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SNP critical care

Alessandro Foti, Frank Dorendorf, Silke Leimkühler
Aldehyde oxidases (AOXs) are molybdo-flavoenzymes characterized by broad substrate specificity, oxidizing aromatic/aliphatic aldehydes into the corresponding carboxylic acids and hydroxylating various heteroaromatic rings. The enzymes use oxygen as the terminal electron acceptor and produce reduced oxygen species during turnover. The physiological function of mammalian AOX isoenzymes is still unclear, however, human AOX (hAOX1) is an emerging enzyme in phase-I drug metabolism. Indeed, the number of xenobiotics acting as hAOX1 substrates is increasing...
2017: PloS One
Loic Yengo, Zhihong Zhu, Naomi R Wray, Bruce S Weir, Jian Yang, Matthew R Robinson, Peter M Visscher
Quantifying the effects of inbreeding is critical to characterizing the genetic architecture of complex traits. This study highlights through theory and simulations the strengths and shortcomings of three SNP-based inbreeding measures commonly used to estimate inbreeding depression (ID). We demonstrate that heterogeneity in linkage disequilibrium (LD) between causal variants and SNPs biases ID estimates, and we develop an approach to correct this bias using LD and minor allele frequency stratified inference (LDMS)...
August 8, 2017: Proceedings of the National Academy of Sciences of the United States of America
Yi Chen, Yan Luo, Heather Carleton, Ruth Timme, David Melka, Tim Muruvanda, Charles Wang, George Kastanis, Lee S Katz, Lauren Turner, Angela Fritzinger, Terence Moore, Robert Stones, Joseph Blankenship, Monique Salter, Mickey Parish, Thomas S Hammack, Peter S Evans, Cheryl L Tarr, Marc W Allard, Errol A Strain, Eric W Brown
Epidemiological findings of a listeriosis outbreak in 2013 implicated Hispanic-style cheese produced by Company A, and pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed on clinical isolates and representative isolates collected from Company A cheese and environmental samples during the investigation. The results strengthened the evidence for cheese as the vehicle. Surveillance sampling and WGS three months later revealed that the equipment purchased by Company B from Company A yielded an environmental isolate highly similar to all outbreak isolates...
May 26, 2017: Applied and Environmental Microbiology
Eric L Patterson, Margaret B Fleming, Kallie C Kessler, Scott J Nissen, Todd A Gaines
The invasive aquatic plant Eurasian watermilfoil (Myriophyllum spicatum L.) can hybridize with the related North American native species northern watermilfoil (M. sibiricum Kom.). Hybrid watermilfoil (M. spicatum × M. sibiricum) populations have higher fitness and reduced sensitivity to some commonly used aquatic herbicides, making management more difficult. There is growing concern that management practices using herbicides in lakes with mixed populations of watermilfoil species may further select for hybrid individuals due to the difference in herbicide sensitivity...
2017: Frontiers in Plant Science
Jing-Lun Liu, Xiao-Ying Chen, Ni-Na Gu, Jin-Ye Zhang, Li-Ping Jiang, Dan Zhang, Guo-Sheng Ren
OBJECTIVE: The objective was to investigate the correlation between single nucleotide polymorphism (SNP) of chromogranin A (CHGA) and prognosis of critically ill patients. METHODS: We screened 357 critically ill patients consecutively admitted to our intensive care unit. The -89/-415/-462 SNP locus in the promoter region and the +9559/+9578/+9590/+9611 SNP locus in exon 7 coding of CHGA were genotyped by polymerase chain reaction and DNA sequencing technology. Subsequently, the correlation between genotype and prognosis of patients was analyzed...
June 2017: Journal of Critical Care
Saila Holopainen, Marjo K Hytönen, Pernilla Syrjä, Meharji Arumilli, Anna-Kaisa Järvinen, Minna Rajamäki, Hannes Lohi
Acute respiratory distress syndrome (ARDS) is the leading cause of death in critical care medicine. The syndrome is typified by an exaggerated inflammatory response within the lungs. ARDS has been reported in many species, including dogs. We have previously reported a fatal familial juvenile respiratory disease accompanied by occasional unilateral renal aplasia and hydrocephalus, in Dalmatian dogs. The condition with a suggested recessive mode of inheritance resembles acute exacerbation of usual interstitial pneumonia in man...
February 2017: PLoS Genetics
Heather A Frey, Molly J Stout, Laurel N Pearson, Methodius G Tuuli, Alison G Cahill, Jerome F Strauss, Luis M Gomez, Samuel Parry, Jenifer E Allsworth, George A Macones
BACKGROUND: Preterm birth is considered a multifactorial condition; however, emerging evidence suggests that genetic variation among individuals may have an important role. Prior studies have suggested that single-nucleotide polymorphisms associated with genes related to the immune system, and particularly the maternal inflammatory response, may be associated with an increased risk of preterm delivery. OBJECTIVE: The objective of the study was to identify single-nucleotide polymorphisms associated with spontaneous preterm birth <37 weeks within a cohort of African-American women...
August 2016: American Journal of Obstetrics and Gynecology
A Primerano, E Colao, C Villella, M D Nocera, A Ciambrone, E Luciano, L D'Antona, M F M Vismara, S Loddo, A Novelli, N Perrotti, Paola Malatesta
We report a case of a woman with a cryptic balanced translocation between chromosomes 5 and 17, suspected during genetic counseling. The woman had a history of previous fetal losses attributed to lissencephaly and intra uterine growth retardation (IUGR) and a daughter with dysmorphic features and mental retardation, previously attributed to a small deletion 5pter, detected years ago by a first generation CGH-array. This peculiar combination of personal and family history suggested the opportunity to carry out a FISH approach, focusing on chromosomes 5 and 17, based on the idea that a malsegregation secondary to a balanced translocation, might have escaped the first CGH array...
2015: Molecular Cytogenetics
Zhiqiang Wu, Luke R Tembrock, Song Ge
DNA sequencing has been revolutionized by the development of high-throughput sequencing technologies. Plummeting costs and the massive throughput capacities of second and third generation sequencing platforms have transformed many fields of biological research. Concurrently, new data processing pipelines made rapid de novo genome assemblies possible. However, high quality data are critically important for all investigations in the genomic era. We used chloroplast genomes of one Oryza species (O. australiensis) to compare differences in sequence quality: one genome (GU592209) was obtained through Illumina sequencing and reference-guided assembly and the other genome (KJ830774) was obtained via target enrichment libraries and shotgun sequencing...
2015: PloS One
Fernanda Majolo, Francis Jackson de Oliveira Paludo, Aline Ponzoni, Pietra Graebin, Fernando Suparregui Dias, Clarice Sampaio Alho
During critical illness and sepsis there is severe antioxidant depletion, and this scenario raises the critical ill patient's mortality risk. Glutathione peroxidase (GPx) is one of the first endogenous antioxidant defense enzymes, and it works cooperatively with superoxide dismutase (SOD) and catalase (CAT) to detoxify free radicals from the cellular environment. Genetic studies are important to understand the complexity of human oxidative stress and how the organism responds to an extreme situation such as critically care conditions...
February 2015: Cytokine
Pardis Taheripour, Mark A DeFord, Emily J Arentson-Lantz, Shawn S Donkin, Kolapo M Ajuwon, Sean C Newcomer
BACKGROUND: The development of long-term vascular disease can be linked to the intrauterine environment, and maternal nutrition during gestation plays a critical role in the future vascular health of offspring. The purpose of this investigation was to test the hypothesis that a high-energy (HE) gestational diet, HE post-weaning diet, or their combination will lead to endothelial dysfunction in offspring. METHODS: Duroc × Landrace gilts (n = 16) were assigned to either a HE (10,144 Kcal/day, n = 8) or normal energy (NE: 6721 Kcal/day, n = 8) diet throughout pregnancy...
2014: BMC Pregnancy and Childbirth
Julie Kaylor, Maria Alfaro, Arjun Ishwar, Charles Sailey, Jeffrey Sawyer, Yuri A Zarate
We describe the case of a male newborn with ring chromosome 13 found to have dysmorphic features, growth retardation, imperforate anus, and ambiguous genitalia. An initial karyotype showed 46,XY,r(13)(p13q34) in the 30 cells analyzed. SNP microarray from peripheral blood revealed not only an 8.14-Mb 13q33.2q34 deletion, but also a duplication of 87.49 Mb suggesting partial trisomy 13q that the patient did not appear to have clinically. Further cytogenetic characterization detected 3 distinct cell lines in the repeated peripheral blood sample: 46,XY,r(13)(p13q34)[89]/ 46,XY,r(13;13)(p13q34)[7]/45,XY,-13[5] and 2 in cultured fibroblasts: 46,XY,r(13)(p13q34)[65]/45,XY,-13[35]...
2014: Cytogenetic and Genome Research
Yongyue Wei, Zhaoxi Wang, Li Su, Feng Chen, Paula Tejera, Ednan K Bajwa, Mark M Wurfel, Xihong Lin, David C Christiani
BACKGROUND: Platelets are believed to be critical in pulmonary-origin ARDS as mediators of endothelial damage through their interactions with fibrinogen and multiple signal transduction pathways. A prior meta-analysis identified five loci for platelet count (PLT): BAD, LRRC16A, CD36, JMJD1C, and SLMO2. This study aims to validate the quantitative trait loci (QTLs) of PLT within BAD, LRRC16A, CD36, JMJD1C, and SLMO2 among critically ill patients and to investigate the associations of these QTLs with ARDS risk that may be mediated through PLT...
March 2015: Chest
B Nevado, M Perez-Enciso
The choice of technology and bioinformatics approach is critical in obtaining accurate and reliable information from next-generation sequencing (NGS) experiments. An increasing number of software and methodological guidelines are being published, but deciding upon which approach and experimental design to use can depend on the particularities of the species and on the aims of the study. This leaves researchers unable to produce informed decisions on these central questions. To address these issues, we developed pipeliner - a tool to evaluate, by simulation, the performance of NGS pipelines in resequencing studies...
January 2015: Molecular Ecology Resources
Lynn G Dressler, Sondra Smolek Jones, Janell M Markey, Katherine W Byerly, Megan C Roberts
AIMS: For more than two decades genomic education of the public has been a significant challenge. As genomic information becomes integrated into daily life and routine clinical care, the need for public education is even more critical. We conducted a pilot study to learn how genomic researchers and ethical, legal, and social implications advisors who were affiliated with large-scale genomic variation studies have approached the issue of educating the public about genomics. METHODS/RESULTS: Semi-structured telephone interviews were conducted with researchers and advisors associated with the SNP/HAPMAP studies and the Cancer Genome Atlas Study...
March 2014: Genetic Testing and Molecular Biomarkers
Daniela Hauer, Ines Kaufmann, Claudia Strewe, Isabel Briegel, Patrizia Campolongo, Gustav Schelling
Critically ill patients are at an increased risk for traumatic memories and post-traumatic stress disorder (PTSD). Memories of one or more traumatic events play an important part in the symptom pattern of PTSD. Studies in long-term survivors of intensive care unit (ICU) treatment demonstrated a clear and vivid recall of traumatic experiences and the incidence and intensity of PTSD symptoms increased with the number of traumatic memories present. Preclinical evidence has clearly shown that the consolidation and retrieval of traumatic memories is regulated by an interaction between the noradrenergic, the glucocorticoid and the endocannabinoid system...
July 2014: Neurobiology of Learning and Memory
Soichiro Ide, Daisuke Nishizawa, Ken-ichi Fukuda, Shinya Kasai, Junko Hasegawa, Masakazu Hayashida, Masabumi Minami, Kazutaka Ikeda
Individual differences in the sensitivity to fentanyl, a widely used opioid analgesic, lead to different proper doses of fentanyl, which can hamper effective pain treatment. Voltage-activated Ca(2+) channels (VACCs) play a crucial role in the nervous system by controlling membrane excitability and calcium signaling. Ca(v)2.3 (R-type) VACCs have been especially thought to play critical roles in pain pathways and the analgesic effects of opioids. However, unknown is whether single-nucleotide polymorphisms (SNPs) of the human CACNA1E (calcium channel, voltage-dependent, R type, alpha 1E subunit) gene that encodes Cav2...
2013: PloS One
David M Engelthaler, Erin Kelley, Elizabeth M Driebe, Jolene Bowers, Carl F Eberhard, Jesse Trujillo, Frederic Decruyenaere, James M Schupp, Joel Mossong, Paul Keim, Jos Even
BACKGROUND: spa typing is a common genotyping tool for methicillin-resistant Staphylococcus aureus (MRSA) in Europe. Given the high prevalence of dominant clones, spa-typing is proving to be limited in its ability to distinguish outbreak isolates from background isolates. New molecular tools need to be employed to improve subtyping of dominant local MRSA strains (e.g., spa type t003). METHODS: Phylogenetically critical, or canonical, SNPs (can-SNPs) were identified as subtyping targets through sequence analysis of 40 MRSA whole genomes from Luxembourg...
2013: BMC Infectious Diseases
Callie M Thompson, Tarah D Holden, Gail Rona, Balaji Laxmanan, R Anthony Black, Grant E OʼKeefe, Mark M Wurfel
OBJECTIVE: To determine whether single nucleotide polymorphisms (SNPs) in TLR1 are associated with mortality, specifically sepsis-associated mortality, in a traumatically injured population. BACKGROUND: Innate immune responses mediated by toll-like receptors (TLRs) induce early inflammatory responses to pathogen and damage-associated molecular patterns. Genetic variation in TLRs has been associated with susceptibility and outcomes in a number of infectious and noninfectious disease states...
January 2014: Annals of Surgery
Nuala J Meyer, Rui Feng, Mingyao Li, Yang Zhao, Chau-Chyun Sheu, Paula Tejera, Robert Gallop, Scarlett Bellamy, Melanie Rushefski, Paul N Lanken, Richard Aplenc, Grant E O'Keefe, Mark M Wurfel, David C Christiani, Jason D Christie
RATIONALE: Acute respiratory distress syndrome (ARDS) behaves as a complex genetic trait, yet knowledge of genetic susceptibility factors remains incomplete. OBJECTIVES: To identify genetic risk variants for ARDS using large scale genotyping. METHODS: A multistage genetic association study was conducted of three critically ill populations phenotyped for ARDS. Stage I, a trauma cohort study (n = 224), was genotyped with a 50K gene-centric single-nucleotide polymorphism (SNP) array...
May 1, 2013: American Journal of Respiratory and Critical Care Medicine
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