REVIEW | doi:10.20944/preprints202109.0507.v1
Subject: Biology, Plant Sciences Keywords: epigenetics; plant development; microsporogenesis; megasporogenesis; male and female gametophytes; embryogenesis; endospermogenesis; sexual and asexual reproduction
Online: 30 September 2021 (09:16:17 CEST)
Plants are exposed to highly fluctuating effects of light, temperature, weather conditions and many other environmental factors throughout their life. As sessile or-ganisms, unlike animals, they are unable to escape, hide or even change their position. Therefore, the growth and development of plants is largely determined by interaction with the external environment, the success of this interaction depends on the ability of the phenotype plasticity, which is largely determined by epigenetic regulation. In addi-tion to how environmental factors can change the patterns of genes expression, epige-netic regulation determines how genetic expression changes during the differentiation of one cell type into another, and how patterns of gene expression are passed from one cell to its descendants. Thus, one genome can generate many 'epigenomes'. Epigenetic modifications acquire special significance during the formation of gametes and plant reproduction, when epigenetic marks are eliminated during meiosis and early embry-ogenesis and later reappear. However, during asexual plant reproduction, when meio-sis is absent or suspended, epigenetic modifications that have arisen in the parental sporophyte can be transmitted to the next clonal generation practically unchanged. In plants that reproduce sexually and asexually, epigenetic variability has different adap-tive significance. In asexuals, epigenetic regulation is of particular importance for im-parting plasticity to the phenotype, when the genotype remains unchanged for many generations of individuals. Of particular interest is the question of the possibility of transferring acquired epigenetic memory to future generations and its potential role for natural selection and evolution. All these issues will be discussed to some extent in this review. In the last two decades, a lot of data on the epigenetic regulation of plants has appeared, as well as works summarizing the accumulated knowledge (Verhoeven and Preite 2013; Pikaard and Scheid 2014; Gehring 2019; Ono and Kinoshita 2021), nevertheless, many questions remain unclear, and a number of results are contradic-tory. New in this area data is constantly emerging. We tried to take into account and discuss the main findings and conclusions in this field.
Wed, 29 September 2021
ARTICLE | doi:10.20944/preprints202109.0503.v1
Subject: Biology, Animal Sciences & Zoology Keywords: mitogenome; transmembrane proteins; substitution matrix; JTT matrix; molecular evolution; partitioned models; mixture models; RY coding; cyto-nuclear discordance
Online: 29 September 2021 (16:57:38 CEST)
Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals. Hydrophobic amino acids in mitochondrially-encoded proteins, which are expected to be found in transmembrane helices, have been hypothesized to be associated with non-historical signals. We tested this hypothesis by comparing the evolution of transmembrane helices and extramembrane segments of mitochondrial proteins from 420 bird species, sampled from most avian orders. We estimated amino acids exchangeabilities for both structural environments and assessed the performance of phylogenetic analysis using each data type. We compared those relative exchangeabilities with values calculated using a substitution dataset for transmembrane helices from a variety of sampled set of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. Models of transmembrane and extramembrane sequence evolution for amino acids and nucleotides exhibited striking differences, but there was no evidence for strong topological data type effects. However, incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit. Thus, we believe that considering protein structure will improve analyses of mitogenomic data, both in birds and in other taxa.
ARTICLE | doi:10.20944/preprints202109.0484.v1
Subject: Biology, Ecology Keywords: analytical index; continental U.S.; Human Footprint; human perception; landscape modification; landscape transformation; systematic conservation planning
Online: 29 September 2021 (10:04:40 CEST)
We assessed how close human perceptions of landscape modification matched a multivariate index based on remotely sensed data of the same locations. Using a Human Footprint (HF) map of the continental U.S. (scaled 0-100), we created three series of aerial images, each with ten images distributed evenly across the 10 deciles of HF score. Using a web-based survey, 290 members of the global public ranked the images in one series based on their perception of the degree of human modification. Respondents also reported age, sex, and country. The degree of correspondence between rankings by respondents and by HF score was high, an average of 1.29 units of difference out of a maximum possible of 5.0. Differences among respondents were not explained by age, sex, or general geographic location. These results suggest that human perception of relative landscape modification conforms closely with the relative ranking made by a multivariate, analytical index.
Tue, 28 September 2021
ARTICLE | doi:10.20944/preprints202109.0474.v1
Subject: Biology, Other Keywords: NELL2; Preproenkephalin; Endoplasmic reticulum; Calcium ion; Protein kinase C; Extracellular signal-regulated kinase (ERK)
Online: 28 September 2021 (13:40:26 CEST)
Preproenkephalin (PPE) is a precursor molecule for multiple endogenous opioid peptides Leu-enkephalin (ENK) and Met-ENK, which are involved in a wide variety of modulatory functions in the nervous system. Despite the functional importance of ENK in the brain, the effect of brain-derived factor(s) on PPE expression is unknown. We report the dual effect of neural epidermal growth factor (EGF)-like-like 2 (NELL2) on PPE gene expression. In cultured NIH3T3 cells, transfection of NELL2 expression vectors induced an inhibition of PPE transcription intracellularly, in parallel with downregulation of protein kinase C signaling pathways and extracellular signal-regulated kinase. Interestingly, these phenomena were reversed when synthetic NELL2 was administered extracellularly. The in vivo disruption of NELL2 synthesis resulted in an increase in PPE mRNA level in the rat brain, suggesting that the inhibitory action of intracellular NELL2 predominates the activation effect of extracellular NELL2 on PPE gene expression in the brain. Biochemical and molecular studies with mutant NELL2 structures further demonstrated the critical role of EGF-like repeat domains in NELL2 for regulation of PPE transcription. These are the first results to reveal the spatio-specific role of NELL2 in the homeostatic regulation of PPE gene expression.
ARTICLE | doi:10.20944/preprints202109.0473.v1
Subject: Biology, Animal Sciences & Zoology Keywords: Cultural Use; Squirrel; gliding squirrel; tribes; Arunachal Pradesh
Online: 28 September 2021 (13:32:46 CEST)
Based on an ethnozoological study carried out from December 2018 to November 2019, this paper attempts to document the usage of squirrel species for various purposes by the Adi, Idu Mishmi, Miju Mishmi, Tangsa, Chakma and Monpa tribe living near the villages adjoining the protected areas located in the districts of East Siang, Lower Dibang Valley, Dibang Valley, Lohit, Changlang and West Kameng of Arunachal Pradesh, India. The paper also describes the use of certain squirrel species as a part of their traditional culture and lists their names in English, Vernacular and Latin names. The study has led to an understanding that eight squirrel species are used by the tribes for cultural, food and medicinal purposes. This work contributes to ethnozoological research by describing a knowledge system of squirrel species use and the association of squirrel species with the cultural believes of the tribes.
Mon, 27 September 2021
ARTICLE | doi:10.20944/preprints202109.0451.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Allelopathy; Gossypium hirsutum; chromosome substitution; sustainable weed management.
Online: 27 September 2021 (12:56:50 CEST)
Palmer amaranth (Amaranthus palmeri) is a problematic common weed species, especially in cotton (Gossypium hirsutum). With the wide use of chemical herbicide and herbicide-tolerant transgenic cotton lines, Palmer amaranth populations have developed tolerance to commonly used herbicides. It is imperative to develop alternative weed control methods to slow the evolution of herbicide-resistant weed populations and provide new sources for weed management. Eleven chromosome substitution (CS) cotton lines CS-B26lo, CS-T17, CS-B16-15, CS-B17-11, CS-B12, CS-T05sh, CS-T26lo, CS-T11sh, CS-M11sh, CS-B22sh, and CS-B22lo were screened for weed-suppressing abilities in this study. The cotton lines were tested using the established stair-step structure methodology, which provided scope to study the effect of individual CS lines on the growth and development of Palmer amaranth weed without any interference of other external factors in the greenhouse. Height (cm) and chlorophyll concentration (cci) were measured for each plant in the system. The data were analyzed as a randomized complete block design using LSD mean comparisons of the genotypes at the P≤ .05 level. The 14th day after establishment resulted in the most significant variation in Palmer amaranth height reduction among the CS lines. Results indicated that CS-B22sh had the highest effect in reducing Palmer amaranth height and chlorophyll concentration with the most heightened susceptibility for Palmer amaranth. The cluster analysis revealed that Enlist® cotton, CS-CS-B22sh, and CS-T26lo were clustered in one group suggesting similar genetic potential with reference to Palmer amaranth growth and development. CS-B22sh showed novel genetic potential to control the growth and development of Palmer amaranth, a major weed in cotton fields. In the future, it will be interesting to investigate if CS-B22sh exudates from its root contain allelochemicals able to impede the growth and development of Palmer amaranth.
Thu, 23 September 2021
ARTICLE | doi:10.20944/preprints202109.0395.v1
Subject: Biology, Plant Sciences Keywords: 2,4-D; upland cotton; chromosome substitution lines; herbicide tolerance; 2,4-D absorption and translocation
Online: 23 September 2021 (08:10:50 CEST)
Upland cotton is sensitive to 2,4-dichlorophenoxyacetic acid (2,4-D), and the identification of potentially 2,4-D tolerant cotton chromosome substitution (CS) lines and understanding tolerance mechanisms provide a significant step into the development and genetic improvement of upland cotton to reduce yield loss caused by 2,4-D herbicide effects including the drifts. Experiments were conducted to understand the possible mechanism of herbicide tolerance in CS-T04-15, CS-T07, and CS-B15sh, 2,4-D herbicide-tolerant cotton CS lines compared with TM-1, the 2,4-D herbicide susceptible recurrent parent of the CS line as control, using [14C]2,4-D. Percent absorption rate and translocation patterns of the 14C-labeled herbicide application at 5.17 kBq at 6 to 48 hours after treatment (HAT) were determined. The tolerant cotton CS lines showed 15-19% [14C]2,4-D uptake while TM-1 exhibited a reduced uptake of only 1.4% [14C]2,4-D at 24 HAT. Distribution of the absorbed [14C]2,4-D showed that 2-5% was translocated outside the treated leaf. In TM-1, 77% of the herbicide was translocated above and below the treated leaf, contrasting with the reduced translocation of 14C-labeled herbicide observed in the tolerant CS lines. Interestingly, CS-T04-15 showed a restricted movement of 14C below the treated leaf at 6 to 48 HAT, suggesting a novel mechanism of herbicide tolerance. This finding is the first report on upland cotton demonstrating a complex differential uptake and translocation associated with herbicide tolerance for [14C]2,4-D in cotton CS lines.
Wed, 22 September 2021
Subject: Biology, Agricultural Sciences & Agronomy Keywords: mimosa bush; control; chemical herbicides; encapsulation; implantation
Online: 22 September 2021 (11:48:04 CEST)
Mimosa bush (Vachellia farnesiana) is an invasive woody weed widely distributed in Australia. While it can be controlled using several mechanical and chemical techniques, this study evaluated a novel new herbicide delivery mechanism that minimizes the risk of spray drift and potential non-target damage. It was developed by Bioherbicides Australia and involves the implantation of encapsulated granular herbicides into the stem of intact plants or into the stump after cutting off plants close to ground level (cut stumped). Trials were implemented near Moree (NSW, Australia) on intact (two trials) plants and cut stumped (two trials) plants. For each trial, an untreated control plus the conventional basal bark application of a liquid formulation of triclopyr/picloram mixed with diesel was included for comparison. Encapsulated glyphosate, aminopyralid/metsulfuron-methyl, hexazinone and clopyralid were also tested in all trials. In addition, triclopyr/picloram, and metsulfuron-methyl were included in at least one of the whole plant trials. Aminopyralid/metsulfuron-methyl was consistently most effective at controlling intact plants, whilst aminopyralid/metsulfuron-methyl and clopyralid provided highest mortality when applied to cut stumps of mimosa bush. Overall, highest efficacy was achieved on single stemmed plants, but with some further refinement of the technique it should be possible to achieve similar results for multi-stemmed species.
Tue, 21 September 2021
ARTICLE | doi:10.20944/preprints202109.0367.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: daily light integral (DLI) maps; LED grow lights; greenhouse integrated PV; adaptive lighting control; year-round cultivation; agrivoltaics
Online: 21 September 2021 (14:31:23 CEST)
High efficacy LED lamps combined with adaptive lighting control and greenhouse integrated photovoltaics (PV) could enable the concept of year-round cultivation and become a feasible option even in the harsh climate of the Nordic countries. Meteorological satellite data of this region was analyzed in a parametric study to evaluate the potential of these technologies. The generated maps showed monthly average temperatures fluctuating from -20°C to 20°C throughout the year. The natural photoperiod and light intensity also changed drastically, resulting in monthly average daily light integral (DLI) levels ranging from 45-50 mol·m-2·d-1 in summer and contrasting with 0-5 mol·m-2·d-1 during winter. To compensate, growth room cultivation independent from outdoor conditions could be used in winter. Depending on the efficacy of the lamps, the electricity required for sole-source lighting at 300 µmol·m-2·s-1 for 16 hours would be between 1.4 and 2.4 kWh·m-2·d-1. Greenhouses with supplementary lighting could help start the cultivation earlier in spring and extend it further into autumn. The energy required for lighting highly depends on several factors such as the natural light transmittance, the light threshold settings and the lighting control protocol, resulting in electric demands between 0.6 and 2.4 kWh·m-2·d-1. Integrating PV on the roof or wall structures of the greenhouse could offset some of this electricity, with specific energy yields ranging from 400 to 1120 kWh·kWp-2·yr-1 depending on the region and system design.
REVIEW | doi:10.20944/preprints202109.0364.v1
Subject: Biology, Horticulture Keywords: stress tolerance; biological mechanisms; biotic/Abiotic stress; hybrid priming; high-quality seeds
Online: 21 September 2021 (14:02:07 CEST)
Farmers and seed companies constantly require high-quality seeds with excellent agronomic performance. However, faced with environmental adversity, limited natural resources and increasing food demand around the globe, more attention has turned to improving crop plant production by implementing efficient strategies. Seed priming technology has shown promising biological improvements leading to suitable agronomic performance in crop plants under adverse environmental conditions. Seeds are subjected to controlled conditions that are conducive to complex physiological, biochemical, and molecular changes, conferring specific stress tolerance to subsequent germination and growth conditions. In this review paper, we aimed to study the recent approaches in the efficiency of hydropriming, osmopriming, chemopriming, hormopriming, nanopriming, matrix priming, biopriming, physical priming and hybrid priming procedures in the production of crop plants under environmental adversity, as well as their biological mechanism changes. All priming methods demonstrated relevant changes in the biological mechanism related to crop plant production by mitigating salinity effects, heavy metals, and flooding stress and enhancing chilling, heat, drought and phytopathogen tolerance. We strongly recommend that researchers combine multiple priming methods, known as hybrid priming, in their investigations to provide novel technologies and additional biological approaches to enhance the knowledge of crop plant science. Thus, the findings shed light on the use of seed priming technology as a key strategy to increase crop plant production under environmental adversity by acquiring stress tolerance and enhancing agronomic traits to meet the global food demand.
Mon, 20 September 2021
ARTICLE | doi:10.20944/preprints202109.0320.v1
Subject: Biology, Physiology Keywords: music; blood-brain barrier; lymphatic system; amyloid-β protein; detrended fluctuation analysis; electroencephalographic patterns.
Online: 20 September 2021 (09:02:40 CEST)
The lymphatic system of the brain meninges and head plays a crucial role in the clearance of amyloid-β protein (Aβ), a peptide thought to be pathogenic in Alzheimer’s disease (AD), from the brain. The development of methods to modulate lymphatic clearance of Aβ from the brain coild be a revolutionary step in the therapy of AD. The opening of the blood-brain barrier (OBBB) by focused ultrasound is considered as a possible tool for stimulation of clearance of Aβ from the brain of humans and animals. Here, we propose an alternative method of non-invasive music-induced OBBB that is accompanied by the activation of clearance of fluorescent Aβ (Fαβ) from the mouse brain. Using confocal imaging, fluorescence microscopy and magnetic resonance tomography, we clearly demonstrate that OBBB by music stimulates the movement of Fαβ and Omniscan in the cerebrospinal fluid and lymphatic clearance of Fαβ from the brain. We propose the extended detrended fluctuation analysis (EDFA) as a promising method for the identification of OBBB markers in the electroencephalographic (EEG) patterns. These pilot results suggest that music-induced OBBB and the EDFA analysis of EEG can be a non-invasive, low cost, labelling free, clinical perspective and completely new approach for the treatment and monitoring of AD.
Fri, 17 September 2021
ARTICLE | doi:10.20944/preprints202109.0316.v1
Subject: Biology, Physiology Keywords: temporal lobe epilepsy; hippocampus; 4-aminopyridine; epilepsy model; long-term potentiation; AMPA receptor.
Online: 17 September 2021 (12:45:31 CEST)
Even brief epileptic seizures can lead to activity-dependent structural remodeling of neural circuitry. Animal models show that the functional plasticity of synapses and changes in the intrinsic excitability of neurons can be crucial for epileptogenesis. However, the exact mechanisms underlying epileptogenesis remain unclear. We induced epileptiform activity in rat hippocampal slices for 15 min using a 4-aminopyridine (4-AP) in vitro model and observed hippocampal hyperexcitability for at least 1 hour. We tested several possible mechanisms of this hyperexcitability, including changes in intrinsic membrane properties of neurons, presynaptic and postsynaptic alterations. Neither input resistance nor other essential biophysical properties of hippocampal CA1 pyramidal neurons were affected by epileptiform activity. The glutamate release probability also remained unchanged, as the frequency of miniature EPSCs and the paired amplitude ratio of evoked responses did not change after epileptiform activity. However, we found an increase in the AMPA/NMDA ratio, suggesting alterations in the properties of postsynaptic glutamatergic receptors. Thus, the increase in excitability of hippocampal neural networks is realized through postsynaptic mechanisms. In contrast, the intrinsic membrane properties of neurons and the probability of glutamate release from presynaptic terminals are not affected in a 4-AP model.
REVIEW | doi:10.20944/preprints202109.0310.v1
Online: 17 September 2021 (12:08:15 CEST)
Cool-season grasses are the most common forage types in livestock operations and amenities. Several of the cool-season grasses establish mutualistic associations with an endophytic fungus of the Epichloe genus. The grasses and endophytic fungi have evolved over a long period of time to form host-fungus specific relationships that confer protection for the grass against various stressors in exchange for housing and nutrients to the fungus. This review provides an overview of the mechanisms by which Epichloe endophytes and grasses interact, including molecular pathways for secondary metabolite production. It also outlines specific mechanisms by which the endophyte helps protect the plant from various abiotic and biotic stressors. Finally, the review provides information on how Epichloe infection of grass and stress affect the rhizosphere environment of the plant.
ARTICLE | doi:10.20944/preprints202109.0309.v1
Subject: Biology, Plant Sciences Keywords: Trichoderma atroviride; volatile organic compounds; tomato; biostimulation; biocontrol; Fusarium wilt disease
Online: 17 September 2021 (12:03:42 CEST)
The promotion of plant growth and suppression of plant disease using beneficial microorganisms is considered an alternative to the application of chemical fertilizers or pesticides in the field. In this study, a coconut-scented antagonistic Trichoderma strain LZ42, previously isolated from Genoderma lucidum-cultivated soil, was investigated for biostimulatory and biocontrol functions in tomato seedlings. Morphological and phylogenetic analyses suggested that strain LZ42 is closely related to T. atroviride. Tomato plants showed increased aerial and root dry weights in greenhouse trials after treatment with T. atroviride LZ42 formulated in talc, indicating the biostimulatory function of this fungus. T. atroviride LZ42 effectively suppressed Fusarium wilt disease in tomato seedlings, with an 82.69% control efficiency, which is similar to that of fungicide treatment. The volatile organic compounds (VOCs) emitted by T. atroviride LZ42 were found to affect the primary root growth direction and promote the root growth of tomato seedlings in root Y-tube olfactometer assays. The fungal VOCs from T. atroviride LZ42 were observed to significantly inhibit F. oxysporum in a sandwiched Petri dish assay. SPME-GC-MS analysis revealed several VOCs emitted by T. atroviride LZ42; the dominant compound was tentatively identified as 6-pentyl-2H-pyran-2-one (6-PP). 6-PP exhibited a stronger ability to influence the direction of the primary roots of tomato seedlings but not the length of the primary roots. The inhibitory effect of 6-PP on F. oxysporum was the highest among the tested pure VOCs, showing a 50% effective concentration (EC50) of 5.76 μL mL-1 headspace. In conclusion, T. atroviride LZ42, which emits VOCs with multiple functions, is a promising agent for the biostimulation of vegetable plants and integrated management of Fusarium wilt disease.
Online: 17 September 2021 (11:49:04 CEST)
In 1984, Susumu Ohno hypothesized that the nylon-degrading enzyme NylB arose de novo via a frameshift mutation within a hypothetical precursor protein (PR.C). However, Ohno never tested his hypothesis or provided supporting biological evidence. For decades, Ohno’s famous frame-shift hypothesis has been uncritically accepted as the correct explanation for the origin of NylB and has been used to illustrate how simple it is for a totally new enzyme to arise spontaneously. In this paper we test Ohno’s hypothesis in light of data not available in 1984. We searched multiple protein databases and found that the NylB protein is widely occurring, has thousands of homologs, and is found in diverse organisms and diverse habitats. Conserved domain searches showed that the NylB sequence is homologous to beta lactamases - a family of highly conserved enzymes. However, our searches showed that there is no evidence for the existence of Ohno’s hypothetical PR.C protein, nor any credible homolog. Our results effectively falsify Ohno's frameshift hypothesis. We extended this analysis to other nylonases and found all the nylonases we examined had large numbers of homologs throughout the biosphere. This falsifies the long-held assumption that all nylonases evolved after the invention of nylon in 1935.
ARTICLE | doi:10.20944/preprints202109.0305.v1
Subject: Biology, Entomology Keywords: Krüppel-homologue 1; juvenile hormone; vitellogenin; RNA interference; nanoparticles; reproduction; dominance; aggression; oogenesis
Online: 17 September 2021 (11:18:45 CEST)
Dominance hierarchies are ubiquitous in invertebrates and vertebrates, but little is known on how genes influence dominance rank. Our gaps in knowledge are specifically significant concerning female hierarchies and in insects. To start filling these gaps we studied the social bumble bee Bombus terrestris, in which social hierarchies among females are common and functionally significant. Dominance rank in this bee is influenced by multiple factors, including juvenile hormone (JH) that is a major gonadotropin in this species. We tested the hypothesis that the JH responsive transcription factor Krüppel homologue 1 (Kr-h1) mediates hormonal influence on dominance behavior in the bumble bee. We first developed and validated a perfluorocarbon nanoparticles-based RNA interference protocol for knocking down Kr-h1 expression. We then used this procedure to show that Kr-h1 mediates the influence of JH not only on oogenesis and wax production, but also on aggression and dominance rank. To the best of our knowledge, this is the first study causally linking a gene to dominance rank in social insects, and one of only a few such studies in insects or in female hierarchies. These findings are important for determining whether there are general molecular principles governing dominance rank across gender and taxa.
Thu, 16 September 2021
ARTICLE | doi:10.20944/preprints202109.0294.v1
Subject: Biology, Horticulture Keywords: bud burst; Classification type; shoot bud; non-shoot bud; ‘Jonagold’; ‘Miyabi Fuji’; ‘Orin’.
Online: 16 September 2021 (16:33:12 CEST)
Being able to ascertain the physiological condition of the buds on a young apple tree before bud burst could help farmers manage their orchards more efficiently, especially if they could do so without destroying the buds in the process. The experiments carried out in this study were conducted with the aim of distinguishing shoot from non-shoot buds before bud burst using a visible/near-infrared spectrometer, a device that does not destroy the buds being tested. Tests on spring-planted (April 30, 2021) trees were conducted to check shoot and non-shoot bud physiology and the winter dormancy of young ‘Jonagold’, ‘Miyabi Fuji’ and ‘Orin’ apple trees. The light absorbance of the shoot buds before bud burst was much lower than the light absorbance of the non-shoot buds as checked on the visible/near-infrared spectrometer. The highest first factor effect was determined by a PCA test conducted on shoot and non-shoot ‘Jonagold’ buds (99.9%) at a range of 640-652 nm, ‘Miyabi Fuji’ buds (99.7%) at 654-680 nm and ‘Orin’ buds (99.6%) at 704-766 nm seven days before bud burst. We also found that the highest level of accuracy, using the Classifier analysis, between shoot and non-shoot ‘Jonagold’ buds (76.6%) was one day before bud burst, for ‘Miyabi Fuji’ buds (82.1%) it was three days before and for ‘Orin’ buds (76.3%) it was two days before. These findings suggest that growers can more effectively manage the development of the young trees in their orchards with a visible/near-infrared spectrometer.
REVIEW | doi:10.20944/preprints202109.0284.v1
Online: 16 September 2021 (13:29:23 CEST)
A single paragraph Arbuscular mycorrhizal fungi (AMF) establish symbiotic relationships with many crops. These soil microbiotas improve the soil fertility through the soil physical, chemical and biological properties. extending the root absorbing area. In return, the symbiont receives plant carbohydrates for the completion of its life cycle. AMF also helps plants to cope with biotic and abiotic stresses such as extreme temperature, heavy metal, diseases, and pathogens. For soil physical properties, the mechanisms used by AMF are the production of a glycoprotein, glomalin, which creates a high quality of soil macro-aggregations. These macro-aggregations control soil erosion, nutrients and organic matter losses. For soil chemical properties, AMF produce acids and an enzyme called phosphatase. This enzyme hydrolyzes the inorganic phosphorus and the rock phosphate (RP) hence making P available in the soil for plant uptake. AMF also are involved in soil nitrogen, carbon and trace element cycling. Regarding the biological component of the soil, AMF influence the composition, diversity and activity of microbial communities in the hydrosphere. They also work in synergy with others soil microorganisms to improve soil fertility, plant growth and resistance against some diseases. In this review, we present the contribution of AMF on soil fertility and importance in polluted soils.
ARTICLE | doi:10.20944/preprints202109.0279.v1
Subject: Biology, Animal Sciences & Zoology Keywords: Primate cognition; scribbles; evolutive anthropology; art; aesthetics
Online: 16 September 2021 (11:20:42 CEST)
This study analyses 749 drawings of five female Bornean orang-utans (Pongo pygmaeus) at Tama Zoological Park in Japan. We searched for differences between individuals but also tried to identify possible temporal changes among the drawings of one individual, Molly, who drew almost 1,300 drawings from 2006 to 2016. An analysis of the drawings was carried out after collecting quantitative and qualitative variables. Our findings reveal evidence of differences in the drawing style of the five individuals as well as creative changes in Molly’s drawing style throughout her lifetime. Individuals differed in terms of the colours used, the space they filled but also the shapes (fan patterns, circles or loops) they drew. Molly drew less and less as she grew older, and we found a significant difference between drawings produced in winter, when orang-utans were kept inside and had less activity, and those produced during other seasons. Our results suggest that the drawing behaviour of these five orang-utans is not random and that differences among individuals might reflect differences of styles, states of mind but also motivation to draw.
Wed, 15 September 2021
Online: 15 September 2021 (15:58:51 CEST)
The relevance of bacteria to subjective experiences or qualia is under-appreciated. Here, I make four proposals. Firstly, living systems traverse sequences of active states that determine their behaviour; these states result from competitive coherence, which depends on a connectivity-based competition between a Next process and a Now process whereby elements in the active state at time n+1 are chosen between the elements in the active state at time n and those elements in the developing n+1 state. Secondly, bacteria should help us link the mental to the physical world given that bacteria were here first, are highly complex, influence animal behaviour and dominate the Earth. Thirdly, the operation of competitive coherence to generate active states in bacteria, brains and other living systems is inseparable from qualia. Fourthly, these qualia become particularly important to the generation of active states in the highest levels of living systems, namely, the ecosystem and planetary levels.
REVIEW | doi:10.20944/preprints202109.0264.v1
Subject: Biology, Other Keywords: choanoflagellates; multicellularity; animal origins; genome editing; electroporation
Online: 15 September 2021 (14:39:19 CEST)
Choanoflagellates, the closest living relatives of animals, have the potential to reveal the genetic and cell biological foundations of complex multicellular development in animals. Here we describe the history of research on the choanoflagellate Salpingoeca rosetta. From its original isolation in 2000 to the establishment of CRISPR-mediated genome editing in 2020, S. rosetta provides an instructive case study in the establishment of a new model organism.
ARTICLE | doi:10.20944/preprints202109.0256.v1
Subject: Biology, Plant Sciences Keywords: germination; Leucadendron; seed storage; seed viability estimation; viability loss
Online: 15 September 2021 (12:19:18 CEST)
Seed viability is routinely measured on seeds that fail to germinate at the end of an experiment. Together with the number of germinants, this is used to estimate viability of the seeds at start of the experiment (i.e., initial viability) and provides the comparative basis on which germination success is determined. We used this standard procedure on 40 Leucadendron species subjected to oscillating temperatures, heat and/or smoke pre-treatments to examine the extent to which they raised germination levels above that of the untreated controls. 16 species showed significantly different levels of estimated initial seed viability between treatments when they should have been unaffected. Loss of viability during the trial was an order of magnitude greater than annual loss during cold storage, which was usually negligible. Lowest levels of estimated initial viability occurred among the poorly germinating controls and confirmed that the heat and smoke treatments had little effect on viability. Species with soil-stored seeds were more vulnerable to this artefact than those with plant-stored seeds. We caution against the routine use of end-of-trial germination and viability of ungerminated seeds as an estimate of initial viability in determining germination success of various treatments. The preference is for estimates of initial viability to be undertaken on a separate sample of seeds in association with the trial.
REVIEW | doi:10.20944/preprints202109.0253.v1
Subject: Biology, Other Keywords: Mycobacteria; Mycobacterium tuberculosis; non-coding RNA; RNA-seq; transcriptome
Online: 15 September 2021 (11:00:59 CEST)
A definitive transcriptome atlas for the non-coding expressed elements of pathogenic mycobacteria does not exist. Incomplete lists of non-coding transcripts can be obtained for some of the reference genomes (e.g. Mycobacterium tuberculosis H37Rv) but to what extent these transcripts have homologues in closely related species or even strains is not clear. This has implications for the analysis of transcriptomic data; non-coding parts of the transcriptome are often ignored in the absence of formal, reliable annotation. Here, we review the state of our knowledge of non-coding RNAs in pathogenic mycobacteria, emphasising the disparities in the information included in commonly used databases. We then proceed to review ways of combining computational solutions for predicting the non- coding transcriptome with experiments that can help refine and confirm these predictions.
REVIEW | doi:10.20944/preprints202102.0145.v4
Subject: Biology, Ecology Keywords: Biodiversity Conservation, Sharks, Sustainable Shark Fishing, Fisheries, Shark Fin Trade
Online: 15 September 2021 (10:54:13 CEST)
A detailed analysis of fishing records has shown that the shark species accessible to global fisheries have been systematically depleted for decades. They were already fished to about 10 percent of their former levels by 2003. Now one species after another is being listed on the IUCN Red List of Threatened Species as their numbers drop towards extinction. Shark depletion has not been well documented and a large proportion of shark mortality has been bycatch, the target species being teleost fish. But with the rise in value of shark fins due to the shark fin trade, at the same time as teleost fish stocks have become severely overfished, sharks, along with tuna, have become the most valuable catches. Fishing on the high seas is scarcely profitable, and so is heavily supported by subsidies. But the shark fin trade, in which organized crime is heavily involved, is driven by enormous profits and provides a powerful demand for the fins of all sharks. Thus it is now being supplied by fisheries around the world. There is no interest in sustainability in consumer countries, and neither the will nor the resources to manage the trade exist. Although some shark fisheries might have been managed sustainably in some regions for certain species for meat, such fisheries are increasingly dependent on the shark fin trade.. The rising global demand for shark fins, coupled with the increasing depletion of the animals supplying that demand, makes commercial fishing for sharks unsustainable. Given their high ecological value across the aquatic ecosystems they inhabit, it is important that they receive more effective measures of protection going far beyond the currently existing ones. In particular, protection of all sharks, manta rays, devil rays and rhino rays through an Appendix I CITES listing should be effected immediately due to the scale of the global take of the shark fin trade and the state of shark depletion amply documented in the literature.
ARTICLE | doi:10.20944/preprints202109.0252.v1
Subject: Biology, Entomology Keywords: Emerald ash borer; Fraxinus spp.; forest pests; invasive populations; north-west Russia; Saint Pe-tersburg; urban pests
Online: 15 September 2021 (09:46:17 CEST)
Emerald ash borer (EAB), Agrilus planipennis, is an invasive beetle of East Asian origin that in North America and Russia killed millions of ash trees (Fraxinus spp.). In September 2020, EAB was de-tected in Saint Petersburg, becoming resonant event for the metropolitan city. The aim of the present study was to investigate occurrence and ecology of EAB in Saint Petersburg. The presence of two distinct enclave populations of EAB was revealed, each of which has (very likely) been established by separate events of “hitchhiking” transport vehicles. Following the invasion, further spread of EAB in Saint Petersburg was slow and locally restricted, main explanation for which is climatic factor. Due to spread by “hitchhiking”, the possibility of EAB further long-distance ge-ographic spread of EAB in the Baltic Sea region (EU) is high, and not only by ground transport (120–130 km distance from EU borders), but also by ferries transporting cars (traditional means of transportation across the Baltic Sea). In certain cases, development of EAB on F. excelsior was more successful (stem portion colonized, larval densities, number of galleries, exit holes, viable larvae, emerged beetles) than in (adjacent) F. pennsylvanica trees. Observed relatively high EAB-sensitivity of F. excelsior therefore questions the efficacy and benefits of the currently ongoing selection and breeding projects against ash dieback (ADB), caused by Hymenoscyphus fraxineus. Inventory, mapping, and monitoring of surviving F. excelsior trees in areas infested by both ADB and EAB are necessary to acquire genetic resource for work on strategic long-term restoration of F. excelsior, tackling (inevitable) invasion of EAB to the EU.
ARTICLE | doi:10.20944/preprints202109.0250.v1
Online: 15 September 2021 (09:16:39 CEST)
Folic acid, one of the 13 essential vitamins, plays an important role in cardiovascular development. Mutations in folic acid synthesis gene 5,10-methylenetetrahydrofolate reductase (MTHFR) is significantly associated with the occurrence of congenital heart disease. However, the mechanisms underlying the regulation of cardiac development by mthfr gene are poorly understood. Here, we exposed zebrafish embryos to excessive folate or folate metabolism inhibitors. And we established a knock-out mutant of mthfr gene in zebrafish by using CRISPR/Cas9. The zebrafish embryos of insufficient or excessive folic acid, and mthfr-/- mutant all gave rise to early pericardial edema and cardiac defect at 3 days after fertilization(dpf). Furthermore, the folic acid treated embryos showed abnormal movement at 5dpf. The expression levels of cardiac marker genes hand2, gata4 and nppa changed in the abnormality of folate metabolism embryos and mthfr-/- mutant, and there is evidence that they are related to the change of methylation level caused by the change of folate metabolism. In conclusion, our study provides a novel model for the in-depth study of MTHFR gene and folate metabolism. And our results reveal that folic acid has a dose-dependent biphasic effect on early cardiac development.
Tue, 14 September 2021
ARTICLE | doi:10.20944/preprints202109.0240.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Gene Silencing; Host–Virus Interaction; RNA Interference; Saccharum officinarum; Sugarcane Yellow Leaf Virus and Target Prediction
Online: 14 September 2021 (12:43:22 CEST)
The Sugarcane yellow leaf virus (SCYLV) is associated with sugarcane yellow leaf disease (SCYLD) and is considered to be the most economically deleterious emerging pathogen that represents a potential threat and danger to sugarcane cultivation in China. Over the last two decades, high genetic diversity in the SCYLV genotypes was observed worldwide, with a greater chance of YLD incidence for sugarcane injury. SCYLV infection has significantly damaged its economic traits and is responsible for substantial losses in biomass production in sugarcane cultivars. This study aims to identify and comprehensively analyze sugarcane microRNAs (miRNAs) as therapeutic targets against SCYLV using plant miRNA prediction tools. Mature sugarcane miRNAs are retrieved and are used for hybridization of the SCYLV. A total of seven common sugarcane miRNAs were selected based on consensus genomic positions. The biologically significant, top ranked ssp-miR528 was consensually predicted to have a potentially unique hybridization site at nucleotide position 4162 for targeting the ORF5 of the SCYLV genome; this was predicted by all the algorithms used in this study. Then, the miRNA–mRNA regulatory network was generated using the Circos algorithm, which was used to predict novel targets. There are no acceptable commercial SCYLV-resistant sugarcane varieties available at present. Therefore, the predicted biological data offer valuable evidence for the generation of SCYLV-resistant sugarcane plants.
ARTICLE | doi:10.20944/preprints202109.0224.v1
Online: 14 September 2021 (08:19:04 CEST)
The major threats to the sustainable supply of forest tree products are adverse climate, pests and diseases. Climate change, exemplified by increased drought, poses a unique threat to global forest health. This is attributed to the unpredictable behavior of forest pathosystems, which can favor fungal pathogens over the host under persistent drought stress conditions in the future. Currently, the effects of drought on tree resistance against pathogens are hypothetical, thus research is needed to identify these correlations. Norway spruce (Picea abies) is one of the most economically important tree species in Europe, and is considered highly vulnerable to changes in climate. Dedicated experiments to investigate how disturbances will affect the Norway spruce - Heterobasidion sp. pathosystem are important, in order to develop different strategies to limit the spread of H. annosum s.l. under the predicted climate change. Here, we report a transcriptional study to compare Norway spruce gene expressions to evaluate the effects of water availability and the infection of Heterobasidion parviporum. We performed inoculation studies of three-year-old saplings in a greenhouse (purchased from a nursery). Norway spruce saplings were treated in either high (+) or low (-) water groups: high water group received double the water amount than the low water group. RNA was extracted and sequenced. Similarly, we quantified gene expression levels of candidate genes in biotic stress and jasmonic acid (JA) signaling pathways using qRT-PCR, through which we discovered a unique preferential defense response of H. parviporum-infected Norway spruce under drought stress at the molecular level. Disturbances related to water availability, especially low water conditions can have negative effects on the tree host and benefit the infection ability of the pathogens in the host. From our RNA-seq analysis, 114 differentially expressed gene regions were identified between high (+) and low (-) water groups under pathogen attack. None of these gene pathways were identified to be differentially expressed from both non-treated and mock-control treatments between high (+) and low (-) water groups. Finally, only four genes were found to be associated with drought in all treatments.
Mon, 13 September 2021
ARTICLE | doi:10.20944/preprints202109.0202.v1
Subject: Biology, Other Keywords: Translesion synthesis; radioresistance; autophagy; REV1; ionizing radiations; etoposide
Online: 13 September 2021 (11:09:07 CEST)
Cancer therapy resistance is a persistent clinical challenge. Recently, inhibition of the mutagenic translesion synthesis (TLS) protein REV1 was shown to enhance tumor cell response to chemotherapy by triggering senescence hallmarks. These observations suggest REV1’s important role in determining cancer cell response to chemotherapy. Whether REV1 inhibition would similarly sensitize cancer cells to radiation treatment is unknown. This study reports a lack of radiosensitization in response to REV1 inhibition by small molecule inhibitors in ionizing radiation-exposed cancer cells. Instead, REV1 inhibition unexpectedly triggers autophagy, which is a known biomarker of radioresistance. Collectively, we report a possible role of REV1 TLS protein in determining cancer treatment outcomes depending upon the type of DNA damage inflicted. Furthermore, we discover REV1 inhibition directly triggers autophagy, an uncharacterized REV1 phenotype, with significant bearing on cancer treatment regimens.
Wed, 8 September 2021
ARTICLE | doi:10.20944/preprints202109.0161.v1
Online: 8 September 2021 (20:25:45 CEST)
For developmental processes we know most of the gene networks controlling specific cell responses. We still have to determine how these networks cooperate and how signals become integrated. The JNK pathway is one of the key elements modulating cellular responses during development. Yet, we still know little on how the core components of the pathway interact with additional regulators or how this network modulates cellular responses in the whole organism in homeostasis or during tissue morphogenesis. We have performed a promoter analysis searching for potential regulatory sequences of puc and identified different specific enhancers directing gene expression in different tissues and at different developmental times. Remarkably, some of these domains respond to the JNK activity, but not all. Altogether, these analyses show that puc expression regulation is very complex and that JNK activities participate in non-previously known processes during the development of Drosophila.
REVIEW | doi:10.20944/preprints202109.0153.v1
Subject: Biology, Plant Sciences Keywords: Biosurfactants; Critical micelle concentration (C.M.C.); Antioxidant; Microorganism; Soil quality; Plant disease management
Online: 8 September 2021 (13:34:43 CEST)
In the current scenario of changing climatic conditions and rising global population, there is always a need to explore novel, efficient, and economical natural products for the benefit of human kind. Biosurfactant is one of the latest explored microbial biomolecules that have been used in numerous fields, including agriculture, pharmaceuticals, cosmetics, food processing, and environment-cleaning industries as raw material, lubrication, wetting, foaming softening, making emulsions, and stabilizing dispersions. The amphiphilic nature of biosurfactant biomolecules showed great advantage, distributing themselves into two immiscible surfaces by reducing interfacial surface tension and increasing the solubility of hydrophobic compounds. Furthermore, their eco-friendly nature, low or even no toxic nature, durability at higher temperatures, and wide range of pH fluctuations making the microbial surfactants preferable compared to their chemical counterparts. Additionally, the biosurfactants can obviate the oxidation flow by eliciting the antioxidant property, antimicrobial, anticancer activity, and drug delivery system, further broadening their applicability in the food, pharmaceutical, and pharma industries. Nowadays, biosurfactant has been broadly utilized to improve the soil quality by improving the concentration of trace elements and mixed with pesticides or applied singly on the plant surfaces for plant disease management. In the present review, we summarise the latest aspect of microbial synthesized biosurfactant compounds, limiting factors of biosurfactant production, and their application in improving soil quality, plant disease management.
ARTICLE | doi:10.20944/preprints202108.0381.v2
Subject: Biology, Agricultural Sciences & Agronomy Keywords: quinoa; genotype; nutritional traits; seed quality
Online: 8 September 2021 (12:37:08 CEST)
Exploiting the relationship between the nutritional properties of seeds and the genetic background, constitutes an essential analysis which contributes to broadening our knowledge regarding the control of the nutritional quality of seeds or any other edible plant structure. This constitutes an important aspect when aiming at improving the nutritional characteristics properties of crops, including those of Chenopodium quinoa Willd (quinoa) which is intended to be one of the main nutrient sources ensuring food security worldwide. Changes in the nutritional properties of quinoa seeds due to the influence exerted by the environment, the genotype, or their interaction, have been already described in previous works, but there is an important limitation in the analyses carried out, including the outcomes that can be translated into agronomical practices by which quality can be improved selecting the most adequate genotype. In the present study, several seed nutritional-related parameters from fifteen quinoa cultivars grown in a particular environmental context were analyzed aiming at targeting compounds that can be determinants of seed quality. Important agronomical and nutritional differences were found among cultivars such as distinct mineral or protein contents and seed viability. More importantly, our analyses revealed key correlations between seed quality-related traits in some cultivars, including those that relate yield and antioxidants or the germination rate. These results highlight the importance of considering the genotypic variation in quinoa when selecting improved quinoa varieties with the best nutritional characteristics for new cultivation environments.
Online: 8 September 2021 (12:31:24 CEST)
Steroid and hopanoid biomarkers can be found in ancient rocks and may give a glimpse of what life was present at that time. Sterols and hopanoids are produced by two related enzymes, though the evolutionary history of this protein family is complicated by losses and horizontal gene transfers, and appears to be widely misinterpretted. Here, I have added sequences from additional species, and re-analysis of the phylogeny of SHC and OSC indicates a single origin of both enzymes among eukaryotes. This pattern is best explained by vertical inheritance of both enzymes from a bacterial ancestor, followed by widespread loss of SHC, and two subsequent HGT events to ferns and ascomycetes. Thus, the last common ancestor of eukaryotes would have been bifunctional for both sterol and hopanoid production. Later enzymatic innovations allowed diversification of sterols in eukaryotes. Contrary to previous interpretations, the LCA of eukaryotes potentially would have been able to produce hopanoids as a substitute for sterols in anaerobic conditions. Without invoking any other metabolic demand, the LCA of eukaryotes could have been a facultative aerobe, living in unstable conditions with respect to oxygen level.
REVIEW | doi:10.20944/preprints202109.0136.v1
Online: 8 September 2021 (08:48:16 CEST)
Onions are an excellent source of a variety of essential antioxidants, polyphenols, and other phytonutrients. These onions were used to enhance the meal's flavour and aroma. Additionally, onions have long been recognised for their ability to change food texture, making it more pleasant for eating. Among the most significant phenolic compounds identified in onions was Quercetin, which has been proven to be very helpful for maintaining good health by reducing the risk of heart disease, cancer, and a number of other severe conditions. Polyphenol extraction is essential for the effective usage and research of these phytochemicals. Previously, the extraction process was complicated by a variety of traditional methods, but with the aid of contemporary technology, the procedure was simplified. Additionally, it was found that red onions had greater health benefits than yellow onions, which were the most commonly used kind at the time. Apart from their health benefits, polyphenols were well recognised for their industrial use in dyeing, polymer manufacturing, and resin synthesis.
Tue, 7 September 2021
CONCEPT PAPER | doi:10.20944/preprints202109.0132.v1
Subject: Biology, Other Keywords: Access and Benefit Sharing (ABS); resource mobilization; Digital Sequence Information (DSI); Post-2020 Global Biodiversity Framework; biodiversity crisis
Online: 7 September 2021 (16:07:18 CEST)
Facing unprecedented global declines in the extent and integrity of ecosystems, the 15th UN Biodiversity Conference (COP-15) in Kunming, China, presents an opportunity for transformative change. However, a lack of consensus on two key issues – resource mobilization and Access and Benefit Sharing (ABS) associated with Digital Sequence Information (DSI) – risks stalling negotiations for an ambitious ‘Post-2020 Global Biodiversity Framework’ as the next 10-year strategic plan under the Convention on Biological Diversity. We highlight systemic misconceptions concerning the financing of biodiversity and the burden this places on the ABS system. In the context of DSI, we caution that conflating ABS with resource mobilization risks disrupting modern science policy built on open access, with potentially severe ramifications for scientific research and innovation. To resolve these tensions, we call for a recalibration of discussions on ABS in order to maximize the value delivered by biodiversity for all of society, including indigenous peoples and local communities.
ARTICLE | doi:10.20944/preprints202109.0128.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Poisonous plants; soil microbial communities; Stellera chamaejasme; Elymus nutans
Online: 7 September 2021 (12:17:21 CEST)
Stellera chamaejasme L. is a fast-spreading unpalatable poisonous plant that grows in the alpine grasslands of the Qinghai-Tibetan Plateau (QTP). The impacts of unpalatable plant species spread on animal health and plant community have been well studied, but studies into their effects on belowground organisms and processes are rare. We carried out a soil metabarcoding study using Illumina MiSeq sequencing to investigate whether the soil bacteria and fungi communities of Stellera are different to the soil microbiome of neighboring palatable grass Elymus nutans Griseb. Total carbon and nitrogen, the ratio of carbon to nitrogen, ammonium nitrogen, and microbial biomass carbon were all significantly greater in Stellera soil compared to Elymus soil, while no significant differences were observed for gravimetric soil moisture, pH or nitrate nitrogen. There were no significant differences in bacterial and fungal abundance between Stellera and Elymus soil. The bacterial species richness was significantly lower in Stellera soil but no significant difference was observed for fungal species richness. The beta diversity and community composition of bacteria and fungi were markedly different between soils. The presence of bacterial phyla Actinobacteria and Verrucomicrobia, and fungal phyla, Basidiomycota and Glomeromycota, were significantly greater under Stellera soil. This study demonstrated that the spread of undesirable unpalatable plants can potentially disrupt existing plant-soil-microbe associations with potential consequences for grassland soil biodiversity and ecosystem functioning.
BRIEF REPORT | doi:10.20944/preprints202109.0122.v1
Subject: Biology, Anatomy & Morphology Keywords: tendon sheath; metacarpophalangeal; rheumatoid arthritis; tenosynovitis; peritendinitis; anatomy
Online: 7 September 2021 (11:49:31 CEST)
Background. MRI-detected inflammation around the metacarpophalangeal (MCP-)joints is prevalent in RA and poses a markedly increased risk of RA-development when present in arthralgia patients. Such inflammation is called ‘peritendinitis’, since anatomy literature reports no presence of a tenosynovial sheath at these tendons. However, the presence or absence of a synovial sheath at these extensor tendons has never been studied. Methods. A macroscopy and microscopy study of extensor-tendons at the MCP-joints of two embalmed human hands was performed. Routine histology was performed with Haematoxylin-Eosin staining. Results. We found evidence for the presence of synovial lining around extensor-tendons at MCP-joints. A delimited space surrounding the extensor digitorum tendon was observed, which was lined with an epithelium representing fibroblast-like synoviocytes. Conclusion. Contrast-enhancement around extensor tendons at MCP joints observed on MRI in RA represents tenosynovitis and thus inflammation of synovial tissue. Further studies with larger numbers of specimen are warranted to study anatomic variants. In addition, the molecular composition of the tenosynovium remains to be characterized.
Subject: Biology, Animal Sciences & Zoology Keywords: Amphipoda; invasive species; population genetics; miogenome; Ponto-Caspian; SNP
Online: 7 September 2021 (10:56:34 CEST)
The Ponto-Caspian region is the main donor of invasive amphipods to freshwater ecosystems, with at least 13 species successfully established in European inland waters. Dikerogammarus spp. and Pontogammarus robustoides are among the most successful, due to their strong invasive impact on local biota. However, genomic knowledge on these invaders is scarce, while phylogeography and population genetics have been based on short fragments of mitochondrial markers or nuclear mi-crosatellites. In this study, we provide: (i) reconstruction of four mitogenomes for four invasive gammarids; (ii) comparison between the structure of the newly obtained mitogenomes and to those from literature; (iii) SNP calling rates for individual D. villosus and D. haemobaphes from different invasion sites across Europe; and (iv) the first time-calibrated full mitogenome reconstruction of several Ponto-Caspian taxa. We have sequenced, assembled and annotated four mitogenomes, each from D. villosus, D. hae-mobaphes, D. bispinosus and Pontogammarus robustoides. We found that, in comparison to other gammarids, the mitogenomes of Ponto-Caspian species show a translocation between the tRNA-E and tRNA-R positions. Phylogenetic reconstruction using the mitogenomes identified that Ponto-Caspian gammarids form a well-supported group that originated in the Miocene. Our study supports paraphyly in the family Gammaridae. These mitogenomes serve as vital genetic resources for the development of new markers for PCR-based identification methods and demographic studies.
REVIEW | doi:10.20944/preprints202109.0119.v1
Subject: Biology, Entomology Keywords: Asian tiger mosquito; feeding pattern; minimum infection rate; emerging arboviruses; dengue virus
Online: 7 September 2021 (10:38:13 CEST)
The aim of the work was to update the distribution range of Aedes (Stegomyia) albopictus Skuse in the Americas, review the blood-feeding patterns and compare the minimum infection rate (MIR) of the dengue virus (DENV) between studies of vertical and horizontal transmission. The current dis-tribution of Ae. albopictus encompasses 21 countries in the Americas. Extensive review has been conducted for the blood-feeding patterns of Ae. albopictus. The results suggest that the mosquito is capable of feeding on 16 species of mammals and five species of avian. Humans, dogs, and rats are the most common host. Eight arboviruses with the potential to infect humans and animals have been isolated in Ae. albopictus. In the United States of America (USA), Eastern equine encephalitis virus, Keystone virus, La Crosse Virus, West Nile virus, and Cache Valley virus were isolated in the Asian mosquito. In Brazil, Mexico, Colombia, and Costa Rica, DENV (all serotypes) has been frequently identified in field-caught Ae. albopictus. Overall, the estimated MIR in Ae. albopictus infected with DENV is similar between horizontal (10.95) and vertical transmission (8.28). However, in vertical transmission, there is a difference in the MIR values if the DENV is identified from larvae or adults (males and females emerged from a collection of eggs or larvae). MIR es-timated from larvae is 14.04 and in adults is 4.04. In conclusion, it has to be highlighted that Ae. albopictus is an invasive mosquito with wide phenotypic plasticity to adapt to broad and new areas, it is highly efficient to transmit the DENV horizontally and vertically, it can participate in the inter-endemic transmission of the dengue disease, and it can spread zoonotic arboviruses across forest and urban settings.
ARTICLE | doi:10.20944/preprints202109.0117.v1
Subject: Biology, Plant Sciences Keywords: Anticandidosic activity; Candida albicans; Quercus suber L.; Methanolic extracts; Traditional pharmacopoeia; Acute Toxicity
Online: 7 September 2021 (10:32:31 CEST)
The cork oak (Quercus suber L.), endemic essence of the Mediterranean Basin, is commonly used in traditional pharmacopoeia. The main objective of this work is to enhance the valorization of this plant species through the study of the anticandidosic activity of cork oak bark methalonic extracts in order to develop an efficient natural formulation for Candidiasis treatment.The anticandidosic activity of methanolic extracts of Q. suber bark stemming from decoction, maceration and Soxhlet methods of extraction in was tested on five different Candida albicans strains. Our results showed that all the tested extracts displayed an inhibitive activity, which varies according to the obtained extract and the tested strain. The best anticandidosic potential was observed with extracts obtained with Soxhlet method. The study of the acute toxicity showed that the lethal dose is 1150 mg/kg in mice, which remained moderately toxic according to Hodge and Sterner classification scale. Thus, this extract can be used in phytotherapy without danger in doses that are below 300 mg/kg of corporal weight. Based on these results, we can conclude that Cork oak bark extracts can be used to treat Candida albicans infections.
ARTICLE | doi:10.20944/preprints202109.0113.v1
Subject: Biology, Other Keywords: GWAS; MDD; Insomnia; eQTL; comorbidity; STRING; gene network; meta-analysis
Online: 7 September 2021 (08:07:18 CEST)
Major depressive disorder (MDD) is one of the most prevalent and disabling mental disorders worldwide. Among the symptoms of MDD, sleep disturbance such as insomnia is prominent and the first reason patients may seek professional help. However, the underlying pathophysiology of this comorbidity is still elusive. Recently, genome-wide association studies (GWAS) have begun to unveil the genetic background of several psychiatric disorders, including MDD and insomnia. Identifying the shared genomic risk loci between comorbid psychiatric disorders could be a valuable strategy to understand their comorbidity. This study seeks to identify the shared genes and biological pathways between MDD and insomnia based on their shared genetic variants. First, we performed a meta-analysis based on the GWAS summary statistics of MDD and insomnia obtained from Psychiatric Genomics Consortium and UK Biobank, respectively. Next, we associated shared genetic variants to genes using two gene mapping strategies: (a) positional mapping based on genomic proximity and (b) expression quantitative trait loci (eQTL) mapping based on gene expression linkage across multiple tissues. As a result, a total of 719 shared genes were identified. Over half (51%) of them are protein-coding genes. Functional enrichment analysis shows that the most enriched biological pathways are related to epigenetic modification, sensory perception, and immunologic signatures. We also identified druggable targets using a network approach. Together these results may provide insights into understanding the genetic predisposition and underlying biological pathways of comorbid MDD and insomnia symptoms.
Mon, 6 September 2021
REVIEW | doi:10.20944/preprints202109.0087.v1
Subject: Biology, Other Keywords: iPSCs; ESC; differentiation; Cardiovascular disease, Myocardial repair
Online: 6 September 2021 (12:03:49 CEST)
Cardiovascular disease (CVD) is one of the contributing factors to more than one-third of human mortality and the leading cause of death worldwide. Cardiac myocyte death is a fundamental process in cardiac pathologies caused by various heart diseases, including myocardial infarction. Thus, strategies for replacing fibrotic tissue in the infarcted region with functional myocardium have long been a goal of cardiovascular research. This review focuses primarily on induced-pluripotent stem cells (iPSCs), which have emerged as perhaps the most promising source of cardiomyocytes for both therapeutic applications and drug testing. We also briefly summarize other stems- and progenitor-cell populations that have been used for regenerative myocardial therapy and attempt to generate cardiomyocytes directly from cardiac fibroblasts (i.e., transdifferentiation), which, if successful, may enable the pool of endogenous cardiac fibroblasts to be used as an in-situ source of cardiomyocytes for myocardial repair.
Fri, 3 September 2021
ARTICLE | doi:10.20944/preprints202109.0058.v1
Subject: Biology, Physiology Keywords: TRPA1; Drosophila melanogaster; isoform; citronellal; menthol; AITC; HC-030031; repellent; avoidance; olfaction
Online: 3 September 2021 (10:35:49 CEST)
The Transient Receptor Potential Ankyrin 1 (TRPA1) cation channels function as broadly-tuned sensors of noxious chemicals in many species. Recent studies identified four functional TRPA1 isoforms in Drosophila melanogaster (dTRPA1(A) to (D)), but their responses to non-electrophilic chemicals are yet to be fully characterized. Methods: We determined the behavioral responses of adult flies to the mammalian TRPA1 non-electrophilic activators citronellal and menthol, and characterized the effects of these compounds on all four dTRPA1 channel isoforms using intracellular Ca2+ imaging and whole-cell patch-clamp recordings. Results: Wild type flies avoided citronellal and menthol in an olfactory test and this behavior was reduced in dTrpA1 mutant flies. Both compounds activate all dTRPA1 isoforms in the heterologous expression system HEK293T, with the following sensitivity series: dTRPA1(C) = dTRPA1(D) > dTRPA1(A) ≫ dTRPA1(B) for citronellal and dTRPA1(A) > dTRPA1(D) > dTRPA1(C) > dTRPA1(B) for menthol. Conclusions: dTrpA1 was required for the normal avoidance of Drosophila melanogaster towards citronellal and menthol. All dTRPA1 isoforms are activated by both compounds, but the dTRPA1(B) is consistently the least sensitive. We discuss how these findings may guide further studies on the physiological roles and the structural bases of chemical sensitivity of TRPA1 channels.
ARTICLE | doi:10.20944/preprints202109.0051.v1
Subject: Biology, Entomology Keywords: Helicoverpa zea; Bollworm; CRISPR; Cry1A; Bt Toxin; Genome Editing; Knockout; Functional Genomics; Resistance
Online: 3 September 2021 (08:19:44 CEST)
Members of the insect ATP binding cassette transporter subfamily C2 (ABCC2) in several moth species are known as receptors for the Cry1Ac insecticidal protein from Bacillus thuringiensis (Bt). Mutations that abolish the functional domains of ABCC2 are known to cause resistance to Cry1Ac, although the reported levels of resistance vary widely depending on insect species. In this study, the function of the ABCC2 gene as putative Cry1Ac receptor in Helicoverpa zea, a major pest of over 300 crops, was evaluated using CRISPR/Cas9 to progressively eliminate different functional ABCC2 domains. Results from bioassays with edited insect lines support that muta-tions in ABCC2 was associated with Cry1Ac resistance ratios (RR) ranging from 7.3- to 39.8-fold. No significant differences in susceptibility to Cry1Ac were detected between H. zea with partial or complete ABCC2 knockout, although highest levels of tolerance were observed when knocking out half of ABCC2. Based on >500-1,000-fold RRs reported in similar studies for closely related moth species, the low RRs observed in H. zea knockouts support that ABCC2 is not a major Cry1Ac receptor in this insect.
Thu, 2 September 2021
ARTICLE | doi:10.20944/preprints202109.0049.v1
Subject: Biology, Plant Sciences Keywords: reflectance; dehydration stress; proximal sensing; vegetation indices; pigments.
Online: 2 September 2021 (16:38:49 CEST)
We compared two approaches to non-invasive proximal sensing of the early changes in fresh-cut lettuce leaf quality: hyperspectral imaging and imaging PAM-fluorometry of chlorophyll contained in the leaves. The assessments made by the imaging techniques were confronted with the quality assessments made by traditional biochemical assays: relative water content and foliar pigment (chlorophyll and carotenoid) composition. The hyperspectral imaging-based approach provided the highest sensitivity to the decline of fresh-cut lettuce leaf quality taking place within 24 h from cutting. Using of the imaging PAM was complicated by (i) weak correlation of the spatial distribution pattern of the Qy parameter with the actual physiological condition of the plant object and (ii) its high degree of heterogeneity. Accordingly, the imaging PAM-based approach was sensitive only to the manifestations of leaf quality degradation only at advanced stages of the process. Sealing the leaves in the polyethylene bags slowed down the leaf quality degradation at the initial stages (< 3 days) but promoted its rate at more advanced stages, likely due to build-up of ethylene in the bags. An approach was developed to the processing of hyperspectral data for non-invasive monitoring of the lettuce leaves with a potential for implementation in greenhouses and packinghouses.
ARTICLE | doi:10.20944/preprints202109.0046.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: growth regulator; ABA; NDGA; Prunus avium; fruit color
Online: 2 September 2021 (15:39:00 CEST)
Abscisic acid (ABA) plays a major role in promoting ripening in sweet cherry, a non-climateric fruit. Exogenous application of ABA has been performed to study fruit ripening and cracking, but this growth regulator is not used for commercial production. To determine the potential of this growth regulator to improve sweet cherry fruit quality, ABA canopy spraying was assayed in four cultivars. Canopy spraying of S-ABA significantly: 1) enhanced sweet cherry fruit color in ‘Glenred’, ‘Lapins’ and 'Bing' cultivars, but not in ‘Royal Rainier’ (a bi-colored cultivar), and 2) decreased fruit size and firmness in ‘Lapins’, ‘Bing’ and ‘Royal Rainier’. Seasonally reproducible effects were seen in ‘Lapins’ (mid/late-maturing) but not in ‘Glenred’ (early-maturing). Canopy spraying of nordihydroguaiaretic acid (NDGA) decreased color and increased fruit size in ‘Lapins’, but not in ‘Glenred’. Direct application of ABA on fruits attached to the tree, without application to the foliage, increased Lapins' fruit color without reducing size. These results suggest a localized fruit response to exogenous ABA application on fruit color development, but that a decrease in fruit size may be due to the effects of exogenous ABA on the tree canopy foliage.
Wed, 1 September 2021
REVIEW | doi:10.20944/preprints202109.0028.v1
Online: 1 September 2021 (15:52:02 CEST)
Glyphosate (N-(phosphonomethyl)glycine) is a herbicide used to kill broadleaf weeds and grass, developed in the early 1970s. The widely occurring degradation product aminomethylphosphonic acid (AMPA) is a result of glyphosate and amino-polyphosphonate degradation. The massive use of the parent compounds leads to the ubiquity of AMPA in the environment, and particularly in water. Considering this, it can be assumed that glyphosate and its major metabolites could pose a potential risk to aquatic organisms. This review summarises current knowledge about residual glyphosate and their major metabolite AMPA in the aquatic environment, including status and toxic effects in aquatic organisms, mainly fish, are reviewed. Based on the above, we identify major gaps in the current knowledge and some directions for future research knowledge about the effects of worldwide use of herbicide glyphosate and its major metabolite AMPA. The toxic effect of glyphosate and their major metabolite AMPA has mainly influenced growth, early development, oxidative stress biomarkers, antioxidant enzymes, haematological, biochemical plasma indices, caused histopathological changes in the aquatic organism.
ARTICLE | doi:10.20944/preprints202109.0022.v1
Online: 1 September 2021 (14:28:58 CEST)
The plague caused by the Yersinia pestis bacterium is primarily a flea-transmitted zoonosis of rodents that can also be conveyed to humans and other mammals. In this work, we analyzed the spatial and temporal distribution of rodents’ populations during active and quiescent periods of the plague in the municipality of Exu, northeastern Brazil. The geospatial analyses had shown that all rodent species occurred through the whole territory of the municipality with different hotspots for the risk of occurrence of the different species. Important fluctuation in the rodent populations was observed with a reduction in the wild rodent fauna following the end of a plague epidemic period, mostly represented by Necromys lasiurus and increase of the commensally species Rattus rattus. A higher abundance of rats might lead to an increased exposure of humans populations, favoring spillovers of plague and other rodent-borne diseases. Our analysis contributed to further highlight the role of the wild rodent species as the amplifier hosts and of the commensally rats (Rattus rattus) as the preserver hosts on the quiescent period on that transmission infection area.
Tue, 31 August 2021
ARTICLE | doi:10.20944/preprints202108.0579.v1
Subject: Biology, Other Keywords: Graph Theory; Computational Geometry; Spatial Statistics; Image analysis; Tessellations; Voronoi Polygons; Delaunay Triangulations; Minimal Spanning Trees; Pitteway Violations
Online: 31 August 2021 (15:58:36 CEST)
Every biological image contains quantitative data that can be used to test hypotheses about how patterns were formed, what entities are associated with one another, and whether standard mathematical methods inform our understanding of biological phenomena. In particular, spatial point distributions and polygonal tessellations are particularly amendable to analysis with a variety of graph theoretic, computational geometric, and spatial statistical tools such as: Voronoi Polygons; Delaunay Triangulations; Perpendicular Bisectors; Circumcenters; Convex Hulls; Minimal Spanning Trees; Ulam Trees; Pitteway Violations; Circularity; Clark-Evans spatial statistics; Variance to Mean Ratios; Gabriel Graphs; and, Minimal Spanning Trees. Furthermore, biologists have developed a number of empirically related correlations for polygonal tessellations such as: Lewis’s Law (the number of edges of convex polygons are positively correlated with the areas of these polygons): Desch’s Law (the number of edges of convex polygons are positively correlated with the perimeters of these polygons); and Errara’s Law (daughter cell areas should be roughly half that of their parent cells’ areas). We introduce a new Pitteway Law that the number of sides of the convex polygons in a Voronoi tessellation of biological epithelia is proportional to the minimal interior angle of the convex polygons as angles less than 90 degrees result in Pitteway violations of the Delaunay dual of the Voronoi tessellation.
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Salmonella enterica; food safety; genome; theory; single nucleotide polymorphisms; recombination; serotype
Online: 31 August 2021 (12:47:33 CEST)
Adenine and thymine homopolymer strings of at least 8 nucleotides (AT 8+mers) were characterized in Salmonella entericasubspecies I. The motif differed between cother taxonomic classes but not between Salmonella enterica serovars. The motif in plasmids was associated with serovar. Approximately 12.3% of the S. enterica motif loci had mutations. Mutability of AT 8+mers suggests that genomes undergo frequent repair to maintain optimal gene content, and that the motif facilitates self-recognition; in addition, serovar diversity is associated with plasmid content. A theory that genome regeneration accounts for both persistence of predominant Salmonella serovars and serovar diversity provides a new framework for investigating root causes of foodborne illness.
ARTICLE | doi:10.20944/preprints202108.0571.v1
Subject: Biology, Plant Sciences Keywords: Arabidopsis thaliana; plastid; co-maturation; post-transcriptional; Nanopore
Online: 31 August 2021 (11:48:48 CEST)
Plastid gene expression involves many post-transcriptional maturation steps resulting in a complex transcriptome composed of multiple isoforms. Although short read RNA-seq has considerably improved our understanding of the molecular mechanisms controlling these processes, it is unable to sequence full-length transcripts. This information is however crucial when it comes to understand the interplay between the various steps of plastid gene expression. Here, the study of the Arabidopsis leaf plastid transcriptome using Nanopore sequencing showed that many splicing and editing events were not independent but co-occurring. For a given transcript, maturation events also appeared to be chronologically ordered with splicing happening after most sites are edited.
Subject: Biology, Forestry Keywords: ecosystem disservices; green infrastructure; site design; tree selection; urban forestry
Online: 31 August 2021 (11:42:48 CEST)
As urban development increases in density, the space to grow urban trees becomes more constrained. In heavily developed areas, small stature trees can be planted to reduce both above- and below-ground conflicts with infrastructure elements. However, even these species have their limits when placed in extremely confining conditions. In this study, we build on past work to determine the minimum planting widths of small stature urban trees. We found that species, stem diameter, and the height at which stem diameter measurements occurred were all strong predictors of trunk flare diameter (adjusted R2 of 0.843). Additionally, we modelled the relationship between planting space and the presence or absence of hardscape conflicts – using the predictions derived from this effort to project the potential cost savings in two United States cities. Study results provide a guideline to create sufficient space for urban trees and minimize infrastructure damage and associated cost savings.
Online: 31 August 2021 (11:41:51 CEST)
Bacillus anthracis, the causative agent of anthrax, has two virulence plasmids: pXO1 and pXO2. Plasmid pXO2 carries the genes of an antiphagocytic capsule synthesis. Plasmid pXO1 carries the genes pagA, lef, and cya encoding anthrax toxins, as well as atxA, which encodes the main regulator of pathogenicity factor expression. In the present paper, we evaluated the polymorphism of the pagA, lef, cya, and atxA genes for 85 B. anthracis strains belonging to different evolutionary lineages and canSNP groups and three B. cereus strains possessing pXO1-like plasmids. We found 19 genotypes (GT) strongly correlated with the main evolutionary lineages; they were mainly correlated with the canSNP group within these lines. In some cases, one GT combined the strains of several canSNP groups, and some canSNP groups were divided into several GTs. The most interesting of such cases were 1) the formation of a separate GT by strains of the A.Br.008/009 group isolated in the former USSR; 2) the presence of a unique GT in some American strains of the A.Br.Aust94 group; 3) the division of the A.Br.001/002 group into two subgroups, one of which may be a transitional link to the group A.Br.Ames; 4) the fact that European isolates of the B.Br.CNEVA group and Arctic strains of the B.Br.001/002 group have a common GT.
Mon, 30 August 2021
SHORT NOTE | doi:10.20944/preprints202108.0549.v1
Subject: Biology, Forestry Keywords: ecosystem disservices; green infrastructure; site design; tree selection; urban forestry
Online: 30 August 2021 (14:39:04 CEST)
As urban development increases in density, the space to grow urban trees becomes more constrained. In heavily developed areas, small stature trees can be planted to reduce both above- and below-ground conflicts with infrastructure elements. However, even these species have their limits when placed in extremely confining conditions. In this study, we build on past work to determine the minimum planting widths of small stature urban trees. We found that species, stem diameter, and the height at which stem diameter measurements occurred were all strong predictors of trunk flare diameter (adjusted R2 of 0.843). Additionally, we modelled the relationship between planting space and the presence or absence of hardscape conflicts – using the predictions derived from this effort to project the potential cost savings in two United States cities. Study results provide a guideline to create sufficient space for urban trees and minimize infrastructure damage and associated cost savings.
ARTICLE | doi:10.20944/preprints202107.0362.v2
Subject: Biology, Agricultural Sciences & Agronomy Keywords: VarroMed®; Varroa destructor; winter treatment; summer-autumn treatment; queen caging; brood interruption
Online: 30 August 2021 (12:52:30 CEST)
VarroMed® is a soft acaricide registered for honey bees on the European Union market since 2017 for Varroa control. Researchers involved were partners of different countries of the Varroa control task force of COLOSS Association. Our goal was to evaluate performances (acaricide efficacy and toxic effects on honey bees) of VarroMed® in different climatic conditions. Our results in the tested apiaries showed an efficacy ranging from 71.2 to 89.3 % in summer/autumn, and from 71.8 % to 95.6 % in winter. No toxic effects on bees were observed, except in one apiary, where severe cold climatic conditions played a crucial role. The treatment could be efficiently applied in brood right as well as in broodless colonies. Integrated pest management (IPM) recommendations for bee-keepers are provided in order to apply the best Varroa control protocol.
ARTICLE | doi:10.20944/preprints202108.0536.v1
Subject: Biology, Other Keywords: interferon gamma; cancer immunotherapy; viral vectors; alphavirus; bone marrow-derived macrophages; spheroids; CD38; Pam3CSK4
Online: 30 August 2021 (10:18:08 CEST)
Interferon gamma (IFNg) is a pleiotropic cytokine that can potentially reprogramme the tumour microenvironment. However, the antitumour immunomodulatory properties of IFNg still need to be validated due to variable therapeutic outcomes in preclinical and clinical studies. We developed a replication-deficient Semliki Forest virus vector expressing IFNg (SFV/IFNg) and evaluated its immunomodulatory antitumour potential in vitro in a model of 3D spheroids and in vivo in immunocompetent 4T1 mouse breast cancer model. We demonstrated that SFV-derived IFN-g stimulated bone marrow macrophages to acquire the tumoricidal M1 phenotype in 3D nonattached conditions. Coculturing SFV/IFNg-infected 4T1 spheroids with BMDMs inhibited spheroid growth. In the orthotopic 4T1 mouse model, intratumoural administration of SFV/IFNg virus particles alone or in combination with the Pam3CSK4 TLR2/1 ligand led to significant inhibition of tumour growth compared to the administration of the control SFV/Luc virus particles. Analysis of the composition of intra-tumoural lymphoid cells isolated from tumours after SFV/IFNg treatment revealed an increase in CD4+ and CD8+ and a decrease in T-reg (CD4+/CD25+/FoxP3+) cell populations. Furthermore, a significant decrease in the populations of cells bearing myeloid cell markers CD11b, CD38 and CD206 was observed. In conclusion, the SFV/IFNg vector induces a therapeutic antitumour T-cell response and inhibits myeloid cell infiltration in treated tumours.
Fri, 27 August 2021
ARTICLE | doi:10.20944/preprints202108.0529.v1
Online: 27 August 2021 (16:32:33 CEST)
Relapses and resistance to therapeutic agents are major barriers for treatment of acute myeloid leukemia (AML) patients. This unfavorable circumstance emphasizes the need for new strategies targeting drug-resistant cells. As IDH mutation is present in the preleukemic stem cells and systematically conserved at relapse, targeting mutant IDH cells would be essential to achieve a long-term remission in the AML subgroup with IDH mutation. Here, using a panel of human AML cell lines and primary AML patient specimens harboring IDH mutation, we showed that the presence of IDH mutation through the production of an oncometabolite (R)-2-HG induces vitamin D receptor related transcriptional programs, priming these AML cells to differentiate with pharmacological doses of ATRA or/and VD. This activation occurs in a CEBP-dependent manner. Accordingly, our findings illuminate potent and cooperative effects of IDH mutation and vitamin D pathway to differentiate in AML, revealing a novel therapeutic approach easily transferable/immediately applicable in clinics for this subgroup of AML patients.
ARTICLE | doi:10.20944/preprints202012.0826.v2
Subject: Biology, Entomology Keywords: Amegilla; Gossypium barbadens; Meskine; pollination efficiency; yields
Online: 27 August 2021 (14:08:15 CEST)
This study was carried out to evaluate the impact of Amegilla calens bee on fruit and seed yields of G. hirsutum in an experimental field, in September 2018 and 2019. The experiments were carried out on 540 flowers divided in four treatments: 120 flowers accessible to all visitors; 120 flowers bagged to avoid all visits; 200 flowers protected and uncovered when they were opened, to allow A. calens visits; 100 flowers bagged then uncovered and rebagged without the visit of insects or any other organism. Bees daily rhythm of activity, its foraging behaviour on flowers, its pollination efficiency, the fruiting rate, the number of seeds per fruit and the percentage of normal seeds were evaluated. Results indicate that among 11 insect species recorded on flowers, X. olivacea ranked second and harvested nectar. Throughout the pollination efficiency of a single flower visit, X. olivacea provoked a significant increase of the podding rate, the mean number of seeds per pod, the percentage of normal seeds and the mean weight of a seed by 39.48 %, 18.19 %, 49.62 % and 31.53 % respectively. The conservation and installation of X. olivacea nests close to P. vulgaris fields is recommended to improve its pod production and seed quality.
Wed, 25 August 2021
ARTICLE | doi:10.20944/preprints202108.0497.v1
Subject: Biology, Plant Sciences Keywords: leaf water content; hyperspectral spectroscopy; leaf water potential; drought; diurnal cycle; plant water status; relative water content; equivalent water thickness; Dracaena marginate; water stress; leaf water variation
Online: 25 August 2021 (15:00:37 CEST)
Water plays a crucial role in maintaining plant functionality and drives many ecophysiological processes. The distribution of water resources is in a continuous change due to global warming affecting the productivity of ecosystems around the globe, but there is a lack of non-destructive methods capable of continuous monitoring of plant and leaf water content that would help us in understanding the consequences of the redistribution of water. We studied the utilization of novel small hyperspectral sensors in the 1350-2450 nm spectral range in non-destructive estimation of leaf water content in laboratory and field conditions. We found that the sensors captured up to 96% of the variation in equivalent water thickness (EWT, g/m2) and up to 90% of the variation in relative water content (RWC). These laboratory findings were supported by field measurements, where repeated leaf spectra measurements were in good agreement (R2=0.79) with a time-lagged change of tree xylem diameter. Further tests were done with an indoor plant (Dracaena marginate Lem.) by continuously measuring leaf spectra while drought conditions developed, which revealed detailed diurnal dynamics of leaf water content. We conclude that close-range hyperspectral spectroscopy can provide a novel tool for continuous measurement of leaf water content at the single leaf level and help us to better understand plant responses to varying environmental conditions.
ARTICLE | doi:10.20944/preprints202108.0484.v1
Subject: Biology, Other Keywords: cyanobacteria; metabolomics; high-resolution mass spectrometry; secondary metabolite induction; culture conditions
Online: 25 August 2021 (10:48:20 CEST)
Cyanobacteria are microorganisms able to adapt to a wide variety of environmental conditions and abiotic stresses. They produce a very large number of metabolites that can participate in the adaptation of cyanobacteria to a large range of resources such as light, temperature, or nutrient. The metabolites variation is one way to understand the physiological status and adaptation of cells. In this study, we aim to understand how the diversity and the dynamics of the whole metabolome is dependent of the growth phases and under control of abiotic factors (e.g. light intensity and temperature). The cyanobacteria Aliinostoc sp. PMC 882.14 was selected for its large number of biosynthetic gene clusters. Metabolomes were analyzed by using mass spectrometry (qTOF-MS/MS) combined with untargeted analysis to investigate the metabolite dynamics. Significant variations were characterized between exponential and stationary phases, whatever the culture conditions (“control”, “higher light”, or “higher temperature”). ”Higher light” and “higher temperature” favored the synthesis of metabolites belonging to the same molecular families. Among highly regulated metabolites, we observe the presence of mycosporine-like amino acids (MAAs), and various variants of somamides, microginins, and microviridins. Through Aliinostoc sp. PMC 882.14, this study shows the importance of knowing the physiological state of cyanobacteria for comparative global metabolomics and questions the regulation processes involve into metabolite families production. Our results also open up new perspectives in the context of the production of targeted bioactive metabolites.
ARTICLE | doi:10.20944/preprints202108.0478.v1
Subject: Biology, Plant Sciences Keywords: antioxidant activity; chlorophyll; glycinebetaine; membrane stability index; salt stress
Online: 25 August 2021 (08:19:23 CEST)
Tagetes genus of Composite family consider one of the most favorite floriculture plant. Therefore, of particular interest examine the salt tolerance of this bedding and coloring agent plant. In this research, was report the role of glycinebetaine (GB) in attenuating the adverse impacts of salt stress in African marigold plant, along with their anti-oxidative capacities and biochemical attributes. The salt stressed African marigold (100 and 150 mM NaCl) was treated with GB at 200 mM, beside untreated control plants. According to the obtained results, the growth characters were negatively in salt stressed plants but a mitigate impact of GB were observed in this respect. Obviously, the morphological as well as some physiological characters were reduced with salinity treatments while GB treatment reverses these effects. Overall, the alleviate impact of GB on the negative impact of salt stress was enhanced through improving total phenolic and antioxidant enzyme activity. Further, it is concluded that GB concentration induces the activities of antioxidative enzymes which scavenged ROS increased under saline conditions.
Tue, 24 August 2021
ARTICLE | doi:10.20944/preprints202108.0476.v1
Subject: Biology, Ecology Keywords: Trophic ecology; ecological plasticity; European catfish; pelagic habitat; littoral habitat; commercial fishermen; stomach content analyses; commercial harvest
Online: 24 August 2021 (16:14:00 CEST)
Ecological information of invasive alien species are crucial for their effective management. How-ever, they are often lacking in newly invaded ecosystems. This is the case of the European catfish Silurus glanis L. in Lake Maggiore where the species is present since 1990 but no scientific infor-mation are available on its ecology. To start filling this knowledge gap, 236 catfish (67 cm to 150 cm of total length) were collected, measured, and dissected for stomach content analyses from three localities and in two habitats (littoral vs. pelagic) in late autumn/early winter. NPUE and BPUE (individuals and biomass (g) per unit effort (m2)) of catfish was generally higher in littoral (NPUE > 0.01; BPUE > 96) than pelagic habitats (NPUE < 0.009; BPUE < 114) but catfish had, on average, larger sizes in pelagic habitats. Overall, 581 individual prey items were recorded belonging to12 taxa. Pelagic catfish specialized their diet exclusively on three prey fish (coregonids, shad and roach) whilst the diet of littoral catfish was more variable, and was dominated by crayfish, perch, and roach. These results highlighted for the first time the interaction of larger catfish with the lake’s pelagic food web, and thus possible consequences are discussed, including the potential contrasting role S. glanis may have for the lake’s fishery.
Subject: Biology, Anatomy & Morphology Keywords: adaptive significance; evolution of gall insects; gall-inducing insects; gall formation mechanism; insect effectors
Online: 24 August 2021 (13:04:19 CEST)
Galls are characteristic plant structures formed by cell size enlargement and/or cell proliferation induced by parasitic or pathogenic organisms. Insects are a major inducer of galls, and insect galls can occur on plant leaves, stems, floral buds, flowers, fruits, or roots. Many of these exhibit unique shapes, providing shelter and nutrients to insects. To form unique gall structures, gall-inducing insects are believed to secrete certain effector molecules and hijack host developmental programs. However, the molecular mechanisms of insect gall induction and development remain largely unknown due to the difficulties associated with the study of non-model plants in the wild. Recent advances in next-generation sequencing have allowed us to determine the biological processes in non-model organisms, including gall-inducing insects and their host plants. In this review, we first summarize the adaptive significance of galls for insects and plants. Thereafter, we summarize recent progress regarding the molecular aspects of insect gall formation.
ARTICLE | doi:10.20944/preprints202108.0464.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Hydrolyzed protein flour; Cassava starch; In-line rheology; Power law; Pseudoplastic
Online: 24 August 2021 (11:35:12 CEST)
The extrusion of food for human and animal consumption is a unit operation that includes mixing, shearing and force to the materials related to the rheological properties of the materials in the extruder. The present work aims to study the rheological behavior of an extruded fish diet incorporating hydrolyzed protein flour processed by extrusion. The measurement was carried out online with a slit die rheometer, defining the rheological models and parameters that fit the process. During the extrusion process, the raw materials used were hydrolyzed protein meal, fish meal and cassava starch. For the results, the evaluated treatments were adjusted to the Power Law, where an increase in the shear rate decreases the viscosity of the material, corresponding to a pseudoplastic behavior. The incorporation of hydrolyzed protein flour presented a significant effect on the value of n and Klp, increasing the viscosity with the increase in the percentage of inclusion of HPH. The models obtained for the prediction of the viscosity are adjusted to the changes in shear rate, temperature and humidity of the system.
ARTICLE | doi:10.20944/preprints202108.0460.v1
Subject: Biology, Horticulture Keywords: Cannabis; cannabinoids; nutrients; nitrogen (N); phosphorus (P); potassium (K); yield; response surface methodology
Online: 24 August 2021 (08:40:44 CEST)
Following legalization, cannabis has quickly become an important horticultural crop in Canada and increasingly so in other parts of the world. However, due to previous legal restrictions on cannabis research there are limited scientific data on the relationship between nitrogen (N), phosphorus (P), and potassium (K) supply (collectively: NPK) and the crop yield and quality. This study examined the response of a high delta-9-tetrahydrocannabinol (THC) Cannabis sativa cultivar grown in deep-water culture with different nutrient solution treatments varying in their concentrations (mg L-1) of N (70, 120, 180, 250, 290), P (20, 40, 60, 80, 100) and K (60, 120, 200, 280, 340) according to a central composite design. Results demonstrated that inflorescence yield responded quadratically to N and P, with the optimal concentrations predicted to be 194 and 59 mg L-1, respectively. Inflorescence yield did not respond to K in the tested range. These results can provide guidance to cultivators when formulating nutrient solutions for soilless cannabis production and demonstrates the utility of surface response design for efficient multi-nutrient optimization.
Mon, 23 August 2021
REVIEW | doi:10.20944/preprints202106.0471.v2
Subject: Biology, Physiology Keywords: Alzheimer’s Disease; microfluidics; lab-on-chip; 3D culture; organ-on-chip
Online: 23 August 2021 (13:38:28 CEST)
Alzheimer’s disease (AD) is a significant health concern worldwide with enormous social and economic impact globally. The gradual deterioration of cognitive functions and irreversible neuronal losses are primary features of the disease. Even after decades of research, most therapeutic options are merely symptomatic, and drugs in clinical practice present numerous side effects. Lack of effective diagnostic techniques prevents the early prognosis of disease, resulting in a gradual deterioration in the quality of life. Furthermore, the mechanism of cognitive impairment and AD pathophysiology is poorly understood. Microfluidics exploits different microscale properties of fluids to mimic environments on microfluidic chip-like devices. These miniature multichambered devices can be used to grow cells and 3D tissues in vitro, analyze cell-to-cell communication, decipher the roles of neural cells like microglia, and gain insights into AD pathophysiology. This review focuses on the applications and impact of microfluidics on AD research. We discuss the technical challenges and possible solutions provided by this new cutting-edge technique to understand disease-associated pathways and mechanisms.
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Microbiome; Diazotroph; Nitrogen fixation bacteria; Random Forest; Network; Trichomona
Online: 23 August 2021 (12:15:31 CEST)
Biofertilizer, an environment-friendly and renewable plant nutrient source, has been widely applied and studied to reduce dependency on chemical fertilizers. However, most studies focus on the effects of biofertilizer on the bacterial and fungal communities, and we still lack an understanding of biofertilizer on the protistan community. Here, the effects of biofertilizer application on the composition and interaction of the protistan community in the wheat rhizosphere were investigated based on a 4-year field experiment. Biofertilizer application altered soil physicochemical properties and the protistan community composition (ANOSIM, p < 0.001), and significantly induced an alpha diversity decline. Random forecast and redundancy analysis demonstrated that nitrogenase activity and available phosphorus were the main drivers. Trichomonas classified to the phylum Metamonada was enriched by biofertilizer, and was significantly positive connections with soil nitrogenase activity and some function genes involved in nitrogen-fixation and nitrogen-dissimilation. Biofertilization loosely connected biotic interactions, while did not affect the stability of the protistan community. Besides, biofertilizer promoted the connections of protists with fungi, bacteria, and archaea. Combined with the conjunct biotic network (protist, fungi, bacteria, and archaea) and interactions between protists and soil physicochemical properties/function genes, protists may act as keystone taxa potentially driving soil microbiome composition and function.
Fri, 20 August 2021
CONCEPT PAPER | doi:10.20944/preprints202108.0422.v1
Subject: Biology, Ecology Keywords: Rainforest; recovery; indicators; logging; grassland; shifting cultivation; forestry; national parks; traditional rights
Online: 20 August 2021 (19:02:09 CEST)
Recovery of forest after logging can be tested in many ways: the presence of particular species of fauna or flora, the similarity of the biodiversity of the recovering forest to that on neighbouring areas of undisturbed forest; or the characteristics of soils and streams whose conditions may have drastically changed during logging. Three cases of rainforest recovery after logging and clearance from Australia and Borneo exhibit different starting and different goals for recovery. Faunal indicators of recovery vary with size and with species dependence of the rainforest. Endemic forest species may have difficulty in recovering. Tree species richness and abundance may recover in two decades, but canopy closure takes longer. Compacted soils may retain low infiltration capacities for many decades. This diversity in recovery rates is confirmed when compared with those used elsewhere. Because the starting points for recovery vary, from damage by tropical cyclones and landslides, to clearance for shifting cultivation, pasture or agriculture, to post-logging conditions, universal indicators may be inappropriate. The desired endpoints of recovery also range from a “wilderness” state to a National Park for human enjoyment, biodiversity preservation, safeguarding rights of traditional forest-dwelling peoples, or a second round of selective logging.
BRIEF REPORT | doi:10.20944/preprints202108.0407.v1
Subject: Biology, Animal Sciences & Zoology Keywords: Hair; HPA-axis; Koalas; Rehabilitation Sanctuary; Stress; Faeces; Glucocorticoids
Online: 20 August 2021 (08:52:07 CEST)
Koalas (Phascolarctos cinereus) are one of Australia's most charismatic native small marsupial species. Unfortunately, populations of koalas are rapidly declining throughout Australia and they continue to face increasing pressure from a changing ecosystem. Negative stimulants in the environment can elicit stress responses through activation of the hypothalamic-pituitary-adrenal (HPA) axis. Depending on the duration of the negative stimulant, the stress response can lead to either acute or chronic side effects, and is shown through the activation of the neuroendocrine stress system and the release of glucocorticoids (e.g., cortisol). Wild koalas entering clinical care face novel stressors that can be out of a wildlife carer's control. In this pilot study, we monitored physiological stress in three wild koalas at a wildlife rehabilitation centre in New South Wales, Australia. Acute and chronic stress was indexed non-invasively, with faecal samples taken to evaluate acute stress, and fur samples taken to evaluate chronic stress. Sampling occurred sporadically over four months, from the start of September 2018 to the end of December 2018. Results attempt to understand the stress response of koalas to negative stimulants in the environment by comparing faecal glucocorticoids on days where a known stressor was recorded with days where no known stressor was recorded. Furthermore, variations in faecal and fur glucocorticoids were compared between the three koalas in this study. To our knowledge, this is the first evidence of stress tracking of wild rescued koalas in a sanctuary. We suggest that further monitoring of baseline, acute and chronic stress will be needed to better understand how koalas respond to negative stimulants associated with clinical care.
Thu, 19 August 2021
ARTICLE | doi:10.20944/preprints202108.0405.v1
Subject: Biology, Anatomy & Morphology Keywords: animal welfare; pigs; deep learning; computer vision; stress detection; facial expression recognition
Online: 19 August 2021 (13:17:08 CEST)
Animal welfare is not only an ethically important consideration in good animal husbandry, but can also have a significant effect on an animal’s productivity. The aim of this paper is to show that a reduction in animal welfare, in the form of increased stress, can be identified in pigs from frontal images of the animals. We train a Convolutional Neural Network (CNN) using a leave-one-out design and show that it is able to discriminate between stressed and unstressed pigs with an accuracy of >90% in unseen animals. Grad-CAM is used to identify the animal regions used, and these support those used in manual assessments such as the Pig Grimace Scale. This innovative work paves the way for further work examining both positive and negative welfare states with a view to the development of an automated system that can be used in precision livestock farming to improve animal welfare.
Subject: Biology, Plant Sciences Keywords: Regeneration; asexual propagation; multicellular organisms; wound repair; maturation
Online: 19 August 2021 (11:27:26 CEST)
Regeneration is usually regarded as a unique plant or some animal species process. In reality, regeneration is a ubiquitous process in all multicellular organisms. It ranges from response to wounding by healing the wounded tissue to whole body neoforming (remaking of the new body). In a larger context, regeneration is one facet of two reproduction schemes that dominate the evolution of life. Multicellular organisms can propagate their genes asexually or sexually. Here I present the view that the ability to regenerate tissue or whole-body regeneration is also determined by the sexual state of the multicellular organisms (from simple animals like hydra and planaria to plants and complex animals). The above idea is manifested here by showing evidence that many organisms, organs, or tissues show inhibited or diminished regeneration capacity when in reproductive status compared to the same organism organs or tissues in nonreproductive conditions or by exposure to sex hormones.
Wed, 18 August 2021
ARTICLE | doi:10.20944/preprints202108.0381.v1
Online: 18 August 2021 (14:00:54 CEST)
Exploiting the relationship between the nutritional properties of seeds and the environment (E), genotype (G) and the GXE interaction, constitutes an essential analysis which contributes to broaden our knowledge regarding the control of the nutritional quality of seeds or of any other edible plant structure. This constitutes an important aspect when aiming at improving the nutri-tional characteristics properties of plant species, including those of Chenopodium quinoa Willd (quinoa) which is intended to be one of the main nutrient sources ensuring food security worldwide. This crop has gained popularity in the last decade achieving a fast-global expansion due to its excellent nutritional and agronomical properties together with the excellent adaptation shown to a wide diversity of agroclimatic conditions. Changes in the nutritional properties of quinoa seeds due to the influence exerted by the environment, the genotype, or their interaction, have been already described in previous works, but there is an important limitation in the anal-yses carried out, including the outcomes that can be translated into agronomical practices by which quality can be improved selecting the most adequate genotype. In here, several seed nu-tritional-related parameters from fifteen quinoa cultivars grown in a particular environmental context were analysed aiming at targeting compounds that can be determinants of seed quality varying with the genetic background. Important nutritional and agronomical differences were found among quinoa varieties highlighting the importance of choosing a proper genotype when cultivating quinoa.
HYPOTHESIS | doi:10.20944/preprints202010.0004.v11
Subject: Biology, Anatomy & Morphology Keywords: carbon-based entity; driving force; energy; evolution; fitness; mechanism; natural selection; speciation; thermodynamics; theory
Online: 18 August 2021 (09:57:59 CEST)
Evolution is fundamental to natural sciences and social sciences. Existing evolutionary theories are incomplete and unable to explain multiple evolutionary issues. To establish a comprehensive and comprehensible evolutionary theory, we employ the concept carbon-based entities (CBEs), which include methane, glucose, proteins, organisms, and other entities chemically containing carbon atoms. We deduce the steps, driving forces, and mechanisms of evolution of CBEs, through integration of geology, physics (particularly the second law of thermodynamics), chemistry (particularly chemical reactions of CBEs), and biology (particularly the essence of reproduction, genomes, and natural selection). We hence establish the Carbon-Based Evolutionary Theory (CBET), which suggests that evolution is the increase in the amount, diversity, and fitness of higher-hierarchy CBEs under natural selection and driven by the organic synthesis tendency on the Earth from the thermodynamic features of the Earth. It provides better explanations for various evolutionary issues (e.g. life origin, neutral mutation, speciation, and evolutionary tempos) than existing evolutionary theories. It reveals the physiochemical roots of biological evolution and the evolutionary roots of multiple social notions important to harmonious development of human society. It refutes from a novel respect some incorrect thermodynamic notions regarding evolution (e.g. negative entropy). It hence removes contradictions between physiochemistry, biology, and social sciences, and bridges them through evolution. The CBET is reliable as per its deduction and applications. Therefore, the CBET is more scientific and comprehensive than existing evolutionary theories, and could have great significance in natural sciences and social sciences. Meanwhile, the CBET is open to optimization and extension.
Tue, 17 August 2021
ARTICLE | doi:10.20944/preprints202108.0358.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Symbiosis; rhizobium; Ferralsol; Haut-Katanga
Online: 17 August 2021 (10:16:48 CEST)
The legume-rhizobium symbiosis plays an important role in the nitrogen (N) assimilation of plants, more particularly in the humid tropical region where soils are deeply weathered and have poor electrochemical properties. On acidic soils of Haut-Katanga, DR Congo it is not clear how application of Bradyrhizobium japonicum affect N allocation among soybean organs (e.g., leaves, seeds). Here, we assessed the effect of Bradyrhizobium japonicum on N content of soybean leaves and seeds cultivated on acidic soils. We conducted two experiments using a split-plot setup with three replicates in two sites (i.e., Kasapa and Kanyameshi). The main plots included three strains of Bradyrhizobium plus the uninoculated control and four varieties of soybean in the subplot. We found that the different strains of Bradyrhizobium did not induce significant effects on the total N content of soybean leaves and seeds in the Kasapa site. In contrast, Bradyrhizobium affected significantly the N content of soybean leaves in the Kanyameshi site. We demonstrated that N content in the soil, which varies between the two sites, positively influences yield and nodulation. We conclude that that the efficiency of the soybean-Bradyrhizobium symbiosis and its influence on the allocation of N through soybean plants strongly depend on the chemical characteristics of the soil and particularly on the initial levels of N in the soils.
Mon, 16 August 2021
ARTICLE | doi:10.20944/preprints202108.0346.v1
Online: 16 August 2021 (14:50:44 CEST)
We report the development of in vitro propagation protocols through adventitious shoot induction pathway for a rare and medicinal Scutellaria havanensis. In vitro propagation studies using nodal explants showed MS medium supplemented with 10µM 6-Benzylaminopurine induced highest number of adventitious shoots in a time dependent manner. A ten - day incubation was optimum for shoot bud induction as longer exposures resulted in hyperhydricity of the explants and shoots induced. We also report preliminary evidence of Agrobacterium tumefaciens EHA105 - mediated gene transfer transiently expressing of green fluorescent protein in this species. Transformation studies exhibited amenability of various explant tissues, internode being the most receptive. As the plant has medicinal value, research was carried out to evaluate its potential antioxidant capacity and the efficacy of methanolic leaf extracts in curbing the viability of human colorectal cancer cell line HCT116. Comparative total polyphenol, and flavonoid content measurement of fresh and air dried leaf extract revealed that the fresh leaf extracts contain higher total polyphenol and flavonoid content. The HCT 116 cell viability assessed by colorimetric assay using a 3-(4, 5-dimethyl-thiazol-2-yl)-2, 5-diphenyltetrazolium bromide, showed a steady growth inhibition after 24 hours of incubation. Scanning Electron Microscopy of leaf surface revealed high density of glandular and non-glandular trichomes. This research provides basis for the conservation of this rare plant and future phytochemical screening and clinical research.
ARTICLE | doi:10.20944/preprints202108.0323.v1
Subject: Biology, Animal Sciences & Zoology Keywords: racehorse; hoof; breakover; gallop; shoeing condition; surface; speed.
Online: 16 August 2021 (11:21:06 CEST)
Understanding the effect of horseshoe-surface combinations on hoof kinematics at gallop is relevant for optimising performance and minimising injury in racehorse-jockey dyads. This intervention study assessed hoof breakover duration in Thoroughbred ex-racehorses from the British Racing School galloping on turf and artificial tracks in four shoeing conditions: barefoot, aluminium-rubber composite (GluShu), aluminium and steel. Shoe-surface combinations were tested in a randomized order and horse-rider pairings (n=14) remained constant. High-speed video cameras (Sony DSC-RX100M5) filmed the hoof-ground interactions at 1000 frames per second. The time taken for a hoof marker wand fixed to the lateral hoof wall to rotate through an angle of 90 degrees during 384 breakover events was quantified using Tracker software. Data were collected for leading and non-leading front and hind limbs, at gallop speeds ranging from 23–56 km h-1. Linear mixed-models assessed whether speed, surface, shoeing condition or any interaction between these parameters (fixed factors) significantly affected breakover duration. Day and horse-rider pair were included as random factors and speed was included as a covariate. The significance threshold was set at p<0.05. For all limbs, breakover times decreased as gallop speed increased (p<0.0005), although a greater relative reduction in breakover duration for hindlimbs was apparent beyond approximately 45 km h-1. Breakover duration was longer on turf compared to the artificial surface (p≤0.04). In the non-leading hindlimb only, breakover duration was affected by shoeing condition (p=0.025) and an interaction between shoeing condition and speed (p=0.023). Future work seeks to relate these results to hoof accelerometer data.
ARTICLE | doi:10.20944/preprints202108.0317.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: COVID-19; Africa; food systems; agriculture
Online: 16 August 2021 (10:47:45 CEST)
Emerging information on the interactions between the COVID-19 pandemic and global food systems has highlighted how the pandemic is accentuating food crises across Africa. Less clear, however, are how the impacts differ between farming systems. Drawing on 50 key informant interviews with farmers, village leaders and extension officers, in South Africa and Tanzania, we identify the effects of COVID-19 and associated measures to curb the spread of the disease on farming production systems, the coping mechanisms adopted by farmers, and explore their longer-term plans for adaptation. We focus on a diverse range of production systems, from small-scale mixed farming systems in Tanzania, to large-scale corporate farms in South Africa. Our findings highlight how COVID-19 restrictions have interrupted the supply chains of agricultural inputs and commodities, increasing the storage time for produce, decreasing income and purchasing power, and reducing labour availability. Farmers’ responses were heterogeneous, with highly diverse small-scale farming systems and those less engaged with international markets least affected by the associated COVID-19 measures. Large-scale farmers were most able to access capital to buffer short-term impacts, whereas smaller-scale farms shared labour, diversified to subsistence produce and sold assets. However, compounded shocks, such as recent extreme climate events, limited the available coping options, particularly for smaller-scale and emerging farmers. The study highlights the need to understand the characteristics of farm systems to better equip and support farmers, particularly in contexts of uncertainty. We propose that policy actions should focus on (i) providing temporary relief and social support and protection to financially vulnerable stakeholders, (ii) job assurance for farmworkers, and engaging an alternative workforce in farming, (iii) investing in farming infrastructure, such as storage facilities, digital communication tools, and extension services, and iv) supporting diversified agroecological farming systems.
REVIEW | doi:10.20944/preprints202108.0315.v1
Subject: Biology, Animal Sciences & Zoology Keywords: amylase; carbohydrates; crustaceans; decapods; digestion; feeding habits; lobster.
Online: 16 August 2021 (09:33:48 CEST)
Decapod crustaceans are a very diverse group and have evolved to suit a wide variety of diets. Alpha-amylases enzymes, responsible for starch and glycogen digestion, have been more thoroughly studies in herbivore and omnivore than in carnivorous species. We used information on the α-amylase of a carnivorous lobster as a connecting thread to provide a more comprehensive view of α-amylases across decapods crustaceans. Omnivorous crustaceans such as shrimps, crabs and crayfish present relatively high amylase activity respect to carnivorous. Yet, contradictory results have been obtained and relatively high activity in some carnivores has been suggested to be a remnant trait from ancestor species. Here we provided information sustaining that high enzyme sequence and overall architecture conservation do not allow high changes in activity, and that differences among species may be more related to number of genes and isoforms, as well as transcriptional and secretion regulation. However, recent evolutionary analyses revealed that positive selection might have also occurred among distant lineages with feeding habits as a selection force. Some biochemical features of decapod α-amylases can be related with habitat or gut conditions, while less clear patterns are observed for other enzyme properties. Likewise, while molt cycle variations in α-amylase activity are rather similar among species, clear relationships between activity and diet shifts through development cannot be always observed. Regarding the adaptation of α-amylase to diet, juveniles seem to exhibit more flexibility than larvae, and it has been described variation in α-amylase activity or number of isoforms due to the source of carbohydrate and its level in diets, especially in omnivore species. In the carnivorous lobster, however, no influence of the type of carbohydrate could be observed. Also, lobsters were not able to fine-regulate α-amylase gene expression in spite of large changes in carbohydrate content of diet, while retaining some capacity to adapt α-amylase activity to very low carbohydrate content in the diets. In this review, we raised arguments for the need of more studies on the α-amylases of less studied decapods groups, including carnivorous species which rely more on dietary protein and lipids, to broad our view of α-amylase in decapods crustaceans.
Sat, 14 August 2021
ARTICLE | doi:10.20944/preprints202108.0308.v1
Subject: Biology, Horticulture Keywords: : carotenoid cleavage dioxygenase; strigolactones; wintersweet
Online: 14 August 2021 (14:36:42 CEST)
Strigolactones (SLs) regulate plant shoot development by inhibiting axillary bud growth and branching. However, the role of SLs in wintersweet (Chimonanthus praecox) shoot branching remains unknown. Here, we identified and isolated two wintersweet genes, CCD7 and CCD8, in-volved in the SL biosynthetic pathway. Quantitative real-time PCR revealed that CpCCD7 and CpCCD8 were down-regulated in wintersweet during branching. When new shoots were formed, expression levels of CpCCD7 and CpCCD8 were almost the same as the control (un-decapitation). CpCCD7 was expressed in all tissues, with the highest expression in shoot tips and roots, while CpCCD8 showed the highest expression in roots. Both CpCCD7 and CpCCD8 localized to chloroplasts in Arabidopsis. CpCCD7 and CpCCD8 overexpression restored the phenotypes of branching mutant max3-9 and max4-1, respectively. CpCCD7 overexpression reduced the rosette branch number, whereas CpCCD8 overexpression lines showed no phenotypic differences compared with wild-type plants. Additionally, the expression of AtBRC1 was significantly up-regulated in transgenic lines, indicating that two CpCCD genes functioned similarly to the homologous genes of the Arabidopsis. Overall, our study demonstrates that CpCCD7 and CpCCD8 exhibit conserved functions in the CCD pathway, which controls shoot development in wintersweet. This research provides a molecular and theoretical basis for further understanding branch development in wintersweet.
Thu, 12 August 2021
HYPOTHESIS | doi:10.20944/preprints202108.0270.v1
Subject: Biology, Other Keywords: T helper differentiation; T helper polarization; Cross-reactivity; Regulatory T cells; Microbiota; Original Antigenic Sin
Online: 12 August 2021 (08:46:55 CEST)
Naive CD4+ T cells engage cognate peptide MHC-II complexes (pMHC-IIs) to differentiate and acquire one of several T helper (Th) fates whose specific trajectories are guided by a dynamic cytokine milieu that develops in response to antigenic entity. This physiological process is often erroneously conflated with a pathological one termed Th polarization. Using the SPIRAL model, we argue here that unlike Th fate choice, innate signaling alone is insufficient to initiate Th polarization in naive CD4+ T cells, that it instead develops from pre-existing memory CD4+ T cells that express cross-reactive TCRs, and that it inevitably leads to immunopathology.
Tue, 10 August 2021
REVIEW | doi:10.20944/preprints202108.0232.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Cyperus exculentus; Neglected/Underutilized Crop species; Biology; Uses; Production constraints
Online: 10 August 2021 (12:33:44 CEST)
Food security relies mainly on a few major crop such as wheat, maize, rice and yam. Many of the cultivated plant such as Cyperus exculentus are still considered invasive plants and are neglected and underutilized. In the perspective to valorization of the species, this systematic review aimed at identifying the biology, production constraints and uses of tigernut for future research directions. Extensive searches were carried out and studies were screened and extracted using established systematic review methods. A total of 175 papers met the inclusion criteria. Approximately 52% and 21.71% of the studies were undertaken in Europe and Africa respectively. Most of the papers reviewed for the study were published between [2010-2015[. The review highlighted the critical research gaps in genetic diversity using SSR makers and evolutionary biology. Further, production constraints and solution approaches for the promotion of the species were the other gaps identified in the reviewed studies. Production constraints were specifically related to the insufficient mineral fertilizers and difficult in harvesting. Tigernut is used in more fields such as food, medicinal, cosmetic, biofuel and fishing and fish breeding. Such investigations would help in decision-making and elaboration of breeding strategies, and advancing steps towards sustainable use of the species.
ARTICLE | doi:10.20944/preprints202108.0225.v1
Subject: Biology, Physiology Keywords: microglia; gut-brain axis; antibiotics; glutamatergic synapses; hippocampus; patch clamp; hippocampal slices.; microbiota; neurons; glutamatergic trasmission
Online: 10 August 2021 (10:04:00 CEST)
‘Dysbiosis’ of the adult gut microbiota, in response to challenges such as infection, altered diet, stress, and antibiotics treatment has been recently linked to pathological alteration of brain func-tion and behavior. Moreover, gut microbiota composition constantly controls microglia matura-tion as revealed by morphological observations and gene expression analysis. However, it is un-clear whether gut microbiota influences microglia functional properties and crosstalk with neu-rons, known to shape and modulate synaptic development and function. Here, we investigated how antibiotic mediated alteration of the gut microbiota influences microglial and neuronal functions in adult mice hippocampus. Hippocampal microglia from adult mice treated with oral antibiotics exhibited increased microglia density, altered basal patrolling activity, and impaired process rearrangement in response to damage. Patch clamp recordings at CA3-CA1 synapses revealed that antibiotics treatment alters neuronal functions, reducing spontaneous postsynaptic glutamatergic currents and decreasing synaptic connectivity, without reducing dendritic spines density. The effect of dysbiosis on neuronal functions are mediated by microglia-neuron cross-talk through the CX3CL1-CX3CR1 axis, as antibiotics treatment of CX3CR1 deficient mice, mod-ulates microglia density and processes rearrangement leaving unaltered synaptic function. To-gether, our findings show that the antibiotics alteration of gut microbiota impairs synaptic effi-cacy, probably through CX3CL1-CX3CR1 signaling supporting microglia as a major player in in the gut-brain axis, and in particular in the gut microbiota-to-neuron communication pathway.
Mon, 9 August 2021
ARTICLE | doi:10.20944/preprints202108.0198.v1
Subject: Biology, Animal Sciences & Zoology Keywords: depolymerizing enzyme; debranching enzyme; xylanase; arabinofuranosidase; feruloyl esterase; arabinoxylan; digestion; growth performance; volatile fatty acid; piglet
Online: 9 August 2021 (14:56:56 CEST)
This study was aimed to investigate the effect of xylan depolymerizing enzyme namely endo-xylanase (Xyn) combined with debranching enzymes namely arabinofuranosidase (Afd) and feruloyl esterase (FE) on digestion, growth performance and intestinal volatile fatty acid profile of piglets. The in vitro experiments were firstly conducted to examine the enzymological properties of Xyn, Afd and FE, the synergy among these enzymes, together with the effect of combination of these enzymes on digestion of piglet diet. The in vivo experiment was then implemented by allocating 270 35-d-old postweaning piglets into 3 treatment groups: control group, Xyn group and (Xyn+Afd+FE) group. Each group had 6 replicates (15 piglets/replicate). The results revealed a satisfying thermostability and pH stability of Xyn, Afd and FE. Combination of Xyn, Afd and FE had a superiority (P < 0.05) over Xyn alone and its combination with Afd or FE in promoting degradation of different bran fibers rich in arabinoxylan (Abx). Treatment with combination of Xyn, Afd and FE had advantages over Xyn alone to induce increasing trends (P < 0.10) of in vitro digestibility of dietary nutrients (dry matter, crude protein, crude ash and gross energy) and piglet growth performance (average daily gain, final body weight and feed efficiency), concurrent with a reduction (P < 0.05) of diarrhea rate and increases (P < 0.05) in cecal acetic acid, butyric acid and total volatile fatty acids concentrations as well as pH value of piglets. Collectively, combination of Xyn, Afd and FE was efficient in benefiting degradation of Abx in brans, as well as improving digestion, growth performance and intestinal volatile fatty acid profile of piglets.
Sat, 7 August 2021
REVIEW | doi:10.20944/preprints202108.0174.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: lactic acid bacteria; food-producing animals; dairy products; health benefits; One health; antimicrobial resistance; probiotics; starter cultures; adjunct cultures; protective cultures.
Online: 7 August 2021 (00:17:15 CEST)
Animal products, in particular dairy and fermented products, are natural, major sources of lactic acid bacteria (LAB). Due to their antimicrobial properties, LAB are used in humans and in animals, with beneficial effects, as probiotics or in the treatment of a variety of diseases. In livestock production, LAB contribute to animal performance, health, and productivity. In the food industry, LAB are applied as bioprotective and biopreservation agents, contributing to improve food safety and quality. However, some studies have described resistance to relevant antibiotics in LAB, with the concomitant risks associated to the transfer of antibiotic resistance genes to foodborne pathogens, their potential dissemination throughout the food chain, and the environment. Here, we summarize the application of LAB in livestock and animal products, as well as the health impact of LAB in animal food products. In general, the beneficial effects of LAB on the human food chain seem to outweigh the potential risks associated with their consumption as part of animal and human diets. However, further studies and continuous monitorization efforts are needed to ensure their safe application in animal products and in the control of pathogenic microorganisms, preventing the possible risks associated with antibiotic resistance and, thus, protecting public health.
Fri, 6 August 2021
ARTICLE | doi:10.20944/preprints202108.0167.v1
Subject: Biology, Physiology Keywords: LED; light; retina; microglia; caspase; apoptosis; Bcl-2; BAX; degeneration
Online: 6 August 2021 (14:04:11 CEST)
Vision is our primary sense as the human eye is the gateway for more than 65% of information reaching the human brain. Today’s increased exposure to different wavelengths and intensities of light from Light Emitting Diodes (LEDs) sources could induce retinal degeneration and accompanying neuronal cell death. Damage induced by chronic phototoxic reactions occurring in the retina accumulates over years and it has been suggested to be responsible for the etiology of many debilitating ocular conditions. In this work, we examined how LED stimulation affects vision by monitoring changes in the expression of death and survival factors as well as microglial activation in LED-induced damage (LID) of the retinal tissue. We found an LED exposure-induced increase in the mRNA levels of major apoptosis-related markers -BAX, Bcl-2, and Caspase-3 and an accompanying wide-spread microglial and Caspase-3 activation. Everyday LED light exposure was accounted for all the described changes in the retinal tissue of mice in this study, indicating that overuse of non-filtered direct LED light can have detrimental effects on the human retina as well.
ARTICLE | doi:10.20944/preprints202108.0160.v1
Subject: Biology, Entomology Keywords: Pyrethroid; pyrethroid resistance; insecticide resistance; insecticide resistance management; vector control; malaria; malaria control; mosquito; Anopheles
Online: 6 August 2021 (11:19:25 CEST)
Pyrethroid resistance is widespread in malaria vectors. However, differential mortality in discriminating dose assays to different pyrethroids is often observed in wild populations. When this occurs, it is unclear if this differential mortality should be interpreted as an indication of differential levels of susceptibility within the pyrethroid class, and if so, if countries should consider selecting one specific pyrethroid for programmatic use over another. A review of evidence from molecular studies, resistance testing with laboratory colonies and wild populations, and mosquito behavioural assays was conducted to answer these questions. Evidence suggests that in areas where pyrethroid resistance exists, different results in insecticide susceptibility assays with specific pyrethroids currently in common use (deltamethrin, permethrin, α-cypermethrin and λ-cyhalothrin) are not necessarily indicative of an operationally relevant difference in potential performance. Consequently, it is not advisable to use rotation between these pyrethroids as an insecticide resistance management strategy. Less commonly used pyrethroids (bifenthrin and etofenprox) may have sufficiently different modes of action, though further work would be needed to examine how this may apply to insecticide resistance management.
Thu, 5 August 2021
REVIEW | doi:10.20944/preprints202108.0141.v1
Online: 5 August 2021 (11:04:09 CEST)
Tomato leaf curl disease (TLCD) is the most common viral disease in the tomato plant. It is caused by begomoviruses, which are viruses that cause plant development to be slowed. Many of the traditional disease management methods are still in use. They are, however, ineffective and out of date. Modern biotechnology is being used to detect illness in tomato plants as early as possible, thus reducing damage to the plants. Through genetic engineering, the spread of viruses may be controlled or prevented entirely. Here reviewed many methods for decreasing or eliminating the viral influence on crop growth through biotechnology and genomics. We also investigated the possibility of genetic engineering to reduce or remove the virus TLCD impact on tomato crop development.
Wed, 4 August 2021
REVIEW | doi:10.20944/preprints202108.0124.v1
Subject: Biology, Anatomy & Morphology Keywords: rhizoremediation; plant growth promoting rhizobacteria; petroleum hydrocarbon-degrading bacteria; salix; contaminated soils; alkanes; polycyclic aromatic hydrocarbons
Online: 4 August 2021 (22:30:31 CEST)
Soil contamination with petroleum hydrocarbons (PHCs) has become a global concern in the word due to intensification of industrial activities. This creates a serious environmental issue, therefore there is a need to find solutions, including application of efficient remediation technologies, or to improve current techniques. Rhizoremediation is a sub-category of the phytoremediation which refers to Phytomanagement that uses plants and their associated microbiota. These green technologies have received a global attention as a cost-effective and possible efficient remediation technique that can be applied to cleanup PHCs-polluted soils. The mechanism of rhizoremediation process is that plant roots stimulate soil microbes to mineralize organic contaminants to H2O and CO2. However, this multipartite interaction is much complex because many biotic and abiotic factors can influence microbial processes in the soil, making the efficiency of rhizoremediation unpredictable. This review reports the progress made on rhizoremediation approaches that can overcome the limitations and improve the efficiency of PHCs-contaminated soils. The addressed approaches in this review include: 1) selecting plants with desired characteristics suitable for rhizoremediation, 2) the exploitation and manipulation of plant microbiome by using inoculant containing plant growth-promoting rhizobacteria (PGPR) or hydrocarbon-degrading microbes, or a combination of both types of organisms, and 3) enhancement of the understanding of how host-plant assembles a beneficial microbiome, and how it functions, under pollutant stress.
ARTICLE | doi:10.20944/preprints202108.0106.v1
Subject: Biology, Anatomy & Morphology Keywords: hormones; Carpathian Indigenus Buffalo; FTAI; sexed semen; OvSynch
Online: 4 August 2021 (10:02:50 CEST)
Although artificial insemination can mean a slow and progressive improvement of animal genetics, in buffalo-cow its practical application is difficult the results are incomparably lower then cattle. The purpose of this article is to develop a new methodology, a well-known technique to make AI biotechnology more applicable to the buffalo, in order to improve the conception rate. The protocol we follow is to stimulate hormonal ovarian activity, inducing the dominant follicle, causing ovulation and scheduling the moment of sexed artificial insemination deep in the uterine horn only ipsilateral to the ovary that will ovulate. The experiment was performed on 40 primiparous buffaloes-cows in two groups for AI separated by two bulls whit 2 Millions female sperm straws. The groups was compiled after a thorough gynecological examination, and subsequently the OvSynch therapeutic protocol was started. The results were 82,5% buffaloes (33/40) had dominant follicle (DF) and inseminated, on hot/cold seasons the distribution was 75%vs90%. The conception rate was 63,6% (21/33), on hot/cold seasons 60%vs66,6%, and after calving 92.5% (20/21) female cattle were obtained. Thus, by implementing UcFTAI protocol, we state that the goal of increasing the genetic potential of CIB by becomes achievable and can be extended to a larger scale. Our Improved Protocol (UcFTAI) aims to reduce waste and maximize OvSynch hormone therapy.
ARTICLE | doi:10.20944/preprints202108.0104.v1
Subject: Biology, Anatomy & Morphology Keywords: quantitative metagenomics; microbiome; obesity; gut microbiota; microbial DNA extraction; sequencing; Simulation; Oxford Nanopore Technologies; MinION
Online: 4 August 2021 (09:44:24 CEST)
Background: The gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. Large-scale sequencing projects allowed characterizing the perturbations of these communities. However, translating these discoveries into clinical applications remains a challenges. To facilitate routine implementation of microbiome profiling in clinical settings, portable, real-time, and low-cost sequencing technologies are needed. Results: Here, we propose a computational and experimental protocol for whole genome quantitative metagenomics studies of human gut microbiome with Oxford Nanopore sequencing technology (ONT) that could be applied to other microbial ecosystems. We developed a bioinformatic protocol to analyse ONT sequences taxonomically and functionally and optimized pre-analytic protocols including stool collection and DNA extraction methods to maximize read length. This is a critical parameter for the sequence alignment and classification. Our protocol was evaluated using simulations of metagenomic communities which reflect naturally occuring compositional variations. Next, we validated both protocols using stool samples from a bariatric surgery cohort, sequenced with ONT, Illumina and SOLiD technologies. Results revealed similar diversity and microbial composition profiles. Conclusion: This protocol can be implemented in the clinical or research setting, bringing rapid personalized whole genome profiling of target microbiome species.
Tue, 3 August 2021
REVIEW | doi:10.20944/preprints202108.0097.v1
Subject: Biology, Anatomy & Morphology Keywords: Goat population; Goat milk; Milk production; Milk composition; Goat cheese; Therapeutic properties
Online: 3 August 2021 (15:57:07 CEST)
Since the 1980s, a growing interest in goat milk was noticed due to the nutritional values and health benefits of this milk, which resulted in increasing goat populations and milk production worldwide. This comprehensive review elaborates on goat milk composition compared to other types of milk. It is also an overview of goat milk production, properties, nourishment-value, applications in dairy products, and potential health benefits. Goat milk composition and its characteristics are slightly different from other types of milk and can be utilized to manufacture many dairy products. Fresh goat milk and goat milk products (e.g., yogurt and kefir were found to provide various potential health benefits, such as anti-inflammatory, prevent cardiovascular disease, anti-diabetic and antihypertensive, strengthen bones, boost immunity, and improve metabolism.
ARTICLE | doi:10.20944/preprints202108.0092.v1
Subject: Biology, Anatomy & Morphology Keywords: petroleum; metagenomics; core microbiota, functional potential, oil fields
Online: 3 August 2021 (15:29:57 CEST)
Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to deci-pher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301,2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 MAGs of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to ar-chaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied. The analysis of the potential functional core in the reservoirs showed that the microbiota was specialized for each site, with 31.7% of the total KEGG orthologies annotated as functions (1,690 genes) common to all oil fields, while 18% of the functions were site-specific, i.e., present only in one of the oil fields. The oil reservoirs with lower level of intervention were the most similar to the potential functional core, while the oil fields with longer history of water in-jection had greater variation in functional profile. These results show how key microorganisms and their functions respond to the distinct physicochemical parameters and interventions of the oil field operations such as water injection and expand the knowledge of biogeochemical trans-formations in these ecosystems.
REVIEW | doi:10.20944/preprints202108.0082.v1
Subject: Biology, Anatomy & Morphology Keywords: vaccines; vaccination; bovine respiratory disease; antigen; adjuvants
Online: 3 August 2021 (13:39:11 CEST)
Vaccination is widely regarded as a cornerstone in animal or herd health and infectious disease management. Nineteen vaccines against the major pathogens implicated in bovine respiratory disease are registered for use in the UK by the Veterinary Medicines Directorate (VMD). However, despite annual prophylactic vaccination, bovine respiratory disease is still conservatively estimated to cost the UK economy approximately £80 million per annum. This review examines the vaccine types available, discusses the surrounding literature and scientific rationale of the limitations and assesses the potential of novel vaccine technologies.
ARTICLE | doi:10.20944/preprints202108.0078.v1
Subject: Biology, Anatomy & Morphology Keywords: biodiversity; insolation, biogeography; lidar; point-cloud; multi-spectral imagery; spatial prediction model; forest canopy
Online: 3 August 2021 (13:05:43 CEST)
Incident solar radiation (insolation) passing through the forest canopy to the ground surface is either absorbed or scattered. This phenomenon, known as radiation attenuation, is measured using the extinction coefficient (K). The amount of radiation at the ground surface of a given site is effectively controlled by the canopy’s surface and structure, determining its suitability for plant species.Menhinick’s and Simpson biodiversity indexes were selected as spatially explicit response variables for the regression equation using canopy structure metrics as predictors. Independent variables include modeled area solar radiation, LiDAR derived canopy height, effective leaf area index data derived from multi-spectral imagery, and canopy strata metrics derived from LiDAR point-cloud data. The results support the hypothesis that, 1.) canopy surface and strata variability may be associated with understory species diversity due to habitat partitioning and radiation attenuation, and that, 2.) such a model can predict both this relationship and biodiversity clustering.The study data yielded significant correlations between predictor and response variables and was used to produce a multiple-linear model comprising canopy relief, texture of heights, and vegetation density to predict understory plant diversity. When analyzed for spatial autocorrelation, the predicted biodiversity data exhibited non-random spatial continuity.
ARTICLE | doi:10.20944/preprints202108.0077.v1
Subject: Biology, Anatomy & Morphology Keywords: arboviruses; Dengue; Chikungunya; molecular biology; qRT-PCR; Aedes aegypti; Burkina Faso
Online: 3 August 2021 (12:48:01 CEST)
Abstract: In 2016, we conducted an entomological survey in a railway transect between Banfora and Ouagadougou, Burkina Faso. The aim was to evaluate the risk factors for arbovirus epidemics, including vector infection status, in areas representative of the country. Aedes aegypti mosquitoes were collected at larval stage from four study sites and reared until adult stage and kept in RNAlater for detection of arbovirus RNA. In the laboratory, the mosquito specimens were screened for dengue virus (DENV) and chikungunya virus (CHIKV) using one step real-time qRT-PCR. We detected one DENV-2 positive pool from Ouagadougou, giving a minimum infec-tion rate (MIR) of 16.67, and 6 CHIKV positive pools, giving a MIR of 66.67 from Ouagadougou, but also in Banfora and Boromo. The qRT-PCR is a useful tool for the surveillance of arboviruses of public health importance in Burkina Faso and may be incorporated into disease surveillance and control programs in Burkina Faso.
Mon, 2 August 2021
ARTICLE | doi:10.20944/preprints202108.0059.v1
Subject: Biology, Anatomy & Morphology Keywords: Ballota nigra; salinity; antioxidant; enzyme activity; phytochemical composition
Online: 2 August 2021 (16:31:13 CEST)
Black horehound (Ballota nigra L.) is one of the important medicinal plants, which is a rich source of health-promoting essential oils. Salinity stress affects plant development and alters the quality and quantity of plants extracts and their composition. This study was aimed to investigate the effect of salinity on morphological, physiological characteristics, and secondary metabolites of B. nigra under greenhouse, and in vitro culture conditions. The plants were treated with different concentrations of NaCl (25, 50, 75, 100 mM) and fresh and dry weight of leaf and stem were measured as well as morphological characteristics of the plant. Plant growth was reduced with the increased salinity concentrations. The results showed that all growth-related traits and SPAD were decreased both in vivo and in vitro. Additionally, increased salt concentration affected the cell membrane integrity. Total phenolics content of plants growing in the greenhouse, increased by 21% at 50 mM NaCl, but at higher stress levels (100 mM NaCl), the amounts were decreased significantly. Total flavonoids contents followed similar patterns, with a slight difference. In addition, the maximum and minimum total phenolics contents of plants growing under in vitro condition were observed at 50 mM NaCl and control treatments, respectively. Increasing the salt concentration significantly affected the total flavonoids content, and as a result, the highest amount was observed in 50 and 75 mM NaCl treatments. Antioxidant activity was also measured. Among the NaCl treatments, the highest DPPH scavenging activities (IC50) under greenhouse and in vitro conditions were detected at 50 mM and 25 mM concentrations, respectively. In general, based on the results, with increasing the salinity level to 75 mM, the activities of CAT and APX were significantly upregulated in both greenhouse and in vitro culture conditions. A correlation between total phenolics and flavonoids contents as well as antioxidant activity were obtained. With shifting salinity stress, the type and the amount of the identified essential oil compounds changed. Compounds such as styrene, tridecanol, germacrene-D, beta-Ionone, beta-bisabolene, and caryophyllene oxide increased compared to the controlled treatment.
ARTICLE | doi:10.20944/preprints202107.0439.v2
Subject: Biology, Anatomy & Morphology Keywords: capital return rate deficiency; expected value; carbon storage; carbon rent; albedo effect
Online: 2 August 2021 (13:28:23 CEST)
Two sets of initial conditions are used in the investigation of capital return rate and carbon storage in boreal forests. Firstly, a growth model is applied in young stands as early as the inventory-based model is applicable. Secondly, the growth model is applied to observed wooded stands. Four sets of thinning schedules are investigated in either case. First, the capital return rate is aspired without any restriction. Second, the number of thinnings is restricted to at most one. Third, thinnings are restricted to the removal of only trees thicker than 237 mm. Fourth, commercial thinnings are omitted. The two sets of initial conditions yield similar results. The capital return rate is a weak function of rotation age, which results in variability in the optimal number of thinnings. Reducing the number of thinnings to one increases timber stock but induces a capital return rate deficiency. The deficiency per excess volume unit is smaller if the severity of any thinning is restricted by the removal of large trees only. Omission of thinnings best applies to spruce-dominated stands with stem count less than 2000/ha. Restricted thinning intensity applies to deciduous stands and dense pine stands. The albedo effect increases the benefits of restricted thinnings and increased clearcuttings instead of contradicting the carbon storage.
COMMUNICATION | doi:10.20944/preprints202108.0036.v1
Subject: Biology, Anatomy & Morphology Keywords: Acinetobacter baumannii, H-NS, natural transformation, naturally competent, DNA acquisition
Online: 2 August 2021 (12:58:22 CEST)
Most Acinetobacter baumannii strains are naturally competent. Although some information is available about factors that enhance or reduce the frequency of transformation of this bacterium, the regulatory elements and mechanisms are barely understood. In this article, we describe studies on the role of H-NS in the regulation of expression of genes related to natural competency and the ability to uptake foreign DNA. The expression levels of the natural transformation-related genes pilA, pilT, pilQ, comEA, comEC, comF, and drpA were significantly increased in a Δhns derivative of Acinetobacter baumannii A118. Complementation of the mutant with a recombinant plasmid harboring hns restored expression levels of six of these genes (pilT remained expressed at high levels) to those of the wild-type strain. The transformation frequency of the A. baumannii A118 Δhns strain was significantly higher than that of the wild-type. Similar, albeit not identical, effects occurred when hns was deleted from the hypervirulent A. baumannii AB5075 strain. Reduction of gene expression in a few cases was not as pronounced as to reach wild-type levels, and expression of comEA was enhanced further. In conclusion, the expression of all seven transformation-related genes was enhanced after deleting hns in A. baumannii A118 and AB5075, and these modifications are accompanied by an increase in the cells’ transformability. The results demonstrate a role of H-NS in A. baumannii’s natural competence.
ARTICLE | doi:10.20944/preprints202108.0002.v1
Online: 2 August 2021 (08:43:20 CEST)
Human Rhinovirus (HRV) is the most common cause of upper respiratory infections and exacerbations of asthma. In this work, we selected 14 peptides (6 from HRV A and 8 from HRV C) encompassing potential CD4 T cell epitopes. Peptides were selected for being highly conserved in HRV A and C serotypes and predicted to bind to multiple HLA II molecules. We found positive T cell recall responses by IFNγ-ELISPOT assays to 8 peptides, validating 7 of them (3 from HRV A and 4 from HRV C) as CD4 T cell epitopes through intracellular cytokine staining assays. Additionally, we verified their promiscuous binding to multiple HLA II molecules by quantitative binding assays. According to their experimental HLA II binding profile, the combination of all these 7 epitopes could be presented and recognized by > 95 % of the world population. We actually determined IFNγ responses to a pool encompassing these CD4 T cell epitopes by intracellular cytokine staining, finding positive responses in 29 out of 30 donors. The CD4 T cell epitopes identified in this study could be key to monitor HRV infections and to develop peptide-based vaccines against most HRV A and C serotypes.
Fri, 30 July 2021
ARTICLE | doi:10.20944/preprints202107.0696.v1
Subject: Biology, Entomology Keywords: Gustation; sugar aversion; German cockroach; olfactory learning; memory; foraging
Online: 30 July 2021 (10:49:30 CEST)