A biomimetic platform for studying root-environment interaction

Aims

Microstructure plays an important role in biological systems. Microstructural features are critical in the interaction between two biological organisms, for example, a microorganism and the surface of a plant. However, isolating the structural effect of the interaction from all other parameters is challenging when working directly with the natural system. Replicating microstructure of leaves was recently shown to be a powerful research tool for studying leaf-environment interaction. However, no such tool exists for roots. Roots present a special challenge because of their delicacy (specifically of root hairs) and their 3D structure. We aim at developing such a tool for roots.

Methods

Biomimetics use synthetic systems to mimic the structure of biological systems, enabling the isolation of structural function. Here we present a method which adapts tools from leaf microstructure replication to roots. We introduce new polymers for this replication.

Results

We find that Polyurethane methacrylate (PUMA) with fast UV curing gives a reliable replication of the tomato root surface microstructure. We show that our system is compatible with the pathogenic soilborne bacterium Ralstonia solanacearum.

Conclusions

This newly developed tool may be used to study the effect of microstructure, isolated from all other effects, on the interaction of roots with their environment.

     

Pseudomonas sp. to Sphingobium indicum: a journey of microbial degradation and bioremediation of Hexachlorocyclohexane

The unusual process of production of hexachlorocyclohexane (HCH) and extensive use of technical HCH and lindane has created a very serious problem of HCH contamination. While the use of technical HCH and lindane has been banned all over the world, India still continues producing lindane. Bacteria, especially Sphingomonads have been isolated that can degrade HCH isomers. Among all the bacterial strains isolated so far, Sphingobium indicum B90A that was isolated from HCH treated rhizosphere soil appears to have a better potential for HCH degradation. This conclusion is based on studies on the organization of lin genes and degradation ability of B90A. This strain perhaps can be used for HCH decontamination through bioaugmentation.     

Therapeutic approaches of melatonin in microwave radiations-induced oxidative stress-mediated toxicity on male fertility pattern of Wistar rats

Microwave (MW) radiation produced by wireless telecommunications and a number of electrical devices used in household or in healthcare institutions may adversely affects the reproductive pattern. Present study aimed to investigate the protective effects of melatonin (is well known antioxidant that protects DNA, lipids and proteins from free radical damage) against oxidative stress-mediated testicular impairment due to long-term exposure of MWs. For this, 70-day-old male Wistar rats were divided into four groups (n?=?6/group): Sham exposed, Melatonin (Mel) treated (2?mg/kg), 2.45?GHz MWs exposed and MWs?+?Mel treated. Exposure took place in Plexiglas cages for 2?h a day for 45 days where, power density (0.21?mW/cm²) and specific absorption rate (SAR 0.14?W/Kg) were estimated. After the completion of exposure period, rats were sacrificed and various stress related parameters, that is LDH-X (lactate dehydrogenase isoenzyme) activity, xanthine oxidase (XO), ROS (reactive oxygen species), protein carbonyl content, DNA damage and MDA (malondialdehyde) were performed. Result shows that melatonin prevent oxidative damage biochemically by significant increase (p?0.001) in the levels of testicular LDH-X, decreased (p?0.001) levels of MDA and ROS in testis (p?0.01). Meanwhile, it reversed the effects of MWs on XO, protein carbonyl content, sperm count, testosterone level and DNA fragmentation in testicular cells. These results concluded that the melatonin has strong antioxidative potential against MW induced oxidative stress mediated DNA damage in testicular cells.     

Identification of 1-chloro-2-formyl indenes and tetralenes as novel antistaphylococcal agents exhibiting sortase A inhibition

Tetralene and indene compounds have shown inhibitory activity against human pathogen, Mycobacterium tuberculosis. Their potential use as antistaphylococcal agent against drug-resistant Staphylococcus aureus has not been explored so far. We determined in vitro antistaphylococcal activity and mechanism of action of these compounds as sortase A inhibitors through in silico analysis followed by biological assays. Tetralene and indene series were tested against S. aureus strains MTCC96, MRSA, and VA30. Three compounds showed significant reduction in MIC in both wild-type and drug-resistant S. aureus strains. In silico absorption, distribution, metabolism, excretion, and toxicity analysis of identified leads and cytotoxicity testing with colorimetric method using Vero and WRL-68 cell lines showed no significant cytotoxic effects. Molecular docking of these molecules with sortase A (PDB: 2KID) showed H-bond interaction with functional site residue Arg197 of sortase A. Sortase A inhibition assay was developed by expressing SrtA_?N from S. aureus strain MTCC96. Tetralene and indene compounds were found to have sortase A inhibitory potential. S. aureus strain MTCC96 treated with these compounds showed surface-sorting inhibition of fibronectin-binding protein and reduction in adherence to host extracellular matrix protein, fibronectin. 1-Chloro, 2-formyl, 6-methoxy, 1-tetralene (Tet-5), 1,5-dichloro, 2-formyl, 1-indene (Tet-20) and 1-chloro, 2-formyl, 5,6-methylenedioxy, and 1-indene (Tet-21) exhibited antistaphylococcal activity along with sortase A inhibition. The results also indicate the possible role of these leads in other reactions essential for cell viability.     

Two new protocols to enhance the production and isolation of human induced pluripotent stem cell lines

There are two critical stages in the retroviral reprogramming of somatic cells to produce human induced pluripotent stem cell (hiPSC) lines. One is the production of high titer virus required to reprogram somatic cells; the other is identification of true hiPSC colonies from heterogeneous cell populations, and their isolation and expansion to generate a sustainable, pluripotent stem cell line. Here we describe simple, time-saving methods to address the current difficulties at these two critical junctures. First, we have developed a method to increase the number of infectious viral units 600-fold. Second, we have developed a TRA-1-81-based positive selection column method for isolating “true” hiPSCs from the heterogeneous cell populations, which overcomes the labor-intensive and highly subjective method of manual selection of hiPSC colonies. We have used these techniques to produce 8 hiPSC lines from human fibroblasts and we believe that they are of considerable utility to researchers in the hiPSC field.     

LIPOPREDICT: bacterial lipoprotein prediction server

Bacterial lipoproteins have many important functions owing to their essential nature and roles in pathogenesis and represent a class of possible vaccine candidates. The prediction of bacterial lipoproteins from sequence is thus an important task for computational vaccinology. A Support Vector Machines (SVM) based module for predicting bacterial lipoproteins, LIPOPREDICT, has been developed. The best performing sequence model were generated using selected dipeptide composition, which gave 97% accuracy of prediction. The results obtained were compared very well with those of previously developed methods.     

Genetic differentiation of wild and cultivated Lens based on molecular markers

Genetic diversity among 83 lentil genotypes including 23 wild types, 19 indigenous varieties, 5 exotic lines and 36 advanced breeding lines was studied using molecular markers. A total of 112 amplicons were produced using 15 RAPD and 8 SSR markers. Dendrogram based on Jaccard similarity coefficient and UPGMA analysis revealed two major clusters and one minor cluster. Cluster I comprised 21 wild accessions of L. orientalis and 1 L. ervoides subspecies. Nineteen Indian varieties grouped together in subcluster IIA indicating their narrow genetic base. Subcluster IIB consisted of 41 genotypes including 5 exotic and 36 advanced breeding lines mainly derived from exotic genotypes. The narrow genetic base of released cultivars and germplasm lines emphasized the need for broadening of genetic base of breeding material using exotic collections and wild species to ascertain genetic improvement upon existing cultivars.     

Identification and annotation of abiotic stress responsive candidate genes in peanut ESTs

Peanut (Arachis hypogaea L.) ranks fifth among the world oil crops and is widely grown in India and neighbouring countries. Due to its large and unknown genome size, studies on genomics and genetic modification of peanut are still scanty as compared to other model crops like Arabidopsis, rice, cotton and soybean. Because of its favourable cultivation in semi-arid regions, study on abiotic stress responsive genes and its regulation in peanut is very much important. Therefore, we aim to identify and annotate the abiotic stress responsive candidate genes in peanut ESTs. Expression data of drought stress responsive corresponding genes and EST sequences were screened from dot blot experiments shown as heat maps and supplementary tables, respectively as reported by Govind et al. (2009). Some of the screened genes having no information about their ESTs in above mentioned supplementary tables were retrieved from NCBI. A phylogenetic analysis was performed to find a group of utmost similar ESTs for each selected gene. Individual EST of the said group were further searched in peanut ESTs (1,78,490 whole EST sequences) using stand alone BLAST. For the prediction as well as annotation of abiotic stress responsive selected genes, various tools (like Vec-Screen, Repeat Masker, EST-Trimmer, DNA Baser, WISE2 and I-TASSER) were used. Here we report the predicted result of Contigs, domain as well as 3D structure for HSP 17.3KDa protein, DnaJ protein and Type 2 Metallothionein protein.