Influence of different Sinorhizobium meliloti inocula on abundance of genes involved in nitrogen transformations in the rhizosphere of alfalfa (Medicago sativa L.)

Inoculation of leguminous seeds with selected rhizobial strains is practised in agriculture to ameliorate the plant yield by enhanced root nodulation and nitrogen uptake of the plant. However, effective symbiosis between legumes and rhizobia does not only depend on the capacity of nitrogen fixation but also on the entire nitrogen turnover in the rhizosphere. We investigated the influence of seed inoculation with two indigenous Sinorhizobium meliloti strains exhibiting different efficiency concerning plant growth promotion on nitrogen turnover processes in the rhizosphere during the growth of alfalfa. Quantification of six target genes (bacterial amoA, nirK, nirS, nosZ, nifH and archaeal amoA) within the nitrogen cycle was performed in rhizosphere samples before nodule formation, at bud development and at the late flowering stage. The results clearly demonstrated that effectiveness of rhizobial inocula is related to abundance of nifH genes in the late flowering phase of alfalfa. Moreover, other genes involved in nitrogen turnover had been affected by the inocula, e.g. higher numbers of amoA copies were observed during flowering when the more effective strain had been inoculated. However, the respective gene abundances differed overall to a greater extent between the three plant development stages than between the inoculation variants.     

Genetic control of the immune response to ferredoxin: linkage and mapping of T cell proliferation and antibody production genes to the MHC of mice

The genetics of the immune response in the mouse were studied by using the antigenically simple, stable, naturally occurring protein ferredoxin (Fd) from Clostridium pasteurianum. The immune status of mice primed and boosted with Fd was assessed by using two parameters of immunity: T cell proliferation and serum antibody production with the ELISA method. In both assay systems, the response has been shown to be H-2 linked: k, b, and s haplotypes respond to Fd, and H-2d mice are nonresponders. It is apparent that different immunoregulatory events modulate the response in the responder strains; these factors become evident in the recombinant analysis of the response and to date an immunoregulatory gene(s) has been mapped to at least the K/I-A subregions. F1 analysis demonstrated a gene dose-dependent response of the strains studied.     

Molecular Typing of Lung Adenocarcinoma on Cytological Samples Using a Multigene Next Generation Sequencing Panel

Identification of driver mutations in lung adenocarcinoma has led to development of targeted agents that are already approved for clinical use or are in clinical trials. Therefore, the number of biomarkers that will be needed to assess is expected to rapidly increase. This calls for the implementation of methods probing the mutational status of multiple genes for inoperable cases, for which limited cytological or bioptic material is available. Cytology specimens from 38 lung adenocarcinomas were subjected to the simultaneous assessment of 504 mutational hotspots of 22 lung cancer-associated genes using 10 nanograms of DNA and Ion Torrent PGM next-generation sequencing. Thirty-six cases were successfully sequenced (95%). In 24/36 cases (67%) at least one mutated gene was observed, including EGFR, KRAS, PIK3CA, BRAF, TP53, PTEN, MET, SMAD4, FGFR3, STK11, MAP2K1. EGFR and KRAS mutations, respectively found in 6/36 (16%) and 10/36 (28%) cases, were mutually exclusive. Nine samples (25%) showed concurrent alterations in different genes. The next-generation sequencing test used is superior to current standard methodologies, as it interrogates multiple genes and requires limited amounts of DNA. Its applicability to routine cytology samples might allow a significant increase in the fraction of lung cancer patients eligible for personalized therapy.     

Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain <1% endogenous DNA, with the majority of sequencing capacity taken up by environmental DNA. Here we present a capture-based method for enriching the endogenous component of aDNA sequencing libraries. By using biotinylated RNA baits transcribed from genomic DNA libraries, we are able to capture DNA fragments from across the human genome. We demonstrate this method on libraries created from four Iron Age and Bronze Age human teeth from Bulgaria, as well as bone samples from seven Peruvian mummies and a Bronze Age hair sample from Denmark. Prior to capture, shotgun sequencing of these libraries yielded an average of 1.2% of reads mapping to the human genome (including duplicates). After capture, this fraction increased substantially, with up to 59% of reads mapped to human and enrichment ranging from 6- to 159-fold. Furthermore, we maintained coverage of the majority of regions sequenced in the precapture library. Intersection with the 1000 Genomes Project reference panel yielded an average of 50,723 SNPs (range 3,062–147,243) for the postcapture libraries sequenced with 1 million reads, compared with 13,280 SNPs (range 217–73,266) for the precapture libraries, increasing resolution in population genetic analyses. Our whole-genome capture approach makes it less costly to sequence aDNA from specimens containing very low levels of endogenous DNA, enabling the analysis of larger numbers of samples.     

Properties and Nematicide Performance of Avermectins

In 1979, the anthelmintic activity of abamectin, a mixture of avermectins B_1a and B_1b, was first reported. Since then, multiple articles have investigated avermectins' degradation and its efficacy against a wide variety of pests under different conditions and using different modes of application. However, there is a gap in the literature of analysing abamectin properties and its performance as a non‐fumigant nematicide when applied liquid or granular vs. new avenues of application based on seed and seedling treatment. Therefore, this article reviewed literature to discuss the mode of action, environmental aspects, the nematicidal effectiveness of treatment forms and the range of activity to address these topics.     

Estimating Encounter Rates and Densities of Three Lemur Species in Northeastern Madagascar

Primate populations, including Madagascar’s lemurs, are threatened worldwide and conservationists need accurate population estimates to develop targeted conservation plans. We sought to fill knowledge gaps for three lemur taxa —white-fronted brown lemur (Eulemur albifrons); eastern woolly lemur (Avahi laniger); and Allocebus/Microcebus, a category combining observations of hairy-eared dwarf lemurs (Allocebus trichotis) and mouse lemurs (Microcebus spp.)— in northeastern Madagascar by estimating their density, examining how their encounter rates and densities vary across three different forest types, and monitoring trends in encounter rates and densities at resurveyed sites, using data from surveys at six forest sites over a 4-year period (2010–2013). Landscape density for white-fronted brown lemur, eastern woolly lemur, and Allocebus/Microcebus was 21.5 (SE 3.67), 57.7 (SE 9.17), and 39.1 (SE 9.55) individuals/km², respectively. There was no difference in density estimates at intact and intermediately degraded forest sites; however, we encountered white-fronted brown lemurs more often in intact forest (1.64 ± SE 0.40 individuals/km) than in intermediately degraded and degraded forest (0.15 ± SE 0.06 and 0.16 ± SE 0.06 individuals/km). In addition, we encountered white-fronted brown lemurs at lower rates in 2013 (0.15 ± SE 0.06 individuals/km) compared to 2010 (0.82 ± SE 0.12 individuals/km) at a resurveyed site. Our findings emphasize that primate researchers must account for variation in how lemur encounter rates and densities differ between intact and degraded forests, and although we observed a decline in white-fronted brown lemur encounter rate at our resurveyed site, we caution that changes in lemur encounter rates may simply reflect lower detection rates rather than lower density. Future research should focus on using conventional distance sampling techniques, which are infrequently used in primate studies, to provide more robust density estimates as a way to accurately assess trends and the effects of anthropogenic pressures on lemur populations.     

Music of metagenomics—a review of its applications,analysis pipeline,and associated tools

Functional & Integrative Genomics - This humble effort highlights the intricate details of metagenomics in a simple, poetic, and rhythmic way. The paper enforces the significance of the...     

Phosphate solubilizing bacteria enhanced growth,oil yield,antioxidant properties and biodiesel quality of Kasumbha

Biodiesel is considered as a potential alternative energy source, but problem exists with the quantity and quality of feedstock used for it. To improve the feedstock quality of biodiesel, a field experiment was conducted under natural conditions. Cultivar Thori of kasumbha was used in the experiment. Commercialized biofertilizers were applied at the rate of 20 kg per acre and chemical fertilizer (diammonium phosphate) was applied as half dose (15 kg/ha). Results indicated that number of leaf plant⁻¹, leaf area, number of seeds capitulum⁻¹ was significantly increased by biofertilizer treatment alone (BF) and combine treatment of biofertilizer and chemical fertilizer (BFCF). Agronomic traits such as plant height, no. of branches of a plant, no. of capitulum/plant was improved significantly by BF treatment over the control. Maximum 1000 seed weight (41%) and seed yield (23%) were recorded in half dose of chemical fertilizers treatment (CFH). Seed oil content and seed phenolics were significantly improved by BF and CF treatments while maximum biodiesel yield was recorded by BF treatment. Maximum oleic acid was recorded by BF treatment while other fatty acids being maximum in control except linoleic acid in BFCF treatment. Results for specific gravity were non-significant while acid value and free fatty acid contents were substantially reduced by BF treatment as compared to other treatments. Maximum value of iodine number was recorded in BFCF treatment while tocopherol contents were improved by BF treatment. It is inferred that biofertilizer treatment alone perform better as compared to other treatments and 50% chemical fertilizer can be replaced using biofertilizer which is a good approach for sustainable environmental-friendly agriculture.Keyword: Green energy, Biofuel, Biodiesel, Kasumbha, Biofertilizers, Fatty acid, NMR     

Lung carcinoids. Tumor angiogenesis in relation to clinicopathologic characteristics

OBJECTIVE: To evaluate the prognostic value of carcinoid angiogenesis for the presence of lymph node metastases, histologic subtype and tumor size. STUDY DESIGN: The study group consisted of 72 resected primary lung carcinoids, 57 typical and 15 atypical. TNM staging was performed. The histologic criteria for carcinoids was based on the Flieder classification. Angiogenesis, expressed as tumor microvessel density, was estimated in sections stained with CD34 antibody, according to Weidner's method. RESULTS: The size of carcinoids was related to the histologic type: the average tumor diameter of typical carcinoids was significantly smaller than the average diameter of atypical carcinoids (P = .003, U = 207, Z = -3.023). Atypical carcinoids represented a more aggressive form of tumors than typical carcinoids; patients with typical carcinoids developed lymph node metastases less frequently (10% vs. 33%) as compared to patients with atypical carcinoids; the difference was statistically significant (P = .032). Tumor angiogenesis failed to distinguish the histologic type of carcinoids and did not indicate the presence or absence of regional lymph node metastases; neither did pTN stage or tumor size. CONCLUSION: Angiogenesis is not a determining factor of the metastatic potential of pulmonary carcinoids.