A non‐canonical role of the p97 complex in RIG‐I antiviral signaling

RIG‐I is a well‐studied sensor of viral RNA that plays a key role in innate immunity. p97 regulates a variety of cellular events such as protein quality control, membrane reassembly, DNA repair, and the cell cycle. Here, we report a new role for p97 with Npl4‐Ufd1 as its cofactor in reducing antiviral innate immune responses by facilitating proteasomal degradation of RIG‐I. The p97 complex is able to directly bind both non‐ubiquitinated RIG‐I and the E3 ligase RNF125, promoting K48‐linked ubiquitination of RIG‐I at residue K181. Viral infection significantly strengthens the interaction between RIG‐I and the p97 complex by a conformational change of RIG‐I that exposes the CARDs and through K63‐linked ubiquitination of these CARDs. Disruption of the p97 complex enhances RIG‐I antiviral signaling. Consistently, administration of compounds targeting p97 ATPase activity was shown to inhibit viral replication and protect mice from vesicular stomatitis virus (VSV) infection. Overall, our study uncovered a previously unrecognized role for the p97 complex in protein ubiquitination and revealed the p97 complex as a potential drug target in antiviral therapy.     

The mouse alpha-amylase multigene family. Sequence organization of members expressed in the pancreas, salivary gland and liver

The DNAs that specify the α-amylase messenger RNAs found in the pancreas, salivary gland and liver of mouse strain A have been isolated by molecular cloning in phage λ. Amylase clones were studied by mRNA/DNA hybrid analysis in the electron microscope, restriction endonuclease site mapping and DNA sequencing. The Amy-2^a gene, which specifies pancreatic α-amylase mRNA, measures 10·1 kb from cap to polyadenylation site and is interrupted by at least 9 intervening sequences. Amy-1^a, which specifies both salivary gland and liver α-amylase mRNAs contains at least 10 introns. The distance between the cap and polyadenylation sites used in the salivary gland and the liver measures 22·9 kb and 20 kb, respectively. Introns are located at very similar, if not identical, positions within comparable regions of Amy-1^a and Amy-2^a. The first intron of Amy-1^a, which interrupts sequences specifying 5′ non-translated regions of salivary gland and liver α-amylase mRNAs, has no counterpart in Amy-2^a. Some introns exhibit considerable sequence homology, suggesting that Amy-1^a and Amy-2^a have evolved by duplication from a common split ancestor sequence. Repetitive sequence elements occur in the introns and flanking regions of these genes. Gene titration by quantitative autoradiography reveals only one copy of Amy-1^a, but two copies of Amy-2^a per haploid mouse genome. In addition to Amy-1^a and Amy-2^a, several other amylase-like DNA sequences exist in the mouse genome. No gross rearrangements of amylase DNA sequences can be detected between germline DNA and that of various mouse tissues.     

Mapping quantitative trait loci (QTLs) for fatty acid composition in an interspecific cross of oil palm

Background  

Marker Assisted Selection (MAS) is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials.     

Noma Affected Children from Niger Have Distinct Oral Microbial Communities Based on High-Throughput Sequencing of 16S rRNA Gene Fragments

We aim to understand the microbial ecology of noma (cancrum oris), a devastating ancient illness which causes severe facial disfigurement in>140,000 malnourished children every year. The cause of noma is still elusive. A chaotic mix of microbial infection, oral hygiene and weakened immune system likely contribute to the development of oral lesions. These lesions are a plausible entry point for unidentified microorganisms that trigger gangrenous facial infections. To catalog bacteria present in noma lesions and identify candidate noma-triggering organisms, we performed a cross-sectional sequencing study of 16S rRNA gene amplicons from sixty samples of gingival fluid from twelve healthy children, twelve children suffering from noma (lesion and healthy sites), and twelve children suffering from Acute Necrotizing Gingivitis (ANG) (lesion and healthy sites). Relative to healthy individuals, samples taken from lesions in diseased mouths were enriched with Spirochaetes and depleted for Proteobacteria. Samples taken from healthy sites of diseased mouths had proportions of Spirochaetes and Proteobacteria that were similar to healthy control individuals. Samples from noma mouths did not have a higher abundance of Fusobacterium, casting doubt on its role as a causative agent of noma. Microbial communities sampled from noma and ANG lesions were dominated by the same Prevotella intermedia OTU, which was much less abundant in healthy sites sampled from the same mouths. Multivariate analysis confirmed that bacterial communities in healthy and lesion sites were significantly different. Several OTUs in the Orders Erysipelotrichales, Clostridiales, Bacteroidales, and Spirochaetales were identified as indicators of noma, suggesting that one or more microbes within these Orders is associated with the development of noma lesions. Future studies should include longitudinal sampling of viral and microbial components of this community, before and early in noma lesion development.     

Ecdysteroids and meiotic reinitiation in Palaemon serratus (Crustacea Decapoda Natantia) and in Locusta migratoria (Insecta orthoptera). A comparative study

Summary

Meiotic reinitiation has been studied in Locusta migratoria and Palaemon serratus in relation to the titre of free ecdysteroids present in the maturing oocyte. In both species meiotic reinitiation is characterized by two meiotic arrests, in prophase I and in metaphase I, and the first meiotic resumption which leads to germinal vesicle breakdown (GVBD) is correlated with increasing titres of ecdysteroids in the oocyte. Meiotic reinitiation has been successfully triggered in the oocytes of both species by incubation with physiological doses of ecdysteroids.     

Analysis and comparison of the pan-genomic properties of sixteen well-characterized bacterial genera

Background  

The increasing availability of whole genome sequences allows the gene or protein content of different organisms to be compared, leading to burgeoning interest in the relatively new subfield of pan-genomics. However, while several studies have analyzed protein content relationships in specific groups of bacteria, there has yet to be a study that provides a general characterization of protein content relationships in a broad range of bacteria.     

Ex vivo characterization of allo-MHC-restricted T cells specific for a single MHC-peptide complex

Alloreactive T cells are thought to be a potentially rich source of high-avidity T cells with therapeutic potential since tolerance to self-Ags is restricted to self-MHC recognition. Given the particularly high frequency of alloreactive T cells in the peripheral immune system, we used numerous MHC class I multimers to directly visualize and isolate viral and tumor Ag-specific alloreactive CD8 T cells. In fact, all but one specificities screened were undetectable in ex vivo labeling. In this study, we report the occurrence of CD8 T cells specifically labeled with allo-HLA-A*0201/Melan-A/MART-1(26-35) multimers at frequencies that are in the range of 10(-4) CD8 T cells and are thus detectable ex vivo by flow cytometry. We report the thymic generation and shaping of tumor Ag-specific, alloreactive T cells as well as their fate once seeded in the periphery. We show that these cells resemble their counterparts in HLA-A*0201-positive individuals, based on their structural and functional attributes.     

Rapid and high-throughput genotyping of Staphylococcus epidermidis isolates by automated multilocus variable-number of tandem repeats: a tool for real-time epidemiology

Fast and reliable genotyping methods allowing real-time epidemiology would be instrumental to discriminate Staphylococcus epidermidis isolates, in order to evaluate potential cross-infections or to follow genome content of infecting strains of this important opportunistic pathogen. We describe an automated multilocus variable-number tandem repeat-based assay (MLVA) for the rapid genotyping of S. epidermidis. Multiplex PCR amplifications using 6 primer pairs targeting gene-regions containing variable numbers of tandem repeats and the mecA gene are resolved by micro-capillary electrophoresis and automatically assessed by cluster analysis. This genotyping technique was evaluated for discriminatory power and reproducibility on 2 sequenced strains, on a collection of 21 strains previously characterized using genotyping reference methods and finally on 65 clinical isolates identified in two different institutions. All steps of this new procedure were developed to ensure rapid turn-around time and moderate costs. Our results suggest that this rapid approach is a valuable epidemiological tool to genotype S. epidermidis isolates in real-time. The rapid analysis of a limited number of evolutionary markers showed a power of discrimination similar to that of pulse-field gel electrophoresis (PFGE) or multilocus sequence type (MLST). This type of rapid and high-throughput methodology opens the possibility to rapidly assess long-term nosocomial transmission or to characterize infecting strains in the general procedure of routine laboratories, in real-time.     

Hydrogen peroxide production by Lactobacillus johnsonii NCC 533 and its role in anti-Salmonella activity

The human intestinal isolate Lactobacillus johnsonii NCC 533 (La1) is a probiotic strain with well-documented antimicrobial properties. Previous research has identified the production of lactic acid and bacteriocins as important factors, but that other unidentified factors are also involved. We used the recently published genome sequence of L. johnsonii NCC 533 to search for novel antipathogen factors and identified three potential gene products that may catalyze the synthesis of the known antimicrobial factor hydrogen peroxide, H(2)O(2). In this work, we confirmed the ability of NCC 533 as well as eight different L. johnsonii strains and Lactobacillus gasseri to produce H(2)O(2) when resting cells were incubated in the presence of oxygen, and that culture supernatant containing NCC 533-produced H(2)O(2) was effective in killing the model pathogen Salmonella enterica serovar Typhimurium SL1344 in vitro.