Characterizing HMW-GS alleles of decaploid Agropyron elongatum in relation to evolution and wheat breeding

Bread wheat quality is mainly correlated with high molecular weight glutenin subunits (HMW-GS) of endosperm. The number of HMW-GS alleles with good processing quality is limited in bread wheat cultivars, while there are plenty of HMW-GS alleles in wheat-related grasses to exploit. We report here on the cloning and characterization of HMW-GS alleles from the decaploid Agropyron elongatum. Eleven novel HMW-GS alleles were cloned from the grass. Of them, five are x-type and six y-type glutenin subunit genes. Three alleles Aex4, Aey7, and Aey9 showed high similarity with another three alleles from the diploid Lophopyrum elongatum, which provided direct evidence for the Ee genome origination of A. elongatum. It was noted that C-terminal regions of three alleles of the y-type genes Aey8, Aey9, and Aey10 showed more similarity with x-type genes than with other y-type genes. This demonstrates that there is a kind of intermediate state that appeared in the divergence between x- and y-type genes in the HMW-GS evolution. One x-type subunit, Aex4, with an additional cysteine residue, was speculated to be correlated with the good processing quality of wheat introgression lines. Aey4 was deduced to be a chimeric gene from the recombination between another two genes. How the HMW-GS genes of A. elongatum may contribute to the improvement of wheat processing quality are discussed

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

Observation of the electromagnetic doubly OZI-suppressed decay J/ψ→ϕπ0J/\psi \rightarrow \phi \pi^{0}

Using a sample of $1.31$ billion $J/\psi$ events accumulated with the BESIII detector at the BEPCII collider, we report the observation of the decay $J/\psi \rightarrow \phi\pi^{0}$, which is the first evidence for a doubly Okubo-Zweig-Iizuka suppressed electromagnetic $J/\psi$ decay. A clear structure is observed in the $K^{+} K^{-}$ mass spectrum around 1.02 GeV/$c^2$, which can be attributed to interference between $J/\psi \rightarrow \phi\pi^{0}$ and $J/\psi \rightarrow K^{+}K^{-}\pi^{0}$ decays. Due to this interference, two possible solutions are found. The corresponding measured values of the branching fraction of $J/\psi \to \phi\pi^{0}$ are $[2.94 \pm 0.16\text{(stat.)} \pm 0.16\text{(syst.)}] \times 10^{-6}$ and $[1.24 \pm 0.33\text{(stat.)} \pm 0.30\text{(syst.)}] \times 10^{-7}$.Comment: 7 pages, 4 figures, published in Phys. Rev.

Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes

<p>Abstract</p> <p>Background</p> <p>Melanoma is the major cause of skin cancer deaths and melanoma incidence doubles every 10 to 20 years. However, little is known about melanoma pathway aberrations. Here we applied the robust Gene Identification Signature Paired End diTag (GIS-PET) approach to investigate the melanoma transcriptome and characterize the global pathway aberrations.</p> <p>Methods</p> <p>GIS-PET technology directly links 5' mRNA signatures with their corresponding 3' signatures to generate, and then concatenate, PETs for efficient sequencing. We annotated PETs to pathways of KEGG database and compared the murine B16F1 melanoma transcriptome with three non-melanoma murine transcriptomes (Melan-a2 melanocytes, E14 embryonic stem cells, and E17.5 embryo). Gene expression levels as represented by PET counts were compared across melanoma and melanocyte libraries to identify the most significantly altered pathways and investigate the expression levels of crucial cancer genes.</p> <p>Results</p> <p>Melanin biosynthesis genes were solely expressed in the cells of melanocytic origin, indicating the feasibility of using the PET approach for transcriptome comparison. The most significantly altered pathways were metabolic pathways, including upregulated pathways: purine metabolism, aminophosphonate metabolism, tyrosine metabolism, selenoamino acid metabolism, galactose utilization, nitrobenzene degradation, and bisphenol A degradation; and downregulated pathways: oxidative phosphorylation, ATPase synthesis, TCA cycle, pyruvate metabolism, and glutathione metabolism. The downregulated pathways concurrently indicated a slowdown of mitochondrial activities. Mitochondrial permeability was also significantly altered, as indicated by transcriptional activation of ATP/ADP, citrate/malate, Mg⁺⁺, fatty acid and amino acid transporters, and transcriptional repression of zinc and metal ion transporters. Upregulation of cell cycle progression, MAPK, and PI3K/Akt pathways were more limited to certain region(s) of the pathway. Expression levels of c-<it>Myc </it>and <it>Trp53 </it>were also higher in melanoma. Moreover, transcriptional variants resulted from alternative transcription start sites or alternative polyadenylation sites were found in <it>Ras </it>and genes encoding adhesion or cytoskeleton proteins such as integrin, β-catenin, α-catenin, and actin.</p> <p>Conclusion</p> <p>The highly correlated results unmistakably point to a systematic downregulation of mitochondrial activities, which we hypothesize aims to downgrade the mitochondria-mediated apoptosis and the dependency of cancer cells on angiogenesis. Our results also demonstrate the advantage of using the PET approach in conjunction with KEGG database for systematic pathway analysis.</p

Acupuncture for persistent allergic rhinitis: a multi-centre, randomised, controlled trial protocol

<p>Abstract</p> <p>Background</p> <p>Allergic rhinitis is one of the most common health complaints worldwide. Complementary and alternative medical approaches have been employed to relieve allergic rhinitis symptoms and to avoid the side effects of conventional medication. Acupuncture has been widely used to treat patients with allergic rhinitis, but the available evidence of its effectiveness is insufficient. Our objective is to evaluate the effectiveness of acupuncture in patients in Korea and China with persistent allergic rhinitis compared to sham acupuncture treatment or waitlist control.</p> <p>Methods</p> <p>This study consists of a multi-centre (two centres in Korea and two centres in China), randomised, controlled trial with three parallel arms (active acupuncture, sham acupuncture, and waitlist group). The active acupuncture and sham acupuncture groups will receive real or sham acupuncture treatment, respectively, three times per week for a total of 12 sessions over four weeks. Post-treatment follow-up will be performed a month later to complement these 12 acupuncture sessions. Participants in the waitlist group will not receive real or sham acupuncture treatments during this period but will only be required to keep recording their symptoms in a daily diary. After four weeks, the same treatment given to the active acupuncture group will be provided to the waitlist group.</p> <p>Discussion</p> <p>This trial will provide evidence for the effectiveness of acupuncture as a treatment for persistent allergic rhinitis. The primary outcome between groups is a change in the self-reported total nasal symptom score (i.e., nasal obstruction, rhinorrhea, sneezing, and itching) from baseline at the fourth week. Secondary outcome measures include the Rhinitis Quality of Life Questionnaire score and total non-nasal symptom score (i.e., headache, itching, pain, eye-dropping). The quantity of conventional relief medication used during the follow-up period is another secondary outcome measure.</p> <p>Trial registration</p> <p>Current Controlled Trials ISRCTN90807007</p

Nuclear ING2 expression is reduced in human cutaneous melanomas

Cutaneous malignant melanoma is a severe and sometimes life-threatening cancer. The molecular mechanism of melanomagenesis is incompletely understood. Deregulation of apoptosis is probably one of the key factors contributing to the progression of melanoma. The inhibitor of growth (ING) family proteins are candidate tumour suppressors which play important roles in apoptosis. Downregulated expression of ING proteins have been reported in several tumour types, including the loss of nuclear expression of p33ING1b in melanoma. As ING2 exhibits 58.9% homology with p33ING1b, we hypothesized that the aberrant expression of ING2 may be involved in melanomagenesis. Here, we used tissue microarray technology and immunohistochemistry to examine ING2 expression in human nevi and melanoma biopsies. Our data showed that nuclear ING2 expression was significantly reduced in radial growth phase (RGP), vertical growth phase (VGP), and metastatic melanomas compared with dysplastic nevi (P<0.05). Our data also revealed that nuclear ING2 expression was not associated with patient's gender, age or tumour thickness, ulceration, American Joint Committee on Cancer (AJCC) stage, tumour subtype, location and 5-year survival (P>0.05). Taken together, our results suggest that nuclear ING2 expression is significantly reduced in human melanomas and that reduced ING2 may be an important molecular event in the initiation of melanoma development

Concept drift over geological times : predictive modeling baselines for analyzing the mammalian fossil record

Fossils are the remains organisms from earlier geological periods preserved in sedimentary rock. The global fossil record documents and characterizes the evidence about organisms that existed at different times and places during the Earth's history. One of the major directions in computational analysis of such data is to reconstruct environmental conditions and track climate changes over millions of years. Distribution of fossil animals in space and time make informative features for such modeling, yet concept drift presents one of the main computational challenges. As species continuously go extinct and new species originate, animal communities today are different from the communities of the past, and the communities at different times in the past are different from each other. The fossil record is continuously increasing as new fossils and localities are being discovered, but it is not possible to observe or measure their environmental contexts directly, because the time is gone. Labeled data linking organisms to climate is available only for the present day, where climatic conditions can be measured. The approach is to train models on the present day and use them to predict climatic conditions over the past. But since species representation is continuously changing, transfer learning approaches are needed to make models applicable and climate estimates to be comparable across geological times. Here we discuss predictive modeling settings for such paleoclimate reconstruction from the fossil record. We compare and experimentally analyze three baseline approaches for predictive paleoclimate reconstruction: (1) averaging over habitats of species, (2) using presence-absence of species as features, and (3) using functional characteristics of species communities as features. Our experiments on the present day African data and a case study on the fossil data from the Turkana Basin over the last 7 million of years suggest that presence-absence approaches are the most accurate over short time horizons, while species community approaches, also known as ecometrics, are the most informative over longer time horizons when, due to ongoing evolution, taxonomic relations between the present day and fossil species become more and more uncertain.Peer reviewe

Comprehensive Genomic Analysis of a BRCA2 Deficient Human Pancreatic Cancer

Capan-1 is a well-characterised BRCA2-deficient human cell line isolated from a liver metastasis of a pancreatic adenocarcinoma. Here we report a genome-wide assessment of structural variations and high-depth exome characterization of single nucleotide variants and small insertion/deletions in Capan-1. To identify potential somatic and tumour-associated variations in the absence of a matched-normal cell line, we devised a novel method based on the analysis of HapMap samples. We demonstrate that Capan-1 has one of the most rearranged genomes sequenced to date. Furthermore, small insertions and deletions are detected more frequently in the context of short sequence repeats than in other genomes. We also identify a number of novel mutations that may represent genetic changes that have contributed to tumour progression. These data provide insight into the genomic effects of loss of BRCA2 function