Co-resistance is the dominant mechanism of co-selection and dissemination of antibiotic resistome in nano zinc oxide polluted soil.

The broader soil bacterial community responses at ecotoxicologically relevant levels of nano ZnO (nZnO) focussing on co-selection of antibiotic resistance (AR) were investigated. nZnO imposed a stronger influence than the bulk counterpart (bZnO) on antibiotic resistance genes (ARGs) with multidrug resistance (MDR) systems being predominant (63 % of total ARGs). Proliferation of biomarker ARGs especially for last resort antibiotic like vancomycin was observed and Streptomyces hosted multiple ARGs.

Whole genome based identification of BAHD acyltransferase gene involved in piperine biosynthetic pathway in black pepper.

Black pepper ( L.), a crop of the genus Piper, is an important spice that has both economic and ecological significance. It is widely regarded as the "King of Spices" because of its pungency, attributed to the presence of piperine.

New insights into bacterial Zn homeostasis and molecular architecture of the metal resistome in soil polluted with nano zinc oxide.

Accumulation of nano ZnO (nZnO) in soils could be toxic to bacterial communities through disruption of Zn homeostasis. Under such conditions, bacterial communities strive to maintain cellular Zn levels by accentuation of appropriate cellular machinery. In this study, soil was exposed to a gradient (50-1000 mg Zn kg) of nZnO for evaluating their effects on genes involved in Zn homeostasis (ZHG).

Soil polluted with nano ZnO reveals unstable bacterial communities and decoupling of taxonomic and functional diversities.

Due to relentless production and disposal of nano zinc oxide (nZnO), it has become critical to comprehend the serious risks large-scale accumulation of nZnO pose to bacterial communities in soil. The primary objective was to evaluate the changes in bacterial community structure and associated functional pathways through predictive metagenomic profiling and subsequent validation through Quantitative Realtime PCR in soil spiked with nZnO (0, 50, 200, 500 and 1000 mg Zn kg) and similar levels of bulk ZnO (bZnO). The results revealed that soil microbial biomass-C, -N, -P, soil respiration and enzyme activities decreased markedly at higher ZnO levels.

Metagenomics indicates abundance of biofilm related genes and horizontal transfer of multidrug resistant genes among bacterial communities in nano zinc oxide polluted soil.

The unsafe and reckless disposal of metal oxide nanoparticles like ZnO (nZnO) into the soil could seriously impact bacterial behavioural responses and functions. Under such stress, biofilm formation is considered to be a robust mechanism for bacterial survival in soil. We examined the response of bacterial metagenomes in soils exposed to varying levels of Zn (50, 200, 500 and 1000 mg kg) as nano Zn oxide (nZnO) in terms of biofilm genesis and regulation and their co-occurrences with multidrug resistance genes (MDRGs) and mobile genetic elements (MGEs).

Transcriptomic meta-analysis reveals biomarker pairs and key pathways in Tetralogy of Fallot.

Tetralogy of Fallot (TOF) is a cyanotic congenital condition contributed by genetic, epigenetic as well as environmental factors. We applied sparse machine learning algorithms to RNAseq and sRNAseq data to select the prospective biomarker candidates. Furthermore, we applied filtering techniques to identify a subset of biomarker pairs in TOF.

Dataset of hybrid berry transcriptome profiling and characterization of species ( and ) using Illumina and Nanopore sequencing.

and are the most popular and economically essential spice crops globally valued for their aromatic alkaloids, especially Piperine. However, Piperine synthesis pathway mechanisms are not yet well known. This work was aimed to generate the full-length comparative berry transcriptome analysis dataset of and by Illumina and Nanopore sequencing platforms.

Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.).

Ginger (Zingiber officinale Rosc.) is an economically important and valuable spice crop around the world. It is used as food, spice, condiment, and medicine.

Analysis of selection signatures reveals important insights into the adaptability of high-altitude Indian sheep breed Changthangi.

Changthangi is a high-altitude sheep breed of India that is adapted to cold and hypoxic climate of Himalayas. In the present study, we analysed population structure of Changthangi and contrasted it with selected Indian and European commercial sheep breeds to detect genomic regions under positive selection. The Illumina OvineSNP50v1 genotype data on 292 animals from seven different sheep breeds i.

Integrated regulatory network based on lncRNA-miRNA-mRNA-TF reveals key genes and sub-networks associated with dilated cardiomyopathy.

Dilated Cardiomyopathy (DCM) is a multifactorial condition often leading to heart failure in many clinical cases. Due to the high number of DCMincidence reported as familial, a gene level network based study was conducted utilizing high throughput next generation sequencing data. We exploited the exome and transcriptome sequencing data in NCBI-SRA database to construct a high confidence scale-free regulatory network consisting of lncRNA, miRNA, mRNA and Transcription Factors (TFs).

Two way network construction and analysis of mRNA, miRNA and lncRNA reveals critical regulators and regulatory modules in cardiovascular diseases.

Background: Cardiovascular diseases contribute to the leading cause of deaths (31%) in the world population.

Objective: The objective of this study is to compile non-coding RNA-gene interaction into a core regulatory network whose dysregulation might play an important role in disease progression.

Method: We applied a structured approach to reconstruct the interaction network of lncRNAs, miRNAs and genes involved in cardiovascular diseases.

MethFinder - A software package for prediction of human tissue-specific methylation status of CpG islands.

Unlabelled: DNA methylation, the highly studied epigenetic mechanism which is involved in the regulatory events of various cellular processes like chromatin structure modifications, chromosomal inactivation, gene expressional patterns, embriyonic developments and transcriptional modification etc. Various high throughput techniques evolved for direct detection of methylation actions as well as information across the entire region. However, despite high throughput technological advances in experimental field, the development of software tools that has been dedicated to the prediction of epigenetic information from specific genome sequences is warranted.

Oncogenic microRNAs as biomarkers of oral tumorigenesis and minimal residual disease.

Objectives: Classical diagnostic methods are not sensitive enough in detecting oral lesions that may progress to cancer and in assessing minimal residual disease (MRD) in oral surgical margins. Altered expression of microRNAs (miRNAs) contributes to human cancer, including oral cancer. Although there are many studies on microRNAs in oral cancer, there is no reported study comparing the expression of microRNAs during oral tumor progression and in oral surgical margins.

Proteomic profiling of high glucose primed monocytes identifies cyclophilin A as a potential secretory marker of inflammation in type 2 diabetes.

Hyperglycemia is widely recognized to be a potent stimulator of monocyte activity, which is a crucial event in the pathogenesis of atherosclerosis. We analyzed the monocyte proteome for potential markers that would enhance the ability to screen for early inflammatory status in Type 2 diabetes mellitus (T2DM), using proteomic technologies. Monocytic cells (THP-1) were primed with high glucose (HG), their protein profiles were analyzed using 2DE and the downregulated differentially expressed spots were identified using MALDI TOF/MS.

Comprehensive patterns in microRNA regulation of transcription factors during tumor metastasis.

In spite of a large body of information about the upstream regulators of metastasis, a process that often plays a limiting factor in therapeutic outcome of cancer patients, the impact of regulatory microRNA patterns remains obscure. This review describes computational analysis of coordinated regulation of genes by di-directional regulation of microRNA and transcription factors that specifically regulate the process of metastasis. We discovered several unexpected modes of regulatory patterns between microRNAs and transcription factors.