Dynamics of viable nitrifier community and nutrient availability in dry tropical forest habitat as affected by cultivation and soil texture

Seasonal dynamics of N-mineralization and the size of the viable community of nitrifying bacteria were studied for a forest site and an adjoining cropland site. The forest site was dominated by Boswellia serrata and Acacia catechu in the tree layer, and by Nyctanthes arbortristis and Zizyphus glaberrima in the shrub layer. Crop sequence on the cropland site was Oryza sativa/Lens culinaris. The soil type in both the sites was ultisol (USDA). The cropland soil had significantly higher bulk density, and clay content but lower organic C, total N and total P than forest soil. The soil moisture content, numbers of ammonia-and nitrite oxidizing bacteria and N-mineralization rates were highest in the wet season and lowest in the dry season, while the size of mineral N and P pools showed a reverse trend in both sites. The numbers of free-living cells of ammonia-and nitrite oxidizing bacteria were significantly related with each other as well as with the soil moisture content and N-mineralization rates. In N-mineralization, NO ₃ ^– was the dominating form in the forest site during rainy season, while in other seasons in this site and in all the seasons in the cropland site, NH ₄ ⁺ -N was predominant. The N-mineralization rate and the number of viable nitrifying cells were consistently higher for the forest soil compared to the clay-rich cropland soil. The combination of low soil organic matter and high clay content suppressed the number of free-living cells of nitrifying bacteria and N-mineralization rates in the cropland site.     

Isolation and Characterization of Antidermatophytic Bioactive Molecules from Piper longum L. Leaves

Piper longum L. (Piperaceae) commonly known as “long pepper” is a well known medicinal plant in ayurveda. Different parts of this plant, such as root, seed, fruit, whole plant etc. are used traditionally in various ailments. Here we have investigated the antidermatophytic activity of sequentially extracted petroleum ether, chloroform, methanol and water extracts from P. longum leaf against Trichophytonmentagrophytes, T. rubrum, T. tonsurans, Microsporum fulvum and M. gypseum. Better activity of chloroform and methanol extracts was observed. The chloroform extract was selected for further study and the MIC value was recorded as 5.0 mg ml⁻¹ against the test organisms. In the chloroform extract, tannins and phenolic compounds were detected. Further activity-guided fractionation of chloroform extract by silica gel column chromatography yielded nine major fractions. Among these, fraction-1, 4, 5 and 7 showed higher antidermatophytic activity. Fraction-4 on further purification by repeated column chromatography yielded a potential antidermatophytic fraction showing MIC value of 0.625 mg ml⁻¹ against T. mentagrophytes and T. rubrum as determined by broth microdilution method. The major compounds were identified as 1,2-benzenedicarboxylic acid, bis(2-ethylhexyl) ester (C₂₄H₃₈O₄] (41.45 %), 2,2-dimethoxybutane (C₆H₁₄O₂] (13.6 %) and β-myrcene (C₁₀H₁₆) (6.75 %) based on GC–MS data.     

Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome

Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the Bacteroidetes, fail to recognize the SD sequence of mRNA in vitro. A cryo-electron microscopy structure of the complete 70S ribosome from F. johnsoniae at 2.8 Å resolution reveals that the ASD is sequestered by ribosomal proteins bS21, bS18 and bS6, explaining the basis of ASD inhibition. The structure also uncovers a novel ribosomal protein—bL38. Remarkably, in F. johnsoniae and many other Flavobacteriia, the gene encoding bS21 contains a strong SD, unlike virtually all other genes. A subset of Flavobacteriia have an alternative ASD, and in these organisms the fully complementary sequence lies upstream of the bS21 gene, indicative of natural covariation. In other Bacteroidetes classes, strong SDs are frequently found upstream of the genes for bS21 and/or bS18. We propose that these SDs are used as regulatory elements, enabling bS21 and bS18 to translationally control their own production.     

Cloning and functional expression of an acyl-ACP thioesterase FatB type from Diploknema (Madhuca) butyracea seeds in Escherichia coli

A cDNA of fatty acyl-acyl carrier protein (ACP) thioesterase (Fat) from developing seed of Madhuca butyracea has been cloned. The deduced amino acid sequence of the cDNA corresponding to the mature polypeptide showed 30-40% and 60-75% identity to the reported FatA and FatB class of plant thioesterases, respectively. This gene, MbFatB, is present as a single copy in M. butyracea genome and the MbFatB protein was detected clearly in seed tissues of this plant but not in that of Indian mustard (Brassica juncea). Heterologous expression of the MbFatB gene driven by different promoters in E. coli wild type and fatty acid beta-oxidation mutant (fadD88) strains resulted production of the recombinant protein with various fusion tags either as biologically inactive (insoluble) or functionally active forms. Expression of functionally active recombinant MbFatB in E. coli affected bacterial growth and cell morphology as well as changed the fatty acid profiles of the membrane lipid and the culture supernatant. Alteration of the fatty acid composition was directed predominantly towards palmitate and to a lesser extent myristate and oleate due to acyl chain termination activity of plant thioesterase in bacteria. Thus, this new MbFatB gene isolated from a non-traditional oil-seed tree can be used in future for transgenic development of oil-seed Brassica, a widely cultivated crop that expresses predominantly oleoyl-ACP thioesterase (FatA) in its seed tissue and has high amount of unwanted erucic acid in edible oil in order to alter the fatty acid profile in a desirable way.     

Structural exploration of tetrahydroisoquinoline derivatives as HDAC8 inhibitors through multi-QSAR modeling study

Abstract

Histone deacetylase 8 (HDAC8) is one of the crucial HDACs responsible for influencing the epigenetic functions of the body. Overexpression of HDAC8 is found to be involved in numerous disease conditions such as tumorigenesis, cell proliferation, cancer, viral infections, neuronal disorders and other epigenetic diseases. Therefore, inhibition of HDAC8 is a primary method to combat these diseases. In this article, a multi-QSAR modeling study on tetrahydroisoquinoline derivatives was conducted to identify important contributions of the structural features of these compounds toward HDAC8 inhibition. All these QSAR modeling techniques were individually validated and justified the observations of each other. The results implied that the tetrahydroisoquinoline moiety may be effective as a cap group than as a linker moiety for HDAC8 inhibition. Different substitutions at the tetrahydroisoquinoline scaffold were also found to be crucial in modulating HDAC8 inhibition.

Communicated by Ramaswamy H. Sarma     

An epi(c)genetic war: Pathogens,cancer and human genome

Cancer is characterized by inter- and intra-tumor heterogeneity and this is also observed in the context of cancers caused by pathogens. Nearly 20% of all cancers are attributable to pathogenic organisms. Pathogenic infections result in deregulation of gene expression both by genetic and epigenetic mechanisms, thereby causing malignant transformation. Another characteristic of pathogen-induced cancers is the occurrence of chronic inflammation due to activation of the innate and adaptive arms of the immune system. This review focuses on the epigenetic changes induced by oncoviruses, parasites, cancer-causing bacteria and ‘endogenous pathogens’ to trigger host cell proliferation indefinitely as well as the inflammation associated with pathogen-induced cancers. The opportunity of targeting components of both pathogen and host epigenetic machinery to limit tumor progression is also discussed.     

Shoot Na+ Exclusion and Increased Salinity Tolerance Engineered by Cell Type–Specific Alteration of Na+ Transport in Arabidopsis

Soil salinity affects large areas of cultivated land, causing significant reductions in crop yield globally. The Na⁺ toxicity of many crop plants is correlated with overaccumulation of Na⁺ in the shoot. We have previously suggested that the engineering of Na⁺ exclusion from the shoot could be achieved through an alteration of plasma membrane Na⁺ transport processes in the root, if these alterations were cell type specific. Here, it is shown that expression of the Na⁺ transporter HKT1;1 in the mature root stele of Arabidopsis thaliana decreases Na⁺ accumulation in the shoot by 37 to 64%. The expression of HKT1;1 specifically in the mature root stele is achieved using an enhancer trap expression system for specific and strong overexpression. The effect in the shoot is caused by the increased influx, mediated by HKT1;1, of Na⁺ into stelar root cells, which is demonstrated in planta and leads to a reduction of root-to-shoot transfer of Na⁺. Plants with reduced shoot Na⁺ also have increased salinity tolerance. By contrast, plants constitutively expressing HKT1;1 driven by the cauliflower mosaic virus 35S promoter accumulated high shoot Na⁺ and grew poorly. Our results demonstrate that the modification of a specific Na⁺ transport process in specific cell types can reduce shoot Na⁺ accumulation, an important component of salinity tolerance of many higher plants.     

DIRECTIONAL AND STABILIZING DENSITY-DEPENDENT NATURAL SELECTION FOR PUPATION HEIGHT IN DROSOPHILA MELANOGASTER

Six populations of Drosophila melanogaster have been kept at extreme population densities, three high and three low, for 175 generations. Larvae from the high density populations pupate 50%-100% higher than larvae from the low density populations. At high larval test densities there is both a directional and a stabilizing component to selection, with viabilities ranging from 0.14 to 0.992, depending on the choice of pupation site. The directional component is stronger on the populations which have evolved at low densities, while the stabilizing component is stronger on the populations which have evolved at high densities. There is no indication that the evolution of this trait, in response to density, has altered its phenotypic plasticity.