ARTICLE | doi:10.20944/preprints202306.0731.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: antispasmodic; heart rate variability; intestinal function; parasympathetic activity
Online: 9 June 2023 (15:50:58 CEST)
The impact of a non-anticholinergic spasmolytic drug (drotaverine hydrochloride) on 23 heart rate (HR), HR variability (HRV) and gastrointestinal tract (GIT) motility in the normal, resting 24 horses was determined. Ten adult riding horses had ECG recordings for 180 minutes after treat-25 ment with drotaverine (180 mg) or saline. Horses from the drotaverine group presented a de-26 creased of GIT contraction for two hours after treatment, but also showed drowsiness. Drotaverine 27 caused a reduction in cardiac vagal modulation of HR at T30 (P=0.050) and T60 (P=0.008) compared 28 to those receiving saline. RMSSD and high frequency (HF) recorded significantly low values after 29 drotaverine treatment by the end of the study, suggesting a decrease in parasympathetic activity. 30 HRV analysis indicated that drotaverine decreased both the low frequency (LF) and Lf/HF ratio 31 reflecting a decrease in sympathetic system. Non linear parameters registered low values after 32 drotaverine administration pointing a diminished in parasympathetic (for SD1) and sympathetic 33 (for SD2) activity. Decreased HRV was suggestive for a pervasive state of sympathetic hypervigi-34 lance of horses. The marked effect of drotaverine on HRV and GIT function in horses should be 35 taken into consideration when evaluating a clinical response to this drug in diseases associated 36 with smooth muscle spasm.
ARTICLE | doi:10.20944/preprints202306.0727.v1
Subject: Biology And Life Sciences, Aquatic Science Keywords: phytoplankton; light measurements; light limitation; coastal ecosystems
Online: 9 June 2023 (14:08:39 CEST)
The use of several light-related variables, such as the Secchi disc depth, the euphotic depth, and in particular, the diffuse attenuation coefficient (Kd), is deeply rooted in phytoplankton research, but these are not the most appropriate indicators of the amount of light available for photosynthesis. We argue that the variable of interest for phytoplankton is the mean light intensity in the mixed layer (Im), which represents the mean light to which phytoplankton cells are exposed throughout their life cycle, while being continuously mixed in the mixed layer. We use empirical data collected in different coastal ecosystems in southern Portugal to demonstrate why Im should be the preferred metric instead of the deeply rooted Kd. We show that, although the relationship between Im and Kd is inversely proportional, it is not always strong or even significant. Different Im values can be associated to the same Kd, but distinct Im have different physiological effects of phytoplankton. Therefore, Kd does not capture the amount of light available for photosynthesis, given that, unlike Im, Kd calculation does not consider the depth of the mixed layer. Therefore, we urge phytoplankton researchers to consider the measurement and calculation of Im when evaluating light-related processes in phytoplankton ecology.
REVIEW | doi:10.20944/preprints202306.0715.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: lectin; carbohydrate; marine animal; toxin; pore-forming protein; innate immunity
Online: 9 June 2023 (12:12:43 CEST)
Glycans play important roles as recognition molecules on cell surfaces in living organisms due to their remarkable structural diversity. Carbohydrates exist in numerous isomeric forms and can adopt diverse structures through various branching patterns. Despite their relatively small molecular weights, they exhibit extensive structural diversity. On the other hand, lectins, also known as carbohydrate-binding proteins, not only recognize and bind to the diverse structures of glycans but also induce various biological reactions based on structural differences. Initially discovered as hemagglutinins in plant seeds, lectins have been found to play significant roles in cell recognition processes in higher vertebrates. However, our understanding of lectins in marine animals, particularly marine invertebrates, remains limited. Recent studies have revealed that marine animals possess novel lectins with unique structures and glycan recognition mechanisms not observed in known lectins. Of particular interest is their role as pattern recognition receptors in the innate immune system, where they recognize glycan structures of pathogens. Furthermore, lectins serve as toxins for self-defense against foreign enemies. Recent discoveries have identified various pore-forming proteins containing lectin domains in fish venoms and skins. These proteins utilize lectin domains to bind target cells, triggering oligomerization and pore formation in the cell membrane. These findings have spurred research into the new functions of lectins and lectin domains. In this review, we present recent findings on the diverse structures and functions of lectins in marine animals.
ARTICLE | doi:10.20944/preprints202306.0705.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Phenology; Tillering; Random Forest; Crop type; Clustering, Unsupervised classification
Online: 9 June 2023 (11:04:40 CEST)
The rising global population amidst the growing concerns of climate change will have a dire consequence on global food security and socio-economic activities. Wheat is one of the most important staple foods consumed by more than four billion people in the world, but climate change impacts account for a decline of 5.5% in wheat yield and predictions indicate that the production could further dwindle by nearly 30% in 2050, due to trends in temperature, precipitation, and carbon dioxide. An effective annual crop estimate is necessary not only to inform government the status of national food security, but also is used to determine the benchmark on which agricultural commodities are priced in the market. Thus, annual crop monitoring and yield estimate is paramount to determine the amount of wheat imports required to make up for the shortfalls in the national wheat production in South Africa, which has been a net importer of wheat since 1998. A joint project between South Africa and Poland investigated satellite based-crop growth monitoring using Sentinel 2 and determined the most distinguishable crop phenology for an accurate winter wheat classification during the growing season from August – December with Random Forest (RF) algorithm. The winter wheat crop was more accurately identified during the crop ‘heading’ stage in October yielding the highest user’s (75.56%) and producer’s (92.52%) accuracies, despite the relatively lower overall accuracy (78.14%) compared to that of December with OA of 83.58% obtained during the maturity stage. This study, therefore, confirms the suitability of sentinel 2 for an effective phenology-based winter wheat crop classification during the heading stage, reducing the ambiguity of spectral confusion created with surrounding grass and maize crops.
ARTICLE | doi:10.20944/preprints202306.0704.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: Pediococcus acidilactici ORE5; Katiki Domokou cheese; probiotic fortification; biopreservation
Online: 9 June 2023 (10:57:07 CEST)
Nowadays, functional foods supplemented with health-promoting microorganisms have attracted the consumers attention due to their health benefits. However, maintaining high cell loads, which consists of an essential requirement for conferring the health effect is a real bottleneck for the food industry, due to viability decline during food processing and storage. Hence, freeze-drying and cell immobilization have been suggested to enhance cell viability. The aim of our study was to assess the effect of freeze-dried immobilized P. acidilactici ORE5 on pistachio nuts on functional regulation of Katiki Domokou-type cheese microbiome. Supplementation of Katiki Domokou-type cheese with free or immobilized P. acidilactici ORE5 culture resulted in cell loads > 8.5 logcfu/g up to 7 days of storage. Both free and immobilized P. acidilactici ORE5 cells suppressed the growth of L. monocytogenes after deliberate inoculation, acting as a protecting shield. SPME GC/MS analysis showed that incorporation of P. acidilactici ORE5 culture in cheese resulted in an improved volatile compounds profile, as verified by the preliminary sensory evaluation. According to Next-Generation Sequencing analysis, a wide range of bacterial diversity was revealed among samples. The most abundant genus was Lactococcus in all samples, while the results showed increased presence of Pediococcus spp. in cheese fortified with P. acidilactici ORE5 culture, highlighting the ability of the strain to survive in the final product. Furthermore, the incorporation of P. acidilactici ORE5 culture in cheese had a significant impact on cheese microbiome composition, as the presence of spoilage bacteria, such as Chryseobacterium, Acinetobacter and Pseudomonas, were significantly lower compared to the control cheese, indicating quality improvement and prolongation of the product’s shelf- life.
ARTICLE | doi:10.20944/preprints202306.0699.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: Biological pretreatment; Ligno-hemicellulolytic enzymes; Corn stover; Enzymatic hydrolysis; Pyrenophora phaeocomes S-1
Online: 9 June 2023 (10:28:39 CEST)
Biological pretreatment of lignocellulosic residues has the potential to serve as a sustainable, less energy-intensive alternative to harsh chemical treatments for enhancing cellulose accessibility, despite the requirement of a lengthy incubation period. The study characterized the simultaneous delignification of corn stover by the white-rot fungus Pyrenophora phaeocomes S-1, as well as the co-production of a ligno-hemicellulolytic enzyme cocktail consisting of laccase, xylanase, and mannanase. The maximum yields of all three components of the cocktail were achieved after just 4 days of incubation under solid-state conditions. Following a 40-day fermentation period, we achieved a cellulose recovery of 44.25 ± 1.72%, attributed to the activities of 133.88 U/gds of laccase, 14.93 U/gds of xylanase, and 1.34 U/gds of mannanase co-produced by the fungus in the medium. Subsequently, through the extraction of biologically treated biomass with 0.5N NaOH after 40 days, the cellulose recovery increased to 66.4 ± 1.39%. Enzymatic hydrolysis of the same, employing only 5 FPU/gds of in-house produced cellulases, resulted in the liberation of 397.84 mg/gds of total reducing sugars after 144h. The findings of this study encourage further optimization of biological pretreatment of lignocellulosic residues and enzymatic hydrolysis to enhance the yields of total reducing sugars for their valorization.
ARTICLE | doi:10.20944/preprints202306.0691.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Root length; MtTGA1; Antioxidant Enzyme; hormones; salt stress
Online: 9 June 2023 (09:18:28 CEST)
The TGACG motif-binding factor1 (TGA1) transcription factor, a significant protein in the bZIP transcription factor family, exhibits a myriad of functions, contributes to numerous biological events, and holds substantial application potential. In this study, our analysis revealed a diverse range of photoregulatory and hormone regulatory elements within the MtTGA1 promoter region. The expression profile of MtTGA1 indicated its highest expression in the root, with its regulation influenced by SA, ABA, BR, and GA. Under salt stress conditions, transgenic plants demonstrated significantly longer root lengths and heightened activities of antioxidant enzymes such as ascorbic acid catalase (APX), peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD) in their roots and leaves compared to control plants. Simultaneously, the levels of endogenous hormones ABA and BR escalated in transgenic plants, with a marked change in the morphology of their leaf cells. Transcriptome analysis identified a total of 193 differentially expressed genes, implicating a wide array of biological processes. Furthermore, we found that MtTGA1 is able to interact with Medicago truncatula SPX domain containing protein 1 (SPX1). In conclusion, the MtTGA1 transcription factor plays a crucial role in enhancing salt tolerance, which provides new insights for improving plant survival under salt stress conditions.
REVIEW | doi:10.20944/preprints202306.0686.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: phosphate homeostasis; transcription factors; phosphate starvation response factors; SPX; proteomics; post-translational; CRISPR; gene editing
Online: 9 June 2023 (08:20:58 CEST)
Plants attained cellular homeostasis of phosphate (Pi) through an integrated response pathway regulated by different families of transcription factors including MYB, WRKY, bHLH and ZFP. The systemic response to Pi limitation showed the critical role played by inositol pyrophosphate (PP-InsPs) as signaling molecule and SPX (SYG1/PHO81/XPR1) domain proteins as sensor of cellular Pi status. Binding of SPX to PP-InsPs regulates the transcriptional activity of the MYB-CC proteins, phosphate starvation response factors (PHR/PHL) as the central regulator of Pi-deficiency response in plants. Vacuolar phosphate transporter, VPT may sense the cellular Pi status by its SPX domain, and vacuolar sequestration is activated under Pi replete condition and the stored Pi is an important resource to be mobilized under Pi deficiency. Proteomic approaches led to new discoveries of proteins associated with Pi-deficient response pathways and post-translational events that may influence plants in achieving Pi homeostasis. This review provides current understanding on the molecular mechanisms at the transcriptional and translational levels for achieving Pi homeostasis in plants highlighting the importance of DNA-protein and protein-protein interactions. The potential strategies for employing the CRISPR technology to modify the gene sequences of key regulatory and response proteins for attaining plant Pi homeostasis are discussed.
REVIEW | doi:10.20944/preprints202306.0673.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: seed size; IKU, ubiquitin; G protein; MAPK; transcription factor; phytohormone; miRNA
Online: 9 June 2023 (05:40:03 CEST)
The size of seeds is particularly important for agricultural development, as it is a key trait that determines yield. It is controlled by the coordinated development of the integument, endosperm, and embryo. Large seeds are one of the important ways to improve the ultimate “sink strength” of crops, providing more nutrients for early plant growth and showing certain tolerance to abiotic stresses. There are several pathways for regulating plant seed size, including the HAIKU (IKU) pathway, ubiquitin-proteasome pathway, G (Guanosine triphosphate) protein regulatory pathway, mitogen-activated protein kinase (MAPK) pathway, transcriptional regulators pathway, phytohormone regulatory pathways including auxin, brassinosteroid (BR), gibberellin (GA), jasmonic acid (JA), cytokinin (CK), Abscisic acid (ABA), and MicroRNAs (miRNAs) regulatory pathway. This article summarized the seed size regulatory network and prospected ways to improve yield. We expect to provide valuable reference to researcher in the related field.
DATA DESCRIPTOR | doi:10.20944/preprints202306.0658.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Genetics and Genomics; Evolutionary Biology; Zoology
Online: 9 June 2023 (03:30:56 CEST)
Snakes are a vital component of wildlife resources and are widely distributed across the globe. Bungarus multicinctus, a highly venomous snake, is found in central and southern China. B. multicinctus is a highly venomous snake and is distributed in central and southern China. Snakes are an ancient group of reptiles, and their genome resources can provide important clues for understanding the evolutionary history of reptiles. Meanwhile, genomic resources play a crucial role in comprehending the evolution of species. So far, the genomic resources of snakes are a rarity. In 2021, a snake sample was collected from Beiliu Longgukeng, Guangxi, which was identified as B. multicinctus through morphological identification. In this study, we present a highly contiguous genome of B. multicinctus with a size of 1.51 Gb. The genome contains a repeat content of 40.15%, with a total length exceeding 620 Mb. Additionally, we annotated a total of 24,869 functional genes. This research is of great significance for comprehending the evolution of B. multicinctus and provides a genomic basis for the genes involved in venom gland function.
ARTICLE | doi:10.20944/preprints202306.0649.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: monocyte, VCAM-1, microsphere, capillary vessel, microemboli
Online: 8 June 2023 (14:02:33 CEST)
The restriction of normal blood flow is the cause of many diseases including stroke and coronary artery diseases. To study the consequences of vessel blockade, previous models mainly focused on major arteries and have been well studied. However, the sequela from interruption of capillary vessels by microemboli was less well characterized. In this study, we exploited polystyrene microspheres as a mimicry of microemboli and found that microspheres of this size can be trapped in capillary vessels of all organs without causing apparent acute morbidities of the host. Interestingly, we accidentally found significantly increased recruitment of monocyte to the brain vasculature expressing low levels of Ly6C expression, but not to other organs. Further study revealed the spleen is the major origin of the recruited monocyte. Most importantly, VCAM-1 which is constitutively expressed on mouse brain vasculature orchestrates the recruitment of monocyte. Blockade of VCAM-1 in mice can substantially reduce monocyte recruitment. Interestingly, monocytes get activated through TNF- signaling which likely happens in the spleen instead of the brain. Collectively, we found a unique monocyte recruitment strategy in the brain comparing to other orangs, in response to capillary blockade induced by polystyrene microspheres.
ARTICLE | doi:10.20944/preprints202306.0648.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2 ORF6 – RAE1 binding; 3D molecular structure modelling; molecular dynamics simulations; cell cycle, cyclin E; R-loops; DNA replication stress
Online: 8 June 2023 (13:52:38 CEST)
ORF6 is responsible for suppressing the immune response of cells infected by the SARS-CoV-2 virus. It is also the most toxic protein of SARS-CoV-2, and its actions are associated with the viral pathogenicity. Here we study in silico and in vitro the structure of the protein, its interaction with RAE1, and the mechanism of action behind its high toxicity. We show both computationally and experimentally that SARS-CoV-2 ORF6, embedded in the membranes of the endoplasmic reticulum, binds to RAE1 and sequesters it in the cytoplasm, thus depleting its availability in the nucleus and impairing nucleocytoplasmic mRNA transport. This negatively affects the cellular genome stability by compromising the cell cycle progression into the S-phase and by promoting the accumulation of RNA-DNA hybrids. Understanding the multiple ways in which ORF6 affects DNA replication may also have important implications for elucidating the pathogenesis of SARS-CoV-2 and developing therapeutic strategies to mitigate its deleterious effects on host cells.
ARTICLE | doi:10.20944/preprints202306.0642.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: basal breast cancer; extracellular matrix remodeling; ferroptosis; transcriptome; text mining
Online: 8 June 2023 (11:21:03 CEST)
(1) Background: Breast cancer is a frequent heterogeneous disorder diagnosed in woman and is a high cause of mortality of them in reason to rapid metastasis and disease recurrence. Ferroptosis can inhibit breast cancer cell growth, improve the sensitivity of chemotherapy and radiotherapy and inhibit distant metastases so potentially acts on tumor micro-environment; (2) Methods: Ferroptosis/Extracellular matrix remodeling literature text-mining results were integrated in breast cancer transcriptome cohort according their distant relapse free survival (DRFS) under adjuvant therapy (anthracyclin+taxanes) and also in MDA-MB-231 transcriptome functional experiments with ferroptosis activations (GSE173905); (3) Results: Ferroptosis/Extracellular matrix remodeling text-mining identified 910 associated genes in at list 10 articles. Univariate Cox analyses censored on breast cancer (GSE25066) selected 252 individual significant genes and 171 of them found with an adverse expression. Functional enrichment of these 171 adverse genes predicted basal breast cancer signatures. By text-mining some ferroptosis significant adverse selected genes shared citations in domain of ECM remodeling such as: TNF, IL6, SET, CDKN2A, EGFR, HMGB1, KRAS, MET, LCN2, HIF1A, TLR4. A molecular score based on expression the eleven genes was found predictive of worst prognosis breast cancer at univariate level: basal subtype, short DRFS, high grade values 3 and 4, estrogen and progesterone receptors negative and nodal stages 2 and 3. This eleven gene signature was validated as regulated by ferroptosis inductors (erastin and RSL3) in triple negative breast cancer cellular model MDA-MB-231.; (4) Conclusions: Crosstalk between ECM remodeling-Ferroptosis functionalities allowed to define a molecular score which have been characterized as an independent adverse parameter in prognosis of breast cancer patients. Gene signature of this molecular score have been validated to be regulated by erastin/RSL3 ferroptosis activators. This molecular score could be promising to evaluate ECM impact of ferroptosis target therapies in breast cancer.
REVIEW | doi:10.20944/preprints202306.0639.v1
Subject: Biology And Life Sciences, Toxicology Keywords: Vaping; e-cigarettes; tobacco flavors; toxicity; regulation
Online: 8 June 2023 (10:59:40 CEST)
On Feb. 6th, 2020, FDA implemented the enforcement priorities against all flavored, cartridge-based e-cigarettes other than menthol and tobacco flavors. This ban undermined the products’ attraction to vapers, so e-cigarette manufacturers added flavorants of other attractive flavors into tobacco-flavored e-cigarettes and re-established attractions. Both the sales of e-cigarettes and posts on social media suggested that the manufacturers’ strategies are likely “successful”. The re-established attraction causes not only a public health issue, but also threats to the health of individual vapers. Research has shown an increase in toxicity associated with the flavorants commonly used in flavored e-cigarettes that are likely added in tobacco-flavored e-cigarettes based on tobacco-derived and synthetic tobacco free nicotine, and these other flavors are associated with higher clinical symptoms not often induced by only natural traditional tobacco flavors. The additional health risks posed by the flavorants are pronounced even without considering the interactions of toxicology of the different tobacco flavorants, and more research should be done to understand the health risks thoroughly and to take proper actions accordingly for regulation of these emerging products.
ARTICLE | doi:10.20944/preprints202305.1521.v2
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: potyvirus; in silico tools; sugarcane mosaic virus; miRNA; RNA interference
Online: 8 June 2023 (10:58:12 CEST)
Sugarcane mosaic virus (SCMV) is a deleterious pathogen which causes widespread Sugarcane mosaic disease (SCMD) and is classified in the genus Potyvirus (Potyviridae), disseminated by the aphid vector. RNA interference (RNAi)-mediated antiviral innate immunity is a key biological process and antiviral defence system to interfere with viral genomes for controlling plant pathogens. The current study aims to analyze sugarcane (Saccharum officinarum L. and Saccharum spp.) locus-derived microRNAs (sof-miRNAs/ssp-miRNAs) with predicted potential for targeting the SCMV +ssRNA-encoded mRNAs, using ‘five algorithms’ approach. The ultimate goal in this research is to mobilize the in silico endogenous predicted sof-miRNAs/ssp-miRNAs to trigger RNAi catalytic pathway experimentally and generate sugarcane cultivars for evaluating potential antiviral resistance monitoring capability and capacity for SCMV. Experimentally validated mature sugarcane (S. officinarum, 2n = 8X = 80) and (S. spp., 2n = 100-120) sof-miRNAs/ssp-miRNAs (n = 28) were acquired for alignment with the SCMV genome. Of the 28 targeting mature locus-derived sof-miRNAs/ssp-miRNAs investigated, one sugarcane miRNA homolog, sof-miR159c, was concluded to localize potential binding site at genomic nucleotide site 3847 targeting CI ORF of SCMV. In order to validate target prediction accuracy, whether the sugarcane sof-miRNA/ssp-miRNA might bind predicted SCMV mRNA target(s), we created an integrated Circos plot. Genome-wide in-silico-predicted miRNA-mediated target gene regulatory network validated interactions that warrant in vivo analysis. The current work provides valuable evidence and biological material for generating SCMV-resistant sugarcane varieties.
ARTICLE | doi:10.20944/preprints202306.0636.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: Clostridioides difficile; COVID-19; SARS-CoV-2
Online: 8 June 2023 (10:55:48 CEST)
The COVID-19 pandemic was associated with increases in some healthcare-associated infections. We investigated the impact of the pandemic on rates and molecular epidemiology of Clostridioides difficile infection (CDI) within one VA Hospital. We anticipated that the potential widespread use of antibiotics for pneumonia during the pandemic might increase CDI rates given that antibiotics are a major risk for CDI. Hospital data on patients with CDI and recurrent CDI (rCDI) were reviewed pre-COVID-19 pandemic (2015 to 2019) and during the pandemic (2020 - 2021). Restriction endonuclease analysis (REA) strain typing was performed on CD isolates recovered from stool samples collected from 10/2019 – 3/2022. CDI case numbers declined 43.2% in 2020 – 2021 compared to the annual mean over the previous 5 years. Stool test positivity rate was also lower during the COVID-19 pandemic (14.3% vs. 17.2%; P = 0.013). Although inpatient volume declined, rates of CDI among inpatients were reduced by 34.2% in 2020 – 2021. Mean monthly cases of rCDI also declined significantly after 2020 [3.38 (95% CI: 2.89 – 3.87) vs. 1.92 (95% CI: 1.27 – 2.56); P = <0.01]. Prior to the pandemic, REA group Y was the most prevalent CD strain among the major REA groups (27.3%). During the first wave of the pandemic from March 8, 2020, through June 30, 2020, there was an increase in the relative incidence of REA group BI (26.7% vs. 9.1%. After adjusting for CDI risk factors, a multivariable logistic regression model revealed that odds of developing an REA group BI CDI increased during the first pandemic wave (OR 6.41, 95% CI: 1.03 – 39.91) compared to the pre-pandemic period. In conclusion, the incidence of CDI and rCDI decreased significantly during the initial waves of the COVID-19 pandemic. In contrast, REA BI (Ribotype 027), a virulent, previously epidemic CD strain and frequently associated with hospital transmission and outbreaks, reappeared as a prevalent strain during the first wave of the pandemic.
ARTICLE | doi:10.20944/preprints202306.0632.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: broiler; duodenum; jejunum; production performance; intestinal barrier; immunoglobulin
Online: 8 June 2023 (10:46:21 CEST)
In order to improve the adaptability of broilers to low-temperature environments and their ability to resist acute cold stress (ACS), 240 one-day-old broilers were selected and randomly divided into three groups. The control treatment (CC) was raised at the conventional feeding temperature from 1-43 days (d), the cold stimulation treatments (CS) were kept at 3 °C below the temperature of CC at 1-d intervals for 3 and 6 hours from 15 to 35 d, namely CS3 and CS6, respectively. Then all broilers were kept at 20 °C from 36 to 43 d. ACS was then carried out at 44 d, and the ambient temperature was dropped to 10 °C for 6 hours. The study investigated the production perfor-mance, as well as levels of intestinal barrier genes (including Claudin-1, E-cadherin, Occludin, ZO-1, ZO-2 and Mucin2), secretory IgA in duodenum and jejunum, and immunoglobulins (IgA and IgG) in serum. The results showed that IMCS could increase the daily weight gain and decrease the feed conversion ratio. During the IMCS, the expression levels of intestinal barrier genes were up-regulated and the content of secretory IgA was increased. When IMCS ceased for one week, the level of immunoglobulins in serum stabilized, and the expression levels of Occludin, ZO-2 and Mucin2 still maintained high levels. After ACS, broilers that received IMCS training maintained the high levels of intestinal barrier genes and secretory IgA.
REVIEW | doi:10.20944/preprints202306.0629.v1
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: glucose metabolism; aerobic glycolysis; Warburg effect; Alzheimer’s disease; amyloid-β; ketogenic diet
Online: 8 June 2023 (10:39:29 CEST)
Alzheimer’s disease (AD) is characterized by the formation of senile plaques consisting fibrillated amyloid-β (Aβ), dystrophic neurites, and the neurofibrillary tangles of tau. The oligomers/fibrillar Aβ damages the neurons or initiate an intracellular signaling cascade for neuronal cell death leading to Aβ toxicity. The Aβ is a 4 kDa molecular weight peptide originating from the C-terminal region of the amyloid precursor protein via proteolytic cleavage. Apart from the typical AD hallmarks, certain deficits in metabolic alterations have been identified. This study describes the emerging features of AD from the aspect of alternation in the main pathway of carbohydrate metabolism in the human brain. Particularly, the neurons in patients with AD favor glycolysis despite a normal mitochondrial function indicating a Warburg-like effect. In addition, certain dietary patterns are well known for their properties in preventing AD. Among those, a ketogenic diet may substantially improve the symptoms of AD. An effective therapeutic method in the treatment, mitigation, and prevention of AD has not yet been established. Therefore, the researchers pursue the development and establishment of novel therapies effective in suppressing AD symptoms and the elucidation of their underlying protective mechanisms against neurodegeneration aiming for AD therapy in near future.
ARTICLE | doi:10.20944/preprints202306.0628.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Staphylococcus aureus; MRSA; mBTL; mBTL-ChNPs; antibiotic resistance; quorum sensing; virulence; biofilm
Online: 8 June 2023 (10:36:45 CEST)
Of late, the focus has been shifted towards quorum sensing inhibitors which reduce bacterial virulence and lower the probability of resistance and refining infections. In this work, meta-bromo-thiolactone (mBTL), a potent quorum and virulence inhibitor against Staphylococcus aureus and MRSA phenotypes, was formulated in chitosan nanoparticles (ChNPs) using ionic gelation method. mBTL-loaded-ChNPs were characterized for particle size, polydispersity index, zeta potential. Morphology was visualized by Transmission Electron Microscopy (TEM), drug release profile and antibiofilm analysis using Confocal Laser Scanning Microscope (CLSM) and Scanning Electron Microscopy (SEM) were performed. Synthesized mBTL-loaded-CNPs showed homogenized nano-size particles ranging from 158+1.3 to 284+5.6 nm with spherical particles that exhibited sustainable release profile over 48 hr at 37 °C. These findings revealed successful preparation of mBTL-loaded-ChNPs, that further showed effective antibiofilm activity at MIC50 (0.5 mg/mL) where all strains displayed reduced biofilm formation compared to untreated strains. CLSM results showed a significant reduction in the number of viable cells, indicating the effectiveness of m-BTL as an antibacterial agent. SEM analysis permitted visualization of biofilm structure in relation to the spatial localization of important biofilm matrix components, the formed biofilms were clearly distinguished in the SEM images. Bacterial cells in the control group were enclosed in thick biofilms. In contrast, there was a considerable reduction in biofilm production when mBTL was present, where bacterial cells seemed less ordered and more scattered with no detectable biofilms. In conclusion, mBTL-loaded-ChNPs is a potential alternative treatment to overcome antimicrobial resistance and condensed MRSA infections.
ARTICLE | doi:10.20944/preprints202305.1053.v2
Subject: Biology And Life Sciences, Food Science And Technology Keywords: consumer awareness; dietary choices; front-of-pack label; Nutri-Score; nutrition labelling
Online: 8 June 2023 (10:06:48 CEST)
Front-of-pack labelling (FOPL) systems, such as the Nutri-Score, play a crucial role in promoting healthy diets and raising consumer awareness. Our study aimed to gather the opinions of Polish experts on the Nutri-Score and its relation to an ideal information system. We conducted a Poland-wide expert opinion study using a cross-sectional design survey with 75 participants, who had an average of 18±13 years of experience and were mainly employed at medical and agricultural universities. The data were collected with CAWI method. The results showed that the most important features of an FOPL system were clarity, simplicity, consistency with healthy eating recommendations, and the ability to objectively compare products within the same group. While more than half of the respondents believed that the Nutri-Score provides an overall assessment of a product’s nutritional value and facilitates quick purchasing decisions, it falls short in helping consumers compose a balanced diet and cannot be applied to all product groups. The experts also expressed concerns about the system’s ability to account for a product’s degree of processing, full nutritional value and carbon footprint. In conclusion, Poland’s current labelling system needs expansion, but the Nutri-Score requires significant and deep changes and validation against national guidelines and expert expectations before implementation.
ARTICLE | doi:10.20944/preprints202306.0613.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Accessions; genetic diversity; morphological traits; SSRs; winged bean
Online: 8 June 2023 (09:25:39 CEST)
Winged bean productivity and the potential to enhance food and nutrition security in sub-Saharan Africa are recurrently affected by several constraints, including but not limited to the lack of genetic improvement. The dearth of adequate information on the genetic diversity that guides the choice of progenitors’ selection among other advantages has been a major setback in planning appropriate improvement programs. This study assessed 15 winged bean accessions for genetic diversity using 10 quantitative traits and 10 microsatellites (SSRs) markers. These accessions were evaluated using RCBD with three replicates for two growing seasons. Ten plants constitute each accession during evaluation from where leaf samples were obtained for SSR marker genotyping. Phenotypic results revealed significant variation (p < 0.05) in the performances of the accessions for the measured traits. H2 estimates varied from 18.92% for seed length to 72.67% for seed weight per plant. Pod weight had a positive and significant correlation with pod length (0.53), pod width (0.70), and number of seeds per pod (0.64). However, the number of seeds per pod negatively correlated with days to maturity (-0.71). The number of seeds per pod was positively predicted by pod weight, seed thickness, and days to maturity. Cluster analysis revealed two genetic groups characterized by different traits. The ten SSRs revealed an average allele count of 4.2, gene diversity of 0.25, and polymorphic information content of 0.22. Analysis of molecular variance revealed within the population of 95% as compared to between population variance of 5%. Phylogeny analysis revealed two primary genetic groups from where five secondary genetic subgroups were identified and only three accessions (TPt-6, TPt-126, and TPt-48) showed genetic purity. This study provides the basis for further studies aimed at exploiting existing variations in winged bean germplasm for its improvement.
ARTICLE | doi:10.20944/preprints202306.0592.v1
Subject: Biology And Life Sciences, Toxicology Keywords: anti-inflammatory assays; murine model; rodent-induced edema
Online: 8 June 2023 (07:34:51 CEST)
Background: Pteropodine (PT) is a component of some plants with potentially useful pharmaco-logical activities for humans. This compound has biomedical properties related to the modulation of the immune system, nervous system, and inflammatory processes. This study addresses the an-ti-inflammatory and antioxidant capacity of pteropodin in a murine model of arthritis and induced edema of the mouse ear. Methods: To evaluate the anti-inflammatory activity, we used the reversed passive Arthus reaction (RPAR), which includes the rat paw edema test, the rat pleurisy test, and a mouse ear edema model. The antioxidant effect was evaluated by determining the myeloperoxidase enzyme activity. Results: PT showed an anti-inflammatory effect in the different specific and non-specific tests. We found a 52 to 74% of inhibitory effect of PT in the rat paw edema test, 52% of reduction of the pleural exudate volume, and low neutrophil count (28%), when compared to the control group. We also found a 81% of inflammatory inhibition of the ear edema, and a significant myeloperoxidase enzyme inhibition by the three doses of PT. Conclusions: PT exerted a potent an-ti-inflammatory effect in the acute inflammation model in rodents.
ARTICLE | doi:10.20944/preprints202306.0600.v1
Subject: Biology And Life Sciences, Aging Keywords: Parkinson; monkey; non-motor symptoms; anxiety; sleep; cognition
Online: 8 June 2023 (07:25:45 CEST)
Abstract Background: Parkinson's disease (PD) is a neurodegenerative disorder featured with motor and non-motor deficits. Using 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) induced dopamine neuron degeneration has been widely used to produce reliable animal models of the PD. However, most of previous preclinical studies focused on the motor dysfunctions, few non-motor symptoms were evaluated. So far there is a lack of comprehensive investigation of the non-motor symptoms in animal models. Objectives: In this study, we aim to use a battery of behavioral methods to evaluate the non-motor symptoms in MPTP-induced non-human primate PD models. Methods: Cognitive functions, sleep and psychiatric behaviors were evaluated in MPTP-treated cynomolgus monkeys. The tests consisted of delayed matching-to-sample (DMTS), physical activity monitor (PAM), apathy feeding task (AFT), human intruder test (HIT), novel fruit test (NFT) and predator confrontation test (PCT). In addition, we tested whether the dopamine receptor agonist pramipexole (PPX) will improve these non-motor symptoms. Results: The present results show that the MPTP-treated monkeys exhibited cognitive deficits, abnormal sleep, and anxiety-like behaviors as compared to the control monkeys. These symptoms were relieved partially by PPX. Conclusions: These results suggest that MPTP-induced PD monkeys displayed non-motor symptoms that were similar to those found in PD patients. PPX treatment showed moderate therapeutic effects on these non-motor symptoms. This battery of behavioral tests may provide a valuable model for future preclinical research.
ARTICLE | doi:10.20944/preprints202306.0586.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: harbor porpoise; aggregation; social behavior; Phocoena phocoena; foraging behavior; large group; transboundary; community science; Salish Sea
Online: 8 June 2023 (04:18:24 CEST)
Harbor porpoise are typically seen in small groups of 1-3 individuals, with aggregations of 20+ individuals treated as rare events. Since the 1990s, the harbor porpoise population in the Salish Sea has seen a significant recovery, which has led to an increased number of observed aggregations that exceed the more usual small group sizes. By combining the observational data of United States and Canadian research organizations, community scientists, and whale watch captains or naturalists, we demonstrate that harbor porpoise aggregations appear to be more common than previously known, with 160 aggregations documented in 2022 alone. Behavioral data also indicated that foraging behaviors were common and social behaviors, like mating, were seen more often during these encounters compared to small groups. Other behaviors that are considered to be rare or unknown, were also observed during these encounters, including cooperative foraging and vessel approach. These aggregations are likely important foraging and social gatherings for harbor porpoises. This holistic approach integrating data from two countries and multiple sources provides an ecosystem level assessment that more effectively reflects the habitat use of harbor porpoise in this region that do not recognize the socio-political boundaries imposed upon the natural world.
ARTICLE | doi:10.20944/preprints202306.0580.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Sugarcane cultivation; development; 2WT; earthing up machine; economic performance
Online: 8 June 2023 (04:01:00 CEST)
Like the most of crops, especially sugarcane needs to be kept upright until it is harvested. Because, lodging of sugarcane has a significant negative effect on cane yield and sugar content of sugarcane. To keep sugarcane upright earthing up is an utmost intercultural operation. In Bangladesh, most of the operations for sugarcane cultivation including earthing up are generally done in traditional method using human labor which increases production costs as well as reduces the income of sugarcane growers. So, a cost effective two-wheeled tractor (2WT) mounted earthing up machine was developed in Bangladesh Sugarcrop Research Institute (BSRI), Pabna to reduce drudgery and cost of sugarcane production. Field tests were conducted in experimental sugarcane field at BSRI and technical and economic performances of the developed earthing up machine were also carried out based on the field test. Average effective field capacity and field efficiency were found 0.16 ha/hr and 77.41 %, respectively for the developed earthing up machine. The earthing up machine was not found economically viable when it is used only for earthing up operation. Besides, when the 2WT was being used as the main driver for other activities including earthing up operation, then the earthing up machine becomes economically beneficial with net cash flow, net present value, internal rate of return, benefit-cost ratio and payback period of BDT 148497/ha, BDT 23184, 3%, 3.81:1 and approximately 1 year, respectively. On the contrary, considering cost of only earthing up tool without 2WT, then it was found economically beneficial with net cash flow, internal rate of return, net present value, benefit-cost ratio and payback period of BDT 16428/ha, BDT 3053, 4.7%, 2.71:1 and approximately 2 years, respectively. Since 2WT is commonly used for versatile farming purposes. Therefore, versatile use of 2WT as prime mover for other machines including earthing up machine can make earthing up machine economically viable and beneficial for sugarcane growers.
CONCEPT PAPER | doi:10.20944/preprints202306.0578.v1
Subject: Biology And Life Sciences, Other Keywords: contemporary conceptualism; cognitive situation; biological systematics; philosophy of systematics; taxonomic theory; taxonomic monism & pluralism; taxonomic nomenclature
Online: 8 June 2023 (03:51:46 CEST)
Biological systematics, exploring the structure of taxonomic diversity (TD), needs a proper conceptualization that would (a) make it complying with certain universal criteria of scientificity and (b) take into account specificity of its studied object. This article outlines a possible conceptual framework for this natural science discipline based on the ideas of contemporary conceptualism. One of the most fundamental of them includes a concept of cognitive situation shaped by three interrelated basic components—ontic, epistemic, and subjective. Its core position is taken by a taxonomic theory (TT) being a conceptual construct resulted from a “summative” effect of all three components and designed for studying TD. The general TT is shown to be composed by a hierarchically arranged array of partial TTs of various levels of generality, and this construct serves as a conceptual justification of taxonomic pluralism. Several kinds of partial TTs are suggested to recognise, viz., ontology- and epistemology-oriented, aspect- and object-based, etc. The aspect-based TTs are of special importance as the conceptual foundations of particular research programs in systematics. The object-based partial TTs are shown to be implemented by concepts of species and homology. A large-scale relation between taxonomic theory and nomenclature is briefly considered.
ARTICLE | doi:10.20944/preprints202306.0573.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Ginger Rhizomes; Moisture Content; Thermal Conductivity; Forced Convection; Drying Temperature
Online: 8 June 2023 (03:25:06 CEST)
This study presents an experimental investigation of the convective drying process of ginger rhizomes (Zingiber officinale). It analyses the effect of moisture content on the thermal properties of dried ginger rhizomes. Drying experiments were conducted under controlled conditions to establish the relationship between moisture content and thermal conductivity. The drying kinetics were examined to provide insights into the drying behaviour of ginger rhizomes and the influence of moisture content on their thermal properties. The results demonstrated a significant impact of initial moisture content and convective drying conditions on the drying process. As drying progressed, the moisture content decreased, leading to a reduction in thermal conductivity. It was observed that drying under convective drying takes 24 hours compared to open sun drying at nine days and solar tunnel drying at eight days. The drying temperature of 60°C was considered optimum. The results show that dried ginger at an absolute moisture content of 6.63% (wb) with a thermal conductivity of 0.0553W/m. K for unblanched ginger, 9.04% (wb) with thermal conductivity of 0.0516W/m. K for blanched ginger, 8.56% (wb) moisture content with a thermal conductivity of 0.0483W/m. K for peeled ginger and 5.98% moisture content with a thermal conductivity of 0.0460W/m. K for unpeeled ginger would be ideal for making powdered ginger rhizomes. These findings have practical implications for the food industry, as they can aid in designing and improving drying processes for ginger rhizomes and similar agricultural products. By understanding the relationship between moisture content and thermal properties, more efficient drying strategies can be developed to minimise energy consumption and maintain the quality of the dried product.
ARTICLE | doi:10.20944/preprints202306.0557.v1
Subject: Biology And Life Sciences, Virology Keywords: coinfection; tick Ixodes persulcatus; virus isolate; tick-borne encephalitis virus (TBEV); ectromelia virus; biological properties of co-isolate; electron microscopy; south of the Russian Far East
Online: 7 June 2023 (13:14:24 CEST)
The phenomenon of pathogens co-infection detected in the half fed on humans I. persulcatus tick in the south of the Far East was studied. Researchs were carried out on PEK, Vero, Vero-E6 cell lines, outbred mice, chicken embryos, using ELISA, PCR, IMFA, plaque formation, and electron microscopy. The tick contained an antigen and a genetic marker of the tick-borne encephalitis virus (TBEV). The patient had post-vaccination antibodies in a titer of 1:200, as a result of which, obviously, an antibody-dependent elimination of TBEV occurred. The tick-borne co-isolate also contained an unknown pathogen (Kiparisovo-144 virus), which, in our opinion, was a trigger for the activation of chronic infection in suckling white mice. In the laboratory coisolate, ectromelia virus was present, as evidenced by paw edema during intradermal infection of mice, characteristic rashes on the chorion-allantoic envilope of chicken embryos, and typical plaques on Vero-E6. The Kiparisovo-144 virus was not pathogenic for white mice and chicken embryos, but successfully multiplied in the PEK, Vero, and Vero-E6 lines. Viral co-infection was confirmed by electron microscopy. Passaging on mice contributed to an increase in the virulence of the co-isolate, whose titer increased by 10,000 times by the 5th passage, which poses a serious epidemiological danger.
BRIEF REPORT | doi:10.20944/preprints202306.0463.v2
Subject: Biology And Life Sciences, Plant Sciences Keywords: Chloroplast genome; Passifloraceae; Passiflora tripartita; poro-poro; Huánuco; Peru
Online: 7 June 2023 (12:23:59 CEST)
Poro-poro is an important native fruit used in traditional Peruvian medicine with relevant agro-industrial and pharmaceutical potential for its antioxidant capacity for human health. However, to date, there have been few genetic studies. The lack of genomic exploration limits the possibility of expanding our knowledge of its molecular evolution, new molecular pathways, genetic traits, and evolutionary relationships. Here, we report the plastid genome sequence of Passiflora tripartita var. mollissima and the reconstructed phylogenetic tree to infer the phylogenetic relationships among Passiflora species. Our phylogenetic analysis showed that poro-poro is most closely related to Passiflora menispermifolia and Passiflora oerstedii. In summary, our study provides the basis for developing new molecular markers that constitutes a valuable resource for studying molecular evolution and domestication. It also provides a powerful foundation for conservation genetics research and plant breeding programs. To our knowledge, this is the first report on the plastid genome of Passiflora tripartita var. mollissima from Peru.
ARTICLE | doi:10.20944/preprints202306.0539.v1
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: MIA; cytokines; chemokines; colony-stimulating factors; Poly (I:C); neurodevelopmental disorders
Online: 7 June 2023 (10:47:26 CEST)
Maternal infections during pregnancy may increase the risk of psychiatric disorders in offspring. We recently demonstrated that activation of peroxisome proliferator-activate receptor‐α (PPARα), with the clinically available agonist fenofibrate, attenuates the neurodevelopmental disturbances induced by maternal immune activation (MIA) in rat offspring. We hypothesized that fenofibrate might reduce MIA-induced cytokine imbalance using a MIA model based on the viral mimetic polyriboinosinic-polyribocytidilic acid [poly (I:C)]. By using the Bio-Plex Multiplex-Immunoassay-System, we measured cytokine/chemokine levels in maternal serum and in the fetal brain of rats treated with fenofibrate, at 6 and 24 hours after poly (I:C). We found that MIA induced time-dependent changes in the levels of several cytokines/chemokines/colony-stimulating factors (CSFs). Specifically, the maternal serum of the poly (I:C)/CTRL group showed increased levels of (i) proinflammatory chemokine macrophage inflammatory protein 1-alpha (MIP-1α), (ii) tumor necrosis factor-alpha (TNF-), the monocyte chemoattractant protein-1 (MCP-1), the macrophage (M-CSF) and granulocyte-macrophage colony-stimulating factor (GM-CSF). Conversely, in the fetal brain of the poly (I:C)/CTRL group, interleukin 12p70 and MIP-1 levels were lower than in veh/CTRL group. Notably, MIP-1, TNF-, GRO/KC, GM-CSF, and M-CSF levels were lower in the poly (I:C)/FEN than in poly (I:C)/CTRL rats, indicating the protective role of the PPARα agonist. PPARα might represent a therapeutic target to attenuate the consequences of MIA.
ARTICLE | doi:10.20944/preprints202306.0532.v1
Subject: Biology And Life Sciences, Behavioral Sciences Keywords: Attention; phonological processing; space
Online: 7 June 2023 (10:04:25 CEST)
Spatial attentional biases can be observed during the processing of linguistic material. For example, we previously reported that healthy subjects overestimate the semantic distance between word stimuli in the right vs left space. Here we explored whether attentional biases are also observed in tasks requiring evaluation of phonological distance between words in the right and left hemispace. Forty-one healthy subjects were presented with triplets of words arranged in space and were asked to indicate the side of space in which the phonological distance between the middle word and an outer word was smaller. In Experiment 1 real words and pseudowords were used, while in Experiment 2 only pseudowords and consonant strings were used. Subjects overestimated the phonological distance between the middle and outer words in the right space. These findings were specific to word stimuli. These results are consistent with the idea that semantic and phonological information may be internally mapped onto spatial representations.
ARTICLE | doi:10.20944/preprints202306.0526.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Dispersal; Connectivity; Movement; Conservation Genomics; Madagascar; Habitat Loss and Fragmentation; Rodents
Online: 7 June 2023 (09:30:53 CEST)
Habitat loss and fragmentation are of concern to conservation biologists worldwide. However, not all organisms are affected equally by these processes, thus it is important to study the effects of living in fragmented habitats on species that differ in lifestyle and habitat requirements. In this study we examined dispersal and connectivity patterns of rodents, one endemic (Eliurus myoxinus) and one invasive (Rattus rattus), in two landscapes containing forest fragments and adjacent continuous forest patches in northwestern Madagascar. We generated genomic (RADseq) data for 66 E. myoxinus and 81 R. rattus individuals to evaluate differences in genetic diversity as well as inbreeding and connectivity in two landscapes. We found higher levels of inbreeding and lower levels of genetic diversity in E. myoxinus compared with R. rattus. We observed related dyads both within and between habitat patches and positive spatial autocorrelation at lower distance classes for both species, with a stronger pattern of spatial autocorrelation in R. rattus. Across each site we identified contrasting migration rates for each species, but these did not correspond to habitat-matrix dichotomies. The relatively low genetic diversity in the endemic E. myoxinus suggests ecological constraints that require further investigation.
REVIEW | doi:10.20944/preprints202306.0521.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: platelet-rich plasma; platelet-rich fibrin; hyaluronic acid; orthobiologics; osteoarthritis; regenerative medicine
Online: 7 June 2023 (08:54:22 CEST)
Platelet and fibrin-rich orthobiologic products, such as autologous platelet concentrates, have been extensively studied and appreciated for their beneficial effects in multiple conditions. PRP and its derivatives, including PRF, have demonstrated encouraging outcomes in clinical and laboratory settings, particularly in the treatment of musculoskeletal disorders such as OA. Although PRP and PRF have distinct characteristics, they share similar properties. The relative abundance of platelets, peripheral blood cells and molecular components in these orthobiologic products stimulate numerous biological pathways. These include inflammatory modulation, augmented neovascularization, and delivery of pro-anabolic stimuli that regulate cell recruitment, proliferation, and differentiation. Furthermore, the fibrinolytic system, which is sometimes overlooked, plays a crucial role in musculoskeletal regenerative medicine by regulating proteolytic activity and promoting the recruitment of inflammatory cells and MSCs in areas of tissue regeneration, such as bone, cartilage, and muscle. PRP acts as a potent signaling agent; however, it diffuses easily, while the fibrin from PRF offers a durable scaffolding effect that promotes cell activity. The combination of fibrin with hyaluronic acid, another well-studied orthobiologic product, has been shown to improve its scaffolding properties, leading to more robust fibrin polymerization. This supports cell survival, attachment, migration, and proliferation. Therefore, the administration of the "power mix" containing HA and autologous PRP + PRF may prove to be a safe and cost-effective approach in regenerative medicine.
ARTICLE | doi:10.20944/preprints202306.0516.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: WPI; pectin; coacervation; microcapsules; propolis
Online: 7 June 2023 (08:34:56 CEST)
Propolis is known to have many benefits, especially in the health sector. Due to the sharp aroma & taste, and the phenolic compounds contained in propolis are easily oxidized & hydrolyzed at high temperatures, the application of propolis in the food sector is still lacking. Microencapsulation with a coacervation complex is used to overcome these problems. The thickness of the coating material is an important factor in the microencapsulation of complex coacervation. This study aimed to determine the coating ratio used to produce propolis microcapsules with the highest phenolic stability during storage and heating. This study consisted of three treatment ratios of whey protein isolate (WPI) & pectin coating materials 1:2, 1:1, and 2:1. The results showed that the yield value ranged from 37.279-40.116%, aw 0.375-0.529, and encapsulation efficiency 85.45-96.44%. The color of the microcapsules produced was bright (L* = 94.28-95.35%), tended to be reddish (a* = 0.07-0.11) & yellowish (b* = 4.36-4.83). The difference in the ratios treatment significantly affected the storage stability, while the heating stability ratio only significantly affected the 2:1 treatment. The best total phenolic stability of propolis microcapsules during storage & heating was obtained by 1:1 treatment with retention values of 97.31% and 63.86%.
REVIEW | doi:10.20944/preprints202306.0515.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: epigenetic; genomic imprinting; ovarian tissue cryopreservation; testicular tissue cryopreservation; Medically Assisted Reproduction
Online: 7 June 2023 (08:32:11 CEST)
Ovarian tissue cryopreservation (OTC) or testicular tissue cryopreservation (TTC) are effective and often the only options for fertility preservation in female or male patients due to oncological, medical, or social aspects. While TTC and resumption of spermatogenesis, either in vivo or in vitro, has still be considered an experimental approach in humans, OTC and autotransplantation has been applied increasingly to preserve fertility with more than 200 live births worldwide. However, the cryopreservation of reproductive cells followed by the resumption of gametogenesis, either in vivo or in vitro, may interfere with sensitive and highly regulated cellular processes. In particular, the epigenetic profile, which includes not just reversible modifications of the DNA itself but also post-translational histone modifications, small non-coding RNAs, gene expression and availability, and storage of related proteins or transcripts, have to be considered in this context. Due to complex reprogramming and maintenance mechanisms of the epigenome in germ cells, growing embryos, and offspring, OTC and TTC are carried out at very critical moments early in the life cycle. Given this background, the safety of OTC and TTC taking into account the epigenetic profile has to be clarified. Cryopreservation of mature germ cells (including Metaphase II oocytes and mature spermatozoa collected via ejaculation or more invasively after testicular biopsy) or embryos has been used successfully for many years in Medically Assisted Reproduction (MAR). However, tissue freezing followed by in vitro or in vivo gametogenesis has become more attractive in the past, while few human studies have analysed the epigenetic effects, with most data deriving from animal studies. In this review, we highlight the potential influence of the cryopreservation of immature germ cells and subsequent in vivo or in vitro growth and differentiation on the epigenetic profile in humans and animals.
ARTICLE | doi:10.20944/preprints202306.0512.v1
Subject: Biology And Life Sciences, Virology Keywords: metatranscriptome; microbiome; SARS-CoV-2; virome
Online: 7 June 2023 (08:23:07 CEST)
The recent global emergence of the SARS-CoV-2 pandemic has accelerated research in several areas of science whose valuable outputs and findings can help to address future health challenges in the event of emerging infectious agents. We performed a multifocus shotgun analysis to compare differences in bacterial spectrum and viral presence through culture-independent RNA sequencing. We compared the microbiome of healthy people versus those with varying degrees of COVID-19 severity. We observed a significant increase in the diversity of microbial species in patients with COVID-19 regardless of disease severity. Some bacterial phyla, such as Actinobacteria, are significantly more abundant in healthy people than in infected people, whereas Bacteroides are less abundant in the latter. Infected people, regardless of severity and symptoms, have the same proportional representation of Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteriales the same. In addition to SARS-CoV-2 and numerous phage groups, we identified sequences of clinically significant viruses such as Human Herpes Virus 1, Human Mastadenovirus D, Molluscum Contagiosum Virus, and Rhinovirus A in several samples. Analyses were performed retrospectively, therefore, in the case of SARS-CoV-2 various WHO variants such as Alpha (B.1.1.7), Delta (B.1.617.2), Omicron (B.1.1.529), and 20C strains are represented. Additionally, the presence of specific virus strains has a certain effect on the distribution of individual microbial taxa.
ARTICLE | doi:10.20944/preprints202306.0478.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Amphibians; Conservation; Islands; Philippines; Priorities.
Online: 7 June 2023 (08:06:48 CEST)
Research efforts toward Philippine biodiversity have increased significantly due to concerns about its natural resources and biodiversity. However, there is an imbalance in the distribution of published studies, with specific territories and organisms receiving more attention. Mindanao, a southern Philippine Island, is known for its high levels of endemism for amphibians and reptiles. Despite this, research on these groups remains unconsolidated. To address this gap, we conducted a biodiversity synthesis focusing on amphibians and reptiles in the faunal region of Mindanao. We found an increasing effort towards herpetofauna over the two decades, yet there is a clear bias in the effort towards amphibians compared to reptiles. In addition, we found that amphibians have a significantly higher species threat index than reptiles and all other vertebrate groups, regardless of ecological status. Yet, threatened herpetofauna species and those facing a greater number of threats are poorly studied, in general. Understanding the factors driving research biases in Mindanao and the Philippines is essential to allow us to redirect research efforts to the most needed areas, particularly to understudied and neglected taxa in Mindanao. This is especially urgent in the face of changing climate, where diverse communities of herpetofauna are at increased risk of extinction. Consequently, by bridging these gaps in biodiversity information, we can effectively contribute to the conservation and understanding of biodiversity in the region.
ARTICLE | doi:10.20944/preprints202306.0506.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: Microbiological quality; traditional fermented African yoghurt; public health concern
Online: 7 June 2023 (07:52:19 CEST)
In this study, the microbiological quality of traditionally made yoghurt from Northern Uganda and Western Kenya were analysed. Six samples of typical traditionally fermented milk were randomly collected from traditional cattle keepers from Karamojong (UG 1) and Acholi (UG 2) in Northern Uganda), and Kalenjin in Western Kenya (KE). Analysis was carried out for microbial quality of the collected samples and was assessed using the conventional methods for total aerobic mesophilic bacteria, total coliform, lactic acid bacteria, Staphylococcus aureus, Listeria monocytogenes, yeasts, and mould counts. The results showed that the pH of the samples was low (2.9- 3.6). The mean aerobic mesophilic bacterial counts were 5.14 x 109 cfu/ml. The mean counts for mesophilic lactobacilli ranged from x 106 to x 108, cfu/ml. The mean thermophilic lactobacilli count ranged from x 107, to x 109, cfu/ml. However, the thermophilic lactococci counts ranged from x 106, to x 109, cfu/ml. On the other hand, the Streptococci counts were between x 106 to x 108 cfu/ml. The mean counts for the non-Sorbitol E. coli was 3.87 x 103 cfu/ml. The results suggest that although the pH of the yoghurt made in the Acholi and Karamojong (Northern Uganda) and in Kalenjin (Kenya) areas was low, the level of bacteria, yeast, and mould counts indicated poor microbiological quality control. This poses public health concerns. Therefore, attention of the appropriate government agencies is needed to ensure that environment of yogurt produced in a traditional setting in most appropriate condition to reduce contamination.
ARTICLE | doi:10.20944/preprints202306.0501.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: Drosophila; miR-274; melanotic mass; growth; JNK signaling; JAK/STAT signaling; found-in-neurons
Online: 7 June 2023 (07:12:24 CEST)
The hematopoietic system plays a crucial role in immune defense response and normal development, and is regulated by various factors from other tissues. The dysregulation of hematopoiesis is associated with melanotic mass formation; however, the molecular mechanisms underlying this process are poorly understood. Here, we observed that the overexpression of miR-274 in the fat body resulted in the formation of melanotic masses. Moreover, abnormal activation of the JNK and JAK/STAT signaling pathways was linked to these consequences. In addition to this defect, miR-274 overexpression in the larval fat body decreased the total tissue mass, leading to a reduction in body weight. miR-274-5p was found to directly suppress the expression of found-in-neurons (fne), which encodes an RNA-binding protein. Similar to the effects of miR-274 overexpression, fne depletion led to melanotic mass formation and growth reduction. Collectively, miR-274 plays a regulatory role in the fne-JNK signaling axis in melanotic mass formation and growth control.
ARTICLE | doi:10.20944/preprints202306.0498.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: infectivity; neutral solution; acidic solution; alkaline solution; deprotonation
Online: 7 June 2023 (07:05:54 CEST)
The preservative qualities of individual ionic compounds on the infectivity of T4 virions were elucidated. T4 virions were immersed in quasi-pure ionic solutions prior to the adsorption process, and the pfu values of these were measured following the conventional method. In neutral ionic solutions, the minimum and the optimum concentrations for preservative qualities were corresponded with the results obtained from the multi-ionic media/buffers. In acid and alkali solutions, phages show tolerances at a pH range of 5-11 in multi-ionic media/buffers. T4 virions show no tolerance in quasi-pure acid, neutral and weak alkaline conditions. The preservative quality of T4 virions was jumped up in over 10-1 mM OH- solution, equivalent to pH value over 10, which is corresponding to the pKa of the deprotonation of the DNA bases G and T. Infectivity was lost below 10-1 mM OH- and higher than 10 mM OH-. These results implicate the maintaining of infectivity of a virion may need the flexibility of the intra-capsid DNA by deprotonation.
ARTICLE | doi:10.20944/preprints202306.0483.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Rice seeds; dehydration rate; RNA-seq; DEGs
Online: 7 June 2023 (03:54:11 CEST)
The transcriptomic analysis of the dehydration rate of mature rice seeds was conducted to explore candidate genes related to the dehydration rate and provide a theoretical basis for breeding and utilization. In this study, we selected Baghlani Nangarhar, an extremely fast dehydration material, and Saturn, a slow dehydration material, based on the results of the previous studies of screening of 165 germplasm materials for dehydration rate phenotypes. Fast dehydration experiment on these two types of seeds was conducted. Four comparative groups were set up under control and dehydration conditions. The differentially expressed genes (DEGs) were quantified by transcriptome sequencing and quantitative real-time PCR (qRT-PCR). GO and KEGG analyses were carried out. The results showed that in Baghlani Nangarhar, 53 DEGs were screened, of which 33 were up-regulated and 20 were down-regulated. Similarly, in Saturn, 25 DEGs were screened, of which 19 were up-regulated and 6 down-regulated. The results of the GO analysis showed that the sites of action of the differentially expressed genes enriched in the fast dehydration modes were concentrated in the cytoplasm, internal components of the membrane and nucleosomes. They play regulatory roles in catalysis, binding, translocation, transcription, protein folding, degradation and replication. They are involved in adaptive responses to adverse external environments such as reactive oxygen species and high temperature. The KEGG analysis showed that the main metabolic pathways enriched are protein processing in the endoplasmic reticulum, amino acid biosynthesis, and oxidative phosphorylation. The key differentially expressed genes and the most important metabolic pathways in the rapidly and slowly dehydrated materials obtained in this study were protein processing in the endoplasmic reticulum and oxidative phosphorylation metabolism, which are presumed to have important regulatory roles in stress/defense, energy metabolism, protein synthesis/folding, and signal transduction during dehydration and drying of mature seeds. The results of this study could potentially provide a valuable reference for further research on the genes and metabolic pathways related to the dehydration rate of mature rice seeds and provide theoretical guidance for the selection and breeding of new rice germplasm that can be rapidly dehydrated at the mature stage.
COMMUNICATION | doi:10.20944/preprints202306.0473.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; echocardiography; left ventricular mass index; the ratio between the E and A waves; deceleration time of early mitral inflow; biomarkers
Online: 7 June 2023 (03:22:53 CEST)
Background: The manifestations, severity, and mortality of COVID-19 are considered to be associated with the changes in various hematological parameters and in immunity. Associations of immunoglobulin G antibodies against severe acute respiratory syndrome-linked coronavirus (IgG-SARS)-positive status with cardiac function and hematological and biochemical parameters in apparently health subjects are poorly understood. Methods: The present cross-sectional study included 307 healthy volunteers (24-69 years of age; 44.8±8.6 years; 80.4% men) and was initiated in 2019 before the COVID-19 pandemic. COVID-19 episodes were confirmed by detection of IgG-SARS against SARS-CoV-2 S1 RBD to reveal 70 IgG-SARS-positive and 237 negative participants. Numerous ultrasound characteristics were assessed by echocardiography, and 15 hematological and biochemical parameters were assayed in the blood. Descriptive and comparative analysis was based on the IgG-SARS status of the participants. Results: The left ventricular mass index, mitral ratio of peak early to late diastolic filling velocity or flow velocity across the mitral valve, and deceleration time of early mitral inflow were decreased (P<0.05) in IgG-SARS-positive participants versus those in IgG-SARS-negative participants according to multivariate logistic regression analysis. Erythrocyte sedimentation rate and platelet count were slightly increased, and blood hemoglobin was decreased in IgG-SARS-positive participants compared with those in IgG-SARS-negative participants. Conclusions: LV filling, inflammation, blood coagulation, and hemoglobin appear to be influenced by COVID-19 infection in healthy participants. These observations contribute to the development of a population recovery strategy after the episodes of COVID-19.
ARTICLE | doi:10.20944/preprints202306.0465.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: Yeast selection; Saccharomyces cerevisiae; Wine microbiology; Autochthonous yeast; “Pago” wine
Online: 6 June 2023 (14:44:08 CEST)
The aim of this study was to isolate and characterize autochthonous Saccharomyces cerevisiae yeasts from Cabernet Sauvignon grape must and to analyze how they impacted the final characteristics of the wines obtained from the same must type. This work was carried out in a “Pago” winery located in Requena, Spain. Twenty-two isolates were obtained from grape must. After molecular identification and typing, 11 different strains were determined. Growth-related parameters and metabolic characteristics (glucose and fructose consumption, and ethanol, glycerol and acetic acid production) were determined by laboratory-scale fermentations (50 mL) of Cabernet Sauvignon must. From 2 L fermentation batches, residual sugar, density, ethanol concentration, titratable and volatile acidities, pH, and polyphenolic and volatile compounds were determined, as well as the sensory attributes of the produced wines. Differences between strains in the growth and metabolic parameters were observed. Eleven S. cerevisiae strain profiles were characterized to establish which strain or strains of the selected yeasts would produce the highest polyphenolic and aromatic concentration of the red Cabernet wines made in the “Pago winery” to then multiply them for their use to make the red wines of this winery.
REVIEW | doi:10.20944/preprints202306.0464.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: Calcium phosphate; calciprotein particles; nanoclusters; intrinsically disordered proteins; crystal toxicity; milk; serum
Online: 6 June 2023 (14:19:16 CEST)
Management of calcium and phosphate in biofluids is key to maintaining physiological mineral homeostasis (i.e., appropriate mineralization of hard tissues and an absence of mineral deposition in soft tissues). This review describes and contrasts the ways vertebrates manage calcium phosphate in two biological fluids (breast milk and serum) and illustrates the benefits of mineral sequestration by proteins. In milk, phosphoprotein-sequestered calcium magnesium phosphates provide nutritional support, whereas in serum, protein-sequestered calcium phosphates control transport and delivery of calcium and phosphate to tissues for biological function or excretion. In addition, subsets of sequestered phosphates in serum have been identified as culprits underlying ectopic deposition of calcium phosphates and toxicity.
REVIEW | doi:10.20944/preprints202306.0462.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: membrane hyperpolarization; SLO3; contraception; potassium channels; sperm; acrosomal exocytosis; capacitation; hyperactivated motility; SLO channels; male fertility
Online: 6 June 2023 (14:01:18 CEST)
Sperm cells must undergo a complex maturation process after ejaculation to be able to fertilize an egg. One component of this maturation is hyperpolarization of the membrane potential to a more negative value. The ion channel responsible for this hyperpolarization, SLO3, was first cloned in 1998, and since then much progress has been made to determine how the channel is regulated and how its function intertwines with various signaling pathways involved in sperm maturation. Although SLO3 was originally thought to be present only in the sperm of mammals, recent evidence suggests that a primordial form of the gene is more widely expressed in some fish species. As with many reproductive genes, SLO3 is rapidly evolving with low conservation between closely related species and different regulatory and pharmacological profiles. Despite these differences, SLO3 appears to have a conserved role in regulating sperm membrane potential and driving large changes in response to stimuli. As with the differences in regulation of the channel, the effect of this hyperpolarization of the membrane potential may vary among mammalian species. Recent discoveries have elucidated the role of SLO3 in these processes in human sperm and provided tools to target the channel to affect human fertility.
ARTICLE | doi:10.20944/preprints202306.0444.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Climate change; Net photosynthetic rate; Chalky grain; Growth; High temperature
Online: 6 June 2023 (11:07:59 CEST)
Global warming causes an alarming increase in temperature which negatively affects growth, physiology, and yield of rice. To gain some insights into the impacts of booting HT (at 42°C, 3 h for 7 days), we investigated its effect in three rice genotypes, namely, N22, KDML105 and IR64. Booting HT caused an extended phenology and lower photosynthesis and plant growth rate but an increase in chalkiness. Although, prolonged phenology from dough to physiological maturity led to longer duration of grain filling, the negative effects of its was significantly lower yield components, yield and harvest index in all rice. Among cultivars, N22 presented adapted ability to maintain leaf gas exchange and compensated vegetative part by an increase in tiller numbers resulting in less affected growth rate. It prolonged phenology that caused extended grain filling. Consequence, N22 was the lowest reduction in number of seed panicle–1, number of filled seeds hill–1, yield, HI as well as the lowest percentage chalkiness. KDML105 adapted to booting HT by maintaining leaf gas exchange, increasing specific leaf area and prolonging phenology. The longest extended phenology together with the maintenance of high photosynthesis during dough grain were associated with moderate yield reduction and chalkiness. However, IR64 showed dramatic reductions in photosynthesis, growth rate, and yield but highest percentage grain chalkiness. Therefore, in response to booting HT, N22, KDML105 and IR64 could be indicated as being heat tolerant, moderately heat sensitive, and heat sensitive, respectively. This can be applied for crop modelling and rice heat tolerance in breeding program.
REVIEW | doi:10.20944/preprints202305.1895.v2
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: lipid membrane; excitable cells; synaptic vesicles; H+ ion; Ca2+ signaling; calcium; binding proteins; signal transduction; G-protein coupled receptors
Online: 6 June 2023 (10:53:32 CEST)
Protons are gaining increasing attention as neurotransmitters due to their extraordinary abilities to rapidly transfer electrical charge, mobilize cellular calcium and modulate ion channels. How all this is possible is currently the subject of in-depth studies and discussions concerning not only neurophysiology, but also biological materials for artificial intelligence. In this short review, some biochemical mechanisms are described by which protons, in combination with calcium, can initiate firing in sensory neurons and transmit impulse across synapses. Furthermore, mechanisms are put forward concerning how three neurotransmitters, glutamate, gamma-aminobutyric acid and acetylcholine, are able to generate protons. The results of the numerous experimental works taken into consideration indicate that protons can play a fundamental role both in the generation and in the transmission of the nerve impulse.
REVIEW | doi:10.20944/preprints202306.0441.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: anti-lipoxygenase peptide; bioactivity; enzymatic hydrolysis; food peptide; food protein; inflammation; lipoxidase; lipoxygenase inhibitory activity.
Online: 6 June 2023 (10:11:09 CEST)
Lipoxygenases are non-heme iron-containing enzymes that catalyze the oxidation of polyunsaturated fatty acids, resulting in the production of lipid hydroperoxides, which are precursors of inflammatory lipid mediators. The enzymes are widely distributed in humans, other eukaryotes, and cyanobacteria. Lipoxygenases hold promise as therapeutic targets for several human diseases, including cancer and inflammation-related disorders. Inhibitors of lipoxygenase have potential applications in pharmaceuticals, cosmetics, and food. Bioactive peptides are short amino acid sequences embedded within parent proteins, which can be released by enzymatic hydrolysis, microbial fermentation, and gastrointestinal digestion. A wide variety of bioactivities have been documented for protein hydrolysates and peptides derived from different biological sources. Recent findings indicate that protein hydrolysates and peptides derived from both edible and non-edible bioresources can act as lipoxygenase inhibitors. In this review, we explore current knowledge on the production of anti-lipoxygenase protein hydrolysates and peptides from millet grains, chia seeds, insects, milk proteins, fish feed, velvet antler blood, fish scales, and feather keratins. We delve into the anti-lipoxygenase activities and modes of action of these protein hydrolysates and peptides, while also highlighting the strengths and shortcomings of previous research. Additionally, we propose potential research directions and areas of improvement that can propel the discovery of anti-lipoxygenase peptides in the near future.
REVIEW | doi:10.20944/preprints202306.0439.v1
Subject: Biology And Life Sciences, Insect Science Keywords: urban zone; mosquitoes; mapping; mosquito-borne diseases; stinkbugs; nuisance
Online: 6 June 2023 (10:07:51 CEST)
Urban environments are frequently populated by different insect species. Some of them are very beautiful and appealing to the people around them, such as ladybugs and butterflies, while some others are molestants and even dangerous to public health. Mosquitoes often inhabit urban environments by staying close to their hosts (humans, birds, etc.), while phytophagous species such as stinkbugs find hosts among ornamental plants and shelters during the winter around humans. This article describes the early discoveries and distribution of two invasive mosquito species, Aedes albopictus, and Ae. japonicus (Diptera: Culicidae), which were recorded in Serbia in 2009 and 2018, respectively. Both species are important for human health, due to their nuisance behavior and because they are vectors of many viruses. On the other hand, in 2015 and 2008, two invasive stinkbug species, Halyomorpha halys and Nezara viridula (Hemiptera: Pentatomidae) were observed to spread, respectively. Since then, these species have disrupted human population in urban areas, but also damaged a range of crops and ornamental plants. All species have been monitored in the territory of Serbia, and establishment and distribution have been confirmed so far.
ARTICLE | doi:10.20944/preprints202306.0437.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Azospirillum brasilense; biological nitrogen fixation; microbial auxin biosynthesis; ATP biosynthesis; micronutrient uptake; light stimulation
Online: 6 June 2023 (10:01:34 CEST)
As the use of microbial inoculants in agriculture rises, it becomes important to understand how the environment may influence microbial ability to promote plant growth. This work examines whether there are light dependencies in the biological functions of Azospirillum brasilense, a commercialized prolific grass-root colonizer. Though classically defined as non-phototrophic, A. brasilense possesses photoreceptors that could perceive light conducted through its host’s roots. Evidence for light dependency of four microbial processes were examined and noted: biological nitrogen fixation (BNF), auxin biosynthesis, ATP biosynthesis, and iron and manganese uptake. Functional mutants of A. brasilense were leveraged and studied in light and dark environments: HM053 (high BNF and auxin production), ipdC (capable of BNF, deficient in auxin production), and FP10 (capable of auxin production, deficient in BNF). HM053 exhibited the highest rate of nitrogenase activity with the greatest light dependency comparing iterations in light and dark environments. The ipdC mutant showed similar behavior with relatively lower nitrogenase activity observed, while FP10 did not show a light dependency. Auxin biosynthesis showed strong light dependencies in HM053 and FP10 strains, but not for ipdC. Iron is involved in the BNF biological process, and light dependency was observed for microbial 59Fe2+ uptake in HM053 and ipdC, but not FP10. Surprisingly, a light dependency for 52Mn2+ uptake was only observed in ipdC. Finally, ATP biosynthesis was sensitive to light across all three mutants favoring blue light over red light compared to darkness with observed ATP levels in descending order for HM053 > ipdC > FP10.
ARTICLE | doi:10.20944/preprints202306.0434.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: Staphylococcus equorum; antibiotic resistance; dairy microbiology; starters; adjunct cultures; cheese
Online: 6 June 2023 (09:52:40 CEST)
In this work, the resistance/susceptibility (R/S) profile of Staphylococcus equorum strains (n=30) from cheese to 16 antibiotics was determined by broth microdilution. The minimum inhibitory concentration (MIC) for all antibiotics was low in most strains, although higher MICs compatible with acquired genes were also noted. Genome analysis of 13 strains showed the S. equorum resistome to be composed of intrinsic mechanisms, acquired mutations, and acquired genes. However, the genetic data did not always correlate with the phenotype. As such, a cat gene providing resistance to chloramphenicol was found on a plasmid in one strain; this was able to provide resistance to Staphylococcus aureus after electroporation. An msr(A) polymorphic gene was identified in five strains. The Mrs(A) variants were associated with variable resistance to erythromycin. All strains harboured a polymorphic fosB/fosD gene, although only one acquired copy was associated with strong resistance to fosfomycin. Similarly, a plasmid-associated blaR1-blaZI operon encoding a penicillinase was identified in five ampicillin- and penicillin G-susceptible strains. Identified genes not associated with resistance further included mph(C) in two strains and norA in all strains. The antibiotic R/S status and gene content of S. equorum strains intended to be employed in food systems should be carefully determined.
REVIEW | doi:10.20944/preprints202306.0421.v1
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: OCd; obsessive-compulsive disorder; microbiota; gut; gut-brain axis; probiotics; fecal transplants; microbial reprogramming
Online: 6 June 2023 (08:53:21 CEST)
This review examines the evidence supporting the role of dysbiosis in the development of obses-sive-compulsive disorders (OCD). We review the molecular mechanisms and role of the microbiota in the microbiota-gut-brain axis, focusing on the endocrine, nervous, and immune pathways. We then propose a model that positions dysbiosis as the central unifying element in the neurochemi-cal, immunological, genetic, and environmental factors leading to OCD. Based on this, we review the animal and human clinical evidence for the use of microbial reprogramming strategies such as probiotic or fecal microbiota transplants to treat OCD. Finally, we discuss the unique challenges that must be addressed in future clinical interventions.
ARTICLE | doi:10.20944/preprints202306.0420.v1
Subject: Biology And Life Sciences, Endocrinology And Metabolism Keywords: diabetes; anaerobic exercise; glut4 gene expression; streptozocin
Online: 6 June 2023 (08:52:56 CEST)
Diabetes is a chronic condition that worsens living conditions and causes significant problems, particularly in the vascular system. Many different treatment options are used to prevent these negative effects of diabetes. The most important of these is changing living conditions and exercising regularly.This study aimed todetermining the impacts of a 6-week anaerobic exercise protocol on the blood glucose levels and Glut4 gene expression in the muscle tissues of streptozocin (STZ)-induced diabetic rats. A total of 45 rats were separate control, sedentary, and exercise groups (n=15 each). The STZ used to induce diabetes in rats was applied once with a single intraperitoneal injection. No diabetes was created in the control group, and no exercise was performed, whereas in the sedentary group, diabetes was induced, and no exercise was applied. It was determined that the Glut4 gene expression in the muscle tissue of the exercise group was importantly increased when compared with the sedentary diabetes group.Glut4 gene is an important gene involved in blood glucose regulation and anaerobic exercise significantly increased the expression level of this gene in our study.
ARTICLE | doi:10.20944/preprints202306.0376.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Obesity; T2DM; Insulin resistance; Vindoline; Adipocyte; Skeletal muscle
Online: 6 June 2023 (08:42:02 CEST)
Type 2 diabetes mellitus (T2DM) has emerged as a major health care concern in modern society, primarily due to lifestyle changes and dietary habits. Obesity-induced insulin resistance is considered as the major pathogenic factor in T2DM. In this study, we have investigated the effect of vindoline, an indole alkaloid of Catharanthus roseus on insulin resistance, oxidative stress and inflammatory responses in high glucose induced insulin resistant L6-myoblast cells, and dexamethasone (IR inducer)/1L-β (inflammation inducer) induced dysfunctional 3T3-L1 adipocytes. Results showed that dexamethasone induced dysfunctional 3T3-L1 adipocytes treated with different concentrations of vindoline significantly enhanced basal glucose consumption, accompanied by increased expression of GLUT-4, IRS-1 and adiponectin. Vindoline treatment significantly suppressed the ROS production and upregulated pro-inflammatory mediators in IL-1β induced dysfunctional adipocytes. Similarly, vindoline treated insulin resistant L6 myoblasts exhibited significantly enhanced glycogen content accompanied with upregulation of IRS-1 and GLUT-4. Thus, in vitro studies of vindoline in insulin resistant skeleton muscle and dysfunctional adipocytes confirmed that vindoline treatment significantly mitigate insulin resistance in myotubes and improves functional status of adipocytes. These results demonstrated that vindoline has the potential to be used as a therapeutic agent to ameliorate obesity-induced T2DM associated insulin resistance profile in adipocytes and skeletal muscles.
ARTICLE | doi:10.20944/preprints202306.0419.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: chalky rice; xylanase activity; cellulase activity; hard water; hardness
Online: 6 June 2023 (08:40:23 CEST)
Global warming has led to the increase in chalky grains of rice, which has also caused the deteriorations of physicochemical and cooking qualities of rice grains. These chalky rice grains are characterized by high α-amylase activity, high protease activity, and low apparent amylose contents, low degree of hardness and stickiness of boiled rice than those of the whole rice grains. In the present paper, we evaluated 14 Japonica unpolished rice grains harvested in Japan in 2021, and these samples (original grains) were divided to two groups (whole grain group and chalky grain one). We found that the chalky rice grains showed higher values of xylanase activity than those of the whole rice grains, while cellulase activity were lower than that of whole rice grains. Using rice grains blended with 30 % of chalky grains as material, we compared sugar and mineral contents and textural properties of the boiled rice grains soaked and boiled in the ordinary water or in the hard water, such as Evian or Contrex. It was shown that the hard water is useful for the prevention of the texture deterioration of the boiled rice grains due to the inhibition of the reduction of endogenous hydrolytic enzymes, such as amylase, proteinase, and xylanase. Furthermore, we found that hard water is useful for the increase of calcium and magnesium intake through the meal with the boiled rice grains soaked and cooked using hard water.
ARTICLE | doi:10.20944/preprints202306.0413.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: PFAS; metabolism; transcriptomics; transcriptome; cross-species analysis
Online: 6 June 2023 (08:22:33 CEST)
In the recent decades, per- and polyfluoroalkyl substances (PFAS) have garnered widespread public attention due to their persistence in the environment and detrimental effects on the health of living organisms, spurring the generation of several transcriptome-centered investigations to understand the biological basis of their mechanism. In this study, we analyzed 2144 publicly available datasets from 7 distinct species to examine the molecular responses to PFAS exposure and determine if there are conserved responses. Our comparative transcriptional analysis revealed that exposure to PFAS is conserved across different tissues, molecules and species. We identified and reported several genes exhibiting consistent and evolutionarily conserved transcriptional re-sponse to PFAS, such as ESR1, HADHA and ID1, as well as several pathways including lipid me-tabolism, immune response and hormone pathways. This study provides the first evidence that distinct PFAS molecules induce comparable transcriptional changes and affect the same metabolic processes across inter-species borders. Our findings have significant implications for under-standing the impact of PFAS exposure on living organisms and the environment. We believe that this study offers a novel perspective on the molecular responses to PFAS exposure and provides a foundation for future research into developing strategies for mitigating the detrimental effects of these substances.
REVIEW | doi:10.20944/preprints202306.0416.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: oculomotor neurons; trochlear motor neurons; abducens motor neurons; extraocular eye muscles; vestibular nuclei connections
Online: 6 June 2023 (08:21:45 CEST)
Extraocular eye muscles (EOMs) are innervated by axons of three ocular motor nuclei, the oculomotor (CNIII), trochlear (CNIV), and abducens (CNVI) neurons. The purpose of this review is to analyze the origin of ocular motor neurons, define the pattern of innervation of nerve fibers that project to the EOMs, pro-vide an overview of vestibular pathway inputs to ocular motor nuclei, and describe congenital disorders that alter the development of ocular motor neurons. Oculomotor neurons originate in the midbrain and innervate the ipsilateral orbit, except for the superior rectus and the levator palpebrae which are contra-laterally innervated. Trochlear motor neurons originate at the midbrain-hindbrain junction and innervate the contralateral superior oblique muscle. Abducens motor neurons originate variously in the rhombomeres r4-6 and innervate the posterior (or lateral) rectus muscle and innervate the retractor bulbi. Genes allow yielding a distinction between special somatic (CNIII, IV) and somatic (CNVI) ocular motor neurons. The ocular motor neurons are innervating somites, which receive innervates vestibular nuclei that connects with the brainstem motor neurons. Development of ocular motor neurons and their axonal projections to the EOMs may be derailed by various genetic causes, resulting in the congenital cranial dysinnervation disorders.
ARTICLE | doi:10.20944/preprints202306.0403.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Water saving; Energy consumption; Partial root drying; organic mulch; Water productivity; Water stress; Climate change
Online: 6 June 2023 (08:05:09 CEST)
Many techniques have been and are being made to find alternatives to water-saving practices. Among them, Partial root drying (PRD), one of the effective approaches, plays a major role in reducing the harmful effects of water deficit stress. An experiment was carried out using irrigation strategies [I1 (100% full irrigation “FI”), I2 (75%FI), I3 (50%FI), and I4 (PRD (50%FI)] and soil organic mulch [L0 (Zero layer organic soil mulch” control”), L1 (Single layer organic soil mulch), L2 (Two layers of organic soil mulch), and L3 (Three layers of organic soil mulch)] to inspect the impact of those treatments for increasing yield, water productivity and saving energy under arid region conditions. To meet the study's objective, two field experiments were carried out at a private farm. Our results demonstrated a general decrease in water stress and salt accumulation inside root-zone area with PRD with L3. The PRD strategy increased fruit yields by 3.7 and 7.3% and water productivity by 51.9 and 53.1% compared with I1 during 2020/2021 and 2021/2022, respectively, while reducing the applied irrigation water by 50 %. The PRD strategy showed superior results in increasing mango yield and water productivity. In general, PRD can be used as good technique to save water and energy up to 50% and enhance productivity along with using organic mulching, ultimately improving mango yield under arid climatic regions. It may prove a good adaptation strategy for current and future water shortage scenarios of climate change.
ARTICLE | doi:10.20944/preprints202306.0404.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Chicken infectious anemia virus; isolation and identification; pathogenicity; whole genome; bioinformatics analysis
Online: 6 June 2023 (08:05:07 CEST)
Chicken infectious anemia (CIA) poses a significant threat to the chicken industry in China. De-spite its non-specific symptoms, the disease is often overlooked. This study aimed to conduct a comprehensive analysis of the etiology and pathology of CIA in Guangxi Province, China. Three strains of the chicken infectious anemia virus (CIAV) were isolated from liver samples of diseased 20-week-old chickens. The complete genomes of these strains were sequenced, and experiments on specific pathogen-free (SPF) chicks revealed that the GX21121 strain exhibited high virulence. Histopathological examination of the deceased chicks showed liver cell necrosis, fibrous-serous exudation, inflammatory cell infiltration, hemorrhage in liver tissues, as well as congestion in lung and renal tissues. Phylogenetic analysis of the genome revealed that the three strains had a close genetic relationship to the Heilongjiang wild-type (GenBank KY486144). The genetic evolu-tion of their VP1 genes indicated that all three CIAV isolates belonged to genotype IIIc. In sum-mary, this study demonstrated the genomic diversity of three CIAV strains in adult layer hens. The isolation and characterization of the GX21121 strain as a highly virulent isolate provide val-uable information for further investigations into the etiology, molecular epidemiology, and viral evolution of CIAV.
ARTICLE | doi:10.20944/preprints202306.0381.v1
Subject: Biology And Life Sciences, Virology Keywords: Astrovirus; Porcine; Encephalitis; Myelitis
Online: 6 June 2023 (07:06:03 CEST)
Recently, astroviruses (AstVs) have been associated with neurological symptoms in pigs, cattle, sheep, minks, muskoxes, alpacas, and humans. To investigate genotypes of porcine astrovirus (PAstV) and neuroinvasive (Ni) PAstV in South Korea, five domestic pigs with neurological symptoms from three farms were tested using reverse transcriptase PCR, histopathology, and in situ hybridization (ISH). All five genotypes of PAstV were detected in brain tissues and coinfection of PAstV with multiple genotypes was observed. To the best of our knowledge, this is the first study to report pig infection by Ni-PAstV with multiple genotypes in South Korea.
ARTICLE | doi:10.20944/preprints202306.0391.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Outcrossing; isolation distance; varietal purity; pollen movement; faba bean pollination
Online: 6 June 2023 (07:04:58 CEST)
Faba bean (Vicia faba L.) is a partially outcrossing species requiring an isolation distance to maintain genetic purity when more than one variety is grown in field conditions. This information is crucial for seed growers and faba bean breeders. A study was conducted at the University of Sydney’s Plant Breeding Institute, Narrabri over two years to examine the extent of natural outcrossing using a creamy white flower characteristic as a morphological marker, which is controlled by a single recessive gene. The white flowered genotype (IX225c) was grown in paired rows of 150 m length in four directions from a central 480 m2 plot of the normal flowered genotype PBA Warda. A beehive was placed in the central plot at flowering time and natural pollination was allowed. At maturity, seed samples were taken from the white flowered genotype at designated intervals along each axis and 100 seeds from each sample were grown in the glasshouse/birdcage to the 4-5 leaf stage and the proportion of plants displaying stipule spot pigmentation (normal flower colour and spotted stipule are linked) was used to determine the percentage of outcrossing. Maximum outcrossing of 2.28% occurred where both genotypes were grown side by side (0 m) and the degree of outcrossing decreased as the distance along each axis from the central plot increased. At 6 m distance the outcrossing was less than 1%, however on occasion it increased to 1% beyond a distance of 100 m, indicating the volatile and unpredictable nature of bee flights. Distance had the major effect on outcrossing, but direction and its interaction had no effect. The results suggest that to limit outcrossing to below 0.5%, a distance of more than 150 m between plots of different faba beans cultivars would be required. It also indicated that Australian faba bean genotypes are mostly self-fertile and a relatively narrow isolation distance will ensure self-fertilization in seed production and breeding programs.
ARTICLE | doi:10.20944/preprints202306.0389.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: body composition; body condition score; body parameters; fat; live weight; ewes condition; im-age analysis
Online: 6 June 2023 (05:54:38 CEST)
Farmers are continually looking for new reliable, objective and non-invasive methods for evaluation of ewe condition. Live weight (LW) and body condition score (BCS) are used by farmers as a basis to determine the condition of the animal. Body composition is an important aspect of monitoring animal condition. The body composition is the amount of fat, lean and bone; knowing the amount of each is important because the information can be used for better strategic management interventions. Experiments were conducted to establish the relationship between body composition and body parameters, at key life’s stages (weaning and pre-mating), using measurements automatically determined by an image processing ap-plication at Lincoln University sheep farm for 88 Coopworth ewes. Computerized Tomography technology was used to develop relationship with body parameters and a subset was used to validate the predicted model. Multivariate linear regression (MLR), artificial neural network (ANNs) and regression tree (RT) statistical analysis methods were evaluated to determine their efficacy to predict body fat, lean and bone. The results showed a correlation between fat, lean and bone determined by CT and the fat, lean, bone weight estimated by live weight and body parameters calculated using the image processing application with R2 values of 0.90 for fat, 0.72 for lean and 0.50 for bone using ANNs statistical model. From these results, farmers can utilize accurate measures of fat which will enhance nutritional and management practices.
ARTICLE | doi:10.20944/preprints202306.0379.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: skeletal muscle; transcriptome; gene expression; Fujian white rabbit; growth stage
Online: 6 June 2023 (04:45:16 CEST)
In China, the demand for rabbit meat is also increasing, and the production for rabbit meat is important. However, the underlying mechanisms of regulate skeletal muscle growth and development in rabbits remain unclear. The purpose of this study was to identify candidate genes related to skeletal muscle growth in rabbits and explore their potential regulatory mechanisms. RNA-seq technique was used to compare the differences of skeletal muscle transcriptome in Fujian white rabbits at different developmental stages (day 20 and 26 of embryos and birth 1, 30 and 60-day-olds) with a total of 25 individual selected. A total of 9737 DEGs that were acquired from the five groups were annotated into three ontologies of the GO database: biological process (BP), cell component (CC), and molecular function (MF). For KEGG analysis, there are 8249 genes were enriched in 1148 pathways, of which 67 pathways were significantly enriched, mainly in Hypertrophic cardiomyopathy (HCM), the PPAR signaling pathway, MAPK signaling pathway. Among all comparison groups, SE was the most abundant AS event. Real-time PCR verified that the expression patterns of differential genes were consistent with the transcriptome sequencing results. These results will provide a molecular regulation mechanism of muscle growth and development in Fujian white rabbits, and should serve an important theoretical basis for improving meat performance and growth rate of Chinese local meat rabbit breeds.
ARTICLE | doi:10.20944/preprints202306.0378.v1
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: Electrodermal activity; Photoplethysmography; Consumer wearables
Online: 6 June 2023 (04:27:30 CEST)
The capability of measuring specific neurophysiological and autonomic parameters plays a crucial role in the objective evaluation of the human’s mental and emotional states. These human aspects are commonly known in scientific literature to be involved in a wide range of processes, such as the stress and arousal. These aspects represent a relevant factor especially in real and operational environment. Neurophysiological autonomic parameters, such as the Electrodermal Activity (EDA) and Photoplethysmographic data (PPG), have been usually investigated through research-graded devices, therefore resulting in a high degree of invasiveness, which could negatively interfere with the monitored user’s activity. For such a reason, in the last decade the recent consumer-grade wearable devices, usually designed for fitness tracking purposes, are receiving an increasing attention from the scientific community, being characterized by higher comfort, easiness of use and, therefore, by higher compatibility with dailylife environments. The present preliminary study aimed at assessing the reliability of a consumer wearable device, i.e., the Fitbit Sense, with respect to a research-graded wearable, i.e., the Empatica E4 wristband, and a laboratory device, i.e., the Shimmer GSR3+. The EDA and PPG were collected among 12 participants while performing multiple resting conditions. The results demonstrated that the EDA and PPG-derived features computed through the wearable and research devices were positively and significantly correlated, while the reliability of the consumer device resulted to be significantly lower.
ARTICLE | doi:10.20944/preprints202306.0225.v2
Subject: Biology And Life Sciences, Plant Sciences Keywords: Auxin; cell wall composition; chlorogenic acid; lignin; pectin; post harvest wounding; tap roots
Online: 6 June 2023 (03:57:18 CEST)
The blackening of cut carrots decreases their shelf life and causes severe economic losses but the molecular and metabolic mechanisms that underpin this phenomenon remain poorly characterized. Studies were therefore undertaken to determine the molecular and metabolic causes of the blackening. The susceptibility of blackening was dependent on the period of time that the crop was stored underground prior to harvest. The structure of the cell walls in the black regions was substantially changed compared to the orange regions. The black regions of carrot batons had decreased immunodetection of xyloglucan, HG-pectin, RG-I pectin, galactan and arabinan but had higher levels of lignin and phenolic compounds compared to the orange regions. Transcript profiling analysis revealed that phytohormone signalling processes were activated in the black regions. Transcripts associated with auxin signalling and ethylene-responsive transcription factors were increased in the black regions. In contrast, the levels of transcripts encoding proteins associated with secondary metabolism were decreased in the black regions. These findings implicate ethylene and auxin-related processes in the control of the primary to secondary metabolism shift that results in lignification and cell wall disruption that underpin the blackening process.
ARTICLE | doi:10.20944/preprints202306.0370.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: miRNA; Buffalo; Estrus; Prognostic biomarker; Gene-Target prediction
Online: 6 June 2023 (03:52:39 CEST)
Buffalo are silent breeders, therefore detecting estrus is a serious challenge. There is a rising need for sensitive and precise biomarkers in this scenario. Recent research on miRNA has demon-strated the importance of these molecules as biomarkers. Though there have been miRNA studies in saliva during the estrous cycle, there have been few miRNA research in blood samples. The current study was designed to look at blood miRNAs during the oestrous cycle in heifers (n=5) to address the issue of silent estrus. On the day of estrus and diestrus, blood samples from 60 heifers were obtained and pooled into (n=5) separate samples. Ultrasonography and progesterone assay was performed to confirm estrus. Then, employing particular miRNA adapters, small RNA se-quencing of miRNA was performed using the Illumina Miseq 2500. The UEA sRNA bioinfor-matics workbench identified 94 substantially differently expressed miRNAs (p>0.05) from these data. In estrus, 63 miRNA were upregulated and 31 miRNA were downregulated. When fold change was increased to (log2foldchange >1; q value less than 0.05), 25 miRNAs were elevated during estrus. miR-497, miR-582, miR-10174, miR-23, miR-223, miR-1296 were upregulated, whereas miR-10167, 671, 1246,122 were downregulated. miR-497 is unusually elevated (log2 foldchange>5) when compared to another miRNA (log2 foldchange >5) miRNet 2.0, Cytoscape, and MIENTURNET network software found that miR-497 has more degree centrality, above 60; it is associated with more than 60 nodes, followed by miR-93
ARTICLE | doi:10.20944/preprints202306.0366.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Liquid liquid phase separation; protein oligomerization; GO; domain-domain interaction; domain linker; intrinsically disordered regions; domain-peptide interaction; beta-sheet; transmembrane helices; post-translational modification
Online: 6 June 2023 (03:43:57 CEST)
Although there are a large number of databases available for regulatory elements, bottleneck has been created by the lack of bioinformatics tools for predicting types of mechanisms underlying actions of regulatory elements. To reduce the gap, we developed ARabidopsis Transcription regulatory Factor Domain-domain interaction Analysis Tool- Liquid-liquid phase separation (LLPS), Oligomerization, GO analysis (ART FounDATion-LOG), a useful toolkit for protein-nucleic acid interactions (PNI) and protein-protein interactions (PPI) analysis based on domain-domain interaction (DDI). LLPS, protein oligomerization, structural properties of protein domains, and protein modifications are major components in orchestrating spatio-temporal dynamics of PPI and PNI. Our goal is to integrate PPI/PNI information into development of prediction model for identifying important genetic variants in peach. The program unified inter-database relational keys by protein domains for facilitating inference from the model species. Key advantage of the program lies in the integrated information of related features: LOG, structural characterization of domain (e.g. domain linker, intrinsically disordered regions, DDI, domain-motif (peptide) interaction, beta-sheet and transmembrane helices), and post-translational modification. We provided simple tests to demonstrate how to use the program. The program may be applied to other eukaryotic organisms. The program codes and data are freely available for download at and https://sourceforge.net/projects/artfoundation-log/.
REVIEW | doi:10.20944/preprints202306.0360.v1
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: eye movements; visual system; mouse vision
Online: 6 June 2023 (02:44:55 CEST)
The mouse visual system recently became the most popular model to study the cellular and circuit mechanisms of sensory processing. However, the importance of eye movements in mice only started to be appreciated recently. Eye movements provide a basis for active sensing and deliver insights into various brain functions and dysfunctions. A plethora of knowledge on the central control of eye movements and their role in perception and behaviour arose from work on primates. However, an overview of the known eye movement types in mice and a comparison to primates is missing.Here, we review the eye movement types described to date in mice and compare them to those observed in primates. We discuss the central neuronal mechanisms for their generation and control. Furthermore, we review the mounting literature on eye movements in mice during head-fixed and freely moving behaviours. Finally, we highlight gaps in our understanding and suggest future directions for research.
ARTICLE | doi:10.20944/preprints202306.0357.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: Cardiomyopathy; myosin RLC; myosin ELC; N-terminal protein modification, S15D-RLC phosphomimetic, super-relaxed state (SRX); Tg mice
Online: 5 June 2023 (16:43:56 CEST)
This study focuses on mimicking constitutive phosphorylation in the N-terminus of the myosin regulatory light chain (S15D-RLC) as a rescue strategy for the mutation-induced cardiac dysfunction in transgenic (Tg) models of restrictive (RCM) and dilated (DCM) cardiomyopathy caused by mutations in myosin essential (ELC) or regulatory (RLC) light chains. S15D-RLC phosphomimetic was reconstituted in left ventricular papillary muscle (LVPM) fibers from two mouse models of cardiomyopathy, RCM-E143K ELC and DCM-D94A RLC, along with their corresponding Tg-ELC and Tg-RLC wild type (WT) mice. The beneficial effects of S15D-RLC in rescuing cardiac function were manifested by S15D-RLC-induced destabilization of the super-relaxed (SRX) state that was observed in both models of cardiomyopathy. S15D-RLC promoted a shift from the SRX state to the disordered relaxed (DRX) state, increasing the number of heads readily available to interact with actin and produce force. Additionally, S15D-RLC reconstituted fibers demonstrated significantly higher maximal isometric force per cross-section of muscle compared with reconstitution with WT-RLC protein. The effects of the phosphomimetic S15D-RLC were compared to those observed for Omecamtiv Mecarbil (OM), a myosin activator shown to bind to the catalytic site of cardiac myosin and increase myocardial contractility. A similar SRX↔DRX equilibrium shift was observed in OM=treated fibers as in S15D-RLC-reconstituted preparations. Additionally, treatment with OM resulted in significantly higher maximal pCa 4 force per cross-section of muscle fibers in both cardiomyopathy models. Our results suggest that both treatments with S15D-RLC and OM may improve the function of myosin motors and cardiac muscle contraction in RCM-ELC and DCM-RLC mice.
ARTICLE | doi:10.20944/preprints202306.0349.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Alkaloids; Cells; Cranichideae; Ergastic substances; Leaf; Micromorphology; Orchidoideae; Rhizomes; Roots; Spiranthinae
Online: 5 June 2023 (16:19:40 CEST)
The orchid genus Brachystele Schltr. comprises 20 species distributed from Mexico to Argentina; 10 are found in Brazil. Anatomical studies of Orchidoideae Lindl. have been scarce, and the anatomy and histochemistry of Brachystele are still largely unknown. We characterized the vegetative organs of B. guayanensis (Lindl.) Schltr. using standard anatomical and histochemical microtechniques. Brachystele guayanensis was observed to display the anatomical characters commonly found in the vegetative organs of representatives of the Orchidaceae and Orchidoideae (including a uniseriate epidermis, thin cuticle, amphistomatic leaves, anomocytic, diacytic and tetracytic stomata, a homogeneous mesophyll, collateral vascular bundles, rhizomes with pericyclic fibers, roots with velamen, uniseriate exodermis, endodermis and pericycle). Histochemical tests confirmed the presence of lignin, proteins, and alkaloids, the lipidic nature of the cuticle, starch grains stored in spiranthosomes in the roots, and the composition of the raphides. Alkaloids were observed in great abundance, especially in the roots, and may have potentially useful medicinal activities, as has been observed in groups phylogenetically related to Brachystele.
ARTICLE | doi:10.20944/preprints202306.0347.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: soil amendment; Fenton reaction; seedling growth; plant proteomics; Lettuce
Online: 5 June 2023 (16:14:19 CEST)
Information regarding physiological and molecular plant responses to the treatment with new biofertilizers is limited. In this study a fast-composting soil amendment (FCA), obtained from solid waste by means of a Fenton reaction, was tested to evaluate the effects on the growth of Lactuca sativa L. var. longifolia seedlings. Growth rate, leaves and roots biomass, chlorophyll concentration and total soluble proteins of seedlings treated with the 2% FCA soil amendment showed significant increase in comparison with control seedlings. Leaf proteomic analysis revealed that the FCA soil amendment induced the up-regulation of proteins belonging to photosynthesis machinery, carbohydrate metabolism and promoted the up-regulation of the water stress response. Root proteomics indicated that FCA strongly induced the organs morphogenesis and developments; root cap development, lateral root formation, post-embryonic root morphogenesis were the main biological processes enriched by the treatment. Overall, our data suggest that addition of FCA formulation to the base soils might ameliorate plant growth by inducing carbohydrates primary metabolism and the differentiation of a robust root system.
ARTICLE | doi:10.20944/preprints202306.0337.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: agricultural management; antagonistic activity; fermentation formulation; copper-containing fungicides
Online: 5 June 2023 (14:31:43 CEST)
Sweet pepper is an important vegetable in the world. Bacterial leaf spot caused by the pathogen Xanthomonas perforans, is a limiting factor that significantly reduces the quality and yield of sweet pepper To control this disease, the use of chemical fungicides is currently the main disease control method. Thus, we want to develop an alternative method by using antagonistic microorganisms. Under this demand, Bacillus amyloliquefaciens PMB04 has strong antagonistic effects against pathogens and can inhibit the occurrence of diseases. B. amyloliquefaciens PMB04 has the potential for the development of a disease control product. Primarily, PMB04 revealed to contain a strong inhibitory effect against all isolated X. perforans strains. In the inoculation assay, the severity of bacterial spot disease on sweet peppers was reduced by PMB04 bacterial suspensions. To increase the convenience of field application for future prospects, the development of PMB04 fermentation liquid was carried out with different ratios of brown sugar and yeast extract in a 30-liter fermentation tank subsequently. Results exhibited that the fermentation liquid of 3-1 formula obtained the highest bacterial population in a 30-liter fermentation tank. The fermentation liquid of 0.5-0.5 formula was the most stable formula under two different conditions in terms of consistent bacterial population and sporulation. In addition, the 200-fold dilution of 3-1 and 0.5-0.5 fermentation liquids revealed best control efficacy on bacterial leaf spot of sweet pepper. Additionally, the results of the 0.5-0.5 fermentation liquid (PMB4FL) with different dilution concentrations also showed that the 200- and 500-fold dilutions had the best control efficacy. To understand the effect of commonly used copper-containing fungicides on sweet peppers on the application of microbial agent PMB4FL, the effects of copper hydroxide and tribasic copper sulfate on the growth of X. perforans strains and B. amyloliquefaciens PMB04 were assayed. The results exhibited that the above two fungicides did not have any inhibitory effect on the growth of PMB04, but had a strong inhibitory effect on the X. perforans strain. In the follow-up control experiment, the treatment of copper hydroxide had no synergistic effect with PMB4FL to control bacterial leaf spot. We concluded that the use of PMB4FL fermentation liquid alone on the leaves can effectively control the occurrence of bacterial leaf spot in sweet pepper crops.
ARTICLE | doi:10.20944/preprints202306.0327.v1
Subject: Biology And Life Sciences, Insect Science Keywords: Circadian clock; Frankliniella occidentalis; Feeding; Mating; Behavior
Online: 5 June 2023 (13:35:11 CEST)
The western flower thrips, Frankliniella occidentalis, is invasive and polyphagous. Its visual signal plays a crucial role in host location, suggesting that thrips has diurnal behavior. However, any diel rhythmicity of the thrips behavior is not yet well understood. This study analyzed the diurnal rhythmicity of the feeding and mating behaviors of thrips, and the patterns were explained in terms of diel rhythmicity by assessing the expression of genes associated with the circadian clock. Most feeding behaviors were observed during photophase in both larvae and adults. In mating behavior, which is mainly exhibited in 2~3 days-old young adults after emergence, most adults copulated at photophase. This diurnal pattern of the mating behavior was further supported by the analysis of a temporal calling behavior for mating, which was biased toward photophase. Four genes associated with the circadian clock were predicted in the F. occidentalis genome: period (PER), Timeless (TIM), Doubletime (DBT), and clock (CLK). All these genes exhibited a characteristic diel pattern in their gene expressions in a 24 h-period. The high expression peaks of these genes except for DBT were observed at photophase. To confirm the functional association of these genes with the feeding and mating behaviors, individual RNA interference specific to each gene was executed by feeding the gene-specific double-stranded RNA. Aside from DBT, suppression of these gene expressions resulted in significant deviations of the diel rhythms of the behaviors. These results suggest that the genetic components of the diel rhythmicity mediate the diurnal feeding and mating behaviors of F. occidentalis.
ARTICLE | doi:10.20944/preprints202306.0320.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: Blueberries; quality; firmness; fungal infection; anthocyanin content; phenolic content; antioxidant capacity
Online: 5 June 2023 (13:04:55 CEST)
Blueberries (Vaccinium corymbosum L.) are becoming increasingly popular for their nutritional and health benefits, and their economic value is therefore increasing. Loss of quality that can occur due to softening and fungal attack is an important consideration when marketing blueberries. Despite the added value of blueberries, no studies have been carried out on how the fruit arrives at the outlets just before purchase by the consumer in terms of firmness, physico-chemical parameters, phenolic compounds and fungal growth. The aim of this work has been, therefore, to investigate possible differences in quality parameters between blueberries purchased from ten different outlets, regardless of the supplier. The results showed that all samples were of acceptable quality, although they all had a low maturity index at the point of sale. On the other hand, differences in the parameters measured were observed between samples of the same cultivar while we could not find differences between conventionally and organically grown blueberries, suggesting that preharvest and postharvest factors could influence the final quality when they reach the consumer.
ARTICLE | doi:10.20944/preprints202306.0310.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: exercise training; aortic stenosis; heart failure; isolated papillary muscle; isolated cardiomyocyte; calcium handling.
Online: 5 June 2023 (10:47:28 CEST)
Aerobic exercise training (AET) has been used in the management of heart disease. AET may, totally or partially, restore the activity and/or expression of proteins that regulate calcium (Ca2+) handling, optimize intracellular Ca2+ flow, and attenuate cardiac functional impairment in failing hearts. However, the literature presents conflicting data regarding the effects of AET on Ca2+ transit and cardiac function in rats with heart failure resulting from aortic stenosis. The objective of this study was to evaluate the effects of AET on calcium handling and cardiac function in rats with heart failure due to aortic stenosis. Wistar rats were distributed into two groups: control (Sham; n= 61) and aortic stenosis (AoS; n= 44). After 18 weeks, the groups were redistributed into: non-exposed to exercise training (Sham, n = 28 and AoS, n = 22) and trained (Sham-ET, n = 33 and AoS-ET, n = 22) for 10 weeks. Treadmill exercise training was performed with a velocity equivalent to the lactate threshold. Echocardiogram, isolated papillary muscle, and isolated cardiomyocyte analyzed cardiac function. During isolated papillary muscle assay and isolated cardimyocyte was evaluated Ca2+. The expression of regulatory proteins of diastolic Ca2+ was analyzed via Western Blot. AET attenuated the diastolic dysfunction and benefited the systolic function. AoS-ET animals presented better response to post-rest contraction, and SERCA2a and L-type Ca2+ channels blocked than the AoS. Furthermore, AET was able to improve aspects of the mechanical function and the responsiveness of the myofilaments to the Ca2+ of the AoS-ET animals. AoS animals presented alteration in the protein expression of the SERCA2a and NCX, and AET restored SERCA2a and NCX levels near normal values. Therefore, AET increased SERCA2a activity, improved the cellular Ca2+ influx mechanism, and increased myofilament responsiveness to Ca2+, attenuating cardiac dysfunction at cellular, tissue, and chamber levels in animals with aortic stenosis and heart failure.
ARTICLE | doi:10.20944/preprints202306.0306.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: microfragmented adipose tissue; regenerative medicine; bone healing, osteotomy, cranial cruciate ligament
Online: 5 June 2023 (10:22:38 CEST)
The aim of this study was to evaluate the effects of autologous microfragmented adipose tissue (MFAT), obtained by mechanical fragmentation, on radiographic bone healing in dogs subjected to tibial plateau levelling osteotomy (TPLO). Twenty dogs with unilateral cranial cruciate disease were enrolled and randomly assigned to the treatment group (MFAT) or the control group (NT). The MFAT group underwent TPLO and autologous MFAT intra-articular administration while the NT group underwent TPLO alone. The adipose tissue was collected from the thigh region and MFAT was obtained by mechanical fragmentation at the end of the surgery. The patients were subjected to X-ray exam preoperatively, immediately postoperatively (T0) and at 4 (T1) and 8 (T2) weeks postoperatively. Two radiographic scores that had previously been described for the evaluation of bone healing after TPLO were used. A 12-point scoring system (from 0 = no healing to 12= complete remodelling) was used at T0, T1 and T2, while a 5-point scoring system (from 0 = no healing to 4 = 76%–100% of healing) was used at T1 and T2. The median healing scores were significantly higher at T1 and T2 for the MFAT group compared with the NT group for the 12-point (p < 0.05) and 5-point (p < 0.05) scoring systems. The intra-articular injection of autologous microfragmented adipose tissue can accelerate bone healing after TPLO without complications.
ARTICLE | doi:10.20944/preprints202306.0293.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Pseudomonas aeruginosa; chronic infection; respiratory; murine model; in vivo; S. aureus
Online: 5 June 2023 (09:50:00 CEST)
Pseudomonas aeruginosa (P. aeruginosa) is an opportunistic pathogen and is the leading cause of infection in patients with cystic fibrosis (CF). The ability of P. aeruginosa to evade host responses and develop into chronic infection causes significant morbidity and mortality. Several mouse models have been developed to study chronic respiratory infections induced by P. aeruginosa, with the bead agar model being the most widely used. However, this model has several limitations, including the requirement for surgical procedures and high mortality rates. Herein, we describe novel and adapted biologically relevant models of chronic lung infection caused by P. aeruginosa. Three methods are described, a clinical isolate infection model, utilizing isolates obtained from patients with CF, an incomplete antibiotic clearance model, leading to bacterial bounce-back and the establishment of chronic infection, and an adapted water bottle chronic infection model. These models circumvent the requirement for surgical procedure and importantly, can be induced with clinical isolates of P. aeruginosa and in wild-type mice. We also demonstrate successful induction of chronic infection in the transgenic βENaC murine model of CF. We envisage that the models described will facilitate the investigations of host and microbial factors, and the efficacy of novel antimicrobials, during chronic P. aeruginosa respiratory infections.
ARTICLE | doi:10.20944/preprints202306.0288.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Early cancer diagnosis; cell free DNA; biomarker; integrative biology; pan cancer
Online: 5 June 2023 (09:20:14 CEST)
Blood-based circulating cell free DNA(cfDNA) detection offers a non-invasive and easily accessible way for early cancer detection. Despite the extensive utility of cfDNA, there are still many challenges to develop the clinical biomarkers. For example, cfDNA with genetic alterations often compose a small portion of the DNA circulating in plasma, which can be confounded by cfDNA contributed by normal cells. Therefore, filtering out the potential false-positive cfDNA mutations from health population will be important for the cancer-based biomarkers. Additionally, many low-frequency genetic alterations are easily overlooked in small amount of cfDNA-based cancer test. We hypothesize that, the combination of diverse types of cancer studies on cfDNA can provide us a new insight to identify low-frequency genetic variant across cancer types for early clinical detection of cancers. By building a standardized computational pipeline for 1358 cfDNA samples across seven cancer types, we prioritize 129 shard genetic variants in the major cancer types. Further functional analysis of the 129 variants found that they are mainly enriched in ribosome pathways such as cotranslational protein targeting to membrane, some of which are tumor suppressor, oncogene and related to cancer initiation. In summary, our integrative analysis revealed the important roles of ribosome proteins as the common biomarkers in early cancer diagnosis.
ARTICLE | doi:10.20944/preprints202306.0279.v1
Subject: Biology And Life Sciences, Virology Keywords: NDV; paramyxovirus; outbreak; pathogenicity
Online: 5 June 2023 (08:43:36 CEST)
In August 2022, in the Moscow region, Russia, on a backyard farm, the mortality was observed at chickens and all 45 birds of this farm died or were slaughtered after onset of symptoms within a few days. Paramyxovirus was isolated from diseased birds. Based on the nucleotide sequences of the F and NP gene fragments, the belonging of virus to subgenotype VII.1 AAvV-1 class II was established. The cleavage site of the F gene 109SGGRRQKRFIG119 and T in 546 and 555 position of NP gene, were typical for the velogenic type. The genetically closest NDV isolates were found in Iran. The mean time of death of 10-day-old chicken embryos upon infection with the minimal infectious dose was 52 hours, which is typical for the velogenic pathotype. The virus caused 100% death of six-week-old chickens during oral infection, as well as 100% mortality of all contact chickens, including those located in remote cages, which proves the ability of virus to spread not only by fecal-oral but also by aerosol route. That demonstrates a high level of pathogenicity and contagiousness of the isolated strain for chicken. However, the mice intranasally infected with high doses of the virus had not die.
ARTICLE | doi:10.20944/preprints202306.0273.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: precision agriculture; durum wheat; Italy; case study; economic impact; agro-environmental impact; sustainability; nitrogen efficiency; profitability
Online: 5 June 2023 (08:32:28 CEST)
The European Green Deal has set a concrete strategic plan to increase farm sustainability. At the same time, the current global challenges, due to climate change and fuels and commodity market crisis, combined with the Covid-19 pandemic and the ongoing war in Ukraine, comprise the need for quality food, but also the reduction of negative external effects of agricultural production, with fair remuneration for the farmers. In response, precision agriculture has great potential to contribute to the sustainable development. Precision agriculture is a farming management that provides a holistic system approach to managing the spatial and temporal crop and soil variability within a field to improve the farm’s performance and sustainability. However, farmers are still hesitant to adopt it. On these premises, the study aims to evaluate the impacts of precision agriculture technologies on farm profitability, agronomic and environmental management by farmers adopting (or not) these technologies, using the case study method. In detail, the work focuses on the period 2014-2022 for two farms that cultivate durum wheat in Central Italy. The results suggest that the implementation of precision technologies can guarantee economic and agri-environmental efficiency. Results could serve as a basis for developing a program to start training in farms as well as suggest policy strategies.
ARTICLE | doi:10.20944/preprints202306.0270.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Mycoplasma pneumoniae; CC16; CCSP; CC10; mass spectrometry; remodeling
Online: 5 June 2023 (08:28:04 CEST)
CC16 plays many protective roles within the lung; however, the complete biological functions, es-pecially regarding the pulmonary epithelium during infection, remain undefined. We have previ-ously shown that CC16 deficient (CC16-/-) mouse tracheal epithelial cells (MTECs) have enhanced Mp burden, compared to CC16 sufficient (WT) MTECs; therefore, in this study, we wanted to fur-ther define how the pulmonary epithelium responds to infection in the context of CC16 deficiency. Using mass spectrometry and quantitative proteomics to analyze proteins secreted apically from MTECs grown at an air-liquid interface, we investigated the protective effects that CC16 elicits within the pulmonary epithelium during Mycoplasma pneumoniae (Mp) infection. When chal-lenged with Mp, WT MTECs have an overall reduction in apical protein secretion, whereas CC16-/- MTECs have increased apical protein secretion compared to their unchallenged controls. Fol-lowing Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) assessment, many of the proteins upregulated from CC16-/- MTECS (unchallenged and during Mp infection) were related to airway remodeling, which were not observed by WT MTECs. These findings sug-gest that CC16 is instrumental in providing protection within the pulmonary epithelium during respiratory infection with Mp, the major causative agent of community-acquired pneumoniae.
ARTICLE | doi:10.20944/preprints202306.0265.v1
Subject: Biology And Life Sciences, Virology Keywords: astrovirus; wild raccoon dog; neurotropic-astrovirus
Online: 5 June 2023 (08:16:12 CEST)
Astroviruses (AstVs) have been detected in a wide range of animal species, including mammals and birds. Recently, a novel AstVs associated with neurological symptoms has been detected in the brain of some mammals. Raccoon dog AstV has been reported recently in China. However, there have been no reports in South Korea. Therefore, the present study aimed to detect and genetically characterize AstVs in intestine and brain tissues of 133 wild raccoon dogs collected in Korea between 2017 and 2019. Seven wild raccoon dogs were positive for AstV, four of which were also detected in brain tissue. Analysis of the capsid protein amino acid sequences of raccoon dog AstVs detected in Korea revealed a high similarity to canine AstVs, suggesting possible interspecies transmission between raccoon dogs and dogs. Phylogenetic and capsid protein amino acid sequence analysis of raccoon dog AstVs detected in brain 17-148B strain belonged to the HMO clade and exhibited conserved sequences found in neurotropic AstVs (NT-AstVs), indicating their potential as NT-AstVs. However, the pathogenicity and transmission routes of the raccoon dog AstV detected in Korea have not yet been elucidated, so further research and continued surveillance for AstV in wild raccoon dogs are needed.
ARTICLE | doi:10.20944/preprints202305.1319.v2
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: attention development; socioeconomic status; bilingualism; cognitive development
Online: 5 June 2023 (08:01:58 CEST)
Abstract: For decades, researchers have suggested the existence of a bilingual cognitive advantage, especially in tasks involving executive functions such as inhibition, shifting, and updating. Recently, an increasing number of studies have questioned whether bilingualism results in change in executive functions, highlighting conflicting data published in the literature. The present study compared the performance of third-, fourth-, and fifth-grade bilingual and monolingual children on attentional and cognitive tasks. Participants were 61 monolingual and 74 bilingual children (M = 114.6 months; SD = 8.48 months) who were tested on two versions of the Attention Network Task (ANT), with and without social stimuli, as well as tests investigating working memory, short-term memory, narrative memory, and receptive vocabulary. Data on families’ socioeconomic status and children’s reasoning abilities were also collected. The results showed that bilingualism and socioeconomic status affected attentional networks in tasks involving social stimuli. In tasks involving non-social stimuli, socioeconomic status only affected the alerting and executive conflict networks. Consistent with the literature, a positive relationship emerged between socioeconomic status and executive control in the context of social stimuli, and a negative relationship emerged between socioeconomic status and the alerting network in the context of non-social stimuli. Interestingly, neither socioeconomic status nor social attentional networks correlated with working memory. Therefore, although more investigations are required, the results suggest that differences in social contexts mainly affect attentional functions.
REVIEW | doi:10.20944/preprints202306.0235.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: β-glucosidase; biocatalysis; biosynthesis; enzyme engineering
Online: 5 June 2023 (04:30:08 CEST)
β-glucosidases (BGLs) play a crucial role in the degradation of lignocellulosic biomass as well as in industrial applications such as pharmaceuticals, foods, and flavors. However, the application of BGLs has been largely hindered by issues such as low enzyme activity, product inhibition, low stability, etc. Many approaches have been developed to engineer BGLs to improve these enzymatic characteristics to facilitate industrial production. In this article, we review the recent advances in BGL engineering in the field, including the efforts from our laboratory. We summarize and discuss the BGL engineering studies according to the targeted functions as well as the specific strategies used for BGL engineering.
ARTICLE | doi:10.20944/preprints202306.0217.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Aquatic microbiology; Bacteria; Microbial ecology; Phytopathogens; Irrigation
Online: 2 June 2023 (15:38:59 CEST)
There is significant lack of information on the presence of plant pathogens in aquifer, increasingly used for irrigation during last decades and considered mostly free of them. In this work, we report the presence of bacteria from the Pseudomonas syringae complex (referred as PsyC) including phytopathogenic bacteria, in groundwater of Avignon, France. Their concentration was variable and inversely correlated with water electrical conductivity. Their mean abundance were hundred times lower than in the river Durance, connected with the aquifer but surprisingly, their genetic structure were more homogeneous. Moreover, most strains (97 %) from groundwater were tested as potentially pathogenic on plants, when in the river they were only 71 %. Determinants of this low diversity and high aggressiveness remain to be identified. We conclude that aquifers must be considered potential plant pathogenic reservoirs even if more surveys are needed to understand the real impact on crops during irrigation. These results could be included in prediction models and new approaches to disease forecasting and surveillance and could lead to adaptation of agricultural practices.
ARTICLE | doi:10.20944/preprints202306.0212.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Cheiridiidae; False scorpions; Levant; Species List; Syarinidae; Taxonomy; Zoogeography
Online: 2 June 2023 (14:16:19 CEST)
The location of Israel at the junction of three continents leads to a unique faunal combination of Palearctic and Afrotropic zoogeographic origins. Following systematic revisions over the past sixty years and the discovery of new species, the only available key to the pseudoscorpions (Arachnida: Pseudoscorpiones) of Israel (Beier 1963) has become outdated. We provide here an up-to-date checklist of the pseudoscorpion species of Israel including distribution maps, and the first illustrated identification key of the Israeli fauna based on morphological characters. Prior to our study this fauna comprised twelve families, 26 genera and 52 morphospecies, including several “subspecies”. We increase this number and list 61 pseudoscorpion morphospecies that belong to 28 genera and fourteen families. Most species are Palearctic and Mediterranean, and only a few are Afrotropic. Two families new to Israel are reported here for the first time: Syarinidae and Cheiridiidae. Both families are cosmopolitan and have representatives in the Mediterranean region. The putative new species are presented here at a genus level and will be described separately elsewhere.
ARTICLE | doi:10.20944/preprints202306.0199.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: mutations; folding free energy change; binding free energy change; single nucleotide variant
Online: 2 June 2023 (11:58:21 CEST)
Development of methods and algorithms to predict the effect of mutations on protein stability, protein-protein, and protein-DNA/RNA binding is necessitated by the needs of protein engineering and for understanding the molecular mechanism of disease-causing variants. The vast majority of the leading methods are either methods with adjustable parameters or machine learning algorithms, both requiring a database of experimentally measured folding and binding free energy changes. These databases are collections of experimental data taken from scientific investigations typically aimed at probing the role of particular residue on the above-mentioned thermodynamics characteristics, i.e., the mutations are not introduced at random and do not necessarily represent mutations originating from single nucleotide variant (SNV). Thus, the reported performance of the leading algorithms assessed on these databases or other limited cases, may not be applicable for predicting the effect of SNVs seen in the human population. Indeed, we demonstrate that the SNVs and non-SNVs are not equally presented in the corresponding databases and the distribution of the free energy changes are not the same. Furthermore, the Pearson correlation coefficients (PCCs) obtained on cases involving SNVs are less impressive than for non-SNVs, indicating that caution should be used in applying them to reveal the effect of human SNVs. All methods are found to underestimate the energy changes by roughly a factor of 2.
ARTICLE | doi:10.20944/preprints202306.0195.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Male infertility; heavy smoking; transcript level; PGAM5; PTPRN2; TYRO3
Online: 2 June 2023 (11:49:29 CEST)
Smoking have been linked to male infertility by affecting the sperm epigenome and genome. In this study, we aimed to determine possible changes in the transcript levels of the PTPRN2, PGAM5, and TYRO3 genes in heavy smokers compared with non-smokers; and to investigate their association with fundamental sperm parameters. One hundred eighteen sperm samples (63 heavy-smokers (G1) and 55 non-smokers (G2) were included in this study. Semen analysis was performed according to WHO guidelines. After total RNA extraction, RT-PCR was used to quantify the transcript levels of studied genes. In G1 a significant decrease in standard semen parameters in comparison to non-smokers has been shown (p<0.05). Moreover, PGAM5 and PTPRN2 were differentially expressed (P≤0.03 and P≤0.01, respectively), and downregulated in spermatozoa of G1 compared to G2. In contrast, no difference was observed for TYRO3 (p≤0.3). In G1, mRNA expression level of studied genes correlated negatively with motility, sperm count, normal form, vitality, and sperm membrane integrity (p<0.05). Therefore, smoking may affect gene expression and male fertility by altering DNA methylation patterns in genes associated with fertility and sperm quality, including PGAM5, PTPRN2, and TYRO3.
ARTICLE | doi:10.20944/preprints202306.0194.v1
Subject: Biology And Life Sciences, Virology Keywords: insect viruses; arthropod virus; distant homology detection; remote homology detection; virulence factor; tospovirus; structure prediction; cypovirus; small protrusion domain
Online: 2 June 2023 (11:45:35 CEST)
Today, the most powerful approach to detect distant homologs of a protein is based on structure prediction and comparison. Yet this approach is still inapplicable to many viral proteins. Therefore, we developed a powerful sequence-based procedure to identify distant homologs of viral proteins. It relies on 3 main principles: 1) Traces of sequence similarity with a protein can persist beyond the significance cutoff of homology detection programs; 2) Candidate homologs can be identified among proteins with weak sequence similarity to the query, by using "contextual" information, e.g. taxonomy or type of host infected; 3) These candidate homologs can be validated using highly sensitive profile-profile comparison.As a test case, we applied our approach to a protein without known homologs, ORF4 of Lake Sinai virus (which infects bees). We discovered that ORF4 is composed of a domain that has homologs in proteins from >20 taxa of viruses infecting arthropods. We called it “Widespread, Intriguing, Versatile” (WIV) domain because it is found in proteins with a wide variety of domain organizations and functions. For example, WIV is encoded by the NSs protein of tospoviruses, a global threat to food security, which infect plants through arthropod vectors; by the protein encoded by RNA2 ORF1 of chronic bee paralysis virus, a widespread virus of bees; and by various proteins of cypoviruses, which infect the silkworm bombyx mori. WIV has a previously unknown structural fold, according to Alphafold predictions. In some viral species, WIV facilitates infection of arthropods, according to bibliographical evidence
ARTICLE | doi:10.20944/preprints202306.0191.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: soil salinity; sodium; chloride; ion transporters; transcriptome factors
Online: 2 June 2023 (11:34:36 CEST)
Sweet sorghum is an important bioenergy grass and valuable forage with a strong adaptability to saline environments. However, little is known about the mechanisms of sweet sorghum coping with ion toxicity under salt stresses. Here, we first evaluated the salt tolerance of a sweet sorghum cultivar “Lvjuren” and determined its ion accumulation traits under NaCl treatments; then explored key genes involved in Na+, Cl−, K+ and NO3− transport using transcriptome profiling and qRT-PCR method. The results showed that the growth and photosynthesis of sweet sorghum were unaffected by 50 and 100 mM NaCl treatments, indicative of a strong tolerance of this species to salt stresses. Under NaCl treatments, sweet sorghum could efficiently exclude Na+ from shoots and accumulate Cl− in leaf sheaths to avoid their overaccumulation in leaf blades; meanwhile, it possessed a prominent ability to sustain NO3− homeostasis in leaf blades. Transcriptome profiling identified several differentially expressed genes associated with Na+, Cl−, K+ and NO3− transport in roots, leaf sheaths and leaf blades of sweet sorghum after 200 mM NaCl treatment for 6 and 48 h. Moreover, transcriptome data and qRT-PCR results indicated that HKT1;5, CLCc and NPF7.3-1 should be key genes involved in Na+ retention in roots, Cl− accumulation in leaf sheaths and maintenance of NO3− homeostasis in leaf blades, respectively. Many TFs were also identified after NaCl treatment, which should play important regulatory roles in salt tolerance of sweet sorghum. This work lays a preliminary foundation for clarifying the molecular basis underlying the adaptation of sweet sorghum to adverse environments.
COMMUNICATION | doi:10.20944/preprints202306.0190.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: organic horticultural practices and production; chemical metabolites; isotopic ratios; multivariate analysis; chemometrics
Online: 2 June 2023 (11:29:22 CEST)
In the last decades, consumers are increasingly interested in organic products and they strongly demand for reliability of the traceability of the organic products they use to buy and eat. Different researches have been carried out over the years to investigate on new and reliable systems to test the authenticity of products obtained using organic cultivation methods. The monitoring of some chemical components, derived from primary and/or secondary metabolism, in horticultural organic and conventional products, has highlighted the diversity induced by the two production techniques while the difference in fertilization practices has been shown to impact on the isotopic distribution of some elements, with particular reference to nitrogen. An integrated system is proposed to validate, through the acquisition of isotopic data and other chemical and biochemical parameters, the authenticity of organic products. This approach is intended to be coupled to the application of chemometric multivariate analysis of isotopic data combined with other quality and nutraceutical parameters, giving the possibility to discriminate organic from conventional products, thanks to the different isotopic signature impressed by the different nitrogenous source combined with the qualitative pattern of the crops, significantly affected by the different treatments. The main perspectives of the presented integrated approach, based on the combined use of chemometric and analytical tools, are linked to the feasibility of applying a reliable system to authenticate productions obtained with organic fertilizers (organic agriculture) respect to those obtained with the use of synthetic fertilizers (conventional agriculture), protect and valorize virtuous farmers and support political stakeholders and decision makers to counteract food fraud.
COMMUNICATION | doi:10.20944/preprints202306.0189.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: RNA-seq; COVID-19; SARS-CoV-2; gene enrichment analysis; enriched pathways; differentially expressed genes; transcriptomics
Online: 2 June 2023 (11:12:22 CEST)
During the infection by SARS-CoV-2, the virus is changing infected host cell into its own factory producing new viral particles. As infection progresses, infected cell undergoes many changes in various pathways. One of the events caused by changes is cytokine storm, which leads to the severe symptoms. In this study, we investigated transcriptomic changes caused by COVID-19 disease using RNA-seq data obtained from COVID-19-positive patients and COVID-19-negative donors. RNA-seq data were collected for the purpose of identification of potential biomarkers associated with a different course of the disease. Here, the first datasets of 96 samples were analyzed to validate the methods. The aim of this publication is to report pilot results. In search of potential biomarkers associated with different disease severity, we performed differential expression analysis of human transcriptome, focusing on COVID-19 positivity and symptom severity. Since we detected plenty of potential biomarkers, we performed KEGG enrichment analysis to get better view of altered pathways. Results show, that affected were pathways related to immune processes and response to infection, also multiple signaling pathways, while most of them were also reported to be influenced by SARS-CoV-2 infection in previous studies.
REVIEW | doi:10.20944/preprints202306.0188.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: bioactive compounds; biorefinery; coffee by-products; functional food ingredients; health benefits; nutraceuticals; sustainability; technological innovation; valorization; waste utilization
Online: 2 June 2023 (11:00:02 CEST)
Coffee production generates significant amounts of by-products, posing challenges for waste management in the industry. Recent research has revealed that coffee by-products are rich in bioactive compounds suitable to produce functional food ingredients and nutraceuticals. In this review, we explore biorefinery strategies for extracting and utilizing bioactive compounds from coffee by-products, including the production of bio-based chemicals and materials, as well as the extraction of phenolic compounds, antioxidants, and dietary fiber for food applications. We propose a stepwise approach for the development of functional food ingredients and nutraceuticals from coffee by-products, covering the identification of needs, comprehensive characterization, in vitro and in vivo research, unraveling the mechanism of action, food and nutraceutical formulation, sensory analysis, shelf-life stability, scale-up, randomized control trials, and biostatistic and bioinformatic integration. Additionally, we discuss the market potential, regulatory issues, and technological innovation surrounding the commercialization of coffee by-product-based products. Emphasizing the importance of regulatory compliance and sustainability in the coffee industry, this review highlights the potential of coffee by-products to be transformed from waste into valuable functional food ingredients and nutraceuticals, offering a promising avenue for waste reduction and promoting sustainability in the coffee industry.
CASE REPORT | doi:10.20944/preprints202304.0698.v2
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: raccoons; canine distemper virus
Online: 2 June 2023 (10:31:55 CEST)
Canine distemper virus (CDV) is a serious contagious disease of canines, cats and sometimes ra-coons. The study included seven raccoons from Timisoara Zoo. The detection of CDV in all raccoons was accomplished using qRT-PCR, but several other exams were also conducted. Clinically, severe digestive disorders were observed, characterized by diarrhea and repeated hematemesis. Pseudomembranous gastroenteritis, congestion and pulmonary edema were found during the ne-cropsy of two racoons. Immunohistochemically, the brown color was highlighted in the examined sectionsand it was present in the cytoplasm of the cells from the germinal centers of the medullary area. Histopathological examination revealed lymphocyte depletion and intranuclear and intracy-toplasmic inclusions in the intestine. Based on the qRT-PCR assay, laboratory tests and lesions ob-served, it was established that the raccoons got infected with CDV, and two of them died as a result. The necropsy, histological lesions and immunohistochemical results are comparable between dogs and racoons. Through the results obtained, it was concluded that the interspecific infection is possible and the epidemiological risk of infection transmitted by racoons to domestic animals, such as dogs and cats, needs to be examined in the future.
ARTICLE | doi:10.20944/preprints202306.0183.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: allelopathy; barnyardgrass; root trait; phytohormone; biotic stress
Online: 2 June 2023 (10:29:48 CEST)
Barnyardgrass (Echinochloa spp.) is a prevalent type of weed in rice fields worldwide. Despite the growing knowledge concerning allelopathic interference with barnyardgrass, little is understood regarding the competitive mechanisms between allelopathic rice and herbicide-resistant barnyardgrass at the plant physiological level. In this context, a hydroponic system was employed to investigate the root morphological traits and different phytohormones levels of two rice cultivars, i.e., the allelopathic rice cultivar “PI312777” (PI) and the non-allelopathic rice cultivar “Lemont” (LE), when co-planted with quinclorac-resistant and -susceptible barnyardgrass, respectively. The results showed that the shoot and root biomass were greater in the allelopathic rice cultivar. Moreover, the treatments at the two time points induced an increase in shoot and root biomass of PI when subjected to barnyardgrass stress. In terms of root morphology, PI exhibited significantly higher fine-root length in diameters <0.5 mm, a greater number of root tips, and longer root tips compared to LE. In addition, the levels of different plant hormones, including auxin (IAA), abscisic acid (ABA), jasmonic acid (JA), and salicylic acid (SA), known for their diverse adaptation strategies to biotic stress, were analysed. The response to quinclorac-resistant barnyardgrass stress was consistent in terms of the content of well-known stress-related hormones, namely SA and JA. The accumulation of SA and JA was observed in both rice cultivars under the stress of quinclorac-resistant barnyardgrass, with higher contents of these hormones in PI than that in LE. The most significant change was observed in IAA and ABA contents in rice, which decreased significantly from 7 days to 14 days under co-culture stress. Additionally, PI contained higher levels of IAA and ABA than LE in the presence of barnyardgrass stress. This research may aid in the development of strategies for reducing the environmental impact of herbicides through the prudent selection of non-chemical herbicide control tactics.
REVIEW | doi:10.20944/preprints202306.0177.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: ferroptosis; cancer; EMT; angiogenesis; metastasis
Online: 2 June 2023 (10:12:45 CEST)
Ferroptosis is a newly discovered iron-dependent form of regulated cell death driven by phospholipid peroxidation, associated with processes including iron overload, lipid peroxidation and dysfunction of cellular antioxidant systems. Ferroptosis is found closely related to many diseases including cancer, at its every stage. Epithelial-mesenchymal transition (EMT) in malignant tumors that originate from epithelia promotes cancer cell migration, invasion and metastasis by disrupting cell-cell and cell-martrix junctions, cell polarity, etc. Recent studies have shown that ferroptosis appears to share multiple initiators and overlapping pathways with EMT in cancers and identify ferroptosis as a potential predictor of various cancer grade and prognosis. Cancer metastasis involves multiple steps including local invasion of cancer cells, intravasation, survival in circulation, arrest at a distant organ site, extravasation and adaptation to foreign tissue microenvironments, angiogenesis and the formation of “premetastatic niche”. Numerous studies have revealed that ferroptosis is closely associated with cancer metastasis. From the cellular perspective, ferroptosis has been implicated in the regulation of cancer metastasis. From the molecular perspective, the signaling pathways activated during the two events interweave. This review briefly introduces the mechanisms of ferroptosis, and discusses how ferroptosis is involved in cancer progression including EMT, cancer angiogenesis, invasion and metastasis.
ARTICLE | doi:10.20944/preprints202306.0174.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: tea (Camellia sinensis); solid phase micro extraction (SPME); two-dimensional comprehensive gas chromatography-olfactometry-mass spectrometry analysis (GC × GC-O-MS); gas chromatog-raphy-ion mobility spectrometry (GC-IMS); aroma compounds
Online: 2 June 2023 (09:59:50 CEST)
Tea (Camellia sinensis) is one of the most popular beverages worldwide. Many types of tea prod-ucts continuously emerge in an endless stream; so, the classification or verification of tea be-comes more difficult. Aroma is a vital indicator of tea quality. The present study deals with the identification of aroma compounds in 18 different kinds of tea belonging to three typical tea va-rieties, including green tea, oolong tea, and black tea, using GC-IMS and GC×GC-O-MS. More-over, the clustering of all 18 tea samples and the in-depth correlation analysis between sensory evaluation and instrumental data were performed using the PCA and OPLS-DA. The results re-vealed that in all 18 kinds of tea, a total of 85 aroma compounds were detected by GC-IMS, whereas 318 were detected by GC×GC-O-MS. The PCA result revealed that green tea, oolong tea, and black tea could be clearly separated based on their peak areas. The OPLS-DA result showed that a total of 49 aroma compounds with VIP value > 1.0 could be considered as the potential in-dicators to quickly classify or verify tea types. This study not only compared the aroma differ-ences across different types of teas, but also provided ideas for the rapid monitoring of tea qual-ity and variety.
BRIEF REPORT | doi:10.20944/preprints202306.0164.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: biofilms; bioelectric effect; electrolysis; plaque index; gingival index
Online: 2 June 2023 (09:48:55 CEST)
Bioelectric effect is known as combinatorial biofilm treatment with low dose of antibiotics with small electricity. When external electric field or current are applied, biofilms can be affected by the electrostatic force, non-uniform distribution of essential electrolytes, induction of low activity of enzyme, and increase of permeability of biofilms. In this work, we have focused on the reduction of applied electric power consumption that could avoid water electrolysis which was one of major challenges for biomedical applications. We have developed a new type of electrical signal that enhances the efficacy of biofilm removal. The results show combination of alternating and direct current remove biofilm effectively without causing electrolysis. We further developed an oral healthcare device as a bioelectric toothbrush and tested in dental clinic. The results demonstrated 75% reduction of gingivitis. In addition, we have tested a mimicked air conditioner biofilms that are root causes of aerobic hygiene infection. The result demonstrates 81.8% increased biofilm removal. In conclusion, a new bioelectric technology has been developed and demonstrated the biofilm removal efficacy without the electrolysis.
REVIEW | doi:10.20944/preprints202306.0170.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: Long-COVID-19; SARS-CoV-2; Endothelial cells; Cognitive dysfunction; Blood Brain Barrier; Neuro-inflammation
Online: 2 June 2023 (09:38:56 CEST)
As the name implies, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a single-stranded RNA virus and a member of the corona virus family, primarily affecting the upper respiratory system and the lungs. Like many other respiratory viruses, SARS-CoV-2 can spread to other organ systems. Apart from causing diarrhea, another most common but debilitating complication caused by the SARS-CoV-2 is neurological symptoms and cognitive difficulties, which occur in up to two thirds of hospitalized covid patients and ranging from shortness of concentration, overall declined cognitive speed to executive or memory function impairment. Neuro-cognitive dysfunction and “brain fog” are frequently present in COVID-19 cases, which can last several months after the infection, leading to disruption of daily life. Cumulative evidence suggests that SARS-CoV-2 affects vasculature in the extra pulmonary systems directly or indirectly, leading to impairment of endothelial function and even multi-organ damage. The post COVID-19 long-lasting neurocognitive impairments have not been studied fully; and the underlying mechanism remains elusive. In this review, we summarize the current understanding of the effects of COVID-19 on vascular dysfunction and how vascular dysfunction leads to cognitive impairment in patients.
REVIEW | doi:10.20944/preprints202306.0166.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Raman, IR, spectroscopy, phytochrome, tetrapyrrole, photoswitch
Online: 2 June 2023 (09:01:39 CEST)
Phytochromes are biological photoswitches that translate light into a physiological function. Spec-troscopic techniques are essential tools in molecular research on these photoreceptors. This review is directed to summarize how resonance Raman and IR spectroscopy contributed to the under-standing of structure, dynamics, and reaction mechanism of phytochromes, outlining the substan-tial experimental and theoretical challenges and describing the strategies to master them. It is shown that the potential of the various vibrational spectroscopic techniques can be most efficient-ly exploited in integral approaches by combination with theoretical methods as well as other ex-perimental techniques.