Structural stability studies in adhesion molecules—role of cation–<Emphasis Type="Italic">π</Emphasis> interactions

Cell adhesion molecules are important for their various roles in many cellular events and responses. In the present study, we have analyzed the roles played by cation–π interactions in the structural stability of adhesion molecules. These interactions are mainly formed by long-range contacts. The occurrence of arginine is higher than lysine to form cation–π interactions. The secondary structure preferences of interacting residues are independent of amino acid class. Cation–π interactions might stabilize the interface between the terminus and core in this class of proteins. The results obtained in the present study will be useful in understanding the contribution of cation–π interactions to the overall stability of adhesion proteins.     

Steeper restitution slopes across right ventricular endocardium in patients with cardiomyopathy at high risk of ventricular arrhythmias

Steep action potential duration (APD) restitution slopes (>1) and spatial APD restitution heterogeneity provide the substrate for ventricular fibrillation in computational models and experimental studies. Their relationship to ventricular arrhythmia vulnerability in human cardiomyopathy has not been defined. Patients with cardiomyopathy [left ventricular (LV) ejection fraction <40%] and no history of ventricular arrhythmias underwent risk stratification with programmed electrical stimulation or T wave alternans (TWA). Low-risk patients (n = 10) had no inducible ventricular tachycardia (VT) or negative TWA, while high-risk patients (n = 8) had inducible VT or positive TWA. Activation recovery interval (ARI) restitution slopes were measured simultaneously from 10 right ventricular (RV) endocardial sites during an S1-S2 pacing protocol. ARI restitution slope heterogeneity was defined as the coefficient of variation of slopes. Mean ARI restitution slope was significantly steeper in the high-risk group compared with the low-risk group [1.16 (SD 0.31) vs. 0.59 (SD 0.19), P = 0.0002]. The proportion of endocardial recording sites with a slope >1 was significantly larger in the high-risk patients [47% (SD 35) vs. 13% (SD 21), P = 0.022]. Spatial heterogeneity of ARI restitution slopes was similar between the two groups [29% (SD 16) vs. 39% (SD 34), P = 0.48]. There was an inverse linear relationship between the ARI restitution slope and the minimum diastolic interval (P < 0.001). In cardiomyopathic patients at high risk of ventricular arrhythmias, ARI restitution slopes along the RV endocardium are steeper, but restitution slope heterogeneity is similar compared with those at low risk. Steeper ARI restitution slopes may increase the propensity for ventricular arrhythmias in patients with impaired left ventricular function.     

Activation of BRCA1/BRCA2-associated helicase BACH1 is required for timely progression through S phase

BACH1 (also known as FANCJ and BRIP1) is a DNA helicase that directly interacts with the C-terminal BRCT repeat of the breast cancer susceptibility protein BRCA1. Previous biochemical and functional analyses have suggested a role for the BACH1 homolog in Caenorhabditis elegans during DNA replication. Here, we report the association of BACH1 with a distinct BRCA1/BRCA2-containing complex during the S phase of the cell cycle. Depletion of BACH1 or BRCA1 using small interfering RNAs results in delayed entry into the S phase of the cell cycle. Such timely progression through S phase requires the helicase activity of BACH1. Importantly, cells expressing a dominant negative mutation in BACH1 that results in a defective helicase displayed increased activation of DNA damage checkpoints and genomic instability. BACH1 helicase is silenced during the G(1) phase of the cell cycle and is activated through a dephosphorylation event as cells enter S phase. These results point to a critical role for BACH1 helicase activity not only in the timely progression through the S phase but also in maintaining genomic stability.     

Overexpression of a diacylglycerol acyltransferase gene in Phaeodactylum tricornutum directs carbon towards lipid biosynthesis

Under nutrient deplete conditions, diatoms accumulate between 15% to 25% of their dry weight as lipids, primarily as triacylglycerols (TAGs). As in most eukaryotes, these organisms produce TAGs via the acyl‐CoA dependent Kennedy pathway. The last step in this pathway is catalyzed by diacylglycerol acyltransferase (DGAT) that acylates diacylglycerol (DAG) to produce TAG. To test our hypothesis that DGAT plays a major role in controlling the flux of carbon towards lipids, we overexpressed a specific type II DGAT gene, DGAT2D, in the model diatom Phaeodactylum tricornutum. The transformants had 50‐ to 100‐fold higher DGAT2D mRNA levels and the abundance of the enzyme increased 30‐ to 50‐fold. More important, these cells had a 2‐fold higher total lipid content and incorporated carbon into lipids more efficiently than the wild type (WT) while growing only 15% slower at light saturation. Based on a flux analysis using ¹³C as a tracer, we found that the increase in lipids was achieved via increased fluxes through pyruvate and acetyl‐CoA. Our results reveal overexpression of DAGT2D increases the flux of photosynthetically fixed carbon towards lipids, and leads to a higher lipid content than exponentially grown WT cells.     

An IPTG Inducible Conditional Expression System for Mycobacteria

Conditional expression strains serve as a valuable tool to study the essentiality and to establish the vulnerability of a target under investigation in a drug discovery program. While essentiality implies an absolute requirement of a target function, vulnerability provides valuable information on the extent to which a target function needs to be depleted to achieve bacterial growth inhibition followed by cell death. The critical feature of an ideal conditional expression system is its ability to tightly regulate gene expression to achieve the full spectrum spanning from a high level of expression in order to support growth and near zero level of expression to mimic conditions of gene knockout. A number of bacterial conditional expression systems have been reported for use in mycobacteria. The utility of an isopropylthiogalactoside (IPTG) inducible system in mycobacteria has been reported for protein overexpression and anti-sense gene expression from a replicating multi-copy plasmid. Herein, we report the development of a versatile set of non-replicating IPTG inducible vectors for mycobacteria which can be used for generation of conditional expression strains through homologous recombination. The role of a single lac operator versus a double lac operator to regulate gene expression was evaluated by monitoring the expression levels of β-galactosidase in Mycobacterium smegmatis. These studies indicated a significant level of leaky expression from the vector with a single lac operator but none from the vector with double lac operator. The significance of the double lac operator vector for target validation was established by monitoring the growth kinetics of an inhA, a rpoB and a ftsZ conditional expression strain grown in the presence of different concentrations of IPTG. The utility of this inducible system in identifying target specific inhibitors was established by screening a focussed library of small molecules using an inhA and a rpoB conditional expression strain.     

Mass spectrometry-based metabolomics application to identify quantitative resistance-related metabolites in barley against Fusarium head blight

Quantitative resistance is generally controlled by several genes. More than 100 resistance quantitative trait loci (QTLs) have been identified in wheat and barley against Fusarium head blight (FHB), caused by Gibberella zeae (anamorph: Fusarium graminearum), implying the possible occurrence of several resistance mechanisms. The objective of this study was to apply metabolomics to identify the metabolites in barley that are related to resistance against FHB. Barley genotypes, Chevron and Stander, were inoculated with mock or pathogen during the anthesis stage. The disease severity was assessed as the proportion of spikelets diseased. The genotype Chevron (0.33) was found to have a higher level of quantitative resistance than Stander (0.88). Spikelet samples were harvested at 48 h post-inoculation; metabolites were extracted and analysed using an LC-ESI-LTQ-Orbitrap (Thermo Fisher, Waltham, MA, USA). The output was imported to an XCMS 1.12.1 platform, the peaks were deconvoluted and the adducts were sieved. Of the 1826 peaks retained, a t-test identified 496 metabolites with significant treatment effects. Among these, 194 were resistance-related (RR) constitutive metabolites, whose abundance was higher in resistant mock-inoculated than in susceptible mock-inoculated genotypes. Fifty metabolites were assigned putative names on the basis of accurate mass, fragmentation pattern and number of carbons in the formula. The RR metabolites mainly belonged to phenylpropanoid, flavonoid, fatty acid and terpenoid metabolic pathways. Selected RR metabolites were assayed in vitro for antifungal activity on the basis of fungal biomass production. The application of these RR metabolites as potential biomarkers for screening and the potential of mass spectrometry-based metabolomics for the identification of gene functions are discussed.     

Structure of microbial communities performing the simultaneous reduction of Fe(II)EDTA.NO2−and Fe(III)EDTA−

BioDeNOx is a combined physicochemical and biological process for the removal of nitrogen oxides (NOx) from flue gas. In the present study, two anaerobic bioreactors performing BioDeNOx were run consecutively (RUN-1 and RUN-2) at a dilution rate of 0.01 h⁻¹ with Fe(II)EDTA.NO²⁻ and Fe(III)EDTA⁻ as electron acceptors and ethanol as electron donor. The measured protein concentration of the reactor biomass of both runs was 120 mg/l. Different molecular methods were used to determine the identity and abundance of the bacterial populations in both bioreactors. Bacillus azotoformans strain KT-1 was recognized as a key player in Fe(II)EDTA.NO²⁻ reduction. PCR-denaturing gradient gel electrophoresis analysis of the reactor biomass showed a greater diversity in RUN-2 than in RUN-1. Enrichments of Fe(II)EDTA.NO²⁻ and Fe(III)EDTA⁻ reducers and activity assays were conducted using the biomass from RUN-2 as an inoculum. The results on substrate turnover, overall microbial diversity, and enrichments and finally activity assays confirmed that ethanol was used as electron donor for Fe(II)EDTA.NO²⁻ reduction. In addition, the Fe(III)EDTA⁻ reduction rate of the microbial community proved to be feasible enough to run the bioreactors, ruling out the chemical reduction of Fe(III)EDTA⁻ with sulfide as was proposed by other researchers.     

C-Phycocyanin Modulates Selenite-Induced Cataractogenesis in Rats

The present investigation is aimed to evaluate the anticataractogenic potential of C-phycocyanin (C-PC), extracted and purified from Spirulina platensis. Enucleated rat lenses were maintained in vitro in Dulbecco’s modified Eagle medium (DMEM). Group I contained DMEM, Group II and Group III contained 100 μM of sodium selenite, Group III was subdivided into three viz IIIa, IIIb, IIIc supplemented with 100, 150, 200 μg of C-PC respectively. In the in vivo study, on tenth day post partum: Group I rat pups received an intraperitoneal injection of saline, Group II, IIIa, IIIb, and IIIc rat pups received a subcutaneous injection of sodium selenite (19 μmol/kg bodyweight) Group IIIa, IIIb, IIIc also received an intraperitoneal injection of 100, 150, 200 mg/kg body weight of C-PC, respectively, from postpartum days?9–14. On termination of the experiment, the lenses from both in vitro and in vivo studies were subjected to morphological examination and subsequently processed to estimate the activities of antioxidant enzymes namely superoxide dismutase, catalase, glutathione peroxidase, glutathione reductase, levels of reduced glutathione and lipid peroxidation products. Sodium selenite-exposed, C-PC-treated rat lenses (Group IIIc), showed significant restoration of antioxidant enzyme activity (p?<?0.05) when compared to their counterpart Group II. Group IIIc conserved the levels of GSH and lipid peroxidation products at near to normal levels as compared with Group II. Results conclude the possible role of C-PC in modulating the antioxidant enzyme status, thereby retarding sodium selenite-induced cataract incidence both in vitro and in vivo.     

Integrating biodiversity and conservation with modern agricultural landscapes

To achieve food security and meet the demands of the ever-growing human populations, farming systems have assumed unsustainable practices to produce more from a finite land area. This has been cause for concern mainly due to the often-irreversible damage done to the otherwise productive agricultural landscapes. Agro-ecology is proclaimed to be deteriorating due to eroding integrity of connected ecological mosaics and vulnerability to climate change. This has contributed to declining species diversity, loss of buffer vegetation, fragmentation of habitats, and loss of natural pollinators or predators, which eventually leads to decline in ecosystem services. Currently, a hierarchy of conservation initiatives is being considered to restore ecological integrity of agricultural landscapes. However, the challenge of identifying a suitable conservation strategy is a daunting task in view of socio-ecological factors that may constrain the choice of available strategies. One way to mitigate this situation and integrate biodiversity with agricultural landscapes is to implement offset mechanisms, which are compensatory and balancing approaches to restore the ecological health and function of an ecosystem. This needs to be tailored to the history of location specific agricultural practices, and the social, ecological and environmental conditions. The offset mechanisms can complement other initiatives through which farmers are insured against landscape-level risks such as droughts, fire and floods. For countries in the developing world with significant biodiversity and extensive agriculture, we should promote a comprehensive model of sustainable agricultural landscapes and ecosystem services, replicable at landscape to regional scales. Arguably, the model can be a potential option to sustain the integrity of biodiversity mosaic in agricultural landscapes.     

Geographical markers for <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> strains with similar technological origins domesticated for rice-based ethnic fermented beverages production in North East India

Autochthonous strains of Saccharomyces cerevisiae from traditional starters used for the production of rice-based ethnic fermented beverage in North East India were examined for their genetic polymorphism using mitochondrial DNA-RFLP and electrophoretic karyotyping. Mitochondrial DNA-RFLP analysis of S. cerevisiae strains with similar technological origins from hamei starter of Manipur and marcha starter of Sikkim revealed widely separated clusters based on their geographical origin. Electrophoretic karyotyping showed high polymorphism amongst the hamei strains within similar mitochondrial DNA-RFLP cluster and one unique karyotype of marcha strain was widely distributed in the Sikkim-Himalayan region. We conceptualized the possibility of separate domestication events for hamei strains in Manipur (located in the Indo-Burma biodiversity hotspot) and marcha strains in Sikkim (located in Himalayan biodiversity hotspot), as a consequence of less homogeneity in the genomic structure between these two groups, their clear separation being based on geographical origin, but not on technological origin and low strain level diversity within each group. The molecular markers developed based on HinfI-mtDNA-RFLP profile and the chromosomal doublets in chromosome VIII position of Sikkim-Himalayan strains could be effectively used as geographical markers for authenticating the above starter strains and differentiating them from other commercial strains.