REVIEW | doi:10.20944/preprints202007.0328.v2
Subject: Biology, Other Keywords: Evolution; Speciation; Crossbreeding; Hybridization; Species spectrum; Polyploidization; Mutation
Online: 30 November 2021 (11:04:43 CET)
Although Darwin‘s evolutionary mutation theory has been widely accepted, many endeavors tried to challenge it. With more and more observation of successful hybridization and hybrids, the sexual isolation between species has become vague. The mechanism of evolution has been expanded from the classical model of evolution to multiple routes of speciation. Furthermore, a fundamental crossbreeding theory has been raised and proved by two lines of evidences: paleopolyploidy and fan-shaped spectrum of species. Ancient genome duplications are widespread throughout eukaryotic lineages, particularly in plants. The genome polyploidization can break through the sexual incompatibility between diploid counterparts to hybridize and produce new species. By comparing characteristics, all species in every taxon, both in the extinct fossil and extant organisms, can be arranged into fan-shaped spectrum according to their similarity: left primitive type-middle advanced type-right primitive type. The species are primitive at the two ends and advanced at the middle. The primitive two species always resemble two types of more primitive species that can be confirmed as their ancestors respectively, and the middle species is half similar to the two ancestors respectively. These suggest that the species in the spectrum come from two different ancestors by crossbreeding and gene combination. As a sum, advanced species originated from crossbreeding of two primitive ancestors, by major method of polyploidization, and proved by results of fan-shaped spectrum of species. Then, sex is the cause, force and opportunity for evolution.
ARTICLE | doi:10.20944/preprints202111.0557.v1
Subject: Biology, Other Keywords: Bacterial nomenclature; archaeal nomenclature; genome taxonomy; shotgun metagenomics; Candidatus names
Online: 30 November 2021 (10:53:50 CET)
Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.
Mon, 29 November 2021
ARTICLE | doi:10.20944/preprints202111.0517.v1
Subject: Biology, Other Keywords: Rhodotorula babjevae; de-novo hybrid assembly; Nanopore sequencing; genome divergence
Online: 29 November 2021 (07:57:39 CET)
The genus Rhodotorula includes basidiomycetous oleaginous yeast species. R. babjevae can produce compounds of biotechnological interest such as lipids, carotenoids and biosurfactants from low value substrates such as lignocellulose hydrolysate. High-quality genome assemblies are needed to develop genetic tools and to understand fungal evolution and genetics. Here, we combined short- and long-read sequencing to resolve the genomes of two R. babjevae strains, CBS 7808 (type strain) and DBVPG 8058 at chromosomal level. Both genomes have a size of 21 Mbp and a GC content of 68.2%. Allele frequency analysis indicated tetraploidy in both strains. They harbor 21 putative chromosomes with sizes ranging from 0.4 to 2.4 Mb. In both assemblies, the mitochondrial genome was recovered in a single contig, which shared 97% pairwise identity. The pairwise identity between the majority of chromosomes ranges from 82% to 87%. We found indications for strain-specific extrachromosomal endogenous DNA. 7,591 protein-coding genes and 7,607 associated transcripts were annotated in CBS 7808 and 7,481 protein-coding genes and 7,516 associated transcripts in DBVPG 8058. CBS 7808 has accumulated a higher number of tandem duplications than DBVPG 8058. We identified large translocation events between putative chromosomes and a high genetic divergence between the two strains.
Fri, 19 November 2021
REVIEW | doi:10.20944/preprints202111.0367.v1
Online: 19 November 2021 (14:56:06 CET)
Telomeres are crucial structures that preserve genome stability. Their progressive erosion over rounds of DNA duplication determines senescence of cells and organisms. Telomere length homeostasis is critical for cancer development then telomere maintenance mechanisms are established targets in cancer treatment. Besides telomere elongation, telomere’s dysfunction impinges on intracellular signalling pathways, in particular DNA damage signalling and repair affecting cancer cell survival and proliferation. This review summarizes and discusses about the recent findings in anti-cancer drug development targeting different “telosome” components.
Thu, 18 November 2021
REVIEW | doi:10.20944/preprints202111.0319.v1
Subject: Biology, Other Keywords: Higher Order Repeats; Non-B DNA; Centromere Protein B; Break-Induced Replication; Molecular Drive
Online: 18 November 2021 (08:27:35 CET)
Centromeres, the chromosomal loci where spindle fibers attach during cell division to segregate chromosomes, are typically found within satellite arrays in plants and animals. Satellite arrays have been difficult to analyze because they comprise megabases of tandem head-to-tail highly repeated DNA sequences. Much evidence suggests that centromeres are epigenetically defined by the location of nucleosomes containing the centromere-specific histone H3 variant cenH3, independently of the DNA sequences where they are located; however, the reason that cenH3 nucleosomes are generally found on rapidly evolving satellite arrays has remained unclear. Recently, long read sequencing technology has clarified the structures of satellite arrays and sparked rethinking of how they evolve, while new experiments and analyses have helped bring both understanding and further speculation about the role these highly repeated sequences play in centromere identification.
Wed, 17 November 2021
ARTICLE | doi:10.20944/preprints202111.0304.v1
Subject: Biology, Other Keywords: amino acid permease; L-aspartic acid; Bacillus licheniformis; whole-cell biocatalyst; fermentation engineering
Online: 17 November 2021 (11:58:31 CET)
Amino acid efflux and influx transport systems play vital roles in industrial microorganisms’ cell growth and metabolism. However, although biochemically characterized, most amino acid transporters remain unknown at the molecular level in Bacillus licheniformis. This study focuses on the molecular and functional characterizations of three transporters, YdgF, YvbW, and YveA, mainly when catalyzing the cross-membrane flux of L-Aspartate. When growing in the minimal medium with L-Asp as the only carbon and nitrogen source, the growth of strains lacking proteins YdgF, YvbW, and YveA was significantly inhibited compared with wild-type strains, while supplementing the expression of the corresponding proteins in the single-gene knockout strains can alleviate the inhibition to some extent. Upon overexpression, the recombinant proteins mediate the accumulation of L-aspartate to varying degrees. Compared with wild-type strains, the single knockout strains of the three protein genes exhibited reduced absorption of L-aspartate. In addition, this paper focuses on the effects of these three proteins on the absorption of β-alanine, L-glutamate, D-serine, D-alanine, and glycine.
Mon, 15 November 2021
TECHNICAL NOTE | doi:10.20944/preprints202111.0256.v1
Subject: Biology, Other Keywords: planarian; maceration; high-content fluorescence microscopy; formaldehyde fixation; RNA FISH; immunocytochemistry; BrdU; phospho-histone H3; tyramide signal amplification
Online: 15 November 2021 (11:44:53 CET)
High-content fluorescence microscopy combines the efficiency of high-throughput techniques with the ability to extract quantitative information from biological systems. The planarian community has developed sensitive and robust assays for whole animals, yet cell based assays, despite their practical aspects, have not been explored to the same extent. Here we describe a modular collection of detailed protocols adapted for fixed planarian cells that enable multiplexed measurements of biomarkers in microwell plates. Methods include the detection of RNA transcripts by RNA fluorescent in situ hybridization combined with tyramide signal amplification using hapten-labeled riboprobes. In addition, immunocytochemical protocols for quantifying proliferating cells by the detection of phosphorylated histone H3 as well as 5-bromo-2'-deoxyuridine incorporation into the nuclear genome are described. The assays are compatible with planarians of virtually any size, as the tissue is disaggregated into a single cell suspension before fixation and staining. By sharing many reagents with established planarian whole mount staining protocols, preparation of samples for high-content microscopy adoption requires little additional investment. Recommendations for successful experimental workflows and common sources of errors are discussed.
Fri, 12 November 2021
ARTICLE | doi:10.20944/preprints202111.0233.v1
Subject: Biology, Other Keywords: animal robots; neuronal electrical signal; electrical stimulation; Direct Digital Synthesis algorithm
Online: 12 November 2021 (15:15:25 CET)
As a stimulus signal, coded electrical signals can control the motion behavior of animals, which has been widely used in the field of animal robots. In current research, most of the stimulus signals used by researchers are traditional waveforms, such as square waves. To enrich the stimulus waveform, a wireless animal robot stimulation system based on neuronal electrical signal characteristics is presented in this paper. The stimulator uses the CC1101 wireless module to control animal behavior through brain stimulation. The LabVIEW-based graphical user interface(GUI) can manipulate brain stimulation remotely while the stimulator powered by battery. Additionally, The spikes of animals have been simulated by this system through Direct Digital Synthesizer(DDS) algorithm. The GUI enable users to customize the combination of these analog spike signals. The recombined signals are sent to the stimulator through CC1101 as stimulus signals. In vivo experiments conducted on five pigeons verified the efficacy of the stimulation mechanism. The analog spike signal with an amplitude of 3-5V successfully caused the pigeon’s turning behavior. The feasibility of the analog spike signals as stimulus signals was successfully verifified. Increased the diversity of stimulus waveforms in the field of animal robots.
Wed, 10 November 2021
REVIEW | doi:10.20944/preprints202111.0194.v1
Subject: Biology, Other Keywords: Complexity; Evolution; Major transitions; Multicellularity; Selective driver; Environment; Size; Division of labor
Online: 10 November 2021 (08:39:39 CET)
In order to understand the evolution of multicellularity, we must understand how and why selection favors the first steps in this process: the evolution of simple multicellular groups. Multicellularity has evolved many times in independent lineages with fundamentally different ecologies, yet no work has yet systematically examined these diverse selective drivers. Here we review recent developments in systematics, comparative biology, paleontology, synthetic biology, theory, and experimental evolution, highlighting ten selective drivers of simple multicellularity. Our survey highlights the many ecological opportunities available for simple multicellularity, and stresses the need for additional work examining how these first steps impact the subsequent evolution of complex multicellularity.
Tue, 9 November 2021
REVIEW | doi:10.20944/preprints202111.0175.v1
Subject: Biology, Other Keywords: atherosclerotic cardiovascular disease (ACVD); atherosclerosis; gut dysbiosis; immune system; gut microbial metabolites; SCFAs; TMAO
Online: 9 November 2021 (13:45:20 CET)
Atherosclerosis is a leading cause of cardiovascular disease and mortality worldwide. Alterations in the gut microbiota composition, known as gut dysbiosis, have been shown to contribute to atherosclerotic cardiovascular disease (ACVD) development through several pathways. Disruptions in gut homeostasis are associated with activation of immune processes and systemic inflammation. The gut microbiota produces several metabolic products, namely trimethylamine (TMA), which is used to produce the proatherogenic metabolite trimethylamine-N-oxide (TMAO). Short chain fatty acids (SCFAs), including acetate, butyrate, and propionate, and certain bile acids (BAs) produced by the gut microbiota lead to inflammation resolution and decrease atherogenesis. Chronic low-grade inflammation is associated to common risk factors for atherosclerosis, including metabolic syndrome, type 2 diabetes mellitus (T2DM), and obesity. Novel strategies for reducing ACVD include the use of nutraceuticals such as resveratrol, modification of glucagon-like peptide 1 (GLP-1) levels, supplementation with probiotics, and administration of prebiotic SCFAs and BAs. Investigation into the relationship between the gut microbiota and its metabolites, and the host immune system could reveal promising insight into ACVD development, prognostic factors, and treatments.
Wed, 3 November 2021
REVIEW | doi:10.20944/preprints202111.0091.v1
Subject: Biology, Other Keywords: microtubule organizing center; centrosome; centriolar plaque; Plasmodium; Toxoplasma gondii; ultrastructure expansion microscopy
Online: 3 November 2021 (16:35:39 CET)
Microtubule organizing centers (MTOCs) perform critical cellular tasks by nucleating, stabilizing and anchoring microtubule’s minus ends. These capacities impact tremendously a wide array of cellular functions ranging from ascribing cell shape to orchestrating cell division and generating motile structures, among others. The phylum Apicomplexa comprises over 6000 single-celled obligate intracellular parasitic species. Many of the apicomplexan are well known pathogens such as Toxoplasma gondii and the Plasmodium species, causative agents of toxoplasmosis and malaria, respectively. Microtubule organization in these parasites is critical for organizing the cortical cytoskeleton, enabling host cell penetration and the positioning of large organelles, drive cell division and direct the formation of flagella in sexual life stages. Apicomplexans are a prime example of MTOC diversity displaying multiple functional and structural MTOCs combinations within a single species. This diversity can only be fully understood in light of each organism's specific MT nucleation requirements and their evolutionary history. Insight into apicomplexan MTOCs had traditionally been limited to classical ultrastructural work by transmission electron microscopy. However, in the past few years, a large body of molecular insight has emerged. In this work we describe the latest insights into nuclear MTOC biology in two major human and animal disease causing Apicomplexans; Toxoplasma gondii and Plasmodium spp.
Mon, 25 October 2021
ARTICLE | doi:10.20944/preprints202110.0367.v1
Subject: Biology, Other Keywords: Bacteria; culturomics; genome; species; sp. nov.,; taxono-genomics
Online: 25 October 2021 (15:47:32 CEST)
Marseille-Q4369 is a strain that we isolated from human healthy skin and characterized by taxono-genomic approach. Marseille-Q4369 exhibited 99.80% 16S rRNA sequence similarity with Agrococcus pavilionensisT the phylogenetically closest bacterium with standing in nomenclature. Furthermore, digital DNA–DNA hybridization revealed a maximum identity similarity of only 52.4% and an OrthoANI parameter provided a value of 93.63% between the novel organism and Agrococcus pavilionensisT. Marseille-Q4369 was observed to be a yellowish-pigmented, Gram-positive, coccoïd, facultative aerobic bacterium, and belonging to the Microbacteriaceae family. The major fatty acids detected are 12-methyl-tetradecanoic acid (66%), 14-methyl-hexadecanoic acid (24%) followed by 13-methyl-tetradecanoic acid (5%). The genome size of strain Marseille-Q4369 was 2,737,735-bp long with a 72,27 % G+C content. Taken altogether, these results confirm the status of this strain as a new member of the Agrococcus genus for which the name of Agrococcus massiliensis is proposed (=CSUR-Q4369 = DSM112404).
ARTICLE | doi:10.20944/preprints202110.0355.v1
Subject: Biology, Other Keywords: Deep Learning; Electrospray; Mass Spectrometry; Metabolomics; Artificial Intelligence; Generative Methods; Chemical Space; Transformers
Online: 25 October 2021 (13:20:47 CEST)
The ‘inverse problem’ of mass spectrometric molecular identification (‘given a mass spectrum, calculate/predict the 2D structure of the molecule whence it came’) is largely unsolved, and is especially acute in metabolomics where many small molecules remain unidentified. This is largely because the number of experimentally available electrospray mass spectra of small molecules is quite limited. However, the forward problem (‘calculate a small molecule’s likely fragmentation and hence at least some of its mass spectrum from its structure alone’) is much more tractable, because the strengths of different chemical bonds are roughly known. This kind of molecular identification problem may be cast as a language translation problem in which the source language is a list of high-resolution mass spectral peaks and the ‘translation’ a representation (for instance in SMILES) of the molecule. It is thus suitable for attack using the deep neural networks known as transformers. We here present MassGenie, a method that uses a transformer-based deep neural network, trained on ~6 million chemical structures with augmented SMILES encoding and their paired molecular fragments as generated in silico, explicitly including the protonated molecular ion. This architecture (containing some 400 million elements) is used to predict the structure of a molecule from the various fragments that may be expected to be observed when some of its bonds are broken. Despite being given essentially no detailed nor explicit rules about molecular fragmentation methods, isotope patterns, rearrangements, neutral losses, and the like, MassGenie learns the effective properties of the mass spectral fragment and valency space, and can generate candidate molecular structures that are very close or identical to those of the ‘true’ molecules. We also use VAE-Sim, a previously published variational autoencoder, to generate candidate molecules that are ‘similar’ to the top hit. In addition to using the ‘top hits’ directly, we can produce a rank order of these by ‘round-tripping’ candidate molecules and comparing them with the true molecules, where known. As a proof of principle, we confine ourselves to positive electrospray mass spectra from molecules with a molecular mass of 500Da or lower, including those in the last CASMI challenge (for which the results are known), getting 49/93 (53%) precisely correct. The transformer method, applied here for the first time to mass spectral interpretation, works extremely effectively both for mass spectra generated in silico and on experimentally obtained mass spectra from pure compounds. It seems to act as a Las Vegas algorithm, in that it either gives the correct answer or simply states that it cannot find one. The ability to create and to ‘learn’ millions of fragmentation patterns in silico, and therefrom generate candidate structures (that do not have to be in existing libraries) directly, thus opens up entirely the field of de novo small molecule structure prediction from experimental mass spectra.
Thu, 21 October 2021
ARTICLE | doi:10.20944/preprints202110.0303.v1
Online: 21 October 2021 (09:47:37 CEST)
Cognitive networks have evolved to cope with uncertain environments in order to make reliable decisions. Such decision making circuits need to respond to the external world in efficient and flexible ways, and one potentially general mechanism of achieving this is grounded in critical states. Mounting evidence has shown that brains operate close to such critical boundaries consistent with self-organized criticality (SOC). Is this also taking place in small-scale living systems, such as cells? Here we explore a recent model of engineered gene networks that have been shown to exploit the feedback between order and control parameters (as defined by expression levels of two coupled genes) to achieve a SOC state. We suggest that such SOC motif could be exploited to generate adaptive behavioral patterns and might help design fast responses in synthetic cellular and multicellular organisms.
Mon, 18 October 2021
REVIEW | doi:10.20944/preprints202110.0258.v1
Subject: Biology, Other Keywords: phylogeny estimation; multiple sequence alignment; phylogenetic placement; phylogenomics; taxon identification; maximum likelihood
Online: 18 October 2021 (15:43:34 CEST)
With the increased availability of sequence data and even of fully sequenced and assembled genomes, phylogeny estimation of very large trees (even of hundreds of thousands of sequences) is now a goal for some biologists. Yet, the construction of these phylogenies is a complex pipeline presenting analytical and computational challenges, especially when the number of sequences is very large. In the last few years, new methods have been developed that aim to enable highly accurate phylogeny estimations on these large datasets, including divide-and-conquer techniques for multiple sequence alignment and/or tree estimation, methods that can estimate species trees from multi-locus datasets while addressing heterogeneity due to biological processes (e.g., incomplete lineage sorting and gene duplication and loss), and methods to add sequences into large gene trees or species trees. Here we present some of these recent advances and discuss opportunities for future improvements.
Fri, 8 October 2021
Subject: Biology, Other Keywords: natural products; biosynthetic gene clusters; synthetic biology; genome mining strategies; modification strategies; design-build-test-learn (DBTL) cycle
Online: 8 October 2021 (09:10:02 CEST)
A wide variety of bacteria, fungi and plants can produce bioactive secondary metabolites, which are often referred to as natural products. With the rapid development of DNA sequencing technology and bioinformatics, a large number of putative biosynthetic gene clusters have been reported. However, only a few natural products can be detected when isolated species are grown under conventional laboratory conditions, as most biosynthetic gene clusters are not expressed or are expressed at extremely low levels at these conditions. With the rapid development of synthetic biology, advanced genome mining and modification strategies have been reported, and they provide new opportunities for discovery of natural products. This review discusses advances in recent years that can accelerate the design, build, test, and learn (DBTL) cycle of natural product discovery, and prospects trends and key challenges for future research directions.
Fri, 1 October 2021
REVIEW | doi:10.20944/preprints202110.0026.v1
Subject: Biology, Other Keywords: Halotolerant/halophilic fungi; Hortaea werneckii; Wallemia ichthyophaga; HOG signal transduction Pathway
Online: 1 October 2021 (14:52:54 CEST)
Sensing and responding to changes in NaCl concentration in hypersaline environments is vital for cell survival. We have identified and characterized key components of the high-osmolarity glycerol (HOG) signal transduction pathway, which is crucial in sensing hypersaline conditions in the extremely halotolerant black yeast Hortaea werneckii and in the obligate halophilic fungus Wallemia ichthyophaga. Both organisms were isolated from solar salterns, their predominating ecological niche. The identified components included homologous proteins of both branches involved in sensing high osmolarity (SHO1 and SLN1) and the homologues of mitogen-activated protein kinase module (MAPKKK Ste11, MAPKK Pbs2, and MAPK Hog1). Functional complementation of the identified gene products in S. cerevisiae mutant strains revealed some of their functions. Structural protein analysis demonstrated important structural differences in the HOG pathway components between halotolerant/halophilic fungi isolated from solar salterns, salt-sensitive S. cerevisiae, the extremely salt-tolerant H. werneckii, and halophilic W. ichthyophaga. Known and novel gene targets of MAP kinase Hog1 were uncovered particularly in halotolerant H. werneckii. Molecular studies of many salt-responsive proteins confirm unique and novel mechanisms of adaptation to changes in salt concentration.
Subject: Biology, Other Keywords: Trypanosoma brucei; cytoskeleton; microtubules; BioID; mass spectrometry
Online: 1 October 2021 (14:04:33 CEST)
Trypanosome brucei, the causative agent of African sleeping sickness, harbours a highly ordered, subpellicular microtubule cytoskeleton that defines many aspects of morphology, motility and virulence. This array of microtubules is associated with a large number of proteins involved in its regulation. Employing proximity-dependent biotinylation assay (BioID) using the well characterized cytoskeleton-associated protein CAP5.5 as a probe we identified CAP50 (Tb927.11.2610). This protein colocalizes with the subpellicular cytoskeleton microtubules but not with the flagellum. Depletion by RNAi results in defects in cytokinesis, morphology and partial disorganization of microtubule arrays. Published proteomics data indicate a possible association of CAP50 with two other, yet uncharacterized, cytoskeletal proteins, CAP52 (Tb927.6.5070) and CAP42 (Tb927.4.1300), which were therefore included in our analysis. We show that their depletion causes phenotypes similar to those described for CAP50 and that they are essential for cellular integrity.
Thu, 30 September 2021
CONCEPT PAPER | doi:10.20944/preprints202109.0530.v1
Subject: Biology, Other Keywords: energy; homeostasis; neural network; behavior; free energy principle
Online: 30 September 2021 (17:49:37 CEST)
Explaining the emergence of behavior and understanding on the basis of neuronal mechanisms is still elusive. One renowned proposal is the Free Energy Principle (FEP), which uses an information-theoretic framework derived from thermodynamic considerations to describe how behavior and understanding would emerge. FEP starts from a whole organism approach, based on mental states and phenomena, mapping them into the neuronal substrate. An alternative approach, the Energy Homeostasis Principle (EHP), initiates a similar explanatory effort, but starting from single neuron phenomena and building up to the whole organism’s behavior and understanding. In this work, we develop the EHP as an alternative but complementary vision to FEP and try to explain how behavior and understanding would emerge from the local requirements of the neurons. Based on EHP and a strict naturalist approach that sees living beings as physical and deterministic systems, we explain scenarios where learning would emerge without the need for volition or goals. Given these starting points, we state several considerations of how we see the nervous system, particularly the role of function, purpose, and the conception of goal-oriented behaviors. We problematize these conceptions, giving an alternative teleology-free framework in which behavior and, ultimately, understanding would still emerge. We reinterpret neural processing explaining basic learning situations up to simple anticipatory behavior. Finally, we end the work with an evolutionary perspective of how this non-goal-oriented behavior appears. We acknowledge that in the current form of our proposal, we are still far from explaining the emergence of understanding. Still, we set the ground for an alternative neuron-based framework to ultimately explain understanding.
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.
Fri, 17 September 2021
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.
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.
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.
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.
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/preprints202109.0113.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.
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.
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
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.
Wed, 25 August 2021
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.
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.
Mon, 26 July 2021
ARTICLE | doi:10.20944/preprints202107.0554.v1
Subject: Biology, Other Keywords: SARS-CoV-2; ORF10; Co-mutations; Intrinsic Protein Disorder; Ubiquitin Ligase Complex
Online: 26 July 2021 (09:07:38 CEST)
The devastating impact of the ongoing coronavirus disease 2019 (COVID-19) on public health, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has made fighting of the COVID-19 pandemic is a top priority in medical research and pharmaceutical development. Surveillance of SARS-CoV-2 mutations is essential for the comprehension of SARS-CoV-2 variant diversity and their impact on virulence and pathogenicity. The SARS-CoV-2 open reading frame 10 (ORF10) protein interacts with multiple human proteins CUL2, ELOB, ELOC, MAP7D1, PPT1, RBX1, THTPA, TIMM8B, and ZYG11B expressed in the lung tissues. Mutations and co-mutations in the emerging SARS-CoV-2 ORF10 variants are expected to impact the severity of the virus and its associated consequences. In this article, We highlight 128 single mutations and 35 co-mutations in the unique SARS-CoV-2 ORF10 variants in this article. The possible predicted effects of these mutations and co-mutations on the secondary structure of ORF10 variants and host protein interactomes are presented. The findings highlight the possible effects of mutations and co-mutations on the emerging 140 ORF10 unique variants from secondary structure and intrinsic protein disorder perspectives.
Mon, 12 July 2021
REVIEW | doi:10.20944/preprints202107.0237.v1
Online: 12 July 2021 (09:38:48 CEST)
Microorganisms including actinomycetes, archaea, bacteria, fungi, yeast, and micro algae are the auspicious source of vital bioactive compounds. In this review, the existing state of the art re-garding antimicrobial molecules from microorganisms has been summarized. The potential an-timicrobial compounds from actinomycetes, particularly Streptomyces sp.; archaea; fungi including endophytic and marine-derived fungi, mushroom; yeast, and microalgae were briefly described. Furthermore, this review briefly summarized the activity and mode of action of bacteriocins, a ribosomally synthesized antimicrobial peptides product of Eurotium sp., Streptomyces parvulus, S. thermophiles, Lactococcus lactis, etc. Bacteriocins have inherent properties such as targeting multi-ple-drug resistant pathogens, which allows them to be considered next-generation antibiotics. Similarly, Glarea lozoyensis derived antifungal lipohexpeptides i.e., pneumocandins, inhibits 1,3-β-glucan synthase of the fungal cell wall and acts as a precursor for the synthesis of caspo-fungin, is also elaborated. In conclusion, this review highlights the possibility of using microor-ganisms as an antimicrobial resource for biotechnological, nutraceutical, and pharmaceutical ap-plications. However, more investigations are still required to separate, purify, and characterize these bioactive compounds and transfer these primary drugs into clinically approved antibiotics.
Wed, 9 June 2021
ARTICLE | doi:10.20944/preprints202106.0257.v1
Subject: Biology, Other Keywords: Extracellular vesicles (EVs); mRNA; fungal pathogen; plant pathogen; Ustilago maydis
Online: 9 June 2021 (10:59:36 CEST)
Extracellular vesicles (EVs) can transfer diverse RNA cargo for intercellular signalling. EV-associated RNAs have been found in diverse fungi and were proposed to be relevant for pathogenesis in animal hosts. In plant-pathogen interactions, small RNAs are exchanged in a cross-kingdom RNAi warfare and EVs were considered to be a delivery mechanism. To extend the search for EV-associated molecules involved in plants-pathogen communication, we have characterised the repertoire of EV-associated mRNAs secreted by the maize smut pathogen, Ustilago maydis. For this initial survey, EVs were isolated from axenic filamentous cultures that mimic infectious hyphae. The EV-associated RNAs were resistant to degradation by RNases and the presence of intact mRNAs was evident. The set of mRNAs enriched inside EVs relative to the fungal cells are functionally distinct from those that are depleted from EVs, particularly overrepresented in metabolic enzyme activities. Intriguingly, mRNAs of some known effectors and other proteins linked to virulence were found in EVs. Furthermore, several mRNAs enriched in EVs are also upregulated during infection, suggesting that EV-associated mRNAs may participate in plant-pathogen interaction.
ARTICLE | doi:10.20944/preprints202106.0256.v1
Online: 9 June 2021 (10:58:20 CEST)
Abstract: Oxidative metabolism is crucial for leukemic stem cell (LSC) function and drug resistance in acute myeloid leukemia (AML). Mitochondrial metabolism also affects the immune system and therefore the antitumor response. Modulation of oxidative phosphorylation (OxPHOS) has emerged as a promising approach to improve therapy outcome for AML patients. However, the effect of mitochondrial inhibitors on the immune compartment in the context of AML is yet to be explored. Immune checkpoints such as the ecto-nucleotidase CD39 and programmed dead ligand 1 (PD-L1) have been reported to be expressed in AML and linked to chemoresistance and poor prognosis. In the present study, we first demonstrated that a novel selective electron transfer chain complex (ETC) I inhibitor, EVT-701, decreased OxPHOS metabolism of murine and human cytarabine (AraC)-resistant leukemic cell lines. Furthermore, we showed that, while AraC induced immune response regulation by increasing CD39 expression and by reinforcing interferon-γ/PD-L1 axis, EVT-701 reduced CD39 and PD-L1 expression in vitro in a panel of both murine and human AML cell lines, especially upon AraC treatment. Altogether, this work uncovers a non-canonical function of ETCI in controlling CD39 and PD-L1 immune checkpoints, thereby improving the anti-tumor response in AML.
Tue, 8 June 2021
ARTICLE | doi:10.20944/preprints202106.0229.v1
Subject: Biology, Other Keywords: The Gulf of Mottama Wetland, Morphometric measurement, catch weight, size group
Online: 8 June 2021 (13:15:52 CEST)
The present study was conducted the status of sea bass from Kokko and Kyuntone of The Gulf of Motttama Wetland (GoMW) area in Thanatpin Township in Bago Region Myanmar from September 2019 to August 2020. Fifty specimens were monthly collected, measured and weighed. Invoices of sea bass were collected for the depot and fish sellers by monthly. In Kokko, mean value of standard length and body weight were highest in March (32.70±1.58, 660.7±112.23). The mean value of standard length was peak in January (31.39±7.16) but peak of body weight was in March (963.24±280.86) in Kyuntone villages. The lowest mean value of standard length and body weight were found in June at both study areas. According to the invoice data revealed that monthly catch weight of sea bass is most abundance in October (829.92) kg in Kokko, (339.12) kg in Kyuntone. Based on price of relations to size group, small size C < 300g (41%) was mostly abundance in Kokko and in Kyuntone small size C < 300g (35%) was second abundance. Specimens were not landed in April and May. In June, young specimens were very rarely seen in both study sites. The important roles of wetland fishes, the economic valuation of GOMW in Myanmar and samples of fishing gear and value chain of sea bass in Myanmar was expressed in this study.
Mon, 7 June 2021
REVIEW | doi:10.20944/preprints202106.0163.v1
Subject: Biology, Other Keywords: white biotechnology; metabolic engineering; non-conventional yeast; oleaginous yeast; cell factory; heterologous expression; biodiversity; Yarrowia lipolytica; Yarrowia clade; GMO
Online: 7 June 2021 (10:50:26 CEST)
Among non-conventional yeasts of industrial interest, the dimorphic oleaginous yeast Yarrowia lipolytica appears as one of the most attractive for a large range of white biotechnology applications, from heterologous proteins secretion to cell factories process development. The past, present and potential applications of wild type, traditionally improved or genetically modified Yarrowia lipolytica strains will be resumed, together with the wide array of molecular tools now available to genetically engineer and metabolically remodel this yeast. The present review will also provide a detailed description of Yarrowia lipolytica strains and highlight the natural biodiversity of this yeast, a subject little touched upon in most previous reviews. This work intends to fill this gap by retracing the genealogy of the main Yarrowia lipolytica strains of industrial interest, by illustrating the search for new genetic backgrounds and by providing data about the main publicly available strains in yeast collections worldwide. At last, it will focus on exemplifying how advances in engineering tools can leverage a better biotechnological exploitation of the natural biodiversity of Yarrowia lipolytica and of other yeasts from the Yarrowia clade.
Wed, 2 June 2021
ARTICLE | doi:10.20944/preprints202106.0047.v1
Online: 2 June 2021 (07:19:08 CEST)
A field experiment was conducted during Kharif 2018, laid out in Randomized Block Design with three replications having seven treatments viz. N omission (T1), N applied as basal and AT (T2), N as basal, AT and PI (T3), N as basal and top dressing at NDVI threshold of 0.75 (T4), at NDVI threshold of 0.8 (T5), at SPAD threshold of 35.0 (T6) and SPAD threshold of 37.5 (T7) with Rice variety Sahabhagidhan.The study revealed that application of 30 kg N/ha as basal dose and top dressing of 20 kg N/ha twice at 35 and 63 DAS guided by NDVI threshold value of 0.8 (T5) was found to be superior over other treatments with respect to productivity. T5 recorded highest grain yield of 4438 kg/ha which was 17.0% higher than that top dressed at NDVI threshold of 0.75 (T4) and 7.1% higher than that top dressed at SPAD threshold value of 37.5 (T7). In case of SPAD meter, nitrogen top dressed at threshold value of 37.5 (T7) produced grain yield of 4143 kg/ha which was 15.0% higher than T6. T5 produced maximum dry matter of 8678 kg/ha with highest grain yield (4438 kg/ha), straw yield (5092 kg/ha) and harvest index 46.0%.
Thu, 27 May 2021
COMMUNICATION | doi:10.20944/preprints202105.0679.v1
Online: 27 May 2021 (14:14:20 CEST)
The study aimed to identify different molds that grow on various food surfaces. As a result, we conducted a case study for the detection of mold on food surfaces based on the “you only look once (YOLO) v5” principle. In this context, a dataset of 2050 food images with mold growing on their surfaces was created. The dataset was trained using the pre-trained YOLOv5 algorithm. In comparison to YOLOv3 and YOLOv4, this current YOLOv5 model had better precision, recall, and average precision (AP), which were 98.10%, 100%, and 99.60%, respectively. The YOLOv5 algorithm was used for the first time in this study to detect mold on food surfaces. In conclusion, the proposed model successfully recognizes any kind of mold present on the food surface. Using YOLOv5, we are currently conducting research to identify the specific species of the detected mold.
Mon, 24 May 2021
REVIEW | doi:10.20944/preprints202105.0572.v1
Subject: Biology, Other Keywords: microalgae; marine bacteria; quorum sensing signals; alkyl quinolones; microbial loop
Online: 24 May 2021 (13:34:11 CEST)
Quorum sensing (QS) describes a process by which bacteria can sense the local cell density of their own species, thus enabling them to coordinate gene expression and physiological processes on a community-wide scale. Small molecules called autoinducers or QS signals, which act as intraspecies signals, mediate quorum sensing. As our knowledge of QS has progressed, so too has our understanding of the structural diversity of QS signals, along with the diversity of bacteria conducting QS and the range of ecosystems in which QS takes place. It is now also clear that QS signals are more than just intraspecies signals. QS signals mediate interactions between species of prokaryotes, and between prokaryotes and eukaryotes. In recent years, our understanding of QS signals as mediators of algae–bacteria interactions has advanced such that we are beginning to develop a mechanistic understanding of their effects. This review will summarize the recent efforts to understand how different classes of QS signals contribute to the interactions between planktonic microalgae and bacteria in our oceans, primarily N-acyl-homoserine lactones, their degradation products tetramic acids, and 2-alkyl-4-quinolones. In particular, this review will discuss the ways in which QS signals alter microalgae growth and metabolism, namely as direct effectors of photosynthesis, regulators of the cell cycle, and as modulators of other algicidal mechanisms. Furthermore, the contribution of QS signals to nutrient acquisition is discussed, and finally how microalgae can modulate these small molecules to dampen their effects.
Mon, 17 May 2021
ARTICLE | doi:10.20944/preprints202105.0394.v1
Subject: Biology, Other Keywords: Modularity; Protein-to-protein interaction networks; Spectral characterization; Tree of life
Online: 17 May 2021 (16:56:57 CEST)
Modularity and organizational hierarchy are important concepts in understanding the structure and evolution of interactions in complex biological systems. In this work, we introduce and use a spectral characterization measure (Spectral Entropy) to quantify modularity in protein-to-protein interaction (PPI) networks in species across the tree of life. We evaluated the relation between the size of a PPI network and its (Spectral Entropy-based) modularity, and found a sigmoidal response between the two. We also found significant differences in the distribution of Spectral Entropy values among the three domains of life (Bacteria, Archaea, Eukaryotes). To explore further correlations with biological traits, we focused solely on bacterial PPI networks, which are the most numerous among the three domains and had associated trait metadata, and investigated how modularity impacts or is impacted by growth, aerobicity, selection and location on the tree of life. We found no relation between maximal growth rate and Spectral Entropy, but a strong dependence between G-C content (a proxy for selection) and Spectral Entropy. We also discovered that Spectral Entropy is negatively affected by phylogenetic placement (evolutionary distance from the last universal common ancestor). The general nature of the Spectral Entropy measure of hierarchical modularity in networks suggests that it will be useful in other settings where structural properties of real-world networks are being compared.
Thu, 6 May 2021
ARTICLE | doi:10.20944/preprints202105.0088.v1
Subject: Biology, Other Keywords: highly pathogenic avian influenza viruses, pathogenicity factors.
Online: 6 May 2021 (13:18:14 CEST)
The H7 subtype of avian influenza viruses (AIV) stands out among other AIV. H7 viruses circulate in ducks, poultry, equine and have repeatedly caused outbreaks of disease in humans. In order to study the pathogenicity factors of H7N1 viruses, several laboratory variants of the A/FPV/Rostock/34 (H7N1) strain were obtained by passages in the chicken lungs. After 10 such passages, a variant was obtained that differed from the parent virus by amino acid substitutions Val109Phe in PB2, Gln621Lys in PB1, Thr32Ala and Leu586Phe in PA Gly140Arg in HA1 and Ala101Thr in HA2 (numbering by H3), Ser82Arg in M2, Arg118Lys and Met124Arg in NS1. No differences were found in proteins NA, NP, M1 and NS2. The resulting variant was hundreds of times more pathogenic for chickens than the original laboratory variant of the virus. The study of intermediate passages showed that the jump in pathogenicity occurs sharply between the fifth and sixth passage through the chicken lungs. By cloning these variants, a pair of strains (R5p and R6p) were obtained, and the complete genomes of these strains were sequenced. Single amino acid substitution was revealed, namely Gly140Arg in HA1. It is important to emphasize that this substitution is a reversion, since Arg is located in position 140 HA1 of original the A/FPV/Rostock/34 (H7N1) virus (GenBank). This amino acid is located at the head part of the hemagglutinin, adjacent to the receptor-binding site. In addition to the increased pathogenicity, R6p differs from R5p by an increased affinity for a negatively charged receptor analogue, an increased affinity for MDCK cells, while maintaining a receptor specificity profile.
Fri, 16 April 2021
ARTICLE | doi:10.20944/preprints202104.0443.v1
Subject: Biology, Other Keywords: Fluoroquinolones; Ciprofloxacin; Untargeted Metabolomics; Mycobacterium tuberculosis; Tuberculosis; GCxGC-TOFMS
Online: 16 April 2021 (11:28:54 CEST)
In the interest of developing more effective and safer anti-Tuberculosis treatment, we aimed for a better understanding of the antimycobacterial action of ciprofloxacin against Mycobacterium tuberculosis (Mtb). We used GCxGC-TOF-MS and well described metabolomics statistical approaches, to investigate and compare the metabolic profiles of Mtb in the presence and absence of the drug. The metabolites that best describe the differences between the compared groups were identified as markers characterizing the changes induced by ciprofloxacin. Malic acid was ranked as the most significantly altered metabolite marker induced by ciprofloxacin, indicative of an inhibition of the tricarboxylic acid (TCA) and glyoxylate cycle of Mtb. The altered fatty acid, myo-inositol and triacylglycerol metabolism seen in this group, supports the previous observations of ciprofloxacin action on the Mtb cell wall. Furthermore, the altered pentose phosphate intermediates, glycerol metabolism markers, glucose accumulation, and the reduction in the glucogenic amino acids specifically, indicates a flux towards DNA (as well as cell wall) repair, also supporting previous findings of DNA damage caused by ciprofloxacin. This study further provides insights useful for designing network whole-system strategies for the identification of possible modes of actions of various drugs and possibly adaptations by Mtb resulting in resistance.
Mon, 12 April 2021
ARTICLE | doi:10.20944/preprints202104.0324.v1
Subject: Biology, Other Keywords: lipids; cerebrospinal fluid, parkinson´s disease, mass-spectrometry, lipidomics
Online: 12 April 2021 (21:16:21 CEST)
Lipid metabolism is clearly associated to Parkinson´s disease (PD). Although lipid homeostasis has been widely studied in multiple animal and cellular models as well as in blood derived from PD individuals, the cerebrospinal fluid (CSF) lipidomic profile in PD remains largely unexplored. In this study, we have characterized the CSF lipidomic imbalance between neurologically intact controls (n=10) and PD subjects (n=20). The combination of dual extraction with ultra-performance liquid chromatography-electrospray ionization quadrupole-time-of-flight mass spectrometry (UPLC-ESI-qToF-MS/MS) allowed to monitor 257 lipid species across all samples. Complementary multivariate and univariate data analysis pointed out that glycerolipids (mono-, di-, and triacylglycerides), saturated and mono/polyunsaturated fatty acids, primary fatty amides, glycerophospholipids (phosphatidylcholines, phosphatidylethanolamines), sphingolipids (ceramides, sphingomyelins), N-acylethanolamines and sterol lipids (cholesteryl esters, steroids) were significantly increased in the CSF of PD compared to control group. These results, despite the limitation of being obtained in a small population, demonstrate and extensive CSF lipid remodelling in PD, shedding new light on the deployment of CSF lipidomics as a promising tool to identify potential lipid markers as well as discriminatory lipid species between PD and other atypical parkinsonisms.
Wed, 24 February 2021
REVIEW | doi:10.20944/preprints202102.0541.v1
Subject: Biology, Other Keywords: Functional food components, Dietary miRNA, XenomiRs, dietary supplementation therapy
Online: 24 February 2021 (10:11:26 CET)
Exogenous miRNAs derived from dietary substances have been shown to be orally transferred to the mammalian system and proven to remain active to regulate host-gene expression. This way they have become an active area of research as functional food components and aspects for dietary supplementation. They are being studied as a new class of metabolically targeted therapeutics that work through diet manipulation and may hold promise for a therapeutic approach in reducing the risk of life-threatening diseases. However, a substantial amount of evidence also defies this dietary miRNA concept in terms of their absorption, bioavailability, cellular uptake and its physiological effects in the mammalian system. But recent advances in the identification of some unique sequence and structural characteristics of dietary miRNAs and a deeper understanding of their stability in host peripheral blood for its cellular uptake have strengthened the whole concept. The review comprehensively summarizes the mechanism for miRNA extracellular transport, absorption through the gastrointestinal tract (GI), stability in peripheral blood, and cellular uptake in mammalian cells. It recapitulates the shreds of evidence, related to the influence of dietary miRNAs on gene expression based on the source of the origin (plant vs animal), and compares their cross-kingdom behaviour in terms of their unique sequence and stem-loop structure properties that help them to get stabilized in the mammalian system. The review also summarizes the parameters required for maintaining the sustainable uptake and bioavailability of the dietary miRNAs with existing examples of successful in-vivo and in-vitro delivery of dietary miRNA for augmented therapy. Lastly, it provides an overview of the available and required databases, webserver, and tools that can be used for the successful identification of potential dietary miRNA candidates.
Mon, 21 December 2020
Online: 21 December 2020 (11:29:19 CET)
The history of life on Earth has been shaped by a series of major evolutionary innovations. While some of these innovations occur repeatedly (e.g., multicellularity), some of the most important evolutionary innovations (e.g., the origin of life itself, eukaryotes, or the genetic code) are evolutionary singularities, arising just once in the history of life. This historical fact has often been interpreted to mean that singularities are particularly difficult, low-probability evolutionary events, thus making the long-term course of life on Earth highly contingent on their chance appearances. Alternatively, singularities may arise from evolutionary priority effects, where first-movers suppress independent origins. In this paper, we disentangle these hypotheses by examining a distinctive innovation: phototrophy. The ability to use light to generate metabolic energy evolved twice, preserving information about the evolution of rare, transformative innovations that is lost in singularities. We show that the two forms of phototrophy occupy opposite ends of several key trade-offs: efficiency of light capture vs. return on investment in photosynthetic infrastructure, dependence on limiting nutrients vs. metabolic versatility, and complexity vs. simplicity. Our results suggest that phototrophy is a 'dual singularity' because phototrophic niche space is too large for the first mover to fully suppress future innovation, but not so large as to support many innovations. While often ignored over geological time scales, ecological interactions, in particular the potential for direct competition and priority effects, plays a fundamental role in the tempo and mode of major evolutionary innovations.
Tue, 15 December 2020
Subject: Biology, Other Keywords: SARS-CoV-2; COVID-19 pandemic; food industry; disinfection trade-offs; one-health
Online: 15 December 2020 (12:58:18 CET)
Industries of the food sector have made a great effort to control SARS-CoV-2 indirect transmission, through objects or surfaces, by updating cleaning and disinfection protocols previously focused on inactivating other pathogens, as well as food spoilage microorganisms. The information, although scarce at the beginning of the COVID-19 pandemic, has started to be sufficiently reliable to avoid over-conservative disinfection procedures. This work reviews the literature to propose a holistic view of the disinfection process where the decision variables, such as type and concentration of active substance, are optimised to guarantee the inactivation of SARS-CoV-2 and other usual pathogens and spoilage microorganisms while minimising possible side-effects on the environment and animal and human health.
Mon, 7 December 2020
REVIEW | doi:10.20944/preprints202007.0613.v3
Subject: Biology, Other Keywords: infective dose; SARS-CoV-2; COVID-19; respiratory viruses; viral load; viral dynamics
Online: 7 December 2020 (11:36:05 CET)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pandemic. Prevention and control strategies require an improved understanding of SARS-CoV-2 dynamics. We did a rapid review of the literature on SARS-CoV-2 viral dynamics with a focus on infective dose. We sought comparisons of SARS-CoV-2 with other respiratory viruses including SARS-CoV-1 and MERS-CoV. We examined laboratory animal, and human studies. The literature on infective dose, transmission, and routes of exposure was limited specially in humans, and varying endpoints were used for measurement of infection. We propose the minimum infective dose of COVID-19 in humans, is higher than 100 particles, possibly slightly lower than the 700 particles estimated for H1N1 influenza. Despite variability in animal studies, there was some evidence that increased dose at exposure correlated with higher viral load clinically, and severer symptoms. Higher viral load measures did not reflect COVID-19 severity. Aerosol transmission seemed to raise the risk of more severe respiratory complications in animals. An accurate quantitative estimate of the infective dose of SARS-CoV-2 in humans is not currently feasible and needs further research. Further work is also required on the relationship between routes of transmission, infective dose, co-infection, and outcomes.
Fri, 27 November 2020
REVIEW | doi:10.20944/preprints202011.0689.v1
Subject: Biology, Other Keywords: Plasmodium vivax; Erythrocyte Invasion Mechanisms; Duffy Negative; Africa; Immunology; Epidemiology
Online: 27 November 2020 (13:08:59 CET)
Plasmodium vivax malaria is a neglected tropical disease, despite being more geographically widespread than any other form of malaria. The documentation of P. vivax infections in different parts of Africa where Duffy-negative individuals are predominant suggested that there are alternative pathways for P. vivax to invade human erythrocytes. Duffy-negative individuals may be just as fit as Duffy-positive individuals and are no longer resistant to P. vivax malaria. In this review, we describe the complexity of P. vivax malaria, characterize pathogenesis and candidate invasion genes of P. vivax, and host immune responses to P. vivax infections. We provide a comprehensive review on parasite ligands in several Plasmodium species that further justify candidate genes in P. vivax. We also summarize previous genomic and transcriptomic studies related to the identification of ligand and receptor proteins in P. vivax erythrocyte invasion. Finally, we identify topics that remain unclear and propose future studies that will greatly contribute to our knowledge of P. vivax.
Mon, 16 November 2020
HYPOTHESIS | doi:10.20944/preprints202008.0607.v2
Subject: Biology, Other Keywords: catalysis; kinetics; time; biological macromolecular enzyme; large biological macro-substrate; catalytic step; catalytic efficiency; turnover number
Online: 16 November 2020 (08:28:55 CET)
Classical enzyme kinetics are summarized and linked with modern discoveries here. The time course of sequential catalytic events by biological macromolecular enzyme is analyzed at the molecular level; the relationships between catalytic efficiency (turnover number), catalytic rate/velocity, the amount of time taken and physical/biochemical conditions of the system are discussed. This writing tries to connect the microscopic molecular behavior of enzyme to kinetic data obtained in experiment, and the hypothesis proposed here provide an interpretation to previous experimental observations and can be testified by future experiments.
Mon, 2 November 2020
REVIEW | doi:10.20944/preprints202011.0069.v1
Subject: Biology, Other Keywords: Fibroblasts; Rheumatoid Arthritis; Cancer; Metabolic Reprogramming; Glycolytic Switch; Systems Biology; Computational Modelling
Online: 2 November 2020 (19:28:02 CET)
Fibroblasts, the most abundant cells in the connective tissue, are key modulators of the extracellular matrix (ECM) composition. These spindle-shaped cells are capable of synthesizing various extracellular matrix proteins and collagen. They also provide the structural framework (stroma) for tissues and play a pivotal role in the wound healing process. While they are maintainers of the ECM turnover and regulate several physiological processes, they can also undergo transformations responding to certain stimuli and display aggressive phenotypes that contribute to disease pathophysiology. In this review, we focus on the metabolic pathways of glucose and highlight metabolic reprogramming as a critical event that contributes to the transition of fibroblasts from quiescent to activated and aggressive cells. We also cover the emerging evidence that allows us to draw parallels between fibroblasts in autoimmune disorders and more specifically in rheumatoid arthritis and cancer. We link the metabolic changes of fibroblasts to the toxic environment created by the disease condition and discuss how targeting of metabolic reprogramming could be employed in the treatment of such diseases. Lastly, we discuss Systems Biology approaches, and more specifically, computational modelling, as a means to elucidate pathogenetic mechanisms and accelerate the identification of novel therapeutic targets.
Wed, 23 September 2020
ARTICLE | doi:10.20944/preprints202009.0550.v1
Subject: Biology, Other Keywords: Heat; Heatwave; Cardiovascular diseases; Respiratory diseases; Hospital admissions; Climate change; ambient temperature; Public health; time series; summer months
Online: 23 September 2020 (10:32:12 CEST)
There is a lack of knowledge concerning the effects of ambient heat exposure on morbidity in Northern Europe. Therefore, this study aimed to evaluate the relationships of daily summer-time temperature and heatwaves with cardiorespiratory hospital admissions in the Helsinki metropolitan area, Finland. Methods: Time-series models adjusted for potential confounders such as air pollution were used to investigate the associations of daily temperature and heatwaves with cause-specific cardiorespiratory hospital admissions, during summer months of 2001-2017. Daily number of hospitalizations was obtained from the national hospital discharge register, weather information from the Finnish Meteorological Institute. Results: Increased daily temperature was associated with decreased risk of total respiratory hospital admissions and asthma. Heatwave days were associated with 20.5% (95% CI: 6.9, 35.9) increased risk of pneumonia admissions and during long or intense heatwaves also with total respiratory admissions in the oldest age group (≥ 75 years). There were also suggestive positive associations between heatwave days and admissions due to myocardial infarction and cerebrovascular diseases. In contrast, risk of arrhythmia admissions was decreased 20.8% (95% CI: 8.0, 31.8) during heatwaves. Conclusions: Heatwaves, rather than single hot days, are a health threat affecting the morbidity even in a Northern climate.
Tue, 22 September 2020
Subject: Biology, Other Keywords: historical kinds; individuation; cultural evolution; evolutionary innovation
Online: 22 September 2020 (08:45:54 CEST)
Two welcome extensions of evolutionary thinking have come to prominence over the last thirty years: the so-called “extended evolutionary synthesis” (EES) and debate about biological kinds and individuals. These two agendas have, however, remained orthogonal to one another. The EES has mostly restricted itself to widening the explanations of adaptation offered by the preceding “modern evolutionary synthesis” by including additional mechanisms of inheritance and variation; while discussion of biological kinds has turned toward philosophical questions of essential vs. contingent properties of life forms and realist vs. epistemological approaches to categorization and classification. Here we attempt to broaden the explanatory scope of evolutionary theory by linking these two agendas. We expand on the mechanistic orientation of the EES, using new understandings of networked systems of components in order to engage the distinct intellectual challenge of the origination of historical kinds. With this phrase we designate a subset of natural kinds that acquires, through evolutionary processes, a quasi-independent lineage-history. Such kinds emerge in both biology and culture, and we enlarge the limited number of historical kinds that have thus far been recognized in evolutionary biology in a series of paradigmatic exemplars, from genes and cell types to rituals and music. For each exemplar we discern specific mechanisms by which it arose and persists; comparing these, we suggest a general unity in the ways in which diverse historical kinds originate.
Mon, 21 September 2020
REVIEW | doi:10.20944/preprints202009.0490.v1
Subject: Biology, Other Keywords: base editing; prime editing; ABE; SCD; sickle cell disease; sickle cell anemia; CRISPR; Cas9
Online: 21 September 2020 (04:23:21 CEST)
Sickle cell disease is characterized by stiff, “sickled” red blood cells that have difficulty moving through the bloodstream and do not efficiently carry oxygen. It is an inherited disease with severely limited treatment options, and is caused by a point mutation. Its prevalence in black and brown communities makes the already limited treatment options even less accessible. Base editing and prime editing are two relatively recent discoveries in the field of genome editing and were developed after the groundbreaking discovery of the CRISPR Cas9 system. While not fully tested, they hold a lot of promise in providing alternative treatment options for sickle cell disease. Both editing systems are able to install individual point mutations in the beta globin gene, which is where the sickle cell mutation occurs, and can thus cure sickle cell disease (in theory). In this paper we outline the mechanisms of CRISPR-Cas9 systems and base and prime editing, and provide insight into how to apply them to treat SCD. Further investigation should be done on specific editing systems and designs to use to ensure optimal treatment of SCD.
Sun, 20 September 2020
ARTICLE | doi:10.20944/preprints202009.0475.v1
Subject: Biology, Other Keywords: Nile tilapia; Oreochromis niloticus; liver; duckweed; Lemna minor; Cu; Zn; Glutathione Peroxidase; GPx; Glutathione-S-Transferase; GST; Superoxide dismutase; SOD; Catalase; CAT; remediation assessment
Online: 20 September 2020 (14:41:41 CEST)
A two-fold integrated research study was conducted; firstly, to understand effects of copper (Cu) and zinc (Zn) on the growth and oxidative stress in Nile tilapia, Oreochromis niloticus; secondly, to study the beneficial effects of the duckweed Lemna minor L. as a heavy metal remover from wastewater. Experiments were conducted in mesocosms with and without duckweed. Tilapia fingerlings were exposed to Cu (0.004 and 0.02 mg/L) and Zn (0.5 and 1.5 mg/L) and fish fed for four weeks. We evaluated the fish growth performance, the hepatic DNA structure using comet assay, the expression of antioxidative genes (superoxide dismutase, SOD; catalase, CAT; glutathione peroxidase, GPx and glutathione-S-transferase, GST) and GPx and GST enzymatic activity. The results showed that Zn exhibited more pronounced toxic effects than Cu. Low dose of Cu did not influence the growth whereas higher doses of Cu and Zn significantly reduced the growth rate of tilapia compared to control, but addition of duckweed prevented weight loss. Further, in the presence of a high dose of Cu and Zn, DNA damage decreased, antioxidant gene expressions and enzymatic activities increased. In conclusion, results suggest that duckweed and Nile tilapia can be suitable candidates in metal remediation wastewater assessment programs.
Sat, 19 September 2020
ARTICLE | doi:10.20944/preprints202009.0459.v1
Online: 19 September 2020 (11:34:12 CEST)
The COVID-19 global pandemic has created dire consequences with an alarming rate of morbidity and mortality. There are not yet vaccine or efficacious treatment options to combat the causative SARS-CoV-2 infection. This paper describes the identification of potentially repurposable drugs for COVID-19 treatment by conducting pathway enrichment analysis on publicly available Gene Expression Omnibus datasets. We first determined SARS-CoV-2 infection-induced alterations of host gene expressions and pathways. We then identified drugs or compounds that target and counter virus-triggered cellular perturbations, suggesting their potential repurposing for COVID-19 treatment. The key findings are that SARS-CoV-2 infection in host cells induces mitochondrial dysfunction, inhibits oxidative phosphorylation, and activates several immune response and pro-inflammatory pathways. Triptolide, the major bioactive component of a traditional Chinese medicine herb, may rescue mitochondrial dysfunction by activating oxidative phosphorylation. Further in vitro and in vivo studies are necessary to verify these results prior to clinical application.
Thu, 17 September 2020
ARTICLE | doi:10.20944/preprints202009.0409.v1
Subject: Biology, Other Keywords: clay; mica; biotite; muscovite; origin of life; origins of life; mechanical energy; work; wet-dry cycles
Online: 17 September 2020 (13:01:15 CEST)
An origin of life between the sheets of micaceous clay is proposed to involve the following steps: 1) evolution of metabolic cycles and nucleic acid replication, in separate niches in biotite mica; 2) evolution of protein synthesis on ribosomes formed by liquid-in-liquid phase separation; 3) repeated encapsulation by membranes of molecules required for the metabolic cycles, replication, and protein synthesis; 4) interactions and fusion of the these membranes containing enclosed molecules; resulting eventually in 5) an occasional living cell, containing everything necessary for life. The spaces between mica sheets have many strengths as a site for life’s origins: mechanochemistry and wet-dry cycles as energy sources, an 0.5-nm anionic crystal lattice with potassium counterions (K+), hydrogen-bonding, enclosure, and more. Mica pieces in micaceous clay are large enough to support mechanochemistry from moving mica sheets. Biotite mica is an iron-rich mica capable of redox reactions, where the stages of life’s origins could have occurred, in micaceous clay.
REVIEW | doi:10.20944/preprints202009.0399.v1
Subject: Biology, Other Keywords: inositide; phosphoinositide; 5-phosphatase; INPP5K; SKIP; phosphatidylinositol 3,4,5-trisphosphate; phosphatidylinositol 4,5-bisphosphate; congenital muscular dystrophy; cataract; intellectual disability; insulin signaling; insulin resistance; endoplasmic reticulum; endoplasmic reticulum stress; unfolded protein response
Online: 17 September 2020 (11:19:10 CEST)
INPP5K (Inositol Polyphosphate 5-Phosphatase K, or SKIP (for Skeletal muscle and Kidney enriched Inositol Phosphatase) is a member of the phosphoinositide 5-phosphatases family. Its protein structure is comprised of a N-terminal catalytic domain which hydrolyses both PtdIns(4,5)P2 and PtdIns(3,4,5)P3, followed by a SKICH domain at the C-terminus which is responsible for protein-protein interactions and subcellular localization of INPP5K. Strikingly, INPP5K is mostly concentrated in the endoplasmic reticulum, although it is also detected at the plasma membrane, in the cytosol and the nucleus. Recently, mutations in INPP5K have been detected in patients with a rare form of autosomal recessive congenital muscular dystrophy with cataract, short stature and intellectual disability. INPP5K functions extend from control of insulin signaling, endoplasmic reticulum stress response and structural integrity, myoblast differentiation, cytoskeleton organization, cell adhesion and migration, renal osmoregulation, to cancer. The goal of this review is thus to summarize and comment recent and less recent data in the literature on INPP5K, in particular on the structure, expression, intracellular localization, interactions and functions of this specific member of the 5-phosphatases family.
Sun, 13 September 2020
REVIEW | doi:10.20944/preprints202009.0279.v1
Subject: Biology, Other Keywords: selection; mutation; genetic drift; adaptation; ploidy drive; genome instability
Online: 13 September 2020 (11:48:30 CEST)
Ploidy is a significant type of genetic variation, describing the number of chromosome sets per cell. Ploidy evolves in natural populations, clinical populations, and lab experiments, particularly in fungi. Despite a long history of theoretical work on this topic, predicting how ploidy will evolve has proven difficult, as it is often unclear why one ploidy state outperforms another. Here, we review what is known about contemporary ploidy evolution in diverse fungal species through the lens of population genetics. As with typical genetic variants, ploidy evolution depends on the rate that new ploidy states arise by mutation, natural selection on alternative ploidy states, and random genetic drift. However, ploidy variation also has unique impacts on evolution, with the potential to alter chromosomal stability, the rate and patterns of point mutation, and the nature of selection on all loci in the genome. We discuss how ploidy evolution depends on these general and unique factors and highlight areas where additional experimental evidence is required to comprehensively explain the ploidy transitions observed in the field and the lab.
Wed, 9 September 2020
ARTICLE | doi:10.20944/preprints202009.0211.v1
Subject: Biology, Other Keywords: New Zealand; biomarkers; environmental health assessment; Anguilla dieffenbachii
Online: 9 September 2020 (11:45:52 CEST)
The Matāura River is the sixth largest river system in New Zealand and has long been subject to agricultural, industrial, and residential land use activities. The catchment has geographic and economic value and is of great cultural importance for local Māori, who have concerns over potential adverse impacts that anthropogenic stressors exert on the health of the river. There is a dearth of information on the impacts of these stressors towards the health of native species such as the longfin eel Anguilla dieffenbachii. This study assessed the environmental status of the Matāura River using biological and chemical methodologies incorporating A. dieffenbachii as a bioindicator species for exposure to combined anthroprogenic stressors. A range of biomarker endpoints were measured in caged and wild-caught eels (when available) to characterize site-specific responses to combined anthropogenic stressors. While there was no clear indication of cumulative impacts moving from pristine headwaters to the lower reaches of the Matāura River biomarkers of xenobiotic metabolization were induced in A. dieffenbachia and there was evidence of chemical contamination in sediments and tissues.
Mon, 7 September 2020
REVIEW | doi:10.20944/preprints202009.0162.v1
Subject: Biology, Other Keywords: amyloids; frozen accident; genetic code; hydrogels; liquid-liquid phase separation; mRNA; polyglycine; rRNA; ribosomes; translational fidelity; tRNA
Online: 7 September 2020 (09:13:11 CEST)
The genetic code evolved by a combination of chaotic and ordered processes. Liquid-liquid phase separation (hydrogels), a chaotic process, constructs diverse membraneless compartments within cells, resulting in regulated hydration and sequestration and concentration of reaction components. Hydrogels relate to chaotic amyloid fiber production. We propose that polyglycine and related hydrogels (i.e. GADV; G is glycine), phase separations, membraneless droplets and amyloid accretions organized protocell domains to drive the earliest evolution of the genetic code and the pre-life to cellular life transition. By contrast, evolution of tRNA, tRNAomes, aminoacyl-tRNA synthetases and translation systems followed highly ordered and systematic pathways, described by well-defined mechanisms and rules. The pathway of evolution of aminoacyl-tRNA synthetases, which tracked evolution of the genetic code, is clarified. Hydrogels and amyloids form a chaotic component, therefore, that complemented otherwise systematic processes. We describe with detail a pre-life world in which hydrogels and amyloids provided the Darwinian selections of the first life.
ARTICLE | doi:10.20944/preprints202004.0281.v2
Online: 7 September 2020 (04:15:59 CEST)
Spike (S) protein of Coronaviruses help in receptor attachment and virus entry into the host cells. While S protein is required for virus entry, it is also important as an immunogen as it is the most accessible part of the virus architecture. S protein form knob like structures (viral spikes) protruding outwards in the form of homotrimers containing an S1 and S2 as monomers. Mutations in structural proteins of virus play crucial role in determining virulence and also in many instances influencing emergence of antibody escape variants and cellular tropism. In this paper we have performed in depth analyses of spike protein sequences from various parts of the world and tried to correlate the data with possible functional relevance of such mutations.
Thu, 3 September 2020
ARTICLE | doi:10.20944/preprints202009.0062.v1
Subject: Biology, Other Keywords: retinitis pigmentosa; TULP1; RPE65; recessive; missense; frameshift
Online: 3 September 2020 (07:16:45 CEST)
Retinitis pigmentosa (RP) clinically and genetically heterogeneous group of inherited retinal disorders (IRD) that result in retinal degeneration. This study aimed to identify the genetic findings of patients with autosomal recessive retinitis pigmentosa (arRP). Whole exome sequencing (WES) was performed in two unrelated Pakistani families underlying arRP. Data analysis and mutation screening was performed for all the known RP genes following bi-directional Sanger sequencing to determine whether any of the candidate variants co-segregated with the disease phenotype in the families. WES data analysis revealed a novel homozygous missense variant (c.1274T>C) in the in Tubby like Protein 1 (TULP1 NM_003322.6) gene in family 1 and a novel homozygous frameshift variant (c.351delC) in the retinoid isomerohydrolase 65 (RPE65 NM_000329.3) gene in family 2. The identified variants perfectly co-segregated with the disease phenotype within the families. Our results strongly suggest that mutations in TULP1 and RPE65 are responsible for the retinal phenotype in the affected individuals. These mutations will increase the mutation spectrum of these genes; furthermore, it will enhance our knowledge and understanding of the underlying molecular mechanisms of retinitis pigmentosa.
REVIEW | doi:10.20944/preprints202009.0058.v1
Subject: Biology, Other Keywords: Emerging infectious diseases; coronaviruses; COVID-19; SARS-CoV; SARS-CoV-2; MERS-CoV; zoonotic diseases
Online: 3 September 2020 (04:54:38 CEST)
The ongoing global pandemic caused by coronavirus disease 2019 (COVID-19) has once again demonstrated the significance of the Coronaviridae family in causing human disease outbreaks. As SARS-CoV-2 was first detected in December 2019, information on its tropism, host range, and clinical presentation in animals is limited. Given the limited information, data from other coronaviruses may be useful to inform scientific inquiry, risk assessment and decision-making. We review the endemic and emerging alpha- and betacoronavirus infections of wildlife, livestock, and companion animals, and provide information on the receptor usage, known hosts, and clinical signs associated with each host for 15 coronaviruses discovered in people and animals. This information can be used to guide implementation of a One Health approach that involves human health, animal health, environmental, and other relevant partners in developing strategies for preparedness, response, and control to current and future coronavirus disease threats.
Tue, 1 September 2020
ARTICLE | doi:10.20944/preprints202009.0012.v1
Online: 1 September 2020 (11:42:14 CEST)
The specificity and potency of venom components gives them a unique advantage in development of various pharmaceutical drugs. Though venom is a cocktail of proteins rarely is the synergy and association between various venom components studied. Understanding the relationship between various components is critical in medical research. Using meta-analysis, we found underlying patterns and associations in the appearance of the toxin families. For Crotalus, Dis has the most associations with the following toxins: PDE; BPP; CRL; CRiSP; LAAO; SVMP P-I & LAAO; SVMP P-III and LAAO. In Sistrurus venom CTL and NGF had most associations. These associations can be used to predict presence of proteins in novel venom and to understand synergies between venom components for enhanced bioactivity. Using this approach, the need to revisit classification of proteins as major components or minor components is highlighted. The revised classification of venom components needs to be based on ubiquity, bioactivity, number of associations and synergies. The revised classification will help in increased research on venom components such as NGF which have high medical importance.
Mon, 31 August 2020
ARTICLE | doi:10.20944/preprints202008.0687.v1
Subject: Biology, Other Keywords: gross chromosomal rearrangements; non-homologous end joining; translocation; Illumina MiSeq; Oxford Nanopore; kluyveromyces marxianus; saccharomyces cerevisiae; URA3 gene
Online: 31 August 2020 (02:54:09 CEST)
Kluyveromyces marxianus (K. marxianus) is a newly emerging industrially relevant yeast. It is known to possess a highly efficient Non-Homologous End Joining (NHEJ) pathway that promotes random integration of non-homologous DNA fragments into its genome. The nature of the integration events was traditionally analyzed by Southern blot hybridization. However, the precise DNA sequence at the insertion sites were not fully explored. We transformed a PCR product of the Saccharomyces cerevisiae URA3 gene (ScURA3) into an uracil auxotroph K. marxianus wildtype strain and picked 24 stable Ura+ transformants for sequencing analysis. We took advantage of rapid advances in DNA sequencing technologies and developed a method using a combination of Illumina MiSeq and Oxford Nanopore sequencing. This approach enables us to uncover the Gross Chromosomal Rearrangements (GCRs) that are associated with the ScURA3 random integration. Moreover, it will shine a light on understanding DNA repair mechanisms in Eukaryotes, which could potentially provide insights for cancer research.
Sun, 30 August 2020
CONCEPT PAPER | doi:10.20944/preprints202008.0661.v1
Subject: Biology, Other Keywords: life definition; living being definition; robot definition; living viruses; extraterrestrial life
Online: 30 August 2020 (11:33:48 CEST)
What is life, what is the difference between something that is alive and something that is not, are viruses living beings, or what would life be like elsewhere in the universe, are questions that still do not have clear-cut answers fully accepted by the scientific community. Based on the fundamental attributes of all living things, I define life as a process that takes place in very ordered organic structures and is characterized by being automatic, interactive and evolutionary. I also define a living being as an organic, highly ordered, automatic, interacting and evolutionary system, and a robot as an ordered automatic and interacting system. Based on this definition and what we know about the biology of viruses, I maintain that they should be considered as living entities. Finally, I explain why if there were life elsewhere in the universe, it would be very similar to what we know on our planet.
ARTICLE | doi:10.20944/preprints202008.0660.v1
Subject: Biology, Other Keywords: Carcharhinidae sharks; Prionace glauca; demographic parameters; exploitation; Gulf of Guinea
Online: 30 August 2020 (11:27:39 CEST)
Prionace glauca, blue shark is a cosmopolitan species. Together with Carcharhinus falciformis, it co-dominated the landings of carcharhinidae sharks at the Artisanal Fishing Port of Cotonou. The objective of this study is to determine the demographic parameters of the blue shark in Gulf of Guinea marine waters. The different routines of the FISAT II v 1.2 software associated with the empirical equations of Froese and Nohland, allowed the evaluation of the different demographic parameters of the blue shark in Benin's marine waters. From August to December 2015, 244 individuals shark sizes; ranging from 175cm to 325cm were sampled. The total asymptotic length obtained was 341.25cm with a growth rate of 0.35/year, which indicates that the species is growing rapidly and the optimal total length of the species is 232.01cm. The age of first maturity of the species is 3 years with a longevity of 10 years. The exploitation rate is E= 0.74 with total mortality being 2.4; natural mortality is 0.6 and fishing mortality is 1.8. The sex ratio remains in favour of males throughout the study period. Monitoring programme were suggested with effective management measures established and executed for sustainability of the blue shark’s stock in the Gulf of Guinea.
Fri, 28 August 2020
ARTICLE | doi:10.20944/preprints202008.0647.v1
Subject: Biology, Other Keywords: Biological Organization Principles; Dynamical Systems; Bayesian Inference and Brian; FEP; Autopoiesis; Evolution; Cognition; Niche; KAM-dynamics Contents
Online: 28 August 2020 (15:08:56 CEST)
The Autopoiesis and Cognition Theory (ACT), by Maturana and Varela, based on the notions of Biological Closure and Structural Coupling, is a well-known theory on how to understand biological organization [1, 2, 3]. Although, for example, the Free Energy Principle framework evokes some entailments of autopoiesis in a more formal setting [4, 5]; and ACT has been used in many fields, its impact has been restricted because it lacks quantitative analysis. Here we present a theoretical framework grounded in accepted and well-developed ideas from Mathematics and Physics which advance the understanding of the Principles of Biological Organization under the guidance of Biological Closure and Structural Coupling. The disciplines of Differential Geometry/Topology, Mechanics and Complex Dynamical Systems provide a powerful, elegant, and well-established body of knowledge to support our Biological Organization Principles (BOP) framework. In particular, Stochastic Mechanics and KAM theory (from Kolmogorov, Arnold and Moser theorem) allow us to develop, using the notions of Biological Closure and Structural Coupling, a central core of BOP termed Dynamical Closure Mechanism. Under the proposed framework, a wide variety of bio- logical phenomena can be understood, shedding new light on biological explanations. However, an understanding of biological organization may require the re-evaluation of dogmas on how we think on biology as it seems inescapable that what is needed is an integration of analysis and notions derived from mathematics, physics, and biology to generate a new landscape of ideas.
ARTICLE | doi:10.20944/preprints202008.0632.v1
Subject: Biology, Other Keywords: Blockchain; P2P Networks; Nucleobase DNA/RNA sequence; Gene Expression; Cell Population; Epigenetics; Methylation; Consensus; Hash Algorithm; Triple Codons; Protein Synthesis; Cryptocurrency
Online: 28 August 2020 (10:33:42 CEST)
The study presents a mathematical modeling for supporting the premise that our body is composed of blockchain systems. A cell population is considered a space with peer-to-peer communication networks for applying blockchain protocol. Transaction is defined as gene expression that constantly occurs for protein synthesis in each cell. The transaction process proceeds according to the blockchain protocol with sharing and recording the data on the blockchain ledger. The premise comes from the clues of the previous research such that the cell population is a complex structured network system having cell-to-cell connections. Although individual cells exhibit stochastic nonlinear dynamic behavior, cell population shows consensus behavior that reaches to ensemble through interaction among cells. It is inferred that gene expression is not regulated by the corresponding cell only nor determined by external intelligence such as the brain. This is achieved through a consensus through stochastic interactions between cells over the whole cell population. These findings imply that mathematical blockchain modeling is a suitable for gene expression process. The original contribution of the study is a methodology for applying mathematically the blockchain protocol to the real biological gene expression process. In other words, the DNA sequence is converted into a numeral bit sequence that makes it possible to implement the blockchain protocol. A new DNA sequence scheme is proposed with adding methylated cytosine and adenine as the 5th and 6th bases for including epigenetic information which has profound effect on gene expression and regulation. The methodology was applied to the real biological synthesis process of protein samples. The protein is composed of amino acids that are encoded by triplet codons of 216 kinds with 6 base RNA sequence. The gene expression information is traced backward from a synthesized protein sample, amino acids of codons, RNA transcript up to DNA sequence. One of the results is a numeric value in the form of a bit sequence with which mathematical blockchain modeling is applicable. The cryptographic authentication and the consensus process are mathematically proven to work properly by the blockchain protocol. It implies that the same protein is synthesized, but with different epigenetic data, then protein's latent material properties will certainly be different. Although the result has not been justified by the biologic experiment yet, it is sure that the biological hidden algorithm inside DNA sequence will be revealed by the binary bit-logic with physical on/off states which is mathematically proven. The research will greatly contribute to disease treatment and medicine development as well as epigenetics in the future.
ARTICLE | doi:10.20944/preprints202008.0633.v1
Subject: Biology, Other Keywords: giant phage; phiKZ; Pseudomonas aeruginosa; nucleoid; pseudo-nucleus; analytical electron microscopy; electron tomography; fluorescent in situ hybridization; stress response
Online: 28 August 2020 (10:29:39 CEST)
Bacteria develop various defense mechanisms against stresses, including the bacteriophage infection. The giant phiKZ phage infection induced the appearance of a pseudo-nucleus inside the bacterial cytoplasm. Here, we used FISH, electron tomography and analytical electron microscopy to study the morphology of this unique nucleus-like shell and to demonstrate the distribution of phiKZ and bacterial DNA in infected P. aeruginosa cells. The maturation of the pseudo-nucleus was traced in short intervals for 40 min after infection. This study was accompanied by the identification of phiKZ and bacterial DNA by real-time RCR. We demonstrated that phage DNA that isolated from the cytoplasm during all infection stages were compacted within the pseudo-nucleus in a specific structure. Bacterial DNA was diminished in the course of infection, but did not completely degrade until at least 40 min after phage application. The content of the total phage DNA, on the other hand, increased. EDX analysis confirmed these results and revealed that, during the infection, Sulfur content in the bacterial cytoplasm increased, which suggests the increase of DNA-binding Met-reach proteins synthesis, which could protect bacterial DNA from stress.
Thu, 27 August 2020
ARTICLE | doi:10.20944/preprints202008.0621.v1
Subject: Biology, Other Keywords: Clustering; Mutation; Amino acid substitution; Structural proteins; Biochemical properties; Functional sub-domains
Online: 27 August 2020 (12:39:30 CEST)
Like other viruses, SARS-COV-2 too mutating and thus creating divergent variants across the world. Protein sequence variation occurs due to non-synonymous single-nucleotide polymorphism (SNP) that alter the amino acid. Amino acid substitutions on homooligomer interfaces may change the structure of the protein and hence alter the regular or known functional activities of a viral protein. Studies reveal that even a single point mutation in virus protein can significantly change their biology, leads to peculiar pathogenic properties. Therefore, an in-depth investigation of the amino acid substitution in the genomic signature of a protein is highly essential for the rapidly evolving virus-like SARS-COV-2. Investigation of world-wide and country-specific substitution features may be crucial and highly essential to decipher pathogenicity. These might be also helpful to precise structure prediction and identification of possible therapeutic targets for effective drug design. We perform extensive analysis towards highlighting and characterizing the amino acid substitution signature occurs in the four structural proteins (Spike-S, Nucleocapsid-N, Membrane-M, Envelope-E) of SARS-COV-2. We use a total of 9587 viral sequences reported from 49 different countries across the globe. In this study, we try to study the amino acid substitution patterns and its impact on change in biochemical properties, thereby possible changes in protein structures. We perform the following analysis: a) isolating and grouping variants we considered, for different protein sequences; b) identifying amino acid substitution type that are frequently and rarely occurring and reporting their location within the sequence; c) change in chemical properties due to amino acid substitution; and f) highlight country-specific divergent variation and substitution signature. In terms of mutational changes, E and M proteins are relatively stable than N and S proteins. A significant quantity of variations is observed in spike (S) proteins. Our study further reveals an interesting fact that the substitution location is random in N protein, whereas the substitution sites in M protein is less varying and almost stable. Substitutions specific to active sub-domains in S and N proteins reveals that sub-domains like Heptapeptide Repeat (HR2), Fusion peptides (FP), and Transmembrane (TM), which are involved in cellular membrane fusion and entry of the virus into the host cells, are significantly mutated. Majority of the substitutions leads to change in biochemical properties (side chain and hydropathy) of amino acid. A good number of exclusive variants are found specific to a particular country. We strongly believe that the current findings will be helpful for protein structure analysis of viral structural proteins and antiviral drug discovery.
HYPOTHESIS | doi:10.20944/preprints202008.0607.v1
Subject: Biology, Other Keywords: catalysis; kinetics; time; biological macromolecular enzyme; large biological macro-substrate; catalytic step; catalytic efficiency; turnover number
Online: 27 August 2020 (09:04:44 CEST)
Classical enzyme kinetics are interpreted from a new angle here, and biological macromolecular enzyme catalysis is viewed and explored at the molecular level. The time course of sequential catalytic events is analyzed, the relationships between catalytic efficiency, catalytic rate/velocity and the amount of time consumed are established. This writing tries to connect the microscopic molecular behavior of enzymes to kinetic data obtained in experiment, and the equations proposed here can be testified and examined by future experiments.
Wed, 26 August 2020
ARTICLE | doi:10.20944/preprints202008.0580.v1
Subject: Biology, Other Keywords: Aminobenzoic acid; cinnamic acid; gene clusters; hydroxybenzoic acid; resveratrol; SLC25 subfamily 44; para-coumaric acid; ubiquinone
Online: 26 August 2020 (10:43:03 CEST)
The solute carrier family 25 (SLC25) participates in the transport of metabolites and cofactors across the membranes of mitochondria, plastids, peroxisomes, and endoplasmic reticulum. By calling for genomic blocks involved in adjacent metabolic reactions, this report introduces gene clusters of the Slc25 subfamily 44, stilbene and chalcone synthases, and subunits of the mitochondrial electron transfer complexes. The Slc25A44 gene was found ubiquitously expressed and transcriptionally co-regulated with energy metabolism genes in human, mouse, and Arabidopsis thaliana. The Slc25A44s also had no homozygous missense mutation and were highly conserved at intra-species level with the majority of polymorphism present in the non-coding regions. When expressed in oocytes, AdSlc25A44 from Arachis duranensis showed transport activity for the common precursors of flavonoids, stilbenoids, and ubiquinone. Accordingly, AdSLC25A44 and its human orthologue HsSLC25A44 elevated the production of para-coumaric, 4-aminobenzoic, and 4-hydroxybenzoic acids in Saccharomyces cerevisiae strains designed to produce para-coumaric acid via different pathways. Moreover, the engineered SLC25 subfamily specific signature, i.e., AdSLC25A44LWW206IQF, had a stronger effect on para-coumaric acid secretion than the native variant. Importantly, the aerobic growth-rate of S. cerevisiae was significantly higher when expressing the AdSLC25A44, HsSLC25A44, or AdSLC25A44LWW206IQF. These results suggest that SLC25A44 is an essential mitochondrion-ER-nucleus zone transporter associated with metabolism of secondary metabolites and energy.
Tue, 25 August 2020
REVIEW | doi:10.20944/preprints202008.0554.v1
Subject: Biology, Other Keywords: Cooperation; Aggregative mulicellularity; Social Conflicts; Evolution; Dictyostelium discoideum
Online: 25 August 2020 (13:34:39 CEST)
The ’social amoeba’ Dictyostelium discoideum, where aggregation of genet- ically heterogeneous cells produces functional collective structures, epitomizes social conflicts associated with multicellular organization. ’Cheater’ populations that have a higher chance – quantified by a positive spore bias – of surviving to the next generation are selectively advantaged. Their spread is thus expected to undermine collective functions over evolutionary times. In this review, we discuss the two main approaches adopted to conceptualize social conflicts in Dictyostelium discoideum: describing spore bias as a property of cell popula- tions (strains), or as a result of individual cell choices during the developmental process. These two points of view are often held equivalent and used inter- changeably. While the population-level view allows for more direct evolutionary inference, however, the cell-level interpretation reveals that such evolutionary predictions may be modified if developmental mechanisms, such as dependence on the environment and intrinsic unpredictability of cell fate choices, are taken into account. We conclude by proposing a set of open questions that in our opinion lie at the core of a multi-scale description of aggregative life cycles, where the formulation of predictive evolutionary models would include cell-level mechanisms responsible for spore bias alongside population-level descriptors of multicellular organization.
Mon, 24 August 2020
ARTICLE | doi:10.20944/preprints202008.0525.v1
Subject: Biology, Other Keywords: Transboundary management; biodiversity; species distributions; Exclusive Economic Zones; marine conservation; collaboration
Online: 24 August 2020 (10:01:05 CEST)
Marine species are declining at an unprecedented rate, catalyzing many nations to adopt conservation and management targets within their jurisdictions. However, marine species are naive to international borders and an understanding of cross-border species distributions is important for informing high-level conservation strategies, such as bilateral or regional agreements. Here, we examined 28,252 distribution maps to determine the number and locations of marine transboundary species. Over 90% of species have ranges spanning at least two jurisdictions, with 58% covering over ten jurisdictions. The highest concentrations of transboundary species are in the USA, Australia, and Indonesia. To effectively protect marine biodiversity, international governance mechanisms—particularly those related to the Convention on Biological Diversity, the Convention on Migratory Species, and Regional Seas Organizations—must be expanded to promote multinational conservation planning, and complimented by a holistic governance framework for biodiversity beyond national jurisdiction.
Sat, 22 August 2020
REVIEW | doi:10.20944/preprints202008.0492.v1
Subject: Biology, Other Keywords: cyclic nucleotides; phosphodiesterases (PDEs); optogenetics; cAMP; cGMP
Online: 22 August 2020 (05:04:04 CEST)
Second messengers, cyclic adenosine 3'-5'-monophosphate (cAMP) and cyclic guanosine 3'-5'-monophosphate (cGMP) are playing important roles in many animal cells by regulating intracellular signaling pathways and modulating cell physiology. Environmental cues like temperature, light and chemical compounds can stimulate cell surface receptors and trigger the generation of second messengers and the following regulations. Spread of cAMP and cGMP is further shaped by cyclic nucleotide phosphodiesterases (PDEs) for orchestration of intracellular microdomain signaling. However, localized intracellular cAMP and cGMP signaling requires further investigation. Optogenetic manipulation of cAMP and cGMP offers new opportunities of spatio-temporally precise study of their signaling mechanism. Light-gated nucleotide cyclases are well developed and applied for cAMP/cGMP manipulation. Recently discovered rhodopsin phosphodiesterase gene from protists established new and direct biological connection between light and PDEs. Light-regulated PDEs are under development and of demand to complete the toolkit of cAMP/cGMP manipulation. In this review, we summarize the state of the art, pros and cons of artificial and natural light-regulated PDEs and discuss potential new strategies of developing light-gated PDEs for optogenetic manipulation.
Wed, 19 August 2020
ARTICLE | doi:10.20944/preprints202008.0410.v1
Subject: Biology, Other Keywords: coronavirus; film; detergent; antiviral; virucide; inactivation; sanitization
Online: 19 August 2020 (10:45:07 CEST)
COVID-19 infection, caused by SARS-CoV-2, is inequitably distributed and more lethal among populations with lower socioeconomic status. Direct contact with contaminated surfaces has been one of the virus sources, as it remains infective up to days. Several disinfectants have been shown to inactivate SARS-CoV-2 but they rapidly evaporate, are flammable or toxic and may be scarce or inexistent for the vulnerable populations. Therefore, we are proposing a simple, easy to prepare, low-cost and efficient antiviral films, made with wide available dishwasher detergent, which can be spread in hands and inanimate surfaces and maintains virucidal activity for longer periods than the current sanitizers. Avian coronavirus (ACoV) was used as model of challenge to test the antivirus efficacy of proposed films. Polystyrene microplates were covered with a thin layer of detergent formula. After drying, the films were exposed to different virus doses for 10 minutes and virus infectivity were determined using embryonated chicken eggs and RNA virus quantification in allantoic fluids by RT-qPCR. The films showed to inactive the ACoV (ranging from 103.66 to 106.66 EID50), which is chemically and morphologically similar to SARSCoV-2 and may constitute an excellent alternative to minimize the spread of Covid-19.
Mon, 17 August 2020
REVIEW | doi:10.20944/preprints202008.0350.v1
Subject: Biology, Other Keywords: cytoplasmic incompatibility; Wolbachia; prophage WO; CifA and CifB; symbiosis
Online: 17 August 2020 (04:35:31 CEST)
Cytoplasmic incompatibility (CI) is the most common symbiont-induced reproductive manipulation. Specifically, symbiont-induced sperm modifications cause catastrophic mitotic defects in the fertilized embryo and ensuing lethality in crosses between symbiotic males and either aposymbiotic females or females harboring a different symbiont strain. However, if the female carries the same symbiont strain, then embryos develop properly, which imparts a relative fitness benefit to symbiont-transmitting mothers. Thus, CI drives maternally transmitted bacteria to high frequencies in arthropod species worldwide. In the past two decades, CI has experienced a boom in interest due in part to its (i) deployment in successful, worldwide efforts to reduce the spread of mosquito-borne diseases, (ii) causation by bacteriophage genes, cifA and cifB, that modify animal reproductive processes, and (iii) important impacts on incipient speciation. This review serves as a gateway to experimental, conceptual, and quantitative themes of CI and outlines significant gaps in our understanding of CI’s mechanism that are ripe for investigation from a diversity of subdisciplines in the life sciences.
Fri, 14 August 2020
REVIEW | doi:10.20944/preprints202008.0308.v1
Subject: Biology, Other Keywords: Hereditary HL; genetics of syndromic and non-syndromic HL; methods for pathogenic locus/gene identification
Online: 14 August 2020 (04:45:23 CEST)
Hearing impairment is an immensely diagnosed genetic cause, 5% of the total world population effects with different kind of congenital hearing loss (HL). In third-world countries or countries where consanguineous marriages are more common the frequency rate of genetic disorders are at its zenith. Approximately, the incidence of hearing afflictions is ostensibly 7-8:1000 individuals whereas it is estimated that about 466 million peoples suffer with significant HL, and of theses deaf cases 34 million are children’s up to March, 2020. Several genes and colossal numbers of pathogenic variants cause hearing impairment, which aided in next-generation with recessive, dominant or X-linked inheritance traits. This review highlights on syndromic and non-syndromic HL (SHL and NSHL), and categorized as conductive, sensorineural and mixed HL, which having autosomal dominant and recessive, and X-linked or mitochondrial mode of inheritance. Many hundred genes involved in HL are reported, and their mutation spectrum becomes very wide. Mapping of pathogenic genes in consanguinity family is facilitated to understand the disease history. Review presents the bases of HL and also focused on various genetic factors that cause deafness like the basics of genetic inheritance, and classic and well-characterized inherited factors of it. It also overviews the application of linkage analysis, SNPs genotyping and whole exome sequencing methods, in mapping and identification of new locus, causative genes and their variants in families inherited with HL. Conclusively, this review supports researchers in understanding the location of chromosome, the causative genes and specific locus which causing deafness in humans.
Thu, 13 August 2020
Subject: Biology, Other Keywords: Non-genetic change, translation errors, phenotypic variability, adaptation, evolution
Online: 13 August 2020 (05:23:46 CEST)
The notion that there is a one to one mapping from genotype to phenotype was overturned a long time ago. It is now well established that besides the genetic background, environmental inputs guide the development of phenotype. In addition, altered RNA and protein molecules also influence phenotype in conjunction with the external environment, leading to ‘non-genetic’ changes. The phenotypic variation we see across all living organisms therefore results from a combination of genetic and non-genetic changes. In spite of the prevalent idea that variability arising from non-genetic changes is transient and does not influence evolution, recent work has shown that it can impact both short and long-term adaptation. In this review, I propose that one way in which non-genetic inputs can affect evolution is by indirectly influencing genetic change. I classify and review the many ways in which non-genetic changes influence genotype and impact cellular fitness across generations, with an emphasis on the enticing idea that non-genetic changes act as stepping stones for genetic adaptation. Overall, I review how non-genetic changes impact phenotype via their influence on the genotype, and thus can play a role in evolutionary change.
Tue, 11 August 2020
Subject: Biology, Other Keywords: RaTG13; SARS-COV-2; Illumina sequencing, amplicon sequencing, NGS; fecal swab
Online: 11 August 2020 (08:06:32 CEST)
RaTG13 beta coronavirus, which exists in the form of a genome sequence, is the closest relative of SARS-CoV-2 reported till date. The sample from which RaTG13 virus was sequenced was a bat fecal swab collected in 2013 from Tongguan, Mojiang, Yunnan province, China. The genome data for RaTG13, MN996532.1, was deposited on 27th Jan 2020 and the raw data (Illumina reads) was deposited a fortnight later on 13th Feb 2020 https://www.ncbi.nlm.nih.gov/sra/SRX7724752[accn]. Comparison of the RNA Seq data of RaTG13 fecal swab sample to the corresponding data from the bat fecal swabs deposited by the same working group indicated that the raw data seemed to be anomalous in several aspects. Thirty percent of the reads did not match with anything. From the rest of the 70%, an abnormal high proportion was contributed by reads derived from eukaryotes (~68%). These matched with the sequences of not one but various bat species (round leaf bats, fruit bats and other bats) and animal species (squirrels, foxes, etc.) as per Krona analysis included with the SRA data. The proportion of the bacterial reads in the swab was exceptionally low, i.e. 0.7%, which is abnormal, compared to the 70-90% bacterial abundance in other bat fecal swabs. Furthermore, we also found another set of raw data associated with RaTG13, amplicon sequencing of the genome (SRX8357956), which was submitted in May 2020. Analysis of the amplicons by BLAST showed that these collectively do not cover the whole genome (MN996532.1). On closer inspection, the dates mentioned in the files of the sequenced amplicons were also found to be older (2017, 2018). Collectively, the anomalies in the raw data of RaTG13 pose an important question about the overall authenticity of the RaTG13 genome sequence.
Sun, 9 August 2020
REVIEW | doi:10.20944/preprints202008.0225.v1
Subject: Biology, Other Keywords: Heat-stable proteins; Heat treatment; Hyperthermophilic proteins; Heat stability; Protein purification
Online: 9 August 2020 (22:00:46 CEST)
Proteins possess complex three-dimensional structures, and these structures are stable only within specific ranges of temperature which mostly correspond to the temperature ranges of the host organisms. However, few exceptional proteins, called heat-stable proteins, are stable at temperatures that are substantially higher than those tolerated by the host organisms themselves. Most of the heat-stable proteins possess heat stability to perform their functions at high temperatures, but some of them are intrinsically heat-stable due to their structure. Heat-stable proteins are usually divided into three or four groups depending upon the intricacies of their structures and thermal behaviors. Their peculiar property, i.e. heat-stability, makes them very valuable in applications such as polymerase chain reaction, industrial processes requiring high temperature, and protein engineering. Heat-stability also makes it feasible to purify such proteins, from the rest of the heat-labile proteins, using a simple heat-treatment method. Moreover, heat treatment can be used as a combined cell-lysis and protein purification step which, as compared to conventional methods, can result in a higher yield of heat-stable proteins. Furthermore, some special heat-stable proteins, i.e. intrinsically disordered proteins (which include the proteins involved in important neurodegenerative diseases), need heat-treatment step, in some cases, as the only way for their successful purification and study. Hence, this paper provides a first-ever comprehensive review of all major aspects of heat-stable proteins, i.e., their structure, evolution, classification, significance, and heat-treatment mediated purification.
Sat, 8 August 2020
SHORT NOTE | doi:10.20944/preprints202008.0205.v1
Subject: Biology, Other Keywords: RaTG13; SARS-COV-2; Illumina sequencing; amplicon sequencing; NGS; fecal swab
Online: 8 August 2020 (06:19:45 CEST)
RaTG13 is the next relative of SARS-CoV-2 derived from bat feces. The Illumina based NGS sequence of RaTG13 MN996532.1 was deposited on 27th Jan 2020 and the raw data, a little later on 13th Feb 2020 https://www.ncbi.nlm.nih.gov/sra/SRX7724752[accn]. The fecal swab sample shows abnormally high reads from eukaryotes which includes not only bats but other animals, as per the NCBI site. Also, comparison of the fecal swab to other bat fecal swabs deposited by the same group on the same date indicates that the fecal swab from which RaTG13 sequence was derived looked abnormal. The proportion of bacteria in this RNA Seq project was only 0.7% in contrast to 70-90% abundance in other fecal swabs from bats. Also, the amplicon sequencing done on the same sample showed large number of gaps and inconsistencies. This poses a question on the authenticity of the RaTG13 sequence also.
Thu, 6 August 2020
BRIEF REPORT | doi:10.20944/preprints202008.0148.v1
Subject: Biology, Other Keywords: Alignment-free software tool; Coronavirus; COVID-19; D614G mutation; Sarbecovirus; SARS-CoV; SARS-CoV-2; Spike glycoprotein
Online: 6 August 2020 (10:12:00 CEST)
As reported by us and others previously (1, 2), the D614G mutation appeared in the spike glycoprotein (SPG) of the SARS-CoV-2 (the pathogen behind COVID-19) at the early stages of the pandemic and then G614 containing variant of SARS-CoV-2 became the predominant strain in most human populations across the world. However, one of the most recent reports from India (3) stated the incidence of G614 to be only 26% in the Indian population. This report is contradictory to the information available through the GenBank (4) SARS-CoV-2 sequence deposits made by various laboratories from India. The above stated report currently circulating in the Indian media is likely to create a public perception that the Indian strain is less contagious and such a notion could be harmful to people’s welfare. In view of this concern we have re-evaluated, updated and recalculated the incidence of the G614 variant in the Indian population by analyzing 395 Indian SARS-CoV-2 genomic sequences available in the GenBank as of June 26, 2020. In our analysis we have categorized the samples by the month in which the samples were collected. We have used an alignment-free software tool named Compare (5, 6), and the Basic Local Alignment Search Tool (BLAST) (7) in the present analysis. We finally inspected each of the 395 sequences physically for the presence of aspartic acid (D) or glycine (G) at the 614th position of the spike glycoprotein. We analyzed an Australian cohort in parallel for comparison. We have found that the prevalence of G614 variant in the Indian samples for the month of June 2020 is 90.6%. The trends are similar with the Australian samples.
Tue, 4 August 2020
Subject: Biology, Other Keywords: adaptive death; ageing; altruism; C. elegans; kin selection; salmon
Online: 4 August 2020 (11:26:31 CEST)
Standard evolutionary theory, supported by mathematical modelling of outbred, dispersed populations predicts that ageing is not an adaptation. We recently argued that in clonal, viscous populations, programmed organismal death could promote fitness through social benefits and has, in some organisms (e.g. Caenorhabditis elegans), evolved to shorten lifespan. Here we review previous adaptive death theory, including consumer sacrifice, biomass sacrifice, and defensive sacrifice types of altruistic adaptive death. In addition we discuss possible adaptive death in semelparous fish, coevolution of reproductive and adaptive death, and adaptive reproductive senescence in C. elegans. We also describe findings from recent tests for the existence of adaptive death in C. elegans using computer modelling. Such models have provided new insights into how trade-offs between fitness at the individual and colony levels mean that senescent changes can be selected traits. Exploring further the relationship between adaptive death and social interactions, we consider examples where adaptive death results more from action of kin than from self-destructive mechanisms and, to describe this, introduce the term adaptive killing of kin.
REVIEW | doi:10.20944/preprints202008.0087.v1
Subject: Biology, Other Keywords: Chronic rhinosinusitis (CR); inflammation; nasal polyps; epithelial to mesenchymal transition (EMT); Polyp derived mesenchymal stem cells (PO-MSCs)
Online: 4 August 2020 (11:07:19 CEST)
Chronic rhinosinusitis is a common inflammatory disease of paranasal sinuses, which causes rhinorrhea, nasal congestion and hyposmia. The genetic predisposition or the exposure to irritants can sustain the inflammatory response and the development of nasal polyposis. Nasal polyps are benign and teardrop-shaped growths that project in the nasal cavities and originate from the ethmoid sinuses. This inflammatory process is associated with high expression of IL-5 cytokine and infiltration of eosinophils. Humanized monoclonal antibodies targeting IL-5 or its receptor, represent a therapeutic strategy in the treatment of nasal polyposis in combination with corticosteroids. The molecular pathogenesis of nasal polyps in CRS patients is associated to the epithelial-mesenchymal transition (EMT), a process in which epithelial cells lose their typical phenotype acquiring a mesenchymal phenotype. TGFβ/SMAD, ERK, and Wnt/β-catenin pathways are altered in EMT during the nasal tissue remodeling. miRNA and inhibitor molecules targeting these altered signaling pathways are able to interfere with EMT; which could lead to alternative therapies. Nasal polyps are an alternative source of mesenchymal stem cells which can be easily isolated from surgical biopsies. A molecular understanding of the biology of PO-MSCs will contribute to delineating inflammatory process underlying the development of nasal polyps.
Sun, 2 August 2020
REVIEW | doi:10.20944/preprints202008.0023.v1
Subject: Biology, Other Keywords: epithelial mesenchymal plasticity (EMP); epithelial mesenchymal transition (EMT); mesenchymal epithelial transition (MET); E/M Hybrid; partial EMT; computational biology; mathematical modeling; cancer
Online: 2 August 2020 (12:07:34 CEST)
The epithelial-mesenchymal (E/M) hybrid state has emerged as an important mediator of the elements of cancer progression facilitated by epithelial mesenchymal plasticity (EMP). We review here the evidence for the presence and prognostic potential of E/M hybrid state in carcinoma, modelling predictions and validations studies to demonstrate stabilised E/M hybrid intermediates along the spectrum of EMP, and computational approaches for characterising and quantifying EMP phenotypes, with particular attention to the emerging realm of single-cell approaches through RNA sequencing and protein-based approaches.
Fri, 31 July 2020
REVIEW | doi:10.20944/preprints202007.0743.v1
Online: 31 July 2020 (10:32:09 CEST)
Cryptosporidiosis is a common illness in young cattle that causes high morbidity and some mortality. A common prophylactic treatment are halofuginone products but it seems likely disease could be reduced by other other pharmacological products or some management strategies. We undertook a systematic review and meta-analyses on key outcomes for treatment of calves before and after 5 days of age with any management strategy, any nutritional strategy or any non-halofuginone product. A systematic literature search was undertaken with data extracted for outcomes = oocyst shedding, diarrhea, mortality and weight gain. Experiments had to describe results for same age animals in contemporary arms. Control animals had to be observed concurrently in planned experiments (pre-post and case-control studies were not eligible). Both randomized and other clinically controlled trials were eligible. Results were subgrouped by study design and outcomes were described in detail where at least two articles described the same treatment strategy. 55 articles were found. Significantly lower incidence of oocyst shedding, diarrhea burden and mortality was reported in many experimental arms, especially when animals started treatment before 5 days old. Weight gain was not mostly affected by treatment, however, by three weeks of age. The evidence base is at least encouraging but insufficient about paromomycin, bumped kinase inhibitors and azithromycin treatment, especially for diarrhea and oocyst shedding, given late or early. Azithromycin is the most promising of these.
Thu, 30 July 2020
ARTICLE | doi:10.20944/preprints202007.0719.v1
Subject: Biology, Other Keywords: SARS-CoV-2; long-term; neutralization antibody; lymphocyte functionality; viral pathogenicity.
Online: 30 July 2020 (12:16:21 CEST)
COVID-19 patients can recover with a median SARS-CoV-2 clearance of 20 days post initial symptoms (PIS). However, we observed some COVID-19 patients with existing SARS-CoV-2 for more than 50 days PIS. This study aimed to investigate the cause of viral clearance delay and the infectivity in these patients. Demographic data and clinical characteristics of 22 long-term COVID-19 patients were collected. SARS-CoV-2 nucleic acid, peripheral lymphocyte count, and functionality were assessed. SARS-CoV-2-specific and neutralization antibodies were detected, followed by virus isolation and genome sequencing. The median age of the studied cohort was 59.83±12.94 years. All patients were clinically cured after long-term SARS-CoV-2 infection ranging from 53 to 112 days PIS. Peripheral lymphocytes counts were normal. Interferon gamma (IFN-ƴ)-generated CD4+ and CD8+ cells were normal as 24.68±9.60% and 66.41±14.87%. However, the number of IFN-ƴ-generated NK cells diminished (58.03±11.78%). All patients presented detectable IgG, which positively correlated with mild neutralizing activity (ID50=157.2, P=0.05). SARS-CoV-2 was not isolated, and a cytopathic effect was lacking. Only three synonymous variants were identified in spike protein coding regions. In conclusion, decreased IFN-γ production by NK cells and low neutralizing antibodies might favor SARS-CoV-2 long-term existence. Further, low viral load and weak viral pathogenicity was observed in COVID-19 patients with long-term SARS-CoV-2 infection.
COMMUNICATION | doi:10.20944/preprints202007.0709.v1
Subject: Biology, Other Keywords: intrinsic multi-drug resistance; acquired multi-drug resistance; circulating tumor cells; single cells; cell clusters; cell monolayer; multi-cellular spheroids; cytometry of reaction rate constant; ovarian cancer
Online: 30 July 2020 (09:01:50 CEST)
Does cell clustering influence intrinsic and acquired multi-drug resistance (MDR) differently? To address this question, we studied cultured monolayers (representing individual cells) and cultured spheroids (representing clusters) formed by drug-naïve (intrinsic MDR) and drug-exposed (acquired MDR) lines of ovarian cancer A2780 cells by cytometry of reaction rate constant (CRRC). MDR efflux was characterized by accurate and robust “cell number vs. MDR efflux rate constant (kMDR)” histograms. Both drug-naïve and drug-exposed monolayer cells presented unimodal histograms; the histogram of drug-exposed cells was shifted towards higher kMDR value suggesting greater MDR activity. Spheroids of drug-naïve cells presented a bimodal histogram indicating the presence of two subpopulations with different MDR activity. In contrast, spheroids of drug-exposed cells presented a unimodal histogram qualitatively similar to that of the monolayers of drug-exposed cells but with a moderate shift towards greater MDR activity. The observed greater effect of cell clustering on intrinsic than on acquired MDR can help guide the development of new therapeutic strategies targeting clusters of circulating tumor cells.
ARTICLE | doi:10.20944/preprints202007.0708.v1
Subject: Biology, Other Keywords: Gold Nanoparticles; Lewis Lung Carcinoma; Radiosensitization; Clonogenic Assay; Comet Assay
Online: 30 July 2020 (08:08:26 CEST)
It has been suggested that particle size plays an important role in determining the genotoxicity of gold nanoparticles (GNPs). The purpose of this study was to compare the potential radio-sensitization effects of two different sized GNPs (3.9 and 37.4 nm) fabricated and examined in vitro in Lewis Lung carcinoma (LLC) as a model of non-small cell lung cancer through use of comet and clonogenic assays. After the treatment of 2Gy X-ray irradiation, both particle sizes demonstrated increased DNA damage when compared to treatment with particles only and radiation alone. This radio-sensitization was further translated into a reduction in cell survival demonstrated by clonogenicity. This work indicates that GNPs of both sizes induce DNA damage in LLC cells at the tested concentrations, whereas the 37.4 nm particle size treatment group demonstrated greater significance in vitro. The presented data aids in the evaluation of the radiobiological response of Lewis Lung carcinoma cells treated with gold nanoparticles.
ARTICLE | doi:10.20944/preprints202005.0463.v2
Subject: Biology, Other Keywords: SARS-CoV-2; COVID-19; genome-wide mutations; transition and transversion; microevolution; disinfectants as mutagens
Online: 30 July 2020 (06:22:00 CEST)
The all-pervasiveness and dynamic nature of the COVID-19 pandemic warrants comprehensive and constant surveillance of the numerous mutations that are accumulating in global SARS-CoV-2 genomes and contributing to the microevoution of the various lineages of the novel coronavirus. This would help us gain insights into the evolving pathogenicity of the virus, and thereby improvise our control and therapeutic strategies. This study explores the genome-wide frequency, gene-wise distribution, and molecular nature, of the large repertoire of point mutations detected across the global dataset of 3,608 SARS-CoV-2 RNA-genomes short-listed from a total 5,485 whole genome sequences deposited in GenBank till 4 June 2020 using a download filter that eliminated all incomplete/gapped sequences. Phylogenomic analysis involving all existing SARS-CoV-2 lineages, represented by 3,740 whole genome sequences from human-source (out of a total of 63,894 sequences stored in the GISAID repository, as on 15 July, 2020), illustrated that the two major-lineages of the virus contributed almost equivalently to the pandemic. However, entities belonging to the early lineages are still mostly spread over Asian countries, whereas those affiliated to recently-derived lineages have a relatively more global distribution. Mutation frequency in the SARS-CoV-2 pan genome was found to be 2.27 × 10-5 nucleotide positions mutated per nucleotide analyzed. An overwhelming majority (count: 1797) of the total 2452 instances of single nucleotide substitution detected (in the SARS-CoV-2 pan genome) were found to be transition mutations with cytidine to uridine (CàU) as the most ubiquitous molecular-type (count: 987). Of the 655 instances of transversion detected, the guanosine to uridine (GàU) variant was most widespread (count: 367). All transcribed and untranscribed loci of the pan genome were found to contain mutation(s). nsp3, and S, N and orf3a, were the most point-mutation-ridden non-structural and structural protein-coding genes, respectively, with 435, 300, 171 and 128 total mutations; 349/86, 192/108, 107/64 and 76/52 transitions/transversions; and 189/48, 106/55, 59/42 and 43/31 CàU/GàU substitutions respectively. Potential mechanistic backgrounds were envisaged for the molecular bias of mutations observed in SARS-CoV-2.
Wed, 29 July 2020
ARTICLE | doi:10.20944/preprints202005.0150.v2
Subject: Biology, Other Keywords: chaperone function; heat-shock proteins; lipid binding; phosphatidylserine; protein refolding
Online: 29 July 2020 (12:18:02 CEST)
HspA1A, a molecular chaperone, translocates to the plasma membrane (PM) of stressed and cancer cells. This translocation results in HspA1A’s cell-surface presentation, which renders tumors radiation insensitive. To specifically inhibit the lipid-driven HspA1A’s PM translocation and devise new therapeutics it is imperative to characterize the unknown HspA1A’s lipid-binding regions and determine the relationship between the chaperone and lipid-binding functions. To elucidate this relationship, we determined the effect of phosphatidylserine (PS)-binding on the secondary structure and chaperone functions of HspA1A. Circular dichroism revealed that binding to PS resulted in minimal modification on HspA1A’s secondary structure. Measuring the release of inorganic phosphate revealed that PS-binding had no effect on HspA1A’s ATPase activity. In contrast, PS-binding showed subtle but consistent increases in HspA1A’s refolding activities. Furthermore, using a Lysine-71-Arginine mutation (K71A; a null-ATPase mutant) of HspA1A we show that although K71A binds to PS with affinities similar to the WT, the kinetics of the binding are significantly different, probably because of the mutant’s inability to achieve specific conformations. These observations suggest a two-step binding model that includes conformational changes and strongly support the notion that the chaperone and lipid-binding activities of HspA1A are dependent but the regions mediating these functions do not overlap. These findings provide the basis for future interventions to inhibit HspA1A’s PM-translocation in tumor cells, making them sensitive to radiation therapy.
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