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New gene origin

Pankaj Soni, Pravata K Pradhan, T R Swaminathan, Neeraj Sood
A cell line, designated as PHF, has been established from caudal fin of Pangasianodon hypophthalmus. The cell line was developed using explant method and PHF cells have been subcultured for more than 72 passages over a period of 14 months. The cells were able to grow at temperatures between 24 and 32° C, with an optimum temperature of 28° C. The growth rate of PHF cells was directly proportional to FBS concentration, with optimum growth observed at 20% FBS concentration. On the basis of immunophenotyping assay, PHF cells were confirmed to be of epithelial type...
March 12, 2018: Acta Tropica
Oneida Espinosa-Álvarez, Paola A Ortiz, Luciana Lima, André G Costa-Martins, Myrna G Serrano, Stephane Herder, Gregory A Buck, Erney P Camargo, Patrick B Hamilton, Jamie R Stevens, Marta M G Teixeira
Trypanosoma rangeli and Trypanosoma cruzi are generalist trypanosomes sharing a wide range of mammalian hosts; they are transmitted by triatomine bugs, and are the only trypanosomes infecting humans in the Neotropics. Their origins, phylogenetic relationships, and emergence as human parasites have long been subjects of interest. In the present study, taxon-rich analyses (20 trypanosome species from bats and terrestrial mammals) using ssrRNA, glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH), heat shock protein-70 (HSP70) and Spliced Leader (SL) RNA sequences, and multilocus phylogenetic analyses using 11 single copy genes from 15 selected trypanosomes, provide increased resolution of relationships between species and clades, strongly supporting two main sister lineages: lineage Schizotrypanum, comprising T...
March 12, 2018: International Journal for Parasitology
José F Muñoz, Juan G McEwen, Oliver K Clay, Christina A Cuomo
Dimorphic fungal pathogens cause a significant human disease burden and unlike most fungal pathogens affect immunocompetent hosts. To examine the origin of virulence of these fungal pathogens, we compared genomes of classic systemic, opportunistic, and non-pathogenic species, including Emmonsia and two basal branching, non-pathogenic species in the Ajellomycetaceae, Helicocarpus griseus and Polytolypa hystricis. We found that gene families related to plant degradation, secondary metabolites synthesis, and amino acid and lipid metabolism are retained in H...
March 14, 2018: Scientific Reports
Verity A Jackson, Dimphna H Meijer, Maria Carrasquero, Laura S van Bezouwen, Edward D Lowe, Colin Kleanthous, Bert J C Janssen, Elena Seiradake
Teneurins are ancient cell-cell adhesion receptors that are vital for brain development and synapse organisation. They originated in early metazoan evolution through a horizontal gene transfer event when a bacterial YD-repeat toxin fused to a eukaryotic receptor. We present X-ray crystallography and cryo-EM structures of two Teneurins, revealing a ~200 kDa extracellular super-fold in which eight sub-domains form an intricate structure centred on a spiralling YD-repeat shell. An alternatively spliced loop, which is implicated in homophilic Teneurin interaction and specificity, is exposed and thus poised for interaction...
March 14, 2018: Nature Communications
Dilruba Sharmin, Yong Guo, Tomoyasu Nishizawa, Shoko Ohshima, Yoshinori Sato, Yusuke Takashima, Kazuhiko Narisawa, Hiroyuki Ohta
Endohyphal bacteria (EHB), dwelling within fungal hyphae, markedly affect the growth and metabolic potential of their hosts. To date, two EHB belonging to the family Burkholderiaceae have been isolated and characterized as new taxa, Burkholderia rhizoxinica (HKI 454T ) and Mycoavidus cysteinexigens (B1-EBT ), in Japan. Metagenome sequencing was recently reported for Mortierella elongata AG77 together with its endosymbiont M. cysteinexigens (Mc-AG77) from a soil/litter sample in the USA. In the present study, we elucidated the complete genome sequence of B1-EBT and compared it with those of Mc-AG77 and HKI 454T ...
March 14, 2018: Microbes and Environments
Darren A Cusanovich, James P Reddington, David A Garfield, Riza M Daza, Delasa Aghamirzaie, Raquel Marco-Ferreres, Hannah A Pliner, Lena Christiansen, Xiaojie Qiu, Frank J Steemers, Cole Trapnell, Jay Shendure, Eileen E M Furlong
Understanding how gene regulatory networks control the progressive restriction of cell fates is a long-standing challenge. Recent advances in measuring gene expression in single cells are providing new insights into lineage commitment. However, the regulatory events underlying these changes remain unclear. Here we investigate the dynamics of chromatin regulatory landscapes during embryogenesis at single-cell resolution. Using single-cell combinatorial indexing assay for transposase accessible chromatin with sequencing (sci-ATAC-seq), we profiled chromatin accessibility in over 20,000 single nuclei from fixed Drosophila melanogaster embryos spanning three landmark embryonic stages: 2-4 h after egg laying (predominantly stage 5 blastoderm nuclei), when each embryo comprises around 6,000 multipotent cells; 6-8 h after egg laying (predominantly stage 10-11), to capture a midpoint in embryonic development when major lineages in the mesoderm and ectoderm are specified; and 10-12 h after egg laying (predominantly stage 13), when each of the embryo's more than 20,000 cells are undergoing terminal differentiation...
March 14, 2018: Nature
Marie C Matrka, Katherine A Cimperman, Sarah R Haas, Geraldine Guasch, Lisa A Ehrman, Ronald R Waclaw, Kakajan Komurov, Adam Lane, Kathryn A Wikenheiser-Brokamp, Susanne I Wells
Esophageal cancer occurs as either squamous cell carcinoma (ESCC) or adenocarcinoma. ESCCs comprise almost 90% of cases worldwide, and recur with a less than 15% five-year survival rate despite available treatments. The identification of new ESCC drivers and therapeutic targets is critical for improving outcomes. Here we report that expression of the human DEK oncogene is strongly upregulated in esophageal SCC based on data in the cancer genome atlas (TCGA). DEK is a chromatin-associated protein with important roles in several nuclear processes including gene transcription, epigenetics, and DNA repair...
March 14, 2018: PLoS Genetics
Marjolein Drent, Petal Wijnen, Aalt Bast
PURPOSE OF REVIEW: Fibrosing interstitial pneumonias are associated with various stages of fibrosis. The cause of this group of syndromes remains largely unknown. For most of these diseases, a genetic basis, environmental factors and certain triggers have been suggested as possible risk factors. Various studies have found an association between genetic polymorphisms, or the presence of certain variant alleles, and the occurrence and/or progression of interstitial pneumonias of unknown origin...
March 13, 2018: Current Opinion in Pulmonary Medicine
Mariia Rabyk, Oleksandr Yushchuk, Ihor Rokytskyy, Maria Anisimova, Bohdan Ostash
The AdpA protein from a streptomycin producer Streptomyces griseus is a founding member of the AdpA family of pleiotropic regulators, known to be ubiquitously present in streptomycetes. Functional genomic approaches revealed a huge number of AdpA targets, leading to the claim that the AdpA regulon is the largest one in bacteria. The expression of adpA is limited at the level of translation of the rare leucyl UUA codon. All known properties of AdpA regulators were discovered on a few streptomycete strains. There are open questions about the true abundance and diversity of AdpA across actinobacterial taxa (and beyond) and about the possible evolutionary forces that shape the AdpA orthologous group in Streptomyces...
March 13, 2018: Journal of Molecular Evolution
Vinicius A C Abreu, Rafael V Popin, Danillo O Alvarenga, Patricia D C Schaker, Caroline Hoff-Risseti, Alessandro M Varani, Marli F Fiore
Cylindrospermopsis raciborskii is a freshwater cyanobacterial species with increasing bloom reports worldwide that are likely due to factors related to climate change. In addition to the deleterious effects of blooms on aquatic ecosystems, the majority of ecotypes can synthesize toxic secondary metabolites causing public health issues. To overcome the harmful effects of C. raciborskii blooms, it is important to advance knowledge of diversity, genetic variation, and evolutionary processes within populations...
2018: Frontiers in Microbiology
Raphaël Méheust, Debashish Bhattacharya, Jananan S Pathmanathan, James O McInerney, Philippe Lopez, Eric Bapteste
BACKGROUND: Eukaryotes evolved from the symbiotic association of at least two prokaryotic partners, and a good deal is known about the timings, mechanisms, and dynamics of these evolutionary steps. Recently, it was shown that a new class of nuclear genes, symbiogenetic genes (S-genes), was formed concomitant with endosymbiosis and the subsequent evolution of eukaryotic photosynthetic lineages. Understanding their origins and contributions to eukaryogenesis would provide insights into the ways in which cellular complexity has evolved...
March 13, 2018: BMC Biology
Ian M MacDonald, Pamela C Sieving
PURPOSE: To review the contributions to ophthalmic genetics through the American Journal of OphthalmologyDesign: Perspective. METHODS: A literature search to retrieve original articles, letters, editorials, and published lectures from 1966 to 2017, providing a 50 year review. Titles were excluded that gave no reference to genetics or presented findings related to a non-genetic ocular condition. RESULTS: From a search of the Scopus database, 719 articles were ascertained...
March 9, 2018: American Journal of Ophthalmology
Steven Parker, Marcin G Fraczek, Jian Wu, Sara Shamsah, Alkisti Manousaki, Kobchai Dungrattanalert, Rogerio Alves de Almeida, Edith Invernizzi, Tim Burgis, Walid Omara, Sam Griffiths-Jones, Daniela Delneri, Raymond T O'Keefe
Noncoding RNAs (ncRNAs) are emerging as key regulators of cellular function. We have exploited the recently developed barcoded ncRNA gene deletion strain collections in the yeast Saccharomyces cerevisiae to investigate the numerous ncRNAs in yeast with no known function. The ncRNA deletion collection contains deletions of tRNAs, snoRNAs, snRNAs, stable unannotated transcripts (SUTs), cryptic unannotated transcripts (CUTs) and other annotated ncRNAs encompassing 532 different individual ncRNA deletions. We have profiled the fitness of the diploid heterozygous ncRNA deletion strain collection in six conditions using batch and continuous liquid culture, as well as the haploid ncRNA deletion strain collections arrayed individually onto solid rich media...
March 12, 2018: PLoS Genetics
Karolina Nemes, Michael C Frühwald
Malignant Rhabdoid Tumor (MRT) is a rare and highly aggressive malignancy primarily affecting infants and young children. The most common anatomic locations are the central nervous system (AT/RT), the kidneys (RTK) and other soft tissues (eMRT). The genetic origin of this disease is linked to mutations in SMARCB1, a gene encoding a core subunit of the SWI/SNF chromatin-remodeling complex. Areas covered: Conventional multimodal treatment may offer a significant survival benefit to certain patients. It remains to be determined, however, which patients will prove resistant to chemotherapy and need novel therapeutic approaches...
March 12, 2018: Expert Opinion on Therapeutic Targets
Farzana Jasmine, Justin Shinkle, Mekala Sabarinathan, Habibul Ahsan, Brandon L Pierce, Muhammad G Kibriya
OBJECTIVES: Relative telomere length (RTL) is a potential biomarker of aging and risk for chronic disease. Previously, we developed a probe-based RTL assay on Luminex platform, where probes for Telomere (T) and reference gene (R) for a given DNA sample were tested in a single well. Here, we describe a method of pooling multiple samples in one well to increase the throughput and cost-effectiveness. METHODS: We used four different microbeads for the same T-probe and four different microbeads for the same R-probe...
March 12, 2018: American Journal of Human Biology: the Official Journal of the Human Biology Council
S Georgin-Lavialle, V Hentgen, K Stankovic Stojanovic, C Bachmeyer, F Rodrigues, L Savey, S Abbara, P-L Conan, T Fraisse, M Delplanque, A Rouet, N Sbeih, I Koné-Paut, G Grateau
Familial Mediterranean Fever (FMF) is the most frequent monogenic auto-inflammatory disease. FMF is an autosomal recessive disease, which affects populations from Mediterranean origin and is associated with MEFV gene mutations encoding for the protein pyrin. Pyrin activation enhances the secretion of interleukin 1 by myelo-monocytic cells. Main features of the disease are acute attacks of serositis mainly located on the abdomen, less frequently on chest and joints, accompanied by fever and biological inflammatory markers elevation...
March 8, 2018: La Revue de Médecine Interne
Nicholas Dusek, Austin J Hewitt, Kaycie N Schmidt, Peter W Bergholz
E. coli are deposited into soil with feces and exhibit subsequent population decline with concomitant environmental selection. Environmentally persistent strains exhibit longer survival times during this selection process and some strains have adapted to soil and sediments. A georeferenced collection of E. coli isolates was developed comprising 3,329 isolates from 1,428 soil samples that were collected from a landscape spanning the transition from the grasslands to the eastern deciduous forest biomes. The isolate collection and sample database were analyzed together to discover how land cover, site characteristics and soil chemistry influence the prevalence of cultivable E...
March 9, 2018: Applied and Environmental Microbiology
Kevin Doello
Cancer tissues and placental ones share many properties such as invasiveness, metastasis and local immunosuppressive effects. The goal of the present article is to hypothesize a theory about cancer origin that links placental and cancerous tissues at molecular level. This hypothesis explain that cancer origin could be due to low hypoxic conditions in the peripheral zones of benign tumors which might up-regulate the expression of IGF2, and, consequently, trophoblastic genes. In fact, many phenotypic characteristics and molecular markers are shared between these two cell types (cancerous and trophoblastics ones), providing evidences to support this hypothesis...
April 2018: Medical Hypotheses
Øivind Skare, Rolv T Lie, Øystein A Haaland, Miriam Gjerdevik, Julia Romanowska, Håkon K Gjessing, Astanand Jugessur
Background: Although both the mother's and father's alleles are present in the offspring, they may not operate at the same level. These parent-of-origin (PoO) effects have not yet been explored on the X chromosome, which motivated us to develop new methods for detecting such effects. Orofacial clefts (OFCs) exhibit sex-specific differences in prevalence and are examples of traits where a search for various types of effects on the X chromosome might be relevant. Materials and Methods: We upgraded our R-package Haplin to enable genome-wide analyses of PoO effects, as well as power simulations for different statistical models...
2018: Frontiers in Genetics
Yi Zhou, Xiang Cao, Yang Yang, Jing Wang, Weidong Yang, Peiling Ben, Lei Shen, Peng Cao, Lan Luo, Zhimin Yin
Glutathione S -transferase Pi (GSTP) was originally identified as one of cytosolic phase II detoxification enzymes and also was considered to function via its non-catalytic, ligand-binding activity. We have reported that GSTP played an anti-inflammatory role in macrophages, suggesting that GSTP may have a protective role in inflammation. In this study, we deleted the murine Gstp gene cluster and found that GSTP significantly decreased the mortality of experimental sepsis and reduced related serum level of high mobility group box-1 protein (HMGB1)...
2018: Frontiers in Immunology
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