Subjects -> BIOLOGY (Total: 3174 journals)
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Showing 401 - 600 of 1720 Journals sorted alphabetically
Cryoletters     Full-text available via subscription   (Followers: 4)
Cuadernos de Neuropsicología     Open Access   (Followers: 1)
Current Applied Science and Technology     Open Access  
Current Bioinformatics     Hybrid Journal   (Followers: 13)
Current Biology     Full-text available via subscription   (Followers: 236)
Current Genomics     Hybrid Journal   (Followers: 8)
Current Landscape Ecology Reports     Hybrid Journal   (Followers: 2)
Current Medical Science     Hybrid Journal   (Followers: 1)
Current Molecular Medicine     Hybrid Journal   (Followers: 2)
Current Opinion in Cell Biology     Hybrid Journal   (Followers: 51)
Current Opinion in Molecular Therapeutics     Full-text available via subscription   (Followers: 8)
Current Opinion in Neurobiology     Hybrid Journal   (Followers: 32)
Current Opinion in Structural Biology     Hybrid Journal   (Followers: 26)
Current Opinion in Systems Biology     Hybrid Journal   (Followers: 2)
Current Pharmacogenomics and Personalized Medicine     Hybrid Journal   (Followers: 3)
Current Protein and Peptide Science     Hybrid Journal   (Followers: 8)
Current Proteomics     Hybrid Journal   (Followers: 4)
Current Protocols in Bioinformatics     Hybrid Journal   (Followers: 1)
Current Protocols in Cell Biology     Hybrid Journal  
Current Protocols in Molecular Biology     Hybrid Journal  
Current Protocols in Mouse Biology     Hybrid Journal  
Current Protocols in Neuroscience     Hybrid Journal  
Current Protocols in Plant Biology     Hybrid Journal   (Followers: 2)
Current Protocols in Protein Science     Hybrid Journal   (Followers: 1)
Current Protocols in Stem Cell Biology     Hybrid Journal  
Current Research in Bacteriology     Open Access   (Followers: 3)
Current Research in Biostatistics     Open Access   (Followers: 8)
Current Research in Chemical Biology     Open Access  
Current Research in Neurobiology     Open Access  
Current Research in Parasitology & Vector-Borne Diseases     Open Access  
Current Research in Structural Biology     Open Access   (Followers: 2)
Current Research in Translational Medicine     Full-text available via subscription   (Followers: 1)
Current Research in Virological Science     Open Access   (Followers: 2)
Current Science     Open Access   (Followers: 117)
Current Stem Cell Reports     Hybrid Journal   (Followers: 4)
Current Stem Cell Research & Therapy     Hybrid Journal   (Followers: 8)
Current Topics in Developmental Biology     Full-text available via subscription   (Followers: 3)
Current Topics in Membranes     Full-text available via subscription   (Followers: 1)
Cytotechnology     Hybrid Journal   (Followers: 10)
Database : The Journal of Biological Databases and Curation     Open Access   (Followers: 10)
Dendrochronologia     Hybrid Journal   (Followers: 1)
Developing World Bioethics     Hybrid Journal   (Followers: 6)
Developmental & Comparative Immunology     Hybrid Journal   (Followers: 5)
Developmental Biology     Hybrid Journal   (Followers: 26)
Developmental Cell     Full-text available via subscription   (Followers: 46)
Developmental Dynamics     Hybrid Journal   (Followers: 4)
Developmental Neurobiology     Hybrid Journal   (Followers: 6)
Dhaka University Journal of Biological Sciences     Open Access  
Diatom Research     Hybrid Journal   (Followers: 3)
Differentiation     Hybrid Journal  
Digital Biomarkers     Open Access   (Followers: 1)
Disease Models and Mechanisms     Open Access   (Followers: 1)
Diseases of Aquatic Organisms     Hybrid Journal  
DNA and Cell Biology     Hybrid Journal   (Followers: 9)
DNA Repair     Hybrid Journal   (Followers: 3)
DNA Research     Open Access   (Followers: 4)
Doklady Physics     Hybrid Journal   (Followers: 1)
Drug Discovery Today: Technologies     Full-text available via subscription   (Followers: 12)
Drug Resistance Updates     Hybrid Journal   (Followers: 3)
e-Jurnal Rekayasa dan Teknologi Budidaya Perairan     Open Access  
Ecocycles     Open Access   (Followers: 4)
Ecohydrology & Hydrobiology     Full-text available via subscription   (Followers: 4)
Ecología en Bolivia     Open Access  
Ecological Engineering     Hybrid Journal   (Followers: 4)
Ecological Questions     Open Access   (Followers: 5)
Ecological Solutions and Evidence     Open Access  
Ecology and Society     Open Access   (Followers: 51)
Ecology Letters     Hybrid Journal   (Followers: 256)
Economics & Human Biology     Hybrid Journal   (Followers: 1)
Ecoprint : An International Journal of Ecology     Open Access   (Followers: 4)
Ecoscience     Hybrid Journal   (Followers: 2)
Ecosystem Health and Sustainability     Open Access   (Followers: 1)
Ecosystems and People     Open Access   (Followers: 4)
Educational Technology Research and Development     Partially Free   (Followers: 45)
EDUSAINS     Open Access  
EFB Bioeconomy Journal     Open Access  
Egyptian Journal of Basic and Applied Sciences     Open Access  
Egyptian Journal of Biology     Open Access  
Egyptian Journal of Natural History     Open Access   (Followers: 1)
EJNMMI Research     Open Access  
Ekologia     Open Access  
el-Hayah     Open Access  
Electromagnetic Biology and Medicine     Hybrid Journal  
eLife     Open Access   (Followers: 97)
Embo Molecular Medicine     Open Access   (Followers: 9)
EMBO reports     Full-text available via subscription   (Followers: 23)
Emotion Review     Hybrid Journal   (Followers: 20)
Endangered Species Research     Open Access   (Followers: 6)
Endocrine Connections     Open Access   (Followers: 4)
Endothelium: Journal of Endothelial Cell Research     Full-text available via subscription   (Followers: 4)
Engineering & Technology     Hybrid Journal   (Followers: 23)
Engineering Economist, The     Hybrid Journal   (Followers: 4)
Engineering in Life Sciences     Hybrid Journal   (Followers: 3)
Engineering Optimization     Hybrid Journal   (Followers: 19)
Ensaios e Ciência : Ciências Biológicas, Agrárias e da Saúde     Open Access  
Environmental Biology of Fishes     Hybrid Journal   (Followers: 4)
Environmental DNA     Open Access   (Followers: 1)
Environmental Dynamics and Global Climate Change     Open Access   (Followers: 22)
Environmental Epigenetics     Open Access   (Followers: 2)
Environmental Microbiology     Hybrid Journal   (Followers: 27)
Environmental Microbiome     Open Access  
Environmental Science & Technology     Hybrid Journal   (Followers: 195)
Enzyme and Microbial Technology     Hybrid Journal   (Followers: 12)
Enzyme Research     Open Access   (Followers: 4)
Epidemiology & Infection     Open Access   (Followers: 23)
Epigenomes     Open Access  
EPMA Journal     Open Access  
Ethiopian Journal of Biological Sciences     Open Access   (Followers: 3)
Ethnobiology and Conservation     Open Access   (Followers: 3)
Ethnobiology Letters     Open Access  
Ethnobotany Research & Applications : a journal of plants, people and applied research     Open Access   (Followers: 2)
Ethnoscientia : Brazilian Journal of Ethnobiology and Ethnoecology     Open Access  
Ethology     Hybrid Journal   (Followers: 11)
Ethology Ecology & Evolution     Hybrid Journal   (Followers: 17)
EuPA Open Proteomics     Open Access   (Followers: 2)
EUREKA : Life Sciences     Open Access  
European Journal of Biological Research     Open Access   (Followers: 1)
European Journal of Biology     Open Access   (Followers: 1)
European Journal of Cell Biology     Hybrid Journal   (Followers: 6)
European Journal of Ecology     Open Access   (Followers: 1)
European Journal of Neuroscience     Hybrid Journal   (Followers: 36)
European Journal of Obstetrics & Gynecology and Reproductive Biology     Hybrid Journal   (Followers: 18)
European Journal of Obstetrics & Gynecology and Reproductive Biology : X     Open Access  
European Journal of Phycology     Hybrid Journal   (Followers: 4)
European Journal of Protistology     Hybrid Journal   (Followers: 5)
European Journal of Soil Biology     Hybrid Journal   (Followers: 3)
European Online Journal of Natural and Social Sciences     Open Access   (Followers: 4)
European Scientific Journal     Open Access   (Followers: 1)
Evidência - Ciência e Biotecnologia - Interdisciplinar     Open Access  
EvoDevo     Open Access   (Followers: 4)
Evolution     Partially Free   (Followers: 142)
Evolution and Human Behavior     Hybrid Journal   (Followers: 23)
Evolution Letters     Open Access   (Followers: 8)
Evolutionary Applications     Open Access   (Followers: 6)
Evolutionary Bioinformatics     Open Access   (Followers: 12)
Evolutionary Biology     Hybrid Journal   (Followers: 25)
Evolutionary Computation     Hybrid Journal   (Followers: 11)
Evolutionary Systematics     Open Access   (Followers: 2)
EXCLI Journal : Experimental and Clinical Sciences     Open Access  
Experimental & Molecular Medicine     Open Access  
Experimental and Applied Acarology     Hybrid Journal   (Followers: 1)
Experimental Parasitology     Hybrid Journal   (Followers: 1)
Expert Opinion on Biological Therapy     Hybrid Journal   (Followers: 4)
Expert Opinion on Environmental Biology     Hybrid Journal  
Expert Review of Proteomics     Hybrid Journal   (Followers: 4)
ExRNA     Open Access  
Extreme Life, Biospeology & Astrobiology - International Journal of the Bioflux Society     Full-text available via subscription   (Followers: 5)
Extremophiles     Hybrid Journal   (Followers: 1)
F&S Science : Official journal of the American Society for Reproductive Medicine     Open Access  
Facta Universitatis, Series : Medicine and Biology     Open Access  
Familial Cancer     Hybrid Journal   (Followers: 2)
FASEB BioAdvances     Open Access  
Fauna Norvegica     Open Access  
Fauna of New Zealand     Open Access  
Febs Journal     Hybrid Journal   (Followers: 26)
Feddes Repertorium     Hybrid Journal  
Fems Yeast Research     Hybrid Journal   (Followers: 11)
FIGEMPA : Investigación y Desarrollo     Open Access   (Followers: 1)
Fire Ecology     Open Access   (Followers: 2)
Fish & Shellfish Immunology     Hybrid Journal   (Followers: 10)
Fish and Shellfish Immunology Reports     Open Access   (Followers: 1)
Fishes     Open Access  
Fitoterapia     Hybrid Journal   (Followers: 4)
Florea : Jurnal Biologi dan Pembelajarannya     Open Access  
Fly     Full-text available via subscription  
Folia Biologica     Free   (Followers: 1)
Folia Histochemica et Cytobiologica     Open Access  
Folia Microbiologica     Hybrid Journal   (Followers: 2)
Folia Primatologica     Full-text available via subscription   (Followers: 4)
Food and Bioproducts Processing     Hybrid Journal   (Followers: 3)
Food and Ecological Systems Modelling Journal     Open Access  
Food and Waterborne Parasitology     Open Access  
Food Webs     Hybrid Journal   (Followers: 1)
Forensic Genomics     Full-text available via subscription   (Followers: 6)
Forest Pathology     Hybrid Journal   (Followers: 1)
Forschung     Hybrid Journal   (Followers: 1)
Foundations of Physics     Hybrid Journal   (Followers: 41)
Free Radical Biology and Medicine     Hybrid Journal   (Followers: 6)
Free Radical Research     Hybrid Journal   (Followers: 2)
Freshwater Science     Full-text available via subscription   (Followers: 14)
Frontiers in Ecology and Evolution     Open Access   (Followers: 45)
Frontiers in Evolutionary Neuroscience     Open Access   (Followers: 7)
Frontiers in Life Science     Hybrid Journal   (Followers: 1)
Frontiers in Marine Science     Open Access   (Followers: 14)
Frontiers in Network Physiology     Open Access   (Followers: 2)
Frontiers in Neurogenesis     Open Access   (Followers: 2)
Frontiers in Neuroprosthetics     Open Access   (Followers: 6)
Frontiers of Biogeography     Open Access   (Followers: 4)
Frontiers of Biology     Hybrid Journal   (Followers: 2)
Frontiers of Environmental Science & Engineering     Hybrid Journal   (Followers: 3)
Frontiers of Medical and Biological Engineering     Hybrid Journal  
Functional & Integrative Genomics     Hybrid Journal   (Followers: 7)
Fundamental and Applied Limnology / Archiv für Hydrobiologie     Full-text available via subscription   (Followers: 3)
Fundamental Research     Open Access  
Fungal Biology     Hybrid Journal   (Followers: 6)
Fungal Biology and Biotechnology     Open Access   (Followers: 2)
Fungal Biology Reviews     Full-text available via subscription   (Followers: 9)
Fungal Diversity     Hybrid Journal   (Followers: 2)
Fungal Ecology     Hybrid Journal   (Followers: 6)
Fungal Genetics Reports     Open Access  

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Journal Cover
Evolutionary Bioinformatics
Journal Prestige (SJR): 0.9
Citation Impact (citeScore): 2
Number of Followers: 12  

  This is an Open Access Journal Open Access journal
ISSN (Print) 1176-9343 - ISSN (Online) 1176-9343
Published by Sage Publications Homepage  [1174 journals]
  • In Silico Identification and Characterization of B12D Family Proteins in
           Viridiplantae

    • Authors: Zainab M Almutairi
      Abstract: Evolutionary Bioinformatics, Volume 18, Issue , January-December 2022.
      B12D family proteins are transmembrane proteins that contain the B12D domain involved in membrane trafficking. Plants comprise several members of the B12D family, but these members’ numbers and specific functions are not determined. This study aims to identify and characterize the members of B12D protein family in plants. Phytozome database was retrieved for B12D proteins from 14 species. The total 66 B12D proteins were analyzed in silico for gene structure, motifs, gene expression, duplication events, and phylogenetics. In general, B12D proteins are between 86 and 98 aa in length, have 2 or 3 exons, and comprise a single transmembrane helix. Motif prediction and multiple sequence alignment show strong conservation among B12D proteins of 11 flowering plants species. Despite that, the phylogenetic tree revealed a distinct cluster of 16 B12D proteins that have high conservation across flowering plants. Motif prediction revealed 41 aa motif conserved in 58 of the analyzed B12D proteins similar to the bZIP motif, confirming that in the predicted biological process and molecular function, B12D proteins are DNA-binding proteins. Cis-regulatory elements screening in putative B12D promoters found various responsive elements for light, abscisic acid, methyl jasmonate, cytokinin, drought, and heat. Despite that, there is specific elements for cold stress, cell cycle, circadian, auxin, salicylic acid, and gibberellic acid in the promoter of a few B12D genes indicating for functional diversification for B12D family members. The digital expression shows that B12D genes of Glycine max have similar expression patterns consistent with their clustering in the phylogenetic tree. However, the expression of B12D genes of Hordeum vulgure appears inconsistent with their clustering in the tree. Despite the strong conservation of the B12D proteins of Viridiplantae, gene association analysis, promoter analysis, and digital expression indicate different roles for the members of the B12D family during plant developmental stages.
      Citation: Evolutionary Bioinformatics
      PubDate: 2022-06-14T11:46:01Z
      DOI: 10.1177/11769343221106795
      Issue No: Vol. 18 (2022)
       
  • Investigating the Genomic Background of CRISPR-Cas Genomes for
           CRISPR-Based Antimicrobials

    • Authors: Hyunjin Shim
      Abstract: Evolutionary Bioinformatics, Volume 18, Issue , January-December 2022.
      CRISPR-Cas systems are an adaptive immunity that protects prokaryotes against foreign genetic elements. Genetic templates acquired during past infection events enable DNA-interacting enzymes to recognize foreign DNA for destruction. Due to the programmability and specificity of these genetic templates, CRISPR-Cas systems are potential alternative antibiotics that can be engineered to self-target antimicrobial resistance genes on the chromosome or plasmid. However, several fundamental questions remain to repurpose these tools against drug-resistant bacteria. For endogenous CRISPR-Cas self-targeting, antimicrobial resistance genes and functional CRISPR-Cas systems have to co-occur in the target cell. Furthermore, these tools have to outplay DNA repair pathways that respond to the nuclease activities of Cas proteins, even for exogenous CRISPR-Cas delivery. Here, we conduct a comprehensive survey of CRISPR-Cas genomes. First, we address the co-occurrence of CRISPR-Cas systems and antimicrobial resistance genes in the CRISPR-Cas genomes. We show that the average number of these genes varies greatly by the CRISPR-Cas type, and some CRISPR-Cas types (IE and IIIA) have over 20 genes per genome. Next, we investigate the DNA repair pathways of these CRISPR-Cas genomes, revealing that the diversity and frequency of these pathways differ by the CRISPR-Cas type. The interplay between CRISPR-Cas systems and DNA repair pathways is essential for the acquisition of new spacers in CRISPR arrays. We conduct simulation studies to demonstrate that the efficiency of these DNA repair pathways may be inferred from the time-series patterns in the RNA structure of CRISPR repeats. This bioinformatic survey of CRISPR-Cas genomes elucidates the necessity to consider multifaceted interactions between different genes and systems, to design effective CRISPR-based antimicrobials that can specifically target drug-resistant bacteria in natural microbial communities.
      Citation: Evolutionary Bioinformatics
      PubDate: 2022-06-08T11:56:48Z
      DOI: 10.1177/11769343221103887
      Issue No: Vol. 18 (2022)
       
  • Wenxiang 3.0: Evolutionary Visualization of α, π, and 3/10
           Helices

    • Authors: John R Jungck, Metehan Cebeci
      Abstract: Evolutionary Bioinformatics, Volume 18, Issue , January-December 2022.
      Wenxiang diagrams illustrate protein helices as spirals on a plane and thus have the advantage over helical wheels of being planar graphs. Wenxiang 3.0 extends the original version by adding 3 major features: (1) individual amino acid residues can be colored according to their evolutionary conservation in comparative multiple sequence alignments using CONSURF encoding; (2) α, π, and 3/10 helices can be illustrated by overlaying arcs representative of the pitches of these helices; and, (3) the physico-chemical properties of amino acids residues in the protein sequence can be re-presented by colored geometric shapes.
      Citation: Evolutionary Bioinformatics
      PubDate: 2022-06-01T05:48:37Z
      DOI: 10.1177/11769343221101014
      Issue No: Vol. 18 (2022)
       
  • Host-Population Microbial Diversity Scaling of Chinese Gut Microbiomes in
           Gout Patients

    • Authors: Jieshang Zhou, Yali Yuan, Pengli Xu, Bin Yi, Hongju Chen, Wei Su
      Abstract: Evolutionary Bioinformatics, Volume 18, Issue , January-December 2022.
      Gout is a prevalent chronic inflammatory disease that affects the life of tens of millions of people worldwide, and it typically presents as gout arthritis, gout stone, or even kidney damage. Research has revealed its connection with the gut microbiome, although exact mechanism is still unclear. Studies have shown the decline of microbiome diversity in gout patients and change of microbiome compositions between the gout patients and healthy controls. Nevertheless, how diversity changes across host individuals at a cohort (population) level has not been investigated to the best of our knowledge. Here we apply the diversity-area relationship (DAR), which is an extension to the classic SAR (species-area relationship) and establishes the power-function model between microbiome diversity and the number of individuals within cohort, to comparatively investigate diversity scaling (changes) of gut microbiome in gout patients and healthy controls. The DAR modeling with a study involving 83 subjects (41 gout patients) revealed that the potential number of microbial species in gout patients is only 70% of that in the healthy control (2790 vs 3900) although the difference may not be statistically significant. The other DAR parameters including diversity scaling and similarity parameters did not show statistically significant differences. We postulate that the high resilience of gut microbiome may explain the lack of significant gout-disease effects on gut microbial diversity at the population level. The lack of statistically significant difference between the gout patients and healthy controls at host population (cohort) level is different from the previous findings at individual level in the existing literature.
      Citation: Evolutionary Bioinformatics
      PubDate: 2022-05-13T07:15:29Z
      DOI: 10.1177/11769343221095858
      Issue No: Vol. 18 (2022)
       
  • Identification of Phosphorylated Proteins Regulated by SDF2L1 in
           Nasopharyngeal Carcinoma Cells

    • Authors: Chengchang Luo, Zunni Zhang, Qisheng Su, Wuning Mo
      Abstract: Evolutionary Bioinformatics, Volume 18, Issue , January-December 2022.
      SDF2L1 is a new type of endoplasmic reticulum stress inducible protein, which is related to poor prognosis of various cancer, we initially studied the low expression level of SDF2L1 in NPC, but the molecular mechanism of SDF2L1 in NPC needs further elucidation. To identify phosphorylated proteins regulated by SDF2L1 in nasopharyngeal carcinoma (NPC), Label-free Quantitative (LFQ) Proteomics and 2D-LC-MS/MS analysis were performed on high metastatic NPC 5-8F cells with overexpression of SDF2L1 and empty segment. Western blotting was applied to validate the differentially expressed phosphorylated proteins (DEPPs). As a result, 331 DEPPs were identified by proteomics, and PARVA phosphorylation (ser8) was validated. The present results suggested that PARVA phosphorylation may be a new promising biomarker for predicting NPC and play a key role in the occurrence and development of NPC.
      Citation: Evolutionary Bioinformatics
      PubDate: 2022-04-28T10:43:58Z
      DOI: 10.1177/11769343221095862
      Issue No: Vol. 18 (2022)
       
  • The Prevalence of Pharmacogenomics Variants and Their Clinical Relevance
           Among the Pakistani Population

    • Authors: Abdul Rafay Khan, Sayed Hajan Shah, Sadia Ajaz, Sadaf Firasat, Aiysha Abid, Ali Raza
      Abstract: Evolutionary Bioinformatics, Volume 18, Issue , January-December 2022.
      Background:Pharmacogenomics (PGx), forming the basis of precision medicine, has revolutionized traditional medical practice. Currently, drug responses such as drug efficacy, drug dosage, and drug adverse reactions can be anticipated based on the genetic makeup of the patients. The pharmacogenomic data of Pakistani populations are limited. This study investigates the frequencies of pharmacogenetic variants and their clinical relevance among ethnic groups in Pakistan.Methods:The Pharmacogenomics Knowledge Base (PharmGKB) database was used to extract pharmacogenetic variants that are involved in medical conditions with high (1A + 1B) to moderate (2A + 2B) clinical evidence. Subsequently, the allele frequencies of these variants were searched among multiethnic groups of Pakistan (Balochi, Brahui, Burusho, Hazara, Kalash, Pashtun, Punjabi, and Sindhi) using the 1000 Genomes Project (1KGP) and ALlele FREquency Database (ALFRED). Furthermore, the published Pharmacogenomics literature on the Pakistani population was reviewed in PubMed and Google Scholar.Results:Our search retrieved (n = 29) pharmacogenetic genes and their (n = 44) variants with high to moderate evidence of clinical association. These pharmacogenetic variants correspond to drug-metabolizing enzymes (n = 22), drug-metabolizing transporters (n = 8), and PGx gene regulators, etc. (n = 14). We found 5 pharmacogenetic variants present at >50% among 8 ethnic groups of Pakistan. These pharmacogenetic variants include CYP2B6 (rs2279345, C; 70%-86%), CYP3A5 (rs776746, C; 64%-88%), FLT3 (rs1933437, T; 54%-74%), CETP (rs1532624, A; 50%-70%), and DPP6 (rs6977820, C; 61%-86%) genes that are involved in drug response for acquired immune deficiency syndrome, transplantation, cancer, heart disease, and mental health therapy, respectively.Conclusions:This study highlights the frequency of important clinical pharmacogenetic variants (1A, 1B, 2A, and 2B) among multi-ethnic Pakistani populations. The high prevalence (>50%) of single nucleotide pharmacogenetic variants may contribute to the drug response/diseases outcome. These PGx data could be used as pharmacogenetic markers in the selection of appropriate therapeutic regimens for specific ethnic groups of Pakistan.
      Citation: Evolutionary Bioinformatics
      PubDate: 2022-04-25T06:17:11Z
      DOI: 10.1177/11769343221095834
      Issue No: Vol. 18 (2022)
       
  • Transcriptome Analysis of MYB Genes and Patterns of Anthocyanin
           Accumulation During Seed Development in Wheat

    • Authors: Paulina Calderon Flores, Jin Seok Yoon, Dae Yeon Kim, Yong Weon Seo
      Abstract: Evolutionary Bioinformatics, Volume 18, Issue , January-December 2022.
      Plants accumulate key metabolites as a response of biotic/abiotic stress conditions. In seed coats, anthocyanins, carotenoids, and chlorophylls can be found. They have been associated as important antioxidants that affect germination. In wheat, anthocyanins can impart the seed coat color which have been recognized as health-promoting nutrients. Transcription factors act as master regulators of cellular processes. Transcription complexes such as MYB-bHLH-WD40 (MBW) regulate the expression of multiple target genes in various plant species. In this study, the spatiotemporal accumulation of seed coat pigments in different developmental stages (10, 20, 30, and 40 days after pollination) was analyzed using cryo-cuts. Moreover, the accumulation of phenolic, anthocyanin, and chlorophyll contents was quantified, and the expression of flavonoid biosynthetic genes was evaluated. Finally, transcriptome analysis was performed to analyze putative MYB genes related to seed coat color, followed by further characterization of putative genes. TaTCL2, an MYB gene, was cloned and sequenced. It was determined that TaTCL2 contains a SANT domain, which is often present in proteins participating in the response to anthocyanin accumulation. Moreover, TaTCL2 transcript levels were shown to be influenced by anthocyanin accumulation during grain development. Interaction network analysis showed interactions with GL2 (HD-ZIP IV), EGL3 (bHLH), and TTG1 (WD40). The findings of this study elucidate the mechanisms underlying color formation in Triticum aestivum L. seed coats.
      Citation: Evolutionary Bioinformatics
      PubDate: 2022-04-13T01:04:14Z
      DOI: 10.1177/11769343221093341
      Issue No: Vol. 18 (2022)
       
  • Corrigendum to “Optimized Next-Generation Sequencing Genotype-Haplotype
           Calling for Genome Variability Analysis”

    • Abstract: Evolutionary Bioinformatics, Volume 18, Issue , January-December 2022.

      Citation: Evolutionary Bioinformatics
      PubDate: 2022-03-14T10:58:23Z
      DOI: 10.1177/11769343221089554
      Issue No: Vol. 18 (2022)
       
  • Metatranscriptomics Analysis Reveals Diverse Viral RNA in Cutaneous
           Papillomatous Lesions of Cattle

    • Authors: Adriana O Fernandes, Gerlane S Barros, Marcus VA Batista
      Abstract: Evolutionary Bioinformatics, Volume 18, Issue , January-December 2022.
      Bovine papillomavirus (BPV) is associated with bovine papillomatosis, a disease that forms benign warts in epithelial tissues, as well as malignant lesions. Previous studies have detected a co-infection between BPV and other viruses, making it likely that these co-infections could influence disease progression. Therefore, this study aimed to identify and annotate viral genes in cutaneous papillomatous lesions of cattle. Sequences were obtained from the GEO database, and an RNA-seq computational pipeline was used to analyze 3 libraries from bovine papillomatous lesions. In total, 25 viral families were identified, including Poxviridae, Retroviridae, and Herpesviridae. All libraries shared similarities in the viruses and genes found. The viral genes shared similarities with BPV genes, especially for functions as virion entry pathway, malignant progression by apoptosis suppression and immune system control. Therefore, this study presents relevant data extending the current knowledge regarding the viral microbiome in BPV lesions and how other viruses could affect this disease.
      Citation: Evolutionary Bioinformatics
      PubDate: 2022-03-14T10:26:29Z
      DOI: 10.1177/11769343221083960
      Issue No: Vol. 18 (2022)
       
  • SPINK5 is a Prognostic Biomarker Associated With the Progression and
           Prognosis of Laryngeal Squamous Cell Carcinoma Identified by Weighted Gene
           Co-Expression Network Analysis

    • Authors: Jian Liu, Jing Zhao, Jiaran Xu, Qing Sun, Xuemei Qin, Guohui Chen, Tianle Gao, Guangping Bai, Zhiqiang Guo
      Abstract: Evolutionary Bioinformatics, Volume 18, Issue , January-December 2022.
      Laryngeal squamous cell carcinoma (LSCC) is one of the most common types of head and neck squamous cell carcinomas (HNSCC) and is the second most prevalent malignancy occurring in the head and neck or respiratory tract, with a high incidence and mortality rate. Survival is limited for patients with LSCC. To identify more biomarkers associated with the prognosis of patients with LSCC, using bioinformatics analysis, this study used The Cancer Genome Atlas (TCGA) LSCC dataset and gene expression profiles of GSE59102 from the Gene Expression Omnibus (GEO). Eighty-one differentially co-expressed genes were identified by weighted gene co-expression network analysis (WGCNA). Next, 10 hub genes (PPL, KRT78, CRNN, PTK7, SCEL, AGRN, SPINK5, AIF1L, EMP1, and PPP1R3C) were screened from a protein-protein interaction (PPI) network. Based on survival analysis, SPINK5 was significantly correlated with survival time in LSCC patients. After verification in the TCGA and HPA databases, SPINK5 was selected as a prognostic biomarker. Finally, the GSEA results showed that downregulation of SPINK5 gene expression may promote tumorigenesis and the development of cancers by the “BASAL CELL CARCINOMA” pathway, and it has been implicated in disrupting DNA damage and repair pathways. Collectively, SPINK5 may serve as a potential prognostic biomarker in LSCC.
      Citation: Evolutionary Bioinformatics
      PubDate: 2022-02-04T09:47:10Z
      DOI: 10.1177/11769343221077118
      Issue No: Vol. 18 (2022)
       
  • Screening of Important Markers in Peripheral Blood Mononuclear Cells to
           Predict Female Osteoporosis Risk Using LASSO Regression Algorithm and SVM
           Method

    • Authors: Hongwei Tang, Qingtian Han, Yong Yin
      Abstract: Evolutionary Bioinformatics, Volume 18, Issue , January-December 2022.
      Background:Osteoporosis is a bone disease that increases the patient’s risk of fracture. We aimed to identify robust marker genes related to osteoporosis based on different bioinformatic methods and multiple datasets.Methods:Three datasets from Gene Expression Omnibus (GEO) were utilized for analysis separately. Significantly differentially expressed genes (DEGs) from comparing high hip and low hip low bone mineral density (BMD) groups in the first dataset were identified for Gene Ontology (GO), Gene set enrichment analysis (GSEA) and Kyoto encyclopedia of genes and genomes (KEGG) to investigate the discrepantly enriched biological processes between high hip and low hip group. Last absolute shrinkage and selection operator (LASSO), SVM model and protein-protein interaction (PPI) regulatory network were performed and generated robust marker genes for downstream TF-target and miRNA-target prediction.Results:Several DEGs between high hip BMD group and low hip BMD group were obtained. And the metabolism-related pathways such as metabolic pathways, carbon metabolism, glyoxylate and dicarboxylate metabolism shown enrichment in these DEGs. Integration with LASSO regression analysis, 8 differential expression genes (SH3BP1, NARF, ANKRD34B, RNF40, ZNF473, AKT1, SHMT1, and VASH1) in GSE62402 were identified as the optimal differential genes combination. Moreover, the SVM validation analysis in GSE56814 and GSE56815 datasets showed that the characteristic gene combinations presented high diagnostic effects, and the model AUC areas for GSE56814 was 0.899 and for GSE56815 was 0.921. Furthermore, the subcellular localization analysis of the 8 genes revealed that 4 proteins were located in the cytoplasm, 3 proteins were located in the nucleus, and 1 protein was located in the mitochondria. Additionally, the related TFs and miRNAs by performing TF-target and miRNA-target prediction for 5 genes (AKT1, SHMT1, ZNF473, RNF40 and VASH1) were investigated from PPI network.Conclusion:The optimal differential genes combination (SH3BP1, NARF, ANKRD34B, RNF40, ZNF473, AKT1, SHMT1, and VASH1) presented high diagnostic effect for osteoporosis risk.
      Citation: Evolutionary Bioinformatics
      PubDate: 2022-01-29T07:09:28Z
      DOI: 10.1177/11769343221075014
      Issue No: Vol. 18 (2022)
       
  • Draft Genome Sequence of Oceanobacillus jordanicus Strain GSFE11, a
           Halotolerant Plant Growth-Promoting Bacterial Endophyte Isolated From the
           Jordan Valley

    • Authors: Tareq Alhindi, Randa Albdaiwi
      Abstract: Evolutionary Bioinformatics, Volume 18, Issue , January-December 2022.
      The bacterium Oceanobacillus jordanicus strain GSFE11 is a halotolerant endophyte isolated from sterilized roots of Durum wheat (Triticum turgidum ssp. Durum) growing in hot and arid environments of Ghor Safi area in the Jordan Valley. The draft genome sequence and annotation of this plant growth-promoting endophytic bacterium are reported in this study. The draft genome sequence of Oceanobacillus jordanicus strain GSFE11 has 3 839 208 bp with a G + C content of 39.09%. A total of 3893 protein-coding genes and 68 RNA coding genes were predicted. Several putative genes that are involved in secretion and delivery systems, transport, adhesion, motility, membrane proteins, plant cell wall modification, and detoxification were identified, some are characteristics of endophytes lifestyle including genes that are involved in metabolism of carbohydrate, genes for xylose, fructose and chitin utilization, quinone cofactors biosynthesis, genes associated with nitrogen, sulfur, phosphate and iron acquisition, in addition to genes involved in the biosynthesis of plant hormone auxin. This study highlights the importance of using genome analysis and phylogenomic analysis to resolve the differences between closely related species, such analysis showed Oceanobacillus jordanicus strain GSFE11 to be a new species closely related to Oceanobacillus picturae (genome size 3.67 Mb), Oceanobacillus jordanicus has higher a number of predicted genes compared with Oceanobacillus picturae (3961 genes vs 3823 genes).
      Citation: Evolutionary Bioinformatics
      PubDate: 2022-01-25T10:53:15Z
      DOI: 10.1177/11769343211071114
      Issue No: Vol. 18 (2022)
       
  • Seasonal Diversity of Microeukaryotes in the Han River, Korea Through 18S
           rRNA Gene Metabarcoding

    • Authors: Tae-June Choi, Adeel Malik, Hyung-Eun An, Jung-Il Kim, Thinh Dinh Do, Chang-Bae Kim
      Abstract: Evolutionary Bioinformatics, Volume 18, Issue , January-December 2022.
      Freshwater ecosystems contain a large diversity of microeukaryotes that play important roles in maintaining their structure. Microeukaryote communities vary in composition and abundance on the basis of temporal and environmental variables and may serve as useful bioindicators of environmental changes. In the present study, 18S rRNA metabarcoding was employed to investigate the seasonal diversity of microeukaryote communities during four seasons in the Han River, Korea. In total, 882 unique operational taxonomic units (OTUs) were detected, including various diatoms, metazoans (e.g., arthropods and rotifers), chlorophytes, and fungi. Although alpha diversity revealed insignificant differences based on seasons, beta diversity exhibited a prominent variation in the community composition as per seasons. The analysis revealed that the diversity of microeukaryotes was primarily driven by seasonal changes in the prevailing conditions of environmental water temperature and dissolved oxygen. Moreover, potential indicator OTUs belonging to diatoms and chlorophytes were associated with seasonal and environmental factors. This analysis was a preliminary study that established a continuous monitoring system using metabarcoding. This approach could be an effective tool to manage the Han River along with other freshwater ecosystems in Korea.
      Citation: Evolutionary Bioinformatics
      PubDate: 2022-01-25T09:33:35Z
      DOI: 10.1177/11769343221074688
      Issue No: Vol. 18 (2022)
       
 
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