Genomes and Genes
Experts and Doctors on humans in Ames, Iowa, United States
Locale: Ames, Iowa, United States
- Tsai I, Zarowiecki M, Holroyd N, Garciarrubio A, Sanchez Flores A, Brooks K, et al. The genomes of four tapeworm species reveal adaptations to parasitism. Nature. 2013;496:57-63 pubmed publisher..We identify new potential drug targets, including some on which existing pharmaceuticals may act. The genomes provide a rich resource to underpin the development of urgently needed treatments and control...
- Andreotti A, Schwartzberg P, Joseph R, Berg L. T-cell signaling regulated by the Tec family kinase, Itk. Cold Spring Harb Perspect Biol. 2010;2:a002287 pubmed publisher..Finally, we describe the complex role of Itk signaling in effector T-cell differentiation and the regulation of cytokine gene expression. Together, these data implicate Itk as an important modulator of T-cell signaling and function. ..
- Tuggle C, Green J, Fitzsimmons C, Woods R, Prather R, Malchenko S, et al. EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human. Mamm Genome. 2003;14:565-79 pubmed..We demonstrate the utility of this software for comparative mapping by localizing 61 genes on the porcine physical map for Chromosomes (Chrs) 5, 10, and 14. ..
- Stickney J, Buss J. Murine guanylate-binding protein: incomplete geranylgeranyl isoprenoid modification of an interferon-gamma-inducible guanosine triphosphate-binding protein. Mol Biol Cell. 2000;11:2191-200 pubmed..The C20-selective impairment in prenylation also identifies mGBP1 as an important model for the study of substrate/geranylgeranyl transferase I interactions. ..
- Barnhill A, Brewer M, Carlson S. Adverse effects of antimicrobials via predictable or idiosyncratic inhibition of host mitochondrial components. Antimicrob Agents Chemother. 2012;56:4046-51 pubmed publisher..Nonetheless, it appears that mitochondrion-associated side effects are a potential aspect of antibiotics whose targets are shared by prokaryotes and mitochondria-an important consideration for future drug design. ..
- Zuerner R, Alt D, Bolin C. IS1533-based PCR assay for identification of Leptospira interrogans sensu lato serovars. J Clin Microbiol. 1995;33:3284-9 pubmed..These results demonstrate that this assay is selective enough to be used for typing leptospiral serovars from clinical material and thus allows leptospiral typing without isolation of the bacteria in pure culture. ..
- Fang I, Slowing I, Wu K, Lin V, Trewyn B. Ligand conformation dictates membrane and endosomal trafficking of arginine-glycine-aspartate (RGD)-functionalized mesoporous silica nanoparticles. Chemistry. 2012;18:7787-92 pubmed publisher..Thus, covalent functionalization of biomolecules on MSN assists in the design of a system for controlling the interface with cancer cells. ..
- Wang Q, Gu Z, Jamal S, Detamore M, Berkland C. Hybrid hydroxyapatite nanoparticle colloidal gels are injectable fillers for bone tissue engineering. Tissue Eng Part A. 2013;19:2586-93 pubmed publisher..Human umbilical cord mesenchymal stem cells were also highly viable when seeded on the colloidal gels. HAp/PLGA NP colloidal gels offer an attractive scheme for injectable filling and regeneration of bone tissue. ..
- Cai W, Wannemuehler Y, Dell Anna G, Nicholson B, Barbieri N, Kariyawasam S, et al. A novel two-component signaling system facilitates uropathogenic Escherichia coli's ability to exploit abundant host metabolites. PLoS Pathog. 2013;9:e1003428 pubmed publisher..Taken altogether, this study describes the first UPEC-associated TCS that functions in controlling the utilization of ?-ketoglutarate in vivo thereby facilitating UPEC adaptation to life inside the urinary tract. ..
- West R, Bailey K. ERP correlates of dual mechanisms of control in the counting Stroop task. Psychophysiology. 2012;49:1309-18 pubmed publisher..These findings support the idea that different regions of the cingulate and anterior frontal cortex underpin proactive and reactive control. ..
- Smagghe B, Trent J, Hargrove M. NO dioxygenase activity in hemoglobins is ubiquitous in vitro, but limited by reduction in vivo. PLoS ONE. 2008;3:e2039 pubmed publisher..Hence, future research to test the role of Hbs in NO scavenging would benefit more from the identification of cognate reductases than from in vitro analysis of NO and O(2) binding. ..
- Kudva I, Griffin R, Krastins B, Sarracino D, Calderwood S, John M. Proteins other than the locus of enterocyte effacement-encoded proteins contribute to Escherichia coli O157:H7 adherence to bovine rectoanal junction stratified squamous epithelial cells. BMC Microbiol. 2012;12:103 pubmed publisher..Ongoing experiments to evaluate their role in RSE adherence should provide both valuable insights into the O157-RSE interactions and new targets for more efficacious anti-adhesion O157 vaccines. ..
- Huang N, Singh N, Yoon K, Loiacono C, Kohut M, Birt D. The immuno-regulatory impact of orally-administered Hypericum perforatum extract on Balb/C mice inoculated with H1n1 influenza A virus. PLoS ONE. 2013;8:e76491 pubmed publisher..perforatum extract. In conclusion, the current study showed that SOCS3 elevation by H. perforatum may cause impaired immune defense against influenza virus infection and lead to higher mortality. ..
- Singh R. Evolving concepts on human SMN pre-mRNA splicing. RNA Biol. 2007;4:7-10 pubmed..Considering an antisense-based strategy confers a unique advantage of sequence specificity, availability of many target worthy cis-elements holds strong potential for antisense-mediated therapy of SMA. ..
- Zhu Y, Hollis J. Tooth loss and its association with dietary intake and diet quality in American adults. J Dent. 2014;42:1428-35 pubmed publisher..People with missing teeth are recommended to monitor their dietary intake to avoid nutrient deficiency and to improve their diet quality for better health. ..
- Maxson J, Luty S, Macmaniman J, Paik J, Gotlib J, Greenberg P, et al. The Colony-Stimulating Factor 3 Receptor T640N Mutation Is Oncogenic, Sensitive to JAK Inhibition, and Mimics T618I. Clin Cancer Res. 2016;22:757-64 pubmed publisher..Because of its similarities to CSF3R T618I, the T640N mutation likely has diagnostic and therapeutic relevance in CNL/aCML. ..
- Ernst C, Kapke P, Yerle M, Rothschild M. The leptin receptor gene (LEPR) maps to porcine chromosome 6. Mamm Genome. 1997;8:226 pubmed
- Zuerner R, Bolin C. Differentiation of Leptospira interrogans isolates by IS1500 hybridization and PCR assays. J Clin Microbiol. 1997;35:2612-7 pubmed..The IS-based typing assays described should be useful for epidemiological analysis of leptospirosis. ..
- Rathmacher J, Nissen S, Panton L, Clark R, Eubanks May P, Barber A, et al. Supplementation with a combination of beta-hydroxy-beta-methylbutyrate (HMB), arginine, and glutamine is safe and could improve hematological parameters. JPEN J Parenter Enteral Nutr. 2004;28:65-75 pubmed..These results show that HMB, arginine, and glutamine can be safely used to treat muscle wasting associated with AIDS and cancer. ..
- Markushin Y, Zhong W, Cavalieri E, Rogan E, Small G, Yeung E, et al. Spectral characterization of catechol estrogen quinone (CEQ)-derived DNA adducts and their identification in human breast tissue extract. Chem Res Toxicol. 2003;16:1107-17 pubmed..Although more breast tissue samples from women with and without breast cancer need to be studied, these results suggest that the N3Ade adducts could serve as biomarkers to predict the risk of breast cancer. ..
- Sharma V. Detection and quantitation of enterohemorrhagic Escherichia coli O157, O111, and O26 in beef and bovine feces by real-time polymerase chain reaction. J Food Prot. 2002;65:1371-80 pubmed..In conclusion, eae- and stx-based R-PCR assays are reliable and sensitive methods for the rapid screening and specific and quantitative detection of important serotypes of EHEC in cattle and in foods of bovine origin. ..
- Glavaski Joksimovic A, Jeftinija K, Jeremic A, Anderson L, Jeftinija S. Mechanism of action of the growth hormone secretagogue, L-692,585, on isolated porcine somatotropes. J Endocrinol. 2002;175:625-36 pubmed
- Zhou C, Inanc F, Modrick J. Distortions induced by radioactive seeds into interstitial brachytherapy dose distributions. Med Phys. 2004;31:3393-405 pubmed..The dosimetry data for a single model 6711 seeds is presented for verification and heterogeneity factor computations using simultaneous and superposition techniques are presented...
- Zhu Y, Hsu W, Hollis J. The impact of food viscosity on eating rate, subjective appetite, glycemic response and gastric emptying rate. PLoS ONE. 2013;8:e67482 pubmed publisher..A slower eating rate and a delayed gastric emptying rate can partly explain for the stronger satiating properties of high viscous semi-solid foods. ..
- Stegemöller E, Hibbing P, Radig H, Wingate J. Therapeutic singing as an early intervention for swallowing in persons with Parkinson's disease. Complement Ther Med. 2017;31:127-133 pubmed publisher..Combined with the improvement in UPDRS clinical measures, therapeutic singing may be an engaging early intervention strategy to address oropharyngeal dysphagia while also benefiting additional clinical symptoms of PD. ..
- Spoth R, Greenberg M. Toward a comprehensive strategy for effective practitioner-scientist partnerships and larger-scale community health and well-being. Am J Community Psychol. 2005;35:107-26 pubmed..The comprehensive strategy would require careful attention to the expansion of networks of effective partnerships, partnership-based research agendas, and requisite policy-making. ..
- Register K, Boisvert A, Ackermann M. Use of ribotyping to distinguish Bordetella bronchiseptica isolates. Int J Syst Bacteriol. 1997;47:678-83 pubmed..There was no association between geographic location and ribotype. The technique which we used may be useful for epidemiologic studies in which the transmission of B. bronchiseptica, both within and between species, is investigated...
- Frana T, Beahm A, Hanson B, Kinyon J, Layman L, Karriker L, et al. Isolation and characterization of methicillin-resistant Staphylococcus aureus from pork farms and visiting veterinary students. PLoS ONE. 2013;8:e53738 pubmed publisher..The most common spa types found in this study were associated with ST5 and expands the range of livestock-associated MRSA types. ..
- Pulit Penaloza J, Simpson N, Yang H, Creager H, Jones J, Carney P, et al. Assessment of Molecular, Antigenic, and Pathological Features of Canine Influenza A(H3N2) Viruses That Emerged in the United States. J Infect Dis. 2017;216:S499-S507 pubmed publisher..Since then, this CIV has caused thousands of infections in dogs in multiple states...
- Sacco R, Register K, Nordholm G. Restriction endonuclease analysis discriminates Bordetella bronchiseptica isolates. J Clin Microbiol. 2000;38:4387-93 pubmed..Based on the results presented herein, the combination of REA and ribotyping should provide valuable information in understanding the molecular epidemiology of B. bronchiseptica infections...
- Habier D, Fernando R, Garrick D. Genomic BLUP decoded: a look into the black box of genomic prediction. Genetics. 2013;194:597-607 pubmed publisher..As genomic BLUP cannot capture short-range LD information well, we recommend Bayesian methods with t-distributed priors. ..
- Joseph R, Norris F. Substrate specificity and recognition is conferred by the pleckstrin homology domain of the Dbl family guanine nucleotide exchange factor P-Rex2. J Biol Chem. 2005;280:27508-12 pubmed..Thus substrate recognition can now be added to the growing list of functions that are being attributed to the PH domain of Dbl family GEFs. ..
- Fridley B, Rabe K, de Andrade M. Imputation methods for missing data for polygenic models. BMC Genet. 2003;4 Suppl 1:S42 pubmed..Thus, we recommend the Gibbs sampler for imputation purposes because of the ease with which it can be extended to more complicated models, the consistency of the results, and the accountability of the variation due to imputation. ..
- Mann F, Prisic S, Hu H, Xu M, Coates R, Peters R. Characterization and inhibition of a class II diterpene cyclase from Mycobacterium tuberculosis: implications for tuberculosis. J Biol Chem. 2009;284:23574-9 pubmed publisher..Thus, we hypothesize that the inability to produce edaxadiene may be a contributing factor in the decreased infectivity and/or virulence of M. bovis relative to M. tuberculosis in humans...
- Messer L, Wang L, Tuggle C, Yerle M, Chardon P, Pomp D, et al. Mapping of the melatonin receptor 1a (MTNR1A) gene in pigs, sheep, and cattle. Mamm Genome. 1997;8:368-70 pubmed
- Sahin O, Fitzgerald C, Stroika S, Zhao S, Sippy R, Kwan P, et al. Molecular evidence for zoonotic transmission of an emergent, highly pathogenic Campylobacter jejuni clone in the United States. J Clin Microbiol. 2012;50:680-7 pubmed publisher..These results provide strong molecular and epidemiological evidence for zoonotic transmission of this emergent clone from ruminants to humans and indicate that C. jejuni clone SA is an important threat to public health...
- Humphries J, Kimber M, Barton Y, Hsu W, Marks N, Greer B, et al. Structure and bioactivity of neuropeptide F from the human parasites Schistosoma mansoni and Schistosoma japonicum. J Biol Chem. 2004;279:39880-5 pubmed
- Singh N, Seo J, Rahn S, Singh R. A multi-exon-skipping detection assay reveals surprising diversity of splice isoforms of spinal muscular atrophy genes. PLoS ONE. 2012;7:e49595 pubmed publisher..Our findings bring new insight into splicing regulation of an essential housekeeping gene linked to neurodegeneration and infant mortality. ..
- Buehler J, Navi D, Lorusso A, Vincent A, Lager K, Miller C. Influenza A virus PB1-F2 protein expression is regulated in a strain-specific manner by sequences located downstream of the PB1-F2 initiation codon. J Virol. 2013;87:10687-99 pubmed publisher..Our data suggest that carrying a full-length PB1-F2 ORF may not be predictive of PB1-F2 expression in infected cells for all influenza A viruses. ..
- Logue C, Barbieri N, Nielsen D. Pathogens of Food Animals: Sources, Characteristics, Human Risk, and Methods of Detection. Adv Food Nutr Res. 2017;82:277-365 pubmed publisher..The influence of the global economy, the movement of people, and food makes understanding production animal-associated disease paramount to being able to address new diseases as they arise. ..
- Zhao X, Dittmer K, Blair H, Thompson K, Rothschild M, Garrick D. A novel nonsense mutation in the DMP1 gene identified by a genome-wide association study is responsible for inherited rickets in Corriedale sheep. PLoS ONE. 2011;6:e21739 pubmed publisher..Affected sheep could be used as animal models for this form of human rickets, and for further investigation of the role of DMP1 in phosphate homeostasis. ..
- Bodnar A, Proulx A, Scott M, Beavers A, Reddy M. Iron bioavailability of maize hemoglobin in a Caco-2 cell culture model. J Agric Food Chem. 2013;61:7349-56 pubmed publisher..These results suggest that maize globin produced in E. coli may be an effective iron fortificant, but overexpressing maize globin in maize endosperm may require a different strategy to increase bioavailable iron content in maize. ..
- Trent J, Hargrove M. A ubiquitously expressed human hexacoordinate hemoglobin. J Biol Chem. 2002;277:19538-45 pubmed..The discovery of histoglobin demonstrates that humans, like plants, differentially express multiple hexacoordinate hemoglobins. ..
- Kudva I, Hovde C, John M. Adherence of non-O157 Shiga toxin-producing Escherichia coli to bovine recto-anal junction squamous epithelial cells appears to be mediated by mechanisms distinct from those used by O157. Foodborne Pathog Dis. 2013;10:375-81 pubmed publisher..These findings have important implications for the development of efficacious modalities for blocking adherence of non-O157 STEC to bovine gastrointestinal epithelial cells. ..
- Esch K, Petersen C. Transmission and epidemiology of zoonotic protozoal diseases of companion animals. Clin Microbiol Rev. 2013;26:58-85 pubmed publisher..To provide this awareness, this review is focused on zoonotic protozoal mechanisms of virulence, epidemiology, and the transmission of pathogens of consequence to pet owners in the United States. ..
- Subedi G, Falconer D, Barb A. Carbohydrate-Polypeptide Contacts in the Antibody Receptor CD16A Identified through Solution NMR Spectroscopy. Biochemistry. 2017;56:3174-3177 pubmed publisher..We used a combination of NMR and 1 Î¼s all-atom computational simulations to identify unexpected contacts between the N45 N-glycan and CD16A polypeptide residues. ..
- Messer L, Wang L, Yelich J, Pomp D, Geisert R, Rothschild M. Linkage mapping of the retinol-binding protein 4 (RBP4) gene to porcine chromosome 14. Mamm Genome. 1996;7:396 pubmed
- Ellingson J, Bolin C, Stabel J. Identification of a gene unique to Mycobacterium avium subspecies paratuberculosis and application to diagnosis of paratuberculosis. Mol Cell Probes. 1998;12:133-42 pubmed publisher..paratuberculosis. The dOH method could be a good alternative to existing assays and will be adapted for specific identification of M. paratuberculosis from faecal samples, mixed bacteriologic cultures, tissue specimens and whole blood...
- Borza T, Iancu C, Pike E, Honzatko R, Fromm H. Variations in the response of mouse isozymes of adenylosuccinate synthetase to inhibitors of physiological relevance. J Biol Chem. 2003;278:6673-9 pubmed..Fructose 1,6-bisphosphate and IMP together may be dynamic regulators of the basic isozyme in muscle, causing potent inhibition of the synthetase under conditions of high AMP deaminase activity. ..
- Brown A, Bohan Brown M, Onken K, Beitz D. Short-term consumption of sucralose, a nonnutritive sweetener, is similar to water with regard to select markers of hunger signaling and short-term glucose homeostasis in women. Nutr Res. 2011;31:882-8 pubmed publisher..Therefore, sucralose may be a relatively inert nonnutritive sweetener with regard to hunger signaling and short-term glucose homeostasis. ..
- Sturms R, DiSpirito A, Fulton D, Hargrove M. Hydroxylamine reduction to ammonium by plant and cyanobacterial hemoglobins. Biochemistry. 2011;50:10829-35 pubmed publisher..These results support the hypothesis that plant and cyanobacterial hemoglobins contribute to anaerobic nitrogen metabolism in support of anaerobic respiration and survival during hypoxia...
- Petersen L, Oh J, Sakaguchi D, Mallapragada S, Narasimhan B. Amphiphilic polyanhydride films promote neural stem cell adhesion and differentiation. Tissue Eng Part A. 2011;17:2533-41 pubmed publisher..These findings have important implications for development of engineered constructs to regulate differentiation and target the growth of transplanted cells in stem cell-based therapies to treat nervous system disorders...
- Jin H, Kanthasamy A, Ghosh A, Yang Y, Anantharam V, Kanthasamy A. ?-Synuclein negatively regulates protein kinase C? expression to suppress apoptosis in dopaminergic neurons by reducing p300 histone acetyltransferase activity. J Neurosci. 2011;31:2035-51 pubmed publisher..These findings expand the role of ?syn in neuroprotection by modulating the expression of the key proapoptotic kinase PKC? in dopaminergic neurons. ..
- Mandell R, Flick R. Rift Valley fever virus: an unrecognized emerging threat?. Hum Vaccin. 2010;6:597-601 pubmed..Rift Valley fever epizootics and epidemics might rapidly overwhelm the capacities of the public health and veterinary medical communities to provide rapid diagnostic testing, distribution of countermeasures and adequate medical care...
- DeLisi M, Vaughn M. The Gottfredson-Hirschi critiques revisited: reconciling self-control theory, criminal careers, and career criminals. Int J Offender Ther Comp Criminol. 2008;52:520-37 pubmed..Further integration between self-control and criminal career research is urged. ..
- Strohbehn C, Sneed J, Paez P, Meyer J. Hand washing frequencies and procedures used in retail food services. J Food Prot. 2008;71:1641-50 pubmed..Implementation would mean lost productivity and potential for dermatitis; thus, active managerial control over work assignments is needed. These benchmarks can be used for training and to guide employee hand washing behaviors. ..
- Ross J, Fernandez de Castro J, Zhao J, Samuel M, Walters E, Rios C, et al. Generation of an inbred miniature pig model of retinitis pigmentosa. Invest Ophthalmol Vis Sci. 2012;53:501-7 pubmed publisher..This large-animal model can serve as a novel tool for the study of the pathogenesis and therapeutic intervention in the most common form of adRP...
- Kim K, Kim J, Dekkers J, Rothschild M. Polar overdominant inheritance of a DLK1 polymorphism is associated with growth and fatness in pigs. Mamm Genome. 2004;15:552-9 pubmed..Further study in pigs can provide important insights into understanding the molecular regulation of imprinted genes that are associated with human UPD14 and sheep callipyge phenotypes. ..
- Serb J, Oakley T. Hierarchical phylogenetics as a quantitative analytical framework for evolutionary developmental biology. Bioessays. 2005;27:1158-66 pubmed..We argue that this application of "hierarchical phylogenetics" can be a unifying analytical approach to the field of EDB. ..
- Chung C, Jiang Y, Cheng D, Birt D. Impact of adenomatous polyposis coli (APC) tumor supressor gene in human colon cancer cell lines on cell cycle arrest by apigenin. Mol Carcinog. 2007;46:773-82 pubmed..These results suggest that APC dysfunction may be critical for apigenin to induce cell cycle arrest in human colon cancer cell lines and furthermore, apigenin enhances APC expression and apoptosis in cells with wild-type APC. ..
- Trabue S, Scoggin K, Tjandrakusuma S, Rasmussen M, Reilly P. Ruminal fermentation of propylene glycol and glycerol. J Agric Food Chem. 2007;55:7043-51 pubmed..The sulfur-containing gases produced during propylene glycol fermentation in the rumen may contribute to the toxic effects seen in cattle when high doses are administered for therapeutic purposes...
- Bannantine J, Bermudez L. No holes barred: invasion of the intestinal mucosa by Mycobacterium avium subsp. paratuberculosis. Infect Immun. 2013;81:3960-5 pubmed publisher..These notable findings are summarized along with added mechanistic details of the early infection model. We conclude by proposing critical next steps to further elucidate the process of M. avium subsp. paratuberculosis invasion. ..
- Gentile D, Choo H, Liau A, Sim T, Li D, Fung D, et al. Pathological video game use among youths: a two-year longitudinal study. Pediatrics. 2011;127:e319-29 pubmed publisher..This study adds important information to the discussion about whether video game "addiction" is similar to other addictive behaviors, demonstrating that it can last for years and is not solely a symptom of comorbid disorders. ..
- Kitikoon P, Vincent A, Gauger P, Schlink S, Bayles D, Gramer M, et al. Pathogenicity and transmission in pigs of the novel A(H3N2)v influenza virus isolated from humans and characterization of swine H3N2 viruses isolated in 2010-2011. J Virol. 2012;86:6804-14 pubmed publisher..Continued monitoring of these H3N2 viruses is necessary to evaluate the evolution and potential loss of population immunity in swine and humans...
- Du Z, Fan B, Zhao X, Amoako R, Rothschild M. Association analyses between type 2 diabetes genes and obesity traits in pigs. Obesity (Silver Spring). 2009;17:323-9 pubmed publisher..Further replication of this research in other pig populations should be considered, so that the possibility of utilizing these genetic markers in pig breeding or in animal model research can be explored. ..
- Johansen K, Johansen J. Cell and molecular biology of the spindle matrix. Int Rev Cytol. 2007;263:155-206 pubmed..However, as reviewed here multiple studies spanning the evolutionary spectrum from lower eukaryotes to vertebrates have provided new and intriguing evidence that a spindle matrix may be a general feature of mitosis. ..
- Kudra L, Sebranek J, Dickson J, Mendonca A, Zhang Q, Jackson Davis A, et al. Control of Salmonella enterica Typhimurium in chicken breast meat by irradiation combined with modified atmosphere packaging. J Food Prot. 2011;74:1833-9 pubmed publisher..This study demonstrated that irradiation is an effective means of reducing Salmonella on meat or poultry, but packaging in either vacuum or MAP had little impact during subsequent refrigerated storage. ..
- Terribilini M, Lee J, Yan C, Jernigan R, Honavar V, Dobbs D. Prediction of RNA binding sites in proteins from amino acid sequence. RNA. 2006;12:1450-62 pubmed..RNABindR is available as a Web tool from http://bindr.gdcb.iastate.edu.). ..
- Coyne S, Radesky J, Collier K, Gentile D, Linder J, Nathanson A, et al. Parenting and Digital Media. Pediatrics. 2017;140:S112-S116 pubmed publisher..The majority of children's media use takes place within a wider family dynamic. An understanding of this dynamic is crucial to understanding child media use as a whole...
- Wang J, Huang X. A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage. BMC Bioinformatics. 2005;6:220 pubmed..Our work shows that it is possible to analyze sequences of deep coverage by using pairwise alignments of the sequences with the finished genome sequence, instead of multiple sequence alignments. ..
- Stanton T, Fournié Amazouz E, Postic D, Trott D, Grimont P, Baranton G, et al. Recognition of two new species of intestinal spirochetes: Serpulina intermedia sp. nov. and Serpulina murdochii sp. nov. Int J Syst Bacteriol. 1997;47:1007-12 pubmed..pilosicoli, respectively. S. hyodysenteriae and S. intermedia DNAs gave the same fragment pattern regardless of the enzyme tested. B. aalborgi was differentiated from the Serpulina species by MboII digestion of the 16S rDNA amplicon...
- Chen S, Bobe G, Zimmerman S, Hammond E, Luhman C, Boylston T, et al. Physical and sensory properties of dairy products from cows with various milk fatty acid compositions. J Agric Food Chem. 2004;52:3422-8 pubmed..Thus, selection of cows for milk fatty acid composition can be used to produce dairy products that are probably more healthful and have a softer texture. ..
- Standage D, Brendel V. ParsEval: parallel comparison and analysis of gene structure annotations. BMC Bioinformatics. 2012;13:187 pubmed publisher..Implemented in C, ParsEval provides the quickest and most feature-rich solution for genome annotation comparison to date. The source code is freely available (under an ISC license) at http://parseval.sourceforge.net/. ..
- Everett K, Hornung L, Andersen A. Rapid detection of the Chlamydiaceae and other families in the order Chlamydiales: three PCR tests. J Clin Microbiol. 1999;37:575-80 pubmed..These three tests permit ready identification of chlamydiae for diagnostic and epidemiologic study. The specificity of these tests indicates that they might also be used to identify chlamydiae without culture or isolation...
- Katani R, Cote R, Kudva I, Debroy C, Arthur T, Kapur V. Comparative genomics of two super-shedder isolates of Escherichia coli O157:H7. PLoS ONE. 2017;12:e0182940 pubmed publisher..Future comparative and functional genomic studies are needed to decipher the precise molecular basis for super shedding in O157. ..
- Anderson C, Bushman B, Bartholow B, Cantor J, Christakis D, Coyne S, et al. Screen Violence and Youth Behavior. Pediatrics. 2017;140:S142-S147 pubmed publisher..Modern social-cognitive theories of social behavior provide useful frameworks for understanding how and why these effects occur...
- Yacisin K, Hsieh J, Weiss D, Ackelsberg J, Lee E, Jones L, et al. Outbreak of non-tuberculous mycobacteria skin or soft tissue infections associated with handling fish - New York City, 2013-2014. Epidemiol Infect. 2017;145:2269-2279 pubmed publisher..A definitive environmental outbreak source was not identified...
- Luangtongkum T, Shen Z, Seng V, Sahin O, Jeon B, Liu P, et al. Impaired fitness and transmission of macrolide-resistant Campylobacter jejuni in its natural host. Antimicrob Agents Chemother. 2012;56:1300-8 pubmed publisher..jejuni will likely decrease in the absence of antibiotic selection pressure...
- Xiao C, Halbur P, Opriessnig T. Complete genome sequence of a newly identified porcine astrovirus genotype 3 strain US-MO123. J Virol. 2012;86:13126 pubmed publisher..Sequence comparison and phylogenetic analysis showed that PAstV3 has the closest relationship with mink AstV and the human AstV strains VA1, VA2, and SG, indicating the same ancestral origin and zoonotic potential of the virus. ..
- El Manzalawy Y, Dobbs D, Honavar V. On evaluating MHC-II binding peptide prediction methods. PLoS ONE. 2008;3:e3268 pubmed publisher..These results underscore the importance of using similarity-reduced datasets in rigorously comparing the performance of alternative MHC-II peptide prediction methods. ..