Variant O89 O-Antigen of E. coli Is Associated With Group 1 Capsule Loci and Multidrug Resistance

<p>Bacterial surface polysaccharides play significant roles in fitness and virulence. In Gram-negative bacteria such as Escherichia coli, major surface polysaccharides are lipopolysaccharide (LPS) and capsule, representing O- and K-antigens, respectively. There are multiple combinations of O:K types, many of which are well-characterized and can be related to ecotype or pathotype. In this investigation, we have identified a novel O:K permutation resulting through a process of major genome reorganization in a clade of E. coli. A multidrug-resistant, extended-spectrum β-lactamase (ESBL)-producing strain – E. coli 26561 – represented a prototype of strains combining a locus variant of O89 and group 1 capsular polysaccharide. Specifically, the variant O89 locus in this strain was truncated at gnd, flanked by insertion sequences and located between nfsB and ybdK and we apply the term O89m for this variant. The prototype lacked colanic acid and O-antigen loci between yegH and hisI with this tandem polysaccharide locus being replaced with a group 1 capsule (G1C) which, rather than being a recognized E. coli capsule type, this locus matched to Klebsiella K10 capsule type. A genomic survey identified more than 200 E. coli strains which possessed the O89m locus variant with one of a variety of G1C types. Isolates from our collection with the combination of O89m and G1C all displayed a mucoid phenotype and E. coli 26561 was unusual in exhibiting a mucoviscous phenotype more recognized as a characteristic among Klebsiella strains. Despite the locus truncation and novel location, all O89m:G1C strains examined showed a ladder pattern typifying smooth LPS and also showed high molecular weight, alcian blue-staining polysaccharide in cellular and/or extra-cellular fractions. Expression of both O-antigen and capsule biosynthesis loci were confirmed in prototype strain 26561 through quantitative proteome analysis. Further in silico exploration of more than 200 E. coli strains possessing the O89m:G1C combination identified a very high prevalence of multidrug resistance (MDR) – 85% possessed resistance to three or more antibiotic classes and a high proportion (58%) of these carried ESBL and/or carbapenemase. The increasing isolation of O89m:G1C isolates from extra-intestinal infection sites suggests that these represents an emergent clade of invasive, MDR E. coli.</p

Functional diversification of Argonautes in nematodes:an expanding universe

In the last decade, many diverse RNAi (RNA interference) pathways have been discovered that mediate gene silencing at epigenetic, transcriptional and post-transcriptional levels. The diversity of RNAi pathways is inherently linked to the evolution of Ago (Argonaute) proteins, the central protein component of RISCs (RNA-induced silencing complexes). An increasing number of diverse Agos have been identified in different species. The functions of most of these proteins are not yet known, but they are generally assumed to play roles in development, genome stability and/or protection against viruses. Recent research in the nematode Caenorhabditis elegans has expanded the breadth of RNAi functions to include transgenerational epigenetic memory and, possibly, environmental sensing. These functions are inherently linked to the production of secondary siRNAs (small interfering RNAs) that bind to members of a clade of WAGOs (worm-specific Agos). In the present article, we review briefly what is known about the evolution and function of Ago proteins in eukaryotes, including the expansion of WAGOs in nematodes. We postulate that the rapid evolution of WAGOs enables the exceptional functional plasticity of nematodes, including their capacity for parasitism

New insights into control of arbovirus replication and spread by insect RNA interference pathways

Arthropod-borne (arbo) viruses are transmitted by vectors, such as mosquitoes, to susceptible vertebrates. Recent research has shown that arbovirus replication and spread in mosquitoes is not passively tolerated but induces host responses to control these pathogens. Small RNA-mediated host responses are key players among these antiviral immune strategies. Studies into one such small RNA-mediated antiviral response, the exogenous RNA interference (RNAi) pathway, have generated a wealth of information on the functions of this mechanism and the enzymes which mediate antiviral activities. However, other small RNA-mediated host responses may also be involved in modulating antiviral activity. The aim of this review is to summarize recent research into the nature of small RNA-mediated antiviral responses in mosquitoes and to discuss future directions for this relatively new area of research

Use of dried blood for measurement of trans fatty acids

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Aerosols in the E3SM Version 1: New Developments and Their Impacts on Radiative Forcing

The new Energy Exascale Earth System Model Version 1 (E3SMv1) developed for the U.S. Department of Energy has significant new treatments of aerosols and lightâ absorbing snow impurities as well as their interactions with clouds and radiation. This study describes seven sets of new aerosolâ related treatments (involving emissions, new particle formation, aerosol transport, wet scavenging and resuspension, and snow radiative transfer) and examines how they affect global aerosols and radiative forcing in E3SMv1. Altogether, they give a reduced total aerosol radiative forcing (â 1.6 W/m2) and sensitivity in cloud liquid water to aerosols, but an increased sensitivity in cloud droplet size to aerosols. A new approach for H2SO4 production and loss largely reduces a low bias in small particles concentrations and leads to substantial increases in cloud condensation nuclei concentrations and cloud radiative cooling. Emitting secondary organic aerosol precursor gases from elevated sources increases the column burden of secondary organic aerosol, contributing substantially to global clearâ sky aerosol radiative cooling (â 0.15 out of â 0.5 W/m2). A new treatment of aerosol resuspension from evaporating precipitation, developed to remedy two shortcomings of the original treatment, produces a modest reduction in aerosols and cloud droplets; its impact depends strongly on the model physics and is much stronger in E3SM Version 0. New treatments of the mixing state and optical properties of snow impurities and snow grains introduce a positive presentâ day shortwave radiative forcing (0.26 W/m2), but changes in aerosol transport and wet removal processes also affect the concentration and radiative forcing of lightâ absorbing impurities in snow/ice.Plain Language SummaryAerosol and aerosolâ cloud interactions continue to be a major uncertainty in Earth system models, impeding their ability to reproduce the observed historical warming and to project changes in global climate and water cycle. The U.S. DOE Energy Exascale Earth System Model version 1 (E3SMv1), a stateâ ofâ theâ science Earth system model, was developed to use exascale computing to address the grand challenge of actionable predictions of variability and change in the Earth system critical to the energy sector. It has been publicly released with new treatments in many aspects, including substantial modifications to the physical treatments of aerosols in the atmosphere and lightâ absorbing impurities in snow/ice, aimed at reducing some known biases or correcting model deficiencies in representing aerosols, their life cycle, and their impacts in various components of the Earth system. Compared to its predecessors (without the new treatments) and observations, E3SMv1 shows improvements in characterizing global distributions of aerosols and their radiative effects. We conduct sensitivity experiments to understand the impact of individual changes and provide guidance for future development of E3SM and other Earth system models.Key PointsA description and assessment of new aerosol treatments in the Energy Exascale Earth System Model Version 1 (E3SMv1) is providedContributions to the total aerosolâ related radiative forcing by individual new treatments and different processes are quantifiedSome of the new treatments are found to depend on model physics and require further improvement for E3SM or other Earth system modelsPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153241/1/jame21034-sup-0001-Figure_SI-S01.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153241/2/jame21034.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153241/3/jame21034_am.pd

Evaluation of Candidate Reference Genes for Gene Expression Normalization in Brassica juncea Using Real Time Quantitative RT-PCR

The real time quantitative reverse transcription PCR (qRT-PCR) is becoming increasingly important to gain insight into function of genes. Given the increased sensitivity, ease and reproducibility of qRT-PCR, the requirement of suitable reference genes for normalization has become important and stringent. It is now known that the expression of internal control genes in living organism vary considerably during developmental stages and under different experimental conditions. For economically important Brassica crops, only a couple of reference genes are reported till date. In this study, expression stability of 12 candidate reference genes including ACT2, ELFA, GAPDH, TUA, UBQ9 (traditional housekeeping genes), ACP, CAC, SNF, TIPS-41, TMD, TSB and ZNF (new candidate reference genes), in a diverse set of 49 tissue samples representing different developmental stages, stress and hormone treated conditions and cultivars of Brassica juncea has been validated. For the normalization of vegetative stages the ELFA, ACT2, CAC and TIPS-41 combination would be appropriate whereas TIPS-41 along with CAC would be suitable for normalization of reproductive stages. A combination of GAPDH, TUA, TIPS-41 and CAC were identified as the most suitable reference genes for total developmental stages. In various stress and hormone treated samples, UBQ9 and TIPS-41 had the most stable expression. Across five cultivars of B. juncea, the expression of CAC and TIPS-41 did not vary significantly and were identified as the most stably expressed reference genes. This study provides comprehensive information that the new reference genes selected herein performed better than the traditional housekeeping genes. The selection of most suitable reference genes depends on the experimental conditions, and is tissue and cultivar-specific. Further, to attain accuracy in the results more than one reference genes are necessary for normalization

The role of triacylglycerol in cardiac energy provision

Triacylglycerols (TAGs) constitute the main energy storage resource in mammals, by virtue of their high energy density. This in turn is a function of their highly reduced state and hydrophobicity. Limited water solubility, however, imposes specific requirements for delivery and uptake mechanisms on TAG-utilising tissues, including the heart, as well as intracellular disposition. TAGs constitute potentially the major energy supply for working myocardium, both through blood-borne provision and as intracellular TAG within lipid droplets, but also provide the heart with fatty acids (FAs) which the myocardium cannot itself synthesise but are required for glycerolipid derivatives with (non-energetic) functions, including membrane phospholipids and lipid signalling molecules. Furthermore they serve to buffer potentially toxic amphipathic fatty acid derivatives. Intracellular handling and disposition of TAGs and their FA and glycerolipid derivatives similarly requires dedicated mechanisms in view of their hydrophobic character. Dysregulation of utilisation can result in inadequate energy provision, accumulation of TAG and/or esterified species, and these may be responsible for significant cardiac dysfunction in a variety of disease states. This review will focus on the role of TAG in myocardial energy provision, by providing FAs from exogenous and endogenous TAG sources for mitochondrial oxidation and ATP production, and how this can change in disease and impact on cardiac function