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Abstract Objectives: To evaluate the performance of the Anoxomat, in comparison with the conventional anaerobic GasPak jar system, for the isolation of obligate anaerobes. Method: Anoxomat, model WS800, and anaerobic GasPak jar system (Oxoid) were evaluated. Anoxomat system utilized a gas mixture of 80% N 2 , 10% CO 2 and 10% H 2 , while the GasPak used a gas mixture of 90% H 2 and 10% CO 2 . An anaerobic indicator within the jars monitored anaerobiosis. A total of 227 obligate anaerobic bacteria comprising 116 stock strains, 5 ATCC reference strains and 106 fresh strains, representing different genera, were investigated for growth on anaerobic agar plates and scored for density, colony sizes, susceptibility zones of antibiotic inhibition and the speed of anaerobiosis (reducing the indicator). Results: The results demonstrate that the growth of anaerobic bacteria is faster inside the Anoxomat jar than in the anaerobic GasPak jar system. Of the 227 strains tested, the colonies of 152 (67%) were larger (by size range of 0.2-2.4 mm) in the Anoxomat at 48 h than in the GasPak jar compared with only 21% (range 0.1-0.3 mm) that were larger in the GasPak than in the Anoxomat. The remaining 12% were equal in their sizes. There was no measurable difference in the colony sizes of the reference strains. The Porphyromonas asaccharolytica strains failed to grow within the GasPak system but grew inside the Anoxomat. With the Anoxomat, anaerobiosis was achieved about 35 min faster than in the GasPak system. The density of growth recorded for 177 (78%) strains was heavier in the Anoxomat than in the GasPak jar. The zones of inhibition of the antibiotics tested were not different in the two systems. Conclusion: The Anoxomat system provided superior growth, in terms of density and colony size, and achieved anaerobiosis more rapidly. Evidently, the Anoxomat method is more reliable and appears to support the growth of strict anaerobes better

Tertiary Conformational Transition In Horse Haemoglobin Induced By Inositol Hexakisphosphate

The red blood cell of the domestic horse contains two haemoglobin types. The two haemoglobins were separated on a column of carboxymethylcellulose. The equilibrium constant, Kequ, for the reaction of 5,5'-dithiobis(2-nitrobenzoate) — DTNB — with the CysF9[93]β sulfhydryl group of each haemoglobin was determined at 25°C as a function of pH. The reactivity of CysF9[93]β is affected by allosteric effectors such as the proton (H+) and inositol hexakisphosphate (inositol-P6). Between pH 5.6 and 9.0 Kequ decreased by about two to four orders of magnitude, demonstrating that H+ is a heterotropic allosteric effector of haemoglobin with respect to its reaction with DTNB. Inositol-P6 also decreased Kequ by about two to four orders of magnitude across the experimental pH range. CysF9[93]β exists in two tertiary conformations, r and t, in dynamic equilibrium. Krt, the equilibrium constant for the r t conformational transition, was determined for each of the two horse haemoglobins from an analysis of the pH dependence of Kequ. The calculations from the pH dependence of Kequ showed that the pKa values of the ionisable groups coupled to the DTNB reaction vary between 5.0 and 8.9. The equilibrium constants, Krt, for the r t tertiary structure transition, were 0.143 ± 0.05 and 0.446 ± 0.22 for the fast and slow stripped horse haemoglobins respectively. In the presence of inositol-P6, Krt for the fast and slow were 2.219 ± 0.79 and 2.214 ± 0.83 respectively. The results show that inositol-P6 increases the relative population of the t tertiary conformation. So, it increases the affinity of CysF9[93]β by changing the relative distribution of two protein conformations

The anaerobic bacteriology of intrapulmonary infections in Kuwait

Objective: The primary objective of this study was to ascertain the association of anaerobic bacteria in intrapulmonary infections and their susceptibility pattern to commonly prescribed antibiotics. Methods: One hundred clinical samples (85 broncho-alveolar lavage and 15 lung abscess aspirates) from suspected intrapulmonary infection cases were investigated in order to determine the role of anaerobic bacteria in these infections. The anaerobic bacterial isolates were identified by using the Vitek Anaerobic Card System and conventional methods. Susceptibility of these isolates was determined by Etest method against eight commonly prescribed antibiotics. Results: A total of 42 anaerobes were isolated, of which Prevotella spp. were the commonest isolates, made up of 42.9% (18/42), followed by Peptostreptococcus spp. 33.3% (14/42). Only two Bacteroides fragilis strains were isolated. All the isolates were sensitive to metronidazole, clindamycin, imipenem and meropenem; however, one Prevotella was resistant to piperacillin-tazobactam. The two B. fragilis isolates were susceptible to metronidazole, imipenem, meropenem and piperacillin-tazobactam, and one was found to be resistant to clindamycin. Conclusion: Overall, Prevotella spp. were found to be the predominant anaerobic bacteria associated with intrapulmonary infections in Kuwait. All the commonly prescribed antibiotics had excellent in vitro activities against nearly all the isolates

Adrenergic Alpha-1 Pathway Is Associated with Hypertension among Nigerians in a Pathway-focused Analysis

The pathway-focused association approach offers a hypothesis driven alternative to the agnostic genome-wide association study. Here we apply the pathway-focused approach to an association study of hypertension, systolic blood pressure (SBP), and diastolic blood pressure (DBP) in 1614 Nigerians with genome-wide data.Testing of 28 pathways with biological relevance to hypertension, selected a priori, containing a total of 101 unique genes and 4,349 unique single-nucleotide polymorphisms (SNPs) showed an association for the adrenergic alpha 1 (ADRA1) receptor pathway with hypertension (p<0.0009) and diastolic blood pressure (p<0.0007). Within the ADRA1 pathway, the genes PNMT (hypertension P(gene)<0.004, DBP P(gene)<0.004, and SBP P(gene)<0.009, and ADRA1B (hypertension P(gene)<0.005, DBP P(gene)<0.02, and SBP P(gene)<0.02) displayed the strongest associations. Neither ADRA1B nor PNMT could be the sole mediator of the observed pathway association as the ADRA1 pathway remained significant after removing ADRA1B, and other pathways involving PNMT did not reach pathway significance.We conclude that multiple variants in several genes in the ADRA1 pathway led to associations with hypertension and DBP. SNPs in ADRA1B and PNMT have not previously been linked to hypertension in a genome-wide association study, but both genes have shown associations with hypertension through linkage or model organism studies. The identification of moderately significant (10(-2)>p>10(-5)) SNPs offers a novel method for detecting the "missing heritability" of hypertension. These findings warrant further studies in similar and other populations to assess the generalizability of our results, and illustrate the potential of the pathway-focused approach to investigate genetic variation in hypertension

Novel functional insights into ischemic stroke biology provided by the first genome-wide association study of stroke in indigenous Africans

\ua9 The Author(s) 2024. Background: African ancestry populations have the highest burden of stroke worldwide, yet the genetic basis of stroke in these populations is obscure. The Stroke Investigative Research and Educational Network (SIREN) is a multicenter study involving 16 sites in West Africa. We conducted the first-ever genome-wide association study (GWAS) of stroke in indigenous Africans. Methods: Cases were consecutively recruited consenting adults (aged &gt; 18 years) with neuroimaging-confirmed ischemic stroke. Stroke-free controls were ascertained using a locally validated Questionnaire for Verifying Stroke-Free Status. DNA genotyping with the H3Africa array was performed, and following initial quality control, GWAS datasets were imputed into the NIH Trans-Omics for Precision Medicine (TOPMed) release2 from BioData Catalyst. Furthermore, we performed fine-mapping, trans-ethnic meta-analysis, and in silico functional characterization to identify likely causal variants with a functional interpretation. Results: We observed genome-wide significant (P-value &lt; 5.0E−8) SNPs associations near AADACL2 and miRNA (MIR5186) genes in chromosome 3 after adjusting for hypertension, diabetes, dyslipidemia, and cardiac status in the base model as covariates. SNPs near the miRNA (MIR4458) gene in chromosome 5 were also associated with stroke (P-value &lt; 1.0E−6). The putative genes near AADACL2, MIR5186, and MIR4458 genes were protective and novel. SNPs associations with stroke in chromosome 2 were more than 77 kb from the closest gene LINC01854 and SNPs in chromosome 7 were more than 116 kb to the closest gene LINC01446 (P-value &lt; 1.0E−6). In addition, we observed SNPs in genes STXBP5-AS1 (chromosome 6), GALTN9 (chromosome 12), FANCA (chromosome 16), and DLGAP1 (chromosome 18) (P-value &lt; 1.0E−6). Both genomic regions near genes AADACL2 and MIR4458 remained significant following fine mapping. Conclusions: Our findings identify potential roles of regulatory miRNA, intergenic non-coding DNA, and intronic non-coding RNA in the biology of ischemic stroke. These findings reveal new molecular targets that promise to help close the current gaps in accurate African ancestry-based genetic stroke’s risk prediction and development of new targeted interventions to prevent or treat stroke

PRIMO: an interactive homology modeling pipeline

The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling

Genome-Wide Association and Trans-ethnic Meta-Analysis for Advanced Diabetic Kidney Disease: Family Investigation of Nephropathy and Diabetes (FIND)

Diabetic kidney disease (DKD) is the most common etiology of chronic kidney disease (CKD) in the industrialized world and accounts for much of the excess mortality in patients with diabetes mellitus. Approximately 45% of U.S. patients with incident end-stage kidney disease (ESKD) have DKD. Independent of glycemic control, DKD aggregates in families and has higher incidence rates in African, Mexican, and American Indian ancestral groups relative to European populations. The Family Investigation of Nephropathy and Diabetes (FIND) performed a genome-wide association study (GWAS) contrasting 6,197 unrelated individuals with advanced DKD with healthy and diabetic individuals lacking nephropathy of European American, African American, Mexican American, or American Indian ancestry. A large-scale replication and trans-ethnic meta-analysis included 7,539 additional European American, African American and American Indian DKD cases and non-nephropathy controls. Within ethnic group meta-analysis of discovery GWAS and replication set results identified genome-wide significant evidence for association between DKD and rs12523822 on chromosome 6q25.2 in American Indians (P = 5.74x10-9). The strongest signal of association in the trans-ethnic meta-analysis was with a SNP in strong linkage disequilibrium with rs12523822 (rs955333; P = 1.31x10-8), with directionally consistent results across ethnic groups. These 6q25.2 SNPs are located between the SCAF8 and CNKSR3 genes, a region with DKD relevant changes in gene expression and an eQTL with IPCEF1, a gene co-translated with CNKSR3. Several other SNPs demonstrated suggestive evidence of association with DKD, within and across populations. These data identify a novel DKD susceptibility locus with consistent directions of effect across diverse ancestral groups and provide insight into the genetic architecture of DKD