Genome-Wide Investigation and Expression Analyses of WD40 Protein Family in the Model Plant Foxtail Millet (Setaria italica L.)

WD40 proteins play a crucial role in diverse protein-protein interactions by acting as scaffolding molecules and thus assisting in the proper activity of proteins. Hence, systematic characterization and expression profiling of these WD40 genes in foxtail millet would enable us to understand the networks of WD40 proteins and their biological processes and gene functions. In the present study, a genome-wide survey was conducted and 225 potential WD40 genes were identified. Phylogenetic analysis categorized the WD40 proteins into 5 distinct sub-families (I–V). Gene Ontology annotation revealed the biological roles of the WD40 proteins along with its cellular components and molecular functions. In silico comparative mapping with sorghum, maize and rice demonstrated the orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of WD40 genes. Estimation of synonymous and non-synonymous substitution rates revealed its evolutionary significance in terms of gene-duplication and divergence. Expression profiling against abiotic stresses provided novel insights into specific and/or overlapping expression patterns of SiWD40 genes. Homology modeling enabled three-dimensional structure prediction was performed to understand the molecular functions of WD40 proteins. Although, recent findings had shown the importance of WD40 domains in acting as hubs for cellular networks during many biological processes, it has invited a lesser research attention unlike other common domains. Being a most promiscuous interactors, WD40 domains are versatile in mediating critical cellular functions and hence this genome-wide study especially in the model crop foxtail millet would serve as a blue-print for functional characterization of WD40s in millets and bioenergy grass species. In addition, the present analyses would also assist the research community in choosing the candidate WD40s for comprehensive studies towards crop improvement of millets and biofuel grasses.     

Effect of Temperature Pre-Exposure on the Locomotion and Chemotaxis of C. elegans

The effect of temperature pre-exposure on locomotion and chemotaxis of the soil-dwelling nematode Caenorhabditis elegans has been extensively studied. The behavior of C. elegans was quantified using a simple harmonic curvature-based model. Animals showed increased levels of activity, compared to control worms, immediately after pre-exposure to 30°C. This high level of activity in C. elegans translated into frequent turns by making ‘complex’ shapes, higher velocity of locomotion, and higher chemotaxis index () in presence of a gradient of chemoattractant. The effect of pre-exposure was observed to be persistent for about 20 minutes after which the behavior (including velocity and ) appeared to be comparable to that of control animals (maintained at 20°C). Surprisingly, after 30 minutes of recovery, the behavior of C. elegans continued to deteriorate further below that of control worms with a drastic reduction in the curvature of the worms'' body. A majority of these worms also showed negative chemotaxis index indicating a loss in their chemotaxis ability.     

Biomarkers of Inflammation,Immunosuppression and Stress Are Revealed by Metabolomic Profiling of Tuberculosis Patients

Although tuberculosis (TB) causes more deaths than any other pathogen, most infected individuals harbor the pathogen without signs of disease. We explored the metabolome of >400 small molecules in serum of uninfected individuals, latently infected healthy individuals and patients with active TB. We identified changes in amino acid, lipid and nucleotide metabolism pathways, providing evidence for anti-inflammatory metabolomic changes in TB. Metabolic profiles indicate increased activity of indoleamine 2,3 dioxygenase 1 (IDO1), decreased phospholipase activity, increased abundance of adenosine metabolism products, as well as indicators of fibrotic lesions in active disease as compared to latent infection. Consistent with our predictions, we experimentally demonstrate TB-induced IDO1 activity. Furthermore, we demonstrate a link between metabolic profiles and cytokine signaling. Finally, we show that 20 metabolites are sufficient for robust discrimination of TB patients from healthy individuals. Our results provide specific insights into the biology of TB and pave the way for the rational development of metabolic biomarkers for TB.     

Complete genome sequence of a peste des petits ruminants virus recovered from wild bharal in tibet, china

For the first time, here we announce the complete genome sequence of a field isolate of Peste des petits ruminants virus (PPRV) derived from macerated rectal tissue of a free living bharal (Pseudois nayaur) that displayed clinical disease consistent with severe infection with PPRV. Further, we compare the full genome of this isolate, termed PPRV Tibet/Bharal/2008, with previously available PPRV genomes, including those of virus isolates from domestic small ruminants local to the area where the reported isolate was collected. The current sequence is phylogenetically classified as a lineage IV virus, sharing high levels of sequence identity with previously described Tibetan PPRV isolates. Indeed, across the entire genome, only 26 nucleotide differences (0.16% nucleotide variation) and, consequently, 9 amino acid changes were present compared to sequences of locally derived viruses.     

Incremental paradigms of motif discovery.

We examine the problem of extracting maximal irredundant motifs from a string. A combinatorial argument poses a linear bound on the total number of such motifs, thereby opening the way to the quest for the fastest and most efficient methods of extraction. The basic paradigm explored here is that of iterated updates of the set of irredundant motifs in a string under consecutive unit symbol extensions of the string itself. This approach exposes novel characterizations for the base set of motifs in a string, hinged on notions of partial order. Such properties support the design of ad hoc data structures and constructs, and lead to develop an O(n(3)) time incremental discovery algorithm.     

Neutrophil integrin assay for clinical studies

The level of expression of neutrophil adhesion molecules may be a useful marker for neutrophil activation in clinical studies. We therefore determined neutrophil integrin expression under various experimental conditions using a Fluorescence Activated Cell Sorter (FACS) after the cells had been labelled with fluorescent conjugated antibodies to the integrin subunits CD11a, CD11b and CD18. Levels of labelled CD11b and CD18 increased after activation with the chemotactic peptide formyl-methionyl-leucyl phenylalanine (fMLP) in a dose- and time-dependent manner, but CD11a did not, indicating that CD11a would not be a useful marker of neutrophil activation. The baseline expression of CD11b and CD18 on unstimulated neutrophils was similar in heparin and EDTA anti-coagulated blood but the response to activation with fMLP was significantly less for the EDTA anti-coagulated samples (p < 0·01 in paired t-test). The labelling of integrins was significantly higher in unfixed whole blood samples compared to samples fixed with 1 per cent paraformaldehyde. However, the increase in labelling induced by fMLP was similar whether or not the samples were fixed after activation. Labelling of CD11b and CD18 was greater for preparations of isolated neutrophils than for neutrophils in whole blood, and the response to fMLP stimulation tended to be lower for the isolated cells. Our results indicate that heparin should be used as anti-coagulant in clinical studies utilizing whole blood if subsequent activation of neutrophils is planned (e.g. to detect in vivo priming), although EDTA may be used if baseline expression alone is to be measured. Fixation of blood samples should not affect the ability to detect neutrophil activation.     

TLR–Dependent Control of Francisella tularensis Infection and Host Inflammatory Responses

Background

Francisella tularensis is the causative agent of tularemia and is classified as a Category A select agent. Recent studies have implicated TLR2 as a critical element in the host protective response to F. tularensis infection, but questions remain about whether TLR2 signaling dominates the response in all circumstances and with all species of Francisella and whether F. tularensis PAMPs are predominantly recognized by TLR2/TLR1 or TLR2/TLR6. To address these questions, we have explored the role of Toll-like receptors (TLRs) in the host response to infections with F. tularensis Live Vaccine Strain (LVS) and F. tularensis subspecies (subsp.) novicida in vivo.

Methodology/Principal Findings

C57BL/6 (B6) control mice and TLR– or MyD88-deficient mice were infected intranasally (i.n.) or intradermally (i.d.) with F. tularensis LVS or with F. tularensis subsp. novicida. B6 mice survived >21 days following infection with LVS by both routes and survival of TLR1^−/−, TLR4^−/−, and TLR6^−/− mice infected i.n. with LVS was equivalent to controls. Survival of TLR2^−/− and MyD88^−/− mice, however, was significantly reduced compared to B6 mice, regardless of the route of infection or the subspecies of F. tularensis. TLR2^−/− and MyD88^−/− mice also showed increased bacterial burdens in lungs, liver, and spleen compared to controls following i.n. infection. Primary macrophages from MyD88^−/− and TLR2^−/− mice were significantly impaired in the ability to secrete TNF and other pro-inflammatory cytokines upon ex vivo infection with LVS. TNF expression was also impaired in vivo as demonstrated by analysis of bronchoalveolar lavage fluid and by in situ immunofluorescent staining.

Conclusions/Significance

We conclude from these studies that TLR2 and MyD88, but not TLR4, play critical roles in the innate immune response to F. tularensis infection regardless of the route of infection or the subspecies. Moreover, signaling through TLR2 does not depend exclusively on TLR1 or TLR6 during F. tularensis LVS infection.     

A Genome-Wide mQTL-seq Scan Identifies Potential Molecular Signatures Regulating Plant Height in Chickpea

The current study employed a high-throughput genome-wide next-generation sequencing-led multiple QTL-seq (mQTL-seq) strategy in two inter- and intra-specific recombinant inbred line (RIL) mapping populations to identify the major genomic regions underlying robust quantitative trait loci (QTLs) regulating plant height in chickpea. The whole genome resequencing discovered 446,475 and 150,434 high-quality homozygous single nucleotide polymorphisms (SNPs) exhibiting polymorphism between tall and dwarf/semi-dwarf mapping parents and bulk/homozygous individuals selected from each of two chickpea RIL populations. These SNP-led mQTL-seq assays in RIL mapping populations scaled-down two longer major genomic regions (1.26–1.34 Mb) underlying robust plant height QTLs into the shorter high-resolution QTL intervals (653.2–756.3 kb) on chickpea chromosomes 3 and 8. This essentially delineated regulatory novel natural SNP allelic variants from brassinosteroid insensitive 1-receptor kinase 1 (BAK1) and gibberellin (GA) 20-oxidase genes governing plant height in chickpea. A strong impact of evolutionary bottlenecks including strong artificial/natural selection on two plant height gene loci during chickpea domestication was observed. The shoot apical meristem-specific expression aside from down-regulation of two plant height genes especially in dwarf/semi-dwarf as compared to tall parents and homozygous mapping individuals of two aforementioned RIL populations was apparent. The integrated genomics-assisted breeding strategy combining mQTL-seq with differential gene expression profiling and functional allelic diversity-based trait domestication study collectively identified potential natural allelic variants of candidate genes underlying major plant height QTLs in chickpea. These functionally relevant molecular signatures can be of immense use for marker-aided genetic enhancement to develop high seed- and pod-yielding non-lodging cultivars restructured with desirable plant height in chickpea.     

Tuberculosis in Africa: learning from pathogenesis for biomarker identification

In Africa, more than 4 million people suffer from active tuberculosis (TB) resulting in an estimated 650,000 deaths every year. The etiologic agent of TB, Mycobacterium tuberculosis, survives in resting macrophages, which control the pathogen after activation by specific T lymphocytes. Here, we describe the basic mechanisms underlying the host response to TB with an emphasis on immunity and discuss diagnostics, drugs, and vaccines for TB. Moreover, we outline our attempts to develop biomarkers, which could help the monitoring of TB clinical trials, provide the basis for new diagnostics, and allow prognosis of outcome of infection and of drug treatment.