<Emphasis Type="Italic">Argonaute-2-</Emphasis>null embryonic stem cells are retarded in self-renewal and differentiation

RNA interference (RNAi) pathways regulate self-renewal and differentiation of embryonic stem (ES) cells. Argonaute 2 (Ago2) is a vital component of RNA-induced silencing complex (RISC) and the only Ago protein with slicer activity. We generated Ago2-deficient ES cells by conditional gene targeting. Ago2-deficient ES cells are defective in the small-RNA-mediated gene silencing and are significantly compromised in biogenesis of mature microRNA. The self-renewal rate of Ago2-deficient ES cells is affected due to failure of silencing of Cdkn1a by ES-cell-specific microRNAs (miRNA) in the absence of Ago2. Interestingly, unlike Dicer- and Dgcr8-deficient ES cells, they differentiate to all three germ layers both in vivo and in vitro. However, early differentiation of Ago2-deficient ES cells is delayed by 2–4 days as indicated by persistence of higher levels of self-renewal/ pluripotency markers during differentiation. Further, appearance of morphological and differentiation markers is also delayed during the differentiation. In this study we show that Ago2 is essential for normal self-renewal and differentiation. Also, our data suggest that self-renewal and differentiation of ES cells are regulated by both siRNA and miRNA pathways.     

Selective constraints in yeast genes with differential expressivity: codon pair usage and mRNA stability perspectives

Protein translation has been elucidated to be dictated by evolutionary constraints, namely, variations in tRNA availabilities and/or variations in codon-anticodon binding that is manifested in biased codon usage. Taking advantage of publicly available mRNA expression and protein abundance data for Saccharomyces cerevisiae, we have performed a comprehensive analysis of the diverse factors guiding translation leading to desired protein levels irrespective of the corresponding high or low mRNA levels. It has been elucidated in this study that different combinations of most abundant/non abundant tRNA isoacceptors are selected for in S. cerevisiae that helps in achieving the optimum speed and accuracy in the protein translation process. This is also accompanied by the strategic location of codon pairs in coherence to mRNA secondary structure folding stability for the above mentioned combinations of tRNA isoacceptors. We thus find that codon pair contextual effects; in addition to tRNA abundance and mRNA folding stability during translation elongation process play plausible roles in maintaining translation accuracy and speed that can achieve desired protein levels.     

Phenotypic and genetic characterization of rhizobia associated with alfalfa in the Hokkaido and Ishigaki regions of Japan

Twenty five rhizobial isolates were obtained from root nodules of Medicago sativa inoculated with soil samples collected from the Sapporo region and Ishigaki Island in Japan. To study their diversity and characterize them in relation to the climatic conditions of their soils of origin, a polyphasic approach analyzing stress tolerance, symbiotic and genetic properties was used. Stress tolerance assays revealed marked variations in salinity, pH and temperature tolerance. Isolates originating from a sub-tropical climate in alkaline soil (Ishigaki Island) tolerated high temperature, salinity and pH levels. Moreover, isolates recovered from a temperate climate in acidic soil (Sapporo) were sensitive to high temperature and salinity, and tolerated acidic pH. Phylogenetic analysis of conserved 16S rRNA and recA genes, and symbiotic nodA and nifDK revealed 25 isolates to be closely related to Ensifer meliloti. Furthermore, the branch patterns of phylogenetic trees constructed from different genes revealed the existence of at least two E. meliloti types in the soils studied. These results may be relevant to programs directed towards improving crop productivity through biofertilization with locally adapted and genetically defined strains.     

Effect of controlled inoculation with specific mycorrhizal fungi from the urban environment on growth and physiology of containerized shade tree species growing under different water regimes

The aim of this work was to evaluate the effects of selected mycorrhiza obtained in the urban environment on growth, leaf gas exchange, and drought tolerance of containerized plants growing in the nursery. Two-year-old uniform Acer campestre L., Tilia cordata Mill., and Quercus robur L. were inoculated with a mixture of infected roots and mycelium of selected arbuscular (maple, linden) and/or ectomycorrhiza (linden, oak) fungi and grown in well-watered or water shortage conditions. Plant biomass and leaf area were measured 1 and 2 years after inoculation. Leaf gas exchange, chlorophyll fluorescence, and water relations were measured during the first and second growing seasons after inoculation. Our data suggest that the mycelium-based inoculum used in this experiment was able to colonize the roots of the tree species growing in the nursery. Plant biomass was affected by water shortage, but not by inoculation. Leaf area was affected by water regime and, in oak and linden, by inoculation. Leaf gas exchange was affected by inoculation and water stress. V _cmax and J _max were increased by inoculation and decreased by water shortage in all species. F _v/F _m was also generally higher in inoculated plants than in control. Changes in PSII photochemistry and photosynthesis may be related to the capacity of inoculated plants to maintain less negative leaf water potential under drought conditions. The overall data suggest that inoculated plants were better able to maintain physiological activity during water stress in comparison to non-inoculated plants.     

Isolation and characterization of rhizobacteria associated with coastal agricultural ecosystem of rhizosphere soils of cultivated vegetable crops

In this study, a total of 80 rhizobacteria was isolated from coastal agricultural ecosystem of cultivated vegetable rhizosphere soils. The isolates were screened for antagonistic activity against Sclerotium rolfsii and Colletotrichum capsici and plant growth promoting traits. The results revealed that 15.0 and 43.7% isolates showed statistically significant inhibition of mycelial growth of S. rolfsii and C. capsici respectively, while 48.7% isolates produced siderophore, 57.5% isolates solubilized phosphate and 21.1% isolates produced indole-3-acetic acid more than 20 μg/mL. However, only three isolates PfS1, PfR2 and BL5 were found positive to all properties tested. The identification of potential bacterial isolates through Microbial Identification System (BIOLOG) and 16S rDNA sequencing of the isolates revealed Bacillus species were dominant in the cultivated vegetable rhizosphere soil of Neil and Havelock Islands, India.     

Bacterial decolorization and detoxification of black liquor from rayon grade pulp manufacturing paper industry and detection of their metabolic products

This study deals with the decolorization of black liquor (BL) by isolated potential bacterial consortium comprising Serratia marcescens (GU193982), Citrobacter sp. (HQ873619) and Klebsiella pneumoniae (GU193983). The decolorization of BL was studied by using the different nutritional as well as environmental parameters. In this study, result revealed that the ligninolytic activities were found to be growth associated and the developed bacterial consortium was efficient for the reduction of COD, BOD and color up to 83%, 74% and 85%, respectively. The HPLC analysis of degraded samples of BL has shown the reduction in peak area compared to control. Further, the GC-MS analysis showed that, most of the compounds detected in control were diminished after bacterial treatment while, formic acid hydrazide, 4-cyclohexane-1,2-dicarboxylic acid, carbamic acid, 1,2-benzenedicarboxylic acid and erythropentanoic acid were found as new metabolites. Further, the seed germination test using Phaseolus aureus has supported the detoxification of bacterial decolorized BL.     

Insights into the molecular correlates modulating functional compensation between monogenic and polygenic disease gene duplicates in human

Functional redundancy by gene duplication appears to be a common phenomenon in biological system and hence understanding its underlying mechanism deserves much attention. Here, we investigated the differences between functional compensation of monogenic and polygenic disease genes which are unexplored till date. We found that the competence of functional buffering varies in the order of non-disease genes>monogenic disease genes>polygenic disease genes. This fact has been explained by the sequence identity, expression profile similarity, shared interaction partners and cellular locations between duplicated pairs. Moreover, we observed an inverse relationship between backup capacity and the non-synonymous substitution rate of disease and non-disease genes while the opposite trend is found for their corresponding paralogs. Logistic regression analysis among sequence identity, sharing of expression profile, interaction partners and cellular locations with backup capacity between duplicated pairs demonstrated that the sharing of expression profile is the most dominant regulator of backup capacity.