Interaction of chloramphenicol with titin I27 probed using single-molecule force spectroscopy

Journal of Biological Physics - Titin is a giant elastic protein which is responsible for passive muscle stiffness when muscle sarcomeres are stretched. Chloramphenicol, besides being a...     

The NLRomes of Zea mays NAM founder lines and Zea luxurians display presence–absence variation,integrated domain diversity,and mobility

Plant pathogens cause significant crop loss worldwide, and new resistance genes deployed to combat diseases can be overcome quickly. Understanding the existing resistance gene diversity within the germplasm of major crops, such as maize, is crucial for the development of new disease-resistant varieties. We analysed the nucleotide-binding leucine-rich repeat receptors (NLRs) of 26 recently sequenced diverse founder lines from the maize nested association mapping (NAM) population and compared them to the R gene complement present in a wild relative of maize, Zea luxurians. We found that NLRs in both species contain a large diversity of atypical integrated domains, including many domains that have not previously been found in the NLRs of other species. Additionally, the single Z. luxurians genome was found to have greater integrated atypical domain diversity than all 26 NAM founder lines combined, indicating that this species may represent a rich source of novel resistance genes. NLRs were also found to have very high sequence diversity and presence–absence variation among the NAM founder lines, with a large NLR cluster on Chr10 representing a diversity hotspot. Additionally, NLRs were shown to be mobile within maize genomes, with several putative interchromosomal translocations identified.     

High throughput sequencing study of foliose lichen-associated bacterial communities from India

Molecular Biology Reports - Lichens comprise highly diverse and complex microbial communities, the majority consisting of mycobiont, photobiont, Basidiomycetes yeast and bacteriobiont (internal...     

Aquatic Microbiology with Reference to Tannin Degradation

Tannins in aquatic environment cause harmful effects to aquatic life. They are inhibitory to microbial growth, respiration and metabolism. A few microorganisms degrade tannins and the factors influencing degradation are discussed. The need for coordinated approach is emphasized.Memoir No. 300, from Centre of Advanced study in Botany, University of Madras.     

Reactive oxygen species generation and mitochondrial dysfunction for the initiation of apoptotic cell death in human hepatocellular carcinoma HepG2 cells by a cyclic dipeptide Cyclo(-Pro-Tyr)

Molecular Biology Reports - Cyclic dipeptides are increasingly gaining importance as considering its significant biological and pharmacological activities. This study was aimed to investigate the...     

An Integrated Workflow for DNA Methylation Analysis

The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes. DNA methylation has a demonstrated role in the genome stability and protection, regulation of gene expression and many other aspects of genome function and maintenance. BS-seq is a relatively unbiased method for profiling the DNA methylation, with a resolution capable of measuring methylation at individual cytosines. Here we describe, as an example, a workflow to handle DNA methylation analysis, from BS-seq library preparation to the data visualization. We describe some applications for the analysis and interpretation of these data. Our laboratory provides public access to plant DNA methylation data via visualization tools available at our “Next-Gen Sequence” websites (http://mpss.udel.edu), along with small RNA, RNA-seq and other data types.     

Efficacy of choline and DHA supplements or enriched environment exposure during early adult obesity in mitigating its adverse impact through aging in rats

IntroductionThe aim of this study was to assess the efficacy of choline and DHA or exposure to environmental enrichment in obese adult and aging rats on alterations in body mass index, serum lipid profile and arterial wall changes, despite stopping high fat diet consumption and interventions during adulthood.Methods21 day old male Sprague Dawley rats were assigned as Experiment-1 & 2 - PND rats were divided into 4 groups with interventions for 7 months (n = 8/group). NC– Normal control fed normal chow diet; OB- Obese group, fed high fat diet; OB + CHO + DHA- fed high fat diet and oral supplementation of choline, DHA. OB + EE- fed high fat diet along with exposure to enriched environment .Experiment-2 had similar groups and interventions as experiment 1 but for next 5 months were fed normal chow diet without any interventions. Body mass index was assessed and blood was analyzed for serum lipid profile. Common Carotid Artery (CCA) was processed for Haematoxylin and eosin, Verhoff Vangeison stains. Images of tissue sections were analyzed and quantified using image J and tissue quant software.ResultsIn experiment.1, mean body mass index (p < 0.001), serum lipid profile (p < 0.01), thickness of tunica intima (p < 0.05), tunica media (p < 0.01) and percentage of collagen fibers (p < 0.01) of CCA were significantly increased in OB compared to NC. These were significantly attenuated in OB + CHO + DHA and OB + EE compared to OB. In experiment.2, mean body mass index (p < 0.01), serum lipid profile (p < 0.05) and thickness of tunica media of CCA (p < 0.01) were significantly increased in OB compared to NC. In OB + CHO + DHA and OB + EE, significant attenuation was observed in mean body mass index and mean thickness of tunica media compared to same in OB.ConclusionAdult obesity has negative impact on body mass index, serum lipid profile and arterial wall structure that persists through aging. Supplementation of choline and DHA or exposure to enriched environment during obesity attenuates these negative impacts through aging.     

Analysis of the Global Architecture of Hemoglobin A2 by Heme Binding Studies and Molecular Modeling

The kinetics of CNProto- and CNDeutero-hemin binding to apohemoglobin A₂ was investigated in a stopped-flow device in 0.05 M potassium phosphate buffer, pH 7, at 10°C. The overall kinetic profile exhibited multiple phases: Phases I–IV corresponding with heme insertion (8.5?13 × 10⁷ M^?1 s^?1), local structural rearrangement (0.21?0.23 s^?1), global αδ structural event (0.071?0.098 s^?1), and formation of the Fe–His bond (0.009?0.012 s^?1), respectively. Kinetic differences observed between apohemoglobin A₂ and apohemoglobin A (previously studied) prompted an analysis of the structures of β and δ chains through molecular modeling. This revealed a structural repositioning of the residues not only at, but also distant from the site of the amino acid substitutions, specifically those involved in the heme contact and subunit interface. A significant global change was observed in the structure of the exon-coded 3 region and provided additional evidence for the designation of this as the subunit assembly domain.