Identification and validation of putative biomarkers by in silico analysis, mRNA expression and oxidative stress indicators for negative energy balance in buffaloes during transition period.

Objective: Transition period is considered from 3 weeks prepartum to 3 weeks postpartum, characterized with dramatic events (endocrine, metabolic, and physiological) leading to occurrence of production diseases (negative energy balance/ketosis, milk fever etc). The objectives of our study were to analyze the periodic concentration of serum beta-hydroxy butyric acid (BHBA), glucose and oxidative markers along with identification, and validation of the putative markers of negative energy balance in buffaloes using in-silico and quantitative real time-polymerase chain reaction (qRT-PCR) assay.

Methods: Out of 20 potential markers of ketosis identified by in-silico analysis, two were selected and analyzed by qRT-PCR technique (upregulated; acetyl serotonin o-methyl transferase like and down regulated; guanylate cyclase activator 1B).

Unveiling the anticancer mechanism of 1,2,3-triazole-incorporated thiazole-pyrimidine-isoxazoles: insights from docking and molecular dynamics simulations.

Cancer is a major global health concern, and the constant search for novel, selective anticancer compounds with low toxicity is never ending. Nitrogen heterocyclic compounds such as pyrimidine and triazole have been identified as potential candidates for cancer treatment. A novel series of 1,2,3-triazole incorporated thiazole-pyrimidine-isoxazole derivatives ) were designed, synthesized and evaluated for antitumorigenic activities against human breast cancer (MCF-7), human lung cancer (A549) and human prostate (PC3 & DU-145) various cell-lines by employing MTT assay using etoposide as the positive control.

Multimodal Imaging of Pancreatic Cancer Microenvironment in Response to an Antiglycolytic Drug.

Lipid metabolism and glycolysis play crucial roles in the progression and metastasis of cancer, and the use of 3-bromopyruvate (3-BP) as an antiglycolytic agent has shown promise in killing pancreatic cancer cells. However, developing an effective strategy to avoid chemoresistance requires the ability to probe the interaction of cancer drugs with complex tumor-associated microenvironments (TAMs). Unfortunately, no robust and multiplexed molecular imaging technology is currently available to analyze TAMs.

Analyzing the effect of heparin on in vitro capacitation and spermatozoal RNA population in goats.

Heparin is a glycosaminoglycan polymer that is commonly used as an anticoagulant. Heparin also induces in vitro capacitation in spermatozoa, although its molecular mechanism is elusive. This study investigated the effect of heparin on in vitro capacitation and spermatozoal RNA (spRNA) population in goats.

Restoration of Altered Oncogenic and Tumor Suppressor microRNA Expression in Breast Cancer and Colorectal Cancer Cell using Epicatechin.

Background: MicroRNAs (miRNA) are small non-coding RNAs that regulate the function of mRNA post-transcriptionally in a tissue-specific manner. miRNA expressions are heavily dysregulated in human cancer cells through various mechanisms, including epigenetic changes, karyotype abnormalities, and miRNA biogenesis defects. miRNAs may act as either oncogenes or tumor suppressors under different conditions.

Prediction of potential molecular markers of bovine mastitis by meta-analysis of differentially expressed genes using combined p value and robust rank aggregation.

Bovine mastitis causes significant economic loss to the dairy industry by affecting milk quality and quantity. Escherichia coli and Staphylococcus aureus are the two common mastitis-causing bacteria among the consortia of mastitis pathogens, wherein E. coli is an opportunistic environmental pathogen, and S.

Analysis of Overexpressed miRNA in Circulation and Cancer Tissue to Develop a Potential microRNA Panel for the Diagnosis of Colorectal Cancer.

Background: Colorectal cancer (CRC) represents the world's fourth deadly cancer, but its early diagnosis can be curative with considerable success rates. This study was aimed to identify CRC-specific microRNAs (miRNAs) in tissue and serum samples to develop a miRNA-based diagnostics panel for the minimal invasive detection of CRC in early conditions.

Methods: By integrating four microarrays in tissue and serum samples of CRC from the Gene Expression Omnibus (GEO) database, we screened out the highly expressed miRNAs in each dataset using the limma R package.

Prediction and Boolean logical modelling of synergistic microRNA regulatory networks during reprogramming of male germline pluripotent stem cells.

Unipotent male germline stem (GS) cells can undergo spontaneous reprogramming to germline pluripotent stem (GPS) cells during in vitro culture. In our previous study, we proposed a Boolean logical model of gene regulatory network (GRN) during reprogramming of GS cells to GPS cells. This study was designed to predict and model synergistic microRNA (miRNA) regulatory network during reprogramming of GS cells into GPS cells.

Comparison of spermatozoal RNA extraction methods in goats.

RNA sequencing (RNAseq) has divulged newer role of spermatozoal RNA in male fertility. This study aimed to evaluate different sperm purification and RNA extraction methods for long-read RNA sequencing of poly(A) transcriptome in goat spermatozoa. Sperm samples were purified by swim-up separation using different purification medium.

Molecular modeling, docking and dynamic simulations of growth hormone receptor (GHR) of .

Growth hormones (GH) have diverse functions like growth promotion, metabolism, appetite, reproduction and social behavior in vertebrates, which is mediated through the growth hormone receptor (GHR). This work was aimed to analyze structural features, homology modeling and molecular docking of GHR protein. A physicochemical characteristic, like molecular weight was 67.

Molecular modeling and co-expression analysis of human stem cell factor as fusion partner to granulocyte colony stimulating factor for improving their bioactivity.

Human granulocyte colony stimulating factor (hG-CSF) is an expensive hematopoietic growth factor that is clinically used in human for the treatment of neutropenia in diseases such as AIDS, aplastic anemia, myelodysplastic syndrome and congenital or chemotherapy-induced neutropenia. Here, through a computational biology approach, we show that human stem cell factor (hSCF) could be a better fusion partner than human thyroid peroxidase (hTPO), human erythropoietin (hEPO) and human interleukin-3 (hIL3) for co-expression with hG-CSF. Molecular modeling of hG-CSF-hSCF fusion protein with hG-CSF and hSCF receptors showed that binding of fusion protein with human granulocyte colony stimulating factor receptor (hG-CSFR) did not inhibit its binding to human stem cell factor receptor (hSCFR) and vice versa.

A Boolean Logical model for Reprogramming of Testes-derived male Germline Stem Cells into Germline pluripotent stem cells.

Background And Objective: Male germline stem (GS) cells are responsible for the maintenance of spermatogenesis throughout the adult life of males. Upon appropriate in vitro culture conditions, these GS cells can undergo reprogramming to become germline pluripotent stem (GPS) cells with the loss of spermatogenic potential. In recent years, voluminous data of gene transcripts in GS and GPS cells have become available.

Examining the co-expression, transcriptome clustering and variation using fuzzy cluster network of testicular stem cells and pluripotent stem cells compared with other cell types.

Stem cells are crucial in the field of tissue regeneration and developmental biology. Embryonic stem cells (ESCs) which are pluripotent in nature are derived from the inner cell mass of blastocyst. The gene expression profiles of ESCs and Induced pluripotent stem cells (iPSCs) were compared to identify the differences.

Pharmacophore modeling coupled with scaffold hopping to identify novel and potent ribosomal S6 kinase (RSK2) protein antagonists as anti-cancer agents.

Communicated by Ramaswamy H. Sarma.

Screening and insilico analysis of deleterious nsSNPs (missense) in human CSF3 for their effects on protein structure, stability and function.

Human granulocyte colony stimulating factor (hG-CSF), known as CSF3, plays an important role in the growth, differentiation, proliferation, survival, and activation of the granulocyte cell lineage such as neutrophils and their precursors. Functional reduction in native CSF3 protein results in reduced proliferation and activation of neutrophils and leads to neutropenia. Single nucleotide polymorphisms (SNPs) in the CSF3 gene may have deleterious effects on the CSF3 protein function.

Structural analysis, molecular docking and molecular dynamics simulations of G-protein-coupled receptor (kisspeptin) in fish.

Kisspeptins are neuropeptide that has emerged as an essential gatekeeper for reproduction and onset of puberty in higher vertebrates including fish. In present study, structural analysis, molecular docking and molecular dynamics simulations of kisspeptin receptor ( were carried out, which is a G-protein-coupled receptor. An open reading frame of is 1101 bp encoding a putative protein of 366 amino acids.

Elucidating the Role of Val-Asn 95 and Arg-Gly 52 Mutations on Structure and Stability of Fibroblast Growth Factor Homologous Factor 2.

Background: Fibroblast growth Factor Homologous Factors (FHFs) belong to a subclass of Fibroblast Growth Factor (FGF) family owing to their high sequence and structural similarities with FGFs. However, despite these similarities, there are properties which set them apart from FGFs. FHFs lack the secretion signal sequence unlike other FGF members, except FGF1 and 2.

Prediction of novel pluripotent proteins involved in reprogramming of male Germline stem cells (GSCs) into multipotent adult Germline stem cells (maGSCs) by network analysis.

Germline stem cells (GSCs) are known to transmit genetic information from parents to offspring. These GSCs can undergo reprogramming to transform themselves into pluripotent stem cells, called as Multipotent adult Germline stem cells (maGSCs). The mechanism of the reprogramming of GSCs to maGSCs is elusive.

Structure based annotation of Helicobacter pylori strain 26695 proteome.

The availability of complete genome sequences of H. pylori 26695 has provided a wealth of information enabling us to carry out in silico studies to identify new molecular targets for pharmaceutical treatment. In order to construe the structural and functional information of complete proteome, use of computational methods are more relevant since these methods are reliable and provide a solution to the time consuming and expensive experimental methods.