DDTRP: Database of Drug Targets for Resistant Pathogens

Emergence of drug resistance is a major threat to public health. Many pathogens have developed resistance to most of the existing antibiotics, and multidrug-resistant and extensively drug resistant strains are extremely difficult to treat. This has resulted in an urgent need for novel drugs. We describe a database called 'Database of Drug Targets for Resistant Pathogens' (DDTRP). The database contains information on drugs with reported resistance, their respective targets, metabolic pathways involving these targets, and a list of potential alternate targets for seven pathogens. The database can be accessed freely at http://bmi.icmr.org.in/DDTRP.     

Phosphate starvation responses are mediated by sugar signaling in <Emphasis Type="Italic">Arabidopsis</Emphasis>

Phosphate (Pi) is one of the least available plant nutrients in soils. It is associated with dynamic changes in carbon fluxes and several crucial processes that regulate plant growth and development. Pi levels regulate the expression of large number of genes including those involved in photosynthesis and carbon metabolism. Herein we show that sugar is required for Pi starvation responses including changes in root architecture and expression of phosphate starvation induced (PSI) genes in Arabidopsis. Active photosynthesis or the supplementation of sugar in the medium was essential for the expression of PSI genes under Pi limiting conditions. Expression of these genes was not only induced by sucrose but also detected, albeit at reduced levels, with other metabolizable sugars. Non-metabolizable sugar analogs did not induce the expression of PSI genes. Although sugar input appears to be downstream of initial Pi sensing, it is absolutely required for the completion of the PSI signaling pathway. Altered expression of PSI genes in the hexokinase signaling mutant gin2 indicates that hexokinase-dependent signaling is involved in this process. The study provides evidence for requirement of sugars in PSI signaling and evokes a role for hexokinase in some components of Pi response mechanism.     

Adsorption mechanism of cadmium on juniper bark and wood

In this study the capacity of sorbents prepared from juniper wood (JW) and bark (JB) to adsorb cadmium (Cd) from aqueous solutions at different pH values was compared. Adsorption behavior was characterized through adsorption kinetics, adsorption isotherms, and adsorption edge experiments. Results from kinetics and isotherm experiments showed that JB (76.3-91.6 micromol Cdg(-1) substrate) had 3-4 times higher adsorption capacity for Cd than JW (24.8-28.3 micromol Cdg(-1)). In addition to higher capacity, JB exhibited a higher strength of adsorption (45.3 versus 9.1 Lmmol(-1)) and faster uptake kinetics (0.0119 versus 0.0083 g micromol(-1)min(-1)) compared to JW. For both these adsorbents, increasing Cd adsorption with increasing solution pH in the range of 2-6 suggests that surface carboxyl groups (RCOOH) might be involved in interaction with Cd. Diffuse reflectance infrared Fourier transform (DRIFT) spectra showed that the surface concentration of carboxyl groups was higher on JB compared to JW. The ratio of Ca released to Cd adsorbed was 1.04 and 0.78 for JB and JW, respectively, indicating that Ca-Cd ion-exchange was the primary mechanism involved. The higher Ca content in JB (15 times more) and the surface RCOOH concentration (2.5 times more) can be attributed to the observed differences in Cd adsorption behavior between the two lignocellulosic adsorbents.     

Nested and TaqMan® probe based quantitative PCR for the diagnosis of Ca. Phytoplasma in coconut palms

The root (wilt) disease caused by phytoplasma (Ca. Phytoplasma) is one of the major and destructive occurs in coconut gardens of Southern India. As this organism could not be cultured in vitro, the early detection in the palm is very much challenging. Hence, proper early diagnosis and inoculum assessment relay mostly on the molecular techniques namely nested and quantitative PCR (qPCR). So, the present study qPCR assay conjugated with TaqMan^® probe was developed which is a rapid, sensitive method to detect the phytoplasma. For the study, samples from different parts of infected coconut palms viz., spindle leaflets, roots and the insect vector—leaf hopper (Proutista moesta) were collected and assessed by targeting 16S rRNA gene. Further, nested PCR has been carried out using p1/p7 and fU5/rU3 primers and resulted in the amplification product size of 890 bp. From this amplified product, specifically a target of 69 bp from the 16S rRNA gene region has been detected through primers conjugated with Taqman probe in a step one instrument. The results indicated that the concentration of phytoplasma was more in spindle leaflets (8.9?×?10⁵ g of tissue) followed by roots (7.4?×?10⁵ g of tissue). Thus, a qPCR approach for detection and quantification of coconut phytoplasma was more advantageous than other PCR methods in terms of sensitivity and also reduced risk of cross contamination in the samples. Early diagnosis and quantification will pave way for the healthy coconut saplings selection and management under field conditions.

     

Computational prediction of small molecules with predicted binding to FGFR3 and testing biological effects in bone cells

Activating anabolic receptor-mediated signaling is essential for stimulating new bone formation and for promoting bone healing in humans. Fibroblast growth factor receptor (FGFR) 3 is reported to be an important positive regulator of osteogenesis. Presently, recombinant proteins are used to stimulate FGFR3 function but have limitations for therapy due to expense and stability. Therefore, there is a need for identification of novel small molecules binding to FGFR3 that promote biological function. In silico molecular docking and high-throughput virtual screening on zinc database identified seven compounds predicted to bind to an active site within the βCʹ-βE loop, specific to FGFR3. All seven compounds fall within an acceptable range of ADME/T properties. Four compounds showed a 30–65% oral absorption rate. Density functional theory analysis revealed a high HOMO-LUMO gap, reflecting high molecular stability for compounds 14977614 and 13509082. Five compounds exhibited mutagenicity, while the other three compounds presented irritability. Computational mutagenesis predicted that mutating G322 affected compound binding to FGFR3. Molecular dynamics simulation revealed compound 14977614 is stable in binding to FGFR3. Furthermore, compound 14977614, with an oral absorption rate of 60% and high molecular stability, produced significant increases in both proliferation and differentiation of bone marrow stromal cells in vitro. Anti-FGFR3 treatment completely blocked the stimulatory effect of 14977614 on BMSC proliferation. Ex vivo treatment of mouse calvaria in organ culture for seven days with 14977614 increased mineralization and expression levels of bone formation markers. In conclusion, computational analyses identified seven compounds that bind to the FGFR3, and in vitro studies showed that compound 14977614 exerts significant biological effects on osteogenic cells.     

Effect of heavy metals on tissue protein of an edible fish Cirrhinus mrigala as dependent on pH and water hardness

The goal of the study was to investigate the influence of nickel and chromium at different pH and water hardness on the protein content of muscle tissues of Cirrhinus mrigala fingerlings by Fourier transform infrared spectroscopy. FTIR spectra revealed significant differences in absorbance intensities between control and metal-exposed muscle tissues, reflecting a change in protein content and state caused by heavy metal toxicity; metal accumulation in tissue was markedly increased at alkaline pH and to a lesser extent in hard water.     

Sequence-Dependent Biophysical Modeling of DNA Amplification

A theoretical framework for prediction of the dynamic evolution of chemical species in DNA amplification reactions, for any specified sequence and operating conditions, is reported. Using the polymerase chain reaction (PCR) as an example, we developed a sequence- and temperature-dependent kinetic model for DNA amplification using first-principles biophysical modeling of DNA hybridization and polymerization. We compare this kinetic model with prior PCR models and discuss the features of our model that are essential for quantitative prediction of DNA amplification efficiency for arbitrary sequences and operating conditions. Using this model, the kinetics of PCR is analyzed. The ability of the model to distinguish between the dynamic evolution of distinct DNA sequences in DNA amplification reactions is demonstrated. The kinetic model is solved for a typical PCR temperature protocol to motivate the need for optimization of the dynamic operating conditions of DNA amplification reactions. It is shown that amplification efficiency is affected by dynamic processes that are not accurately represented in the simplified models of DNA amplification that form the basis of conventional temperature cycling protocols. Based on this analysis, a modified temperature protocol that improves PCR efficiency is suggested. Use of this sequence-dependent kinetic model in a control theoretic framework to determine the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is discussed.     

Biodiversity values of abandoned teak,Tectona grandis plantations in southern Western Ghats: Is there a need for management intervention?

Abandoned plantations could potentially support a large number of native tree species through succession and restore the original tree community. In order to assess the ability of abandoned teak plantations to recover through regeneration, teak stands from 29 to 80 years old were sampled for seedling and sapling density, species richness and the use by large ungulates in the southern Western Ghats using 10 m circular plots. The influence of the forest-plantation edge was also studied. There was regeneration of a species-rich tree community in the understorey of abandoned teak plantations. However, regeneration was arrested, and thereby the large girth-class tree community remained species-poor. There was no significant change in the tree species richness with distance from natural forest, suggesting that the forest-plantation edge had little influence on the penetration of native tree species inside plantations. Asian elephant and Indian gaur dung densities were significantly lower in the plantations than in the forest. Indian gaur and sambar used the younger plantations intensively, and the density of their dung was negatively correlated with age of the plantation. Abandonment of mature teak stands arrested the succession of native trees. We provide evidence that abandoned teak plantations might not serve as suitable habitats for large herbivores during the dry months of the year in the region. The study highlights the need for active management of mature teak plantations inside wildlife reserves, in order to promote succession and improve the habitat for wild flora and fauna in the Western Ghats.     

Polymorphisms in transcobalamin II gene is associated with coronary artery disease in Indian population

Transcobalamin (TCII) is a key enzyme involved in intracellular transport of vitamin B12. We had earlier shown that vitamin B12 levels are associated with Coronary Artery Disease (CAD). Herein, we evaluated the association of four nonsynonymous single nucleotide polymorphisms (SNPs) of TCII gene with CAD in 1398 individuals (589 CAD cases and 809 controls). Using logistic regression, we found that three SNPs (G1196A, C776G and C1043T) were significantly associated with CAD and one (G1196A) with vitamin B12 levels even after controlling for confounding factors. Thus, polymorphisms in TCII gene may play an important role in the etiology of CAD.