Bioinformatics analysis of myelin-microbe interactions suggests multiple types of molecular mimicry in the pathogenesis of multiple sclerosis.

Multiple sclerosis (MS) is a devastating autoimmune disease that leads to the destruction of the myelin sheath in the human central nervous system (CNS). Infection by viruses and bacteria has been found to be strongly associated with the onset of MS or its severity. We postulated that the immune system's attack on the myelin sheath could be triggered by viruses and bacteria antigens that resemble myelin sheath components.

Unveiling Recurrence Patterns: Analyzing Predictive Risk Factors for Breast Cancer Recurrence after Surgery.

Objectives: Breast cancer (BC) stands as the second-leading cause of female-specific cancer-related fatalities globally, necessitating comprehensive research to address its critical aspects. This study aimed to explore the time intervals between surgery and disease recurrence in BC patients and their survival utilizing various parametric and semi-parametric models.

Methods: After the examination of data collected from 2010 to 2021 at a BC Center in Tehran, Iran, 171 cases met the criteria for analysis out of 2246 datasets.

Genetic variance components of the growth curve for Isfahan indigenous chicken.

Background: Being able to model a growth curve using three or four non-linear functional parameters could help explain the growth phenomenon in a precise way and would allow the comparison of an animal's development rate, optimize management and feeding strategies and guide animal production strategies.

Objective: The goal of this study was to estimate the genetic parameters of growth traits of Isfahan indigenous chicken in Iran and to determine the best non-linear model describing the growth curve.

Methods: The prediction of additive genetic parameters was performed using the REML method by WOMBAT.

Genetic analysis of growth curve in Moghani Sheep using Bayesian and restricted maximum likelihood.

This study was conducted to predict the genetic (co)variance components of growth curve parameters of Moghani sheep breed using the following information: birth weight (N = 7278), 3-mo-old weight (N = 5881), 6-mo-old weight (N = 5013), 9-mo-old weigh (N = 2819], and 12-mo-old weight (N = 2883). The growth parameters (A: maturity weight, B: growth rate, and K: maturity rate) were calculated using Gompertz, Logistic, Brody, and Von Bertalanffy nonlinear models via NLIN procedure of SAS software. The aforementioned models were compared using Akaike information criterion, root mean square error, adjusted co-efficient of determination.

RNA-Seq Profiling between Commercial and Indigenous Iranian Chickens Highlights Differences in Innate Immune Gene Expression.

The purpose of the current study was to examine transcriptomic-based profiling of differentially expressed innate immune genes between indigenous and commercial chickens. In order to compare the transcriptome profiles of the different chicken breeds, we extracted RNA from blood samples of the Isfahan indigenous chicken (as indigenous) and Ross broiler chicken (as commercial) breeds. RNA-Seq yielded totals of 36,763,939 and 31,545,002 reads for the indigenous and commercial breeds, respectively, with clean reads then aligned to the chicken reference genome (Galgal5).

A new gene tree algorithm employing DNA sequences of bovine genome using discrete Fourier transformation.

Within the realms of human thoughts on nature, Fourier analysis is considered as one of the greatest ideas currently put forwarded. The Fourier transform shows that any periodic function can be rewritten as the sum of sinusoidal functions. Having a Fourier transform view on real-world problems like the DNA sequence of genes, would make things intuitively simple to understand in comparison with their initial formal domain view.

investigation of uncoupling protein function in avian genomes.

Introduction: The uncoupling proteins () are involved in lipid metabolism and belong to a family of mitochondrial anionic transporters. In poultry, only one homologue has been identified and experimentally shown to be associated with growth, feed conversion ratio, and abdominal fat according to its predominant expression in bird muscles. In endotherm birds, cell metabolic efficiency can be tuned by the rate of mitochondrial coupling.

Estimation of genetic parameters for production, reproduction, and growth curve of Fars indigenous chicken.

Iranian native chicken, including Fars indigenous chicken, is an important genetic resource due to its adaptation to stressful environmental conditions, good endurance and resistance to disease. The aim of this research was to determine the genetic infrastructure of Fars indigenous chicken using several nonlinear functions. The dataset included body weight at hatch (BW1), body weight at the 8th week (BW8), body weight at the 12th week (BW12), weight at sexual maturity (WSM), age at sexual maturity (ASM), number of eggs in the first 12 weeks of laying period (EN), egg weight at the first day of laying (EW1), average egg weight at the 28thday of laying (EW28), and average egg weight at weeks 28, 30, and 32 of the laying period (AEW).

Isoprenoid biosynthesis regulation in poplars by methylerythritol phosphate and mevalonic acid pathways.

It is critical to develop plant isoprenoid production when dealing with human-demanded industries such as flavoring, aroma, pigment, pharmaceuticals, and biomass used for biofuels. The methylerythritol phosphate (MEP) and mevalonic acid (MVA) plant pathways contribute to the dynamic production of isoprenoid compounds. Still, the cross-talk between MVA and MEP in isoprenoid biosynthesis is not quite recognized.

Genome-Wide Characterization and Expression Analysis of Fatty acid Desaturase Gene Family in Poplar.

Fatty acid desaturases (FADs) modulate carbon-carbon single bonds to form carbon-carbon double bonds in acyl chains, leading to unsaturated fatty acids (UFAs) that have vital roles in plant growth and development and their response to environmental stresses. In this study, a total of 23 candidates were identified from the poplar genome and clustered into seven clades, including FAB2, FAD2, FAD3/7/8, FAD5, FAD6, DSD, and SLD. The exon-intron compositions and conserved motifs of the PtFADs, clustered into the same clade, were considerably conserved.

An Integrated Bioinformatics Approach to Identify Network-Derived Hub Genes in Starving Zebrafish.

The present study was aimed at identifying causative hub genes within modules formed by co-expression and protein-protein interaction (PPI) networks, followed by Bayesian network (BN) construction in the liver transcriptome of starved zebrafish. To this end, the GSE11107 and GSE112272 datasets from the GEO databases were downloaded and meta-analyzed using the MetaDE package, an add-on R package. Differentially expressed genes (DEGs) were identified based upon expression intensity N(µ = 0.

Probabilistic prediction of segmental body composition in Iranian children and adolescents.

Background: Adolescents' body composition is considered an important measure to evaluate health status. An examination of any of the segmental compartments by anthropometric indices is a more usable method than direct methods.

Objectives: To propose a method based on the network approach for predicting segmental body composition components in adolescent boys and girls using anthropometric measurements.

Constraint-Based, Score-Based and Hybrid Algorithms to Construct Bayesian Gene Networks in the Bovine Transcriptome.

Bayesian gene networks are powerful for modelling causal relationships and incorporating prior knowledge for making inferences about relationships. We used three algorithms to construct Bayesian gene networks around genes expressed in the bovine uterus and compared the efficacies of the algorithms. Dataset GSE33030 from the Gene Expression Omnibus (GEO) repository was analyzed using different algorithms for hub gene expression due to the effect of progesterone on bovine endometrial tissue following conception.

Network Meta-Analysis of Chicken Microarray Data following Avian Influenza Challenge-A Comparison of Highly and Lowly Pathogenic Strains.

The current bioinformatics study was undertaken to analyze the transcriptome of chicken () after influenza A virus challenge. A meta-analysis was carried out to explore the host expression response after challenge with lowly pathogenic avian influenza (LPAI) (H1N1, H2N3, H5N2, H5N3 and H9N2) and with highly pathogenic avian influenza (HPAI) H5N1 strains. To do so, ten microarray datasets obtained from the Gene Expression Omnibus (GEO) database were normalized and meta-analyzed for the LPAI and HPAI host response individually.

Following the Trace of HVS II Mitochondrial Region Within the Nine Iranian Ethnic Groups Based on Genetic Population Analysis.

The Iranian gene pool is seen as an important human genetic resource for investigating the region connecting Mesopotamia and the Iranian plateau. The main objective of this study was to explore gene flow in nine Iranian ethnic/subpopulation groups (402 samples) by examining mtDNA HVS2 sequence variations. This then allowed us to detect mtDNA HVS2 sequence mutations in two independent thalassemia and cystic fibrosis patient sample groups.

Non-extensive thermodynamic entropy to predict the dynamics behavior of COVID-19.

The current world observations in COVID-19 are hardly tractable as a whole, making situations of information to be incompleteness. In pandemic era, mathematical modeling helps epidemiological scientists to take informing decisions about pandemic planning and predict the disease behavior in the future. In this work, we proposed a non-extensive entropy-based model on the thermodynamic approach for predicting the dynamics of COVID-19 disease.

Bayesian estimate of genetic parameters for growth traits in Lori Bakhtiari sheep.

The information of birth (10,017 records), weaning (9439 records), 6 months (7669 records), 9 months (4536 records), and yearling weights (417 records) collected from 1989 to 2016 by the Lori Bakhtiari (Sholi) sheep breeding station located in Shahrekord were used to estimate the genotypic and phenotypic parameters of growth traits of Lori Bakhtiari sheep. The components of variance and genetic parameters were estimated by the Bayesian statistical method based on the Gibbs sampling technique due to the high accuracy of this method. Factors including birth year, lamb sex, birth type, and maternal age at lambing have significant effects on all of these traits (P < 0.

Association analysis and molecular tagging of phytochemicals in the endangered medicinal plant licorice (Glycyrrhiza glabra L.).

Licorice (Glycyrrhiza glabra L.) is a medicinal plant species valued in many countries in Asia and Europe for its phytochemical characteristics. Licorice biodiversity is becoming threatened nowadays in Iran due to increasing demand and a drastic decline of its natural habitats.

Mathematical prediction of the spreading rate of COVID-19 using entropy-based thermodynamic model.

In the COVID-19 pandemic era, undoubtedly mathematical modeling helps epidemiological scientists and authorities to take informing decisions about pandemic planning, wise resource allocation, introducing relevant non-pharmaceutical interventions and implementation of social distancing measures. The current coronavirus disease (COVID-19) emerged in the end of 2019, Wuhan, China, spreads quickly in the world. In this study, an entropy-based thermodynamic model has been used for predicting and spreading the rate of COVID-19.

Genetic analysis of sexual size dimorphism in Markhoz goat.

Genetic bases of sexual size dimorphism (SSD) in Markhoz goat (5268 kids descended from 242 sires and 1499 dams) were unraveled as it was thought that sex-specific genetic mechanism is in the place governing SSD of birth weight (BW), weaning weight at 90 days of age (WW_90d), and post-weaning weights at 6 (W6), 9 (W9), and 12 (W12) months of age. Male kids excelled for BW, WW_90d, W6, W9, and W12 than their female counterparts in the tune of 10, 17, 14, 17, and 23%, respectively. Estimates of sexual dimorphism levels (expressed as M/F) were 1.

RNA-Seq Bayesian Network Exploration of Immune System in Bovine.

Background: The stress is one of main factors effects on production system. Several factors (both genetic and environmental elements) regulate immune response to stress.

Objectives: In order to determine the major immune system regulatory genes underlying stress responses, a learning Bayesian network approach for those regulatory genes was applied to RNA-Seq data from a bovine leukocyte model system.

A new DNA sequence entropy-based Kullback-Leibler algorithm for gene clustering.

Information theory is a branch of mathematics that overlaps with communications, biology, and medical engineering. Entropy is a measure of uncertainty in the set of information. In this study, for each gene and its exons sets, the entropy was calculated in orders one to four.

WITHDRAWN:Identification of bovine uterine transcriptomic hub genes using Bayesian network algorithms.

Ahead of Print article withdrawn by publisher.