Bioinformatic Tools - Science topic

Background: Protein phosphatases (PP2Cs) are the main classes of protein phosphatases in plants, having pivotal functions in different plant stages and abiotic stresses. The PP2C genes are suggested to have critical roles in barley by exposure to heat and cold treatments. Objectives: We surveyed HvPP2C genes from the barley genome in the present st...

Exploration of avian gametologous genes, i.e., homologous genes located on both the Z and W chromosomes, provides a crucial information about the underlying mechanism pertaining to the evolution of these chromosomes. The domestic chicken (Gallus gallus (Linnaeus 1758); GGA) traditionally serves as the primary reference subject of these comparative...

Main conclusion Due to harsh lifestyle changes, in the present era, nutritional security is needed along with food security so it is necessary to include underutilized cereal crops (UCCs) in our daily diet to counteract the rising danger of human metabolic illness. We can attain both the goal of zero hunger and nutritional security by developing im...

Secondary metabolites (SMs) from environmental bacteria offer viable solutions for various health and environmental challenges. Researchers are employing advanced bioinformatic tools to investigate less-explored microorganisms and unearth novel bioactive compounds. In this research area, our understanding of SMs from environmental Gram-negative bac...

Sperm maturation in the epididymis is based on interactions with proteins from epididymal fluid (EF). The aim of the study was to profile canine EF proteome and investigate correlations between EF protein content and epididymal spermatozoa (ES) motion parameters. Twenty-three male dogs were divided into two groups: good sperm motility (GSM) and poo...

Humans are colonized with commensal bacteria soon after birth, and, while this colonization is affected by lifestyle and other factors, bacterial colonization proceeds through well-studied phases. However, less is known about phage communities in early human development due to small study sizes, inability to leverage large databases, and lack of ap...

The miRNAs regulate various biological processes in the mammalian body system. The role of miR-181a in the development, progression, and expansion of cancers is well-documented. However, the role of miR-181a in adipogenesis; lipid metabolism; obesity; and obesity-related issues such as diabetes mellitus needs to be explored. Therefore, in the prese...

The intestinal barrier comprises a single layer of epithelial cells tightly joined to form a physical barrier. Disruption or compromise of the intestinal barrier can lead to the inadvertent activation of immune cells, potentially causing an increased risk of chronic inflammation in various tissues. Recent research has suggested that specific dietar...

During the SARS-CoV-2 pandemic, wastewater-based genomic surveillance (WWGS) emerged as an efficient viral surveillance tool that takes into account asymptomatic cases and can identify known and novel mutations and offers the opportunity to assign known virus lineages based on the detected mutations profiles. WWGS can also hint towards novel or cry...

Streptococcus pneumoniae (SPN) infection has resulted in significant morbidity and mortality worldwide in children and adults. It is responsible for colonizing the human nasopharynx and can also cause diseases, including otitis media, pneumonia, bacteraemia, and meningitis. SPN is exhibiting resistance to multiple antibiotics and current vaccines h...

The emergence and rapid spread of the plasmid-mediated colistin-resistant mcr-1 gene introduced a serious threat to public health. In 2021, a multi-drug resistant, mcr-1 positive Escherichia coli EC1945 strain, was isolated from pig caecal content in Croatia. Antimicrobial susceptibility testing and whole genome sequencing were performed. Bioinform...

The coronavirus disease 2019 (COVID-19) pandemic is still ongoing, with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continuing to evolve and accumulate mutations. While various bioinformatics tools have been developed for SARS-CoV-2, a well-curated mutation-tracking database integrated with in silico evaluation for molecular diagno...

Glaucoma, a neurodegenerative disorder that leads to irreversible blindness, remains a challenge because of its complex nature. MicroRNAs (miRNAs) are crucial regulators of gene expression and are associated with glaucoma and other diseases. We aimed to review and discuss the advantages and disadvantages of miRNA-focused molecular studies in glauco...

Background Japanese encephalitis virus (JEV) remains a predominant cause of Japanese encephalitis (JE) globally. Its infection is usually accompanied by disrupted blood‒brain barrier (BBB) integrity and central nervous system (CNS) inflammation in a poorly understood pathogenesis. Productive JEV infection in brain microvascular endothelial cells (B...

Interleukin-17F (IL-17F), considered a pro-inflammatory cytokine, has been shown to contribute to skeletal tissue degradation and hence chronic inflammation in rheumatoid arthritis (RA). In this study we utilized bioinformatics tools to analyze the effect of three exonic SNPs (rs2397084, rs11465553, and rs763780) on the structure and function of th...

The potential therapeutic role of the Dental Pulp Stem Cells Secretome (SECR) in a rat model of experimentally induced Temporomandibular Joint (TMJ) Osteoarthritis (OA) was evaluated. Proteomic profiling of the human SECR under specific oxygen tension (5% O2) and stimulation with Tumor Necrosis Factor-alpha (TNF-α) was performed. SECR and respectiv...

This paper proposes the use of bioinformatics tools to study the frequencies of alterations found in Fanconi Anemia (FA) genes, through cell lineage, drug activity (CellMinerCDB) in 4 databases (NCI-60, CCLE-Broad-MIT, GDSC-MGH-Sanger, and CTRP-Broad-MIT) evaluating expression, copy variation and mutation, and 32 cancer samples (cBioPortal) were an...

During the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), positive-sense genomic RNA and subgenomic RNAs (sgRNAs) are synthesized by a discontinuous process of transcription characterized by a template switch, regulated by transcription-regulating sequences (TRS). Although poorly known about makeup and dynamics of sgRN...

In the rapidly evolving field of bioinformatics, the analysis of Next-Generation Sequencing (NGS) data has become increasingly intricate, with a plethora of specialized tools addressing specific aspects of this domain. However, the fragmented nature of these tools often hinders comprehensive data mining. Introducing PipenGeneX, a pioneering framewo...

Atrial fibrillation (AF) is a prevalent cardiac arrhythmia worldwide and is characterized by a high risk of thromboembolism, ischemic stroke, and fatality. The precise molecular mechanisms of AF pathogenesis remain unclear. The purpose of this study was to use bioinformatics tools to identify novel key genes in AF, provide deeper insights into the...

Background: Periodontits (PD) and Alzheimer’s disease (AD) are both associated with ageing and clinical studies increasingly evidence their association. However, specific mechanisms underlying this association remain undeciphered, and immune-related processes are purported to play a signifcant role. The accrual of publicly available transcriptomic...

Pancreatic cancer cells undergo intricate metabolic reprogramming to sustain their survival and proliferation. p53 exhibits a dual role in tumor cell ferroptosis. However, the precise role and mechanisms underlying wild-type p53 activation in promoting ferroptosis in pancreatic cancer cells remain obscure. In this study, we applied bioinformatics t...

Global rates of multi-drug resistance continue to rise, posing a significant challenge in the fight against antimicrobial resistance worldwide. Multi-drug efflux pumps are a significant contributor to this burden. Understanding connections between the diverse network of efflux pump genes, and their interactions with other genes, is important for un...

In higher organisms, individual cells respond to signals and perturbations by epigenetic regulation or transcriptional adaptation. However, in addition to shifting the expression level of individual genes, the adaptive response of cells can also lead to shifts in the proportions of different cell types. Recent methods such as scRNA-seq allow for th...

Advances in metagenomics analysis with the advent of next-generation sequencing have extended our knowledge of microbial communities as compared to conventional techniques providing advanced approach to identify novel and uncultivable microorganisms based on their genetic information derived from a particular environment. Shotgun metagenomics invol...

Myocardial infarction (MI) is a leading cause of mortality. To better understand its molecular and cellular mechanisms, we used bioinformatic tools and molecular experiments to explore the pathogenesis and prognostic markers. Differential gene expression analysis was conducted using GSE60993 and GSE66360 datasets. Hub genes were identified through...

Recientes investigaciones han relacionado la microbiota intestinal con la salud humana en múltiples aspectos. La evolución de los estilos de vida ha determinado un cambio en la composición de las bacterias intestinales, así como la implicación que la comunidad de estas ejerce sobre la salud. Actualmente, se conoce que la mayoría de las bacterias pr...

Accurate lipid annotation is crucial for understanding the role of lipids in health and disease and identifying therapeutic targets. However, annotating the wide variety of lipid species in biological samples remains challenging in untargeted lipidomic studies. In this work, we present an optimized lipid annotation workflow based on the combination...

Multiple sequence alignment (MSA) is essential for understanding genetic variations controlling phenotypic traits in all living organisms. The post-analysis of MSA results is a difficult step for researchers who do not have programming skills. Especially those working with large scale data and looking for potential variations or variable sample gro...

Absent in animals and with only seven enzymatic reactions toward the synthesis of chorismate and aromatic amino acids, the shikimate pathway is a crucial target for developing antimicrobial agents and herbicides. Although this pathway has been extensively studied in microorganisms related to human health, it reveals complexities in plants, as it ta...

Leptospirosis is a neglected zoonosis frequently reported worldwide, caused by a spirochete of the genus Leptospira. It is capable of infecting domestic animals, free-living animals, and humans. Among wild animals, the role of bats in the epidemiology of leptospirosis has been investigated but is far from being elucidated. The Amazonian biome has t...

Microbial communities exert a substantial influence on human health and have been unequivocally associated with a spectrum of human maladies, encompassing conditions such as anxiety1, depression2, hypertension3, cardiovascular diseases4, obesity4,5, diabetes6, inflammatory bowel disease7, and cancer8,9. This intricate interplay between microbiota c...

We introduce MutAmore, a bioinformatics tool that renders individual photos of, e.g., protein three-dimensional (3D) structures for protein mutations into an easily understandable movie format. MutAmore provides a streamlined pipeline casting single amino-acid variations (SAVs) into a dynamic 3D protein mutation movie which provides a qualitative p...

Argonaute proteins are instrumental in regulating RNA stability and translation. AGO2, the major mammalian Argonaute protein, is known to primarily associate with microRNAs, a family of small RNA ‘driver’ sequences, and identifies its targets primarily via a ‘seed’ mediated partial complementarity process Despite numerous studies, a definitive expe...

Hepatitis A and B are two crucial viral infections that still dramatically affect public health worldwide. Hepatitis A Virus (HAV) is the main cause of acute hepatitis, whereas Hepatitis B Virus (HBV) leads to the chronic form of the disease, possibly cirrhosis or liver failure. Therefore, vaccination has always been considered the most effective p...

The discovery of new targets for preventing bovine anaplasmosis has moved away from focusing on proteins that have already been extensively studied in Anaplasma marginale , including the Major Surface Proteins, Outer Membrane Proteins, and Type IV Secretion System proteins. An alternative is moonlighting or multifunctional proteins, capable of perf...

The ocular surface (OS) enzymes are of great interest due to their potential for novel ocular drug development. We aimed first to profile and classify the enzymes of the OS to describe major biological processes and pathways that are involved in the maintenance of homeostasis. Second, we aimed to compare the enzymatic profiles between the two most...

Biosynthetic gene clusters (BGCs) are a subset of consecutive genes present within a variety of organisms to produce specialized metabolites (SMs). These SMs are becoming a cornerstone to produce multiple medications including antibacterial and anticancer agents. Natural products (NPs) also play a pivotal role in enhancing the virulence of ESKAPE p...

PTEN and PIK3CA mutations are the most prevalent PI3K pathway alterations in prostate, breast, colorectal, and endometrial cancers. p110β becomes the prominent PI3K isoform upon PTEN loss. In this study, we aimed to understand the molecular mechanisms of PI3K dependence in the absence of PTEN. Using online bioinformatical tools, we examined two pub...

Background Diabetic foot ulcers (DFU) are a serious complication of diabetes that lead to significant morbidity and mortality. Recent studies reported that exosomes secreted by human adipose tissue-derived mesenchymal stem cells (ADSCs) might alleviate DFU development. However, the molecular mechanism of ADSCs-derived exosomes in DFU is far from be...

Sorcin (Sri), a member of penta EF-hand protein family plays a diverse role in maintaining calcium homeostasis, cell cycle and vesicular trafficking. Sri is highly conserved amongst mammals and consists of N-terminal glycine rich domain and C-terminal calcium binding domain that mediates its dimerization and interacts with different compounds. In t...

Background: Neoantigens are patient- and tumor-specific peptides that arise from somatic mutations. They stand as promising targets for personalized therapeutic cancer vaccines. The identification process for neoantigens has evolved with the use of next-generation sequencing technologies and bioinformatic tools in tumor genomics. However, in silico...

With the fast-growing and evolving omics data, the demand for streamlined and adaptable tools to handle the analysis continues to grow. In response to this need, we introduce Auto Bioinformatics Analysis (AutoBA), an autonomous AI agent based on a large language model designed explicitly for conventional omics data analysis. AutoBA simplifies the a...

Gastric cancer (GC) is a highly heterogeneous, complex disease and the fifth most common cancer worldwide (about 1 million cases and 784,000 deaths worldwide in 2018). GC has a poor prognosis (the 5-year survival rate is less than 20%), but there is an effort to find genes highly expressed during tumor establishment and use the related proteins as...

Background Cardio-facio-cutaneous (CFC) syndrome is a RASopathy subtype that presents with unique craniofacial dysmorphology, congenital heart disease, dermatologic abnormalities, growth retardation, and intellectual disability. This study describes the phenotypic spectrum of CFC in China and its association with CFC syndrome gene variants. Result...

Background: Fasciolosis is a global parasitic disease caused by liver trematodes such as Fasciola hepatica, affecting various mammals, including sheep, goats, cattle, pigs, and humans worldwide. Cathepsin L (Cat L) found in the life stages of F. gigantica is associated with the pathology of the fluke. Given the detrimental impact of fasciolosis on...

The DMP (DUF679 membrane proteins) family is a plant-specific gene family that encodes membrane proteins. The DMP family genes are suggested to be involved in various programmed cell death processes and gamete fusion during double fertilization in Arabidopsis. However, their functional relevance in other crops remains unknown. This study identified...

Pairs of sense and antisense transcriptions that are adjacent at their 5′ and 3′ regions are called divergent and convergent transcription, respectively. However, the structural properties of divergent/convergent transcription in different species or RNA biotypes are poorly characterized. Here, we developed CCIVR2, a program that facilitates identi...

Background Spondylocostal dysostosis is a rare genetic disorder caused by mutations in DLL3 , MESP2 , LFNG , HES7 , TBX6 , and RIPPLY2 . A particular form of this disorder characterized by the association of spondylocostal dysostosis with multiple pterygia has been reported and called spondylospinal thoracic dysostosis. Both disorders affect the sp...

Background Neisseria gonorrhoeae (gonococcus) is the causative agent of the sexually transmitted disease gonorrhea, for which no vaccines exist. Efforts are being made to identify potential vaccine protein antigens, and in this study, an immunoproteomics approach was used to identify protein signatures in gonococci that were recognized by sera from...

Whole-exome sequencing (WES) in families with an unexplained tendency for venous thromboembolism (VTE) may favor detection of low-frequency variants in genes with known contribution to hemostasis or associated with VTE-related phenotypes. WES analysis in six family members, three of whom affected by documented VTE, filtered for MAF < 0.04 in 192 ca...

Objective: The primary aim of this investigation is to comprehensively examine the detrimental effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on the WISP3 gene. This objective will be accomplished through intricate evaluations encompassing protein stability prediction, amino acid conservation analysis, investigation of protein-p...

Advances in genomics resources have facilitated the evolution of cereal crops with enhanced yield, improved nutritional values, and heightened resistance to various biotic and abiotic stresses. Genomic approaches present a promising avenue for the development of high-yielding varieties, thereby ensuring food and nutritional security. Significant im...

Introduction: Co-normalization of RNA profiles obtained using different experimental platforms and protocols opens avenue for comprehensive comparison of relevant features like differentially expressed genes associated with disease. Currently, most of bioinformatic tools enable normalization in a flexible format that depends on the individual datas...

With the fast-growing and evolving omics data, the demand for streamlined and adaptable tools to handle the analysis continues to grow. In response to this need, we introduce Auto Bioinformatics Analysis (AutoBA), an autonomous AI agent based on a large language model designed explicitly for conventional omics data analysis. AutoBA simplifies the a...

Purpose The primary objective of this study was to construct competing endogenous RNA (ceRNA) networks and evaluate the prognostic significance of tumor-infiltrating immune cells (TIICs) and key biomarkers within the ceRNA networks in colon adenocarcinoma (COAD) patients. Methods Comprehensive bioinformatics tools were used to screen differentiall...

The impact of the COVID-19 pandemic caused by the SARS-CoV-2 virus underscored the crucial role of laboratorial tests as a strategy to control the disease, mainly to indicate the presence of specific antibodies in human samples from infected patients. Therefore, suitable recombinant antigens are relevant for the development of reliable tests, and s...

Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology and bioinfor...

Background: The liver plays an important role in maintaining copper homeostasis. Copper ion accumulation was elevated in HCC tissue samples. Copper homeostasis is implicated in cancer cell proliferation and angiogenesis. The potential of copper homeostasis as a new theranostic biomarker for molecular imaging and the targeted therapy of HCC has been...

Background Protein Kinase C-epsilon (PKCε) is a member of the novel subfamily of PKCs (nPKCs) that plays a role in cancer development. Studies have revealed that its elevated expression levels are associated with cervical cancer. Previously, we identified pathogenic variations in its different domains through various bioinformatics tools and molecu...

Background Safety of probiotic strains that are used in human and animal trials is a prerequisite. Genome based safety assessment of probiotics has gained popularity due its cost efficiency and speed, and even became a part of national regulation on foods containing probiotics in Indonesia. However, reliability of the safety assessment based only o...