Mapping codon usage of the translation initiation region in porcine reproductive and respiratory syndrome virus genome

<p>Abstract</p> <p>Background</p> <p>Porcine reproductive and respitatory syndrome virus (PRRSV) is a recently emerged pathogen and severely affects swine populations worldwide. The replication of PRRSV is tightly controlled by viral gene expression and the codon usage of translation initiation region within each gene could potentially regulate the translation rate. Therefore, a better understanding of the codon usage pattern of the initiation translation region would shed light on the regulation of PRRSV gene expression.</p> <p>Results</p> <p>In this study, the codon usage in the translation initiation region and in the whole coding sequence was compared in PRRSV ORF1a and ORFs2-7. To investigate the potential role of codon usage in affecting the translation initiation rate, we established a codon usage model for PRRSV translation initiation region. We observed that some non-preferential codons are preferentially used in the translation initiation region in particular ORFs. Although some positions vary with codons, they intend to use codons with negative CUB. Furthermore, our model of codon usage showed that the conserved pattern of CUB is not directly consensus with the conserved sequence, but shaped under the translation selection.</p> <p>Conclusions</p> <p>The non-variation pattern with negative CUB in the PRRSV translation initiation region scanned by ribosomes is considered the rate-limiting step in the translation process.</p

Neutrino decay as a possible interpretation to the MiniBooNE observation with unparticle scenario

In a new measurement on neutrino oscillation $\nu_{\mu}\to\nu_e$, the MiniBooNE Collaboration observes an excess of electron-like events at low energy and the phenomenon may demand an explanation which obviously is beyond the oscillation picuture. We propose that heavier neutrino $\nu_2$ decaying into a lighter one $\nu_1$ via the transition process $\nu_{\mu}\to \nu_e+X$ where $X$ denotes any light products, could be a natural mechanism. The theoretical model we employ here is the unparticle scenario established by Georgi. We have studied two particular modes \nu_\mu\to \nu_e+\Un and $\nu_\mu\to \nu_e+\bar\nu_e+\nu_e$. Unfortunately, the number coming out from the computation is too small to explain the observation. Moreover, our results are consistent with the cosmology constraint on the neutrino lifetime and the theoretical estimation made by other groups, therefore we can conclude that even though neutrino decay seems plausible in this case, it indeed cannot be the source of the peak at lower energy observed by the MiniBooNE collaboration and there should be other mechanisms responsible for the phenomenon.Comment: 14 pages, conclusions are changed; published version for EPJ

Quantum and Classical Magnetoresistance in Ambipolar Topological Insulator Transistors with Gate-tunable Bulk and Surface Conduction

Weak antilocalization (WAL) and linear magnetoresistance (LMR) are two most commonly observed magnetoresistance (MR) phenomena in topological insulators (TIs) and often attributed to the Dirac topological surface states (TSS). However, ambiguities exist because these phenomena could also come from bulk states (often carrying significant conduction in many TIs) and are observable even in non-TI materials. Here, we demonstrate back-gated ambipolar TI field-effect transistors in (Bi0.04Sb0.96)(2)Te-3 thin films grown by molecular beam epitaxy on SrTiO3(111), exhibiting a large carrier density tunability (by nearly 2 orders of magnitude) and a metal-insulator transition in the bulk (allowing switching off the bulk conduction). Tuning the Fermi level from bulk band to TSS strongly enhances both the WAL (increasing the number of quantum coherent channels from one to peak around two) and LMR (increasing its slope by up to 10 times). The SS-enhanced LMR is accompanied by a strongly nonlinear Hall effect, suggesting important roles of charge inhomogeneity (and a related classical LMR), although existing models of LMR cannot capture all aspects of our data. Our systematic gate and temperature dependent magnetotransport studies provide deeper insights into the nature of both MR phenomena and reveal differences between bulk and TSS transport in TI related materials

Curcumin Blocks Small Cell Lung Cancer Cells Migration, Invasion, Angiogenesis, Cell Cycle and Neoplasia through Janus Kinase-STAT3 Signalling Pathway

Curcumin, the active component of turmeric, has been shown to protect against carcinogenesis and prevent tumor development. However, little is known about its anti-tumor mechanism in small cell lung cancer (SCLC). In this study, we found that curcumin can inhibit SCLC cell proliferation, cell cycle, migration, invasion and angiogenesis through suppression of the STAT3. SCLC cells were treated with curcumin (15 µmol/L) and the results showed that curcumin was effective in inhibiting STAT3 phosphorylation to downregulate of an array of STAT3 downstream targets ,which contributed to suppression of cell proliferation, loss of colony formation, depression of cell migration and invasion. Curcumin also suppressed the expression of proliferative proteins (Survivin, Bcl-XL and Cyclin B1), and invasive proteins (VEGF, MMP-2, MMP-7 and ICAM-1).Knockdown of STAT3 expression by siRNA was able to induce anti-invasive effects in vitro. In contrast, activation of STAT3 upstream of interleukin 6 (IL-6) leads to the increased cell proliferation ,cell survival, angiogenesis, invasion, migration and tumor growth. Our findings illustrate the biologic significance of IL-6/JAK/STAT3 signaling in SCLC progression and providenovel evidence that the pathway may be a new potential target for therapy of SCLC. It was concluded that curcumin is a potent agent in the inhibition of STAT3 with favorable pharmacological activity,and curcumin may have translational potential as an effective cancer therapeutic or preventive agent for SCLC

Phylogenomic reappraisal of the family Rhizobiaceae at the genus and species levels, including the description of Ectorhizobium quercum gen. nov., sp. nov.

The family Rhizobiaceae contains 19 validly described genera including the rhizobia groups, many of which are important nitrogen-fixing bacteria. Early classification of Rhizobiaceae relied heavily on the poorly resolved 16S rRNA genes and resulted in several taxonomic conflicts. Although several recent studies illustrated the taxonomic status of many members in the family Rhizobiaceae, several para- and polyphyletic genera still needed to be elucidated. The rapidly increasing number of genomes in Rhizobiaceae has allowed for a revision of the taxonomic identities of members in Rhizobiaceae. In this study, we performed analyses of genome-based phylogeny and phylogenomic metrics to review the relationships of 155-type strains within the family Rhizobiaceae. The UBCG and concatenated protein phylogenetic trees, constructed based on 92 core genes and concatenated alignment of 170 single-copy orthologous proteins, demonstrated that the taxonomic inconsistencies should be assigned to eight novel genera, and 22 species should be recombined. All these reclassifications were also confirmed by pairwise cpAAI values, which separated genera within the family Rhizobiaceae with a demarcation threshold of ~86%. In addition, along with the phenotypic and chemotaxonomic analyses, a novel strain BDR2-2T belonging to a novel genus of the family Rhizobiaceae was also confirmed, for which the name Ectorhizobium quercum gen. nov., sp. nov. was proposed. The type strain is BDR2-2T (=CFCC 16492T = LMG 31717T)

Prognostic significance of the neutrophil to lymphocyte ratio in patients with non-small cell lung cancer: a systemic review and metaanalysis,”

Abstract: Neutrophil to Lymphocyte Ratio (NLR) was recently demonstrated as a useful index in predicting the prognosis of Non-Small Cell Lung Cancer (NSCLC). Thus, a meta-analysis was performed to demonstrate the relationship between NLR and overall survival (OS), progress-free survival (PFS) or disease free survival (DFS) in patients with NSCLC. We searched for relevant literatures in PubMed, EMBASE and Cochrane library and pooled the eligible studies and synthesized hazard ratios (HRs) using Stata 12.0. Final analysis of NSCLC patients from 12 eligible studies was performed. Combined HR suggested that high NLR had an unfavorable effect on patients&apos; OS (n=1700 in 11 studies; HR= 1.43, 95% CI: 1.25-1.64; I^2=80.2%, P&lt;0.01) and PFS (n=664 in 5 studies, HR=1.37, 95% CI: 1.07-1.74; I^2=70.8%, P=0.004). Subgroup analysis based on cutoff shown that, compared with other subgroups, the subgroup with a cutoff of 5 had a significantly poorer survival (HR=1.87, 95% CI 1.49-2.34) with less heterogeneity (I^2=21.3%, P=0.28). However, subgroup analysis based on treatment method indicated that the &quot;surgery&quot; subgroup seemed to have not a significant impact on survival (HR=1.32, 95% CI 0.99-1.77; I^2=80.0%, P=0.063) compared with the chemotherapy subgroup (HR=1.61, 95% CI 1.24-2.10; I^2=82.6%, P&lt;0.01). Additionally, combined odds ratio (OR) suggested high NLR was associated inversely with response to treatment (n = 276 in 2 studies; OR = 1.73, 95% CI: 1.04-2.88; I^2=0%, P=0.40). This study suggests high NLR (especially with a cutoff of 5) seems to be associated with a worse prognosis in patients with NSCLC as well as a worse response to treatments