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De Novo

Tatjana Ćosić, Martin Raspor, Jelena Savić, Aleksandar Cingel, Dragana Matekalo, Snežana Zdravković-Korać, Slavica Ninković
Kohlrabi (Brassica oleracea var. gongylodes) is an important vegetable crop that is able to undergo shoot regeneration in culture from intact seedlings in a single-step regeneration process, using cytokinin as the only plant growth regulator. In this work, we present the expression profiles of seven organogenesis-related genes over the time course of shoot regeneration from intact seedlings of kohlrabi cv. Vienna Purple on shoot regeneration media containing trans-zeatin, cis-zeatin, benzyl adenine or thidiazuron...
November 8, 2018: Journal of Plant Physiology
Ying Li, Xiangbin Jia, Huidan Wu, Guanglei Xun, Jianjun Ou, Qiumeng Zhang, Honghui Li, Ting Bai, Zhengmao Hu, Xiaobing Zou, Kun Xia, Hui Guo
SHANK3 has been identified as the causative gene of 22q13.3 microdeletion syndrome phenotype. De novo mutations (DNMs) of SHANK3 were subsequently identified in patients with several neurodevelopmental disorders, including autism spectrum disorders (ASDs), schizophrenia (SCZ), a Rett syndrome-like phenotype, and intellectual disability (ID). Although broad developmental phenotypes of these patients have been described in single studies, few studies have reviewed the genotype and phenotype relationships using a relatively large cohort of patients with SHANK3 DNMs...
December 9, 2018: American Journal of Medical Genetics. Part A
Ana Carolina Tahira, André Rocha Barbosa, Arthur Sant'Anna Feltrin, Vinicius Daguano Gastaldi, Victor Hugo Calegari de Toledo, José Geraldo de Carvalho Pereira, Bianca Cristina Garcia Lisboa, Viviane Neri de Souza Reis, Ana Cecília Feio Dos Santos, Mariana Maschietto, Helena Brentani
The male-biased prevalence of certain neurodevelopmental disorders and the sex-biased outcomes associated with stress exposure during gestation have been previously described. Here, we hypothesized that genes distinctively targeted by only one or both homologous proteins highly conserved across therian mammals, SOX3 and SRY, could induce sexual adaptive changes that result in a differential risk for neurodevelopmental disorders. ChIP-seq/chip data showed that SOX3/SRY gene targets were expressed in different brain cell types in mice...
December 9, 2018: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
Adrian Wlodarczak, Magdalena Lanocha, Artur Jastrzebski, Maciej Pecherzewski, Marek Szudrowicz, Waldemar Jastrzebski, Joanna Nawrot, Maciej Lesiak
OBJECTIVES: The Magmaris-ACS Registry is the first assessment of the Magmaris implantation in the acute coronary syndrome (ACS) population. BACKGROUND: Bioresorbable vascular scaffolds (BRS), the newest coronary stent technology, was developed to overcome the limitations of the metallic drug-eluting stents (DES). Current promising data of the Magmaris in patients with stable angina have encouraged to validate the second generation BRS in ACS indications. METHODS: The study population consisted of the consecutive patients who underwent PCI with the Magmaris BRS in the settings of ACS...
December 10, 2018: Catheterization and Cardiovascular Interventions
Rui Faria, Pragya Chaube, Hernán E Morales, Tomas Larsson, Alan R Lemmon, Emily Moriarty Lemmon, Marina Rafajlović, Marina Panova, Mark Ravinet, Kerstin Johannesson, Anja M Westram, Roger K Butlin
Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis...
December 8, 2018: Molecular Ecology
Jason K Sa, Seung Won Choi, Junfei Zhao, Yeri Lee, Jing Zhang, Doo-Sik Kong, Jung Won Choi, Ho Jun Seol, Jung-Il Lee, Antonio Iavarone, Raul Rabadan, Do-Hyun Nam
Hypermutagenesis refers to marked increase in the number of mutations due to continuous mutagenic process. Hypermutated tumors, have being found in several tumor types, are associated with inherited or acquired alterations in DNA repair pathways. Hypermutation has been observed in a subset of adult glioma patients as a direct result of temozolomide(TMZ)-induced mutagenesis. In present study, we have identified a rare subset of treatment-naïve adult gliomas with de novo hypermutator phenotype and explored the evolution of spontaneous and treatment-induced hypermutagenesis...
December 11, 2018: International Journal of Cancer. Journal International du Cancer
Bibiana K Y Wong, V Reid Sutton
Aicardi syndrome is a rare, severe neurodevelopmental disorder classically characterized by the triad of infantile spasms, central chorioretinal lacunae, and agenesis of the corpus callosum. Aicardi syndrome only affects females, with the exception of a few males with a 47, XXY chromosome constitution. All cases are de novo and the only cases of definitive recurrence in families are in identical twins. It is now recognized that individuals with Aicardi syndrome commonly exhibit a variety of other neuronal migration defects, eye anomalies, and other somatic features, including skin, skeletal, and craniofacial systems...
December 10, 2018: American Journal of Medical Genetics. Part C, Seminars in Medical Genetics
Taichi Imaizumi, Yukiko Mogami, Nobuhiko Okamoto, Keiko Yamamoto-Shimojima, Toshiyuki Yamamoto
Microdeletions in 1p35.2 region are rare and there are only two reports 1,2 . Here, we report an additional patient with a de novo 1p35.2 microdeletion. An 18-month-old boy was born at 38 weeks of gestation by vaginal delivery. His birth weight was 2452 g (-1.2 SD), length was 49 cm (+0.3 SD), and occipitofrontal circumference (OFC) was 31.6 cm (-1.1 SD). This article is protected by copyright. All rights reserved.
December 10, 2018: Congenital Anomalies
Jeroen J Smits, Jaap Oostrik, Andy J Beynon, Sarina G Kant, Pia A M de Koning Gans, Liselotte J C Rotteveel, Jolien S Klein Wassink-Ruiter, Rolien H Free, Saskia M Maas, Jiddeke van de Kamp, Paul Merkus, Wouter Koole, Ilse Feenstra, Ronald J C Admiraal, Cornelis P Lanting, Margit Schraders, Helger G Yntema, Ronald J E Pennings, Hannie Kremer
ATP2B2 encodes the PMCA2 Ca2+ pump that plays an important role in maintaining ion homeostasis in hair cells among others by extrusion of Ca2+ from the stereocilia to the endolymph. Several mouse models have been described for this gene; mice heterozygous for loss-of-function defects display a rapidly progressive high-frequency hearing impairment. Up to now ATP2B2 has only been reported as a modifier, or in a digenic mechanism with CDH23 for hearing impairment in humans. Whole exome sequencing in hearing impaired index cases of Dutch and Polish origins revealed five novel heterozygous (predicted to be) loss-of-function variants of ATP2B2...
December 8, 2018: Human Genetics
Xiao-Ya Sun, Yan-Hui Wang, Zhuo-Er Dong, Hao-Yang Wu, Ping-Ping Chen, Qiang Xie
Wing polymorphism is common in a wide variety of insect species. However, few studies have reported on adaptations in the wing polymorphism of insects at molecular level, in particular for males. Thus, the adaptive mechanisms need to be explored. The remarkable variability in wing morphs of insects is well represented in the water striders (Hemiptera: Gerridae). Within this family, Gigantometra gigas (China, 1925), the largest water strider known worldwide, displays macropterous and apterous males. In the present study, we used de novo transcriptome assembly to obtain gene expression information and compared body and leg-component lengths of adult males in different wing morphs...
November 1, 2018: Journal of Insect Science
Claire Marks, Charlotte M Deane
Motivation: Accurate prediction of loop structures remains challenging. This is especially true for long loops where the large conformational space and limited coverage of experimentally-determined structures often leads to low accuracy. Co-evolutionary contact predictors, which provide information about the proximity of pairs of residues, have been used to improve whole-protein models generated through de novo techniques. Here we investigate whether these evolutionary constraints can enhance the prediction of long loop structures...
December 10, 2018: Bioinformatics
Sree Rohit Raj Kolora, Anne Weigert, Amin Saffari, Stephanie Kehr, Maria Beatriz Walter Costa, Cathrin Spröer, Henrike Indrischek, Manjusha Chintalapati, Konrad Lohse, Gero Doose, Jörg Overmann, Boyke Bunk, Christoph Bleidorn, Annegret Grimm-Seyfarth, Klaus Henle, Katja Nowick, Rui Faria, Peter F Stadler, Martin Schlegel
Background: Lacerta viridis and L. bilineata are sister species of European green lizards (eastern and western clades respectively), which until recently were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the L. viridis complex. The population history of these sister species and processes driving divergence are unknown. We constructed high quality de novo genome assemblies for both L...
December 10, 2018: GigaScience
Guoli Ji, Wenbin Ye, Yaru Su, Moliang Chen, Guangzao Huang, Xiaohui Wu
Summary: Alternative splicing (AS) is a well-established mechanism for increasing transcriptome and proteome diversity, however, detecting AS events and distinguishing among AS types in organisms without available reference genomes remains challenging. We developed a de novo approach called AStrap for AS analysis without using a reference genome. AStrap identifies AS events by extensive pair-wise alignments of transcript sequences and predicts AS types by a machine-learning model integrating more than 500 assembled features...
December 7, 2018: Bioinformatics
Elaine A Yu, Peter J Hu, Saurabh Mehta
Background: Insulin regulates fatty acids (FAs) in the blood; conversely, FAs may mediate insulin sensitivity and are potentially modifiable risk factors of the diabetogenic state. Objective: The objective of our study was to examine the associations between plasma concentrations of FAs, fasting plasma glucose (FPG), and glycated hemoglobin (HbA1c) among individuals (n = 1433) in the NHANES (2003-2004). Design: Plasma concentrations of 24 individual FAs were considered individually and in subgroups, per chemical structure...
September 1, 2018: American Journal of Clinical Nutrition
Jean L Mbisa, Peter Kirwan, Anna Tostevin, Juan Ledesma, David F Bibby, Alison Brown, Richard Myers, Amin S Hassan, Gary Murphy, David Asboe, Anton Pozniak, Stuart Kirk, O Noel Gill, Caroline Sabin, Valerie Delpech, David T Dunn
Background: Drug-resistant minority variants (DRMinVs) detected in patients who recently acquired HIV-1 can be transmitted, generated de novo through virus replication, or technical errors. The first are likely to persist and result in treatment failure while the latter two could be stochastic and transient. Methods: Ultra-deep sequencing of plasma samples from 835 individuals with recent HIV-1 infection in the UK was performed to detect DRMinVs at mutation frequency between 2-20%...
December 11, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
Fábio Tadeu Arrojo Martins, Berenice Dias Ramos, Edi Lúcia Sartorato
HDR syndrome is a rare autosomal dominant disorder caused by mutations in the GATA3 gene and characterized by hypoparathyroidism, sensorineural deafness and renal abnormalities. Here we report a Brazilian family, from which the proband, his mother and his grandfather were diagnosed with bilateral sensorineural hearing loss. Molecular screening of the GJB2, GJB6 and MTRNR1 genes in the proband showed no alterations; however, whole exome sequencing detected a heterozygous mutation, c.1099C > T (p.Arg367*), in the GATA3 gene...
November 14, 2018: Genetics and Molecular Biology
Michael McCaul, Mike Clarke, Stevan R Bruijns, Peter W Hodkinson, Ben de Waal, Jennifer Pigoga, Lee A Wallis, Taryn Young
Introduction: An adaptive guideline development method, as opposed to a de novo guideline development, is dependent on access to existing high-quality up-to-date clinical practice guidelines (CPGs). We described the characteristics and quality of CPGs relevant to prehospital care worldwide, in order to strengthen guideline development in low-resource settings for emergency care. Methods: We conducted a descriptive study of a database of international CPGs relevant to emergency care produced by the African Federation for Emergency Medicine (AFEM) CPG project in 2016...
December 2018: African Journal of Emergency Medicine Revue Africaine de la Médecine D'urgence
Ingrid Koeter, Gro Stensröd, Aud Hunsbedt Nilsen, Rigmor Lund, Colette Haslam, Marianne De Sèze, Rajagopalan Sriram, John Heesakkers
Aims: This study investigated user perception and adherence related to a hydrophilic-coated urinary catheter (LoFric® Origo™), available for male patients who practice intermittent catheterization. Design: The study had a prospective observational design, including patients from 19 European hospitals. Methods: A total of 416 patients were eligible for the study; 179 experienced catheter users and 237 de novo. Two questionnaires were filled out, one describing background data and a second, 8 weeks later, evaluating catheter features...
January 2019: Nursing Open
Kan Yaguchi, Takahiro Yamamoto, Ryo Matsui, Masaya Shimada, Atsuko Shibanuma, Keiko Kamimura, Toshiaki Koda, Ryota Uehara
Recently, we observed that tetraploidization of certain types of human cancer cells resulted in upregulation of centrosome duplication cycles and chronic generation of the extra centrosome. Here, we investigated whether tetraploidy-linked upregulation of centrosome duplication also occurs in non-cancer cells using tetraploidized parthenogenetic mouse embryos. Cytokinesis blockage at early embryonic stage before de novo centriole biogenesis provided the unique opportunity in which tetraploidization can be induced without transient doubling of centrosome number...
2018: Communicative & Integrative Biology
Sara Louise Dahl, Joshua S Woodworth, Christian Johann Lerche, Elisabeth Præstekjær Cramer, Pia Rude Nielsen, Claus Moser, Allan Randrup Thomsen, Niels Borregaard, Jack Bernard Cowland
Lipocalin-2 is a constituent of the neutrophil secondary granules and is expressed de novo by macrophages and epithelium in response to inflammation. Lipocalin-2 acts in a bacteriostatic fashion by binding iron-loaded siderophores required for bacterial growth. Mycobacterium tuberculosis (M.tb) produces siderophores that can be bound by lipocalin-2. The impact of lipocalin-2 in the innate immune response toward extracellular bacteria has been established whereas the effect on intracellular bacteria, such as M...
2018: Frontiers in Immunology
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