Identification of Host-Specific Bacteroidales 16S rDNA Sequences from Human Sewage and Ruminant Feces

The need to identify the source of fecal contamination of water has led to the development of various fecal source identification methods, a field known as microbial source tracking (MST). One promising method of MST focuses on fecal members of the order Bacteroidales, some of which exhibit a high degree of host-specificity. In order to identify host-specific Bacteroidales genetic markers, a ∼1060 bp section of Bacteroidales 16S rDNA was amplified from human sewage (n = 6), and bovine (n = 6) and ovine fecal (n = 5) samples and used for the generation of three clone libraries. Phylogenetic analysis of sequences from the three clone libraries revealed that the Bacteroidales species found in both human sewage and bovine and ovine feces were a highly diverse group of organisms, many of which were not represented by previously characterised 16S rDNA. Ovine and bovine feces appear to host similar populations of Bacteroidales species and these species were more diverse and less closely related to cultivated species than the Bacteroidales population found in human sewage. Species of Bacteroidales from the ruminant and human feces formed isolated clusters containing putatively host-specific sequences. These sequences were subsequently exploited for the design of host-specific primers which were used in MST studies

ASTM G132 testing for evaluating abrasion resistance of WC-Co hardmetal

The current test method experimentally simulates two-body abrasive wear of WC-6wt% Co hardmetal using modified pin abrasion tester configuration (ASTM G132). Silicon carbide (SiC) and alumina (Al2O3) with different sizes ranging from 22μm to 200 μm were used as abrasives in this test. Experiments were performed for different normal force from 4 to 16 N with constant sliding speed of 150 mm/s for 30 m sliding distance. Worn surface morphology and topography were characterized through SEM and white light interferometry. The obtained results clearly highlights the potential of pin abrasion tester for characterizing two body abrasion of hardmetals

Evidence for diversifying selection of genetic regions of encoding putative collagen-like host-adhesive fibers in Pasteuria penetrans

© FEMS 2018. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.Pasteuria spp. belong to a group of genetically diverse endospore-forming bacteria (phylum: Firmicutes) that are known to parasitize plant-parasitic nematodes and water fleas (Daphnia spp.). Collagen-like fibres form the nap on the surface of endospores and the genes encoding these sequences have been hypothesised to be involved in the adhesion of the endospores of Pasteuria spp. to their hosts. We report a group of 17 unique collagen-like genes putatively encoded by Pasteuria penetrans (strain: Res148) that formed five different phylogenetic clusters and suggest that collagen-like proteins are an important source of genetic diversity in animal pathogenic Firmicutes including Pasteuria. Additionally, and unexpectedly, we identified a putative collagen-like sequence which had a very different sequence structure to the other collagen-like proteins but was similar to the protein sequences in Megaviruses that are involved in host-parasite interactions. We, therefore, suggest that these diverse endospore surface proteins in Pasteuria are involved in biological functions, such as cellular adhesion; however, they are not of monophyletic origin and were possibly obtained de novo by mutation or possibly through selection acting upon several historic horizontal gene transfer events.Peer reviewedFinal Published versio

Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition

This study was designed to assess the influence of three soil DNA extraction procedures, namely the International Organization for Standardization (ISO-11063, GnS-GII and modified ISO procedure (ISOm), on the taxonomic diversity and composition of soil bacterial and fungal communities. The efficacy of each soil DNA extraction method was assessed on five soils, differing in their physico-chemical characteristics and land use. A meta-barcoded pyrosequencing approach targeting 16S and 18S rRNA genes was applied to characterize soil microbial communities. We first observed that the GnS-GII introduced some heterogeneity in bacterial composition between replicates. Then, although no major difference was observed between extraction procedures for soil bacterial diversity, we saw that the number of fungal genera could be underestimated by the ISO-11063. In particular, this procedure underestimated the detection in several soils of the genera Cryptococcus, Pseudallescheria, Hypocrea and Plectosphaerella, which are of ecological interest. Based on these results, we recommend using the ISOm method for studies focusing on both the bacterial and fungal communities. Indeed, the ISOm procedure provides a better evaluation of bacterial and fungal communities and is limited to the modification of the mechanical lysis step of the existing ISO-11063 standard

Improved X‐ray diffraction from Bacillus megaterium penicillin G acylase crystals through long cryosoaking dehydration

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/89569/1/S1744309111040462.pd

Whispers of Doubt Amidst Echoes of Triumph in NLP Robustness

Do larger and more performant models resolve NLP's longstanding robustness issues? We investigate this question using over 20 models of different sizes spanning different architectural choices and pretraining objectives. We conduct evaluations using (a) out-of-domain and challenge test sets, (b) behavioral testing with CheckLists, (c) contrast sets, and (d) adversarial inputs. Our analysis reveals that not all out-of-domain tests provide insight into robustness. Evaluating with CheckLists and contrast sets shows significant gaps in model performance; merely scaling models does not make them adequately robust. Finally, we point out that current approaches for adversarial evaluations of models are themselves problematic: they can be easily thwarted, and in their current forms, do not represent a sufficiently deep probe of model robustness. We conclude that not only is the question of robustness in NLP as yet unresolved, but even some of the approaches to measure robustness need to be reassessed.Comment: To appear at NAACL 24 - main conference. The code is available at: https://github.com/utahnlp/scaling_robustness

Superantigen profiles of emm and emm-like typeable and nontypeable pharyngeal streptococcal isolates of South India

<p>Abstract</p> <p>Background</p> <p>The major virulence factors determining the pathogenicity of streptococcal strains include M protein encoded by <it>emm </it>and <it>emm</it>-like (<it>emmL</it>) genes and superantigens. In this study, the distribution of <it>emm, emmL </it>and superantigen genes was analyzed among the streptococcal strains isolated from the patients of acute pharyngitis.</p> <p>Methods</p> <p>The streptococcal strains were isolated from the throat swabs of 1040 patients of acute pharyngitis. The <it>emm </it>and <it>emmL </it>genes were PCR amplified from each strain and sequenced to determine the <it>emm </it>types. The dot-blot hybridization was performed to confirm the pathogens as true <it>emm </it>nontypeable strains. The presence of eleven currently known superantigens was determined in all the strains by multiplex PCR.</p> <p>Results</p> <p>Totally, 124 beta-hemolytic streptococcal strains were isolated and they were classified as group A streptococcus (GAS) [15.3% (19/124)], group C streptococcus (GCS) [59.7% (74/124)] and group G streptococcus (GGS) [25.0% (31/124)]. Among 124 strains, only 35 strains were <it>emm </it>typeable and the remaining 89 strains were <it>emm </it>nontypeable. All GAS isolates were typeable, whereas most of the GCS and GGS strains were nontypeable. These nontypeable strains belong to <it>S. anginosus </it>[75.3% (67/89)] and <it>S. dysgalactiae </it>subsp. <it>equisimilis </it>[24.7% (22/89)]. The <it>emm </it>and <it>emmL </it>types identified in this study include <it>emm12.0 </it>(28.6%), <it>stG643.0 </it>(28.6%), <it>stC46.0 </it>(17.0%), <it>emm30.11 </it>(8.5%), <it>emm3.0 </it>(2.9%), <it>emm48.0 </it>(5.7%), <it>st3343.0 </it>(2.9%), <it>emm107.0 </it>(2.9%) and <it>stS104.2 </it>(2.9%). Various superantigen profiles were observed in typeable as well as nontypeable strains.</p> <p>Conclusions</p> <p>Multiplex PCR analysis revealed the presence of superantigens in all the typeable strains irrespective of their <it>emm </it>types. However, the presence of superantigen genes in <it>emm </it>and <it>emmL </it>nontypeable strains has not been previously reported. In this study, presence of at least one or a combination of superantigen coding genes was identified in all the <it>emm </it>and <it>emmL </it>nontypeable strains. Thus, the superantigens may inevitably play an important role in the pathogenesis of these nontypeable strains in the absence of the primary virulence factor, M protein.</p

Antimicrobial Peptides: Versatile Biological Properties

Antimicrobial peptides are diverse group of biologically active molecules with multidimensional properties. In recent past, a wide variety of AMPs with diverse structures have been reported from different sources such as plants, animals, mammals, and microorganisms. The presence of unusual amino acids and structural motifs in AMPs confers unique structural properties to the peptide that attribute for their specific mode of action. The ability of these active AMPs to act as multifunctional effector molecules such as signalling molecule, immune modulators, mitogen, antitumor, and contraceptive agent makes it an interesting candidate to study every aspect of their structural and biological properties for prophylactic and therapeutic applications. In addition, easy cloning and recombinant expression of AMPs in heterologous plant host systems provided a pipeline for production of disease resistant transgenic plants. Besides these properties, AMPs were also used as drug delivery vectors to deliver cell impermeable drugs to cell interior. The present review focuses on the diversity and broad spectrum antimicrobial activity of AMPs along with its multidimensional properties that could be exploited for the application of these bioactive peptides as a potential and promising drug candidate in pharmaceutical industries.</jats:p