Molecular mechanism of MBX2319 inhibition of Escherichia coli AcrB multidrug efflux pump and comparison with other inhibitors

Efflux pumps of the resistance nodulation division (RND) superfamily, such as AcrB, make a major contribution to multidrug resistance in Gram-negative bacteria. The development of inhibitors of the RND pumps would improve the efficacy of current and next-generation antibiotics. To date, however, only one inhibitor has been cocrystallized with AcrB. Thus, in silico struc- ture-based analysis is essential for elucidating the interaction between other inhibitors and the efflux pumps. In this work, we used computer docking and molecular dynamics simulations to study the interaction between AcrB and the compound MBX2319, a novel pyranopyridine efflux pump inhibitor with potent activity against RND efflux pumps of Enterobacteriaceae species, as well as other known inhibitors (D13-9001, 1-[1-naphthylmethyl]-piperazine, and phenylalanylarginine-ß-naphthyl-amide) and the binding of doxorubicin to the efflux-defective F610A variant of AcrB. We also analyzed the binding of a sub- strate, minocycline, for comparison. Our results show that MBX2319 binds very tightly to the lower part of the distal pocket in the B protomer of AcrB, strongly interacting with the phenylalanines lining the hydrophobic trap, where the hydrophobic por- tion of D13-9001 was found to bind by X-ray crystallography. Additionally, MBX2319 binds to AcrB in a manner that is similar to the way in which doxorubicin binds to the F610A variant of AcrB. In contrast, 1-(1-naphthylmethyl)-piperazine and phenylalanylarginine-ß-naphthylamide appear to bind to somewhat different areas of the distal pocket in the B protomer of AcrB than does MBX2319. However, all inhibitors (except D13-9001) appear to distort the structure of the distal pocket, impairing the proper binding of substrates

The secret(ion) life of worms

The secretomes of plant and human parasitic nematodes reveal molecular similarities that reflect the shared need to counter host defenses

An ovary transcriptome for all maturational stages of the striped bass (Morone saxatilis), a highly advanced perciform fish

<p>Abstract</p> <p>Background</p> <p>The striped bass and its relatives (genus <it>Morone</it>) are important fisheries and aquaculture species native to estuaries and rivers of the Atlantic coast and Gulf of Mexico in North America. To open avenues of gene expression research on reproduction and breeding of striped bass, we generated a collection of expressed sequence tags (ESTs) from a complementary DNA (cDNA) library representative of their ovarian transcriptome.</p> <p>Results</p> <p>Sequences of a total of 230,151 ESTs (51,259,448 bp) were acquired by Roche 454 pyrosequencing of cDNA pooled from ovarian tissues obtained at all stages of oocyte growth, at ovulation (eggs), and during preovulatory atresia. Quality filtering of ESTs allowed assembly of 11,208 high-quality contigs ≥ 100 bp, including 2,984 contigs 500 bp or longer (average length 895 bp). Blastx comparisons revealed 5,482 gene orthologues (E-value < 10^-3), of which 4,120 (36.7% of total contigs) were annotated with Gene Ontology terms (E-value < 10^-6). There were 5,726 remaining unknown unique sequences (51.1% of total contigs). All of the high-quality EST sequences are available in the National Center for Biotechnology Information (NCBI) Short Read Archive (GenBank: <ext-link ext-link-id="SRX007394" ext-link-type="gen">SRX007394</ext-link>). Informative contigs were considered to be abundant if they were assembled from groups of ESTs comprising ≥ 0.15% of the total short read sequences (≥ 345 reads/contig). Approximately 52.5% of these abundant contigs were predicted to have predominant ovary expression through digital differential display <it>in silico </it>comparisons to zebrafish (<it>Danio rerio</it>) UniGene orthologues. Over 1,300 Gene Ontology terms from Biological Process classes of Reproduction, Reproductive process, and Developmental process were assigned to this collection of annotated contigs.</p> <p>Conclusions</p> <p>This first large reference sequence database available for the ecologically and economically important temperate basses (genus <it>Morone</it>) provides a foundation for gene expression studies in these species. The predicted predominance of ovary gene expression and assignment of directly relevant Gene Ontology classes suggests a powerful utility of this dataset for analysis of ovarian gene expression related to fundamental questions of oogenesis. Additionally, a high definition Agilent 60-mer oligo ovary 'UniClone' microarray with 8 × 15,000 probe format has been designed based on this striped bass transcriptome (eArray Group: Striper Group, Design ID: 029004).</p

Characterization of casein and alpha lactalbumin of African elephant (Loxodonta africana) milk

The current research reports partial characterization of the caseins and alpha-lactalbumin (alpha-LA) of the African elephant with proposed unique structure-function properties. Extensive research has been carried out to understand the structure of the casein micelles. Crystallographic structure elucidation of caseins and casein micelles is not possible. Consequently, several models have been developed in an effort to describe the casein micelle, specifically of cow milk. Here we report the characterization of African elephant milk caseins. The kappa-caseins and beta-caseins were investigated, and their relative ratio was found to be approximately 1:8.5, whereas alpha-caseins were not detected. The gene sequence of beta-casein in the NCBI database was revisited, and a different sequence in the N-terminal region is proposed. Amino acid sequence alignment and hydropathy plots showed that the kappa-casein of African elephant milk is similar to that of other mammals, whereas the beta-casein is similar to the human protein, and displayed a section of unique AA composition and additional hydrophilic regions compared with bovine caseins. Elephant milk is destabilized by 62% alcohol, and it is speculated that the beta-casein characteristics may allow maintenance of the colloidal nature of the casein micelle, a role that was previously only associated with K-casein. The oligosaccharide content of milk was reported to be low in dairy animals but high in some other species such as humans and elephants. In the milk of the African elephant, lactose and oligosaccharides both occur at high levels. These levels are typically related to the content of alpha-LA in the mammary gland and thus point to a specialized carbohydrate synthesis, where the whey protein alpha-LA plays a role. We report the characterization of African elephant alpha-LA. Homology modeling of the alpha-LA showed that it is structurally similar to crystal structures of other mammalian species, which in turn may be an indication that its functional properties, such as lactose synthesis, should not be impaired

Computational and phylogenetic validation of nematode horizontal gene transfer

Sequencing of expressed genes has shown that nematodes, particularly the plant-parasitic nematodes, have genes purportedly acquired from other kingdoms by horizontal gene transfer. The prevailing orthodoxy is that such transfer has been a driving force in the evolution of niche specificity, and a recent paper in BMC Evolutionary Biology that presents a detailed phylogenetic analysis of cellulase genes in the free-living nematode Pristionchus pacificus at the species, genus and family levels substantiates this hypothesis

Genetic drift, not life history or RNAi, determine long term evolution of transposable elements

Transposable elements (TEs) are a major source of genome variation across the branches of life. Although TEs may play an adaptive role in their host’s genome, they are more often deleterious, and purifying selection is an important factor controlling their genomic loads. In contrast, life history, mating system, GC content, and RNAi pathways, have been suggested to account for the disparity of TE loads in different species. Previous studies of fungal, plant, and animal genomes have reported conflicting results regarding the direction in which these genomic features drive TE evolution. Many of these studies have had limited power, however, because they studied taxonomically narrow systems, comparing only a limited number of phylogenetically independent contrasts, and did not address long-term effects on TE evolution. Here we test the long-term determinants of TE evolution by comparing 42 nematode genomes spanning over 500 million years of diversification. This analysis includes numerous transitions between life history states, and RNAi pathways, and evaluates if these forces are sufficiently persistent to affect the long-term evolution of TE loads in eukaryotic genomes. Although we demonstrate statistical power to detect selection, we find no evidence that variation in these factors influence genomic TE loads across extended periods of time. In contrast, the effects of genetic drift appear to persist and control TE variation among species. We suggest that variation in the tested factors are largely inconsequential to the large differences in TE content observed between genomes, and only by these large-scale comparisons can we distinguish long-term and persistent effects from transient or random changes

Superconducing Alloys with Weak and Strong Scattering: Anderson's Theorem and a Superconductor-Insulator Transition

We have studied the effects of strong impurity scattering on disordered superconductors beyond the low impurity concentration limit. By applying the full CPA to a superconductiong A-B binary alloy, we calculated the fluctuations of the local order parameters $\Delta_{A}, \Delta_{B}$ and charge densities, $n_{A}, n_{B}$ for weak and strong on site disorder. We find that for narrow band alloy s-wav e superconductors the conditions for Anderson's theorem are satisfied in general only for the case of particle-hole symmetry. In this case it is satisfied regardless whether we are in the weak or strong scattering regimes. Interestingly, we find that strong scattering leads to band splitting and in this regime for any band filling we have a critical concentration where a superconductor-insulator quantum phase transition occurs at T=0.Comment: 28 pages, 13 figure

Tourism policy and destination marketing in developing countries: the chain of influence

Tourism marketers including destination marketing organisations (DMOs) and international tour operators play a pivotal role in destination marketing, especially in creating destination images. These images, apparent in tourist brochures, are designed to influence tourist decision-making and behaviour. This paper proposes the concept of a “chain of influence” in destination marketing and image-making, suggesting that the content of marketing materials is influenced by the priorities of those who design these materials, e.g. tour operators and DMOs. A content analysis of 2,000 pictures from DMO and tour operator brochures revealed synergies and divergence between these marketers. The brochure content was then compared to the South African tourism policy, concluding that the dominant factor in the chain of influence in the South African context is in fact its organic image

Medical Student Engagement in a Virtual Learning Environment Positively Correlates with Course Performance and Satisfaction in Psychiatry

This article is made available for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.Introduction There has been a move to a “flipped classroom” (FC) in medical education. The FC promotes active learning and utilizes independent preparation prior to in-class sessions. Few studies have evaluated the effectiveness of the FC approach in medical education, specifically via virtual learning. The purpose of this study evaluates student and faculty perceptions of the FC approach and relationships between student engagement and performance. Method The first-year medical student psychiatry curriculum was redesigned with an FC approach and subsequently altered by COVID-19 to a virtual learning environment. A mixed-method approach was used to examine both qualitative assessment and quantitative performance data. Students and facilitators were invited to participate in surveys regarding the curriculum changes. Student performance data was collected via quizzes and examinations. Engagement was evaluated by student participation in National Board of Medical Examiners–style multiple-choice questions delivered via Top Hat®. Correlational analyses were used to evaluate associations between engagement and performance. T-tests were used to compare student satisfaction across 2019 and 2020. Results Performance on in-class questions was positively associated with class rank and performance (p < 0.005). More students were either satisfied or strongly satisfied (91.5%) in 2020 compared to 85.7% in 2019 (two-tailed t-test, p = 0.04). Most students (81.3%) preferred in-class questions to lectures. In 2020, 62.6% of student comments were positive regarding the psychiatry curriculum vs 33.3% in 2019. Over 61.5% of facilitators felt positive towards the changes. Conclusion Our results demonstrate a positive relationship between engagement and class performance. Students and facilitators positively perceived the approach, with students preferring in-class questions compared to lectures. Future research should evaluate overall performance on standardized tests, third-year clerkships, and number of students matching into psychiatry