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New gene origin

Rohit Randhawa, Ajay Duseja, Harish Changotra
Various case-control studies have shown association of single nucleotide polymorphism rs12303764(G/T) in ULK1 with crohn's disease. The techniques used in these studies were time consuming, complicated and require sophisticated/expensive instruments. Therefore, in order to overcome these problems, we have developed a new, rapid and cost effective Tetra-primer ARMS-PCR assay to genotype single nucleotide polymorphism rs12303764(G/T) of ULK1 gene. We manually designed allele specific primers. DNA fragment amplified using outer primers was sequenced to obtain samples with known genotypes (GG, GT and TT) for further use in the development of T-ARMS-PCR assay...
October 25, 2016: Molecular Biology Reports
Xin Yu, Heyi Zheng, Matthew T V Chan, William Ka Kei Wu
Highly up-regulated in liver cancer (HULC) was originally identified as the most overexpressed long non-coding RNA in hepatocellular carcinoma. Since its discovery, the aberrant up-regulation of HULC has been demonstrated in other cancer types, including gastric cancer, pancreatic cancer, osteosarcoma and hepatic metastasis of colorectal cancer. Recent discoveries have also shed new light on the upstream molecular mechanisms underlying HULC deregulation. As an oncogene, HULC promotes tumorigenesis by regulating multiple pathways, such as down-regulation of EEF1E1, promotion of abnormal lipid metabolism, and up-regulation of sphingosine kinase 1...
October 25, 2016: Journal of Cellular and Molecular Medicine
Magdalena Zaborowska, Jonatan Tillander, Rickard Brånemark, Lars Hagberg, Peter Thomsen, Margarita Trobos
Staphylococci and enterococci account for most deep infections associated with bone-anchored percutaneous implants for amputation treatment. Implant-associated infections are difficult to treat; therefore, it is important to investigate if these infections have a biofilm origin and to determine the biofilm antimicrobial susceptibility to improve treatment strategies. The aims were: (i) to test a novel combination of the Calgary biofilm device and a custom-made susceptibility MIC plate (Sensititre(®) ), (ii) to determine the biofilm formation and antimicrobial resistance in clinical isolates causing implant-associated osteomyelitis, and (iii) to describe the associated clinical outcome...
October 25, 2016: Journal of Biomedical Materials Research. Part B, Applied Biomaterials
Pierre F Ray, Aminata Toure, Metzler-Guillemain, Michael J Mitchell, Christophe Arnoult, Charles Coutton
Infertility, defined by the inability of conceiving a child after one year is estimated to concern approximately 50 million couples worldwide. As the male gamete is readily accessible and can be studied by a simple spermogram it is easier to subcategorize male than female infertility. Subjects with a specific sperm phenotype are more likely to have a common origin thus facilitating the search for causal factors. Male infertility is believed to be often multifactorial and caused by both genetic and extrinsinc factors, but severe cases of male infertility are likely to have a predominant genetic etiology...
October 25, 2016: Clinical Genetics
Edgar Teddy Quispe-Soto, Gloria M Calaf
Global cancer burden increased to 14.1 million new cases in 2012; and breast cancer is the most common cancer in women worldwide, with nearly 1.7 million new cases diagnosed in 2012. Curcumin is the major bioactive ingredient extracted from the rhizome of the plant Curcuma longa (turmeric). Paclitaxel is a microtubule-stabilizing agent originally isolated from the bark of Taxus brevifolia. Curcumin and paclitaxel were evaluated with two human breast cancer cell lines as the luminal MCF-7 and the basal-like MDA-MB-231 that are either positive or negative for hormonal receptors estrogen receptor, progesterone receptor and HER2, respectively...
October 19, 2016: International Journal of Oncology
Abdoulaye Diane, W David Pierce, Sandra E Kelly, Sharon Sokolik, Faye Borthwick, Miriam Jacome-Sosa, Rabban Mangat, Jesus Miguel Pradillo, Stuart McRae Allan, Megan R Ruth, Catherine J Field, Rebecca Hutcheson, Petra Rocic, James C Russell, Donna F Vine, Spencer D Proctor
Obesity and its metabolic complications have emerged as the epidemic of the new millennia. The use of obese rodent models continues to be a productive component of efforts to understand the concomitant metabolic complications of this disease. In 1978, the JCR:LA-cp rat model was developed with an autosomal recessive corpulent (cp) trait resulting from a premature stop codon in the extracellular domain of the leptin receptor. Rats that are heterozygous for the cp trait are lean-prone, while those that are homozygous (cp/cp) spontaneously display the pathophysiology of obesity as well as a metabolic syndrome (MetS)-like phenotype...
2016: Frontiers in Nutrition
Pengjun Xu, Roberto Feuda, Bin Lu, Haijun Xiao, Robert I Graham, Kongming Wu
BACKGROUND: Retrotransposed genes are different to other types of genes as they originate from a processed mRNA and are then inserted back into the genome. For a long time, the contribution of this mechanism to the origin of new genes, and hence to the evolutionary process, has been questioned as retrogenes usually lose their regulatory sequences upon insertion and generally decay into pseudogenes. In recent years, there is growing evidence, notably in mammals, that retrotransposition is an important process driving the origin of new genes, but the evidence in insects remains largely restricted to a few model species...
2016: Mobile DNA
F B Pereira, J L Luque
Molecular and morphological characterization of two species of Cucullanidae from freshwater fish in Brazil are provided, one of which represented an undescribed taxon. Cucullanus opisthoporus n. sp. was collected in Cichla melaniae from River Xingu, State of Pará, and in C. pinima from River Jamarí, State of Rondônia. Nematodes referable to Cucullanus grandistomis were collected in Oxydoras niger from River Xingu. The new species has an appendage in the tail tip, ventrally covered by small spines, which is an exclusive feature of Cucullanus tucunarensis...
October 25, 2016: Journal of Helminthology
Camila González, Liliana Godoy, Ma Angélica Ganga
Volatile phenols are aromatic compounds produced by some yeasts of the genus Brettanomyces as defense against the toxicity of hydroxycinnamic acids (p-coumaric acid, ferulic acid and caffeic acid). The origin of these compounds in winemaking involves the sequential action of two enzymes: coumarate decarboxylase and vinylphenol reductase. The first one converts hydroxycinnamic acids into hydroxystyrenes, which are then reduced to ethyl derivatives by vinylphenol reductase. Volatile phenols derived from p-coumaric acid (4-vinylphenol and 4-ethylphenol) have been described as the major contributors to self-defeating aromas associated with stable, gouache, wet mouse, etc...
October 22, 2016: Antonie Van Leeuwenhoek
Diyendo Massilani, Silvia Guimaraes, Jean-Philip Brugal, E Andrew Bennett, Malgorzata Tokarska, Rose-Marie Arbogast, Gennady Baryshnikov, Gennady Boeskorov, Jean-Christophe Castel, Sergey Davydov, Stéphane Madelaine, Olivier Putelat, Natalia N Spasskaya, Hans-Peter Uerpmann, Thierry Grange, Eva-Maria Geigl
BACKGROUND: Climatic and environmental fluctuations as well as anthropogenic pressure have led to the extinction of much of Europe's megafauna. The European bison or wisent (Bison bonasus), one of the last wild European large mammals, narrowly escaped extinction at the onset of the 20th century owing to hunting and habitat fragmentation. Little is known, however, about its origin, evolutionary history and population dynamics during the Pleistocene. RESULTS: Through ancient DNA analysis we show that the emblematic European bison has experienced several waves of population expansion, contraction, and extinction during the last 50,000 years in Europe, culminating in a major reduction of genetic diversity during the Holocene...
October 21, 2016: BMC Biology
Magali Ranchou-Peyruse, Cyrielle Gasc, Marion Guignard, Thomas Aüllo, David Dequidt, Pierre Peyret, Anthony Ranchou-Peyruse
The formation water of a deep aquifer (853 m of depth) used for geological storage of natural gas was sampled to assess the mono-aromatic hydrocarbons attenuation potential of the indigenous microbiota. The study of bacterial diversity suggests that Firmicutes and, in particular, sulphate-reducing bacteria (Peptococcaceae) predominate in this microbial community. The capacity of the microbial community to biodegrade toluene and m- and p-xylenes was demonstrated using a culture-based approach after several hundred days of incubation...
October 21, 2016: Microbial Biotechnology
Reza Fotouhi-Ardakani, Shahriar Dabiri, Soheila Ajdari, Mohammad Hossein Alimohammadian, Elnaz AlaeeNovin, Neda Taleshi, Parviz Parvizi
The polymorphism and genetic diversity of Leishmania genus has status under discussion depending on many items such as nuclear and/or mitochondrial genes, molecular tools, Leishmania species, geographical origin, condition of micro-environment of Leishmania parasites and isolation of Leishmania from clinical samples, reservoir host and vectors. The genetic variation of Leishmania species (L. major, L. tropica, L. tarentolae, L. mexicana, L. infantum) were analyzed and compared using mitochondrial (COII and Cyt b) and nuclear (nagt, ITS-rDNA and HSP70) genes...
October 17, 2016: Infection, Genetics and Evolution
Félix LaRoche-Johnston, Caroline Monat, Benoit Cousineau
BACKGROUND: Group II introns are catalytically active RNA and mobile retroelements present in certain eukaryotic organelles, bacteria and archaea. These ribozymes self-splice from the pre-mRNA of interrupted genes and reinsert within target DNA sequences by retrohoming and retrotransposition. Evolutionary hypotheses place these retromobile elements at the origin of over half the human genome. Nevertheless, the evolution and dissemination of group II introns was found to be quite difficult to infer...
October 20, 2016: BMC Evolutionary Biology
Jenna F DuMond, Xue Zhang, Yuichiro Izumi, Kevin Ramkissoon, Guanghui Wang, Marjan Gucek, Xujing Wang, Maurice B Burg, Joan D Ferraris
NFAT5 is a transcription factor originally identified because it is activated by hypertonicity and that activation increases expression of genes that protect against the adverse effects of the hypertonicity. However, its targets also include genes not obviously related to tonicity. The transactivating domain of NFAT5 is contained in its c-terminal region, which is predicted to be unstructured. Unstructured regions are common in transcription factors particularly in transactivating domains where they can bind co-regulatory proteins essential to their function...
October 7, 2016: Physiological Genomics
Jyoti Rao, Boris Greber
Human embryonic stem cells (hESCs) present a fascinating and powerful system for generating specialized cell types of the human body. Culture and directed differentiation of these cells however requires an understanding of the pluripotent ground state and of how cell lineage decisions in this system are made. In this review, we highlight both these aspects in light of recent findings and technical progress. Hence, advances in culturing the human preimplantation embryo beyond the implantation barrier and in analyzing it at the single-cell level shed new light on the hESC tissue of origin...
October 19, 2016: Stem Cells
Soledad Sagastume, Raquel Martín-Hernández, Mariano Higes, Nuno Henriques-Gil
BACKGROUND: There is great controversy as to whether Microsporidia undergo a sexual cycle. In the paradigmatic case of Nosema ceranae, although there is no morphological evidence of sex, some meiosis-specific genes are present in its reduced genome and there is also high intraspecific variability, with incongruent phylogenies having been systematically obtained. The possibility of sexual recombination is important from an epidemiological standpoint, particularly as N. ceranae is considered to be a major factor in the current disquieting epidemic of widespread bee colony losses...
October 18, 2016: BMC Evolutionary Biology
Deepti Varshney, Akanksha Jaiswar, Alok Adholeya, Pushplata Prasad
BACKGROUND: Subtilisin-like serine proteases or Subtilases in fungi are important for penetration and colonization of host. In Hypocreales, these proteins share several properties with other fungal, bacterial, plant and mammalian homologs. However, adoption of specific roles in entomopathogenesis may be governed by attainment of unique biochemical and structural features during the evolutionary course. Due to such functional shifts Subtilases coded by different family members of Hypocreales acquire distinct features according to respective hosts and lifestyle...
October 19, 2016: BMC Evolutionary Biology
Agnieszka Rybarczyk, Paulina Jackowiak, Marek Figlerowicz, Jacek Blazewicz
Since the beginning of the 21st century, an increasing interest in the research of ribonucleic acids has been observed in response to a surprising discovery of the role that RNA molecules play in the biological systems. It was demonstrated that they do not only take part in the protein synthesis (mRNA, rRNA, tRNA) but also are involved in the regulation of gene expression. Several classes of small regulatory RNAs have been discovered (e.g. microRNA, small interfering RNA, piwiRNA). Most of them are excised from specific double-stranded RNA precursors by enzymes that belong to the RNaseIII family (Drosha, Dicer or Dicer-like proteins)...
October 19, 2016: Acta Biochimica Polonica
Zhijie Pan, Rong Liu, Pei Zhang, Hua Zhou, Yiqi Fu, Jianying Zhou
Raoultella planticola is a gram-negative bacterium that rarely causes diseases in humans. Here, we present a case of hospital-acquired pneumonia caused by R. planticola that likely originated in the gastrointestinal tract. To the best of our knowledge, this is the second report describing the detection of the gene New Delhi Metallo-β-lactamase-1 (blaNDM-1) in multidrug-resistant R. planticola. Clinical samples were collected for bacterial culture and antimicrobial susceptibility testing from a patient during hospitalization...
October 18, 2016: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
Erina Takai, Yasushi Totoki, Hiromi Nakamura, Mamoru Kato, Tatsuhiro Shibata, Shinichi Yachida
Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies. The genomic landscape of the PDAC genome features four frequently mutated genes (KRAS, CDKN2A, TP53, and SMAD4) and dozens of candidate driver genes altered at low frequency, including potential clinical targets. Circulating cell-free DNA (cfDNA) is a promising resource to detect molecular characteristics of tumors, supporting the concept of "liquid biopsy".We determined the mutational status of KRAS in plasma cfDNA using multiplex droplet digital PCR in 259 patients with PDAC, retrospectively...
2016: Advances in Experimental Medicine and Biology
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