ARTICLE | doi:10.20944/preprints202110.0209.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Rpi-genes; parental lines; hybrid progeny; dRenSeq; SCAR markers.
Online: 14 October 2021 (08:38:05 CEST)
(1) Background: Although resistance to pathogens and pests has been researched in many potato cultivars and breeding lines with DNA markers, there is scarce evidence as to the efficiency of the marker-assisted selection (MAS) for these traits when applied at the early stages of breeding. A goal of this study was to estimate the potential of affordable DNA markers to track Rpi disease resistance genes, that are effective against the pathogen Phytophthora infestans, as a practical breeding tool on a progeny of 68 clones derived from a cross between the cultivar Sudarynya and 13/11-09. (2) Methods: this population was studied for four years to elucidate the distribution of LB resistance and other agronomical desirable or simple to phenotype traits such as tuber and flower pigmentation, capacity and structure of yield. LB resistance was phenotypically determined through natural and artificial infection and the presence/absence of nine Rpi genes was assessed via 11 sequence-characterized amplified region (SCAR) markers. To aid this analysis, the profile of Rpi genes in the 13/11-09 parent was established using diagnostic resistance gene enrichment sequencing (dRenSeq) as a gold standard. (3) Results: at the early stages of a breeding program, MAS can halve the workload when screening the segregation of F1 offspring and selected SCAR markers for Rpi-genes provide useful tools.
REVIEW | doi:10.20944/preprints202004.0528.v1
Online: 30 April 2020 (11:09:28 CEST)
Sugarcane is an important industrial crop of semitropical and tropical areas. Due to the importance of this crop it is cultivated on nearly 20 million hectares by more than 90 countries. This crop belongs to family Poaceae, a grass family which is economically vital tracheophyte family that has properties much like that of wheat, maize, rice and sorghum. The Poaceae family is globally vital for providing dietary macromolecules, carbohydrates, and different nutrients. The most important item of sugarcane for the consumption is sucrose that gets accumulated in the stalk internodes. Sucrose is taken out and refined by different mills which is used as a sweetener in human food industries and in the fermentation industry. Large production of alcohol is attained by Brazilian sugarcane industries.
REVIEW | doi:10.20944/preprints202202.0200.v1
Subject: Life Sciences, Microbiology Keywords: antibiotic resistance genes; antibiotic resistance gene database; annotation of antibiotic resistance genes
Online: 17 February 2022 (04:52:10 CET)
As the prevalence of antimicrobial resistance genes is increasing in microbes, we are facing the return of the preantibiotic era. Consecutively, the number of studies concerning antibiotic resistance and its spread in the environment is rapidly growing. Next generation sequencing technologies are widespread used in many areas of biological research and antibiotic resistance is no exception. For the rapid annotation of whole genome sequencing and metagenomic results considering antibiotic resistance, several tools and data resources were developed. These databases, however can differ fundamentally in the number and type of genes and resistance determinants they comprise. Furthermore, the annotation structure and metadata stored in these resources can also contribute to their differences. Several previous reviews were published on the tools and databases of resistance gene annotation, however, to our knowledge, no previous review focused solely and in depth on the differences in the databases. In this review, we compare the most well-known and widely used antibiotic resistance gene databases based on their structure and content. We believe that this knowledge is fundamental for selecting the most appropriate database for a research question and for the development of new tools and resources of resistance gene annotation.
ARTICLE | doi:10.20944/preprints202006.0144.v1
Subject: Life Sciences, Other Keywords: Corynebacterium pseudotuberculosis; RNA-Seq; co-expression networks; influence genes; stress condition; causal genes
Online: 12 June 2020 (08:46:02 CEST)
Corynebacterium pseudotuberculosis is a Gram-positive bacterium that causes caseous lymphadenitis, a disease that predominantly affects sheep, goat, cattle, buffalo, and horses, but has also been recognized in other animals. This bacterium generates a severe economic impact on countries producing meat. Gene expression studies using RNA-seq is one of the most commonly used techniques to perform transcriptional experiments. Computational analysis on such data through reverse-engineering algorithms leads to a better understanding of the genome-wide complexity of gene interactomes, enabling the identification of genes having the most significant functions inferred by the activated stress response pathways. In this study, we identified the influential or causal genes from four RNA-seq data-sets from different stress conditions (high iron, low iron, acid, osmosis, and PH) in C. pseudotuberculosis, using a consensus-based network inference algorithm called miRsig and identified the causal genes in the network using the miRinfluence tool, which is based on the influence diffusion model. We found that over 50\% of the genes identified as influential have some essential cellular functions in the genomes. In the strains analyzed, most of the causal genes have crucial roles or participate in processes associated with response to extracellular stresses, pathogenicity, membrane components, and essential genes. This research brings new insight into the understanding of virulence and infection by C. pseudotuberculosis.
REVIEW | doi:10.20944/preprints201901.0035.v3
Online: 24 October 2019 (11:04:57 CEST)
EuAP2 genes are famous for their role in flower development. A legacy of the founding member of this subfamily of transcription factor, whose mutants lacked petals in Arabidopsis. However, studies of other euAP2 genes in several species have accumulated evidence highlighting the diverse roles of euAP2 genes in other aspects of plant development. Here, we emphasize other developmental roles of euAP2 genes in various species and suggest a shift from regarding euAP2 genes as just flowering genes to consider the global role they may be playing in plant development. We hypothesize that their almost universal expression profile and pleiotropic effects of their mutation suggest their involvement in fundamental plant development processes.
ARTICLE | doi:10.20944/preprints202012.0297.v1
Subject: Life Sciences, Biochemistry Keywords: Rhizobium; species complex; bacterial taxonomy; core genes; housekeeping genes; average nucleotide identity; speciation; genospecies
Online: 12 December 2020 (11:51:22 CET)
Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at around 96% ANI, implying that it is a 'natural' unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, "R. indicum" and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterise isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterising the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.
ARTICLE | doi:10.20944/preprints202105.0751.v1
Subject: Life Sciences, Biochemistry Keywords: Recessive Alleles; Heterozygote advantage; Lethal Genes
Online: 31 May 2021 (11:37:33 CEST)
The article derives the probability for lethal recessive alleles in the case of recessive disadvantage or advantage. It is shown that the recessive advantage of a lethal gene can be detected by the ratio of heterozygotes and homozygotes. This demonstrates that the higher IQ of certain ethnic groups cannot be explained by the recessive advantage of lethal genes. The article shows that lethal genes can survive in the population if some lineages of families have much more children than the average.
ARTICLE | doi:10.20944/preprints202105.0283.v1
Online: 13 May 2021 (11:20:29 CEST)
Wheat (Triticum aestivum L.) being a staple food crop is an important nutritional source providing protein and minerals. It is important to fortify staple cereals like wheat with essential minerals to overcome the problems associated with malnutrition. The experiment was designed to evaluate the status of 11 micronutrients including grain iron (GFe) and zinc (GZn) in 62 wheat cultivars released between 1911 and 2016 in Pakistan. Field trials were conducted over two years and GFe and GZn were quantified by both inductively coupled plasma optical emission spectroscopy (ICP-OES) and energy dispersive X-ray fluorescence spectrophotometer (EDXRF). The GZn ranged from 18.4 to 40.8 mg/kg by ED-XRF and 23.7 to 38.8 mg/kg by ICP-OES. Similarly, GFe ranged from 24.8 to 44.1 mg/kg by ICP-OES and 26.8 to 36.6 mg/kg by EDEXR. The coefficient of correlation was higher for GZn (r=0.90), compared to GFe (r=0.68). Modern cultivars like Zincol-16 and AAS-2011 showed higher GFe and GZn along with improved yield components. Old wheat cultivars WL-711, C-518 and Pothowar-70 released before 1970 also exhibited higher value of GFe and GZn, however their agronomic performance was poor. Multivariate analysis using ten micronutrients (Al, Ca, Cu, K, Mg, Mn, Na and P) along with agronomic traits, and genome-wide SNP markers identified the potential cultivar with improved yield, biofortification trait and wider genetic diversity. Genetic gain analysis identified significant increase in grain yield (0.4% year-1), while there was negative gain for GFe (-0.11% year-1) and GZn (-0.15% year-1) over the span of 100 years. The Green Revolution Rht-B1 and Rht-D1 genes had strong association with plant height, and grain yield (GY), while semi-dwarfing alleles had negative effect on GFe and GZn contents. This study provided a valuable insight into biofortification status of wheat cultivars deployed historically in Pakistan and is a valuable source to initiate a breeding strategy for simultaneous improvement in wheat phenology and biofortification.
ARTICLE | doi:10.20944/preprints202209.0283.v1
Subject: Medicine & Pharmacology, Veterinary Medicine Keywords: Wolinella; Virulence genes; Helicobacter pylori; genomic homology
Online: 20 September 2022 (02:06:43 CEST)
Wolinella spp. and Helicobacter spp. have been repeatedly reported in the oral cavity of dogs and are associated with periodontal disease. Wolinella strains predominate in the oral cavity of dogs. The only known species of this genus, Wolinella succinogenes, was considered non-pathogenic until sequence analysis of its genome revealed homologous genes resembling virulence factors in Helicobacter pylori. This has led researchers to question the nonpathogenic status of W. succinogenes. The cagA and babA genes are examples of crucial virulence factors in H. pylori pathogenesis; thus, the present study evaluated the prevalence of these genera and assessed the Wolinella strain genome in terms of the presence of these virulence factors. Multiple specific PCR tests were performed on oral secretion samples collected from 62 dogs by sterile cytobrush to evaluate the genera, species, and presence of virulence genes. The species-specific 16s rRNA genes from the Helicobacter and Wolinella genera were detected in 58.06% and 83.87% of the oral samples, respectively. H. pylori were not detected in the specimens. No cagA and babA genes were detected in the Wolinella spp. or non-pylori Helicobacter genomes. Our results confirmed that Wolinella spp. is the predominant population compared to Helicobacter in the oral cavity of dogs. Apparently, the incidence of Helicobacter infections is generally associated with non-pylori Helicobacter organisms. Despite the hypothesis of genomic homology between W. succinogenes and H. pylori, cagA and babA virulence genes were not identified in any of the oral samples from the dogs.
ARTICLE | doi:10.20944/preprints202108.0260.v1
Subject: Life Sciences, Biochemistry Keywords: Reporter Genes; PET Imaging; Radiotracers; SNAPTag; Xenograft
Online: 11 August 2021 (12:28:16 CEST)
There is a need for versatile in vivo nuclear imaging reporter systems to foster preclinical and clinical research. We explore the applicability of the SNAPTag and novel radiolabeled small-molecule ligands as a versatile reporter gene system for in vivo nuclear imaging. SNAPTag is a high-affinity protein tag used in a variety of biochemical research areas and based on the suicide DNA repair enzyme O6-methylguanine methyl transferase (MGMT). Its ligands are well suited for reporter gene imaging as the benzyl guanine core scaffold can be derivatized with fluorescent or radiolabeled moieties for various applications. Three guanine-based SNAPTag ligands ([18F]FBBG, [18F]pFBG and [18F]mFBG) were synthesized in high yields and were (radio)chemically characterized. HEK293 cells were engineered to express the SNAPTag on the cell surface and served as cell model to assess target affinity by radiotracer uptake assays, Western blotting and SDS-PAGE autoradiography. A subcutaneous HEK293-SNAPTag xenograft model in immunodeficient mice was used for in vivo evaluation of [18F]FBBG amd [18F]pFBG while the biodistribution of [18F]mFBG was characterized in naïve animals. The results were validated by ex vivo biodistribution studies and immunofluorescence staining of the xenografts. All three radiotracers were produced in high radiochemical purity, molar activity and good yields. Western blot analysis revealed successful SNAPTag expression by the transfected HEK293 cells. In vitro testing revealed high target affinity of all three tracers with an up to 191-fold higher signal in the HEK293-SNAPTag cells compared to untransfected cells. This was further supported by a prominent radioactive protein band at the expected size in the SDS-PAGE autoradiograph of cells incubated with [18F]FBBG or [18F]pFBG. The in vivo studies demonstrated high uptake in HEK293-SNAP xenografts compared to HEK293 xenografts with excellent tumor-to-muscle ratios (7.5 ± 4.2 for [18F]FBBG and 10.6 ± 6.2 for [18F]pFBG). In contrast to [18F]pFBG and its chemical analogue [18F]mFBG, [18F]FBBG showed no signs of unspecific bone uptake and defluorination in vivo. Radiolabeled SNAPTag ligands bear great potential for clinical applications such as in vivo tracking of cell populations, antibody fragments and targeted radiotherapy. With excellent target affinity, good stability, and low non-specific binding, [18F]FBBG is a highly promising candidate for further preclinical evaluation.
REVIEW | doi:10.20944/preprints202107.0355.v1
Subject: Medicine & Pharmacology, Allergology Keywords: circadian rhythms; clock genes; glioblastoma; tretament; chronotherapy
Online: 15 July 2021 (10:18:02 CEST)
Gliomas are solid tumors of the Central Nervous System (CNS) that originated from different glial cells. The World Health Organization (WHO) classified these tumors into four groups (I-IV) with increasing malignancy. Glioblastoma (GBM) is the most common and aggressive type of brain tumor classified as a grade IV. GBM are resistant to conventional therapies with poor prognosis after diagnosis even when the Stupp protocol that combines surgery and radiochemotherapy is applied. Nowadays, few novel therapeutic strategies have been used to improve GBM treatment, looking for higher efficiency and lower side effects, but with relatively modest results. The circadian timing system temporally organizes the physiology and behavior of most organisms and daily regulates several cellular processes in organs, tissues, and even in individual cells, including tumor cells. The potentiality of the function of the circadian clock on cancer cells modulation as a new target for novel treatments with a chronobiological basis offers a different challenge that needs to be considered in further detail. The present review will discuss state of the art regarding GBM biology, the role of the circadian clock in tumor progression, and new chrono-chemotherapeutic strategies applied for GBM treatment.
ARTICLE | doi:10.20944/preprints202102.0508.v1
Subject: Biology, Anatomy & Morphology Keywords: Swine; Archaea; Energy Metabolism; CAZyme genes; ARGs
Online: 23 February 2021 (09:54:38 CET)
Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n=76), Denmark (n=100), and France (n=100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (P<0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray-Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus Methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus Methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32%, 11.67%, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being: AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.
ARTICLE | doi:10.20944/preprints202010.0403.v1
Subject: Life Sciences, Biochemistry Keywords: Trichoderma harzianum; Subtilase genes; Bioinformatics analysis; Nematode
Online: 19 October 2020 (17:15:04 CEST)
The subtilase family is the second largest family of serine proteases. Some fungi including Trichoderma species can capture and kill nematodes by secreting hydrolytic enzymes or toxins, among which serine proteases are important enzymes that allow fungi to infect nematodes. Subtilase can degrade nematode and insect body walls. In this study, subtilase family genes were identified from the Trichoderma harzianum genome database, and bioinformatics analysis of the characteristics and evolutionary status of these genes, along with structural and functional analyses of their proteins, was performed. Gene structure analysis revealed that all the 41 subtilase genes contained introns, while some did not have upstream or downstream regions. Chromosome localisation showed that subtilase family members were unevenly distributed in 22 Trichoderma chromosomes, and 3 clusters were present, indicating that they may be hot spots of subtilase genes. Conserved motif analyses showed these proteins contained a commonly conserved motif, and motifs belonging to the same subfamily remained highly similar. The upstream region of the subtilase genes were enriched with different type and numbers of cis-elements, indicating that subtilase genes are likely to play a role in the response to diverse stresses. Transcription of 31 genes was increased after 5 days of infection with nematodes, whereas that of 10 genes decreased. In these subtilase genes, ThSBT4, ThSBT5, ThSBT12, ThSBT27, ThSBT34, ThSBT35, ThSBT38, and ThSBT40 showed significantly upregulated expression with a log2 fold change value of more than 4, and ThSBT35 showed the highest peak. These results laid a theoretical foundation for further research on the function of the subtilase genes and the mechanism of the resistance response.
REVIEW | doi:10.20944/preprints201902.0179.v1
Subject: Keywords: Histocompatibility complex (MHC) genes, disease resistance, fish
Online: 19 February 2019 (11:14:48 CET)
The basic pattern of MHC variation in fish, with MHC class I versus class II, and polymorphic classical versus nonpolymorphic nonclassical, is similar in fish and mammals. Nevertheless, in many or all teleost fishes, important differences with mammalian or human MHC were observed: (1) The allelic/haplotype diversification levels of classical MHC class I genes tend to be much higher than in mammals; (2) Teleost fish classical MHC class I and class II loci are not linked. The present article summarizes previous studies that performed quantitative trait loci (QTL) analysis for mapping differences in teleost fish disease resistance, and discusses them from MHC point of view. Overall, those studies suggest the possible importance of genomic regions including classical MHC class II and nonclassical MHC class I genes, whereas similar observations were not made for the genomic regions with the highly diversified classical MHC class I alleles. The present study is a review and discussion of the fish MHC situation.
REVIEW | doi:10.20944/preprints202201.0186.v1
Subject: Behavioral Sciences, Behavioral Neuroscience Keywords: habituation learning; habituation genes; habituation pathways; neurodevelopmantal disorders
Online: 13 January 2022 (10:57:23 CET)
Habituation, the most ancient and fundamental form of learning, manifests already before birth. Neuroscientists have been fascinated for decades by its function as a firewall protecting our brains from sensory information overload and its indispensability for higher cognitive processing. Evidence that habituation learning is affected in autism and related monogenic neurodevelopmental syndromes and their animal models has exponentially grown, but the potential of this convergence to advance both fields is still largely unexploited.In this review, we provide a systematic overview of the genes that to date have been demonstrated to underlie habituation across species. We describe the biological processes they converge on, and highlight core regulatory pathways and repurposable drugs that may alleviate the habituation deficits associated with their dysregulation. We also summarize currently used habituation paradigms and extract the most important arguments from literature that support the crucial role of habituation for cognition in health and disease. We conclude that habituation is a powerful tool to overcome current bottlenecks in research, diagnostics and treatment of neurodevelopmental disorders.
ARTICLE | doi:10.20944/preprints202111.0326.v1
Subject: Life Sciences, Genetics Keywords: SNP; calpaincalpastatin system genes; genomic association; tenderization; ageing
Online: 18 November 2021 (13:48:09 CET)
The most important factor that determines beef tenderness is its proteolytic activity and the balance between calpain1 protease activity and calpastatin inhibition is especially important, while contributions could arise from calpain2 and possibly calpain3. These processes are however affected by the meat aging process itself. To determine whether genotypes in the calpaincalpastatin system can enhance tenderness throughout a 20 day aging period, South African purebred beef bulls (n=166) were genotyped using the Illumina BovineHD SNP BeadChip, through genebased association analysis targeting the cast, capn3, capn2 and capn1 genes. The WarnerBratzler shear force (WBSF) and myofibril fragment length (MFL) of Longissimus thoracis et lumborum (LTL) steaks were evaluated between d 3 d 20 of aging, with protease enzyme activity in the first 20 h postmortem. Although several of the 134 SNP associated with tenderness, only seven SNP in the cast, capn2 and capn1 genes sustained genetic associations, additive to agingassociated increases in tenderness for at least three of the four aging periods. While most genomic associations were relatively stable over time, some genotypes within SNP responded differently to aging, resulting in altered genomic effects over time. The level of aging at which genomic associations are performed is an important factor that determines whether SNP affect tenderness phenotypes.
ARTICLE | doi:10.20944/preprints202111.0140.v1
Subject: Biology, Animal Sciences & Zoology Keywords: Streptococcus uberis; mastitis; typing; antimicrobial susceptibility; resistance genes
Online: 8 November 2021 (13:12:44 CET)
Intrammary infections are a major problem for dairy sheep farms, and Streptococcus uberis is one of the main etiological agents of ovine mastitis. Surveys on antimicrobial resistance are still limited in sheep and characterization of isolates is important for acquiring information on resistance and for optimizing therapy. In this study, a sampling of 124 S. uberis isolates collected in Sardinia (Italy) from sheep milk was analysed by multilocus-sequence typing (MLST) and pulsed field gel electrophoresis (PFGE) for genetic relatedness. All isolates were also subjected to antimicrobial susceptibility analysis by the disk diffusion test using a panel of 14 antimicrobials. Resistance genes were detected by PCR assays. MLST analysis revealed that the isolates were grouped into 86 sequence types (STs), of which 73 were new genotypes, indicating a highly diverse population of S. uberis. The most frequently detected lineage was the clonal complex (CC)143, although representing only 13.7% of all characterized isolates. A high level of heterogeneity was also observed among the SmaI PFGE profiles, with 121 unique patterns. Almost all (96.8%) isolates were resistant to at least one antimicrobial, while all exhibited phenotypic susceptibility to oxacillin, amoxicillin-clavulanic acid and ceftiofur. Of the antimicrobials tested, the highest resistance rate was found against streptomycin (93.5%), kanamycin (79.8%) and gentamicin (64.5%), followed by novobiocin (25%) and tetracycline-TE (19.3%). Seventy-four (59.7%) isolates were simultaneously resistant to all aminoglycosides tested. Seventeen isolates (13.7%) exhibited multidrug resistance. All aminoglycosides-resistant isolates were PCR negative for aad-6 and aphA-3’ genes. Among the TE-resistant isolates, the tetM gene was predominant, indicating that the resistance mechanism is mainly mediated by the protection of ribosomes and not through the efflux pump. Three isolates were resistant to erythromycin, and two of them harboured the ermB gene. This is the first study reporting a detailed characterization of the S. uberis strains circulating in Sardinian sheep. Further investigations will be needed to understand the relationships between S. uberis genotypes, mastitis severity, and intra-mammary infection dynamics in the flock, as well as to monitor the evolution of antimicrobial resistance.
ARTICLE | doi:10.20944/preprints202107.0405.v1
Subject: Life Sciences, Biochemistry Keywords: Sheep; E. coli; shiga-toxin; antimicrobial resistance genes
Online: 19 July 2021 (11:12:01 CEST)
Inappropriate antimicrobial treatment can pose a risk for developing resistance against antimi-crobial drugs in bacteria. Close human contact might have a higher chance of being transmitted to humans from sheep if the sheep population is a potential reservoir of zoonotic pathogens such as shiga toxin-producing Escherichia coli (E. coli) (STEC). Therefore, this study aimed to exam-ine the sheep population in rural Bangladesh for antimicrobial resistant STEC. We screened 200 faecal samples collected from sheep in three Upazila from the Chattogram district. Phenotypical-ly positive E. coli isolates were examined for two shiga toxin-producing genes – stx1 and stx2. PCR positive STEC isolates were investigated for the presence of antimicrobial resistance genes- blaTEM, sul1 and sul2. In total, 123 of the 200 tested samples were confirmed positive E. coli by cul-tured based methods. PCR results show 17(13.8%) E. coli isolates harboured ≥ one virulent gene (stx1 or/and stx2) of STEC. Six of the tested STEC isolates exhibited blaTEM gene; eight STEC isolates had sul1 gene, and sul2 gene was detected in ten STEC isolates. To our knowledge, this study is the first to reveal a significant proportion of STEC isolated from sheep in rural Bangla-desh harbouring antimicrobial resistance genes.
REVIEW | doi:10.20944/preprints202107.0203.v1
Online: 8 July 2021 (13:30:31 CEST)
Clopidogrel is one of the thienopyridine antiplatelet drugs commonly used as a prophylactic medication to prevent coagulation in vessels and cardiovascular events. The molecule of clopidogrel is metabolized in the liver via phase-I and phase-II metabolism pathways. The sulfenic acid clopidogrel metabolite undergoes phase-II metabolism through conjugation with glutathione by the glutathione-s-transferase (GST) to form a glutathione conjugate of clopidogrel (inactive metabolite). A glutaredoxin enzyme removes the glutathione conjugated with clopidogrel to form cis-thiol-clopidogrel. This review focused on the polymorphisms of genes related to phase-II metabolism during the clopidogrel bioactivation process. Overall, no well-controlled studies were done about the relationship between the clopidogrel bioactivation process and genes related to phase-II metabolism’s enzymes. Nevertheless, some polymorphisms of G6PD, GCLC, GCLM, GSS, GST, GSR, HK, and GLRX genes could be responsible for clopidogrel resistance due to low glutathione conjugate or glutaredoxin plasma levels. Studies needed to be concerned with the relationship between clopidogrel resistance and phase-II metabolism issues in the near future.
ARTICLE | doi:10.20944/preprints202106.0719.v1
Subject: Engineering, Automotive Engineering Keywords: foam; flocculation; FLO genes; Saccharomyces; fuel-ethanol; FLO8
Online: 30 June 2021 (08:59:57 CEST)
Many contaminant yeast strains able to survive inside fuel ethanol industrial vats show detrimental cell surface phenotypes, such as filamentation, invasive growth, flocculation, biofilm formation and excessive foam production. Previous studies have linked some of these phenotypes to the expression of FLO genes, and the presence of gene length polymorphisms causing the expansion of FLO gene size appears to result in stronger flocculation and biofilm formation phenotypes. We have performed here a molecular analysis of FLO1 and FLO11 gene polymorphisms present in contaminant strains of S. cerevisae from Brazilian fuel ethanol distilleries showing strong foaming phenotypes during fermentation. The size variability of these genes was correlated with cellular hydrophobicity, flocculation and highly foaming phenotypes in these yeast strains. Our results also show that deleting the major activator of FLO genes (the FLO8 gene) from the genome of a contaminant and highly foaming industrial strain avoids problematic foam formation, flocculation, invasive growth and biofilm production by the engineered (flo8∆::BleR / flo8Δ::kanMX) yeast strain. Thus, the characterization of highly foaming yeasts and the influence of FLO8 in this phenotype opens new perspectives for yeast strain engineering and optimization in the sugarcane fuel-ethanol industry.
REVIEW | doi:10.20944/preprints201909.0222.v1
Subject: Life Sciences, Genetics Keywords: hearing impairment; novel murine genes; gene enrichment; africa
Online: 19 September 2019 (11:27:27 CEST)
The prevalence of congenital hearing impairment (HI) is highest in Africa. Estimates evaluated genetic causes to account for 31% of HI cases in Africa, but the identification of associated causative genes mutations have been challenging. In this study, we reviewed the potential roles, in humans, of 38 novel genes identified in a murine study. We gathered information from various genomic annotation databases and performed functional enrichment analysis using online resources i.e. genemania and g.proflier. Results revealed that 27/38 genes are express mostly in the brain, suggesting additional cognitive roles. Indeed, HERC1- R3250X had been associated with intellectual disability in a Moroccan family. A homozygous 216-bp deletion in KLC2 was found in two siblings of Egyptian descent with spastic paraplegia. Up to 27/38 murine genes have link to at least a disease, and the commonest mode of inheritance is autosomal recessive (n=8). Network analysis indicates that 20 other genes have intermediate and biological links to the novel genes, suggesting their possible roles in HI. This study will contribute to advance our knowledge in unravelling the biological roles of novel murine HI genes in humans and could enhance the understanding of the genetic causes of HI in Africans.
ARTICLE | doi:10.20944/preprints201906.0082.v1
Subject: Biology, Anatomy & Morphology Keywords: hox genes; temporal collinearity; axial patterning; gastrulation; xenopus
Online: 11 June 2019 (04:03:46 CEST)
Kondo and collaborators recently reported the absence of Hox temporal collinearity in Xenopus tropicalis. They found none in the initiation of accumulation of Hox transcripts (detected via RNA seq). And none in the initial expression sequence of primary unprorocessed transcripts (Identified by using qRT-PCR against introns or intron-exon boundaries). Nor in the initial acquisition by Hox gene DNA of a mark for active chromatin. These findings are in conflict with the idea that temporal collinearity has to do with the initiation of Hox gene transcription or with the opening of and a progression from repressed to active states in Hox chromatin. But collinear acquisition of the same active chromatin mark has been shown by others in murine 5’ Hoxd cluster genes.The reason for this difference is unknown . This careful study thus indicated that the initiation phase of Hox expression shows no temporal collinearity in X. tropicalis. A previous study in X. laevis from the same group also showed that the sequence of times for reaching (normalised) half maximal Hox expression showed no temporal collinearity. These conclusions are likely to be correct. These authors do however also conclude that “experimental evidence for the temporal collinearity hypothesis is not strong” There is however strong evidence that Hox temporal collinearity does occur in early vertebrate embryos. Below. I present and discuss 3 lines of evidence to resolve the present conflict I argue that Hox temporal collinearity actually does exist and that it is part of a central mechanism in early development.
ARTICLE | doi:10.20944/preprints201807.0113.v1
Online: 6 July 2018 (09:37:08 CEST)
Bidirectional gene promoters affect the transcription of two genes, leading to the hypothesis that they should exhibit protection against genetic or epigenetic changes in cancer. Therefore, they provide an excellent opportunity to learn about promoter susceptibility to somatic alteration in tumors. We tested this hypothesis using data from genome-scale DNA methylation (14 cancer types), simple somatic mutation (10 cancer types), and copy number variation profiling (14 cancer types). For DNA methylation, the difference in rank differential methylation between tumor and tumor-adjacent normal matched samples based on promoter type was tested by Wilcoxon rank sum test. Logistic regression was used to compare differences in simple somatic mutations. For copy number alteration, a mixed effects logistic regression model was used. The change in methylation between non-diseased tissues and their tumor counterparts was significantly greater in single compared to bidirectional promoters across all 14 cancer types examined. Similarly, the extent of copy number alteration was greater in single gene compared to bidirectional promoters for all 14 cancer types. Furthermore, among 10 cancer types with available simple somatic mutation data, bidirectional promoters were slightly more susceptible. These results suggest that selective pressures related with specific functional impacts during carcinogenesis drive the susceptibility of promoter regions to somatic alteration.
REVIEW | doi:10.20944/preprints201806.0373.v1
Subject: Biology, Physiology Keywords: archaic human genes; obesity; diabetes mellitus; Indigenous Australians
Online: 25 June 2018 (08:13:36 CEST)
Indigenous Australians have been particularly affected by type 2 diabetes mellitus due to their genetic susceptibility and a range of environmental risk factors. Recent genetic studies link predisposition to some diseases, including diabetes, to archaic humans, such as Neanderthals and Denisovans, suggesting persistence of ancient alleles in the genomes of modern humans. In this review we discuss the evolutionary role of the negative genetic selection associated with an adopted Western lifestyle as well as DNA variants influencing predisposition to obesity and diabetes in the Australian Indigenous population. We review the contribution of the ancient gene/pathways to the modern human phenotypes including the Neanderthal haplotype-tagging SNPs in NTRK2 gene, which may continue to play a role in obesity in Indigenous Australians.
ARTICLE | doi:10.20944/preprints201804.0325.v1
Subject: Biology, Animal Sciences & Zoology Keywords: mastitis; dairy cow; S. aureus; genotypes; virulence genes
Online: 25 April 2018 (08:04:51 CEST)
Staphylococcus aureus (S. aureus) is recognized worldwide as one of the major agents of dairy cow intra-mammary infections. This microorganism can express a wide spectrum of pathogenic factors used to attach, colonize, invade and infect the host. The present study evaluated 120 isolates from eight different countries that were genotyped by RS-PCR and investigated for 26 different virulence factors to increase the knowledge on the circulating genetic lineages among the cow population with mastitis. New genotypes were observed for South African strains while for all the other countries new variants of existing genotypes were detected. For each country, a specific genotypic pattern was found. Among the virulence factors, fmtB, cna, clfA and leucocidins genes were the most frequent. The sea and sei genes were present in seven out of eight countries; seh showed high frequency in South American countries (Brazil, Colombia, Argentina), while sel was harboured especially in one Mediterranean country (Tunisia). The etb, seb and see genes were not detected in any of the isolates, while only two isolates were MRSA (Germany and Italy) confirming the low diffusion of methicillin resistance microorganism among bovine mastitis isolates. This work demonstrated the wide variety of S. aureus genotypes found in dairy cattle worldwide. This condition suggests that considering the region of interest might help to formulate strategies for reducing the infection spreading.
ARTICLE | doi:10.20944/preprints201803.0002.v1
Subject: Life Sciences, Molecular Biology Keywords: ark shell; transcriptome; growth; metabolism; differentially expressed genes
Online: 1 March 2018 (04:47:45 CET)
To understand the molecular mechanism associated with growth variability in bivalves, the Solexa/Illumina technology was employed to analyze the transcriptomic profiles of extreme growth rate differences (fast- VS. slow-growing individuals) in one full-sib family of the ark shell Scapharca subcrenata. De novo assembly of S. subcrenata transcriptome yielded 276,082,016 raw reads, which were assembled into 98,502 unique transcripts by Trinity strategy. A total of 6,357 differentially expressed genes (DEGs) were obtained between fast- and slow-growing individuals, with 580 up-regulated expression and 5777 down-regulated expression. Functional annotation revealed that the largest proportion of DEGs were classified to the large or small subunit ribosomal protein, all of which showed significantly lower expression levels in fast-growing group than those in slow-growing group. GO enrichment analysis identified the maximum of DEGs to biological process, followed by molecular function and cellular component. Most of the top enriched KEGG pathways were related to energy metabolism, protein synthesis and degradation. These findings reveal the link between gene expression and contrasting phenotypes in ark shells, which support that fast-growing individuals may be resulted from decreased energy requirements for metabolism maintenance, accompanying with greater efficiency of protein synthesis and degradation in bivalves.
REVIEW | doi:10.20944/preprints202209.0412.v1
Subject: Medicine & Pharmacology, Clinical Neurology Keywords: Huntington’s disease; circadian rhythm; clock genes; adult neurogenesis; chemogenetics
Online: 27 September 2022 (04:45:35 CEST)
Huntington’s disease (HD) causes progressive movement disorders and cognitive deficits. Besides, sleep disturbances and emotional distress are prominent clinical signatures of HD. The experimental subjects and HD human brains display altered regenerative plasticity resulting from aberrant neurogenic and nonneurogenic areas. Sleep disorders, emotional disruption, and cognitive deficits have been linked to impaired cell cycle events of neural stem cells (NSC) in neurodegenerative disorders. In a physiological state, circadian clock gene pathways play important roles in the regulation of the proliferation and differentiation of NSC, whereas the irregular circadian clock pathway is attributed to impairment in the neurogenic process. The recent advancement of chemogenetic-based approaches represents a potential scientific tool to rectify the abnormal circadian clock which may aid in mitigating neurogenic failure in the brain. Notably, GABAergic vasoactive intestinal peptide (VIP)-expressing neurons in the brain plays a key role in the regulation of neuroplasticity and circadian rhythm. Thus, this conceptual review article addresses the potential link between sleep disorder and aberrant neurogenic events in HD and proposes chemogenetic kindling of vasoactive intestinal peptide (VIP) -expressing GABAergic neurons in the brain as a therapeutic strategy for reprogramming the clock gene pathways in mitigating the neurodegenerative failure in HD.
ARTICLE | doi:10.20944/preprints202206.0389.v1
Subject: Life Sciences, Microbiology Keywords: Ricefish; Microbiome; Ampicillin; Erythromycin; Immune and Stress-Related Genes
Online: 29 June 2022 (03:05:46 CEST)
Antibiotics have been used in various fields such as livestock farm and fish farm as well as hospital in order to treat diseases caused by bacteria. However, the antibiotics that are not completely decomposed, but remains as residue and discharge to aquatic environment, can cause an imbalance in the gut flora of host, as well as regulate abnormal host gene regulatory system. We investigated the effects of chronic exposure with the low concentrations of erythromycin and ampicillin on gut microbiome and immune and stress-related gene expression using Korea native ricefish (Oryzias latipes). As a result of microbiome analysis, the proportion of Proteobacteria was increased in the ricefish when exposed to erythromycin and ampicillin chronically, whereas the proportion of other bacterial phyla decreased. In addition, the immune and stress-related genes were significantly influenced in the ricefish under the chronic antibiotics exposure. These results show that the internal microbial flora and the host gene expression are susceptible even in the low concentration of chronic antibiotic existing environments. This study provides the importance of the appropriate use of antibiotics dose to maintain the sustainable and healthy aquaculture industry and water ecosystem.
ARTICLE | doi:10.20944/preprints202103.0197.v1
Subject: Life Sciences, Biochemistry Keywords: Systems biology; cervical cancer; prognostic biomarker; differentially expressed genes.
Online: 5 March 2021 (21:25:47 CET)
Nowadays, cervical cancer (CC) is treated as the leading cancer among women throughout the world. Despite effective vaccination and improved surgery and treatment, CC remains its fatality rate about half of the infected populations globally. The major screening biomarkers and therapeutic target identification have now become a global concern. The present study, we have employed systems biology approaches to retrieve the potential biomarkers and pathways from the transcriptomic profiling. Initially, we have identified 76 of each up-regulated and down-regulated gene from a total of 4,643 differentially expressed genes. The up-regulatory genes are mainly concentrating on immune-inflammatory response and the down-regulatory genes are on receptor binding and gamma-glutamyltransferase. The involved pathways associated with these genes were also assessed through pathway enrichment and they were mainly focused on different cancer pathways, immunoresponse, and cell cycle pathways. After the subsequent enrichment of these genes, we have identified 12 hub genes, which play a crucial role in CC. Furthermore, the survival of the hub genes was also assessed, and among them, finally, CXCR4 has identified as one of the most potential differentially expressed gene that might play a vital role to the survival of CC patients. Thus CXCR4 could be used as a prognostic biomarker and development of a drug target for CC.
ARTICLE | doi:10.20944/preprints202101.0185.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Maize; Prolificacy; Linkage analysis; GWAS; Candidate genes; Ethylene signaling
Online: 11 January 2021 (11:28:54 CET)
For the different harvest targets, the requirement for the prolificacy trait of maize was also different, so prolificacy is of great significance for modern production. Although some QTLs and genes associated with prolificacy in teosinte have been reported, the genetic mechanism of prolificacy in maize has not been fully elucidated. In this study, two RIL populations and GWAS population were used to genetic research of prolificacy trait in maize, with multi-environment. Combine linkage analysis and Genome-wide association study has identified a total of 13 QTLs and 8 significant SNPs. There were two genes related to tissue differentiation in the stable QTL qP9-2, and two significant SNPs corresponding to three genes were in QTL qP5-1 and QTL qP7-1, respectively. Four candidate genes GRMZM2G317262, GRMZM2G317584, GRMZM5G882364 and GRMZM2G141679 were finally screened out by qRT-PCR analysis. Based on the function of candidate genes, ethylene signaling pathway plays an important role in the formation of prolificacy in maize. It has deepened our understanding of the formation mechanism of prolificacy and laid a foundation for breeding new varieties with various prolificacy in maize.
ARTICLE | doi:10.20944/preprints202009.0089.v1
Subject: Life Sciences, Microbiology Keywords: Pasteurella multocida; antimicrobial resistance genes; antimicrobial susceptibility patterns; swine
Online: 4 September 2020 (07:47:26 CEST)
Forty-eight Pasteurella multocida isolates were recovered from porcine pneumonic lungs collected in Norwestern Spain (2017- 2019). These isolates were characterized for their minimal inhibition concentrations to twelve antimicrobial agents and for the appearance of eight resistance genes: tetA, tetB, blaROB1, blaTEM, ermA, ermC, mphE and msrE. Relevant resistance percentages were shown to teracyclines, sulphamethoxazole/trimethoprim and tiamulin, thus suggesting that P. multocida isolates were mostly susceptible to amoxicillin, ceftiofur, enrofloxacin, florfenicol, marbofloxacin and macrolides. 29.2% of isolates were resistant to more than two antimicrobials. The tetracycline resistance genes (tetA and tetB) were detected in 22.9% of the isolates, but none was positive to both simultaneously; blaROB1 and blaTEM genes were found in one third of isolates but both genes were detected simultaneously in only one isolate. ermC gene was observed in 41.7% of isolates, a percentage that decreased until 22.9% for msrE; finally, ermA was harboured by 16.7% and mphE was not found in any of them. Six clusters were established based on hierarchical clustering analysis on antimicrobial susceptibility for the twelve antimicrobials. Generally, it was unable to foresee the antimicrobial susceptibility pattern for each family and the association of each particular isolate inside the clusters established from the presence or absence of the resistance genes analyzed.
CONCEPT PAPER | doi:10.20944/preprints202004.0358.v1
Subject: Life Sciences, Microbiology Keywords: MDR typhoid; metal resistant genes; water toxicity; gut microbiome
Online: 20 April 2020 (02:27:07 CEST)
AMR and drug void have caused huge panic today with few thousand death per year. MDR Typhoid was a serious old disease and caused serious health hazard in humen and animals demanding an update on molecular biology of the status on transferable genetic elements. R-plasmids combined in F’-plasmid and the new MDR conjugative plasmids were shown abundant in Sanmonella ranging 70-440kb with similarities. BlaTEM, blaCTX-M, blaOXA, blaNDM mdr genes were abundant in >50 plasmids analyzed and metal resistant gene clusters are predominant in most large plasmids. Among the acetyltransferase all catA1, aacA1 and aac-1b-cr genes were located. Abundant streptomycin phosphotransferases (StrAB) and rarely colistin resistant Mcr-5/9 phosphoethanolamine–lipid A transferase were detected. Altered isomeric dihydropterote synthases (Sul1/2/3) were present giving sulfamethoxazole resistance and dhfr gene frequently associated giving trimethoprim resistance. Metal resistant gene clusters like SilABC (CusABC), PcoAB, RcnA, terABC, and merABCXT etc were found in many Salmonella enterica plasmids. Toxin genes like HipA and virulence genes like spvABD were located in few plasmids increasing virulence and pathogenesis. Drug efflux genes tetA or tetB and OqxB, floR, CmlA were frequent where as QepA and EamA genes were rarely seen. Thus, Salmonella metal resistant genes combined with antibiotic resistant genes has tried to overcome the both toxic antibiotics and metalions causing Typhoid AMR. Such acquisition spreads salmoniasis in the live stocks (pig, cow, chicken) where toxic soil and water dominate increasing chance of MDR typhoid in human.
ARTICLE | doi:10.20944/preprints201911.0282.v1
Subject: Biology, Animal Sciences & Zoology Keywords: Nile tilapia; pseudomonas; antibiotic resistance; biofilm formation; virulence genes
Online: 24 November 2019 (14:11:40 CET)
Pseudomonas aeruginosa (P. aeruginosa) produces a suite of virulence factors that are coordinated by Quorum Sensing (QS) contributing to its disease-causing ability in aquaculture. The present study is first of its kind to obtain information regarding the presence and distribution of five QS genes, three virulence genes viz: lasI, lasR, rhlI, rhlR, rhlAB, toxA, aprA and plcH and seven of the Extended-spectrum βlactamases (blaVEB, blaPER, blaTEM,, blaSHV, blaCTX-M1, blaCTX-M2 and blaCTX-M3) of Pseudomonas species isolated from fish meat by direct PCR. Bacterial identification was based mainly on conventional biochemical techniques using the Vitek 2, automated system. Phenotypic sensitivity of antibiotics was established by the agar disc diffusion technique through 16 various antimicrobial drugs. Quantification of their in vitro production of numerous virulence genes outside the cell that are QS dependent namely, pyocyanin, elastase, alkaline protease, biofilm and cytotoxicity of Vero cell was as well executed. Fifteen genes demonstrated an enormous variety in their association. The total number of Pseudomonas species isolates were 30/100 to be identified by the API 20NE system as P. aeruginosa 12/30 (40%), P. fluorescens 8/30 (27%), P. putida 6/30 (20%) and P. alkylphenolia 4/30 (13%). The outcomes of this study have great significance for the strategic designation of QS quenching.
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Oral cancer; Oropharyngeal cancer; Tumor-suppressor genes; Promoter hypermethylation
Online: 19 March 2019 (12:56:24 CET)
Silencing of tumor suppressor genes (TSGs) by DNA promoter hypermethylation is an earlyevent in carcinogenesis; Hence TSGs may serve as early tumor biomarkers. We determinedthe promoter methylation levels of p16INK4a, RASSF1A, TIMP3 and PCQAP/MED15 TSGs in salivary DNA from oral cancer (OC), and oropharyngeal cancer (OPC) patients, using methylation specific PCR coupled with densitometry analysis. We assessed the association between DNA methylation of individual TSGs with OC and OPC risk factors. We evaluated the performance and the clinical validity of this quadruple methylation marker panel in discriminating OC and OPC patients from healthy controls using CombiROC web tool. Our study reported that RASSF1A, TIMP3 and PCQAP/MED15 TSGs were significantly hypermethylated in OC and OPC cases compared to healthy controls. We found that DNA methylation levels of TSGs were significantly augmented by smoking, alcohol use and betel quid chewing by indicating that the fact that frequent exposure to risk factors may drive oral and oropharyngeal carcinogenesis through TSG promoter hypermethylation. Also, this quadruple-methylation marker panel of p16INK4a, RASSF1A, TIMP3 and PCQAP/MED15 TSGs demonstrated excellent diagnostic accuracy in the early detection of OC at 91.7% sensitivity and 92.3% specificity, and OPC at 99.8% sensitivity and 92.1% specificity, from healthy controls.
ARTICLE | doi:10.20944/preprints201809.0274.v1
Subject: Chemistry, Food Chemistry Keywords: rice bran; rice genes; rice cultivars; metabolic pathway; metabolomics
Online: 15 September 2018 (19:34:43 CEST)
Rice (Oryza sativa L.) processing yields ~60 million metric tons of bran annually. Rice genes producing bran metabolites of nutritional and human health importance were assessed across 17 diverse cultivars from seven countries using non-targeted metabolomics and resulted in 378-430 metabolites. Gambiaka cultivar had the highest number and Njavara had the lowest number of metabolites. The 71 rice bran compounds of significant variation by cultivar included 21 amino acids, seven carbohydrates, two metabolites from cofactors and vitamins, 33 lipids, six nucleotides, and two secondary metabolites. Tryptophan, -ketoglutarate, γ-tocopherol/β-tocopherol and γ-tocotrienol are example bran metabolites with extensive cultivar variation and genetic information. 34 rice bran components that varied between cultivars linked to 535 putative biosynthetic genes using to the OryzaCyc 4.0, Plant Metabolic Network database. Rice genes responsible for bran composition with animal and human health importance is available for rice breeding programs to utilize in crop improvement.
ARTICLE | doi:10.20944/preprints201808.0272.v1
Subject: Life Sciences, Microbiology Keywords: Staphylococcus aureus, meat, raw milk, antibiotics; antibiotic resistance genes
Online: 15 August 2018 (13:58:11 CEST)
Background: Staphylococcus aureus (S. aureus) occasionally threatens the life of the host as a persistent pathogen even though it is normal flora of humans and animals. We characterized drug resistance in S. aureus isolated from animal carcasses and milk samples from the abattoirs and dairy farms in the Eastern Cape Province. Methods: A 1000 meat swab samples and 200 raw milk samples were collected from selected abattoirs and dairy farms in the Eastern Cape Province, South Africa. S. aureus was isolated and positively identified using biochemical tests and confirmed by molecular methods. Antibiotic susceptibility test against 14 different antibiotics was performed against all isolates. Antibiotic resistance genes were also detected. Results: Of the 1200 samples collected, 134 (11.2%) samples were positive for S. aureus. Resistance ranged from 71.6% for penicillin G to 39.2% for tetracycline. Resistance gene (blaZ) was detected in 13 (14.9%), while msrA was found in 31 (52.5%) of S. aureus isolates. Conclusions: The present result shows the potential dissemination of multidrug-resistant S. aureus strains in the dairy farms and abattoirs in the Eastern Cape. Therefore, this implies that the organism may rapidly spread through food and pose serious public health risk
ARTICLE | doi:10.20944/preprints202209.0362.v1
Subject: Life Sciences, Genetics Keywords: RNA-Seq; Vitamin K; Comorbidities; Differential Expressed Genes; Variant analysis
Online: 23 September 2022 (09:13:29 CEST)
Systems genetics is key for integrating a large number of variants associated with diseases. Vitamin K (VK) is one of the scarcely studied conditions in lieu of ascertaining either the differentially expressed genes (DEGs) or variants in an individual subpopulation of diseased phenotypes associated with VK, viz. myocardial infarction, renal failure, prostate cancer, thrombosis, thrombocytopenia, coagulation related diseases to name a few. In this work, we have screened characteristic DEGs common to three VK-related diseases, viz. myocardial infarction, renal failure and prostate cancer and asked whether or not any DEGs in addition to pathogenic variants are common to these conditions. We attempt to bridge the gap in finding characteristic biomarkers and discuss the role of long noncoding RNAs (lncRNAs) in the biogenesis of VK deficiencies.
ARTICLE | doi:10.20944/preprints202208.0341.v1
Subject: Medicine & Pharmacology, Psychiatry & Mental Health Studies Keywords: Schizophrenia; cell types proportions; differential expression genes; functional pathways; CIBERSORTx
Online: 18 August 2022 (10:54:05 CEST)
Schizophrenia (SCZ) is a severe mental disorder that may result in hallucinations, delusions, and extremely disordered thinking. How each cell type in the brain contributes to SCZ occurrence is still unclear. Here, we leveraged the human dorsolateral prefrontal cortex bulk RNA-seq data, then used the RNA-seq deconvolution algorithm CIBERSORTx to generate SCZ brain single-cell RNA-seq data for a comprehensive analysis to understand SCZ-associated brain cell types and gene expression changes. Firstly, we observed that the proportions of brain cell types in SCZ differed from normal samples. Among these cell types, astrocyte, pericyte, and PAX6 cells were found to have a higher proportion in SCZ patients (astrocyte: SCZ = 0.163, Control = 0.145, P.adj = 4.9×10-4; pericyte: SCZ = 0.057, Control = 0.066, P.adj = 1.1×10-4; PAX6 : SCZ = 0.014, Control = 0.011, P.adj = 0.014), while the L5/6_IT_CAR3 cells and LAMP5 cells are the exact opposite (L5/6_IT_Car3 : SCZ = 0.102, Control = 0.108, P.adj = 0.016; LAMP5 : SCZ = 0.057, Control = 0.066, P.adj = 2.2×10-6). Next, we investigated gene expression in cell types and functional pathways in SCZ. We observed chemical synaptic transmission dysregulation in two types of GABAergic neurons (PVALB and LAMP5), and immune reaction involvement in GABAergic neurons (SST) and non-neuronal cell types (endothelial and oligodendrocyte). Furthermore, we observed that some differential expression genes from bulk RNA-seq displayed cell-type-specific abnormal in the expression of molecules in SCZ. Finally, the cell types with the SCZ-related transcriptomic changes could be considered to belong to the same module since we observed two major similar coordinated transcriptomic changes across these cell types. Together, our results offer novel insights into cellular heterogeneity and the molecular mechanisms underlying SCZ.
ARTICLE | doi:10.20944/preprints202101.0320.v2
Subject: Biology, Plant Sciences Keywords: Boechera; Brassicaceae; CENH3; APOLLO; apomixis associated genes; cell division; apomeiosis
Online: 20 December 2021 (10:40:57 CET)
Apomictic plants (reproducing via asexual seeds), unlike sexual individuals, avoid meiosis and egg cell fertilization. Consequently, apomixis is very important for fixing maternal genotypes in the next plant generations. Despite the progress in the study of apomixis, molecular and genetic regulation of the latter remains poorly understood. So far APOLLO (Aspartate Glutamate Aspartate Aspartate histidine exonuclease) is one of the very few described genes associated with apomixis in Boechera species. The centromere-specific histone H3 variant encoded by CENH3 gene is essential for cell division. Mutations in CENH3 disrupt chromosome segregation during mitosis and meiosis since the attachment of spindle microtubules to a mutated form of the CENH3 histone fails. This paper presents in silico characteristic of APOLLO and CENH3 genes, which may affect apomixis. Also, we characterize the structure of CENH3, study expression levels of APOLLO and CENH3 in gynoecium/siliques of the natural diploid apomictic and sexual Boechera species at the stages of before and after fertilization. While CENH3 was a single copy gene in all Boechera species, the APOLLO gene have several polymorphic alleles associated with sexual and apomictic reproduction in the Boechera genera. Expression of the APOLLO apo-allele during meiosis was upregulated in gynoecium of apomict B. divaricarpa downregulating after meiosis until 4th day after pollination (DAP). On the 5th DAP, expression in apomictic siliques increased again. In sexual B. stricta gynoecium and siliques APOLLO apo-allele did not express. Expression of the APOLLO sex-allele during and after meiosis in gynoecium of sexual plants was several times higher than that in apomictic gynoecium. However, after pollination the sex-allele was downregulated in sexual siliques to the level of apomicts and increased sharply on the 5th DAP, while in apomictic siliques it almost did not express. At the meiotic stage, the expression level of CENH3 in the gynoecium of apomicts was two times lower than that of the sexual Boechera, decreasing in both species after meiosis and keep remaining very low in siliques of both species for several days after artificial pollination until the 4th DAP, when the expression level raised in sexual B. stricta siliques exceeding 5 times the level in apomictic B. divaricarpa siliques. We also discuss polymorphism and phylogeny of the APOLLO and CENH3 genes.
REVIEW | doi:10.20944/preprints202108.0348.v1
Subject: Life Sciences, Microbiology Keywords: Enteric pathogenic Escherichia coli; E. coli pathotypes; Virulence factor genes
Online: 17 August 2021 (08:16:59 CEST)
Abstract: Escherichia coli are remarkably versatile microorganisms and important members of the normal intestinal microbiota of humans and animals. This harmless commensal organism can acquire a mixture of comprehensive mobile genetic elements that contain genes encoding viru-lence factors, becoming an emerging human pathogen capable of causing a broad spectrum of intestinal and extraintestinal diseases. Nine definite enteric E. coli pathotypes have been well characterized, causing diseases ranging from various gastrointestinal disorders to urinary tract infections. These pathotypes employ many virulence factors and effectors subverting the func-tions of host cells to mediate its virulence and pathogenesis. This review summarizes new de-velopments in our understanding of diverse virulence factors associated encoding genes used by different pathotypes of enteric pathogenic E. coli to cause intestinal and extraintestinal diseases in humans.
ARTICLE | doi:10.20944/preprints202102.0234.v1
Subject: Biology, Anatomy & Morphology Keywords: Principal Component Analysis, RNA-seq, prostate cancer, biomarkers, RNA genes
Online: 9 February 2021 (10:26:47 CET)
Prostate cancer (Pca) is a highly heterogeneous disease and the second more common tumor in males. Molecular and genetic profiles have been used to identify subtypes and guide therapeutic intervention. However, roughly 26% of primary Pca are driven by unknown molecular lesions. We use Principal Component Analysis (PCA) and custom RNAseq-data normalization to identify a gene expression signature which segregates primary PRAD from normal tissues. This Core-Expression Signature (PRAD-CES) includes 33 genes and accounts for 39% of data complexity along the PC1-cancer axis. The PRAD-CES is populated by protein-coding (AMACR, TP63, HPN) and RNA-genes (PCA3, ARLN1) sparsely found in previous studies, validated/predicted biomarkers (HOXC6, TDRD1, DLX1), and/or cancer drivers (PCA3, ARLN1, PCAT-14). Of note, the PRAD-CES also comprises six over-expressed LncRNAs without previous Pca association, four of them potentially modulating driver’s genes TMPRSS2, PRUNE2 and AMACR. Overall, our PCA capture 57% of data complexity within PC1-3. GO enrichment and correlation analysis involving major clinical features (i.e., Gleason Score, AR Score, TMPRSS2-ERG fusion and Tumor Cellularity) suggest that PC2 and PC3 gene signatures might describe more aggressive and inflammation-prone transitional forms of PRAD. Of note, surfaced genes may entail novel prognostic biomarkers and molecular alterations to intervene. Particularly, our work uncovered RNA genes with appealing implications on Pca biology and progression.
ARTICLE | doi:10.20944/preprints202010.0472.v1
Subject: Biology, Anatomy & Morphology Keywords: BLB Resistance; Xa genes; Xoo; Molecular characterization; Rice; LRR; S_TKc
Online: 23 October 2020 (09:13:39 CEST)
Globally, rice is utilized as staple food, belongs to the family Poaceae. From the past few decades under variable climate conditions, it greatly affected by the bacterial leaf blight (BLB) disease caused by a bacterium Xanthomonas oryzae pv. oryzae (Xoo). Scientists studied causes of the disease and found more than 61 isolates of Xoo. About 39 Xa genes were noted that cause race specifically resistance either individually or in pairs against Xoo. The canvas on the characterization of these genes is still unrevealed. In this study, amino acid sequences of Xa15, Xa19, Xa20 and Xa21 were mined and used for motif-domain identification, characterization, and comparative analysis. It includes screening of physical and chemical characteristics, sequence comparison to find sequence similarity between them and their phylogenetic comparison with other Xa genes and other species based upon LRR and S_TKc domains to find evolutionary relationship among them. The comparison-based modeling was performed and assessed by different tools to gain better understanding and structural evaluation. The results showed identified domains are specific in function, each domain involved in resistance against biotic and abiotic stresses through regulating different cellular processes. This study also revealed high similarity (>98% sequence identity) between these genes and encode a similar leucine-rich repeat receptor kinase like protein. It will optimize the breeding programs as it will be useful for the selection of effective genes to produce resistance in rice varieties against the specific strains of Xoo that will be more effective against BLB than the other Xa genes.
ARTICLE | doi:10.20944/preprints202009.0699.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: SVM; MRMR; Bootstrap; Genes; Gene Expression; Biological Relevance; Subject Classification
Online: 29 September 2020 (09:09:52 CEST)
Selection of biologically relevant genes from high dimensional expression data is a key research problem in gene expression genomics. Most of the available gene selection methods are either based on relevancy or redundancy measure, which are usually adjudged through post selection classification accuracy. Through these methods the ranking of genes was done on a single high-dimensional expression data, which leads to the selection of spuriously associated and redundant genes. Hence, we developed a statistical approach through combining Support Vector Machine with Maximum Relevance and Minimum Redundancy under a sound statistical setup for the selection of biologically relevant genes. Here, the genes are selected through statistical significance values computed using a non-parametric test statistic under a bootstrap based subject sampling model. Further, a systematic and rigorous evaluation of the proposed approach with nine existing competitive methods was carried on six different real crop gene expression datasets. This performance analysis was carried out under three comparison settings, i.e. subject classification, biological relevant criteria based on quantitative trait loci, and gene ontology. Our analytical results showed that the proposed approach selects genes that are more biologically relevant as compared to the existing methods. Moreover, the proposed approach was also found to be better with respect to the competitive existing methods. The proposed statistical approach provides a framework for combining filter, and wrapper methods of gene selection.
BRIEF REPORT | doi:10.20944/preprints202009.0655.v1
Subject: Life Sciences, Biochemistry Keywords: urinary tract infections; multi-drug resistance; biofilm; virulence genes; WGS
Online: 27 September 2020 (02:40:41 CEST)
Background: Extraintestinal pathogenic Escherichia coli (ExPEC) is the most common cause of urinary tract infections (UTIs). They are often multidrug-resistant (MDR), making them challenging to treat. Additionally, virulence mechanisms as biofilm formation are associated with persistent UTIs. Aims: To reveal a possible association between patients’ risk factors and UTIs caused by MDR or biofilm-forming ExPECs and characterize ExPECs causing asymptomatic bacteriuria, community- (CA), or hospital-acquired (HA) UTIs in hospitalized patients in Brazil. Methods: Bacterial DNA was extracted from the urine of 63 hospitalized patients and sequenced using short-read sequencing. Antibiotic susceptibility was evaluated using VITEK-2, and the biofilm-forming, adhesion, and invasion abilities were quantitatively assessed. Results: Antibiotic resistance rates were high, and the majority of UTIs were complicated CA-UTIs. Most MDR- and ESBL-producing E. coli isolates belonged to high-risk lineages and were associated with UTIs in patients with comorbidities and over 60 years of age. The mortality rate of patients infected with MDR-isolates was higher than of those infected with non-MDR isolates. Most isolates were biofilm-forming, but no association with patients’ risk factors was found. Conclusions: Complicated UTIs caused by MDR- and biofilm-forming bacteria are frequently found in hospitalized patients in Brazil suffering from a UTI and are associated with high-risk lineages.
ARTICLE | doi:10.20944/preprints202001.0048.v1
Subject: Biology, Horticulture Keywords: cis-regulatory element; data mining; NBS-LRR resistance genes; Zucchini
Online: 5 January 2020 (17:22:10 CET)
Although Cucurbita pepo is one of the most variable species of the plant kingdom, Zucchini morphotype has undergone intensive breeding that has led to a narrow genetic base making the crop vulnerable to pest and diseases. This vulnerability makes the knowledge of resistance genes of utmost importance. In this study, a data mining search of Zucchini summer squash genome database was conducted to identify and annotate members of the NBS-encoding gene family. In order to characterize the retrieved genes in detail, they have been studied in the bases of phylogenetic relationships, structural diversity, conserved protein motifs, gene duplications and promoter region analysis. Our study shows that the NBS-encoding gene family is relatively small in Zucchini (34 members, which are separated into non-TIR- and TIR-NBS-LRR subfamilies) with a significantly lower number of R-genes than in other species. Duplications have not played a major role in the expansion of this type of genes in C. pepo. Among the cis-regulatory elements presented in these sequences, six motifs are over-represented. These elements were reported to be involved in pathogens or plant stress induced responses. These results will contribute to the identification, isolation and characterization of candidate R-genes, thereby providing insight into NBS gene family evolution in the species.
Subject: Biology, Plant Sciences Keywords: soybean; strigolactones; biosynthesis and signaling genes; expression patterns; salt stress
Online: 3 October 2019 (14:01:36 CEST)
Strigolactones (SLs) are a novel emerging plant hormones, which play important roles in regulating plant organ development and environmental stress tolerance. Even though the SL related genes have been identified and well characterized in some plants. The information of SL related genes in soybean is not fully established yet, especially in response to salt stress. In this study, we identified nine SL biosynthesis genes: two D27, two CCD7, two CCD8, and three MAX1, and seven SL signaling genes: two D14, two MAX2 and three D53 in soybean genome. We found that SL biosynthesis and signaling genes are conserved during evolution in different species. Syntenic analysis of these genes revealed their location on nine chromosomes as well as existence of ten pairs of duplication genes. Moreover, plant hormone and stress-responsive elements were identified in the promoter regions of SL biosynthesis and signaling genes. By using quantitative real-time PCR (qRT-PCR), we confirmed that SL genes have different tissue expression in roots, stems and leaves. Further, we also explored the expression profiles of SL biosynthesis and signaling genes under salt stress. These results suggested that SL signaling genes may play important regulatory roles in response to salt stress. In conclusion, we identified and provided valuable information on the soybean SL biosynthesis and signaling genes, and established a foundation for further functional analysis of soybean SL related genes in response to salt stress.
ARTICLE | doi:10.20944/preprints201903.0262.v1
Subject: Biology, Anatomy & Morphology Keywords: Hox genes, Retinoids, BMP, Gastrulation, Xenopus, Timing, Time Space Translation
Online: 28 March 2019 (10:33:43 CET)
The vertebrate anterior-posterior (A-P) body axis arises due to time space translation (TST). BMP dependent Hox temporal collinearity in early embryonic mesoderm generates the initial vertebrate axial pattern because the Hox codes associated with sequential times are frozen sequentially by BMP inhibiting signals from the embryonic organiser or node. There are three reasons why it is now opportune to review TST. 1/ It has become clear that this mechanism is highly relevant for current and emergent directions in medicine. Making a particular tailored stem cell or culturing a specific organoid in vitro both depend on it. 2/ This unexpected and perhaps unlikely sounding mechanism has recently been thoroughly validated. 8 recent primary publications from 6 major groups confirm that TST is the mechanism for primary axial patterning in the 4 best investigated vertebrate embryos. 3/ Its mechanism is now becoming clear. Previous publications propose it involves Hox regulation of cell movement during gastrulation or sequential stabilisation of Hox codes by anti BMP as above. Neither of these processes works alone but together they amount to a very convincing mechanism.
ARTICLE | doi:10.20944/preprints201801.0266.v1
Subject: Life Sciences, Genetics Keywords: injury; soccer; genetics; ankle injuries; knee injuries; dna testing; genes
Online: 29 January 2018 (04:13:08 CET)
Genetics plays an integral role in athletic performance and is increasingly becoming recognised as an important risk factor for injury. Ankle and knee injuries are the most common injuries sustained by soccer players. Often these injuries result in players missing training and matches, which can incur significant costs to clubs. This study aimed to identify genotypes associated with ankle and knee injuries in soccer players and how these impacted the number of matches played. 289 soccer players including 46 professional, 98 semi-professional and 145 amateur players were genetically tested. Ankle and knee injuries and the number of matches played were recorded during the 2014/15 season. Four genes were assessed in relation to injury. Genotypes found to be associated with injury included the TT genotype of the GDF5 gene, TT and CT genotypes of AMPD1 gene, TT genotype of COL5A1 and GG genotype of IGF2 gene. These genes were also associated with a decrease in the number of matches played.
ARTICLE | doi:10.20944/preprints201706.0086.v2
Subject: Biology, Plant Sciences Keywords: arsenic pollution; differential display; genes; resistance; rice crop; soil contamination
Online: 22 June 2017 (05:16:08 CEST)
The main objective of the present study was to investigate arsenate [As (V)] resistance genes in rice cultivars grown in arsenic contaminated Egyptian soil in order to genetically induce resistance against arsenic in the local rice varieties as well as defining contaminated rice grains and/or soil. Three local rice cultivars; Sakha 102-104 were cultivated on modified Murashige and Skoog Basal Medium (MS medium) containing elevated concentrations of arsenate (0.1, 1 and 10 mg/l). The three varieties showed different resistant attitudes against arsenate with Sakha 104 being the most resistant. Extracted messenger RNA (mRNA) from treated and untreated Sakha 104 plantlets was scanned using differential display to demonstrate the arsenate resistant genes using three different arbitrary primers. About 100 different RNAs with (1500 bp - 50 bp) were obtained from which seven were up-regulated genes, subjected to DNA cloning using TOPO TA system and the selected clones were sequenced. The sequence analysis described four genes out of the seven namely disease resistance protein RPM1, Epstein-Barr virus EBNA-1-like, CwfJ family protein and outer membrane lipoprotein OmlA while the other three genes were hypothetical proteins. It is concluded the four induced genes in the resistant rice cultivar considered as a direct response to arsenic soil pollution. Genes detected in the present study can be used as geno-sensors for rice grains and soil contamination with As (V). Moreover, local rice cultivars may be genetically modified with such genes to induce high resistance and to overcome arsenic soil pollution.
ARTICLE | doi:10.20944/preprints202202.0232.v1
Subject: Biology, Entomology Keywords: Small RNA sequencing; miRNAs; Target prediction; Chemosensory-associated genes; Apolygus lucorum
Online: 18 February 2022 (10:01:58 CET)
MicroRNAs (miRNAs) are a class of small non-coding RNAs, which function as regulators of gene expression and contribute in numerous physiological processes. However, little is known referring to miRNAs function in insect chemosensation. In the current study, nine small RNA libraries were constructed and sequenced from the antennae of nymphs, adult males and females of Apolygus lucorum. In total, 399 miRNAs were identified including 275 known and 124 novel miRNAs. Known miRNAs were classified into 71 families, amongst which, 23 families were insect-specific. Expression profile analysis showed that miR-7-5p_1 was the most abundant miRNAs in the antennae of A. lucorum. Altogether, 69708 target genes related to biogenesis, membrane and binding activities were predicted for 399 miRNAs. Particularly, 15 miRNAs were found to target 16 olfactory genes. These miRNAs could be involved in regulation of olfactory-associated genes ex-pression. Comparing the antennae of nymphs, adult males and females, 94 miRNAs were found to be differentially expressed. The expression levels of some differentially expressed miRNAs measured by qPCR were consistent with sequencing results. This study provides a global miRNAs transcriptome in the antennae of A. lucorum and valuable information for further investigation on miRNA-mRNA interactions, especially the functions of miRNAs in regulating chemosensation.
ARTICLE | doi:10.20944/preprints202112.0381.v2
Subject: Life Sciences, Genetics Keywords: DNA transcription factors; genes; finitely-generated groups; free groups; aperiodic order
Online: 10 January 2022 (11:52:04 CET)
Transcription factors (TFs) are proteins that recognize specific DNA fragments in order to decode the genome and ensure its optimal functioning. TFs work at the local and global scales by specifying cell type, cell growth and death, cell migration, organization and timely tasks. We investigate the structure of DNA-binding motifs with the theory of finitely generated groups. The DNA ‘word’ in the binding domain -the motif- may be seen as the generator of a finitely generated group Fdna on four letters, the bases A, T, G and C. It is shown that, most of the time, the DNA-binding motifs have subgroup structure close to free groups of rank three or less, a property that we call ‘syntactical freedom’. Such a property is associated to the aperiodicity of the motif when it is seen as a substitution sequence. Examples are provided for the major families of TFs such as leucine zipper factors, zinc finger factors, homeo-domain factors, etc. We also discuss the exceptions to the existence of such a DNA syntactical rule and their functional role. This includes the TATA box in the promoter region of some genes, the single nucleotide markers (SNP) and the motifs of some genes of ubiquitous role in transcription and regulation.
REVIEW | doi:10.20944/preprints202111.0509.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: hox genes; gene cluster; larva; evolutionary novelties; Spiralia; Lophotrochozoa; Annelida; Rotifera
Online: 26 November 2021 (13:28:22 CET)
The decoding of genomes of a larger number of animal species have provided further insights into the genomic Hox gene organization and with this indicated the evolutionary changes during the radiation of several clades. The expansion of gene expression studies during development and life history stages of more species, complete the picture of the relationship between cluster organisation and temporal and spatial correlation of the Hox activity. Now these results open the opportunity to look deeper into the regulatory pathways that form these patterns and identify what exact changes caused the evolution of the application of this iconical gene set for the evolution of new larval forms and new structures. Here we review recent progress of Hox gene related research in the large clade Spiralia, that comprises Annelida, Mollusca, Lophophorata, Platyhelminthes, Nemertea and others. Albeit their relationship to each other is not resolved yet, there are emerging patterns that indicate that Hox genes are mainly used for patterning late, adult body parts and that Hox genes are often not expressed on the larval stages. Hox genes seem also often recruited for the formation of morphological novelties. Together with the emerging genomic information Hox genes show a much more dynamic evolutionary history than previously assumed.
ARTICLE | doi:10.20944/preprints202110.0281.v1
Subject: Biology, Animal Sciences & Zoology Keywords: selective pressures; mitochondrial protein-coding genes; subterranean voles; adaptations; subterranean lifestyle.
Online: 19 October 2021 (15:01:42 CEST)
The current study evaluates the selection signals in the evolution of mitochondrial DNA of voles, subfamily Arvicolinae, during the colonization of subterranean environments. The comparative sequence analysis of mitochondrial protein-coding genes of eight subterranean vole species (Prometheomys schaposchnikowi, three species of the genus Ellobius: E. talpinus, E. fuscocapillus and E. lutescens, two species of the genus Terricola: T. subterraneus and T. daghestanicus, Lasiopodomys mandarinus and Hyperacrius fertilis) and their closest aboveground relatives using codon-substitution models was applied. The highest number of selection signatures was detected in genes ATP8 and CYTB. The relaxation of selection was observed in most mtDNA protein-coding genes. In mole voles (genus Ellobius) the signatures of adaptive evolution of mitochondrial genes related to subterranean niche were most pronounced. The number of selection signatures was found to be independent of the evolutionary age of the lineage but fits the degree of specialization to the subterranean niche. The common trends of selective pressures were observed among the evolutionary ancient and highly specialized subterranean rodent families and phylogenetically young lineages of voles. It suggests that the signatures of adaptations in individual mitochondrial protein-coding genes associated with the colonization of the subterranean niche may appear within a rather short evolutionary timespan.
ARTICLE | doi:10.20944/preprints202009.0269.v1
Subject: Life Sciences, Microbiology Keywords: escherichia coli; dogs; virulence genes; antibiotic resistance; WGS; ST372; clonal structure
Online: 12 September 2020 (09:56:27 CEST)
Under one-health perspective and the worldwide antimicrobial resistance concern, we investigate extraintestinal pathogenic Escherichia coli (ExPEC), uropathogenic E. coli (UPEC), and multidrug resistant (MDR) E. coli from 197 isolates recovered from healthy dogs in Spain between 2013 and 2017. Ninety-one (46.2%) isolates were classified as ExPEC and/or UPEC including 50 clones, among which (i) four clones were dominant (B2-CH14-180-ST127, B2-CH52-14-ST141, B2-CH103-9-ST372 and F-CH4-58-ST64815) and (ii) 15 had been shown to be displayed by previously published isolates causing extraintestinal infections in humans. Twenty-eight (14.2%) isolates were classified as MDR, associated with B1, D and E phylogroups and included 24 clones, of which eight had also been identified among human isolates causing infections. We selected 23 ST372 strains, 21 healthy dogs faecal isolates and two human clinical isolates for whole genome sequencing and built a SNP-tree with these 23 genomes and 174 genomes (128 from canine strains and 46 from human strains) obtained from public databases. The analysis of these 197 genomes allowed to identify six clusters. Cluster 1 comprised 74.6% of the strain genomes that were mostly composed of canine strain genomes (P < 0.00001). Clusters 4 and 6 also included canine strain genomes, while clusters 2, 3 and 5 were significantly associated with human strain genomes. All these findings suggest that dogs are reservoirs of ExPEC, UPEC and MDR E. coli isolates with zoonotic potential.
ARTICLE | doi:10.20944/preprints202002.0463.v1
Subject: Life Sciences, Microbiology Keywords: E. coli; clonal structure; ST88; ST141; ST131; ST1193; virulence genes; resistance
Online: 29 February 2020 (10:25:09 CET)
Escherichia coli is the main pathogen responsible for extraintestinal infections. A total of 196 clinical E. coli consecutively isolated during 2016 in Spain (100 from Lucus Augusti hospital in Lugo) and France (96 from Beaujon hospital in Clichy) were characterized. Phylogroups, clonotypes, sequence types (STs), O:H serotypes, virulence factor (VF)-encoding genes and antibiotic resistance were determined. Approximately 10% of the infections were caused by ST131 isolates in both hospitals and approximately 60% of these infections were caused by isolates belonging to only 10 STs (ST10, ST12, ST58, ST69, ST73, ST88, ST95, ST127, ST131, ST141). ST88 isolates were frequent especially in Spain while ST141 isolates significantly predominated in France. The 23 ST131 isolates displayed four clonotypes: CH40-30, CH40-41, CH40-22 and CH40-298. Only 13 (6.6%) isolates were carriers of ESBL enzymes. However, 37.2% of the isolates were multidrug-resistant (MDR). Approximately 40% of the MDR isolates belonged to only four of the dominant clones (B2-CH40-30-ST131, B2-CH40-41-ST131, C-CH4-39-ST88 and D-CH35-27-ST69). Among the remaining MDR isolates two isolates belonged to B2-CH14-64-ST1193 i.e the new global emergent MDR clone. To our knowledge, it is the first identification of this emergent clone in Spain. Moreover, a hybrid ExPEC/enteroaggregative isolate belonging to A-CH11-54-ST10 clone was identified.
REVIEW | doi:10.20944/preprints201911.0236.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: Hox genes; limb development; main body axis; timing; time space translation
Online: 20 November 2019 (10:31:55 CET)
This article is a tribute to Lewis Wolpert on the occasion of the recent 50th anniversary of the publication of his article ‘Positional Information and the Spatial Pattern of Differentiation’. This tribute relates to another of his ideas: his early ‘Progress Zone’ timing model for limb development. Recent evidence is reviewed that a mechanism sharing features with this model patterns the main body axis in early vertebrate development. This tribute celebrates the golden era of Developmental Biology.
ARTICLE | doi:10.20944/preprints201908.0009.v1
Subject: Biology, Animal Sciences & Zoology Keywords: tea polyphenol; serum hormone; enzyme activity; immune function, enzyme-related genes
Online: 1 August 2019 (05:18:08 CEST)
The present study was conducted to evaluate the effects of dietary supplementation of tea polyphenol （TP） on serum hormone, serum enzyme activity, antioxidant-related and immune-related gene expression of laying hens under heat stress. A total of 288 Chinese yellow chicken (186 days old) were randomly distributed among two treatments, each of which included 6 replicates of 24 hens. Dietary treatments were that the basal diet was supplemented with 200 mg / kg tea polyphenol. The study lasted for 7 weeks, including 1 week of adaptation and 6 weeks of the formal test. The content of high-density lipoprotein cholesterol (HDL-C) and total protein (TP) in serum significantly decreased by dietary supplementation with tea polyphenol. Dietary tea polyphenol supplementation improved serum superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) enzyme activity and decreased serum malondialdehyde (MDA) content in treatments compared to the control. However, supplementation of tea polyphenol did not affect the activity of serum catalase (CAT). The results indicated that long-term feeding of tea polyphenols help to increase the amount of hormones (FSH, E2) associated with reproduction in laying hens and thus improve egg production. It also improved the immune function of laying hens in high temperature environments. Adding tea polyphenols to the diet can significantly increase the serum IgG, IgM content of the laying hens and can upregulate the IgA content. Dietary supplementation of tea polyphenols in the laying hens significantly increased the expression of antioxidant enzyme-related genes (SOD, CAT and GPX1) in the liver. Moreover, the addition of tea polyphenols significantly increased the expression of immune-related genes (Interferon-γ (INF-γ), Interleukin 2 (IL-2) and Interleukin 4 (IL-4)) in the spleen. It is concluded that addition of tea polyphenols has a positive effect on antioxidant activity and immune function of laying hens.
ARTICLE | doi:10.20944/preprints201905.0321.v1
Subject: Keywords: Hox genes, Hox collinearity, Noether’s Theory, Anterior Posterior axis, Rotational symmetry
Online: 27 May 2019 (14:14:36 CEST)
Hox Gene Collinearity (HGC) is a fundamental property that determines the development of many animal clades including Vertebrates. In the Hox gene clusters the genes are located in a sequence Hox1, Hox2, Hox3,… along the 3’ to 5’ direction of the cluster in the chromosome. During Hox cluster activation the Hox genes are expressed sequentially in the ontogenetic units D1, D2, D3,… along the anterior (A)- Posterior (P) axis of the early embryo. This collinearity, first observed by E.B. Lewis, is surprising because the spatial extent of these structures (Hox clusters and embryos) differ by about 4 orders of magnitude. Biomolecular mechanisms alone cannot explain this correlation. Long range physical interactions like diffusion or electric attractions should be involved. A biophysical model (BM) has been formulated which cooperates with the biomolecular processes and describes the data successfully. Hundred years ago E. Noether made a fundamental discovery in Mathematics and Physics. She proved rigorously that a physical system obeying a symmetry law (e.g.rotations or self similarity) is linked to a conserved physical quantity. It is argued here that HGC obeys a ‘primitive’ self similarity symmetry of the genes of a Hox cluster along a finite straight line. In the case of Vertebrates, the associated partially conserved quantity is the ever increasing ‘ratchet’- like gene ordering where some Hox genes are missing. Another application of Noether’s Theory is performed to rotationally symmetric embryos like the sea urchin.
Subject: Biology, Horticulture Keywords: transcriptome; Solanum lycopersicum; RNA-seq; light intensity distributions; differentially expressed genes
Online: 19 March 2019 (10:42:26 CET)
Plants grown under fluctuating light impact plant developments compared with those grown under non-fluctuating light conditions. However, our knowledge on the underlying regulatory mechanisms is still quite limited, particularly from the transcriptional perspective. In order to investigate the influence of different light intensity distributions on tomato plant development, we designed three fluctuating light intensity distributions with the non-fluctuating light intensity as control and compared the transcriptional differences after five weeks of treatment. We found plant height and aerial/root weight were significantly reduced under all fluctuating light treatments. Transcriptome analysis revealed that the number of up and down regulated genes had a distinct distribution pattern between different treatments and control. The largest difference between the numbers of down and up regulated genes was found between treatment 1 and 3, reaching to a total of 416 genes. The number and type of the top 20 enriched pathways differed between treatments and control. The largest number of genes enriched was involved in the biosynthesis of secondary metabolites. These results provide insights into the transcriptional regulations of tomato under different light intensity distributions.
ARTICLE | doi:10.20944/preprints201810.0565.v1
Subject: Medicine & Pharmacology, Other Keywords: EZH2; epigenetic regulation; DZNep; tumor-related genes; head and neck cancer
Online: 24 October 2018 (10:34:10 CEST)
EZH2 overexpression is associated with tumor proliferation, metastasis, and poor prognosis. Targeting and inhibiting EZH2 may be an effective therapeutic strategy for head and neck squamous cell carcinoma (HNSCC). We previously analyzed EZH2 mRNA expression in a well-characterized dataset of 230 (110 original and 120 validation cohorts) human head and neck cancer samples. This study aimed to investigate the effects of inhibiting EZH2, either via RNA interference or via pharmacotherapy, on HNSCC growth. EZH2 upregulation was significantly correlated with recurrence (P < 0.001) and the methylation index of tumor suppressor genes (P < 0.05). DNMT3A was significantly upregulated upon EZH2 upregulation (P = 0.043). Univariate analysis revealed that EZH2 upregulation was associated with poor disease-free survival (log-rank test, P < 0.001). In multivariate analysis, EZH2 upregulation was evaluated as a significant independent prognostic factor of disease-free survival (hazard ratio: 2.085, 95% confidence interval: 1.390–3.127; P < 0.001). Cells treated with RNA interference and DZNep, an EZH2 inhibitor, showed the most dramatic changes in expression, accompanied with a reduction in the growth and survival of FaDu cells. These findings suggest that EZH2 upregulation is correlated with tumor aggressiveness and adverse patient outcomes in HNSCC. Evaluation of EZH2 expression might help predict the prognosis of HNSCC patients.
ARTICLE | doi:10.20944/preprints201809.0201.v1
Subject: Life Sciences, Molecular Biology Keywords: Suprachiasmatic nucleus (SCN); Circadian clock; Soleus Muscle (SM); Brown adipose tissue (BAT); liver; 6-meal feeding; Respiratory exchange ratio (RER); Clock genes; metabolic genes; Shift work.
Online: 11 September 2018 (14:21:48 CEST)
Restricted feeding is well known to affect expression profiles of both clock and metabolic genes. However, it is unknown whether these changes in metabolic gene expression result from changes in the molecular clock or in feeding behavior. Here we eliminated the daily rhythm in feeding behavior by providing 6-meals evenly distributed over the light/dark-cycle. Animals on this 6-meals-a-day feeding schedule retained the normal day/night difference in physiological parameters including body temperature and locomotor activity. The daily rhythm in respiratory exchange ratio (RER), however, was significantly phase-shifted through increased utilization of carbohydrates during the light phase and increased lipid oxidation during the dark phase. This 6-meals-a-day feeding schedule did not have a major impact on the clock gene expression rhythms in the master clock but did have mild effects on peripheral clocks. By contrast, genes involved in glucose and lipid metabolism showed differential expression. Concluding, eliminating the daily rhythm in feeding behavior in rats does not affect the master clock and only mildly affects peripheral clocks, but disturbs metabolic rhythms in liver, skeletal muscle and brown adipose tissue in a tissue-dependent manner. Thereby a clear daily rhythm in feeding behavior strongly regulates timing of peripheral metabolism, separately from circadian clocks.
SHORT NOTE | doi:10.20944/preprints202208.0003.v1
Subject: Earth Sciences, Palaeontology Keywords: Cannabis; hemp; pollen; retting; bacteria; molecular biomarkers; 16S rRNA genes; historical records
Online: 1 August 2022 (04:28:27 CEST)
Documenting prehistoric and historical hemp retting for fiber extraction is important in the study of human uses of this iconic plant and its cultural implications. In paleoecology, hemp retting is usually inferred from indirect proxies, notably anomalously high percentages of Cannabis pollen in lake sediments, but some recent studies have also used specific molecular biomarkers (cannabinol, Cannabis DNA) as a more straightforward evidence. Here we provide direct evidence of hemp retting by identifying phylogenetic signatures (16S rRNA genes) from pectinolytic bacteria actually responsible for the fermentation process that separates the fiber from the stalk, namely Bacillus, Clostridium, Escherichia, Massilia, Methylobacterium, Pseusomonas, Rhizobium and Rhodobacter. These analyses have been performed in the sediments from an Iberian lake previously considered as an important hemp retting site during the last five centuries, on the basis of Cannabis pollen abundances. The good match between biomarker and pollen evidence, in the context of the recent historical development of hemp industry in Spain, can be useful to interpret paleoecological records from other similar lakes in the way toward a more regional view on the introduction, spreading, uses and associated cultural connotations of Cannabis in the Iberian Peninsula within European and Mediterranean contexts.
ARTICLE | doi:10.20944/preprints202110.0228.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: flax; Fusarium oxysporum; differential expression genes; GO enrichment analysis; KEGG enrichment analysis
Online: 15 October 2021 (14:32:42 CEST)
A plant’s early response to pathogen stress is a vital indicator of its disease resistance. In order to study the response mechanism of resistant and susceptible flax cultivars to Fusarium oxysporum f. sp. lini (Foln), we applied RNA-sequencing to analyze transcriptomes of flax with Foln 0.5, 2 and 8 hours post inoculation (hpi). We found a significant difference in the number of differential expression genes (DEGs) between resistant and susceptible flax clutivars. The number of DEGs in the Fusarium-resistant cultivar increased dramatically at 2 hpi, and a large number of DEGs participated in the Fusarium-susceptible cultivar response to Foln infection 0.5 hpi. GO enrichment analysis determined that the up-regulated DEGs of both flax cultivars were enriched such as oxidoreductase activity and oxidation-reduction process. At the same time, the genes involved in diterpenoid synthesis were up-regulated in resistant cultivar, while those involved in extracellular region, cell wall and organophosphate ester transport were down-regulated in susceptible cultivar. KEGG enrichment analysis showed the genes encoded WRKY 22 and WRKY33 which involved in MAPK signaling pathway were up-regulated expressed in S-29 and down-regulated expressed in R-7, negatively regulated the disease resistance of flax; The genes encoded Hsp 90 family which in involved in plant pathogen interaction pathway were up-regulated in R-7 and down-regulated in S-29, which positively regulated the disease resistance of flax; The genes encoded MYC2 transcription factor and TIFY proteins which involved in plant hormone signaling pathway were up-regulated in R-7, and regulated the jasmonic acid metabolism of flax and the signal transduction of plant hormones. Meanwhile seven regulatory genes with the most correlation were screened out, Among Lus10025000.g and Lus10026447.g regulated other genes expressed both in plant hormone signal transduction pathway and MAPK signal pathway. In conclusion, these findings will facilitate further studies on the function of these candidate genes in flax of response to Fusarium stress, and the breeding of disease-resistant flax cultivar.
ARTICLE | doi:10.20944/preprints202101.0603.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Clock genes; Hepatocellular carcinoma; Ki67; Radiotherapy; Transgenic Per2::luc mice; γ-H2AX
Online: 29 January 2021 (08:15:35 CET)
This study investigates whether a chronotherapeutic treatment of hepatocellular carcinoma (HCC) may improve treatment efficacy and mitigate side effects on healthy liver (HL). HCC was induced in Per2::luc mice which were irradiated at four time points of the day. Proliferation and DNA-double strand breaks were investigated in irradiated and non-irradiated organotypic slice culture (OSC) and ex vivo samples by detection of Ki67 and γ-H2AX. OSC proved useful to determine dose-dependent effects on proliferation and DNA damage but appeared unsuited to test the chronotherapeutic approach. Irradiation of ex vivo samples was most effective at the proliferation peaks in HCC at ZT02 (early inactivity phase) and ZT20 (late activity phase). Irradiation effects on HL were minimal at ZT20. Ex vivo samples revealed disruption in daily variation and down-regulation of all investigated clock genes except Per1 in non-irradiated HCC as compared with HL. Irradiation affected rhythmic clock gene expression in HL and HCC at all ZTs except at ZT20. Irradiation at ZT20 had no effect on total leukocyte numbers. Our results indicate ZT20 as the optimal time point for irradiation of HCC in mice. Translational studies are now needed to evaluate whether the late activity phase is the optimal time point for irradiation of HCC in man.
ARTICLE | doi:10.20944/preprints202012.0496.v1
Subject: Life Sciences, Biochemistry Keywords: Hungateiclostridium thermocellum; adaptive laboratory evolution; RNA-seq; cellulosomal genes; EMP pathway; monosaccharides
Online: 21 December 2020 (10:36:00 CET)
Hungateiclostridium thermocellum ATCC 27405 is a promising bacterium with a robust ability to degrade lignocellulosic biomass complexes, including crystalline cellulose components, through a multienzyme cellulosomal system. In contrast, it exhibits poor growth on simple monosaccharides such as fructose and glucose. This phenomenon raises many important questions concerning its glycolytic pathways and sugar transport systems. Until now, the detailed mechanisms of H. thermocellum adaptation to growth on monosaccharides have been poorly explored. In this study, adaptive laboratory evolution was applied to train the bacterium on monosaccharides, and genome resequencing was used to detect the genes that had mutated during adaptation. RNA-seq data of the 1st-generation culture growing on either fructose or glucose revealed that several glycolytic genes in the EMP pathway were expressed at lower levels in these cells than in cellobiose-grown cells. After 8 generations of culture on fructose and glucose, the evolved H. thermocellum strains grew faster and yielded greater biomass than the nonadapted strains. Genomic screening also revealed several mutation events in the genomes of the evolved strains, especially in genes responsible for sugar transport and central carbon metabolism. Consequently, these genes could be applied as targets for further metabolic engineering to improve this bacterium for bioindustrial usage.
REVIEW | doi:10.20944/preprints202010.0538.v1
Subject: Life Sciences, Biochemistry Keywords: γ-aminobutyric acid; lactic acid bacteria; glutamate decarboxylase; fermented foods; GAD genes
Online: 27 October 2020 (08:38:21 CET)
Glutamate decarboxylase (L-glutamate-1-carboxylase, GAD; EC 126.96.36.199) is a pyridoxal 5-phosphate-dependent enzyme, which catalyzes the irreversible α-decarboxylation of L-glutamic acid to γ-aminobutyric acid (GABA) and CO2. The enzyme is widely distributed in eukaryotes as well as prokaryotes, where it – together with its reaction product GABA - fulfils very different physiological functions. The occurrence of gad genes encoding GAD has been shown for many microorganisms, and GABA-producing lactic acid bacteria (LAB) have been a focus of research during recent years. A wide range of traditional foods produced by fermentation based on LAB offer the potential of providing new functional food products enriched with GABA that may offer certain health-benefits. Different GAD enzymes and genes from several strains of LAB have been isolated and characterized recently. GABA-producing LAB, biochemical properties of their GAD enzymes, and possible applications are reviewed here.
CONCEPT PAPER | doi:10.20944/preprints202007.0454.v1
Subject: Life Sciences, Genetics Keywords: gene evolution; gene formation; long non-coding RNA genes; pseudogenes; USP18; GGT5
Online: 20 July 2020 (04:39:41 CEST)
A small phylogenetically conserved sequence of 11,231 bp termed FAM247 is repeated in human chromosome 22 by segmental duplications. This sequence forms part of diverse genes that span evolutionary time, the protein genes being the earliest as they are present in zebrafish and/or mice genomes, the long non-coding RNA genes and pseudogenes the most recent as they appear to be present only in the human genome. We propose that the conserved sequence provides a nucleation site for new gene development at evolutionary conserved chromosomal loci where the FAM247 sequences reside. The FAM247 sequence also carries information in its open reading frames that provides protein exon amino acid sequences; one exon plays an integral role in immune system regulation, specifically, the function of ubiquitin specific protease (USP18) in the regulation of interferon. An analysis of this multifaceted sequence and the genesis of genes that contain it are presented.
ARTICLE | doi:10.20944/preprints202004.0064.v1
Subject: Life Sciences, Virology Keywords: erythroparvovirus, tetraparvovirus, protein sequence analyses, overlapping genes, overlapping reading frames VP1, capsid
Online: 6 April 2020 (14:20:35 CEST)
30 years ago, researchers noticed that the capsid (VP1) gene of B19 parvovirus might encode a second protein, called "X", in an overlapping reading frame. Since then, experimental approaches failed to detect it. In contrast, sequence analyses can reliably predict whether a protein is expressed from an overlapping frame, provided that it is beneficial to the virus and thus under selection pressure. We used a dedicated software, Synplot2, to identify regions of VP1 likely to encode functional proteins in overlapping frames. Synplot2 detected the X open reading frame and confirmed it is under highly significant selection pressure. We discovered that the X protein is homologous to the ARF1 protein of human parvovirus 4, another suspected protein encoded in a frame overlapping VP1. These findings provide compelling evidence that the X protein must be expressed and functional. We predict that it contains a predicted transmembrane region. We found that the X frame contains a potential AUG start codon in parvovirus B19 and in all related species. Yet no currently known viral transcript has the potential to encode the X protein in a monocistronic fashion. Therefore, the X protein is probably expressed either from an unmapped monocistronic mRNA, or translated by a non-canonical mechanism from the VP1 mRNA or from a short transcript, R3, which has no currently known function. Finally, Synplot2 also detected proteins likely to be expressed from a frame overlapping VP1 in species distantly related to parvovirus B19: porcine parvovirus 2 and bovine parvovirus 3.
ARTICLE | doi:10.20944/preprints201912.0354.v1
Subject: Biology, Other Keywords: Lactobacillus helveticus; probiotics; whole genome sequencing; PacBio; probiotic genes; bacteriocins; gene expression
Online: 26 December 2019 (10:56:44 CET)
Whole-genome DNA sequencing of Lactobacillus D75 and D76 strains (Vitaflor, Russia) was performed using the PacBio RS II platform, followed by de novo assembly with SMRT Portal 2.3.0. The average nucleotide identity (ANI) test showed that both strains belong to the Lactobacillus helveticus, but not the L. acidophilus as previously assumed. 31 exopolysaccharide (EPS) production genes (nine of which form a single genetic cluster), 13 adhesion genes, 38 milk protein and 11 milk sugar utilization genes, 13 genes for and against specific antagonistic activity, aight antibiotic resistance genes, and also three CRISPR blocks and eight Cas I-B system genes were identified in the genomes of the both strains. The expression of some genes was confirmed. In fact, the presence of identified genes suggests that L. helveticus D75 and D76 are able to form biofilms on the outer mucin layer, inhibit the growth of pathogens and pathobionts, utilize milk substrates with the formation of digestible milk sugars and bioactive peptides, resist bacteriophages and show some genome-determined resistance to antibiotics, stimulate the host’s immune system. Pathogenicity genes have not been identified. The study results confirm the safety and high probiotic potential of the strains.
ARTICLE | doi:10.20944/preprints201809.0553.v1
Subject: Life Sciences, Virology Keywords: Citrus bark cracking viroid; differentially expressed genes; hop; pathogen; transcriptome analysis; viroids
Online: 28 September 2018 (05:26:31 CEST)
Viroids are smallest pathogen that consist of non-capsidated, single-stranded non-coding RNA replicons and exploits host factors for their replication and propagation. The severe stunting disease caused by Citrus bark cracking viroid (CBCVd) is a serious threat, which spread rapidly within hop gardens. In this study, we employed comprehensive transcriptome analyses to dissect host-viroid interactions and identify gene expression changes associated with disease development in hop. Our analysis revealed that CBCVd-infection resulted in the massive modulation of activity of over 2000 genes. Expression of genes associated with plant immune responses (protein kinase and mitogen-activated protein kinase), hypersensitive responses, phytohormone signaling pathways, photosynthesis, pigment metabolism, protein metabolism, sugar metabolism and modification and others were altered, which could be attributed to systemic symptom development upon CBCVd-infection in hop. In addition, genes encoding RNA-dependent RNA polymerase, pathogenesis-related protein, chitinase as well as those related to basal defense responses were up-regulated. The expression levels of several genes identified from RNA sequencing analysis were confirmed by qRT-PCR. Our systematic comprehensive CBCVd-responsive transcriptome analysis provides a better understanding and insights into complex viroid-hop plant interaction. This information will assist further in the development of future measures for the prevention of CBCVd spread in hop fields.
ARTICLE | doi:10.20944/preprints201709.0100.v1
Subject: Medicine & Pharmacology, Other Keywords: alpha; thalassemia; deletional; cut-off; number of genes; microcytic anemia; differential diagnosis
Online: 21 September 2017 (04:47:16 CEST)
Most of α-thalassemia cases are caused by deletions of the structural α-globin genes. The degree of microcytosis and hypochromia has been correlated with the number of affected α-globin genes, suggesting a promising role of hematologic parameters as predictive diagnostic tools. However, specific cut-off points for these parameters to discriminate between the different subtypes of α-thalassemia remain to be clearly defined. Six hematologic parameters (total number of erythrocytes, hemoglobin concentration, mean corpuscular volume, mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration and red cell distribution width) were evaluated in 174 cases of deletional α-thalassemia (92 heterozygous α+ thalassemia, 39 homozygous α+ thalassemia, 34 heterozygous α0 thalassemia and 9 cases of Hb H disease). A good correlation between the number of deleted alpha genes and MCV (r = -0.672, p<0.001), MCH (r = -0.788, p<0.001) and RDW (r = 0.633, p<0.001) was observed. The deletion of at least two alpha genes in adult individuals with microcytosis without iron deficiency and normal values of Hb A2 and Hb F should be discarded when MCH levels are lower than 23.15 pg. Furthermore, MCH <21.90 pg and/or MCV <70.80 fL are strongly suggestive of the presence of one α0 allele. Finally, an accurate presumptive diagnosis of Hb H disease can be made if both RDW ≥20% and MCH <18.45 pg are seen.
ARTICLE | doi:10.20944/preprints202208.0133.v1
Subject: Life Sciences, Microbiology Keywords: Abscisic acid biosynthetic genes; aquaporins; Biofilm forming bacteria; growth traits; oxidative injury; Tomato
Online: 8 August 2022 (05:48:17 CEST)
Use of rhizosphere microorganisms provides an alternative or supplement to conventional plant breeding to improve water deficit tolerance of tomato plants. Experiment was carried out to explore the effect of two microbial species, AMF (Rhizophagus irregularis) and Bacillus subtilis, in single and co-application, on growth, colonization, and molecular aspects of tomato plants under drought stress. Co-inoculated plants showed less reduction in growth traits, photosynthetic pigments, colonization rate, and increased compatible solutes like proline which help in sustaining relative water content than non-inoculated plants. Inoculation considerably enhanced proline dehydrogenase activity, and significantly reduced both Δ1-pyrroline-5-carboxylate reductase Δ1-pyrroline-5-carboxylate synthetase activity causing lower proline accumulation in inoculated plants under drought stress. Co-inoculated plants showed obvious upregulation of antioxidant system, thus facilitating amelioration of oxidative stress through exclusion of reactive oxygen species. No inoculation under drought stress upregulated abscisic acid related genes expression but have no effect in plants inoculated either sole or mixed inoculation. Expression of aquaporin genes was upregulated in plants co-inoculated and with AMF alone under normal condition. However the expression of aquaporin genes were decreased or unaffected in plants inoculated with Bacillus subtilis but increased in non-inoculated plants. Co-applied AMF and bacillus subtilis substantially increase drought tolerance by upregulating proline metabolism, antioxidant enzymes and aquaporin genes. Therefore our results suggest that co-inoculation mediated drought tolerance is linked with increased proline accumulation, enhanced antioxidant enzyme activities and differential regulation of ABA biosynthetic and aquaporin genes, which is vital for osmotic adjustment of host plant.
ARTICLE | doi:10.20944/preprints202004.0016.v2
Subject: Life Sciences, Biochemistry Keywords: glaucoma; retina ganglion cell degeneration; microarray; genes coordination; notch signaling pathway; complement cascade
Online: 23 February 2021 (12:44:20 CET)
Glaucoma is a multifactorial neurodegenerative disease, characterized by degeneration of the retinal ganglion cells (RGCs). There has been little progress in developing efficient strategies for neuroprotection in glaucoma. We profiled the retina transcriptome of Lister Hooded rats at 2 weeks after optic nerve crush (ONC) and analyzed the data from the Genomic Fabric Paradigm (GFP) to bring additional insights into the molecular mechanisms of the retinal remodeling after induction of RGC degeneration. GFP considers for the expression of each gene 3 independent characteristics: level, variability and correlation with each other gene. Thus, the 17,657 quantified genes our study generated a total of 155,911,310 values to analyze. This represents 8,830x more data per condition than a traditional transcriptomic analysis. ONC led to a 57% reduction in RGC numbers as detected by retrograde labeling with DiI. We observed a higher Relative Expression Variability after ONC. Gene expression stability was used as a measure of transcription control and disclosed a robust reduction in the number of very stably expressed genes. Predicted Protein-Protein interaction (PPI) analysis with STRING revealed axon and neuron projection as mostly decreased processes, consistent with RGC degeneration. Conversely, immune response PPIs were found among up-regulated genes. Enrichment analysis showed that Complement Cascade and Notch Signaling Pathway, as well as Oxidative Stress and Kit Receptor Pathway were affected after ONC. To expand our studies of altered molecular pathways, we examined the pair-wise coordination of gene expressions within each pathway and within the entire transcriptome using Pearson correlations. ONC increased the number of synergistically coordinated pairs of genes and the number of similar profiles mainly in Complement Cascade and Notch Signaling Pathway. This deep bioinformatic study provides novel insights beyond the regulation of individual gene expression and discloses changes in the control of expression of Complement Cascade and Notch Signaling functional pathways that may be relevant for both RGC degeneration and remodeling of the retinal tissue after ONC.
COMMUNICATION | doi:10.20944/preprints202012.0753.v2
Subject: Keywords: HOX genes; Hox gene collinearity; spatial collinearity; temporal collinearity; vertebrates; elongated gene cluster
Online: 4 January 2021 (08:30:15 CET)
Hox gene collinearity (HGC) is a multiscalar property of many animal phyla particularly important during embryogenesis. It relates events occurring in Hox clusters inside the chromosome DNA and embryonic tissues. These two entities differ in size by more than four orders of magnitude. HGC is observed as spatial collinearity (SC) where the Hox genes are located in the order H1, H2, H3 … along the 3’ to 5’ direction of the DNA sequence. The corresponding embryonic tissues (E1, E2, E3, …) are activated along the Anterior – Posterior axis in the same order. Besides this collinearity a temporal collinearity (TC) has been also observed in many vertebrates. According to TC first is H1 expressed in E1, later is H2 in E2, followed by H3,… Lately doubt has been raised whether TC really exists. A biophysical model (BM) has been formulated and tested in the last twenty years. According to BM, physical forces are created which pull the Hox genes one after the other driving them to a transcription factory domain where they are transcribed. The existing experiments support this BM description. In the present work two equivalent realizations of BM are presented which explain the recent findings on TC as observed in the vertebrates.
ARTICLE | doi:10.20944/preprints202001.0341.v1
Subject: Life Sciences, Microbiology Keywords: Listeria spp.; food; food contact surfaces; genotyping; virulence genes; toxin-antitoxin system mazEF
Online: 29 January 2020 (03:42:54 CET)
This study aimed to evaluate the hazards posed by foodborne bacteria of the Listeria genus by analyzing prevalence, diversity and virulence of Listeria spp. in food and food manufacturing plants. Seventy five isolates obtained from the routine analysis of 653 samples by three diagnostic laboratories in Northern Italy were genotipically differentiated by Repetitive Extragenic Palindrome (rep) PCR with the GTG5 primer, identified by sequencing the 16S rRNA gene and examined by specific PCR tests for the presence of L. monocytogenes virulence determinants occasionally found to occur in other species of the genus. The identity of the amplification products was confirmed by sequencing. Fifty seven isolates were identified as L. innocua, 12 as L. monocytogenes, 5 as L. welshimeri and one as L. seeligeri. All L. monocytogenes isolates belonged to the serotype 1/2a and were predicted to be virulent for the presence of the inlJ internalin gene. Potentially virulent strains of L. innocua, L. seeligeri and L. welshimeri, carrying the L. monocytogenes inlA gene and/or hly gene, were identified, and most isolates were found to possess the toxin-antitoxin system mazEF for efficient adaptation to heat shock. Results indicated the need to reinforce food contamination prevention measures against all Listeria species by efficiently defining their environmental distribution.
ARTICLE | doi:10.20944/preprints201912.0093.v1
Subject: Life Sciences, Genetics Keywords: mixed linear model; genotyping-by-sequencing; functional validation; RT-qPCR; resistance genes; GWAS
Online: 7 December 2019 (12:41:39 CET)
Meloidogyne javanica causing root-knot nematode in soybean is an important problem in soybean areas, leading to several yield losses. Some accessions have been identified carrying resistance loci to this nematode specie. In this study, a set of 317 soybean accessions were characterized for resistance to M. javanica. Genome-wide association study (GWAS) was performed using SNPs from genotyping-by-sequencing (GBS), and a region of 29.2 Kbp on chromosome 13 was identified. The haplotype analysis showed that SNPs were able to discriminate susceptible and resistant accessions, leading to 25 accessions sharing the resistance locus. Furthermore, 5 accessions may be new M. javanica resistance sources. The screening of the SNPs in the USDA soybean germplasm showed that several accessions previous reported as resistance to other nematodes also showed the resistance haplotype on chromosome 13. High levels of concordance among the phenotypes of Brazilian cultivars and the SNPs in chromosome 13 were observed. A in silico analysis of the mapped region on soybean genome revealed a presence of 5 genes with structural similarity with major resistance genes. The expression levels of the candidate genes in the interval demonstrated a potential pseudogene, and other two model genes up-regulated in the resistance source after pathogen infection. The SNPs associated to the region conferring resistance is a important tool for introgression of the resistance by marker-assisted selection in soybean breeding programs.
ARTICLE | doi:10.20944/preprints201911.0244.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: activated inflammatory macrophages; quercetin; pro-/anti-inflammatory cytokine genes; STAT3 protein phosphorylation; TLR2
Online: 20 November 2019 (16:04:42 CET)
Our previous studies demonstrated that quercetin (Q) could be ingested and metabolized by macrophages and exerted prophylactic immuno-stimulatory activity and therapeutic anti-inflammatory effects on lipopolysaccharide (LPS)-treated macrophages ex vivo. To further clarify its possible anti-inflammatory mechanism, Q was selected to treat mouse peritoneal macrophages that obtained from female BALB/c mice exposed to LPS i.p. for 12 h. Relative gene expression of pro-/anti-inflammatory (TNF-α/IL-10) cytokines and components of inflammation-related intracellular signaling pathways (TLR2, TLR4, NF-κB, JAK2 and STAT3) was analyzed using two-step reverse transcription (RT) and real-time quantitative polymerase chain reaction (qPCR). STAT3 protein phosphorylation was determined using an in-cell ELISA method. As a result, Q and its metabolite quercetin-3-O-β-D-glucuronide (Q3G) decreased TNF-α gene expression amounts and ratios of pro-/anti-inflammatory (TNF-α/IL-10) cytokine gene expressions, but increased IL-10 gene expression amounts in activated inflammatory macrophages, supporting a substantial anti-inflammatory potential of Q and Q3G treatments. However, Q3G had lower effects than those of Q. Importantly, Q inhibited TLR2 gene expression and phosphorylation of STAT3 protein in the inflamed cells. Our results are the first report to suggest that Q inhibits LPS-induced inflammation ex vivo through suppressing TLR2 gene expression and STAT3 protein phosphorylation in activated inflammatory macrophages. Q has potential to further apply for treating inflammation-associated diseases.
Subject: Medicine & Pharmacology, Veterinary Medicine Keywords: l. monocytogenes; humans; animals; food; antimicrobial and virulence genes; bioinformatic analysis; prfA phylogenetic analysis
Online: 17 November 2019 (09:48:54 CET)
Serious outbreaks of foodborne disease have been caused by Listeria monocytogenes found in retail delicatessens and the severity of disease is significant, with high hospitalization and mortality rates. Little is understood about the formidable public health threat of L. monocytogenesin all four niches, humans, animals, food and environment in Egypt. This study analyzed the presence of L. monocytogenes collected from the four environmental niches and bioinformatic analysis was implemented to analyze and compare the data. PCR was used to detect virulence genes encoded by pathogenicity island (LIPI-1). prfA amino acid substation that causes constitutive expression of virulence was common in 77.7% of isolates. BLAST analysis did not match other isolates in the NCBI database suggesting this may be a characteristic of the region associated with these isolates. A second group included the NH1 isolate originating in China, and BLAST analysis showed this prfA allele was shared with isolates from other global locations such as Europe and North America. Identification of possible links and transmission pathways between the four niches, helps to decrease the risk of disease in humans, to take more specific control measures in the context of disease prevention, to limit economic losses associated with food recalls and highlightens the need to treatment options.
ARTICLE | doi:10.20944/preprints202208.0143.v1
Subject: Life Sciences, Microbiology Keywords: non-typhoidal Salmonella; ERIC-PCR typing; WGS; virulence-related genes; SPIs; Salmonella virulence plasmids; prophages
Online: 8 August 2022 (10:07:34 CEST)
In this work, we analysed human isolates of nontyphoidal Salmonella enterica subsp. enterica (NTS), which were collected from salmonellosis cases in Armenia from 1996 to 2019. This disease became a leading food-borne bacterial infection in the region, with the younger age groups especially affected. The isolates were characterised by serotyping, Enterobacterial Repetitive Intergenic Consensus (ERIC-PCR) typing, and whole genome sequencing (WGS). The main serotypes were S. Typhimurium, S. Enteritidis, and S. Arizonae. ERIC-PCR indicated a high degree of clonality among S. Typhimurium strains, which were also multidrug-resistant and produced extended spectrum beta-lactamases. During the study period, the frequency of S. Typhimurium and S. Arizonae isolations were decreasing, but with the increase of S. Enteritidis and other NTS. A total of 42 NTS isolates were subjected to WGS and explored for virulence-related traits and the corresponding genetic elements. Some virulence and genetic factors were shared by all NTS serotypes, while the main differences were attributed to the serotype-specific diversity of virulence genes, SPIs, virulence plasmids, and phages. The results indicated the variability and dynamics in the epidemiology of salmonellosis and a high virulence potential of human NTS isolates circulating in the region.
ARTICLE | doi:10.20944/preprints202202.0357.v1
Subject: Life Sciences, Molecular Biology Keywords: granulosa cells; heat stress; apoptosis; oxidative stress; RNA-seq; transcriptomics; differentially expressed genes; signaling pathways
Online: 28 February 2022 (11:08:42 CET)
Heat stress affects the granulosa cells (GCs) and ovarian follicular microenvironment, causing poor oocyte developmental competence and fertility. This study aimed to investigate the physical responses and global transcriptomic changes in bovine GCs to acute heat stress (43 ℃ for 2 h) in-vitro and gave essential insights into the general interaction at cell–stress nexus. Heat-stressed GCs exhibited transient proliferation senescence, resumed proliferation at 48 h post-stress. While post-stress immediate culture-media change had a relatively positive effect on proliferation resumption. Increased accumulation of reactive oxygen species and apoptosis was observed in heat stress group. In spite of the upregulation of pro-apoptotic and caspase executioner genes, antioxidants and anti-apoptotic genes were also upregulated in heat-stressed GCs. Progesterone and Estrogen hormones along with steroidogenic genes expression, declined significantly, in spite of the upregulation of genes involved in cholesterol synthesis. Out of 12385 differentially expressed genes (DEGs), 330 significant DEGs (75 upregulated, 225 downregulated) were subjected to KEGG functional pathway annotation, gene ontology enrichment, and STRING network analyses. Based on the manual query of DEGs, pathway and enrichment analyses, a vast interplay observed among all major signaling pathways strongly evidence the repression of cellular transcriptional and proliferation activity, averting the effects of heat stress through remodeling of cellular structural proteins and energetic-homeostasis. This study presents detailed responses of acute heat-stressed GCs at physical, transcriptional, and pathway levels and presents interesting insights into future studies regarding GCs adaptation and their interaction with oocyte and reproductive system at ovarian level.
HYPOTHESIS | doi:10.20944/preprints201908.0087.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: Hox genes; collinearity; segmental identity; chromatin modifications; vertebral malformations; vertebrae; Hox synteny; somitogenesis; Notch pathway
Online: 7 August 2019 (03:51:41 CEST)
It is not understood how the numbers and identities of vertebrae are controlled during mammalian development. The remarkable robustness and conservation of segmental numbers may suggest a digital nature of the underlying process. Here I propose a mechanism that allows cells to obtain and store the segmental information in digital form, and to produce a pattern of chromatin accessibility that in turn regulates Hox gene expression specific to the metameric segment. The model requires that a regulatory element be present such that the number of occurrences of the motif between two consecutive Hox genes equals the number of segments under the control of the anterior gene. This is true for the recently discovered HRC3 motif, associated with histone modifications and developmental genes. The finding not only allows correctly predicting the numbers of segments using only sequence information, but also resolves the 40-year-old enigma of the function of temporal and spatial collinearity of Hox genes. The logic of the mechanism is illustrated in an animated video: https://youtu.be/4a3XOQ7Lz28. I also discuss how different aspects of the proposed mechanism can be tested experimentally.
ARTICLE | doi:10.20944/preprints201907.0051.v1
Subject: Life Sciences, Genetics Keywords: lung cancer; molecular signature; molecular pathway; differentially expressed genes; protein-protein interaction; reporter biomolecules and bioinformatics
Online: 3 July 2019 (08:54:37 CEST)
Lung cancer is one of the most important health risks worldwide for human. Non-small cell lung cancer (NSCLC) is the most common cause of premature death from malignant disease. This study provides in-depth insights from systems biology analyses to identify molecular to inform systemic drug targeting in NSCLC. Gene expression profiles from non small cell lung cancer were analyzed with genome-scale biomolecular networks (I,e., protein-protein interaction, transcriptional and post transcriptional regulatory networks). The aim of the study was to determine the pathways and expression profile of the genes to discover molecular signature at RNA and protein levels which could serve as potential drug targets for therapeutics innovation and the identification of novel targets. Eight proteins, six TFs and seven miRNAs came into prominence as potential drug targets. The differential expression profiles of these reporter biomolecules were cross-validated by independent RNA-Seq and miRNA-Seq. Risk discrimination performance of the reporter biomolecules NPR3, JUN, PPARG, TP53, CKMT1A, SP3 and TFAP2A were also evaluated. Total 213 drugs and 7 proteins were found for non small cell lung cancer through dgidb. Among these identified drugs seven drugs such as- Gemcitabine, Carboplatin, paclitaxel, Docetaxel, Crizotinib, Bevacizumab and Gemcitabine is used for NSCLC which is approved by National Cancer Institute. The molecular signatures and repurposed drugs presented here permit further attention for experimental studies which are offer significant potential as biomarkers and candidate therapeutics for precision medicine approaches to clinical management of NSCLC.
ARTICLE | doi:10.20944/preprints202206.0196.v1
Subject: Life Sciences, Microbiology Keywords: biofilm formation; S. aureus; CRA plating test; CVMP test; ica genes; bap gene; foods; public health; Bangladesh
Online: 14 June 2022 (06:10:13 CEST)
Staphylococcus aureus is a major food-borne pathogen. The ability of S. aureus to produce biofilm is a significant virulence factor triggering its persistence in hostile environments. In this study, we screened a total of 420 different food samples and human hand swabs to detect S. aureus and to determine their biofilm formation ability. Samples analyzed were meat, milk, egg, fish, fast foods, and hand swabs. S. aureus were detected by culturing, staining, biochemical, and PCR. Biofilm formation ability was determined by Congo Red Agar (CRA) plate and Crystal Violet Microtiter Plate (CVMP) tests. The icaA, icaB, icaC, icaD, and bap genes involved in the synthesis of bio-film-forming intracellular adhesion compounds were detected by PCR. About 23.81% (100/420; 95% CI: 14.17-29.98%) samples harbored S. aureus as revealed by detection of the nuc gene. CRA plate revealed 20% of S. aureus isolates as strong biofilm producers, while 69% and 11% as in-termediate and non-biofilm producers, respectively. By the CVMP staining method, 20%, 77%, and 3% of the isolates were found strong, intermediate, and non-biofilm producers. Furthermore, 21% of S. aureus isolates carried at least one biofilm-forming gene, where icaA, icaB, icaC, icaD, and bap genes were detected in 15%, 20%, 7%, 20%, and 10% of the S. aureus isolates, respectively. Bivariate analysis showed high significant correlations (p<0.001) between any of the two adhesion genes of S. aureus isolates. To the best of our knowledge, this is the first study in Bangladesh describing the detection of biofilm-forming S. aureus from foods and hand swabs with molecular-based evidence. Our findings suggest that food samples should be deemed a potential reservoir of biofilm-forming S. aureus that indicates a potential public health significance.
ARTICLE | doi:10.20944/preprints202111.0266.v1
Subject: Engineering, Biomedical & Chemical Engineering Keywords: Pan-Cancer; somatic point mutations; cancer subtyping; biomarker discovery; driver genes; per-sonalized medicine; health data analytics
Online: 15 November 2021 (13:51:33 CET)
The advent of high throughput sequencing has enabled researchers to systematically evaluate the genetic variations in cancer, resulting in identifying many cancer-associated genes. Although cancers in the same tissue are widely categorized in the same group, they demonstrate many differences concerning their mutational profiles. Hence there is no “silver bullet” for the treatment of a cancer type. This reveals the importance of developing a pipeline to identify cancer-associated genes accurately and re-classify patients with similar mutational profiles. Classification of cancer patients with similar mutational profiles may help discover subtypes of cancer patients who might benefit from specific treatment types. In this study, we propose a new machine learning pipeline to identify protein-coding genes mutated in a significant portion of samples to identify cancer subtypes. We applied our pipeline to 12270 samples collected from the International Cancer Genome Consortium (ICGC), covering 19 cancer types. Here we identified 17 different cancer subtypes. Comprehensive phenotypic and genotypic analysis indicates distinguishable properties, including unique cancer-related signaling pathways, in which, for most of them, targeted treatment options are currently available. This new subtyping approach offers a novel opportunity for cancer drug development based on the mutational profile of patients. We also comprehensive study the causes of mutations among samples in each subtype by mining the mutational signatures, which provides important insight into their active molecular mechanisms. Some of the pathways we identified in most subtypes, including the cell cycle and the Axon guidance pathways, are frequently observed in cancer disease. Interestingly, we also identified several mutated genes and different rates of mutation in multiple cancer subtypes. In addition, our study on “gene-motif” suggests the importance of considering both the context of the mutations and mutational processes in identifying cancer-associated genes. The source codes for our proposed clustering pipeline and analysis are publicly available at: https://github.com/bcb-sut/Pan-Cancer.
ARTICLE | doi:10.20944/preprints202010.0316.v1
Subject: Life Sciences, Biochemistry Keywords: Type 2 diabetes; cancer; shared pathways; shared genes and proteins; relationship between cancer and type 2 diabetes
Online: 15 October 2020 (09:47:35 CEST)
Obesity, type 2 diabetes, and different forms of cancers are among the leading human diseases and highly complex in terms of diagnostic and therapeutic approaches. Diabetes and cancer are among the most frequent and complex diseases and based on epidemiological evidence and study it can be concluded that the patients suffering from diabetes are considered to be significantly at higher risk for a number of cancer types. Both these diseases are among the highly complex and heterogeneous in nature. There are a number of evidences which support the hypothesis that these diseases interlinked and obesity may aggravate the risk(s) of both these diseases type 2 diabetes and different types of cancers. Multi-level unwanted alterations such as (epi-)genetic alterations, changes at the transcriptional level, and altered signaling pathways (receptor, cytoplasmic, and nuclear level) are the major source which promotes a number of complex diseases and such heterogeneous level of complexities are considered as the major barrier in the development of therapeutic. With so many known challenges, it is critical to understand the relationships and the common shared causes between type 2 diabetes and cancer which is difficult to unravel and understand. Furthermore, the real complexity arises during diagnosis from contended corroborations that specific drug(s) (individually or in combination) during diagnosis process of type 2 diabetes may increase or decrease the cancer risk or affect cancer prognosis. In this review article, we have presented the recent and most updated evidences from the studies where the origin, biological background, correlation between them have been presented or proved. Furthermore, we have summarized the methodological challenges and tasks that are frequently encountered. we have also outlined the physiological links between type 2 diabetes and cancers. Finally, we have presented and summarized the outline of the hallmarks for both these diseases diabetes and cancer.
ARTICLE | doi:10.20944/preprints202005.0471.v2
Subject: Life Sciences, Genetics Keywords: DNA oligomers; harmonic progression; hyperbolic rules; matrices; tensor product; quantum informatics; oligomer sums method; genomes; genes; viruses; proteins; long Russian texts; phonetic sequences
Online: 21 June 2020 (15:26:04 CEST)
The author's method of oligomer sums for analysis of oligomer compositions of eukaryotic and prokaryotic genomes is described. The use of this method revealed the existence of general rules for cooperative oligomeric organization of a wide list of genomes. These rules are called hyperbolic because they are associated with hyperbolic sequences including the harmonic progression 1, 1/2, 1/3, .., 1/n. These rules are demonstrated by examples of quantitative analysis of many genomes from the human genome to the genomes of archaea and bacteria. The hyperbolic (harmonic) rules, speaking about the existence of algebraic invariants in full genomic sequences, are considered as candidates for the role of universal rules for the cooperative organization of genomes. The described phenomenological results were obtained as consequences of the previously published author's quantum-information model of long DNA sequences. The oligomer sums method was also applied to the analysis of long genes and viruses including the COVID-19 virus; this revealed, in characteristics of many of them, the phenomenon of such rhythmically repeating deviations from model hyperbolic sequences, which are associated with DNA triplets. In addition, an application of the oligomer sums method are shown to the analysis of the following long sequences: 1) amino acid sequences in long proteins like the protein Titin; 2) phonetic sequences of long Russan literary texts (for checking of thoughts of many authors that phonetic organization of human languages is deeply connected with the genetic language). The topics of the algebraic harmony in living bodies and of the quantum-information approach in biology are discussed.
ARTICLE | doi:10.20944/preprints201812.0018.v2
Subject: Biology, Other Keywords: colorectal cancer; differentially expressed genes; biomarkers; protein-protein interaction; reporter biomolecules; candidate drugs; systems biology; drug repositioning
Online: 29 December 2018 (07:05:05 CET)
Background and objectives: Colorectal cancer (CRC) is the second most common cause of cancer-related death in the world, but early diagnosis ameliorates the survival of CRC. This report directed to identify molecular biomarker signatures in CRC. Materials and Methods: We analyzed two microarray datasets (GSE35279 and GSE21815) from Gene Expression Omnibus (GEO) to identify mutual differentially expressed genes (DEGs). We integrated DEGs with protein-protein interaction and transcriptional/post-transcriptional regulatory networks to identify reporter signaling and regulatory molecules; utilized functional overrepresentation and pathway enrichment analyses to elucidate their roles in biological processes and molecular pathways; performed survival analyses to evaluate their prognostic performance; and applied drug repositioning analyses through Connectivity map (CMap) and geneXpharma tools to hypothesize possible drug candidates targeting reporter molecules. Results: A total of 727 up-regulated and 99 down-regulated DEGs were detected. The PI3K-Akt signaling, Wnt signaling, ECM-interaction, and cell cycle were identified as significantly enriched pathways. Ten hub proteins (ADNP, CCND1, CD44, CDK4, CEBPB, CENPA, CENPH, CENPN, MYC, and RFC2), 10 transcription factors (ETS1, ESR1, GATA1, GATA2, GATA3, AR, YBX1, FOXP3, E2F4, and PRDM14) and 2 miRNAs (miR-193b-3p and miR-615-3p) were detected as reporter molecules. The survival analyses through Kaplan Meier curves indicated remarkable performance of reporter molecules in estimation of survival probability in CRC patients. In addition, several drug candidates including anti-neoplastic and immunomodulating agents were repositioned. Conclusions: This study presents biomarker signatures at protein and RNA levels with prognostic capability in CRC. We think that the molecular signatures and candidate drugs presented in this study might be useful in future studies indenting development of accurate diagnostic and/or prognostic biomarker screens and efficient therapeutic strategies in CRC.
ARTICLE | doi:10.20944/preprints202112.0377.v1
Subject: Life Sciences, Genetics Keywords: pig genome; gamma/delta T-cell; TRG locus; TRG genes; gamma/delta high species; Cetartiodac-tyla; Immunogenomics; evolution
Online: 23 December 2021 (10:02:37 CET)
The domestic pig (Sus scrofa) is a species representative of the Suina, one of the four suborders within Cetartiodactyla. In this paper, we reported our analysis of the pig TRG locus in comparison with the loci of species representative of the Ruminantia, Tylopoda and Cetacea suborders. The pig TRG genomic structure reiterates the peculiarity of the organization of Cetartiodactyla loci in TRGC “cassettes”, each containing the basic V-J-J-C unit. Eighteen genes arranged in four TRGC cassettes, form the pig TRG locus. All the functional TRG genes were expressed, and the TRGV genes preferentially rearrange with the TRGJ genes within their own cassette, which correlates the diversity of the gamma-chain repertoire with the number of cassettes. Among them, the TRGC5, located at the 5’ end of the locus, is the only cassette that retains a marked homology with the corresponding TRGC cassettes of all the analyzed species. The preservation of the TRGC5 cassette for such a long evolutionary time presumes a highly specialized function of its genes, which could be essential for the survival of species. Therefore, the maintenance of this cassette in pigs confirms that it is the most evolutionarily ancient within Cetartiodactyla, and it has undergone a process of duplication to give rise to the other TRGC cassettes in the different artiodactyl species in a lineage-specific manner.
ARTICLE | doi:10.20944/preprints202010.0449.v1
Subject: Biology, Anatomy & Morphology Keywords: comparative genomics; plant-parasitic nematodes; phylogenomics; parasite-specific genes; pest control; de novo gene birth; horizontal gene transfers
Online: 22 October 2020 (09:01:30 CEST)
Plant-parasitic nematodes cause expressive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. The chemical methods that have been deployed to control nematodes were largely banned from use due to their poor specificity and high toxicity. Hence, there is an urgent need for the development of cleaner and more specific control methods. Recent advances in nematode genomics, including in phytoparasitic species, provide an unprecedented opportunity to identify genes and functions specific to these pests. Using phylogenomics, we compared 61 nematode genomes, including 16 for plant-parasitic species and identified more than 24,000 protein families specific to these parasites. In the genome of Meloidogyne incognita, one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein databases. Among these phytoparasites-specific proteins, ca. 1,000 shared the same properties as known secreted effectors involved in essential parasitic functions. Of those, 68 were novel and showed strong expression during the endophytic phase of the nematode life cycle, based on both RNA-seq and RT-qPCR analyses. Besides effector candidates, transcription-related and neuro-perception functions were enriched in phytoparasites-specific proteins, revealing interesting targets for nematode control methods. This phylogenomics analysis, constitutes an unprecedented resource for the further understanding of the genetic basis of nematode adaptation to phytoparasitism and for the development of more efficient control methods.
ARTICLE | doi:10.20944/preprints202007.0477.v1
Subject: Life Sciences, Genetics Keywords: Autism; Schizophrenia; Mental Depression; Ataxia; Fragile X; Parkinson’s disease; Mitochondria; Genes’ expression; Tissues; neurological disorders; nervous systems disorders
Online: 21 July 2020 (11:07:07 CEST)
The art of observing and describing behaviors has driven diagnosis and informed basic science in Psychiatry. In recent times, studies of mental illness are focused on understanding the brain’s neurobiology but there is a paucity of information on the potential contributions from peripheral activity to mental health. In Precision Medicine, this common practice leaves a gap between bodily behaviors and genomics that we here propose to address with a new layer of inquiry that includes genes’ expression on tissues inclusive of brain, heart, muscle-skeletal and organs for vital bodily functions. We interrogate genes’ expression on human tissue as a function of disease-associated genes. By removing genes linked to disease from the typical human set, and recomputing the genes’ expressions on the tissues, we can compare the outcomes across mental illnesses, well-known neurological conditions, and non-neurological ones. We find that major neuropsychiatric conditions that are behaviorally defined today (e.g. Autism, Schizophrenia, Depression) through DSM-observation criteria, have strong convergence with well-known neurological ones (e.g. Ataxias, Parkinson), but less overlap with non-neurological ones. Surprisingly, tissues majorly involved in the central control, coordination, adaptation and learning of movements, emotion and memory are maximally affected in psychiatric diagnoses along with peripheral heart and muscle-skeletal tissues. Our results underscore the importance of considering both the brain-body connection and the contributions of the peripheral nervous systems to mental health.
ARTICLE | doi:10.20944/preprints202204.0248.v1
Subject: Life Sciences, Molecular Biology Keywords: granulosa cells; heat stress; integrated analysis; transcriptomics; metabolomics; differentially ex-pressed genes; metabolites; signaling pathways; metabolic pathways; cancer pathways
Online: 27 April 2022 (05:08:15 CEST)
Previous studies reported the physical, transcriptomics and metabolomics changes in in-vitro acute heat stressed bovine granulosa cells. Granulosa cells exhibited transient proliferation senescence, oxidative stress, increased rate of apoptosis, and decline in steroidogenic activity. This study performs joint integration and network analysis of metabolomics and transcriptomics data to further narrow down and elucidate the role of differentially expressed genes, important metab-olites and relevant cellular and metabolic pathways in acute heat-stressed granulosa cells. Among significant (Raw P-value <0.05) metabolic pathways where metabolites and genes did converge, this study found Vitamin B6 metabolism, Glycine, serine and threonine metabolism, Phenylalanine metabo-lism, Arginine biosynthesis, Tryptophan metabolism, Arginine and proline metabolism, Histidine metabolism, and Glyoxylate and dicarboxylate metabolism. Important significant convergent bio-logical pathways included, ABC transporters and Protein digestion and absorption, while func-tional signaling pathways included cAMP, mTOR, and AMPK signaling pathways together with Ovarian steroidogenesis pathway. Among caner pathways, the most important pathway was Central carbon metabolism in cancer. Through multiple analysis query, Progesterone, Serotonin, citric acid, Pyridoxal, L-Lysine, Succinic acid, L-Glutamine, L-Leucine, L-Threonine, L-Tyrosine, Vitamin B6, Choline, and CYP1B1, MAOB, VEGFA, WNT11, AOX1, ADCY2, ICAM1, PYGM, SLC2A4, SLC16A3, HSD11B2 and NOS2 appeared to be important enriched metabolites and genes, respectively. These genes, metabolites, metabolic, cellular and cell signaling pathways com-prehensively elucidate the mechanisms underlying the intricate fight between death and survival in acute heat-stressed bovine granulosa cells, and essentially help further our understanding and future quest of research in this direction.
ARTICLE | doi:10.20944/preprints202208.0181.v1
Subject: Life Sciences, Other Keywords: COVID-19; SARS-CoV-2; disease severity; blood leukocyte transcriptome; WGCNA; transcriptional modules; differentially expressed genes; COVID-19 transcriptional markers
Online: 9 August 2022 (14:59:44 CEST)
The transcriptional response of human blood leukocytes to SARS-CoV-2 infection was investigated focusing on the differences between mild and severe cases and between age subgroups. Weighted gene co-expression network analysis and comparative gene expression analysis were used. Three transcriptional modules positively associated with the traits of interest and their respective high hierarchy genes were identified. Enrichment analyses showed that the yellow module, associated with severe cases and older patients, had an overrepresentation of genes involved in inflammatory and innate immune responses, and neutrophil activation. The magenta and black modules, associated with disease severity and younger patients, contained genes related to innate immunity and inflammation and genes that regulate those responses. Subnetworks for these modules were constructed using genes enriched for innate immunity, inflammation, immunoregulation and differentially expressed genes (severe vs. mild). Their analysis evidenced that immunoregulatory functions are more activated in the modules associated with younger patients, what may help to explain the better disease course and faster recovery observed in younger COVID-19 patients. Comparative gene expression analysis between severe and mild groups, followed by gene enrichment and normalized gene expression analyses, revelated a set of 23 potential biomarkers for COVID-19 severity, of which 13 are newly described.
ARTICLE | doi:10.20944/preprints202009.0171.v1
Subject: Biology, Physiology Keywords: protein-protein interaction network; GPx; glutathione peroxidases genes; ciliate protists; copper; metals; antioxidant system; free-radicals; ROS; reactive oxygen species
Online: 8 September 2020 (04:59:18 CEST)
Glutathione peroxidases (GPxs) form a broad family of antioxidant proteins essential for maintaining redox homeostasis in eukaryotic cells. In this study, we used an integrative approach that combines bioinformatics, molecular biology, and biochemistry to investigate the role of GPxs in reactive oxygen species detoxification in the unicellular eukaryotic model organism Tetrahymena thermophila. Both phylogenetic and mechanistic empirical model analyses provided indications about the evolutionary relationships among the GPXs of Tetrahymena and the orthologous enzymes of phylogenetically related species. In-silico gene characterization and text mining were used to predict the functional relationships between GPxs and other physiologically-relevant processes. The GPx genes contain conserved transcriptional regulatory elements in the promoter region, which suggest that transcription is under tight control of specialized signaling pathways. The bioinformatic findings were next experimentally validated by studying the time course of copper (Cu)-dependent regulation of gene transcription and enzymatic activity. Results emphasize the role of GPxs in the detoxification pathways that, by complex regulation of Cu-dependent GPx gene expression, enables Tetrahymena to survive in high Cu concentrations and the associated redox environment.
HYPOTHESIS | doi:10.20944/preprints202002.0147.v3
Subject: Medicine & Pharmacology, General Medical Research Keywords: new coronavirus; 2019-nCoV; superinfection therapy (SIT); apathogenic dsRNA virus; interferon-dependent antiviral genes; broad-spectrum antiviral treatment; clinically tested.
Online: 20 March 2020 (09:31:54 CET)
The transmission characteristic of COVID-19 is of similar magnitude to severe acute respiratory syndrome-related coronavirus (SARS-CoV) and the 1918 pandemic influenza. The virus is now in more than 100 countries and on nearly all continents. The World Health Organization (WHO) declared the COVID-19 outbreak a pandemic. There is no current evidence from random clinical trials (RCTs) to recommend any specific anti-COVID-19 treatment for patients with suspected or confirmed COVID-19 infection. In order to mitigate the impact of the COVID-19 outbreak, here we propose an innovative superinfection therapeutic (SIT) strategy, which could complement the development of prophylactic vaccines. SIT is based on clinical observations that unrelated viruses might interact in co-infected patients. During SIT, the patient benefit from superinfection with an apathogenic dsRNA virus such as the infectious bursal disease virus (IBDV), which is a powerful activator of the interferon-dependent antiviral gene program. An attenuated vaccine strain of IBDV was already successfully administered to resolve acute and persistent infections induced by two completely different viruses, the hepatitis B (DNA) and C (RNA) viruses (HBV/HCV). Importantly, the epidemiological efficacy of a similar strategy to SIT had already been successfully tested in large controlled trials. Standard live orally administered enterovirus vaccines that stimulate the production of endogenous interferon of the host mitigated the seasonal outbreaks of influenza and other associated acute respiratory infections in 152,042 individuals without adverse reactions.
ARTICLE | doi:10.20944/preprints202002.0234.v1
Subject: Life Sciences, Virology Keywords: adeno-associated virus; protein sequence analysis; overlapping genes; amino acid depletion; cysteine depletion; tyrosine depletion; capsid design; membrane-binding amphipathic helix
Online: 17 February 2020 (02:42:39 CET)
Adeno-associated viruses (AAVs, genus dependoparvovirus) are promising gene therapy vectors. In strains AAV1-12, the capsid gene VP1 encodes a recently discovered protein, MAAP, in an overlapping frame. MAAP binds the cell membrane by an unknown mechanism. We discovered that MAAP is also encoded in bovine AAV and in porcine AAVs (which have shown promise for gene transfer into muscle tissues), in which it is probably translated from a non-canonical start codon. MAAP is predicted to be mostly disordered except for a predicted C-terminal, membrane-binding amphipathic α-helix. MAAP has a highly unusual composition. In particular, it lacks internal methionines, and is devoid of tyrosines in most strains. Unexpectedly, we discovered that the N-terminus of VP1 also lacks several amino acids. In all AAVs that encode MAAP, the first 200 aas of VP1 are devoid of internal methionines, probably owing to a selection against ATG codons that could prevent translation of MAAP and of capsid isoforms (VP2, VP3). The N-terminus of VP1 also lacks cysteines, likely to avoid the formation of disulfide bridges when it becomes exposed outside of the capsid during post-endocytic trafficking. Finally, the region common to VP1 and VP2 lacks tyrosine in the vast majority of AAVs that encode MAAP. Avoiding these "forbidden" aas in MAAP and VP1 when creating recombinant AAV capsids might increase the efficiency of capsid design. Conversely, the presence of "forbidden" aas in some rare strains probably indicates that they have unusual properties that could help us understand the viral cycle.
ARTICLE | doi:10.20944/preprints202012.0697.v1
Subject: Life Sciences, Biochemistry Keywords: Repeat-Induced Point Mutations; RIP; Accessory Chromosome; Genome Compartmentalization; GC Content; Genetic Variation; Fusarium circinatum; Transposable Elements; Interstitial Telomeric Repeats; Effector Genes.
Online: 28 December 2020 (12:18:11 CET)
Repeat-Induced Point mutations (RIP) serves as a genome defence mechanism that impedes the deleterious consequences of repeated motifs such as transposable elements in fungi. Genomic regions with RIP are biased for adenosine and thymine transitions and the cumulative influence of RIP is thought to have a considerable impact on genome composition. We investigated the impact of RIP on localized genomic regions and whole-genome sequences for representatives of the pine pathogen, Fusarium circinatum. We set out to determine the intraspecific variation in acquired RIP and the role of RIP in the development of diverse F. circinatum sub-genomic compartments. The results of the study show that the AT-enriched sub-genomic compartment accounts for ca. 97% of the calculated RIP and was further prominent in both core and accessory genomic regions. However, more extensive RIP was observed in the accessory sub-compartment and more variable regions of the genome. Regions with RIP indicated increased intrinsic curvature of the DNA which may influence DNA-protein interactions and may promote constitutive heterochromatin formation. The results show that RIP is an important source of functional novelty and genome variation. RIP contributes to the evolution of the genetic landscape and differentiation of diverse sub-genomic compartments of this important fungal pathogen.
ARTICLE | doi:10.20944/preprints202103.0379.v1
Subject: Life Sciences, Biochemistry Keywords: γδ T cell; T cell receptor; TRA/TRD locus; Variable, Diversity, Joining and Constant genes; complementarity determining region-3; δ chain; somatic hypermutation; Camelidae
Online: 15 March 2021 (12:32:41 CET)
The role of γδ T cells in vertebrate immunity is still an unsolved puzzle. Species such as humans and mice display a low percentage of these T lymphocytes (i.e., “γδ low species”) with a restricted diversity of γδ T cell receptors (TR). Conversely, artiodactyl species (i.e., “γδ high species”) ac-count for a high proportion of γδ T cells with large γ and δ chain repertoires. The genomic organisation of the TR γ (TRG) and δ (TRD) loci has been determined in sheep and cattle, noting that a wide number of germline genes that encode for γ and δ chains characterise their genomes. Taking advantage from the current improved version of the genome assembly, we have investigated the genomic structure and gene content of the dromedary TRD locus, which, as in the other mammalian species, is nested within the TR alpha (TRA) genes. The most remarkable finding was the identification of a very limited number of variable germline genes (TRDV) compared to sheep and cattle, which supports our previous expression analyses for which the somatic hypermutation mechanism is able to enlarge and diversify the primary repertoire of dromedary δ chains. Furthermore, the comparison between genomic and expressed sequences reveals that D genes, up to four incorporated in a transcript, greatly contribute to the increased diversity of the dromedary δ chain antigen binding-site.
Subject: Biology, Anatomy & Morphology Keywords: T cell receptor; dolphin genome; TRB locus; TRBV; TRBJ; TRBD and TRBC genes; TRA and TRB gene expression analysis; multiple sequence alignments (MSA); 3D modelisation; IMGT
Online: 11 February 2021 (13:26:26 CET)
Bottlenose dolphin (Tursiops truncatus) belongs to the Cetartiodactyla and similarly to the other cetaceans represent the most successful mammalian colonization of the aquatic environment. Here we report a genomic, evolutionary and expression study of Tursiops truncatus T cell receptor beta (TRB) genes. Although the organization of the dolphin TRB locus is similar to that of the other artiodactyl species, with three in tandem D-J-C clusters located at its 3’ end, its uniqueness is given by the reduction of the total length due essentially to the absence of duplications and to the deletions that have drastically reduced the number of the germline TRBV genes. We have analyzed the relevant mature transcripts from two subjects. The simultaneous availability of rearranged TRA and TRB cDNA from the peripheral blood of one of the two specimens, and the human/dolphin amino acids multi sequence alignments, allowed us to calculate the most likely interactions at the protein interface between the alpha/beta heterodimer in complex with major histocompatibility class I (MH1) protein. Interacting amino acids located in the CDR-IMGT of the dolphin variable V alpha and beta domains were identified. According to comparative modelisation, the atome pair contact sites analysis between the human MH1 grove (G) domains and the TR V domains confirms conservation of the structure of the dolphin TR/pMH.
REVIEW | doi:10.20944/preprints201809.0217.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: Premature ovarian insufficiency, POI; Gene therapy; Menopause; SAL-like 4 genes, SALL4; Follicle-stimulating hormone (FSH); Basonuclin-1; Replication-incompetent adenoviral vector, Ad; Stem cells, SC.
Online: 12 September 2018 (11:06:42 CEST)
Premature ovarian insufficiency (POI) is a highly prevalent disorder, characterized by the development of menopause before age of 40. Most cases are idiopathic; however, in some women the cause of this condition (e.g. anticancer treatment, genetic disorders, and enzymatic defects) may be identified. Although hormone replacement therapy, the principal therapeutic approach for POI, helps to alleviate the related symptoms, this does not effectively solve the issue of fertility. Assisted reproductive techniques also lack efficacy in these women. Thus, the effective approach to manage the patients with POI is highly warranted. Several mechanisms, associated with POI, have been identified, including lack of FSH receptor functioning, alterations in the apoptosis control, mutations in Sal-like 4 genes, thymulin or basonuclin-1 deficiency etc. The above-mentioned may be good targets for gene therapy in order to correct defects, leading to POI. The goal of this review is to summarize the current experience on the POI studies, that employed gene therapy, and to discuss the possible future directions in this field.
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Neuroendocrine Neoplasms; NOTCH; cancer driven genes; mutational mechanism; germline mutations.; small cell lung carcinoma; pancreatic NET; small bowel NET; medullary thyroid carcinoma; malignant castration-resistant prostatic cells
Online: 23 July 2019 (10:34:50 CEST)
Neuroendocrine neoplasms (NENs) comprise a heterogeneous group of rare malignancies mainly originated from hormones secreting cells, which are widespread in human tissues. The identification of mutations in ATRX/DAXX genes in sporadic NENs, as well as the high burden of mutations scattered throughout MEN-1 gene in both sporadic and inherited syndromes, provided new insights into the molecular biology of tumour development. Other molecular mechanisms, such as the NOTCH signaling pathway, have shown to play an important role in the pathogenesis of NENs. NOTCH receptors are expressed on neuroendocrine cells and generally, act as tumour suppressor proteins, but in some contexts can function as oncogenes. The biological heterogeneity of NENs suggests that to fully understand the roles and the potential therapeutic implications of gene mutations and NOTCH signaling in NENs, a comprehensive analysis of genetic alterations, NOTCH expression patterns and their potential roles across all NEN subtypes is required.