PCR amplification of DNA sequence related to the hrpD gene of Xanthomonas cucurbitae in leaf spot disease of pumpkin and their antagonism by soil bacteria

A sensitive and specific assay was developed to detect and biological control of bacterial leaf spot of pumpkin, Xanthomonas cucurbitae was identified on the basis of the morphological, biochemical and molecular assay. The antibiotic sensitivity of the isolate showed that, Carbenicillin revealed highest antibacterial activity with 29 ± 0.00 mm zone of inhibition against isolated bacterial strain. Isolated bacterial strains from soil were also identified by biochemical and molecular characterisation. By analysing morphological and biochemical characteristics and 16S rDNA of three bacterial strains isolated from soil was matched 96% with Bacillus subtilis, 98% with Bacillus brevis and 97% with Pseudomonas fluorescens strain. They were subjected to the antagonistic activity against Xanthomonas cucurbitae by disc diffusion method. Among them, B. subtilis showed significant positive antagonistic activity with 17.0 ± 0.28 mm zone of inhibition against Xanthomonas cucurbitae. The presence of DNA sequence related to the hrpD gene successfully amplified in some isolates of Xanthomonas cucurbitae.     

Gut microbiota composition is associated with environmental landscape in honey bees

There is growing recognition that the gut microbial community regulates a wide variety of important functions in its animal hosts, including host health. However, the complex interactions between gut microbes and environment are still unclear. Honey bees are ecologically and economically important pollinators that host a core gut microbial community that is thought to be constant across populations. Here, we examined whether the composition of the gut microbial community of honey bees is affected by the environmental landscape the bees are exposed to. We placed honey bee colonies reared under identical conditions in two main landscape types for 6 weeks: either oilseed rape farmland or agricultural farmland distant to fields of flowering oilseed rape. The gut bacterial communities of adult bees from the colonies were then characterized and compared based on amplicon sequencing of the 16S rRNA gene. While previous studies have delineated a characteristic core set of bacteria inhabiting the honey bee gut, our results suggest that the broad environment that bees are exposed to has some influence on the relative abundance of some members of that microbial community. This includes known dominant taxa thought to have functions in nutrition and health. Our results provide evidence for an influence of landscape exposure on honey bee microbial community and highlight the potential effect of exposure to different environmental parameters, such as forage type and neonicotinoid pesticides, on key honey bee gut bacteria. This work emphasizes the complexity of the relationship between the host, its gut bacteria, and the environment and identifies target microbial taxa for functional analyses.     

Tyrosine phosphorylation directs TACE into extracellular vesicles via unconventional secretion

When studying how HIV‐1 Nef can promote packaging of the proinflammatory transmembrane protease TACE (tumor necrosis factor‐α converting enzyme) into extracellular vesicles (EVs) we have revealed a novel tyrosine kinase‐regulated unconventional protein secretion (UPS) pathway for TACE. When TACE was expressed without its trafficking cofactor iRhom allosteric Hck activation by Nef triggered translocation of TACE into EVs. This process was insensitive to blocking of classical secretion by inhibiting endoplasmic reticulum (ER) to Golgi transport, and involved a distinct form of TACE devoid of normal glycosylation and incompletely processed for prodomain removal. Like most other examples of UPS this process was Golgi reassembly stacking protein (GRASP)‐dependent but was not associated with ER stress. These data indicate that Hck‐activated UPS provides an alternative pathway for TACE secretion that can bypass iRhom‐dependent ER to Golgi transfer, and suggest that tyrosine phosphorylation might have a more general role in regulating UPS.      

Assessment of the inhibitory effects and molecular docking of some sulfonamides on human serum paraoxonase 1

Paraoxonase‐1 (PON1) is an organophosphate hydrolyzer and antiatherogenic enzyme. Due to the PON1's crucial functions, inhibitors and activators of PON1 must be known for pharmacological applications. In this study, we investigated the in vitro effects of some sulfonamides compounds on human serum PON1 (hPON1). For this aim, we purified the hPON1 from human serum with high specific activity by using simple chromatographic methods, and after the purification processes, we investigated in vitro interactions between the enzyme and some sulfonamides (2‐amino‐5‐methyl‐1,3‐benzenedisulfonamide, 2‐chloro‐4‐sülfamoilaniline, 4‐amino‐3‐methylbenzenesulfanilamide, sulfisoxazole, sulfisomidine, and 5‐amino‐2‐methylbenzenesulfonamide). IC₅₀, K_i values, and inhibition types were calculated for each sulfonamide. 2‐amino‐5‐methyl‐1,3‐benzenedisulfonamide and 2‐chloro‐4‐sülfamoilaniline exhibited noncompetitive inhibition effect, whereas 4‐amino‐3‐methylbenzenesulfanilamide, sulfisoxazole, and sulfisomidine exhibited mixed type inhibition. On the other hand, 5‐amino‐2‐methylbenzenesulfonamide showed competitive inhibition and so molecular docking studies were performed for this compound in order to assess the probable binding mechanism into the active site of hPON1.     

Identification of marker genes in Alzheimer's disease using a machine-learning model

Alzheimer''s Disease (AD) is one of the most common causes of dementia, mostly affecting the elderly population. Currently, there is no proper diagnostic tool or method available for the detection of AD. The present study used two distinct data sets of AD genes, which could be potential biomarkers in the diagnosis. The differentially expressed genes (DEGs) curated from both datasets were used for machine learning classification, tissue expression annotation and co-expression analysis. Further, CNPY3, GPR84, HIST1H2AB, HIST1H2AE, IFNAR1, LMO3, MYO18A, N4BP2L1, PML, SLC4A4, ST8SIA4, TLE1 and N4BP2L1 were identified as highly significant DEGs and exhibited co-expression with other query genes. Moreover, a tissue expression study found that these genes are also expressed in the brain tissue. In addition to the earlier studies for marker gene identification, we have considered a different set of machine learning classifiers to improve the accuracy rate from the analysis. Amongst all the six classification algorithms, J48 emerged as the best classifier, which could be used for differentiating healthy and diseased samples. SMO/SVM and Logit Boost further followed J48 to achieve the classification accuracy.     

新疆块根芍药(Paeonia anomala)内生细菌XJU-PA-1的鉴定及特性分析

目的:从新疆块根芍药(Paeonia anomala)内生菌中筛选出1株对植物病原菌有抑菌活性的内生菌并对其进行鉴定及特性分析.方法:采用琼脂扩散法进行抑菌实验,基于形态特征,生理生化特性,16S rDNA序列分析并G+C mol%含量对XJU-PA-1进行鉴定.结果:XJU-PA-1对玉米小班病菌和苹果半点落叶病菌有抑菌活性,抑菌圈直径都超过20mm.XJU-PA-1与DQ010109 Bacillus subtilis的16S rDNA序列的同源性达到100%,G+Cmol%含量为54.5%.结论:XJU-PA-1对两种致病菌有较强的抑菌能力,被鉴定为枯草芽孢杆菌(Bacillus subtilis) ,在GenBank数据库的注册号为EU741698.     

In vivo sequence variability of human immunodeficiency virus type 1 envelope gp120: association of V2 extension with slow disease progression.

According to the rate of depletion of CD4 cell counts, we grouped 12 cases of human immunodeficiency virus type 1 (HIV-1) infection as 6 rapid (21.0 to 33.8 cells per microl per month) and 6 slow (0.9 to 7.9 cells per microl per month) progressors and determined the individual viral quasispecies patterns by sequencing the genome region encoding the V1, V2, and V3 loops of envelope protein. Although the quasispecies structures varied widely from one individual to another, a strong correlation was observed between a low rate of disease progression and a high degree of genetic diversity of HIV-1. Furthermore, the V2 loop extension was observed specifically in individuals with slow or no disease progression, whereas basic amino acid substitutions in V3 characteristic of a viral phenotype shift from non-syncytium inducing to syncytium inducing were observed in patients with advanced stages of disease regardless of their rate of disease progression. Studies with recombinant viruses suggested that elongation of V2 potentially restricts the capacity of HIV-1 to replicate in macrophages. Thus, our results suggest the association of distinct sequence features of both V3 and V2 with particular patterns of disease progression. Elongation of the V2 loop may be a good predictor of slow disease progression, while basic substitutions of V3 without elongation of V2 are characteristic of rapid progression.     

Glucose deprivation induced upregulation of phosphoenolpyruvate carboxykinase modulates virulence in Leishmania donovani

Various physiological stimuli trigger the conversion of noninfective Leishmania donovani promastigotes to the infective form. Here, we present the first evidence of the effect of glucose starvation, on virulence and survival of these parasites. Glucose starvation resulted in a decrease in metabolically active parasites and their proliferation. However, this was reversed by supplementation of gluconeogenic amino acids. Glucose starvation induced metacyclogenesis and enhanced virulence through protein kinase A regulatory subunit (LdPKAR1) mediated autophagy. Glucose starvation driven oxidative stress upregulated the antioxidant machinery, culminating in increased infectivity and greater parasitic load in primary macrophages. Interestingly, phosphoenolpyruvate carboxykinase (LdPEPCK), a gluconeogenic enzyme, exhibited the highest activity under glucose starvation to regulate growth of L. donovani by alternatively utilising amino acids. Deletion of LdPEPCK (Δpepck) decreased virulent traits and parasitic load in primary macrophages but increased autophagosome formation in the mutant parasites. Furthermore, Δpepck parasites failed to activate the Pentose Phosphate Pathway shunt, abrogating NADPH/NADP⁺ homoeostasis, conferring increased susceptibility towards oxidants following glucose starvation. In conclusion, this study showed that L. donovani undertakes metabolic rearrangements via gluconeogenesis under glucose starvation for acquiring virulence and its survival in the hostile environment.