REVIEW | doi:10.20944/preprints202101.0549.v1
Subject: Life Sciences, Biochemistry Keywords: Japanese encephalitis virus; birds; genotype shift; JEV genotype I; JEV genotype III
Online: 26 January 2021 (16:47:47 CET)
Japanese encephalitis (JE) is a vaccine preventable disease caused by the Japanese encephalitis virus (JEV), which is primarily prevalent in Asia. JEV is a Flavivirus, classified into a single serotype with five genetically distinct genotypes (I, II, III, IV, and V). JEV genotype III (GIII) had been the most dominant strain and caused numerous out breaks in the JEV endemic countries until 1990. However, recent data shows the emergence of genotype I (GI) as a dominant genotype and it is gradually displacing GIII. The exact mechanism of this genotype displacement is still unclear. The virus can replicate in mosquito vectors and vertebrate hosts to maintain its zoonotic life cycle; pigs and aquatic wading birds act as an amplifying/reservoir hosts, and humans and equines are the dead end hosts. The important role of pigs as an amplifying host for JEV is well known. However, the influence of other domestic animals especially birds that live in high abundance and close proximity to human is not well studied. Here, we strive to briefly highlight the role of birds in JEV zoonotic transmission, discovery of birds as a natural reservoirs and amplifying host for JEV, species of birds susceptible to JEV infection, and the proposed effect of JEV on poultry industry in future perspective which have been neglected for a long times. We also discussed the recent in vitro and in vivo studies which show that the newly emerged GI viruses replicated more efficiently in bird-derived cells and ducklings/chicks than GIII, and an important role of birds in the JEV genotype shift from GIII to GI.
ARTICLE | doi:10.20944/preprints202101.0513.v1
Subject: Life Sciences, Biochemistry Keywords: Aleppo pine; conifers; phytosulfokine; plant growth regulators; somatic embryogenesis
Online: 26 January 2021 (14:21:31 CET)
Organogenesis and somatic embryogenesis have been widely applied as the two main regeneration pathways in plant tissue culture. However, recalcitrance is still a main restriction in the clonal propagation of many woody species, especially in conifers. They undergo a “phase change” that leads to significant loss of organogenic and embryogenic capacity, thus reducing the responsive tissues or organs to juvenile material, and narrowing the competence window. In this sense, in vitro regeneration of mature conifer trees has been a long-cherished goal in many laboratories worldwide. In this work, apical shoot buds were used as explants for both organogenesis and somatic embryogenesis in order to cloning mature trees of Aleppo pine. Reinvigorated axillary shoots were submitted to somatic embryogenesis induction through the manipulation of culture media, including the use of auxins such as 2,4-D and NAA, cytokinins (BA and kinetin) and phytosulfokine (50, 100 and 200 nM). Although somatic embryos could not be obtained, embryogenic-like tissue was produced followed by the appearance of actively proliferating non-embryogenic calli and differences between treatments were found, especially when phytosulfokine was added to the induction media. Organogenic system produced reinvigorated shoots from both BA treatments tested (22 and 44 µM), from juvenile somatic trees and adult trees, and ex-vitro acclimatized plants were developed.
Subject: Life Sciences, Biochemistry Keywords: Course-based undergraduate research experience (CURE); repetition; iteration
Online: 26 January 2021 (11:37:54 CET)
Course-based undergraduate research experiences (CUREs) provide students with opportunities for the same gains that apprenticed research with faculty members offer. As their popularity increases, it is important that critical elements of CUREs are supported by thoughtful design. Student experiences in CUREs can provide important insights into why CUREs are so effective. We present evidence from students who participated in CUREs at the introductory, intermediate, and advanced levels, as well as from graduate teaching assistants for an introductory lab course that included a CURE. Students and teaching assistants describe repetition as a valuable element in CUREs and other laboratory experiences. We used student work and open-ended interviews to identify which of five previously described elements of CUREs students found important. Because repetition was particularly salient, we characterized how students described repetition as they experienced it in courses that contained full-length or “micro”-CUREs. In prompted interviews, students described how repetition in CUREs provided cognitive (learning concepts) and practical (learning technical skills) value. Recent graduates who had participated in CUREs at each level of their Biology education were particularly aware that they placed value in repetition and acknowledged it as motivational in their own learning. Many students described repetition in metacognitive terms, which also suggests that as students advance through laboratory and CURE curricula, their understanding of how repetition supports their learning becomes more sophisticated. Finally, we integrated student descriptions to suggest ways in which repetition can be designed into CUREs or other laboratory courses to support scientific learning and enhance students’ sense of scientific identity.
ARTICLE | doi:10.20944/preprints202012.0293.v2
Subject: Life Sciences, Biochemistry Keywords: Hsp70; biomarker; glioblastoma; NK cells; clinical study
Online: 26 January 2021 (11:33:34 CET)
Despite rapid progress in the treatment of many cancers, glioblastoma remains a devastating disease with dismal prognosis. The aim of this study was to identify immune-related biomarkers that more effectively predict outcome of glioblastoma. Since heat shock protein 70 (Hsp70) and IL-2 are known to increase the expression of activatory NK cell receptors, recognizing aggressive human tumor cells that present Hsp70 on their cell surface, extracellular Hsp70 levels were determined in glioma patients together with activatory NK cell receptors. All gliomas are membrane Hsp70-positive (mHsp70+) and high grade gliomas more frequently show an overexpression of Hsp70 in the nucleus and cytosol. Significantly increased extracellular Hsp70 levels are detected predominantly in glioblastomas with large necrotic areas. Overall survival (OS) is more favorable in patients with low Hsp70 serum levels indicating that a high Hsp70 expression is associated with an unfavorable prognosis. Elevated frequencies of NK cells are associated with a more favorable outcome. Of caution, a glucocorticoid therapy reduces the prevalence of NK cells. In summary, elevated frequencies of Hsp70-reactive NK cells at diagnosis and lower Hsp70 levels predict a more favorable prognosis in glioblastoma patients.
ARTICLE | doi:10.20944/preprints202101.0531.v1
Subject: Life Sciences, Biochemistry Keywords: Priming; RNAi; Tribolium castaneum; Host-parasite interaction; Bacillus thuringiensis
Online: 26 January 2021 (10:50:41 CET)
Insects possess an array of defense molecules allowing them to fight infections. They can also show a form of immune memory, named priming. However, the involvement of insect immune defense mechanisms in priming is unclear, since invertebrates lack the molecular machinery present in vertebrates to build an immune memory. In the red flour beetle Tribolium castaneum, larvae can be primed via the oral route with Bacillus thurigiensis var. tenebrionids (Btt). This results in changes in the expression of a large number of genes, among which some belong to families of ancient defense genes. In the present work, we tested whether three chosen candidate genes (a Thaumatin, a C-type Lectin and an Osiris-like gene) could be involved in the survival to a Btt exposure, as well as in the priming phenotype. We assessed changes in their expression over time and according to the priming treatment, knocked them down individually by RNA interference (RNAi), and observed how it affected survival upon challenge. The quantification of gene expression patterns in our larvae with RT-qPCR showed that up- and/or down-regulation of the genes, after the priming treatment, was quite volatile and time dependent. Upon knock-down, we did not observe the expected decrease in survival to Btt or the abolishment of the priming phenotype. We conclude that knocking down genes individually is probably insufficient to affect survival and priming in our system. This gives us insight into the complexity of the molecular processes underpinning priming.
Mon, 25 January 2021
REVIEW | doi:10.20944/preprints202101.0521.v1
Subject: Life Sciences, Molecular Biology Keywords: Data integration; multi-omics; integration strategies; genomics
Online: 25 January 2021 (16:19:31 CET)
Metabolomics deals with multiple and complex chemical reactions within living organisms and how these are influenced by external or internal perturbations. It lies at the heart of omics profiling technologies not only as the underlying biochemical layer that reflects information expressed by the genome, the transcriptome and the proteome, but also as the closest layer to the phenome. The combination of metabolomics data with the information available from genomics, transcriptomics, and proteomics offers unprecedented possibilities to enhance current understanding of biological functions, elucidate their underlying mechanisms and uncover hidden associations between omics variables. As a result, a vast array of computational tools have been developed to assist with integrative analysis of metabolomics data with different omics. Here, we review and propose five criteria – hypothesis, data types, strategies, study design and study focus – to classify statistical multi-omics data integration approaches into state-of-the-art classes under which all existing statistical methods fall. The purpose of this review is to look at various aspects that lead the choice of the statistical integrative analysis pipeline in terms of the different classes. We will draw a particular attention to metabolomics and genomics data to assist those new to this field in the choice of the integrative analysis pipeline.
REVIEW | doi:10.20944/preprints202101.0517.v1
Subject: Life Sciences, Biochemistry Keywords: Gram-negative bacterial; Metabolite transporter; pathways; metabolic engineering approaches
Online: 25 January 2021 (15:49:13 CET)
Metabolite transport across cellular membranes is a key feature of living organisms. Specialized proteins or protein complexes mediate such transport processes and are accessible to genetic engineering approaches. This special issue will reflect on the different transport between cellular compartments. It will provide an overview about different transporter classes and metabolic engineering approaches in different organisms ranging from Bacteria to Eukarya. The transport mechanisms energetics of these compounds were thought little of, and most consideration was given to the designing of metabolic pathways. Gram-negative microbes discharge a wide scope of proteins whose capacities incorporate biogenesis of organelles, for example, pilli and flagella, supplement securing, destructiveness, and efflux of medications and different poisons. Six particular emission frameworks have been appeared to intervene protein send out through the inward and external layers of Gram-negative microbes. These pathways are exceptionally monitored all through the Gram-negative bacterial species. In Gram-positive microscopic organisms, discharged proteins are usually moved across the single layer by the Sec pathway or the two-arginine (Tat) pathway. Recently efforts focused on transporter and metabolite engineering, visualize the improvement and enhancement of microbial cell to pass such metabolites these metabolite carrier proteins are inserted into the inner membrane of mitochondria across the inner membrane, specialized carrier proteins are necessary that mediate the transport into and out of the mitochondrial matrix. Two main strategies for metabolic engineering in plants: the introduction of genes encoding new enzymes and the use of TFs controlling specialized metabolic pathways
HYPOTHESIS | doi:10.20944/preprints202101.0514.v1
Subject: Life Sciences, Biochemistry Keywords: Senescence; Immortalization; Epithelial to Mesenchymal Transition; Carcinogenesis; Hypothesis
Online: 25 January 2021 (15:31:18 CET)
The origin of cancer remains one of the most important enigmas in modern biology. The prevailing paradigm has failed to grasp a comprehensive view of the disease. Naturally, therapies developed under the current assumptions are inadequate and cancer is practically an incurable disease. Meanwhile, descriptive studies continuously extend the molecular complexity of cancer without an equivalent advancement in its understanding. Furthermore, they tend to accumulate inconsistencies inexplicable under the classical view. This paper presents a compelling theory of the origin of carcinomas. By hypothesis, a series of generic events in epithelial tissues promoted by cellular aging and inflammation enables the reactivation of developmental programs. The origin of carcinomas in vivo is described as the time-ordered cell state transitions undergone by epithelial cells in the hyperplasia due to replicative senescence and inflammation towards a mesenchymal undifferentiated endogenous cell state with cancerous behavior. In support of the theory, the molecular, cellular, and histopathological evidence is critically reviewed. A plausible model for the origin of carcinomas is presented to explain the mechanism underlying carcinogenesis from an evolutive and developmental perspective. The implications of the hypothesis in the current strategies for cancer prevention and treatment are discussed along with rational alternatives and some predictions for possible experimental validation.
ARTICLE | doi:10.20944/preprints202101.0500.v1
Subject: Life Sciences, Biochemistry Keywords: origin of life; disspative structuring; prebiotic chemistry; abiogenisis; adenine
Online: 25 January 2021 (13:57:05 CET)
I describe the non-equilibrium thermodynamics and the photochemical mechanisms which may have been involved in the dissipative synthesis, proliferation, and evolution of the fundamental molecules at the origin of life from simpler and more common precursor molecules such as HCN, H2O and CO2 under the impressed UVC photon flux of the Archean. The fundamental molecules absorb strongly in this UVC region and exhibit strong coupling between their electronic excited and ground states which endows them with efficient photon disipative capacity (broad wavelength absorption and rapid radiationless dexcitation) suggestive of dissipative structuring. The autocatalytic nature of the synthesized molecules in dissipating the same photochemical potential that directed their synthesis leads to their proliferation. The non-linearity in the photochemical and chemical reaction rates provides numerous stationary states which can be reached by amplification of a molecular concentration fluctuation near a bifurcation, promoting the system into states of generally higher photon disspative efficacy. An example is given of the UV photochemical dissipative structuring, proliferation, and evolution of molecules on route to the nucleobase adenine from the common precursor molecules HCN and H2O occurring within a fatty acid vesicle. The kinetic equations are resolved under different environmental conditions, providing a non-equilibrium thermodynamic analysis of the appearance of an early important molecule for the origin of life.
ARTICLE | doi:10.20944/preprints202012.0287.v2
Subject: Life Sciences, Biochemistry Keywords: ABCB1; bortezomib; CXCR4; gene expression; MAF; MARCKS; multiple myeloma; mRNA; POMP; PSMB5; refractory; RPL5; TXN; XBP1; sensitive
Online: 25 January 2021 (13:17:31 CET)
Proteasome inhibitors, like bortezomib, play a key role in the treatment of multiple myeloma (MM); however, most patients eventually relapse and eventually show multiple drug resistance, and the molecular mechanisms of this resistance remain unclear. The present study examines the expression of previously-described genes that may influence resistance to bortezomib treatment at the mRNA level (ABCB1, CXCR4, MAF, MARCKS, POMP, PSMB5, RPL5, TXN and XBP1). mRNA expression was determined in 73 MM patients treated with bortezomib-based regimens (30 bortzomib-sensitive and 43 bortezomib-refractory patients) and 11 healthy controls. RPL5 was significantly down-regulated in multiple myeloma patients as compared with healthy controls. Moreover, POMP was significantly up-regulated in MM patients refractory to bortezomib-based treatment. In multivariate analysis, high expression of PSMB5 and CXCR and autologous stem cell transplantation were independent predictors of progression-free survival, and high expression of POMP and RPL5 was associated with shorter overall survival.
BRIEF REPORT | doi:10.20944/preprints202101.0495.v1
Subject: Life Sciences, Microbiology Keywords: Sulforaphane; Alcohol; Burkholderia; Binge drinking; MHS cells; Melioidosis
Online: 25 January 2021 (13:03:02 CET)
Binge drinking is associated with increased mortality and morbidity. Burkholderia pseudomallei, the causative agent of pneumonic melioidosis can occur in healthy humans; however, binge alcohol intoxication is a major risk factor. Previous findings indicate that a single binge alcohol episode increases Burkholderia spp. infection by reducing alveolar macrophage function. The aim of this study was to test the ability of the phytonutrient sulforaphane (SFN) to rescue the phagocytic function of alveolar macrophages when infected with Burkholderia spp. in vitro. B. thailandensis E264 was used as a useful BSL-1 model to determine the effects of SFN pre-treatment. The primary outcome was macrophage phagocytic killing, while the secondary outcome was the nuclear factor (erythroid-derived 2)-like (Nrf2) signaling response measured by western blot analysis. Results indicate that alveolar macrophages pre-treated with SFN (5 M) and challenged with 0.2% (v/v) alcohol for 3 or 8 h prior to live B. thailandensis infection improved intracellular killing of B. thailandensis ~2-fold compared to MH-S cells treated with alcohol alone. These data demonstrate that SFN may be an effective pre-treatment option to prevent alcohol mediated immune dysfunction and restore macrophage phagocytic killing of Burkholderia spp. and other similar opportunistic pathogens.
Subject: Life Sciences, Biochemistry Keywords: single particle tracking; single molecule biophysics; fluorescence
Online: 25 January 2021 (12:26:31 CET)
Single particle tracking (SPT) is a powerful class of methods for studying the dynamics of biomolecules inside living cells. The techniques reveal the trajectories of individual particles, with a resolution well below the diffraction limit of light, and from them the parameters defining the motion model, such as diffusion coefficients and confinement lengths. Most existing algorithms assume these parameters are constant throughout an experiment. However, it has been demonstrated that they often vary with time as the tracked particles move through different regions in the cell or as conditions inside the cell change in response to stimuli. In this work, we propose an estimation algorithm to determine time-varying parameters of systems that discretely switch between different linear models of motion with Gaussian noise statistics, covering dynamics such as diffusion, directed motion, and Ornstein-Uhlenbeck dynamics. Our algorithm consists of three stages. In the first stage, we use a sliding window approach, combined with Expectation Maximization (EM) to determine maximum likelihood estimates of the parameters as a function of time. These results are only used to roughly estimate the number of model switches that occur in the data to guide the selection of algorithm parameters in the second stage. In the second stage, we use change detection (CD) techniques to identify where the models switch, taking advantage of the off-line nature of the analysis of SPT data to create non-causal algorithms with better precision than a purely causal approach. Finally, we apply EM to each set of data between the change points to determine final parameter estimates. We demonstrate our approach using experimental data generated in the lab under controlled conditions.
REVIEW | doi:10.20944/preprints202101.0471.v1
Subject: Life Sciences, Biochemistry Keywords: aptamer; aptasensor; diagnosis; imaging; sequencing; therapeutics; probes; fluorescence; pathogenic bacteria; cancer cells; monoclonal antibodies; SELEX; nucleic acids
Online: 25 January 2021 (10:18:16 CET)
Issues presented by the application of monoclonal antibodies in diagnostic assays and as curative agents can make the use of such molecules cost-prohibitive and sometimes even unsafe. This has warranted the development of short single-stranded oligonucleotides known as Aptamers. The structural malleability of these short DNA or RNA nucleotide segments allows them to exist in distinct conformations. SELEX (Systematic Evolution of Ligands by Exponential Enrichment) is a multi-step process for synthesis of aptamers. Each step of this procedure is governed by a diverse set of factors that influence production efficiency, binding affinity, and specificity of the oligonucleotides. Headway in aptamer research has been made in recent years by the introduction of newer iterations of the SELEX process. A greater number of studies are now being carried out to incorporate aptamers into existing disease detection tools and therapies. An overview has been given first on the key aptamer properties and the process of their production (with its newer iterations), contrasting each of them with that of monoclonal antibodies. Possible manifold applications afforded due to unique aptamer characteristics are also discussed. A keen review is further provided on the design, development and use of fluorescent aptamers in bioimaging, sequencing or profiling, and treatment of pathogenic bacteria and tumor cells.
ARTICLE | doi:10.20944/preprints202101.0470.v1
Subject: Life Sciences, Biochemistry Keywords: Citrus fruits; patulin, dietary intake, variation in patulin; liquid chromatography
Online: 25 January 2021 (10:16:09 CET)
The research aims to discover the natural occurrence of patulin (PAT) in selected citrus fruits from the central cities of Punjab and Pakistan's Northern cities. Total 2970 samples of twelve citrus fruits; kinnow, orange, grapefruits, bitter orange, mausami, red blood, pineapple, sweet orange, rough lime, sweet lime, kagzi lime and lemon were examined using liquid chromatography fitted with UV detector. The limit of detection (LOD) and quantification limit was 0.04 and 0.12 µg/kg, respectively. The results have shown that 56% of samples of citrus fruits from Punjab's central cities, Pakistan, were discovered to be infected from PAT. The elevated amounts of PAT ranging from 0.04 to 1150 µg/kg were found in citrus fruit samples from Multan cities. Furthermore, 31.7% of samples of citrus fruits from Northern cities of Pakistan were discovered to be infected with PAT, and the elevated amounts were found ranging from 0.04-320 µg/kg from Swat city. About 22.1% of samples of citrus fruits have levels of PAT greater than the suggested limits established by the European Union (EU). PAT's dietary intake levels ranged from 0.10-1.11 µg/kg bw/day from the central cities of Punjab, Pakistan, and 0.13-1.93 µg/kg bw/day were documented from Northern cities of Pakistan.
REVIEW | doi:10.20944/preprints202101.0461.v1
Subject: Life Sciences, Biochemistry Keywords: Diuretic hormone; sleep, feeding; metabolism; ion transport peptide; tachykinin; short neuropeptide F; insulin-like peptide; neuromodulation
Online: 25 January 2021 (09:23:22 CET)
Leucokinins (LKs) constitute a family of neuropeptides identified in numerous insects and many other invertebrates. The LKs act on G-protein coupled receptors that display only distant relations to other known receptors. In adult Drosophila, 26 neurons/neurosecretory cells of three main types express LK. The four brain interneurons are of two types, and these are implicated in several important functions in the fly’s behavior and physiology, including feeding, sleep-metabolism interactions, state-dependent memory formation, as well as modulation of gustatory sensitivity and nociception. The 22 neurosecretory cells (ABLKs) of the abdominal neuromeres coexpress LK and a diuretic hormone (DH44), and together these regulate water and ion homeostasis and associated stress, as well as food intake. In Drosophila larvae, LK neurons modulate locomotion, escape responses, and aspects of ecdysis behavior. A set of lateral neurosecretory cells, ALKs, in the brain express LK in larvae, but inconsistently so in adults. These ALKs coexpress three other neuropeptides and regulate water and ion homeostasis, feeding and drinking, but the specific role of LK is not yet known. This review summarizes Drosophila data on embryonic lineages of LK neurons, functional roles of individual LK neuron types, interactions with other peptidergic systems, and orchestrating functions of LK.
ARTICLE | doi:10.20944/preprints202101.0460.v1
Subject: Life Sciences, Biochemistry Keywords: feeding trial; growth; maintenance; nutrient evaluation; protein utilization; Thai swamp buffalo
Online: 25 January 2021 (09:23:11 CET)
Interpretation of increased gain in the bovine animals is difficult to be validated due to inherent genetic variation to meet their requirement for energy and protein, and those may relate to the bull species, e.g., Thai swamp buffalo. Therein, the study aimed at investigating and predicting protein requirement systems, with providing abundant energy intake 2.20 Mcal/kg DM for maintenance and growth of Thai swamp buffaloes using the comparative prolonged feeding trial for 90 days. Sixteen bull Thai swamp buffaloes at the initial (Age: 18-24 months; BW: 233 ± 25.0 kg) were as-signed into four treatment groups, four buffaloes each, fed 5.42, 6.96, 8.94, and 10.71% DM crude protein (CP). CP intake, BW, and physiological fluid were determined. The net CP requirements for maintenance and growth of Thai swamp buffaloes were 5.41 g CP/kg W0.75 and 0.46 g CP/g average daily gain (ADG), respectively. Our results indicated that CP requirement increases, when BW increases. An increased dietary CP resulted in an increased number at blood urine nitrogen (N), N absorption, total volatile fatty acid, urinary purine derivative, and the microbial N. Notably, the net CP requirement for growth of Thai swamp buffalo was higher than it reported in NRC, but the maintenance was lower.
Fri, 22 January 2021
ARTICLE | doi:10.20944/preprints202101.0456.v1
Subject: Life Sciences, Biochemistry Keywords: Citrus fruits; patulin; dietary intake; variation in patulin; liquid chromatography
Online: 22 January 2021 (14:33:10 CET)
The research aims to discover the natural occurrence of patulin (PAT) in selected citrus fruits from the central cities of Punjab and Pakistan's Northern cities. Total 2970 samples of twelve citrus fruits; kinnow, orange, grapefruits, bitter orange, mausami, red blood, pineapple, sweet orange, rough lime, sweet lime, kagzi lime and lemon were examined using liquid chromatography fitted with UV detector. The limit of detection (LOD) and quantification limit was 0.04 and 0.12 µg/kg, respectively. The results have shown that 56% of samples of citrus fruits from Punjab's central cities, Pakistan, were discovered to be infected from PAT. The elevated amounts of PAT ranging from 0.04 to 1150 µg/kg were found in citrus fruit samples from Multan cities. Furthermore, 31.7% of samples of citrus fruits from Northern cities of Pakistan were discovered to be infected with PAT, and the elevated amounts were found ranging from 0.04-320 µg/kg from Swat city. About 22.1% of samples of citrus fruits have levels of PAT greater than the suggested limits established by the European Union (EU). PAT's dietary intake levels ranged from 0.10-1.11 µg/kg bw/day from the central cities of Punjab, Pakistan, and 0.13-1.93 µg/kg bw/day were documented from Northern cities of Pakistan
ARTICLE | doi:10.20944/preprints202011.0032.v2
Subject: Life Sciences, Biophysics Keywords: Non-ionizing Radiation; Millimeter waves; Novel biomedical applications; Yeast; Non-invasive devices
Online: 22 January 2021 (14:31:18 CET)
Nonionizing millimeter-waves (MMW) interact with cells in a variety of ways. Here the inhibited cell division effect was investigated using 85-105 GHz MMW irradiation within the ICNIRP (International Commission on Non-Ionizing Radiation Protection) non-thermal 20 mW/cm2 safety standards. We irradiated using radiation with a power density of about 1.0 mW/cm2 over 5-6 hours on 50 cells/μl samples of Saccharomyces cerevisiae model organism. This resulted in 62% growth rate reduction compared to the control (sham). The effect was specific for 85-105 GHz range, and was energy and cell density dependent. Irradiation of wild type and Δrad52 (DNA damage repair gene) deleted cells presented no differences of colony growth profiles indicating non-thermal MMW treatment does not cause permanent genetic alterations. Dose versus response relations studied using a standard horn antenna (~1.0 mW/cm2) and compared to that of a compact waveguide (17.17 mW/cm2) for increased power delivery resulted in complete termination of cell division via non-thermal processes supported by temperature rise measurements. Combinations of MMW mediated Structure Resonant Energy Transfer (SRET), membrane modulations eliciting signaling effects, and energetic resonance with biomolecules are conjectured to be responsible for the observations reported. Our results suggest innovative applications of nonionizing radiation procedures for yeast related diseases and other targeted biomedical outcomes.
REVIEW | doi:10.20944/preprints202101.0446.v1
Subject: Life Sciences, Biochemistry Keywords: Diuretic hormone; behavior; sleep; feeding; neuromodulation; neurohormone
Online: 22 January 2021 (12:48:25 CET)
Leucokinins (LKs) constitute a neuropeptide family first discovered in a cockroach and later identified in numerous insects and several other invertebrates. The LK receptors are only distantly related to other known receptors. Among insects, there are many examples of species where genes encoding LKs and their receptors are absent. Furthermore, genomics has revealed that LK signaling is lacking in several of the invertebrate phyla and in vertebrates. In insects, the number and complexity of LK expressing neurons vary, from the simple pattern in the larva of Drosophila where the entire CNS has 20 neurons of three main types, to cockroaches with about 250 of many different types. Common to all studied insects is the presence or 1-3 pairs of LK-expressing neurosecretory cells in each abdominal neuromere of the ventral nerve cord, that, at least in some insects, regulate secretion in Malpighian tubules. This review summarizes the diverse functional roles of LK signaling in insects, as well as other arthropods and mollusks. These functions include regulation of ion and water homeostasis, feeding, sleep-metabolism interactions, state-dependent memory formation, as well as modulation of gustatory sensitivity and nociception. Other functions are implied by the neuronal distribution of LK, but remain to be investigated.
ARTICLE | doi:10.20944/preprints202101.0443.v1
Subject: Life Sciences, Biochemistry Keywords: Trichome; type IV; K-seq; QTLs mapping; QTL-seq; tomato; Solanum pimpinellifolium
Online: 22 January 2021 (12:11:59 CET)
Trichomes are a common morphological defense against pests, in particular, type IV glandular trichomes have been associated with resistance against different invertebrates. Cultivated tomatoes usually lack or have a very low density of type IV trichomes. Thus, specific breeding programs to incorporate these natural defences, that are common within the Solanum genus, might improve a more sustainable management. We have identified a S. pimpinellifolium accession with very high density of this type of trichomes. Two F2 mapping populations using two different parents have been developed, characterized and genotyped using a new genotype methodology, K-seq. We have been able to build an ultra-dense genetic map with 147,326 markers with an average distance between markers of 0.2 cM that has allowed us to perform a detailed mapping. We have used two different families and two different approaches, QTL mapping and QTL-seq, to identify several QTLs implicated in the control of trichome type IV developed in this accession on the chromosomes 5, 6, 9 and 11. The QTL located on chromosome 9 is a major QTL that has not been previously reported in S. pimpinellifolium that increases by a factor of 9 the density of trichomes.
ARTICLE | doi:10.20944/preprints202101.0439.v1
Subject: Life Sciences, Biochemistry Keywords: Rift Valley fever virus; non-structural NSs protein; interferon antagonist; nuclear filaments; PXXP motifs
Online: 22 January 2021 (09:47:33 CET)
Rift valley fever virus (RVFV) is a mosquito-borne bunyavirus that causes an important disease in ruminants, with great economic losses. The infection can be also transmitted to humans; therefore it is considered a major threat to both human and animal health. In a previous work, we described a novel RVFV variant selected in cell culture in the presence of the antiviral agent favipiravir that was highly attenuated in vivo. This variant displayed 24 amino acid substitutions in different viral proteins when compared to its parental viral strain, two of them located in the NSs protein that is known to be the major virulence factor of RVFV. By means of a reverse genetics system, in this work we have analyzed the effect that one of these substitutions, P82L, has in viral attenuation in vivo. Rescued viruses carrying this single amino acid change were clearly attenuated in BALB/c mice while their growth in an IFN-competent cell line as well as the production of IFN-β did not seem to be affected. However, the pattern of nuclear NSs accumulation was modified in cells infected with the mutant viruses. These results unveil a new RVFV virulence marker highlighting the multiple ways of NSs protein to modulate viral infectivity.
Thu, 21 January 2021
ARTICLE | doi:10.20944/preprints202101.0428.v1
Subject: Life Sciences, Biochemistry Keywords: Arabidopsis thaliana; indole-3-acetic acid; indole-3-acetamide; indole glucosinolate; seed maturation; seed size; cell proliferation; plant growth
Online: 21 January 2021 (15:03:42 CET)
The major auxin, indole-3-acetic acid (IAA), is associated with a plethora of growth and developmental processes including embryo development, expansion growth, cambial activity, and the induction of lateral root growth. Accumulation of the auxin precursor indole-3-acetamide (IAM) induces stress related processes by stimulating abscisic acid (ABA) biosynthesis. How IAM signaling is controlled is, at present, unclear. Here, we characterize an ami1/rooty double mutant, that we initially generated to study the metabolic and phenotypic consequences of a genetic blockade of the indole glucosinolate and IAM pathways in Arabidopsis thaliana. Our mass spectrometric analyses of the mutant revealed that the combination of the two mutations is not sufficient to fully prevent the conversion of IAM to IAA. The detected strong accumulation of IAM was, however, recognized to substantially impair seed development. We further show by genome-wide expression studies that the double mutant is broadly affected in its translational capacity, and that a small number of cell proliferation and plant growth regulating transcriptional circuits are repressed by the high IAM content in the seed. In accordance with the previously described growth reduction in response to elevated IAM levels, our data support the hypothesis that IAM is a growth repressing counterpart to IAA.
REVIEW | doi:10.20944/preprints202101.0425.v1
Subject: Life Sciences, Biochemistry Keywords: Goat; Sheep; Small Ruminants; Animal Models; Regenerative Medicine.
Online: 21 January 2021 (15:01:17 CET)
Medical and translational scientific research requires the use of animal models as an initial approach to the study of new therapies and treatments, but when the objective is an exploration of translational potentialities, classical models fail to adequately mimic problems in humans. Among the larger animal models that have been explored more intensely in recent decades, small ruminants, namely sheep and goats, have emerged as excellent options. The main advantages associated to the use of these animals in research works are related to their anatomy and dimensions very similar to those of humans in most physiological systems, in addition to their low maintenance and feeding costs, tendency to be docile, long life expectancies and few ethical complications raised in society. The most obvious disadvantages are the significant differences in some systems such as the gastrointestinal, and the reduced amount of data that limits the comparison between works and the validation of the characterization essays. Despite everything, recently these species have been increasingly used as animal models for diseases in different systems, and the results obtained open doors for their more frequent and advantageous use in the future. The purpose of this review is to summarize the general principles related to the use of small ruminants as animal models, with focus on regenerative medicine, to group the most relevant works and results published recently and to highlight the potentials for the near future in medical research.
ARTICLE | doi:10.20944/preprints202009.0270.v2
Subject: Life Sciences, Biochemistry Keywords: caprine arthritis-encephalitis virus; goat; antigens; antibodies; proviral DNA
Online: 21 January 2021 (12:46:50 CET)
Aim: The aim of this study was to use a multi target approach to testing with both serological tests and an in-house real-time molecular test to investigate the prevalence of the caprine arthritis-encephalitis virus (CAEV) in goats from three hobbyist farms in the Republic of Tatarstan, Russia. Materials and Methods: We have approached the detection of using a multi target approach testing with both ELISA and an in-house real-time PCR test to investigate the prevalence of CAEV in goats. Animals from three hobbyist farms were used in this study. The animals from two farms (n=13 for F1 and n=8 for F2) had clinical signs of arthritis and mastitis. In the third farm (n=15 for F3), all goats were homebred and had no contact with imported animals. Results: CAEV antibodies (ELISA targets TM env and gag genes) were detected in serum samples from two farms (F1 and F2), indicating a seroprevalence 87.50-92.31%. Specific CAEV antibodies were also detected in milk samples. CAEV proviral DNA was detected in 53.85-62.50%. Results from all tests performed in the third farm (F3) were negative, indicting all tests were 100% specific.Conclusion: Results of this work show that CAEV is circulating and present in small hobbyist goat farms in Russia. Serological and molecular tests could be of importance for CAEV control and eradication programs in Russia for hobbyist goat farms.
Subject: Life Sciences, Biochemistry Keywords: D-amino acids; homochirality; molecular modeling; secondary structure occupancy; stability
Online: 21 January 2021 (12:44:27 CET)
On the primitive Earth, both L- and D-amino acids would have been present. However, only L-amino acids are essential blocks to construct proteins in modern life. To study the relative stability of D-amino acid substituted peptides, a variety of computational methods were applied. Ten prebiotic amino acids (Gly, Ala, Asp, Glu, Ile, Leu, Pro, Ser, Thr, and Val) were previously determined by multiple meteorite, spark discharge, and hydrothermal vent studies. Some previously reported early Earth polypeptide analogs were focused on in this study. Tripeptides composed of only Asp, Ser, and Val exemplified that different positions (i.e., N-terminus, C-terminus, and middle) made a difference in the minimal folding energy of peptides, while the chemical classification of amino acid (hydrophobic, acidic, or hydroxylic) did not show a significant difference. Hierarchical cluster analysis for dipeptides with all possible combinations of the proposed ten prebiotic amino acids and their D-amino acid substituted derivatives generated five clusters. Primordial simple polypeptides were modeled to test the significance of molecular fluctuations, secondary structure occupancies, and folding energy differences based on these clusters. We found peptides with α-helices, long β-sheets, and long loops are usually less sensitive to D-amino acid replacements in comparison to short β-sheets. Intriguingly, amongst 129 D-amino acid residues, mutation sensitivity profiles presented that the ratio of more to less stable residues was about 1. In conclusion, some combinations of a mixture of L- and D-amino acids can potentially act as essential building blocks of life.
BRIEF REPORT | doi:10.20944/preprints202101.0416.v1
Subject: Life Sciences, Biochemistry Keywords: Respiratory Syncytial Virus, Molecular Diagnostic, Respiratory Viruses, Coronavirus, Bronchiolitis
Online: 21 January 2021 (12:12:25 CET)
Over two years (2012-2014), 719 nasopharyngeal samples were collected from 6 weeks to 12 months old infants presenting at emergency department with moderate to severe acute bronchiolitis. Viral testing was performed and we found 98% positive samples including 90% Respiratory Syncytial Virus, 34% Human Rhino Virus, and 55% viral co-detections with predominance of RSV/HRV co-infections (30%). Interestingly, we found that the risk of being infected by HRV is higher in the absence of RSV, suggesting interferences or exclusion mechanisms between these two viruses. Conversely, Coronavirus infection had no impact on the likelihood of co-infection involving HRV and RSV. Bronchiolitis is the leading cause of hospitalizations in infants before 12 months of age, and many questions about its role in the later chronic respiratory diseases (asthma and chronic obstructive pulmonary disease) do exist. Role of virus detection and burden of viral codetections need to be further explored, in order to understand the physiopathology of chronic respiratory diseases, a major public health issue.
ARTICLE | doi:10.20944/preprints202101.0414.v1
Subject: Life Sciences, Biochemistry Keywords: 5-Hydroxymethylfurfural; Biocatalysis; 2,5-Di(hydroxymethyl)furan; Fusarium; Whole Cells; Biotransformation; Platform Chemical; Biomass; Bioreactor
Online: 21 January 2021 (10:14:47 CET)
2,5-Di(hydroxymethyl)furan (DHMF) is a high-value chemical block than can be synthesized from 5-hydroxymethylfurfural (HMF), a platform chemical that results from the dehydration of biomass-derived carbohydrates. In this work, the HMF biotransformation capability of different Fusarium species was evaluated and F. striatum was selected to produce DHMF. The effects of the inoculum size, glucose concentration and pH of the media over DHMF production were evalu-ated by a 23 factorial design. A substrate feeding approach was found suitable to overcome the toxicity effect of HMF towards the cells when added at high concentrations (>75 mM). The pro-cess was successfully scaled-up at bioreactor scale (1.3 L) with excellent DHMF production yields (95%) and selectivities (98%). DHMF was purified from the reaction media with high recovery and purity by organic solvent extraction with ethyl acetate.
Wed, 20 January 2021
ARTICLE | doi:10.20944/preprints202101.0391.v2
Subject: Life Sciences, Biochemistry Keywords: Sustainable Development Goals; Ethnobotany; Human Health; Poverty; Traditional Knowledge; Sustainable Agriculture
Online: 20 January 2021 (11:04:41 CET)
Sustainable Development Goals (SDGs) envisaged under Agenda 2030 are a set of seventeen goals which envisage a holistic approach towards attaining certain targets keeping humankind and the planet at center. There are total 169 targets spread across seventeen goals covering wide ranging issues and challenges the world is facing in the twenty-first century. And they are to be achieved by 2030. Concerted efforts of all the stakeholders ranging from indigenous communities, common citizens, scientists, policy makers, world leaders are needed to achieve all the goals and targets Of the seventeen goals, at least seven goals are of interest to the ethnobotanists and are associated with traditional ethnobotanical knowledge. Therefore to achieve those set of goals, a thorough understanding is required to disentangle the intricacies involving traditional ethnobotanical knowledge, indigenous people as traditional knowledge holders and their future role. Understanding relationships between traditional ethnobotanical knowledge and indigenous communities, seeking cooperation from and establishing partnerships with them would help us design policies to achieve intended outcomes of SDGs. In this paper, particular attention is attracted towards the potential role of traditional ethnobotanical knowledge in achieving select sustainable development goals and targets.
Tue, 19 January 2021
REVIEW | doi:10.20944/preprints202101.0393.v1
Subject: Life Sciences, Biochemistry Keywords: Breast cancer; Angiogenesis; Lymphangiogenesis; Cancer Stem cells, microRNA; EP4 receptor; Immune check-point inhibitor
Online: 19 January 2021 (17:40:53 CET)
Formation of new blood (angiogenesis) and lymphatic (lymphangiogenesis) vessels are major events associated with most epithelial malignancies, including breast cancer. Angiogenesis is essential for cancer cell survival. Lymphangiogenesis is critical in maintaining tumoral interstitial fluid balance and importing tumor-facilitatory immune cells. Both vascular routes also serve as conduits for cancer metastasis. Intratumoral hypoxia promotes both events by stimulating multiple angiogenic/lymphangiogenic growth factors. Studies on tumor-associated lymphangiogenesis and its exploitation for therapy have received less attention from the research community than those on angiogenesis. Inflammation is a key mediator of both processes, hijacked by many cancers by aberrant expression of the inflammation-associated enzyme cyclo-oxygenase (COX)-2. In this review, we focus on breast cancer and show that COX-2 is a major promoter of both events, primarily resulting from the activation of Prostaglandin (PG) E receptor EP4 on tumor cells, tumor-infiltrating immune cells, and endothelial cells; and induction of oncogenic microRNAs. COX-2/EP4 pathway also promotes additional events in breast cancer progression, such as cancer cell migration, invasion, and stimulation of stem–like cells. Based on a combination of studies using multiple breast cancer models, we show that EP4 antagonists hold a major promise in breast cancer therapy in combination with other modalities including immune check-point inhibitors
REVIEW | doi:10.20944/preprints202101.0391.v1
Subject: Life Sciences, Biochemistry Keywords: Sustainable Development Goals; Ethnobotany; Human Health; Poverty; Traditional Knowledge; Sustainable Agriculture
Online: 19 January 2021 (16:48:15 CET)
Sustainable Development Goals (SDGs) envisaged under Agenda 2030 are a set of seventeen goals which envisage a holistic approach towards attaining certain targets keeping humankind and the planet at center. There are a total 169 targets spread across seventeen goals covering wide ranging issues and challenges the world is facing in the twenty-first century. And they are to be achieved by 2030. Concerted efforts of all the stakeholders ranging from indigenous communities, common citizens, scientists, policy makers, world leaders are needed to achieve all the goals and targets Of the seventeen goals, at least seven goals are of interest to the ethnobotanists and are associated with traditional ethnobotanical knowledge. Therefore to achieve those set of goals, a thorough understanding is required to disentangle the intricacies involving traditional ethnobotanical knowledge, indigenous people as traditional knowledge holders and their future role. Understanding relationships between traditional ethnobotanical knowledge and indegenous communities, seeking cooperation from and establishing partnerships with them would help us design policies to achieve intended outcomes of SDGs. In this paper, particular attention is attracted towards the potential role of traditional ethnobotanical knowledge in achieving select sustainable development goals and targets.
REVIEW | doi:10.20944/preprints202101.0388.v1
Subject: Life Sciences, Biochemistry Keywords: Thymic selection; T-cell development; T-cell receptor (TCR); mathematical modelling; multiscale models; complex systems; ordinary differential equations (ODE); agent-based models.
Online: 19 January 2021 (16:39:50 CET)
The thymus hosts the development of a specific type of adaptive immune cells called T cells. T cells orchestrate the adaptive immune response through recognition of antigen by the highly variable T-cell receptor (TCR). T-cell development is a tightly coordinated process comprising lineage commitment, somatic recombination of Tcr gene loci and selection for functional, but non-self-reactive TCRs, all interspersed with massive proliferation and cell death. Thus, the thymus produces a pool of T cells throughout life capable of responding to virtually any exogenous attack while preserving the body through self-tolerance. The thymus has been of considerable interest to both immunologists and theoretical biologists due to its multiscale quantitative properties, bridging molecular binding, population dynamics and polyclonal repertoire specificity. Here, we review mathematical modelling strategies that were reported to help understand the flexible dynamics of the highly dividing and dying thymic cell populations. Furthermore, we summarize the current challenges to estimating in vivo cellular dynamics and to reaching a next-generation multiscale picture of T-cell development.
CONCEPT PAPER | doi:10.20944/preprints201910.0311.v3
Subject: Life Sciences, Biochemistry Keywords: virtual reality; biological evolution; immersive reality
Online: 19 January 2021 (10:54:11 CET)
Technological advances made Virtual and Mixed Reality (VMR) accessible at our fingertips. However, only recently VMR has been explored for the teaching of biology. Here, we highlight how VMR applications can be useful in biology education, discuss about caveats related to VMR use that can interfere with learning, and look into the future of VMR applications in the field. We then propose that the combination of VMR with Machine Learning and Artificial Intelligence can provide unprecedented ways to visualise how species evolve in self-sustained immersive virtual worlds, thereby transforming VMR from an educational tool to the centre of biological interest.
Mon, 18 January 2021
ARTICLE | doi:10.20944/preprints202101.0360.v1
Subject: Life Sciences, Biochemistry Keywords: DNA sequences; genomes; percentages of n-plets; binary-oppositions, tensor family of matrices; tetra-groupings; quantum biology
Online: 18 January 2021 (16:15:00 CET)
The article presents the author's results of studying hidden rules of structural organizations of long DNA sequences in eukaryotic and prokaryotic genomes. The results concern some rules of percentages (or probabilities) of n-plets in genomes. To reveal such rules, the author uses a tensor family of matrix representations of interrelated DNA-alphabets of 4 nucleotides, 16 doublets, 64 triplets, and 256 tetraplets. If percentages of each of these n-plets in tested genomic DNA-texts are disposed into appropriate cells of appropriate matrices, unexpected rules of invariance of total sums of their percentages in certain tetra-groupings of n-plets are revealed. The author connects the received results about these genomic percentages rules with a supposition of P. Jordan, who is one of the creators of quantum mechanics and quantum biology, that life's missing laws are the rules of chance and probability of the quantum world. Algebraic features of the genomic matrices of percentages of n-plets are analyzed and discussed. The received results can be used for further development of quantum biology.
Subject: Life Sciences, Biochemistry Keywords: Leishmania; Leishmania viruses; Phylogeny; Coevolution; endosymbiont protozoan viruses
Online: 18 January 2021 (15:00:54 CET)
The description of the genus Leishmania as causative agents of leishmaniasis occurred during this modern age. But evolutionary studies suggest that the origin of Leishmania can be traced back to the Mesozoic era. Subsequently, during its evolutionary process, it sustained a worldwide dispersion predating the breakup of the Gondwana supercontinent. It is assumed that this parasite evolved from monoxenic Trypanosomatidae. Phylogenetic studies locate the dixenous Leishmania in a well-supported clade, recently named subfamily Leishmaniinae, which includes also monoxenous trypanosomatids. Virus-Like Particles were reported in many species of this family. So far, several Leishmania species have been reported as infected by Leishmania RNA Virus (LRV) and Leishbunyavirus (LBV). Since the first descriptions of LRV decades ago, differences in its genomic structure have been highlighted, leading to the designation of a LRV1 in L. (Viannia) species and a LRV2 in other L. (Leishmania) species. There are strong indications of virus infecting Leishmania spp. ability to enhance parasitic survival both in human and experimental infections, through highly complex and specialized mechanisms. Phylogenetic analyzes of these viruses have shown that their genomic differences correlate with the infected parasite species, suggesting a coevolutionary process. Herein, we will present unpublished results regarding the relationship Leishmania – endosymbiotic Leishmania viruses and will explore what has been described in the literature, and what is known about this association that could contribute to discussions about the worldwide dispersion of Leishmania.
REVIEW | doi:10.20944/preprints202101.0337.v1
Subject: Life Sciences, Biochemistry Keywords: Diffuse intrinsic pontine glioma; molecular biology; patient derived xenografts; genetically engineered mouse model; humanized mouse model
Online: 18 January 2021 (12:50:14 CET)
Diffuse intrinsic pontine gliomas (DIPGs) account for ~15% of pediatric brain tumors, which invariably present with poor survival regardless of treatment mode. Several seminal studies have revealed that 80% of DIPGs harbor H3K27M mutation coded by HIST1H3B, HIST1H3C and H3F3A genes. The H3K27M mutation has broad effects on gene expression and is considered a tumor driver. Determination of the effects of H3K27M on posttranslational histone modifications and gene regulations in DIPG is critical for identifying effective therapeutic targets. Advanced animal models play critical roles in translating these cutting-edge findings into clinical trial development. Here, we review current molecular research progress associated with DIPG. We also summarize DIPG animal models, highlighting novel genomic engineered mouse models (GEMMs) and innovative humanized DIPG mouse models. These models will pave the way towards personalized precision medicine for the treatment of DIPGs.
Subject: Life Sciences, Biochemistry Keywords: HIV viral load; external quality assessment; verification; quality; thermostable; PrimeStore MTM
Online: 18 January 2021 (12:24:31 CET)
The tiered laboratory framework for HIV viral load monitoring accommodates a range of HIV viral load testing platforms, with quality assessment critical to ensure quality patient testing. HIV plasma viral load testing is challenged by the instability of viral RNA. An approach using an RNA stabilizing buffer is described for the Xpert® HIV-1 Viral Load (Cepheid) assay and was tested in remote laboratories in South Africa. EDTA-plasma panels with known HIV viral titres were prepared in PrimeStore molecular transport medium for per-module verification and per-instrument external quality assessment. The panels were transported at ambient temperatures to 13 testing laboratories during 2017 and 2018, tested according to standard procedures and uploaded to a web portal for analysis. A total of 275 quality assessment specimens (57 verification panels and two EQA cycles) were tested. All participating laboratories met study verification criteria (n=171 specimens) with an overall concordance correlation coefficient (ρc) of 0.997 (95% confidence interval [CI]: 0.996 to 0.998) and a mean bias of -0.019 log cp/mL (95% CI: -0.044 to 0.063). The overall EQA ρc (n=104 specimens) was 0.999 (95% CI: 0.998 to 0.999), with a mean bias of 0.03 log cp/mL (95% CI: 0.02 to 0.05). These panels are suitable for use in quality monitoring of Xpert® HIV-1 VL and are applicable to laboratories in remote settings.
REVIEW | doi:10.20944/preprints202101.0325.v1
Subject: Life Sciences, Biochemistry Keywords: pediatric cancer; nanoparticles; drug delivery system; liposome; leukemia; lymphoma; osteosarcoma; Ewing sarcoma; glioma; blood-brain barrier
Online: 18 January 2021 (11:58:32 CET)
Cancer is the second biggest cause of death in children. With the development of chemotherapy, there is a substantial increase in overall survival rate over recent 30 years. However, the overall mortality rate in children with cancer still remains 25%, and many survivors experience a decline in overall quality of life and long-term adverse effects caused by treatments. Although cancer cells share common characteristics, pediatric cancers are different from adult cancers in their prevalence, mutation load, and drug response. Therefore, there is an urgent unmet need to develop therapeutic approaches specifically designed for children with cancer. Nanotechnology can potentially overcome the deficiencies of conventional methods of administering chemotherapy and ultimately improve clinical outcomes. The nanoparticle-based drug delivery systems can decrease the toxicity of therapy, provide a sustained or controlled drug release, improve pharmacokinetic properties of loading contents, and achieve a targeted drug delivery with achievable modifications. Further, therapeutic approaches based on combining nanoformulated drugs with novel immunotherapeutic agents are emerging. In this review, we discuss the recently developed nanotechnology-based strategies for treating blood and solid pediatric cancers.
REVIEW | doi:10.20944/preprints202101.0307.v1
Subject: Life Sciences, Biochemistry Keywords: gametogenesis; oocytes; pathways; signaling; stem cells; differentiation; tumor; cancer
Online: 18 January 2021 (09:14:54 CET)
In the present era, infertility is one of the major issues which restricts many couples to have their own kids. Infertility is the inability to achieve a clinical pregnancy after regular unprotected sexual intercourse for the period of one year or more. Various factors including defective male or female germ cell development, unhealthy and improper lifestyles, diseases like cancer and associated chemo-or-radiation therapies, congenital disorders etc. may be responsible for infertility. Therefore, it is highly important to understand the basic concepts of germ cell development including primordial germ cell (PGC) formation, specification, migration, entry to genital ridges and their molecular mechanisms, activated pathways, paracrine and autocrine signaling, along with possible alteration which can hamper germ cell development and can cause adversities like cancer progression and infertility. Knowing all these aspects in a proper way can be very much helpful in improving our understanding about gametogenesis and finding possible ways to cure related disorders. Here in this review, various aspects of gametogenesis especially female gametes and relevant factors causing functional impairment have been thoroughly discussed.
REVIEW | doi:10.20944/preprints202101.0304.v1
Subject: Life Sciences, Biochemistry Keywords: Vascular Endothelial Growth Factors (VEGFs); VEGF-A; PlGF; VEGF-B; VEGF-C; VEGF-D; angiogenesis; lymphangiogenesis; CCBE1; proteases; ADAMTS3; plasmin; cathepsin D; KLK3; prostate-specific antigen (PSA); thrombin; wound healing; metastasis; proteolytic activation; vascular biology
Online: 18 January 2021 (09:05:58 CET)
Specific proteolytic cleavages turn on, modify, or turn off the activity of vascular endothelial growth factors (VEGFs). Proteolysis is most prominent among the lymphangiogenic VEGF-C and VEGF-D, which are synthesized as precursors that need to undergo enzymatic removal of their C- and N-terminal propeptides before they can activate their receptors. The activating cleavage of VEGF-C is mediated by at least five different proteases: plasmin, ADAMTS3, prostate-specific antigen, cathepsin D, and thrombin. All of these proteases except for ADAMTS3 can also activate VEGF-D. Processing by different proteases results in distinct forms of the "mature" growth factors, which differ in affinity and receptor activation potential. The “default” VEGF-C-activating enzyme ADAMTS3 does not activate VEGF-D and therefore, VEGF-C and VEGF-D do function in different contexts. VEGF-C itself is also regulated in different contexts by different proteases. During embryonic development, ADAMTS3 activates VEGF-C. In contrast, thrombin and plasmin likely activate VEGF-C/-D during tissue injury-induced lymphangiogenesis, and PSA and cathepsin D perhaps during tumor-associated pathological lymphangiogenesis. Additionally, cathepsin D from saliva might activate latent VEGF-C/-D upon wound licking, thereby accelerating healing. Similar to tyrosine kinase receptors and VEGFs themselves, these activating proteases could be targeted to modulate angiogenesis and lymphangiogenesis in relevant diseases.
Fri, 15 January 2021
REVIEW | doi:10.20944/preprints202101.0301.v1
Subject: Life Sciences, Biochemistry Keywords: immune response; nutritional supplement; cancer; oncoxin
Online: 15 January 2021 (15:45:55 CET)
Purpose: This study aimed to determine the efficacy and safety of Oncoxin as an antitumoral supplement, and to describe its mechanism of action. Methods: We performed this scoping review according to the recommendations of the Joanna Briggs Institute and included patients older than 18 years-old who have any kind of tumor and receive Oncoxin as a supplement. We focused on the efficacy in terms of antitumoral properties, quality of life and survival, safety in terms of adverse events, and the mechanism of action. We did not limit for language or setting. We searched MEDLINE (Pubmed), EMBASE (Scopus), LILACS, and the Cochrane Central Register of Controlled Trials (CENTRAL) from inception to nowadays. Results: We found a promising increment of survival when taking Oncoxin as a supplementary treatment. Additionally, the quality of life increased in terms of Karnofsky and EORTC scales. Regarding the mechanism of action, studies suggest it modifies inflammatory mediators’ expression, as evidenced by the reduction of COX-2, IL-1β, IL-6, TNF-α, IL-1β, IL-12, and IFN-γ. Besides, it promotes an arrest in the progression of cells from G1 into S, along with an increase in p27 and a decrease in cyclin D1 and pRb. Conclusions: We found promising complementary effects of Oncoxin to the standard treatment of cancer patients in diverse scenarios, with putative robust mechanisms of action. In addition to clinically relevant impacts verified in clinical trials, as well as it decreases the levels of pro-inflammatory cytokines, it can also decrease cytokines with antitumor activity such as IFN-γ, which should be further explored in larger trials and the long term.
Thu, 14 January 2021
ARTICLE | doi:10.20944/preprints202101.0280.v1
Subject: Life Sciences, Biochemistry Keywords: metabolic pathways; mechanistic model; Transcriptomic
Online: 14 January 2021 (18:01:26 CET)
In the last decade, different omic technologies have experiences an exponential technological advancement. However, metabolomics has not followed a similarly vertiginous improving improvement and are far from genomics or transcriptomics in terms of throughput, cost and even accuracy. Therefore, genome-scale in-silico methodologies to estimate metabolic activities from genomic data constitute an active field. The solutions available fall into two extremes: those with few assumptions about the relationships among proteins and metabolites, which are easy-to-use but less accurate and those that account for the complex relationships among molecules and proteins defined in the metabolic pathways, which are more accurate but require mathematical skills. Here, we introduce Metabolica, an algorithm that considers the complex functional relationships among all the molecules and proteins involved in the metabolic pathway analyzed but keeping an easy use that do not require of advanced mathematical skills. Metabolica has been implemented in a freely available software R package. The software inputs transcriptomic data and infers the activities of the reactions that produce the different metabolites in the pathway analyzed. An example shows how detected dysregulated metabolites in several cancers are related to patient survival.
ARTICLE | doi:10.20944/preprints202101.0277.v1
Subject: Life Sciences, Biochemistry Keywords: mucormycosis; Mucor lusitanicus; Mucorales; RNAi; exonuclease; wex1 gene; virulence; virulence factor.
Online: 14 January 2021 (14:39:17 CET)
Mucormycosis is a lethal disease caused by Mucorales, which are emerging as human pathogens with virulent behavior. Antifungal resistance and ineffective treatments are two major causes that explain the high mortality for this disease. Consequently, the research community is searching for virulence determinants that could be repurposed as targets to develop new treatments against mucormycosis. Our work explores an RNA interference (RNAi)-based approach to find targets involved in the virulence of Mucorales. A transcriptome-wide analysis compared sRNAs and their target mRNAs in two Mucor lusitanicus different pathotypes, virulent and avirulent, generating a list of 75 loci selected by their differential sRNA accumulation in these strains. As a proof of concept and validity, an experimental approach characterized two loci showing opposite behavior, confirming that RNAi activity causes their differential expression in the two pathotypes. We generated deletion mutants for two loci and a knockin-strain overexpressing for one these loci. Their functional analysis in murine virulence assays identified the gene wex1, a putative DEDDy exonuclease with RNase domains, as an essential factor for virulence. The identification of wex1 showed the potential of our approach to discover virulence factors not only in Mucorales but also in any other fungal model with an active RNAi machinery. But, more importantly, it adds a new layer to the biological processes controlled by RNAi in M. lusitanicus, confirming that the Dicer-dependent RNAi pathway can silence gene expression to promote virulence.
REVIEW | doi:10.20944/preprints202101.0275.v1
Subject: Life Sciences, Biochemistry Keywords: Vicia faba; legume improvement; quality traits; disease resistance
Online: 14 January 2021 (14:18:29 CET)
Faba bean (Vicia faba L.) was considered a minor crop in the Canadian prairies until recently, but its potential for cultivation is increasing due to its positive environmental impact and economic value. This review provides a historical summary of faba bean improvement in western Canada. Although traditional breeding methods have proved useful, in the last decade faba bean improvement has benefited from advances in genetics, biochemistry and molecular breeding tools. The overall breeding goal is to develop high yielding germplasm with improved agronomic characteristics that will be of economic value to the emerging faba bean sectors, including the plant protein industry. To maximize value and acceptance by producers, processors and the food industry as a source of protein and dietary fibre, future faba bean varieties need to be high-yielding, have diverse seed size classes, disease resistance, genetically low vicine-convicine concentration, and have wider adaptation to different agro-ecological zones of Canada. The experiences over the last 40 years of faba bean improvement in western Canada may be useful to other breeding programs globally located in regions with similar agroecology. In the past 10–15 years, faba bean genetic development in Canada has benefited greatly from research and development interactions with most of the faba bean research programs in northern Europe.
REVIEW | doi:10.20944/preprints202101.0272.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: Metabolic reprogramming; Warburg effect; Cancer metabolism
Online: 14 January 2021 (13:30:44 CET)
The expression "metabolic reprogramming" is more and more encountered in the literature since the mid-1990s. It seems to encompass several notions depending on the author, but the lack of a clear definition allows it to be used as a "catch-all" expression. With the increased interest in metabolism, and more specifically, in the Warburg effect in cancer research, it seems appropriate to discuss this expression and related concepts in detail.
Subject: Life Sciences, Biochemistry Keywords: nanopore; translocation slowdown; mobility; polymer sequencing; bandwidth; diffusion
Online: 14 January 2021 (09:53:00 CET)
A major obstacle faced by nanopore-based polymer sequencing and analysis is the high speed of translocation of an analyte (nucleotide, DNA, amino acid (AA), peptide) through the pore; the rate currently exceeds available detector bandwidth. Except for one method that uses an enzyme ratchet to sequence DNA, attempts to resolve the problem satisfactorily have been largely unsuccessful. Here a counterintuitive method based on reversing the pore voltage, and, with some analytes, increasing their mobility, is described. A simplified Fokker-Planck model shows a significant increase in translocation times for single nucleotides and AAs (up from ~10 ns to ~1 ms). More realistic simulations show that with a bi-level positive-negative pore voltage profile all four nucleotides in DNA (dAMP, dTMP, dCMP, and dGMP) and the 20 proteinogenic amino acids can be trapped inside the pore long enough for detection with bandwidths of ~1-10 Khz.
ARTICLE | doi:10.20944/preprints202101.0262.v1
Subject: Life Sciences, Biochemistry Keywords: lifespan; aging; radioresistance; ionizing radiation; Agronaute; Piwi; Drosophila melanogaster
Online: 14 January 2021 (08:07:44 CET)
Small RNAs are essential for the coordination of many cellular processes, including the regulation of gene expression patterns, the prevention of genomic instability, and the suppression of mutagenic transposon activity. These processes determine aging, longevity, and sensitivity of cells and an organism to stress factors (particularly, ionizing radiation). The biogenesis and activity of small RNAs are provided by proteins of the Argonaute family. These proteins participate in the processing of small RNA precursors and the formation of an RNA-induced silencing complex. However, the role of Argonaute proteins in the regulation of lifespan and radioresistance remains poorly explored. We studied the effect of knockdown of Argonaute genes (AGO1, AGO2, AGO3, piwi) in various tissues on the Drosophila melanogaster lifespan and survival after the γ-irradiation at a dose of 700 Gy. In most cases, these parameters were reduced or did not change significantly in flies with tissue-specific RNA interference. Surprisingly, piwi knockdown in both the fat body and the nervous system caused a lifespan increase. But changes in radioresistance depended on the tissue in which the gene was knocked out. In addition, analysis of changes in retrotransposon levels and expression of stress response genes allowed us to determine associated molecular mechanisms.
Tue, 12 January 2021
ARTICLE | doi:10.20944/preprints202101.0232.v1
Subject: Life Sciences, Biochemistry Keywords: CaSR; Homer1; mTOR; osteoblast; osteocyte; AKT; chaperone function
Online: 12 January 2021 (17:21:02 CET)
We recently found that in human osteoblasts Homer1 complexes to CaSR and mediates AKT initiation via mTORC2 leading to beneficial effects in osteoblasts including -catenin stabilization and mTORC1 activation (doi: 10.1074/jbc.RA118.006587). Herein we further investigated the relationship between Homer1 and CaSR and demonstrate a link between the protein levels of CaSR and Homer1 in human osteoblasts in primary culture. Thus, when siRNA was used to suppress the CaSR, we observed upregulated Homer1 levels and when siRNA was used to suppress Homer1 we observed downregulated CaSR protein levels using immunofluorescence staining of cultured osteoblasts as well as western blot analyses of cell protein extracts. This finding was confirmed in vivo as the bone cells from osteoblast specific CaSR(-/-) mice showed increased Homer1 expression compared to wild-type. Furthermore, when the commonly used osteosarcoma cell lines MG63 and SAOS-2 were compared to primary osteoblasts, higher levels of Homer1 protein were associated with increased protein levels of the CaSR as well as mTOR and Rictor. CaSR and Homer1 protein were both expressed in osteocytes embedded in the long bones of wild-type mice, and immunofluorescent studies of these cells revealed that Homer1 protein sub-cellular localization was markedly altered in the osteocytes of CaSR(-/-) mice compared to wt. The study identifies additional roles for Homer1 in the control of the protein level and subcellular localization of CaSR in cells of the osteoblast lineage, in addition to its established role of mTORC2 activation downstream of the receptor.
REVIEW | doi:10.20944/preprints202012.0578.v2
Subject: Life Sciences, Biochemistry Keywords: Unfolded protein response; Endoplasmic reticulum stress; Glucose-regulated protein 78 kD; Inflammatory Bowel Diseases; Crohn’s disease; Fibrosis; Wound healing
Online: 12 January 2021 (17:03:10 CET)
Endoplasmic reticulum (ER) stress triggers a series of signaling and transcriptional events termed the unfolded protein response (UPR). Severe ER stress is associated with the development of fibrosis in different organs including lung, liver, kidney, heart, and intestine. ER stress is an essential response of epithelial and immune cells in the pathogenesis of inflammatory bowel disease (IBD) including Crohn’s disease. Intestinal epithelial cells are susceptible to ER stress-mediated damage due to secretion of a large amount of proteins that are involved in mucosal defense. In other cells, ER stress is linked to myofibroblast activation, extracellular matrix production, macrophage polarization, and immune cell differentiation. This review focuses on the role of UPR in the pathogenesis in IBD from an immunologic perspective. The roles of macrophage and mesenchymal cells in the UPR from in vitro and in vivo animal models are discussed. The links between ER stress and other signaling pathways such as senescence and autophagy are introduced. Recent advances in the understanding of the epigenetic regulation of UPR signaling are also updated here. The future directions of development of the UPR research and therapeutic strategies to manipulate ER stress levels are also reviewed.
ARTICLE | doi:10.20944/preprints202101.0227.v1
Subject: Life Sciences, Biochemistry Keywords: tRNAs; tRNA-modifying enzyme; TRMT2A; methyltransferase; tRNA hypomethylation; tRNA-derived small RNAs; tRNA-derived stress-induced RNAs; angiogenin.
Online: 12 January 2021 (15:17:29 CET)
Transfer RNA (tRNA) molecules contain various post-transcriptional modifications that are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation to gene expression control and cellular stress response. Recent evidence indicates that tsRNAs are also modified, however, the impact of tRNA epitranscriptome deregulation on tsRNAs generation is only now beginning to be uncovered. The 5-methyluridine (m5U) modification at position 54 of cytosolic tRNAs is one of the most common and conserved tRNA modifications among species. The tRNA methyltransferase TRMT2A catalyzes this modification, but its biological role remains mostly unexplored. Here, we show that TRMT2A knockdown in human cells induces m5U54 tRNA hypomodification, resulting in angiogenin (ANG) dependent tsRNA formation. More specifically, m5U54 hypomodification is followed by ANG overexpression and tRNA cleavage near the anticodon, resulting in accumulation of 5’tRNA-derived stress-induced RNAs (5’tiRNAs), in particular 5’tiRNA-GlyGCC and 5’tiRNA-GluCTC. Additionally, transcriptomic analysis confirms that down-regulation of TRMT2A and consequently m5U54 hypomodification impacts the cellular stress response and RNA stability, which is often correlated with tsRNA generation. Accordingly, exposure to oxidative stress conditions induces TRMT2A down-regulation and tsRNA formation in mammalian cells. These results establish a link between tRNA demethylation and ANG-dependent tsRNAs formation and unravel m5U54 as a tRNA cleavage protective mark.
ARTICLE | doi:10.20944/preprints202101.0226.v1
Subject: Life Sciences, Biochemistry Keywords: Arabidopsis thaliana; callose; cell plate; cross wall; cytokinesis; homogalacturonans; katanin; KNOLLE syntaxin; microtubules; phragmoplast
Online: 12 January 2021 (15:13:01 CET)
Cytokinesis is accomplished in higher plants by the phragmoplast, creating and conducting the cell plate, to separate daughter nuclei by a new cell wall. The microtubule-severing enzyme p60-katanin plays an important role in the centrifugal expansion and timely disappearance of phragmoplast microtubules. Consequently, aberrant structure and delayed expansion rate of the phragmoplast occur in p60-katanin mutants. Here, the consequences of p60-katanin malfunction in cell plate/daughter wall formation were investigated by transmission electron microscopy (TEM), while deviations in the chemical composition of cell plate/new cell wall were identified by immunolabeling and confocal microscopy, in root cells of the fra2 Arabidopsis thaliana mutant. It was found that, apart from defective phragmoplast microtubule organization, cell plates/new cell walls appeared also faulty in structure, being unevenly thick and perforated by large gaps. In addition, demethylesterified homogalacturonans were prematurely present in fra2 cell plates, while callose content was significantly lower than in the wild-type. Furthermore, KNOLLE syntaxin disappeared from newly formed cell walls in fra2 earlier than in the wild-type. Taken together, these observations indicate that delayed cytokinesis, due to faulty phragmoplast organization and expansion, results in a loss of synchronization between cell plate growth and its chemical maturation.
CONCEPT PAPER | doi:10.20944/preprints202005.0321.v2
Subject: Life Sciences, Biochemistry Keywords: trans-species O-glycosylation; trans-species functional bridge; phenotype-specific plasma glycosylation; glycosidic exclusion; ontogenetic Tn formation
Online: 12 January 2021 (12:33:29 CET)
The coevolution of species drives diversity in animals and plants and contributes to natural selection, whereas in host–parasite coevolution, a parasite may complete an incomplete evolutionary/developmental function by utilizing the host cell’s machinery. Analysis of related older data suggests that Plasmodium falciparum (P. falciparum), the pathogen of malaria tropica, cannot survive outside its human host because it is unable to perform the evolutionarily first protein glycosylation of serologically A-like, O-GalNAcα1-Ser/Thr-R, Tn antigen (“T nouvelle”) formation, owing to its inability for synthesizing the amino sugar N-acetyl-d-galactosamine (GalNAc). This parasite breaks the species barrier via hijacking the host's physiological A-like/Tn formation through abundantly expressing serine residues and creating hybrid A-like/Tn structures, which in the human blood group O(H) are attacked by the germline-encoded nonimmune polyreactive immunoglobulin M (IgM), exerting the highly anti-A/B/H-aggressive isoagglutinin activities. These activities physiologically undergo the ABO(H) blood group phenotype formation, occurring on the surfaces of red blood cells (RBC), epithelial and endothelial cells and on plasma proteins by identical glycosylation, performed by the ABO(H)-allelic glycotransferases, phenotypically downregulating the anti-A/B/H-reactive IgM (isoagglutinin) activities in the non-O blood groups. ABO(H) phenotype diversity, this way glycosidically linked and molecularly connected to humoral immunity, becomes exposed to the evolution.
Mon, 11 January 2021
ARTICLE | doi:10.20944/preprints202101.0207.v1
Subject: Life Sciences, Biochemistry Keywords: severe fever with thrombocytopenia syndrome; cat; companion animals; viral hemorrhagic fever; pathology
Online: 11 January 2021 (17:48:51 CET)
ABSTRACT: A woman in her 50s showed symptoms of fever, loss of appetite, vomiting, and general fatigue 2 days after she was bitten by a sick cat, which had later died, in Yamaguchi prefecture, western Japan, in June 2016. She subsequently died of multiorgan failure, and an autopsy was performed to determine the cause of death. However, the etiological pathogens were not quickly identified. The pathological features of the patient were retrospectively re-examined, and the pathology of the regional lymph node at the site of the cat bite was found to show necrotizing lymphadenitis with hemophagocytosis. The pathological features were noticed to be similar to those of patients reported to have severe fever with thrombocytopenia syndrome (SFTS). Therefore, the lymph node section was retrospectively tested immunohistochemically for SFTSV antigen, which revealed the presence of SFTSV antigen. The sick cat also showed similar symptoms and laboratory findings similar to those shown in human SFTS cases. It is highly possible that the patient was infected with SFTSV through the sick cat’s bite. If a patient gets sick in an SFTS-endemic region after a cat bite, SFTS should be considered in the differential diagnosis.
ARTICLE | doi:10.20944/preprints202101.0205.v1
Subject: Life Sciences, Biochemistry Keywords: communication; childbirth; satisfaction; quality of care
Online: 11 January 2021 (17:46:12 CET)
The study aims to identify the difference in communication needs of women giving birth and women during puerperium. An additional goal includes the analysis of the experience and communication needs through the context of a woman's approach to childbirth. The study is a prospective, cross-sectional, self-report survey. 521 women between 5 and 10 days after birth participated in the study. Women perceived information provided by the medical staff as the most helpful aspect of verbal communication both during labour and puerperium. Maintaining eye contact with the medical staff was perceived as the most helpful aspect of non-verbal communication. Women were more satisfied with communication during labour and birth than in the maternity ward and those after non-instrumental childbirth were more satisfied with communication compared to the instrumental birth group. Women perceiving childbirth as the natural, physiological process considered verbal and non-verbal communication during and after childbirth as less helpful than women perceiving birth as more risky and requiring interventions. The results of the study emphasize the importance of verbal and non-verbal communication during birth and puerperium and different communication needs during labour and early postpartum. It also showed that women who perceive labour as a physiological process seem to be less dependent on the communication with the medical staff than women who accept medical interventions during labour and birth as necessary.
ARTICLE | doi:10.20944/preprints202101.0198.v1
Subject: Life Sciences, Virology Keywords: epidemiological history of HCV-2; HCV-2 subtypes; evolutionary demography of HCV-2; phylodynamics of HCV-2 in Italy and Albania; HCV-2 Re estimation
Online: 11 January 2021 (13:10:30 CET)
Newly characterising 245 Italian and Albanian HCV-2 NS5B sequences collected between 2001 and 2016 was used to reconstruct the origin and dispersion pathways of HCV-2c. The tree of a subset of these sequences aligned with 247 publicly available sequences was reconstructed in spatio-temporal scale using the Bayesian approach, and the effective replication number (Re) was estimated using the birth-death model. Our findings show that HCV-2c was the most prevalent subtype in Italy and Albania, and that GT2 originated in Guinea Bissau in the XVI century and spread to Europe in the XX century. The HCV-2c subtype had two internal nodes respectively dating back to the 1930s and 1950s having as most probable locations Ghana and Italy, respectively. Phylodynamic analysis revealed an exponential increase in the effective number of infections and Re in both Italy between the 1950s and 1980s, and Albania between the 1990s and the early 2000s. It seems very likely that HCV-2c reached Italy from Africa at the time of the second Italian colonisation (1936-1941), but did not reach Albania until the period of dramatic migration to Italy in the 1990s.
ARTICLE | doi:10.20944/preprints202101.0195.v1
Subject: Life Sciences, Biochemistry Keywords: miRNA; Tuberculosis; differential expression analysis
Online: 11 January 2021 (12:59:32 CET)
Molecular studies regarding regulatory elements such as small ncRNAs and their mechanisms are poorly understood in infectious diseases. Tuberculosis is one of the oldest infectious diseases of humanity, and it is still a challenge to prevent and treat it. The control of the infection as well as its diagnosis are still complex, and treatments used are linked to several side effects. This study aimed to investigate miRNA’s expression profile to identify possible biomarkers for tuberculosis. We applied NGS techniques to investigate miRNA’s global expression profile from blood samples of infected patients with tuberculosis, their respective healthy physicians, and external healthy individuals as controls. Samples from 22 individuals run through a differential expression, target genes, gene set enrichment, and miRNA-gene network analysis. We observed 153 altered miRNAs, among which, only three DEmiRNAs (hsa-let-7g-5p, hsa-miR-486-3p and hsa-miR-4732-5p) were found between the investigated patients and their respective physicians. These DEmiRNAs are suggested to play an important role in granuloma regulation and their immune physiopathology. Our results propose that miRNAs may be involved in immune modulation, regulating the repertoire of genes expressed in the immune system’s cells. Our findings encourage the application of miRNAs as potential biomarkers for tuberculosis.
REVIEW | doi:10.20944/preprints202101.0193.v1
Subject: Life Sciences, Biochemistry Keywords: gasotransmitters; hydrogen sulfide; cardiovascular system; circulation; hemostasis; erythrocytes; therapeutic potential.
Online: 11 January 2021 (12:48:43 CET)
this review summarizes current knowledge of the hydrogen sulfide role in cardiovascular system, the proposed mechanisms of its action and the prospects for its applicability in the treatment of cardiovascular diseases. Hydrogen sulfide was recently recognized as gasotransmitter – simple signaling molecule which freely penetrates the cell membrane and regulates a number of biological functions. In humans endogenous H2S is generated via enzymatic and non-enzymatic pathways and its content varies in different tissues and is strictly regulated. In cardiovascular system H2S is produced by myocardial, vascular and blood cells and regulates a number of vital functions. Numerous experimental data prove that endogenously generated as well as exogenously administered H2S exerts a wide range of actions in cardiovascular system, including vasodilator/vasoconstrictor effects, regulation of blood pressure, pro-apoptotic and anti-proliferative effects in the vascular smooth muscle cells, influence on angiogenesis and erythropoiesis, myocardial cytoprotection in ischemia-reperfusion injury, oxygen sensing, inhibition of platelet aggregation and blood coagulation, modification of erythrocyte microrheological properties (aggregability and deformability). Understanding of molecular mechanisms of H2S action and molecular crosstalk between H2S, NO, and CO is essential for the development of its diagnostic and therapeutic potential.
ARTICLE | doi:10.20944/preprints202101.0186.v1
Subject: Life Sciences, Biochemistry Keywords: Docosahexaenoic acid (DHA); long chain omega-3 fatty acids; maternal supplementation; pregnancy outcomes; anthropometry; birth weight; birth length; head circumference
Online: 11 January 2021 (11:38:57 CET)
Long-chain omega-3 fatty acid status during pregnancy may influence newborn anthropometry and duration of gestation. Evidence from high-quality trials from LMICs is limited. We conducted a double-blind, randomized, placebo-controlled trial among 957 pregnant women (singleton gestation, 14-20 weeks’ gestation at enrollment) in India to test the effectiveness of 400 mg/d algal docosahexaenoic acid (DHA) compared to placebo provided from enrollment through delivery. Among 3379 women who were screened, 1171 were found eligible; 957 enrolled and were randomized. The intervention was two microencapsulated algal DHA (200 X 2= 400 mg/d) or two microencapsulated soy and corn oil placebo tablets to be consumed daily from enrollment (20 weeks) through delivery. The primary outcome was newborn anthropometry (birth weight, length, head circumference). Secondary outcomes were gestational age and 1 and 5 min Appearance, Pulse, Grimace, Activity, and Respiration (APGAR) score. The groups (DHA; n=478 and placebo; n=479) were well balanced at baseline. There were 902 live births. Compliance with the intervention was similar across groups (DHA: 88.5%; placebo: 87.1%). There were no significant differences between DHA and placebo group for birth weight (2750.6 ± 421.5 vs. 2768.2 ± 436.6 g, p=0.54), length (47.3 ± 2.0 vs. 47.5 ±2.0 cm, p=0.13) or head circumference (33.7 ± 1.4 vs 33.8 ± 1.4 cm, p=0.15). The mean gestational age at delivery was similar between groups (DHA: 38.8 ± 1.7 placebo: 38.8 ± 1.7 wk, p= 0.54) as were APGAR scores at 1 and 5 min. Supplementing mothers through pregnancy with 400mg/d DHA did not impact the offspring birthweight, length or head circumference.
REVIEW | doi:10.20944/preprints202101.0184.v1
Subject: Life Sciences, Biochemistry Keywords: Alzheimer’s Disease; antibacterial; anti-biofilm; antifungal; antiviral; bacteria; infectious burden; parasites; pathogens; viruses
Online: 11 January 2021 (11:28:10 CET)
Alzheimer’s disease (AD) is a chronic neurodegenerative disease associated with the overproduction and accumulation of amyloid-β peptide and hyperphosphorylation of tau proteins in the brain. Despite extensive research on the amyloid-based mechanism of AD pathogenesis, the underlying cause of AD remains poorly understood. No disease-modifying therapies currently exist, and numerous clinical trials have failed to demonstrate any benefits. The recent discovery that the amyloid-β peptide has antimicrobial activities supports the possibility of an infectious aetiology of AD and suggests that amyloid-β plaque formation might be induced by infection. AD patients have a weakened blood-brain barrier and immune system and are thus at elevated risk of microbial infections. Such infections can cause chronic neuroinflammation, production of the antimicrobial amyloid-β peptide, and neurodegeneration. Various pathogens, including viruses, bacteria, fungi, and parasites have been associated with AD. Most research in this area has focused on individual pathogens, with herpesviruses and periodontal bacteria being most frequently implicated. The purpose of this review is to highlight the potential role of multi-pathogen infections in AD. Recognition of the potential coexistence of multiple pathogens and biofilms in AD's aetiology may stimulate the development of novel approaches to its diagnosis and treatment. Multiple diagnostic tests could be applied simultaneously to detect major pathogens, followed by anti-microbial treatment using antiviral, antibacterial, antifungal, and anti-biofilm agents.
ARTICLE | doi:10.20944/preprints202101.0179.v1
Subject: Life Sciences, Biochemistry Keywords: oral squamous cell carcinoma; HLA class I; antigen processing machinery; immune cell infiltration; immune escape; prognosis
Online: 11 January 2021 (10:47:25 CET)
Progression of oral squamous cell carcinoma (OSCC) has been associated with an escape of tumor cells from the host immune surveillance due to an increased knowledge of its underlying molecular mechanisms and its modulation by the tumor microenvironment and immune cell repertoire. In this study the expression of HLA class I (HLA-I) antigens and of components of the antigen processing machinery (APM) was analyzed in 160 pathologically classified human papilloma virus (HPV)-negative OSCC lesions and correlated to the intra-tumoral immune cell response, IFN- signaling and to the patients outcome. A heterogeneous, but predominantly lower constitutive protein expression of HLA-I APM components was found in OSCC sections when compared to non-neoplastic cells. Tumoral HLA-I APM component expression was further categorized into the three major phenotypes HLA-Ihigh/APMhigh, HLA-Ilow/APMlow and HLA-Idiscordant high/low/APMhigh. In the HLA-Ihigh/APMhigh group, the highest frequency of intra-tumoral CD8+ T cells and lowest number of CD8+ T cells close to FoxP3+ cells was found. Patients within this group presented the most unfavorable survival, which was significantly evident in stage T2 tumors. Despite a correlation with the number of intra-tumoral CD8+ T cells, tumoral JAK1 expression as a surrogate marker for IFN- signaling was not associated with HLA-I/APM expression. Thus, the presented findings strongly indicate the presence of additional factors involved in the immunomodulatory process of HPV-negative OSCC with a possible tumor-burden-dependent complex network of immune escape mechanisms beyond HLA-I/APM components and T cell infiltration in this tumor entity.
REVIEW | doi:10.20944/preprints202101.0178.v1
Subject: Life Sciences, Biochemistry Keywords: metalloproteins; zinc transporters; metal chelators; antibiotic resistance; antimicrobials
Online: 11 January 2021 (10:20:01 CET)
Zinc is a redox-inert trace element that is second only to iron in abundance in biological systems. In cells, zinc is typically buffered and bound to metalloproteins, but may also exist as a labile or chelatable (free ion) form. Zinc plays a critical role in prokaryotes and eukaryotes ranging from structural to catalytic to replication to demise. This review discusses the influential properties of zinc on various mechanisms of bacterial proliferation and synergistic action as anti-microbial element. We also touch upon the significance of zinc among eukaryotic cells and how it may modulate their survival and death through its inhibitory or modulatory effect on certain receptors, enzymes, and signaling proteins. A brief discussion on zinc chelators is also presented and chelating agents may be used with or against zinc to affect therapeutics against human diseases. Overall, the multidimensional effects of zinc in cells attest to the growing numbers of scientific research that reveal the consequential prominence of this remarkable transition metal in human health and disease.
ARTICLE | doi:10.20944/preprints202101.0173.v1
Subject: Life Sciences, Biochemistry Keywords: SARS-CoV-2; genetic diversity; molecular surveillance; natural selection; non-synonymous substitution
Online: 11 January 2021 (09:50:55 CET)
In December 2019, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the province of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. We performed genomic analysis to identify the changes in genetic diversity of SARS-CoV-2 between December 2019 and November 2020, and through molecular surveillance, we monitored the mutations that could be involved in viral fitness. We analyzed 2,213 complete genomes from 6 geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified 7 frequent mutations that resulted in non-synonymous substitutions (dN). Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein emerged recently and have spread in Oceania and Europe. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.
REVIEW | doi:10.20944/preprints202101.0171.v1
Subject: Life Sciences, Biochemistry Keywords: microgravity; spaceflight; immunology; pathogens; macrophages; bacteria; viruses; innate immune response; adaptive immune response
Online: 11 January 2021 (09:44:52 CET)
Immune dysfunction has long been reported by medical professionals regarding astronauts suffering from opportunistic infections both during their time in space and a short time period afterwards once back on Earth. Various species of prokaryotes on board these space missions or cultured in a microgravity analogue exhibit increased virulence, enhanced formation of biofilms, and in some cases develop specific resistance for specific antibiotics. This poses a substantial health hazard to the astronauts confined in constant proximity to any present bacterial pathogens on long space missions with a finite number of resources including antibiotics. Furthermore, some bacteria cultured in microgravity develop phenotypes not seen in Earth gravity conditions, providing novel insights into bacterial evolution and research.
Fri, 8 January 2021
Subject: Life Sciences, Biochemistry Keywords: Collaboration; annotate; WormBase; C. elegans; Course-based undergraduate research experience (CURE); genetics; scientific community
Online: 8 January 2021 (16:55:14 CET)
Course-based Undergraduate Research Experiences (CUREs) provide the same benefits as individual, mentored faculty research while expanding the availability of research opportunities. One important aspect of CUREs is student’s engagement in collaboration. We developed a partnership with the Caenorhabditis elegans (C. elegans) database, WormBase, in which students submitted annotations of published manuscripts to the website. This activity provided students with a collaborative research activity that benefitted the greater scientific community and enhanced students’ understanding of molecular genetics during the COVID-19 pandemic. WormBase relies on community annotators to read published articles and input phenotypic data. Students submitted a total of nine annotations directly to WormBase, which were curated by WormBase to ensure correctness and to reduce overlap from redundant annotations. Due to the stress on students during this time of crisis, qualitative data were collected in lieu of quantitative pre-post analyses. Students described their learning experiences in terms of interactions with the scientific community and the “real world”, content knowledge and competencies, and changes in perspectives and use of resources. Students also reported that this activity was helpful in their understanding of critical molecular genetics concepts. Most students reported on cognitive processes that represent mid-level Bloom’s categories. The shift to online learning during the COVID-19 pandemic created an immediate need for meaningful, collaborative experiences in CUREs. By partnering with WormBase, students gained insight into the scientific community and contributed as community members. We describe possible modifications for future courses, potential expansion of the WormBase collaboration, and future directions for quantitative analysis.
ARTICLE | doi:10.20944/preprints202101.0164.v1
Subject: Life Sciences, Biochemistry Keywords: Arbutus unedo L. Artificial Pollination, Breeding, Drought stress, Microscopy, Pollen, Physiological performance
Online: 8 January 2021 (14:08:49 CET)
Arbutus unedo L. is a small Ericaceae tree with a circum-Mediterranean distribution. It has a huge ecological impact on southern Europe forests and a great economic importance, as a source of phytochemicals with bioactive properties and for fruit production. On the foreseen climate change context, breeding towards drought tolerance is necessary in order to ameliorate plant performance. The aim of this work was therefore to study the reproduction mechanisms of strawberry tree, obtain new genetic combinations by hybridization and select genotypes more tolerant to drought stress. A morphological analysis of flowers and pollen was carried out, and controlled pollinations performed both in vitro and ex vitro. The very first approach on strawberry tree breeding by means of hybridization is also presented. Several physiological parameters were evaluated on 26 genotypes submitted to a water deficit regime. Plant behavior under drought greatly varied among genotypes, which showed a high phenotype plasticity. Three genotypes that were able to cope with water restriction without compromising net CO2 assimilation were identified as highly tolerant to drought stress. The results obtained elucidate the reproduction mechanisms of strawberry tree and open the way for a long-term breeding program based on the selection of drought tolerant plants.
ARTICLE | doi:10.20944/preprints202003.0437.v2
Subject: Life Sciences, Biochemistry Keywords: antivirals; broad-spectrum; CRISPR; Cas9; SARS; COVID-19
Online: 8 January 2021 (13:53:55 CET)
All RNA viruses deliver their genomes into target host cells through processes distinct from normal trafficking of cellular RNA transcripts. The delivery of viral RNA into most cells hence triggers innate antiviral defenses that recognize viral RNA as foreign. In turn, viruses have evolved mechanisms to subvert these defenses, allowing them to thrive in target cells. Therefore, drugs activating defense to exogenous RNA could serve as broad-spectrum antiviral drugs. Here we show that transcriptional signatures associated with cellular responses to the delivery of a non-viral exogenous RNA sequence into human cells predict small molecules with broad-spectrum antiviral activity. In particular, transcriptional responses to the delivery of Cas9 mRNA into human hematopoietic stem and progenitor cells (HSPCs) highly matches those triggered by small molecules with broad-spectrum antiviral activity such as emetine, homoharringtonine, pyrvinium pamoate and anisomycin, indicating that these drugs are potentially active against other RNA viruses. Furthermore, these drugs have been approved for other indications and could thereby be repurposed to novel viruses. We propose that the antiviral activity of these drugs to SARS-CoV-2 should therefore be determined as they have been shown as active against other coronaviruses including SARS-CoV-1 and MERS-CoV. Indeed, two of these drugs- emetine and homoharringtonine- were independently shown to inhibit SARS-CoV-2 as this article was in preparation. These drugs could also be explored as potential adjuvants to COVID-19 vaccines in development due to their potential effect on the innate antiviral defenses that could bolster adaptive immunity when delivered alongside vaccine antigens.
Subject: Life Sciences, Biochemistry Keywords: CA3-CA1 synapses; NMDA; AMPA; systems biology; multiscale modeling; synaptic plasticity; long term potentiation; long term depression; hippocampus
Online: 8 January 2021 (13:17:31 CET)
Inside hippocampal circuits, neuroplasticity events that individual cells may undergo during synaptic transmissions occur in the form of Long Term Potentiation (LTP) and Long Term Depression (LTD). The high density of NMDA receptors expressed on the surface of the dendritic CA1 spines confers to hippocampal CA3-CA1 synapses, the ability to easily undergo NMDA-mediated LTP and LTD, that is essential for some forms of explicit learning in mammals. Providing a comprehensive kinetic model that can be used for running computer simulations of the synaptic transmission process is currently a major challenge. Here, we propose a compartmentalized kinetic model for CA3-CA1 synaptic transmission. Our major goal was to tune our model in order to predict the functional impact caused by disease associated variants of NMDA receptors related to severe cognitive impairment. Indeed, for variants Glu413Gly and Cys461Phe, our model predicts negative shifts in the glutamate affinity and changes in the kinetic behavior, consistent with experimental data. These results pinpoint to the predictive power of this multiscale viewpoint, which aims to integrate the quantitative kinetic description of large interaction networks typical of system biology approaches with a focus on the quality of few, key, molecular interactions typical of structural biology ones.
ARTICLE | doi:10.20944/preprints202101.0155.v1
Subject: Life Sciences, Biochemistry Keywords: Aquaponics; Tilapia; Clarias; Bacteroidetes, Proteobacteria, Actinobacteria, extracellular enzymes, Pseudomonas flourescens; Pseudomonas veronii, plant growth promotion, In vitro antagonistic
Online: 8 January 2021 (13:01:18 CET)
Aquaponics are food production systems advocated for food security and health. Their sustainability from a nutritional and plant health perspective is, however, a significant challenge. Recirculated aquaculture systems (RAS) form a major part of aquaponic systems but knowledge about their potential to benefit plant growth and suppress their pathogens is limited. The current study tested if the diversity and function of microbial communities in two commercial RAS were specific to the fish species used (Tilapia or Clarias) and sampling site (fish tanks and wastewaters), and whether they confer benefits to plants and have in vitro antagonistic potential towards plant pathogens. Microbial diversity and composition was found to be dependent on fish species and sample site. The Tilapia RAS hosted higher bacterial diversity than the Clarias RAS; but the latter hosted higher fungal diversity. Both Tilapia and Clarias RAS hosted bacterial and fungal communities that promoted plant growth, inhibited plant pathogens and encouraged biodegradation. The production of extracellular enzymes, related to nutrient availability and pathogen control, by bacterial strains isolated from the Tilapia and Clarias systems, makes them a promising tool in aquaponics and in their system design.
REVIEW | doi:10.20944/preprints202101.0151.v1
Subject: Life Sciences, Biochemistry Keywords: complement system; proteolytic cascade; convertase; inhibitor; structural biology; molecular mechanism
Online: 8 January 2021 (11:54:36 CET)
The complement system is part of the innate immune response, where it provides immediate protection from infectious agents and plays a fundamental role in homeostasis. Complement dysregulation occurs in several diseases, where the tightly regulated proteolytic cascade turns offensive. Prominent examples are atypical hemolytic uremic syndrome, paroxysmal nocturnal hemoglobinuria and Alzheimer’s disease. Therapeutic intervention targeting complement activation may allow treatment of such debilitating diseases. In this review, we describe a panel of complement targeting nanobodies that allow modulation at different steps of the proteolytic cascade, from the activation of the C1 complex in the classical pathway to formation of the C5 convertase in the terminal pathway. Thorough structural and functional characterization has provided a deep mechanistic understanding of the mode of inhibition for each of the nanobodies. These complement specific nanobodies are novel powerful probes for basic research and offer new opportunities for in vivo complement modulation.
ARTICLE | doi:10.20944/preprints202011.0565.v2
Subject: Life Sciences, Biochemistry Keywords: pelvic organ prolapse (POP); uterine prolapse; heavy load carrying
Online: 8 January 2021 (11:34:54 CET)
Heavy load carrying of water, firewood, and sand/stones is a ubiquitous activity for women living in developing countries. Although the intra-abdominal pressure associated with heavy load carrying is hypothesized to increase the risk of pelvic organ prolapse (POP) among women, relevant epidemiologic data are lacking. We conducted a comparative study involving two exploratory cross-sectional studies among convenience samples of women carrying heavy loads, with different characteristics: (1) as part of their activities for daily living, in Shinyanga region, Tanzania; and (2) working as sand miners in Pokhara, Nepal. Women were categorized has having “low” or “high” load-carrying exposures based on the measured weights of the loads being carried at the time of the survey, as well as on self-reported duration and frequency of load carrying. A summary score for lower abdominal discomfort suggestive of POP was generated using questions from the Pelvic Organ Prolapse Distress Inventory (POPDI-6). Women with higher load carrying exposures had on average higher discomfort scores in both Tanzania (adjusted prevalence difference (PDa)=3.7; 95% CI: -3.8-11.3; p=0.33) and Nepal (PDa=9.3; 95% CI: -4.9-23.6; p=0.18). We identified trends suggestive of an association between increasing heavy load carrying exposures and symptoms of lower abdominal discomfort. Our findings underscore the need for larger epidemiologic studies of the potential adverse reproductive health effects of heavy load carrying activities on women in developing countries.
REVIEW | doi:10.20944/preprints202101.0135.v1
Subject: Life Sciences, Biochemistry Keywords: Global Alignment; Local Alignment; Heuristic Algorithm; Exhaustive Algorithm
Online: 8 January 2021 (10:30:03 CET)
Sequence analysis program is outlined that analyzes and investigates homology between various nucleic acid or protein sequence. The dot matrix technique compares the sequences and the consensus sequence is obtained by superimposing on each other all the dot matrices. Local Alignment and Global Alignment both sequence from start to end is the best possible alignment over the entire duration between the two sequences. This method is more important to align with two closely related sequences roughly the same length. This method may not able to generate optimal results for divergent sequences and variable length sequence because between the two sequences it does not recognize very similar local region.
ARTICLE | doi:10.20944/preprints202101.0130.v1
Subject: Life Sciences, Biochemistry Keywords: Geniposide; NF-ĸB; IEC-6; Signaling pathway; Cell migration
Online: 8 January 2021 (08:35:25 CET)
The nuclear factor-ĸB (NF-ĸB) transcriptional system is a major effector pathway involved in inflammatory responses. Previous studies found that a Gardenia decoction (GD) inhibited the expression of NF-κB in a lipopolysaccharide (LPS)-stimulated mouse intestinal injury model. Herein, we hypothesized that geniposide (GE), a component of Gardenia jasminoides Ellis, also exerts anti-inflammatory effects and inhibits NF-ĸB activity in LPS-induced intestinal epithelial cells (IEC-6). IEC-6 cells were stimulated with LPS, following which the effects of GE on NF-ĸB signaling in the IEC-6 cells were examined by western blotting to detect IĸB phosphorylation/degradation. The expression of NF-κB was determined by immunofluorescence assay (IFA). Enzyme-linked immunosorbent assay (ELISA) was used to detect the inhibitory effect of GE on the release of tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and interleukin-1β (IL-1β) activated by LPS in IEC-6 cells. In addition, the migration ability of IEC-6 cells was observed by the scratch method. These results showed that GE dose-dependently downregulated levels of the proinflammatory cytokines TNF-α, IL-6 and IL-1β that had been upregulated by LPS and suppressed the phosphorylation of IĸB and NF-ĸB induced by LPS. Our findings indicated that GE could reduce LPS-induced NF-ĸB signaling and proinﬂammatory expression in IEC-6 cells and significantly enhance the migration of IEC-6 cells. Moreover, GE inhibited the expression of NF-κB, nuclear transfer, and transcriptional activity in IEC-6 cells. GE could block the synthesis of inflammatory factors of IEC-6 cells by inhibiting activation of the IĸB/NF-κB signaling pathway induced by LPS.
Wed, 6 January 2021
CASE REPORT | doi:10.20944/preprints202101.0132.v1
Online: 6 January 2021 (20:38:36 CET)
To date, uncertainty remains about how long the protective immune responses against SARS-CoV-2 persists and the first reports of suspected reinfection began to be described in recovered patients months after the first episode. Viral evolution may favor reinfections, and the recently described spike mutations, particularly in the receptor binding domain (RBD) in SARS-CoV-2 lineages circulating in the UK, South Africa, and most recently in Brazil, have raised concern on their potential impact in infectivity and immune escape. We report the first case of reinfection from genetically distinct SARS-CoV-2 lineage presenting the E484K spike mutation in Brazil, a variant associated with escape from neutralizing antibodies.
Subject: Life Sciences, Biochemistry Keywords: evolution; darwinism; genetic code; RNA; homoestasis; physics
Online: 6 January 2021 (15:06:41 CET)
The physics–biology continuum relies on the fact that life emerged from prebiotic molecules. Here, I argue that life emerged from the physical coupling between the synthesis of nucleic acids and the synthesis of amino acid polymers. Owing to this physical coupling, amino acid polymers (or proto-phenotypes) maintained the physicochemical parameter equilibria (proto-homeostasis) in the immediate environment of their encoding nucleic acids (or proto-genomes). This protected the proto-genome physicochemical integrity (i.e., atomic composition) from environmental physicochemical stresses, and therefore increased the probability of reproducing the proto-genome without variation. From there, genomes evolved depending on the biological activities they generated in response to environmental fluctuations. Thus, a genome generating an internal environment whose physicochemical parameters guarantee homeostasis and genome integrity has a higher probability to be reproduced without variation and therefore to reproduce the same phenotype in offspring. Otherwise, the genome is modified by the imbalances of the internal physicochemical parameters it generates, until new emerging biological activities maintain homeostasis. In sum, evolution depends on feedforward and feedback loops between genome and phenotype, since the internal physicochemical conditions that a genome generates in response to environmental fluctuations in turn either guarantee the stability or direct the variation of the genome.
REVIEW | doi:10.20944/preprints202101.0120.v1
Subject: Life Sciences, Biochemistry Keywords: mTOR; ATP; protein synthesis; autophagy; amino acids; nutrition; adipose tissue; muscle; sarcopenia; mitochondria
Online: 6 January 2021 (14:32:22 CET)
Background. Sarcopenia, defined as the loss of skeletal muscle mass and function, is a major clinical problem in many chronic illnesses, in cancer and in the elderly. Exercise and adequate nutrition, peculiarly dependents on availability of essential amino acids, considered the primary strategies for prevention and treatment of protein synthetic deficits, affect both the efficient scavenging of aged and overused protein molecules and the renewal, by maintaining muscular protein synthesis. Many questions still remain about the regulation of protein syntheses and degradation. Degradation of inefficient proteins or organelles is performed by the sum of micro and macro-autophagy plus ubiquitin-proteasome system, activities known as proteostasis, necessary to preserve and promote protein masses and consequently, the body’s reserves. However, how protein synthesis is regulated, and how activation of the mTOR complex may modulate and transduce the flow of information provided by exercise and nutrition to balance proteostasis and syntheses, is far from being fully understood. We suggest that energy production and availability, thus also mitochondria, may have a pivotal role in synchronizing activity and functional outcomes of protein syntheses, and that those syntheses, since higly energy demanding, are main effectors of AMPK dependent autophagy activation by consuming ATP and producing AMP. Conclusion. While in normal conditions protein syntheses drive autophagy activation by decreasing ATP to AMP ratio, conversely autophagy may be inefficiently activated when chronic both low production and consumption of ATP would result in lowest concentrations of AMP, and therefore both blunted rates of protein syntheses and autophagy would be observed. We suggest that this functional hypothesis may explain sarcopenia in many pathological conditions , as in cancer or in aging muscles.
REVIEW | doi:10.20944/preprints202101.0116.v1
Subject: Life Sciences, Biochemistry Keywords: Bioinformatics; Graphs; Medical genetics; sequencing methods
Online: 6 January 2021 (12:06:39 CET)
High-quality chromosome-scale haplotype sequences— of diploid genomes, polyploid genomes and metagenomes — provide important insights into genetic variation associated with disease and biodiversity. However, whole-genome short read sequencing does not yield haplotype information that spans whole chromosomes directly. Computational assembly of shorter haplotype fragments is required for haplotype reconstruction, which can be challenging owing to limited fragment lengths and high haplotype and repeat variability across genomes. Recent advancements in long-read and chromosome-scale sequencing technologies, alongside computational innovations, are improving the reconstruction of haplotypes at the level of whole chromosomes. Here, we review recent methodological progress in these areas and discuss perspectives that could enable routine high-quality haplotype reconstruction in clinical and evolutionary studies.
REVIEW | doi:10.20944/preprints202101.0114.v1
Subject: Life Sciences, Biochemistry Keywords: HIV-1; HIV-1 splicing; HIV-1 oversplicing; HIV-1 latency
Online: 6 January 2021 (11:49:59 CET)
HIV-1 transcribes only one kind of transcript – the full length genomic RNA. To make the mRNA transcripts for the accessory proteins Tat and Rev, the genomic RNA must completely splice. The mRNA transcripts for Vif, Vpr, and Env must splice but not completely. Genomic RNA (which also functions as mRNA for the Gag and Gag/Pro/Pol precursor polyproteins) must not splice at all. HIV-1 can tolerate a surprising range in the relative abundance of individual transcript types, and a surprising amount of aberrant and even odd splicing; however, it must not over-splice, which results in the loss of full length genomic RNA and has a dramatic fitness cost. Cells typically do not tolerate unspliced/incompletely spliced transcripts, so HIV-1 has to circumvent this cell policing mechanism to allow some splicing while suppressing most. Splicing is controlled by RNA secondary structure, cis-acting regulatory sequences which bind splicing factors, and the viral protein Rev. There is still much work to be done to clarify the combinatorial effects of these splicing regulators. These control mechanisms represent attractive targets to induce over-splicing as an antiviral strategy. Finally, splicing has been implicated in latency, but to date there is little supporting evidence for such a mechanism. In this review we apply what is known of cellular splicing to understand splicing in HIV-1, and also present data from our newer and more sensitive deep sequencing assays quantifying the different HIV-1 transcript types.
Subject: Life Sciences, Biochemistry Keywords: super-resolution microscopy; advanced light microscopy; quantitative microscopy; live-cell microscopy; SMLM; STORM; SIM; STED; expansion microscopy; influenza virus; viral replication
Online: 6 January 2021 (10:40:59 CET)
With an estimated 3 to 5 million human cases annually and the potential to infect domestic and wild animal populations, influenza viruses are one of the greatest health and economic burdens to our society  and pose an ongoing threat of large-scale pandemics. Despite our knowledge of many important aspects of influenza virus biology, there is still much to learn about how influenza viruses replicate in infected cells, for instance how they use entry receptors or exploit host cell trafficking pathways. These gaps in our knowledge are due, in part, to the difficulty of directly observing viruses in living cells. In recent years, advances in light microscopy, including super-resolution microscopy and single-molecule imaging, have enabled many viral replication steps to be visualised dynamically in living cells. In particular, the ability to track single virions and their components, in real time, now allows specific pathways to be interrogated providing new insights to various aspects of the virus-host cell interaction. In this review, we discuss how state-of-the-art imaging technologies, notably quantitative live-cell and super-resolution microscopy, are shedding new nanoscale and molecular insights into influenza virus replication and revealing new opportunities for developing antiviral strategies.
Tue, 5 January 2021
REVIEW | doi:10.20944/preprints202101.0098.v1
Subject: Life Sciences, Biochemistry Keywords: Cell proliferation; congenital heart disease; embryonic lethality, folliculogenesis; neuropsychological profile; prolonged cell cycle; short stature; Turner syndrome
Online: 5 January 2021 (14:13:38 CET)
Turner syndrome (TS) is a chromosomal disorder that is caused by a missing or structurally abnormal second sex chromosome. Subjects with TS are at an increased risk of developing intrauterine growth retardation, low birthweight, short stature, congenital heart diseases, infertility, obesity, dyslipidemia, hypertension, insulin resistance, type 2 diabetes mellitus, metabolic syndrome, and cardiovascular diseases (stroke and myocardial infarction). The underlying pathogenetic mechanism of TS is unknown. The assumption that X chromosome-linked gene haploinsufficiency is associated with the TS phenotype is questioned since such genes have not been identified. Thus, other pathogenic mechanisms have been suggested to explain this phenotype. Morphogenesis encompasses a series of events that includes cell division, the production of migratory precursors and their progeny, differentiation, programmed cell death and integration into organs and systems. The precise control of the growth and differentiation of cells is essential for normal development. The cell cycle frequency and the number of proliferating cells are essential in cell growth. 45,X cells have a failure to proliferate at a normal rate, leading to a decreased cell number in a given tissue during organogenesis. A convergence of data indicates an association between a prolonged cell cycle and the phenotypical features in Turner syndrome. This review aims to examine old and new findings concerning the relationship between a prolonged cell cycle and TS phenotype. These studies reveal a diversity of phenotypic features in TS that could be explained by reduced cell proliferation. The implications of this hypothesis for our understanding of the TS phenotype and its pathogenesis are discussed. It is not surprising that 45,X monosomy leads to cellular growth pathway dysregulation with profound deleterious effects on both embryonic and later stages of development. The prolonged cell cycle could represent the beginning of the pathogenesis of TS, leading to a series of phenotypic consequences in embryonic/fetal, neonatal, pediatric, adolescence, and adulthood life.
Subject: Life Sciences, Biochemistry Keywords: continuous cropping obstacles; Panax quinquefolius L.; phenolic acids; soil bacterial community composition; soil nutrients
Online: 5 January 2021 (11:46:53 CET)
This study aims to verify the time-variant feature of American ginseng (AG) continuous cropping obstacles and to explore the factors impeding continuous cropping. We verified the feature with a plant-soil feedback pot experiment and then investigated the factors by comparing the properties of control soils that had not been previously used for growing ginseng (CS) with those of soils with a 10-year-crop-rotation cycle following the growth of AG (RS). It’s found that the survival rate of AG in RS was lower than that in CS. The RS had lower pH, available potassium content, and urease activity. Additionally, p-coumaric, p-hydroxybenzoic, vanillic, caffeic, and cinnamic acid levels were lower in RS than in CS, but salicylic acid levels showed the opposite pattern. RS had higher Rhodanobacter and lower Acidothermus, Sphingomonas relative abundances in bacterial community. It’s also found that many bacteria were substantially correlated with phenolic acids and soil physiochemical properties. Results indicate that even after 10-year crop rotation, the negative effects of prior continuous cropping of AG has not been eliminated. The growth of AG can be affected negatively with deterioration of soil physicochemical properties and with lower levels of phenolic acids which promote pathogen reproduction. Probiotics reduction also weighs. Moreover, biotic factors are interrelated with abiotic ones. Therefore, it can be inferred that the comprehensive change of soil properties is the main obstacle for continuous cropping.
ARTICLE | doi:10.20944/preprints202101.0078.v1
Subject: Life Sciences, Biochemistry Keywords: Protein Oligomerization; Angiogenin (h-ANG); tRNA; ALS; stress granules; NMR spectroscopy
Online: 5 January 2021 (10:58:21 CET)
Protein oligomerzation is key to countless physiological processes, but also to abnormal amyloid conformations implicated in over 25 mortal human diseases. Angiogenin (h-ANG), a ribonuclease A family member, produces RNA fragments that regulate ribosome formation, the creation of new blood vessels and stress granule function. Too little h-ANG activity leads abnormal protein oligomerization resulting in Amyotrophic Lateral Sclerosis (ALS) or Parkinson’s disease. While a score of disease linked h-ANG mutants has been studied by X-ray diffraction, some elude crystallization. There is also debate regarding the structure that RNA fragments adopt after cleavage by h-ANG. Here, to better understand the beginning of the process that leads to aberrant protein oligomerization, the solution secondary structure and residue-level dynamics of WT h-ANG and two mutants: H13A and R121C, are characterized by multidimensional heteronuclear NMR spectroscopy under near physiological conditions. All three variants are found to adopt well folded and highly rigid structures in solution, although the elements of secondary structure are somewhat shorter than those observed in cystallography studies. R121C alters the environment of nearby residues only. By constrast, the mutation H13A affects local residues as well as nearby active site residues residues K41 and H119. The conformation characterization by CD and 1D 1H NMR spectroscopies of tRNAAla before and after h-ANG cleavage reveals a retention of most duplex structure and little or no G-quadruplex formation.
BRIEF REPORT | doi:10.20944/preprints202101.0070.v1
Online: 5 January 2021 (10:13:04 CET)
High prevalence of various infectious diseases including but not limited to HCV, HBV and HIV alongside TB in Pakistani population indicates there must be similarly high prevalence of these, if not higher, amongst (intravenous drug users) IDUs serve as a reservoir for infectious diseases, blood borne as well as others due to injection abuse, poor hygiene and bad quality of life. This continues to be a serious threat in spreading out of these diseases, decreased health quality of the society and increased death rate. This survey study was conducted to check the prevalence of HCV, HBV, HIV and TB in several drug rehabilitation centers in Punjab region of Pakistan. 78 centers were either visited or contacted via phone and 21 out of them cooperated to share their data. An analysis of respondent centers returned useable data revealed that only 7.2% patient were found positive for Hepatitis B. While, 33.23% patients were positive for HCV, 8.74% patients were positive for HIV and 0.87% were positive for TB. What is worrisome is the absence of proper periodic screenings for these as well as other potential infections. Also we found out that upon diagnosis of these diseases mostly rehabilitation centers refuse admittance, which aggravates the problem further as well as leaves those IDUs and their families helpless, who are looking for it. Majority of the respondent centers, doctors, psychologists believed that the patients, partner of the patients and their immediate family members must be offered for infection screenings regularly.
Mon, 4 January 2021
COMMUNICATION | doi:10.20944/preprints202101.0065.v1
Subject: Life Sciences, Biochemistry Keywords: COVID-19; Angiotensin Converting Enzyme 2 (ACE2); Adverse outcome pathway(AOP); Molecular initiation Event (MIE); Key event (KE); Adverse Outcome (AO)
Online: 4 January 2021 (16:37:08 CET)
Increasing global concern over COVID-19 has recently brought greater attention to studies due to the ease of person-to-person transmission and the current lack of effective antiviral therapy. Here, we proposed the application of the adverse outcome pathway (AOP) framework to support re-search on the pathogenesis of viral disease. We first constructed adverse outcome pathways (AOPs) applicable to COVID-19 management to understand whether the infection causes severe acute respiratory distress. Based on the AOP framework where mechanistic elucidation of the pathway from the interaction of chemicals (or viruses) to apical endpoints is represented, our COVID-19 AOP indicated that the molecular initiating event (MIE) was angiotensin-converting enzyme 2 (ACE2) interaction, and the key events (KEs) were the increased pro-inflammatory cytokines in immune cells, with increased mortality as an apical adverse outcome (AO). However, there is still limited information on the toxicity mechanisms of AOPs in COVID-19; therefore, detailed KEs and AOs on toxicity mechanisms will be required to fill these gaps in the data. This study demonstrated that the COVID-19 AOP framework is a suitable tool to design new drugs and to integrate crowded-sourced information for the battle against the COVID-19 pandemic.
Subject: Life Sciences, Biophysics Keywords: double-stranded DNA; DNA dynamical models; correlated oscillations in macromolecules; epigenetic changes
Online: 4 January 2021 (16:35:40 CET)
A fully analytical treatment of the base-pair and codon dynamics in double-stranded DNA molecules is introduced, by means of a realistic treatment which considers different mass values for G, A, T, and C nucleotides and takes into account the intrinsic three-dimensional, helicoidal geometry of DNA in terms of a Hamitonian in cylindrical coordinates. Within the framework of the Peyrard-Dauxois-Bishop model we consider the coupling between stretching and stacking radial oscillations as well as the twisting motion of each base pair around the helix axis. By comparing the linearized dynamical equations for the angular and radial variables when going from the bp local scale to the longer triplet codon scale, we report an underlying hierarchical symmetry. The existence of synchronized collective oscillations of the base-pairs and their related codon triplet units are disclosed from the study of their coupled dynamical equations. The possible biological role of these correlated, long-range oscillation effects in double standed DNA molecules containing mirror-symmetric codons of the form XXX, XX’X, X’XX’, YXY, and XYX is discussed in terms of the dynamical equations solutions and their related dispersion relations.
ARTICLE | doi:10.20944/preprints202012.0712.v2
Subject: Life Sciences, Biochemistry Keywords: path integral; importance sampling; financial options; combat analysis
Online: 4 January 2021 (13:29:01 CET)
Background: Forecasting nonlinear stochastic systems most often is quite difficult, without giving in to temptations to simply simplify models for the sake of permitting simple computations. Objective: Here, two basic algorithms, Adaptive Simulated Annealing (ASA) and path-integral codes PATHINT/PATHTREE (and their quantum generalizations qPATHINT/qPATHTREE) are offered to detail such systems. Method: ASA and PATHINT/PATHTREE have been effective to forecast properties in three disparate disciplines in neuroscience, financial markets, and combat analysis. Applications are described for COVID-19. Results: Results of detailed calculations have led to new results and insights not previously obtained. Conclusion: These 3 applications give strong support to a quite generic application of these tools to stochastic nonlinear systems.
ARTICLE | doi:10.20944/preprints202101.0045.v1
Subject: Life Sciences, Biochemistry Keywords: Kombucha tea; microbial diversity; bacterial cellulose; Komagataeibacter xylinus; repetitive elements sequence-based rep-PCR; typing
Online: 4 January 2021 (13:24:41 CET)
Bacterial cellulose (BC) is receiving great attention due to its unique properties such as high purity, water retention capacity, high mechanical strength, and biocompatibility. However, the production of BC has been limited because of high cost and low productivity. In this light, the isolation of new BC producing bacteria and selection of high productive strains became a promising issue. Kombucha tea is a fermented beverage in which the bacteria fraction of the microbial community is composed mostly by strains belonging to the genus Komagataeibacter. In this study Kombucha tea production trials were performed starting from a previous batch, and bacterial isolation was conducted along cultivation time. From the whole microbial pool, 46 isolates were tested for their ability in producing BC. The obtained BC yield ranged from 0.59 g/L, for the isolate K2G36, to 23 g/L for K2G30 used as the reference strain. The genetic intraspecific diversity of the 46 isolates was investigated using two repetitive-sequence-based PCR typing methods, which are the enterobacterial repetitive intergenic consensus (ERIC) elements and the (GTG)5 sequences, respectively. The results obtained using two different approaches revealed the suitability of the fingerprints techniques, showing a discrimination power, calculated as D index, of 0.94 for (GTG)5 rep-PCR and 0.95 for ERIC rep-PCR. In order to improve the sensitivity of the applied method, a combined model from the two genotyping experiments was performed, allowing to discriminate among strains.
REVIEW | doi:10.20944/preprints202101.0035.v1
Subject: Life Sciences, Biochemistry Keywords: GWAS; genetics; Mendelian Randomization; causal inference
Online: 4 January 2021 (12:36:41 CET)
With the rapidly increasing availability of large genetic data sets in recent years, Mendelian Randomization (MR) has quickly gained popularity as a novel secondary analysis method. Leveraging genetic variants as instrumental variables, MR can be used to estimate the causal effects of one phenotype on another even when experimental research is not feasible, and therefore has the potential to be highly informative. It is dependent on strong assumptions however, often producing strongly biased results if these are not met. It is therefore imperative that these assumptions are well-understood by researchers aiming to use MR, in order to evaluate their validity in the context of their analyses and data. The aim of this perspective is therefore to further elucidate these assumptions and the role they play in MR, as well as how different kinds of data can be used to further support them.
REVIEW | doi:10.20944/preprints202101.0026.v1
Subject: Life Sciences, Biochemistry Keywords: 20S proteasome; protein degradation; intrinsically disordered proteins; enzyme functional cycle; peptides; peptidome; proteome; oxidative stress
Online: 4 January 2021 (12:16:42 CET)
Four decades of proteasome research have yielded extensive information on ubiquitin-dependent proteolysis. The archetype of proteasomes is a 20S barrel-shaped complex that does not rely on ubiquitin as a degradation signal but can degrade substrates with a considerable unstructured stretch. Since roughly half of all proteasomes in most eukaryotic cells are free 20S complexes, ubiquitin-independent protein degradation may coexist with ubiquitin-dependent degradation by the highly regulated 26S proteasome. This article reviews recent advances in our understanding of the biochemical and structural features that underlie the proteolytic mechanism of 20S proteasomes. The two outer α-rings of 20S proteasomes provide a number of potential docking sites for loosely folded polypeptides. The binding of a substrate can induce asymmetric conformational changes, trigger gate opening, and initiate its own degradation through a protease-driven translocation mechanism. Consequently, the substrate translocates through two additional narrow apertures augmented by the β-catalytic active sites. The overall pulling force through the two annuli results in a protease-like unfolding of the substrate and subsequent proteolysis in the catalytic chamber. Although both proteasomes contain identical β-catalytic active sites, the differential translocation mechanisms yield distinct peptide products. Non-overlapping substrate repertoires and product outcomes rationalize cohabitation of both proteasome complexes in cells.
ARTICLE | doi:10.20944/preprints202101.0004.v1
Subject: Life Sciences, Biochemistry Keywords: shipyard welders; PM2.5 metal components; urinary metals; insulin resistance
Online: 4 January 2021 (08:38:23 CET)
Certain studies have reported various insulin resistance responses to ambient heavy metal pollution, but few have reported such responses to occupational heavy metal pollution. Even fewer have demonstrated a relationship between mixture effects of heavy metals and insulin resistance in welding workers. Overall, we recruited 53 welders and 48 administrative staff from a shipyard located in northern Taiwan. Personal exposure to heavy metals was monitored for PM2.5 and urine. Blood samples from each participant were collected from the antecubital vein after fasting. Urine samples from each participant were collected in the same period as blood samples. The geometric mean levels for chromium (Cr), manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), and cadmium (Cd) in the PM2.5 of the personal breathing zone and urinary Mn of welders were significantly higher than those in administrative staffs. Ambient Cr, Co, Ni, and Cu levels in the PM2.5 and urinary Cd were positively related to HOMA2-IR after adjusting for personal covariates (PM2.5-Cr: β=0.036, 95%C.I.: 0.002 to 0.070; PM2.5-Co: β=0.040, 95%C.I.: 0.002 to 0.077; PM2.5-Ni: β=0.054, 95%C.I.: 0.013 to 0.094; PM2.5-Cu: β=0.049, 95%C.I.: 0.010 to 0.088; U-Cd: β=0.209, 95%C.I.: 0.052 to 0.366, respectively). Our findings indicated the PM2.5 metal components and urinary metals were associated with increased insulin resistance in shipyard welders.
Subject: Life Sciences, Biochemistry Keywords: Azanucleoside; DMSO; DNA methylation, epigenetics; phosphorylation; restriction factor; triphosphohydrolase; methyltransferase inhibitor
Online: 4 January 2021 (08:19:38 CET)
Sterile α motif and histidine-aspartate domain–containing protein 1 (SAMHD1) is a multifunctional protein that limits cellular dNTP availability, interacts with specific retroviral proteins to induce degradation. Regulation of dNTP availability is crucial for cell cycle regulation and DNA stability. Demethylating agents such as azacytidine are in clinical use for cancer therapy, and reduce methylation of the SAMHD1 promoter and SAMHD1 gene expression. Here, we evaluated the effect of azacytidine on global DNA methylation in feline lymphocytes, and specifically on the abundance and cellular distribution of phosphorylated and non-phosphorylated SAMHD1. Azacytidine increased cellular and nuclear SAMHD1 but did not increase phosphorylated SAMHD1. Phosphorylation is essential for SAMHD1 stability and function but is unaffected by demethylation. The findings suggest that treatment with azacytidine could increase viral restriction, and they lend support to development of in vivo models utilizing azacytidine to modulate SAMHD1 activity.
Thu, 31 December 2020
ARTICLE | doi:10.20944/preprints202012.0824.v1
Online: 31 December 2020 (15:44:07 CET)
Since the accident of Fukushima Nuclear Power plant in 2011, people have been more interested in radiation safety in life. This study investigated the level of exact recognition of 6 warning pictograms enacted and utilized as per Korea Industrial Regulation in relation to medical & natural radiation safety at this time. Unless people recognize pictogram prepared for radiation safety correctly in accordance with its purpose, safety would be severely intimidated. The result of corroboratively analyzing recognition of radiation safety pictogram is as follows. First, some 63.3% of respondents negatively responded on understanding 6 pictograms related to radiation in life, showing low level of understanding. Second, the average mark of correct response on the questions asking the meaning of 6 pictograms presented in relation to radiation safety in life was 2.79 point (standard deviation 1.447 point), which was relatively low. As seen above, the level of recognition & comprehension is low, because education related to life radiation safety in the school is insufficient and the present warning pictogram established by Korea Industrial Regulation needs to be revised & supplemented. This study is meaningful in that the method of using pictogram is presented as one of diverse efforts to improve life radiation safety.
ARTICLE | doi:10.20944/preprints202012.0820.v1
Subject: Life Sciences, Biochemistry Keywords: Sophora japonica; Adipogenesis; AMPK; 3T3-L1 pre-adipocytes
Online: 31 December 2020 (14:24:18 CET)
Background: The world-wide rate of obesity is increasing continuously, representing a serious medical threat since it is associated with a variety of diseases including type 2 diabetes, cardiovascular disease, and numerous cancers. Sophora japonica is used as a traditional herb for medicinal purposes in eastern Asia. However, the anti-obesity effects of S. japonica fruit have not been explored. Objective: The aim of this study is to investigate the inhibition of adipocyte differentiation and adipogenesis by an ethanol extract of S. japonica fruit (EESF) in 3T3-L1 pre-adipocytes. Methods: MTT assay, Oil Red O staining, and Triglyceride contents were used to investigate lipid accumulation in 3T3-L1 cells to clarify adipocyte differentiation. The expression levels of various molecular signals associated with adipogenesis and lipogenesis were examined by western blot analysis. Results: Our results demonstrate that EESF suppressed the terminal differentiation of 3T3-L1 pre-adipocytes in a dose-dependent manner, as confirmed by a decrease in lipid droplet number and lipid content through Oil Red O staining. EESF significantly reduced the accumulation of cellular triglyceride, which was associated with a significant inhibition of the levels of pro-adipogenic transcription factors, downregulated the expression levels of adipocyte-specific proteins. Furthermore, EESF treatment effectively increased the phosphorylation of AMPK and ACC. Conclusions: These results together indicate that EESF has significant effects on the inhibition of adipogenesis and acts by stimulating the AMPK signaling pathway. Further studies will be needed to identify the active compounds in S. japonica.
ARTICLE | doi:10.20944/preprints202012.0817.v1
Subject: Life Sciences, Biochemistry Keywords: COVID-19; OC43; coronavirus; pandemic; influenza; historical revisionism; corpus linguistics
Online: 31 December 2020 (13:47:00 CET)
COVID-19 is the first known coronavirus pandemic. Nevertheless, the seasonal circulation of the four milder coronaviruses of humans – OC43, NL63, 229E and HKU1 – raises the possibility that these viruses are the descendants of more ancient coronavirus pandemics. This proposal arises by analogy to the observed descent of seasonal influenza subtypes H2N2 (now extinct), H3N2 and H1H1 from the pandemic strains of 1957, 1968 and 2009, respectively. Recent historical revisionist speculation has focussed on the influenza pandemic of 1889-1892, based on molecular phylogenetic reconstructions that show the emergence of human coronavirus OC43 around that time, probably by zoonosis from cattle. If the “Russian influenza”, as The Times named it in early 1890, was not influenza but caused by a coronavirus, the origins of the other three milder human coronaviruses may also have left a residue of clinical evidence in the 19th century medical literature and popular press. In this paper, we search digitised 19th century British newspapers for evidence of previously unsuspected coronavirus pandemics. We conclude that there is little or no corpus linguistic signal in the UK national press for large-scale outbreaks of unidentified respiratory disease for the period 1785 to 1890.
REVIEW | doi:10.20944/preprints202012.0810.v1
Subject: Life Sciences, Immunology Keywords: Krebs cycle; tricarboxylic acid cycle; cellular immunity; immunometabolism
Online: 31 December 2020 (13:16:37 CET)
Tricarboxylic acid cycle (TCA) is a series of chemical reactions in aerobic organisms used to generate energy via the oxidation of acetyl-CoA derived from carbohydrates, fatty acids, and proteins. In the eukaryotic system, the TCA cycle completely occurs in mitochondria, while the intermediates of the TCA cycle are retained in mitochondria due to their polarity and hydrophilicity. Under conditions of cell stress, mitochondria become disrupted and release their contents, which act as danger signals in the cytosol. Of note, the TCA cycle intermediates may also leak from dysfunctioning mitochondria and regulate cellular processes. Increasing evidence shows that the metabolites of the TCA cycle are substantially involved in the regulation of immune responses. In this review, we aimed to provide a comprehensive systematic overview of the molecular mechanisms of each TCA cycle intermediate that may play key roles in regulating cellular immunity in cell stress and discuss their implications for immune activation and suppression.
ARTICLE | doi:10.20944/preprints202012.0809.v1
Subject: Life Sciences, Biochemistry Keywords: Long-term care; care homes; nursing homes; dementia; quality improvement; palliative care
Online: 31 December 2020 (13:16:03 CET)
Important policy developments in dementia and palliative care in nursing homes between 2010 and 2015 in Flanders, Belgium might have influenced which people die in nursing homes and how they die. We aimed to examine differences between 2010 and 2015 in the prevalence and characteristics of residents with dementia in nursing homes in Flanders, and their palliative care service use and comfort in the last week of life. We used two retrospective epidemiological studies, including 198 residents in 2010 and 183 in 2015, who died with dementia in representative samples of nursing homes in Flanders. We found a 23%-point increase in dementia prevalence (P-value<0.001), with a total of 11%-point decrease in severe to very severe cognitive impairment (P=0.04). Controlling for this difference in resident characteristics, in the last week of life, there were increases in the use of pain assessment (+20%-point; P<0.001) and assistance with eating and drinking (+10%-point; P=0.02) but no change in total comfort. The higher prevalence of dementia in nursing homes with no improvement in residents’ total comfort while dying emphasize an urgent need to better support nursing homes in improving their capacities to provide timely and high-quality palliative care services to more residents dying with dementia.
REVIEW | doi:10.20944/preprints202012.0807.v1
Subject: Life Sciences, Biochemistry Keywords: Mechanosensitive channel; Corynebacterium glutamicum; L-glutamate secretion
Online: 31 December 2020 (13:00:44 CET)
After the discovery of Corynebacterium glutamicum from the avian feces contaminated soil, its enigmatic L-glutamate secretion by corynebacterial MscCG-type mechanosensitive channels has been utilized for the industrial monosodium glutamate production. Bacterial mechanosensitive channels are activated directly by increased membrane tension upon hypoosmotic downshock, thus the physiological significance of the corynebacterial L-glutamate secretion has been considered as adjusting turgor pressure by releasing cytoplasmic solutes. In this review, we present information that corynebacterial mechanosensitive channels have been evolutionally specialized as carriers to secrete L-glutamate into the surrounding environment in their habitats rather than osmotic safety valves. The lipid modulation activation of MscCG channels in L-glutamate production can be explained by the “Force-From-Lipids” and “Force-From-Tethers” mechanosensing paradigms and differs significantly from the mechanical activation upon hypoosmotic shock. The review also provides information on the search for possibilities that Corynebacterium glutamicum was originally a gut bacterium in the avian host in the aim of understanding physiological roles of corynebacterial mechanosensing. Corynebacterium glutamicum is able to secrete L-glutamate by mechanosensitive channels in the gut microbiota and help the host brain function via the microbiota-gut-brain axis.
COMMUNICATION | doi:10.20944/preprints202012.0804.v1
Subject: Life Sciences, Biochemistry Keywords: white collar; mucormycosis; virulence; Mucorales; Mucor lusitanicus
Online: 31 December 2020 (12:46:05 CET)
Mucolares are an ancient group of fungi encompassing the causal agents for the lethal infection mucormycosis. The high lethality rates, the emerging character of this disease, and the broad antifungal resistance of its causal agents are mucormycosis features alarming clinicians and researchers. Thus, the research field around mucormycosis is currently focused on finding specific weaknesses and targets in Mucorales for developing new treatments against mucormycosis. In this work, we tested the role of the white-collar genes family in the virulence potential of Mucor lusitanicus. In this regard, the study of the role in virulence of the three genes of this family, mcwc-1a, mcwc-1b, and mcwc-1c, resulted in a marked functional specialization, as only mcwc-1a was essential to maintain the virulence potential of M. lusitanicus. The traditional role of wc-1 genes regulating light-dependent responses is a thoroughly studied field, whereas their role in virulence remains uncharacterized. In this work, we investigated the mechanism involving mcwc-1a in virulence from an integrated transcriptomic and functional approach during the host-pathogen interaction. Our results revealed mcwc-1a as a master regulator controlling an extensive gene-network. Further dissection of this gene-network clustering its components by type of regulation and functional criteria disclosed a multifunctional mechanism depending on diverse pathways. In the absence of phagocytic cells, mcwc-1a controlled pathways related to cell motility and cytoskeleton that could be associated with the essential tropism during tissue invasion. After phagocytosis, several oxidative responding pathways dependent on mcwc-1a were activated during the germination of M. lusitanicus spore inside of phagocytic cells, which is the first stage of the infection. The third relevant group of genes involved in virulence and regulated by mcwc-1a belonged to the “unknown function,” indicating that new and hidden pathways are involved in virulence. The unknown function category is especially pertinent in the study of mucormycosis, as it is highly enriched in specific fungal genes that represent the most promising targets for developing new antifungal compounds. These results essentially unveil a complex multifunctional mechanism used by wc-1 genes to regulate the pathogenic potential in Mucorales that could also apply to other fungal pathogens.
REVIEW | doi:10.20944/preprints202012.0796.v1
Subject: Life Sciences, Biochemistry Keywords: HIV-1; HSV-1/2; CD4; CD8; Vaccines; Infection; Immunity; Keratitis
Online: 31 December 2020 (12:18:00 CET)
Tissue resident memory T cells (TRM) were first described in 2009. While initially the major focus was on CD8 TRM, there has been recently an increased interest in defining the phenotype and the role of CD4 TRM in diseases. Circulating CD4 T cells seed tissue CD4 TRM, but there also appears to be an equilibrium between CD4 TRM and blood CD4 T cells. CD4 TRM are more mobile than CD8 TRM, usually localized deeper within the dermis/lamina propria and yet may exhibit synergy with CD8 TRM in disease control. This has been demonstrated in herpes simplex infections in mice. In human recurrent herpes infections, both CD4 and CD8 TRM persisting between lesions may control asymptomatic shedding through interferon gamma secretion, although this has been more clearly shown for CD8 T cells. The exact role of the CD4/CD8 TRM axis in the trigeminal ganglia and/or cornea in controlling recurrent herpetic keratitis is unknown. In HIV, CD4 TRM have now been shown to be a major target for productive and latent infection in cervix. In HSV and HIV co-infections, CD4 TRM persisting in the dermis support HIV replication. Further understanding of the role of CD4 TRM and their induction by vaccines may help control sexual transmission by both viruses.
REVIEW | doi:10.20944/preprints202012.0795.v1
Subject: Life Sciences, Biochemistry Keywords: T cells; chimeric antigen receptor; transgenic T-cell receptor; tumor-infiltrating lymphocytes; exhaustion; terminal differentiation; senescence; apoptosis; adoptive cell transfer; immunotherapy
Online: 31 December 2020 (12:16:55 CET)
Over the last decades, cellular immunotherapy has revealed its curative potential. However, the inherent physiological characteristics of immune cells can limit the potency of this approach. Best defined in T cells, dysfunction associated with terminal differentiation, exhaustion, senescence, and activation-induced cell death undermine adoptive cell therapies. In this review, we concentrate on how the multiple mechanisms that articulate the various forms of immune dysfunction impact cellular therapies primarily involving conventional T cells, but also other lymphoid subtypes, in addition to the various strategies put in place to circumvent these effects. The repercussions of immune cell dysfunction across the full life cycle of cell therapy, from the source material, during manufacturing, and after adoptive transfer are discussed. Applicable to cellular products prepared from native and unmodified immune cells, as well as genetically engineered therapeutics, the understanding and potential modulation of dysfunctional features is key to the development of improved cellular immunotherapies.
ARTICLE | doi:10.20944/preprints202012.0789.v1
Subject: Life Sciences, Biochemistry Keywords: glioblastoma; DCE-MRI; interstitial flow; convection; diffusion; The Cancer Imaging Archive
Online: 31 December 2020 (11:36:28 CET)
Background: Glioblastoma is the deadliest, yet most common, brain tumor in adults, with poor survival and response to aggressive therapy. Therapeutic failure results from a number of causes inherent to these tumors. Imaging, computational, and drug delivery approaches can aid in the quest to access and kill each tumor cell in patients. One factor, interstitial fluid flow, is a driving force therapeutic delivery. However, convective and diffusive transport mechanisms are un-der-studied. In this study, we examine the application of a novel image analysis method to meas-ure fluid flow and diffusion in glioblastoma patients with MRI and compare to patient outcomes. Methods: Building on a prior imaging methodology tested and validated in vitro, in silico and in preclinical models of disease, here we apply our analysis method to archival patient data from the Ivy GAP dataset. Results: We characterize interstitial fluid flow and diffusion patterns in patients. We find strong correlations between flow rates measured within tumors and in the surrounding parenchymal space, where we hypothesized that velocities would be higher. Looking at overall magnitudes, there is significant correlation with both age and survival in this patient cohort. Additionally, we find that tumor size nor resection significantly alter the velocity magnitude. Last, we map the flow pathways in patient tumors and find variability in degree of directionality that we hypothesize in future studies may lead to information concerning treatment, invasive spread, and progression. Conclusions: Analysis of standard DCE-MRI in patients with glioblastoma offers more infor-mation regarding transport within and around tumor, can be measured post-resection and mag-nitudes correlate with patient prognosis.
ARTICLE | doi:10.20944/preprints202012.0784.v1
Subject: Life Sciences, Biochemistry Keywords: Bacillus subtilis; flow cytometry; gastrointestinal health; peripheral blood mononuclear cells (PBMC); probiotic; short chain fatty acid
Online: 31 December 2020 (09:46:43 CET)
Probiotics make up a large and growing segment of the commercial market of dietary supplements and are touted as offering a variety of human health benefits. Some of the purported positive impacts of probiotics include, but are not limited to, stabilization of the gut microbiota, prevention of gastrointestinal disorders and modulation of the host immune system. Current research suggests that the immunomodulatory effects of probiotics are strain specific and vary in mode of action. Here, we examined the immunomodulatory properties of Bacillus subtilis strain DE111 in a healthy human population. In a randomized, double blind, placebo-controlled four-week intervention, we examined peripheral blood mononuclear cells (PBMCs) at basal levels pre- and post-treatment as well as in response to stimulation with bacterial lipop