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World Journal of Gastrointestinal Pathophysiology 2022年第1期13卷 1-14页

作者： Sarah El-Nakeep Gastroenterology and Hepatology Unit Department of Internal MedicineFaculty of MedicineAin Shams UniversityCairo 11591Egypt

Hepatocellular carcinoma(HCC)is the second cause of cancer-related *** diagnosis of HCC depends mainly on-fetoprotein,which is limited in its diagnostic and screening *** is an urgent need for a biomarker that detects early HCC to give the patients a chance for curative *** targets of therapy could enhance survival and create future alternative curative *** silico analysis provides both;discovery of biomarkers,and understanding of the molecular pathways,to pave the way for treatment *** review discusses the role of in silico analysis in the discovery of biomarkers,molecular pathways,and the role the author has contributed to this area of *** also discusses future aspirations and current limitations.A literature review was conducted on the topic using various databases(PubMed,Science Direct,and Wiley Online Library),searching in various reviews,and editorials on the topic,with overviewing the author’s own published and unpublished *** review discussed the steps of the validation process from in silico analysis to in vivo validation,to incorporation into clinical practice *** addition,reviewing the recent lines of research of bioinformatic studies related to *** conclusion,the genetic,molecular and epigenetic markers discoveries are hot areas for HCC *** will enhance our ability to accomplish this understanding in the near *** face certain limitations that we need to overcome.

关键词： Hepatocellular carcinoma in silico analysis Bioinformatics Biomarkers Molecular pathways Genetics Epigenetics

LTR retrotransposon prediction in algae genome of Coccomyxa Sp.c169,***,***,*** genome using in silico analysis

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LTR retrotransposon prediction in algae genome of Coccomyxa ...

Natural products for infectious microbes and diseases:an overview of sources,compounds,and chemical diversities

中国藻类学会第八次会员大会暨第十六次学术讨论会

作者： Xiayuan Liang,Cui Zhao,Tao Liu Laboratory of Genetics and Breeding of Marine Organism,Ocean University of China, Qingdao,Shandong,China,266003

LTR retrotransposon is recognized as a kind of transposable element.A series of research on TEs revealed that those once thought as "junk DNA" to be functional or at least have effect on the evolution of *** in silico analysis,researchers successfully predicted LTR retrotransposons in rice grape tree and other advanced plants. Algae take possession of an important position in evolution *** prokaryote to complex multicellular eudicots,algae genomes deserve a thorough *** our research,we introduce others work:two LTR retrotransposon prediction biosoftwares LTRTRUC and LTRINDER which utilizing unique structure to define a LTR retroelement, have been introduced into our work to detect potential new LTR retroelements in algae *** this in silico analysis we attend to investigate the existence and dynamic of full-length LTR retrotransposon in *** made our strategy using the LTRTRUC and LTRINDER to scan the algae genome for data,sequences then put on bioinformatics databases Pfam and NCBI to identify the super families of Copia or Gypsy while using blastp and blastx(e1) to find the ORF of reverse transcriptase and clustalW2 for *** investigation include alignments,phylogenic analyze and *** species were taken into our research:***.c169, Chlamydomonasreinhardtii,Volvoxcarteri,Ectocarpus *** we have gain 311 LTR retrotransposon excluding ***69,23 elements for 10mb genome of Chlamydomonas reinhardtii;63 elements for30mb genome of Volvox carteri;225 elements found for 214mb genome of Ectocarpus *** copies and highly similar retroelements were classified into same *** indicates that LTR retrotransposon is part of algae *** a large scale,their LTR sequences most are200-400 *** length is about 4k-6k for Copia,10k for *** retroelements were regarded as the main portion of prediction LTR *** LTR elements are somehow diffe

关键词： LTR retrotransposon in silico analysis algae prediction

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Science China(Life Sciences) 2022年第6期65卷 1123-1145页

作者： Lu Luo Jun Yang Cheng Wang Jie Wu Yafang Li Xu Zhang Hui Li Hui Zhang Yumei Zhou Aiping Lu Shilin Chen Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China Institute of Basic Medical Sciences Chinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100006China Institute of Hematology&Blood Diseases Hospital Chinese Academy of Medical Sciences&Peking Union Medical CollegeTianjin 300020China weMED Health Houston 77054USA Institute of Botany Chinese Academy of SciencesBeijing 100093China Akupunktur Akademiet Aabyhoej 8230Denmark The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine Guangzhou 518033China School of Chinese Medicine Hong Kong Baptist UniversityHong Kong 999077China

As coronavirus disease 2019(COVID-19) threatens human health globally,infectious disorders have become one of the most challenging problem for the medical *** products(NP) have been a prolific source of antimicrobial agents with widely divergent structures and a range of vast biological activities.A dataset comprising 618 articles,including 646 NP-based compounds from 672 species of natural sources with biological activities against 21 infectious pathogens from five categories,was assembled through manual selection of published *** data were used to identify 268 NP-based compounds classified into ten groups,which were used for network pharmacology analysis to capture the most promising lead-compounds such as agelasine D,dicumarol,dihydroartemisinin and *** distribution of maximum Tanimoto scores indicated that compounds which inhibited parasites exhibited low diversity,whereas the chemistries inhibiting bacteria,fungi,and viruses showed more structural diversity.A total of 331 species of medicinal plants with compounds exhibiting antimicrobial activities were selected to classify the family *** family Asteraceae possesses various compounds against ***,the family Anacardiaceae has compounds against Salmonella typhi,the family Cucurbitacea against the human immunodeficiency virus(HIV),and the family Ancistrocladaceae against *** review summarizes currently available data on NPbased antimicrobials against refractory infections to provide information for further discovery of drugs and synthetic strategies for anti-infectious agents.

关键词： natural product infectious pathogen drug discovery drug development in silico analysis

analysis of EST-SSRs in silver birch(Betula pendula Roth.)

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Journal of Forestry Research 2016年第3期27卷 639-646页

作者： Ertugrul Filiz Ilhan Dogan Ibrahim Ilker Ozyigit Department of Crop and Animal Production Cilimli Vocational SchoolDuzce University Department of Molecular Biology and Genetics Izmir Institute of Technology Department of Biology Faculty of ScienceRahatlayadururken Manas University Department of Biology Faculty of Science and ArtsMarmara University

Simple sequence repeats（SSRs） defined as sequence repeat units between 1 and 6 bp occur abundantly in both coding and non-coding regions in eukaryotic genomes and these repeats can affect gene expression. In this study, ESTs（expressed sequence tags） of Betula pendula（silver birch） were analyzed for in silico mining of ESTSSRs, protein annotation, open reading frames（ORFs）,designing primers, and identifying codon repetitions. In ***, the frequency of ESTs containing SSRs was 7.8 %with an average of 1SSR/4. 78 kb of EST sequences. A total of 188 SSRs was identified by using MISA software and dinucleotide SSR motifs（65.9 %） were found to be the most abundant type of repeat motif followed by tri-（27.1 %）,tetra-（4.8 %）, and penta-（2.2 %） motifs. Based on ORF analysis, 175 of 178 sequences were predicted as ORFs and the most frequent SSRs were detected in 50 UTR（58.43 %）,followed by in ORF（31.46 %） and in 30UTR（8.43 %）. 102 of 178 ESTs were annotated as ribosomal protein, transport protein, membrane protein, carrier protein, binding protein,and transferase protein. For a total of 102 SSRs（57.3 %）with significant matches, a set of 102 primers（100 %） with forward and reverse strands was designed by using Primer 3 software. Serine（Ser, 19.6 %） was predominant in putative encoded amino acids and most of amino acids showed nonpolar（35.3 %） nature. Our data provide resources for *** and can be useful for in silico comparative analyses of Betulaceae species, including SSR mining.

关键词： Silver birch (Betula pendula) Betulaceae -EST-SSR SSR mining in silico analysis

DEFB126 polymorphisms and association with idiopathic asthenozoospermia in China

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Asian Journal of Andrology 2022年第6期24卷 607-614页

作者： Jiao-Yu He Jian-Ying Peng Qiu-Fu Li Xiao-Li Lin Yan-Ru Cui Shi-Yu Ma Shi-Yun Fan Yi-Ran Liu Zhi-Lin Song Jun-Hang Deng Xia Wei Xian-Ping Ding Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengdu 610065China Chongqing Nanchuan Biotechnology Research Institute Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and ChongqingChongqing 400000China

Idiopathic asthenozoospermia,a common factor in male infertility,is characterized by altered sperm motility function in fresh *** theβ-defensin 126(DEFB126)protein is associated with asthenozoospermia,DEFB126 gene polymorphisms have not been extensively ***,the association between DEFB126 gene polymorphisms and asthenozoospermia requires further *** was performed by semen analysis,karyotype analysis,and Y microdeletion detection,and 102 fertile men and 106 men with asthenozoospermia in Chengdu,China,were selected for DEFB126 gene sequence *** nucleotide mutations and two nucleotide deletions in the DEFB126 gene were ***11467417(317-318 del/del),rs11467497(163-166 wt/del),c.152T>C,and c.227A>G were significantly different between the control and asthenozoospermia groups,likely representing high-risk genetic factors for asthenozoospermia among ***126 expression was not observed in sperm with rs11467497 homozygous deletion and was unstable in sperm with rs11467417 homozygous *** rs11467497 four-nucleotide deletion leads to truncation of DEFB126 at the carboxy-terminus,and the rs11467417 binucleotide deletion produces a non-stop messenger RNA(mRNA).The above deletions may be responsible for male hypofertility and infertility by reducing DEFB126 affinity to sperm *** on in silico analysis,the amino acids 51M and 76K are located in the highly conserved domain;c.152T>C(M51T)and c.227A>G(K76R)are predicted to be damaging and capable of changing alternative splice,structural and posttranslational modification sites of the RNA,as well as the secondary structure,structural stability,and hydrophobicity of the protein,suggesting that these mutations are associated with asthenozoospermia.

关键词： β-defensin 126 idiopathic asthenozoospermia in silico analysis single-nucleotide polymorphisms

The relevance of dipeptides and tripeptides in the bioactivity and taste of dry-cured ham

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Food Production, Processing and Nutrition 2019年第1期1卷 114-127页

作者： Marta Gallego Leticia Mora Fidel Toldrá Instituto de Agroquímica y Tecnología de Alimentos (CSIC)

Dry-cured ham has been described as a good source of bioactive peptides and taste-active *** of them are dipeptides and tripeptides that are released in a large amount from different muscle proteins due to the action of exopeptidases during the dry-cured ham *** potential of dipeptides and tripeptides to exert bioactivities and impart taste characteristics to dry-cured ham has been evaluated using the BIOPEP database,since in silico approaches are a time-and cost-effective alternative to empirical *** of the studied dipeptides and tripeptides showed ACE and DPP inhibitory activities as well as imparted bitter *** fact,more than one bioactivity and/or taste could be assigned to a given peptide sequence,and there could be a correlation between both,like ACE inhibitory and bitter EA,EI and LG ***,several dipeptides such as EK,KP,LA,PL,PP,RG,and VE,among others,were found to be multifunctional(ACE and DPP IV inhibitory)which would be determined by their structure,sequence and amino acid *** silico analysis evidences the relevance of dipeptides and tripeptides in the bioactivity and taste of dry-cured hams,but further empirical assays including in vitro and in vivo studies are necessary to confirm such theoretical *** degradation of the small peptides during gastrointestinal digestion and intestinal absorption as well as interactions with the food matrix could reduce their bioavailability and bioaccessibility,and modify their biological activities.

关键词： Small peptides Biological activity Sensory Ham in silico analysis Multifunctional peptides

Genome-Wide Identification of ALDH Gene Family under Salt and Drought Stress in Phaseolus vulgaris

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Phyton-International Journal of Experimental Botany 2024年第11期93卷 2883-2907页

作者： Abdil Hakan Eren Department of Pharmacy Services Kırıkhan Vocational SchoolHatay Mustafa Kemal UniversityHatay326Turkiye

Background:Aldehyde dehydrogenase(ALDH)genes constitute an important family of supergenes that play key roles in synthesizing various biomolecules and maintaining cellular homeostasis by catalyzing the oxidation of aldehyde *** climate change increasing the exposure of plants to abiotic stresses such as salt and drought,ALDH genes have been identiﬁed as important contributors to stress *** particular,they help to reduce stress-induced lipid ***:This study aims to identify and characterize members of the ALDH supergene family in Phaseolus vulgaris through a genome-wide bioinformatic analysis and investigate their role in response to abiotic stressors such as drought and salt ***:Genome-wide identiﬁcation of 26 ALDH genes in *** was performed using bioinformatics *** identiﬁed ALDH proteins were ana-lyzed for molecular weight,amino acid number,and exon *** analysis was performed to clas-sify ***,Arabidopsis thaliana,and Glycine max ALDH proteins into different *** links between these genes and functions related to growth,development,stress responses,and hormone signaling were identiﬁed by cis-element analysis in promoter *** silico expression,analysis was performed to assess gene expression levels in different plant ***:RT-qPCR results showed that the expression of ALDH genes was signif-icantly altered under drought and salt stress in *** study provides a comprehensive characterization of the ALDH supergene family in ***,highlighting their potential role in abiotic stress ***:Theseﬁndings provide a basis for future research on the functional roles of ALDH genes in enhancing plant resis-tance to environmental stressors.

关键词： Aldehyde dehydrogenase common bean digital gene expression drought and salt stress genome-wide analysis in silico analysis

MicroRNA exhibit altered expression in the inflamed colonic mucosa of ulcerative colitis patients

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World Journal of Gastroenterology 2017年第29期23卷 5324-5332页

作者： Swati Valmiki Vineet Ahuja Jaishree Paul School of Life Sciences Jawaharlal Nehru University Department of Gastroenterology All India Institute of Medical Sciences

To investigate the miRNA expression in colonic mucosal biopsies from endoscopically inflamed and non inflamed regions of ulcerative colitis (UC) patients. METHODSColonic mucosal pinch biopsies were analyzed from the inflamed and non inflamed regions of same UC patient. Total RNA was isolated and differential miRNA profiling was done using microarray platform. Quantitative Real Time PCR was performed in colonic biopsies from inflamed (n = 8) and non-inflamed (n = 8) regions of UC and controls (n = 8) to validate the differential expression of miRNA. Potential targets of dysregulated miRNA were identified by using in silico prediction tools and probable role of these miRNA in inflammatory pathways were predicted. RESULTSThe miRNA profile of inflamed colonic mucosa differs significantly from the non-inflamed. Real time PCR analysis showed that some of the miRNA were differentially expressed in the inflamed mucosa as compared to non inflamed mucosa and controls (miR-125b, miR-223, miR-138, and miR-155), while (miR-200a) did not show any significant changes. In contrast to microarray, where miR-378d showed downregulation in the inflamed mucosa, qRT-PCR showed a significant upregulation in the inflamed mucosa as compared to the non inflamed. The in silico prediction analysis revealed that the genes targeted by these miRNAs play role in the major signaling pathways like MAPK pathway, NF-κB signaling pathway, cell adhesion molecules which are all assciated with UC. CONCLUSIONThe present study reports disease specific alteration in the expression of miR-125b, miR-155, miR-223 and miR-138 in UC patients and also predict their biological significance.

关键词： Ulcerative colitis Colon mucosa MicroRNA Microarray qRT-PCR in silico analysis

Identification of functional tumor necrosis factor-alpha promoter variants associated with Helicobacter pylori infection in the Sudanese population: Computational approach

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World Journal of Gastroenterology 2022年第2期28卷 242-262页

作者： Abeer Babiker Idris Alaa B Idris Manal A Gumaa Mohammed Babiker Idris Amanda Elgoraish Mohamed Mansour Dalia Allam Bashir MO Arbab Nazar Beirag El-Amin M Ibrahim Mohamed A Hassan Department of Agricultural Science and Technology Institute of Natural and Applied SciencesErciyes UniversityKayseri 38039Turkey Department of Medical Microbiology Faculty of Medical Laboratory SciencesUniversity of KhartoumKhartoum 11111Sudan Department of Neurosurgery Ribat University HospitalKhartoum 11111Sudan BioMérieux Clinical and Application Advisor Al-Jeel Medical Co.Riyadh 11422Saudi Arabia Department of Epidemiology Tropical Medicine Research InstituteKhartoum 11111Sudan Department of Gastroenterology Ibn Sina Specialized HospitalKhartoum 11111Sudan Department of Gastroenterology Modern Medical CentreKhartoum 11111Sudan Biosciences College of HealthMedicine and Life SciencesBrunel UniversityLondon UB83PHUxbridgeUnited Kingdom Department of Translation Bioinformatics Detavax BiotechKayseri 38350Turkey

BACKGROUND Helicobacter pylori(***)is a ubiquitous bacterium that affects nearly half of the world’s population with a high morbidity and mortality *** within the tumor necrosis factor-alpha(TNF-A)promoter region are considered a possible genetic basis for this *** To functionally characterize the genetic variations in the TNF-A 5’-region(-584 to+107)of Sudanese patients infected with *** using in silico *** An observational study was carried out in major public and private hospitals in Khartoum state.A total of 122 gastric biopsies were taken from patients who had been referred for *** DNA was *** of the TNF-A-1030 polymorphism was performed using PCR with confronting two-pair primer to investigate its association with the susceptibility to *** infection in the Sudanese ***,Sanger sequencing was applied to detect single nucleotide polymorphisms in the 5’-region(-584 to+107)of TNF-A in ***-infected *** analyses were used to predict whether these mutations would alter transcription factor binding sites or composite regulatory elements in this region.A comparative profiling analysis was conducted in 11 species using the ECR browser and multiple-sequence local alignment and visualization search engine to investigate the possible ***,a multivariate logistic regression model was constructed to estimate odds ratios and their 95%confidence intervals for the association between TNF-A-1030,sociodemographic characteristics and *** *** were statistically significant if PA,-76)was located at the in silico-predicted promoter region(-146 to+10),and it was predicted to alter transcription factor b

关键词： 5’-region Promoter TNF-A Helicobacter pylori in silico analysis Sudan

TrFAST: A Tool to Predict Signaling Pathway-specific Transcription Factor Binding Sites

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Genomics, Proteomics & Bioinformatics 2012年第6期10卷 354-359页

作者： Umair Seemab Qurrat ul Ain Muhammad Sulaman Nawaz Zafar Saeed Sajid Rashid National Centre for Bioinformatics Quaid-i-Azam University Department of Computer Science Quaid-i-Azam University

Recent advances in the development of high-throughput tools have significantly revolutionized our understanding of molecular mech- anisms underlying normal and dysfunctional biological processes. Here we present a novel computational tool, transcription factor search and analysis tool （TrFAST）, which was developed for the in silico analysis of transcription factor binding sites （TFBSs） of sig- naling pathway-specific TFs. TrFAST facilitates searching as well as comparative analysis of regulatory motifs through an exact pattern matching algorithm followed by the graphical representation of matched binding sites in multiple sequences up to 50 kb in length. TrFAST is proficient in reducing the number of comparisons by the exact pattern matching strategy. In contrast to the pre-existing tools that find TFBS in a single sequence, TrFAST seeks out the desired pattern in multiple sequences simultaneously. It counts the GC con- tent within the given multiple sequence data set and assembles the combinational details of consensus sequence（s） located at these regions, thereby generating a visual display based on the abundance of unique pattern. Comparative regulatory region analysis of multi- ple orthologous sequences simultaneously enhances the features of TrFAST and provides a significant insight into study of conservation of non-coding cis-regulatory elements. TrFAST is freely available at http：//***/***.

关键词： TrFAST Transcription factor binding sites in silico analysis Signaling pathway Pattern searching