Virulence profile of different phylogenetic groups of locally isolated community acquired uropathogenic E. coli from Faisalabad region of Pakistan

ABSTRACT: BACKGROUND: Uropathogenic E.coli (UPEC) are among major pathogens causing urinary tract infections. Virulence factors are mainly responsible for the severity of these emerging infections. This study was planned to investigate the distribution of virulence genes and cytotoxic effects of UPEC isolates with reference to phylogenetic groups (B2, B1, D and A) to understand the presence and impact of virulence factors in the severity of infection in Faisalabad region of Pakistan. METHODS: In this study phylogenetic analysis, virulence gene identification and cytotoxicity of 59 uropathogenic E.coli isolates obtained from non-hospitalized patients was studied. RESULTS: Among 59 isolates, phylogenetic group B2 (50%) was most dominant followed by groups A, B1 (19% each) and D (12 %). Isolates present in group D showed highest presence of virulence genes. The prevalence hlyA (37%) was highest followed by sfaDE (27%), papC (24%), cnf1 (20%), eaeA (19%) and afaBC3 (14%). Highly hemolytic and highly verotoxic isolates mainly belonged to group D and B2. We also found two isolates with simultaneous presence of three fimbrial adhesin genes present on pap, afa, and sfa operons. This has not been reported before and underlines the dynamic nature of these UPEC isolates. CONCLUSIONS: It was concluded that in local UPEC isolates from non-hospitalized patients, group B2 was more prevalent. However, group D isolates were most versatile as all were equipped with virulence genes and showed highest level of cytotoxicity.     

Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome

? Premise of the study: Next-generation sequencing (NGS) technologies are frequently used for resequencing and mining of single nucleotide polymorphisms (SNPs) by comparison to a reference genome. In crop species such as chickpea (Cicer arietinum) that lack a reference genome sequence, NGS-based SNP discovery is a challenge. Therefore, unlike probability-based statistical approaches for consensus calling and by comparison with a reference sequence, a coverage-based consensus calling (CbCC) approach was applied and two genotypes were compared for SNP identification. ? Methods: A CbCC approach is used in this study with four commonly used short read alignment tools (Maq, Bowtie, Novoalign, and SOAP2) and 15.7 and 22.1 million Illumina reads for chickpea genotypes ICC4958 and ICC1882, together with the chickpea trancriptome assembly (CaTA). ? Key results: A nonredundant set of 4543 SNPs was identified between two chickpea genotypes. Experimental validation of 224 randomly selected SNPs showed superiority of Maq among individual tools, as 50.0% of SNPs predicted by Maq were true SNPs. For combinations of two tools, greatest accuracy (55.7%) was reported for Maq and Bowtie, with a combination of Bowtie, Maq, and Novoalign identifying 61.5% true SNPs. SNP prediction accuracy generally increased with increasing reads depth. ? Conclusions: This study provides a benchmark comparison of tools as well as read depths for four commonly used tools for NGS SNP discovery in a crop species without a reference genome sequence. In addition, a large number of SNPs have been identified in chickpea that would be useful for molecular breeding.     

Program death-1 engagement upon TCR activation has distinct effects on costimulation and cytokine-driven proliferation: attenuation of ICOS,IL-4, and IL-21, but not CD28, IL-7, and IL-15 responses

The program death 1 (PD-1) receptor and its ligands, PD-1 ligand (PD-L)1 and PD-L2, define a novel regulatory pathway with potential inhibitory effects on T, B, and monocyte responses. In the present study, we show that human CD4(+) T cells express PD-1, PD-L1, and PD-L2 upon activation, and Abs to the receptor can be agonists or antagonists of the pathway. Under optimal conditions of stimulation, ICOS but not CD28 costimulation can be prevented by PD-1 engagement. IL-2 levels induced by costimulation are critical in determining the outcome of the PD-1 engagement. Thus, low to marginal IL-2 levels produced upon ICOS costimulation account for the greater sensitivity of this pathway to PD-1-mediated inhibition. Interestingly, exogenous IL-2, IL-7, and IL-15 but not IL-4 and IL-21 can rescue PD-1 inhibition, suggesting that among these cytokines only those that activate STAT5 can rescue PD-1 inhibition. As STAT5 has been implicated in the maintenance of IL-2Ralpha expression, these results suggest that IL-7 and IL-15 restore proliferation under conditions of PD-1 engagement by enhancing high-affinity IL-2R expression and hence, IL-2 responsiveness.     

BAD,a Proapoptotic Protein,Escapes ERK/RSK Phosphorylation in Deguelin and siRNA-Treated HeLa Cells

This study has been undertaken to explore the therapeutic effects of deguelin and specific siRNAs in HeLa cells. The data provided clearly show the silencing of ERK 1/2 with siRNAs and inhibition of ERK1/2 with deguelin treatment in HeLa cells. Additionally, we are providing information that deguelin binds directly to anti-apoptotic Bcl-2, Bcl-xl and Mcl-1 in the hydrophobic grooves, thereby releasing BAD and BAX from dimerization with these proteins. This results in increased apoptotic activity through the intrinsic pathway involved in rupture of mitochondrial membrane and release of cytochrome C. Evidence for inhibition of ERK1/2 by deguelin and escape of BAD phosphorylation at serine 112 through ERK/RSK pathway has been further fortified by obtaining similar results by silencing ERK 1/2 each with specific siRNAs. Increase in BAD after treatment with deguelin or siRNAs has been interpreted to mean that deguelin acts through several alternative pathways and therefore can be used as effective therapeutic agent.     

Determination of bacterially derived auxins using a microplate method

Rapid and efficient methods for determining the ability of soil and rhizosphere bacteria to produce key metabolites which are useful in growth promotion or suppression of plant growth are needed. A microplate method was developed and compared to a standard method for assays of auxin compounds produced by bacteria. The microplate method was similar to the standard method in accuracy of determination, required less chemical reagents, and considerably reduced the time required for analyses.     

Estimation of Genetic Divergence and Character Association Studies in Local and Exotic Diversity Panels of Soybean (<i>Glycine max</i> L.) Genotypes

The availability of favorable genetic diversity is a thriving vitality for the success of a breeding program. It provides a firm basis of selecting superior breeding lines for the development of high yielding crop genotypes. In this context, present investigation aimed to generate information on genetic divergence and character association in a diversity panel of 123 local and exotic soybean genotypes. Analysis of variance revealed significant response of the evaluated genotypes based on studied attributes. It depicted the probability of selecting desirable soybean genotypes by focusing on character association studies and genetic diversity analysis. Correlation analysis revealed that seed yield per plant showed high positive correlation with 100-seed weight followed by pods per plant and plant height. Furthermore, path coefficient analysis exposed that pods per plant had maximum direct contribution in seed yield per plant followed by 100-seed weight, days to flowering and SPAD measurement. Genotype named “G-10” showed maximum yield per plant followed by 24607, G-52, 24593, Arisoy, 24566, 17426, A-3127, 24570 and 24567. Genetic diversity analysis grouped the evaluated germplasm into 17 clusters. All clusters showed zero intra-cluster variability; while inter-cluster divergence ranged from 9.00 to 91.11. Cluster V showed maximum inter-cluster distance with cluster XII followed by that of between V and VIII. Moreover, cluster IV with superior genotypes (G-10, 24607, 24593 and 24566), VI (17426 and 24567), XIII (24570) and X (Arisoy and G-52) showed above mean values for most of the studied characters. Overall, the results of hybridization between the superior genotypes of these cluster pairs might be useful for soybean breeding with improving agronomic traits and adaptability.     

Urease and Serine Protease inhibitory alkaloids from Isatis tinctoria

Phytochemical investigations on the alkaloidal fraction of the whole plant of the Isatis tinctoria led to the isolation of the alkaloids 1-6., 3′-Hydroxyepiglucoisatisin (3), Epiglucoisatisin (2) were found to be potent urease inhibitors in a concentration-dependent manner with IC₅₀ values 25.63 ± 0.74, 37.01 ± 0.41 and 31.72 ± 0.93, 47.33 ± 0.31 μM against Bacillus pasteurii & Jack bean urease, respectively. Compounds 3 and 2 also showed potent inhibitory potential against α-chymotrypsin with IC₅₀ values of 23.40 ± 0.21 and 27.45 ± 0.23 μM, respectively.