'Myxococcus xanthus belongs to the delta class of the proteobacteria and is notable for its complex life-style with social behaviors and relatively large genome. Although previous observations have suggested the existence of horizontal gene transfer in M. xanthus, its ability to take up exogenous DNA via natural transformation has not ... More
Gastroenteritis outbreak caused by waterborne norovirus at a New Zealand ski resort.
AuthorsHewitt J, Bell D, Simmons GC, Rivera-Aban M, Wolf S, Greening GE,
JournalAppl Environ Microbiol
PubMed ID17965205
'In July 2006, public health services investigated an outbreak of acute gastroenteritis among staff and visitors of a popular ski resort in southern New Zealand. The source of the outbreak was a drinking water supply contaminated by human sewage. The virological component of the investigation played a major role in ... More
Expression/localization patterns of sirtuins (SIRT1, SIRT2, and SIRT7) during progression of cervical cancer and effects of sirtuin inhibitors on growth of cervical cancer cells.
AuthorsSingh S, Kumar PU, Thakur S, Kiran S, Sen B, Sharma S, Rao VV, Poongothai AR, Ramakrishna G
Journal
PubMed ID25794641
'Sirtuins belong to the family of class III histone deacetylases; its role in neoplasia is controversial as both tumor-suppressive and promoting functions have been reported. There are very few reports available, where expressions of sirtuin isoforms are comprehensively analyzed during neoplasia. Therefore, in the present study, the expression of SIRT1, ... More
The altered landscape of the human skin microbiome in patients with primary immunodeficiencies.
AuthorsOh J, Freeman AF, Park M, Sokolic R, Candotti F, Holland SM, Segre JA, Kong HH,
Journal
PubMed ID24170601
'While landmark studies have shown that microbiota activate and educate host immunity, how immune systems shape microbiomes and contribute to disease is incompletely characterized. Primary immunodeficiency (PID) patients suffer recurrent microbial infections, providing a unique opportunity to address this issue. To investigate the potential influence of host immunity on the ... More
Effect of the metabolic environment at key stages of follicle development in cattle: focus on steroid biosynthesis.
AuthorsWalsh SW, Mehta JP, McGettigan PA, Browne JA, Forde N, Alibrahim RM, Mulligan FJ, Loftus B, Crowe MA, Matthews D, Diskin M, Mihm M, Evans AC,
JournalPhysiol Genomics
PubMed ID22414914
'Cellular mechanisms that contribute to low estradiol concentrations produced by the preovulatory ovarian follicle in cattle with a compromised metabolic status are largely unknown. To gain insight into the main metabolic mechanisms affecting preovulatory follicle function, two different animal models were used. Experiment 1 compared Holstein-Friesian nonlactating heifers (n = ... More
Integrative analysis of genomic aberrations associated with prostate cancer progression.
AuthorsKim JH, Dhanasekaran SM, Mehra R, Tomlins SA, Gu W, Yu J, Kumar-Sinha C, Cao X, Dash A, Wang L, Ghosh D, Shedden K, Montie JE, Rubin MA, Pienta KJ, Shah RB, Chinnaiyan AM,
JournalCancer Res
PubMed ID17804737
'Integrative analysis of genomic aberrations in the context of trancriptomic alterations will lead to a more comprehensive perspective on prostate cancer progression. Genome-wide copy number changes were monitored using array comparative genomic hybridization of laser-capture microdissected prostate cancer samples spanning stages of prostate cancer progression, including precursor lesions, clinically localized ... More
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression.
AuthorsCheng Y, Wu W, Kumar SA, Yu D, Deng W, Tripic T, King DC, Chen KB, Zhang Y, Drautz D, Giardine B, Schuster SC, Miller W, Chiaromonte F, Zhang Y, Blobel GA, Weiss MJ, Hardison RC,
JournalGenome Res
PubMed ID19887574
'The transcription factor GATA1 regulates an extensive program of gene activation and repression during erythroid development. However, the associated mechanisms, including the contributions of distal versus proximal cis-regulatory modules, co-occupancy with other transcription factors, and the effects of histone modifications, are poorly understood. We studied these problems genome-wide in a ... More
Bat white-nose syndrome: a real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructans.
AuthorsMuller LK, Lorch JM, Lindner DL, O'Connor M, Gargas A, Blehert DS,
JournalMycologia
PubMed ID22962349
'The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene ... More
Viral multiplex quantitative PCR assays for tracking sources of fecal contamination.
AuthorsWolf S, Hewitt J, Greening GE,
JournalAppl Environ Microbiol
PubMed ID20061455
'Human and animal fecal pollution of the environment presents a risk to human health because of the presence of pathogenic viruses and bacteria. To distinguish between human and animal sources of pollution, we designed specific real-time reverse transcription (RT)-PCR assays for human and animal enteric viruses, including norovirus genogroups I, ... More
Rapid polymerase chain reaction diagnosis of white-nose syndrome in bats.
AuthorsLorch JM, Gargas A, Meteyer CU, Berlowski-Zier BM, Green DE, Shearn-Bochsler V, Thomas NJ, Blehert DS,
JournalJ Vet Diagn Invest
PubMed ID20224080
'A newly developed polymerase chain reaction (PCR)-based method to rapidly and specifically detect Geomyces destructans on the wings of infected bats from small quantities (1-2 mg) of tissue is described in the current study (methods for culturing and isolating G. destructans from bat skin are also described). The lower limits ... More
Multiple sclerosis with abnormal cerebrospinal fluid--a case report.
AuthorsRatnagopal P, Puvanendran K,
JournalAnn Acad Med Singapore
PubMed ID1803976
Multiple sclerosis is an uncommon demyelinating condition in Singapore. The commonest mode of presentation here is in the form of Devic's syndrome. Although our patients here have shown classical findings with respect to clinical features, neuroimaging studies and electrophysiologic tests, abnormal cerebrospinal fluid changes have not been reported locally. We ... More
Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut.
AuthorsReyes A, Wu M, McNulty NP, Rohwer FL, Gordon JI,
Journal
PubMed ID24259713
Bacterial viruses (phages) are the most abundant biological group on Earth and are more genetically diverse than their bacterial prey/hosts. To characterize their role as agents shaping gut microbial community structure, adult germ-free mice were colonized with a consortium of 15 sequenced human bacterial symbionts, 13 of which harbored one ... More
Symbiotic bacteria appear to mediate hyena social odors.
All animals harbor beneficial microbes. One way these microbes can benefit their animal hosts is by increasing the diversity and efficacy of communication signals available to the hosts. The fermentation hypothesis for mammalian chemical communication posits that bacteria in the scent glands of mammals generate odorous metabolites used by their ... More
Acute-phase CD8 T cell responses that select for escape variants are needed to control live attenuated simian immunodeficiency virus.
AuthorsHarris M, Burns CM, Becker EA, Braasch AT, Gostick E, Johnson RC, Broman KW, Price DA, Friedrich TC, O'Connor SL,
Journal
PubMed ID23785211
The overall CD8 T cell response to human/simian immunodeficiency virus (HIV/SIV) targets a collection of discrete epitope specificities. Some of these epitope-specific CD8 T cells emerge in the weeks and months following infection and rapidly select for sequence variants, whereas other CD8 T cell responses develop during the chronic infection ... More
Targeted resequencing implicates the familial Mediterranean fever gene MEFV and the toll-like receptor 4 gene TLR4 in Behçet disease.
AuthorsKirino Y, Zhou Q, Ishigatsubo Y, Mizuki N, Tugal-Tutkun I, Seyahi E, Özyazgan Y, Ugurlu S, Erer B, Abaci N, Ustek D, Meguro A, Ueda A, Takeno M, Inoko H, Ombrello MJ, Satorius CL, Maskeri B, Mullikin JC, Sun HW, Gutierrez-Cruz G, Kim Y, Wilson AF, Kastner DL, Gül A, Remmers EF,
JournalProc Natl Acad Sci U S A
PubMed ID23633568
Genome-wide association studies (GWAS) are a powerful means of identifying genes with disease-associated common variants, but they are not well-suited to detecting genes with disease-associated rare and low-frequency variants. In the current study of Behçet disease (BD), nonsynonymous variants (NSVs) identified by deep exonic resequencing of 10 genes found by ... More
Sustained release of bone morphogenetic protein 2 via coacervate improves the osteogenic potential of muscle-derived stem cells.
AuthorsLi H, Johnson NR, Usas A, Lu A, Poddar M, Wang Y, Huard J,
Journal
PubMed ID23884640
Muscle-derived stem cells (MDSCs) isolated from mouse skeletal muscle by a modified preplate technique exhibit long-term proliferation, high self-renewal, and multipotent differentiation capabilities in vitro. MDSCs retrovirally transduced to express bone morphogenetic proteins (BMPs) can differentiate into osteocytes and chondrocytes and enhance bone and articular cartilage repair in vivo, a ... More
Identification of soil bacteria susceptible to TiO2 and ZnO nanoparticles.
AuthorsGe Y, Schimel JP, Holden PA,
JournalAppl Environ Microbiol
PubMed ID22798374
Because soil is expected to be a major sink for engineered nanoparticles (ENPs) released to the environment, the effects of ENPs on soil processes and the organisms that carry them out should be understood. DNA-based fingerprinting analyses have shown that ENPs alter soil bacterial communities, but specific taxon changes remain ... More
Open chromatin structures regulate the efficiencies of pre-RC formation and replication initiation in Epstein-Barr virus.
AuthorsPapior P, Arteaga-Salas JM, Günther T, Grundhoff A, Schepers A,
JournalJ Cell Biol
PubMed ID22891264
Whether or not metazoan replication initiates at random or specific but flexible sites is an unsolved question. The lack of sequence specificity in origin recognition complex (ORC) DNA binding complicates genome-scale chromatin immunoprecipitation (ChIP)-based studies. Epstein-Barr virus (EBV) persists as chromatinized minichromosomes that are replicated by the host replication machinery. ... More
Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine.
AuthorsPreidis GA, Saulnier DM, Blutt SE, Mistretta TA, Riehle KP, Major AM, Venable SF, Finegold MJ, Petrosino JF, Conner ME, Versalovic J,
JournalFASEB J
PubMed ID22267340
Beneficial microbes and probiotics show promise for the treatment of pediatric gastrointestinal diseases. However, basic mechanisms of probiosis are not well understood, and most investigations have been performed in germ-free or microbiome-depleted animals. We sought to functionally characterize probiotic-host interactions in the context of normal early development. Outbred CD1 neonatal ... More
Targeted detection of in vivo endogenous DNA base damage reveals preferential base excision repair in the transcribed strand.
Endogenous DNA damage is removed mainly via base excision repair (BER), however, whether there is preferential strand repair of endogenous DNA damage is still under intense debate. We developed a highly sensitive primer-anchored DNA damage detection assay (PADDA) to map and quantify in vivo endogenous DNA damage. Using PADDA, we ... More
Energy use efficiency is characterized by an epigenetic component that can be directed through artificial selection to increase yield.
AuthorsHauben M, Haesendonckx B, Standaert E, Van Der Kelen K, Azmi A, Akpo H, Van Breusegem F, Guisez Y, Bots M, Lambert B, Laga B, De Block M,
JournalProc Natl Acad Sci U S A
PubMed ID19897729
Quantitative traits, such as size and weight in animals and seed yield in plants, are distributed normally, even within a population of genetically identical individuals. For example, in plants, various factors, such as local soil quality, microclimate, and sowing depth, affect growth differences among individual plants of isogenic populations. Besides ... More
Regulation of fat cell mass by insulin in Drosophila melanogaster.
AuthorsDiAngelo JR, Birnbaum MJ,
JournalMol Cell Biol
PubMed ID19822665
A phylogenetically conserved response to nutritional abundance is an increase in insulin signaling, which initiates a set of biological responses dependent on the species. Consequences of augmented insulin signaling include developmental progression, cell and organ growth, and the storage of carbohydrates and lipids. Here, we address the evolutionary origins of ... More
Viremia in acute herpes zoster.
AuthorsSatyaprakash AK, Tremaine AM, Stelter AA, Creed R, Ravanfar P, Mendoza N, Mehta SK, Rady PL, Pierson DL, Tyring SK,
JournalJ Infect Dis
PubMed ID19469706
A phase 2 trial was conducted to evaluate the efficacy of a topical antiviral, sorivudine, as an adjuvant to valacyclovir for the treatment of acute herpes zoster. In this randomized, placebo-controlled, double-blind trial, 25 patients were treated with either sorivudine or placebo cream. All patients began 7 days of valacyclovir ... More
Identification and characterization of mefloquine efficacy against JC virus in vitro.
AuthorsBrickelmaier M, Lugovskoy A, Kartikeyan R, Reviriego-Mendoza MM, Allaire N, Simon K, Frisque RJ, Gorelik L,
JournalAntimicrob Agents Chemother
PubMed ID19258267
Progressive multifocal leukoencephalopathy (PML) is a rare but frequently fatal disease caused by the uncontrolled replication of JC virus (JCV), a polyomavirus, in the brains of some immunocompromised individuals. Currently, no effective antiviral treatment for this disease has been identified. As a first step in the identification of such therapy, ... More
Use of elemental analysis to determine comparative performance of established DNA quantification methods.
AuthorsEnglish CA, Merson S, Keer JT
JournalAnal Chem
PubMed ID16808475
Quantification of genomic DNA is critical for many analyses in molecular biology. Current methods include optical density (OD) measurements or fluorescent enhancement but both approaches have limitations on achievable accuracy. In this study we performed an elemental analysis to quantify genomic DNA to provide an independent value for comparing the ... More
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.
AuthorsLloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C
JournalNature
PubMed ID31142855
'Inflammatory bowel diseases, which include Crohn''s disease and ulcerative colitis, affect several million individuals worldwide. Crohn''s disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative ... More
Respiratory Syncytial Virus induces the classical ROS-dependent NETosis through PAD-4 and necroptosis pathways activation.
AuthorsMuraro SP, De Souza GF, Gallo SW, Da Silva BK, De Oliveira SD, Vinolo MAR, Saraiva EM, Porto BN
JournalSci Rep
PubMed ID30242250
'Respiratory syncytial virus (RSV) is a major cause of diseases of the respiratory tract in young children and babies, being mainly associated with bronchiolitis. RSV infection occurs primarily in pulmonary epithelial cells and, once infection is established, an immune response is triggered and neutrophils are recruited. In this study, we ... More
Locus-specific concordance of genomic alterations between tissue and plasma circulating tumor DNA in metastatic melanoma.
AuthorsCalapre L, Giardina T, Robinson C, Reid AL, Al-Ogaili Z, Pereira MR, McEvoy AC, Warburton L, Hayward NK, Khattak MA, Meniawy TM, Millward M, Amanuel B, Ziman M, Gray ES
JournalMol Oncol
PubMed ID30312528
'Circulating tumor DNA (ctDNA) may serve as a surrogate to tissue biopsy for noninvasive identification of mutations across multiple genetic loci and for disease monitoring in melanoma. In this study, we compared the mutation profiles of tumor biopsies and plasma ctDNA from metastatic melanoma patients using custom sequencing panels targeting 30 ... More
Exploring the influence from whole blood DNA extraction methods on Infinium 450K DNA methylation.
AuthorsHjorthaug HS, Gervin K, Mowinckel P, Munthe-Kaas MC
JournalPLoS One
PubMed ID30540848
'Genome-wide DNA methylation studies are becoming increasingly important in unraveling the epigenetic basis of cell biology, aging and human conditions. The aim of the present study was to explore whether different methods for extracting DNA from whole blood can affect DNA methylation outcome, potentially confounding DNA methylation studies. DNA was ... More
Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI.
AuthorsBoers R, Boers J, de Hoon B, Kockx C, Ozgur Z, Molijn A, van IJcken W, Laven J, Gribnau J
JournalGenome Res
PubMed ID29222086
DNA methylation is a well-known epigenetic modification that plays a crucial role in gene regulation, but genome-wide analysis of DNA methylation remains technically challenging and costly. DNA methylation-dependent restriction enzymes can be used to restrict CpG methylation analysis to methylated regions of the genome only, which significantly reduces the required ... More
A 1204-single nucleotide polymorphism and insertion-deletion polymorphism panel for massively parallel sequencing analysis of DNA mixtures.
AuthorsHwa HL, Chung WC, Chen PL, Lin CP, Li HY, Yin HI, Lee JC
JournalForensic Sci Int Genet
PubMed ID29128546
Massively parallel sequencing (MPS) technology enables the simultaneous analysis of a huge number of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (indels). MPS also enables the detection of the alleles of minor contributors in a highly unbalanced DNA mixture. In this study, we established a 1204-marker panel optimized for MPS ... More
Total circulating cell-free miRNA in plasma as a predictive biomarker of the thyroid diseases.
AuthorsCaglar O, Cayir A
JournalJ Cell Biochem
PubMed ID30506793
Thyroid cancer is a common endocrine cancer. Great progress has been made in resolving its molecular mechanisms in recent years. The molecular changes observed in thyroid cancer can be used as biomarkers for diagnostic, prognostic and therapeutic purposes. MicroRNAs (miRNAs) are important components in biological and metabolic pathways, such as ... More