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National Animal Disease Center

facilityAmes, Iowa, United States

Research output, citation impact, and the most-cited recent papers from National Animal Disease Center (United States). Aggregated across the NobleBlocks index of 300M+ scholarly works.

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National Animal Disease Center

Top-cited papers from National Animal Disease Center

Physiological Changes at Parturition and Their Relationship to Metabolic Disorders
Jesse P. Goff, R.L. Horst
1997· Journal of Dairy Science1.1Kdoi:10.3168/jds.s0022-0302(97)76055-7

Most of the metabolic diseases of dairy cows-milk fever, ketosis, retained placenta, and displacement of the abomasum-occur within the first 2 wk of lactation. The etiology of many of those metabolic diseases that are not clinically apparent during the first 2 wk of lactation, such as laminitis, can be traced back to insults that occurred during early lactation. In addition to metabolic disease, the overwhelming majority of infectious disease, in particular mastitis, becomes clinically apparent during the first 2 wk of lactation. Three basic physiological functions must be maintained during the periparturient period if disease is to be avoided: adaptation of the rumen to lactation diets that are high in energy density, maintenance of normocalcemia, and maintenance of a strong immune system. The incidence of both metabolic and infectious diseases is greatly increased whenever one or more of these physiological functions are impaired. This paper discusses the etiological role of each of these factors in the development of common diseases encountered during the periparturient period.

In-feed antibiotic effects on the swine intestinal microbiome
Torey Looft, Timothy A. Johnson, Heather K. Allen, Darrell O. Bayles +4 more
2012· Proceedings of the National Academy of Sciences1.1Kdoi:10.1073/pnas.1120238109

Antibiotics have been administered to agricultural animals for disease treatment, disease prevention, and growth promotion for over 50 y. The impact of such antibiotic use on the treatment of human diseases is hotly debated. We raised pigs in a highly controlled environment, with one portion of the littermates receiving a diet containing performance-enhancing antibiotics [chlortetracycline, sulfamethazine, and penicillin (known as ASP250)] and the other portion receiving the same diet but without the antibiotics. We used phylogenetic, metagenomic, and quantitative PCR-based approaches to address the impact of antibiotics on the swine gut microbiota. Bacterial phylotypes shifted after 14 d of antibiotic treatment, with the medicated pigs showing an increase in Proteobacteria (1-11%) compared with nonmedicated pigs at the same time point. This shift was driven by an increase in Escherichia coli populations. Analysis of the metagenomes showed that microbial functional genes relating to energy production and conversion were increased in the antibiotic-fed pigs. The results also indicate that antibiotic resistance genes increased in abundance and diversity in the medicated swine microbiome despite a high background of resistance genes in nonmedicated swine. Some enriched genes, such as aminoglycoside O-phosphotransferases, confer resistance to antibiotics that were not administered in this study, demonstrating the potential for indirect selection of resistance to classes of antibiotics not fed. The collateral effects of feeding subtherapeutic doses of antibiotics to agricultural animals are apparent and must be considered in cost-benefit analyses.

Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms
Karin D. E. Everett, R. Mitchell Bush, Arthur A. Andersen
1999· INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY1.1Kdoi:10.1099/00207713-49-2-415

The current taxonomic classification of Chlamydia is based on limited phenotypic, morphologic and genetic criteria. This classification does not take into account recent analysis of the ribosomal operon or recently identified obligately intracellular organisms that have a chlamydia-like developmental cycle of replication. Neither does it provide a systematic rationale for identifying new strains. In this study, phylogenetic analyses of the 16S and 23S rRNA genes are presented with corroborating genetic and phenotypic information to show that the order Chlamydiales contains at least four distinct groups at the family level and that within the Chlamydiaceae are two distinct lineages which branch into nine separate clusters. In this report a reclassification of the order Chlamydiales and its current taxa is proposed. This proposal retains currently known strains with > 90% 16S rRNA identity in the family Chlamydiaceae and separates other chlamydia-like organisms that have 80-90% 16S rRNA relatedness to the Chlamydiaceae into new families. Chlamydiae that were previously described as 'Candidatus Parachlamydia acanthamoebae' Amann, Springer, Schönhuber, Ludwig, Schmid, Müller and Michel 1997, become members of Parachlamydiaceae fam. nov., Parachlamydia acanthamoebae gen. nov., sp. now. 'Simkania' strain Z becomes the founding member of Simkaniaceae fam. nov., Simkania negevensis gen. nov., sp. nov. The fourth group, which includes strain WSU 86-1044, was left unnamed. The Chlamydiaceae, which currently has only the genus Chlamydia, is divided into two genera, Chlamydia and Chlamydophila gen. nov. Two new species, Chlamydia muridarum sp. nov. and Chlamydia suis sp. nov., join Chlamydia trachomatis in the emended genus Chlamydia. Chlamydophila gen. nov. assimilates the current species, Chlamydia pecorum, Chlamydia pneumoniae and Chlamydia psittaci, to form Chlamydophila pecorum comb. nov., Chlamydophila pneumoniae comb. nov. and Chlamydophila psittaci comb. nov. Three new Chlamydophila species are derived from Chlamydia psittaci: Chlamydophila abortus gen. nov., sp. nov., Chlamydophila caviae gen. nov., sp. nov. and Chlamydophila felis gen. nov., sp. nov. Emended descriptions for the order Chlamydiales and for the family Chlamydiaceae are provided. These families, genera and species are readily distinguished by analysis of signature sequences in the 16S and 23S ribosomal genes.

A Microassay for 1,25-Dihydroxyvitamin D Not requiring High Performance Liquid Chromatography: Application to Clinical Studies*
Timothy A. Reinhardt, Ronald L. Horst, John W. Orf, Bruce W. Hollis
1984· The Journal of Clinical Endocrinology & Metabolism805doi:10.1210/jcem-58-1-91

This report describes a microassay for 1,25-dihydroxyvitamin D [1,25-(OH)2D] in plasma which does not require high performance liquid chromatography. The assay involves rapid extraction and preliminary purification on a C-18 Sep-Pak cartridge, followed by final purification on a silica Sep-Pak using hexane-isopropanol. Quantitation of 1,25-(OH)2D is achieved using a nonequilibrium assay employing 1,25-(OH)2D receptor from calf thymus. The method is sensitive to 1.5 pg/tube, with B50 occurring at 9 pg/tube and a useful assay range of 1.5-40 pg/tube. The intra- and interassay coefficients of variation are 6.5% and 11.5%, respectively, and the method is linear over a wide range of sample dilutions. In addition, this assay measures both 1,25-(OH)2D2 and 1,25-(OH)2D3 with equal affinity. The importance of using an assay with equal affinity for 1,25-(OH)2D2 and 1,25-(OH)2D3 is demonstrated by the findings that 25-hydroxyvitamin D2 (250HD2) constituted 38.9% of the total 25-OHD found in clinical samples (12.6 +/- 0.7 ng/ml 25-OHD2 vs. 20.1 +/- 0.5 ng/ml 25-OHD3; n = 807). Results of this new assay have been compared to those of the assay of Horst et al. (21), which employs Sephadex LH-20 and high performance liquid chromatography sample purification. The correlation coefficient was r2 = 0.96, and the slope was 1.05. Using this new assay, plasma 1,25-(OH)2D concentrations were as follows: normal adults, 37.4 +/- 2.2 pg/ml (n = 22); chronic renal failure, 10.6 +/- 1.5 pg/ml (n = 7); anephrics, undetectable (n = 10); infant cord blood, 22.9 +/- 4.4 pg/ml (n = 7); and hyperparathyroidism, 68.9 +/- 5.0 pg/ml (n = 13). This assay should be particularly useful in pediatric or other studies in which sample size is limited.

Comparison of the Pathogenicity of Two US Porcine Reproductive and Respiratory Syndrome Virus Isolates with that of the Lelystad Virus
Patrick G. Halbur, P. S. Paul, M. L. Frey, John G. Landgraf +4 more
1995· Veterinary Pathology770doi:10.1177/030098589503200606

One hundred 4-week-old cesarean-derived colostrum-deprived pigs were inoculated with one of two different US porcine reproductive and respiratory syndrome virus (PRRSV) isolates (VR2385, VR2431) or the European Lelystad virus to detect and compare the location and amount of virus antigen. Interstitial pneumonia, myocarditis, lymphadenopathy, and encephalitis were consistently seen in all three groups; however, disease and lesions were more severe in the VR2385 group. Immunohistochemical evaluation of formalin-fixed tissues revealed virus antigen in alveolar macrophages in lungs of 22/25, 14/25, 14/25, and 0/25 of the VR2385, VR2431, Lelystad, and control pigs, respectively. Follicular macrophages and dendritic cells in the lymph nodes of 14/25, 10/25, 10/25, and 0/25 pigs from the VR2385, VR2431, Lelystad, and control groups, respectively, stained positive for virus antigen. Similar cells in the tonsils from 25/25, 21/25, 23/25, and 0/25 pigs from the VR2385, VR2431, Lelystad, and control groups, respectively, stained positive for virus antigen. Other tissues and cells in which virus antigen was detected included macrophages and endothelial cells in the heart, macrophages, and interdigitating cells in the thymus, macrophages and dendritic cells in the spleen and Peyer's patches, and macrophages in hepatic sinusoids, renal medullary interstitium, and adrenal gland. PRRSV persisted in macrophages in the lung, tonsil, lymph node, and spleen for at least 28 days. Significantly more PRRSV antigen was detected in the lung (P < 0.01), lymph nodes (P < or = 0.05), and tonsils (P < 0.05) of the VR2385 pigs than was detected in the same tissues of the VR2431 and Lelystad pigs. The cell types in which PRRSV antigen was detected and the distribution of PRRSV antigen-positive cells within particular tissues and organs were generally similar for the different virus inoculation groups despite differences in virulence of the isolates.

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
Matthew B. Hufford, Arun S. Seetharam, Margaret Woodhouse, Kapeel Chougule +4 more
2021· Science724doi:10.1126/science.abg5289

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.

Marked suppression of secondary hyperparathyroidism by intravenous administration of 1,25-dihydroxy-cholecalciferol in uremic patients.
Eduardo Slatopolsky, Carol Weerts, J Thielan, R.L. Horst +2 more
1984· Journal of Clinical Investigation686doi:10.1172/jci111639

Current evidence suggests that administration of 1,25(OH)2D3 to patients with chronic renal insufficiency results in suppression of secondary hyperparathyroidism only if hypercalcemia occurs. However, since the parathyroid glands possess specific receptors for 1,25(OH)2D3 and a calcium binding protein, there is considerable interest in a possible direct effect of 1,25(OH)2D3 on parathyroid hormone (PTH) secretion independent of changes in serum calcium. Recent findings indicate substantial degradation of 1,25(OH)2D3 in the intestine, therefore, it is possible that while oral administration of the vitamin D metabolite increases intestinal calcium absorption, the delivery of 1,25(OH)2D3 to peripheral target organs may be limited. We therefore compared the effects of orally or intravenously administered 1,25(OH)2D3 on the plasma levels of 1,25(OH)2D3 and the effects of these two modes of treatment on PTH secretion. Whereas oral administration of 1,25(OH)2D3 in doses adequate to maintain serum calcium at the upper limits of normal did not alter PTH levels, a marked suppression (70.1 +/- 3.2%) of PTH levels was seen in all 20 patients given intravenous 1,25(OH)2D3. Temporal studies suggested a 20.1 +/- 5.2% decrease in PTH without a significant change in serum calcium with intravenous 1,25(OH)2D3. In five patients the serum calcium was increased by the oral administration of calcium carbonate, the decrement in serum i-PTH was only 25 +/- 6.65% when compared with 73.5 +/- 5.08% (P less than 0.001) obtained by the administration of intravenous 1,25(OH)2D3. Thus, a similar serum calcium achieved by intravenous 1,25(OH)2D3 rather than calcium carbonate has a greater suppressive effect in the release of PTH. These studies indicate that 1,25(OH)2D3 administered intravenously rather than orally may result in a greater delivery of the vitamin D metabolite to peripheral target tissues other than the intestine and allow a greater expression of biological effects of 1,25(OH)2D3 in peripheral tissues. The use of intravenous 1,25(OH)2D3 thus provides a simple and extremely effective way to suppress secondary hyperparathyroidism in dialysis patients.

Differentiation of Brucella abortus bv. 1, 2, and 4, Brucella melitensis, Brucella ovis, and Brucella suis bv. 1 by PCR
Betsy J. Bricker, Shirley M. Halling
1994· Journal of Clinical Microbiology583doi:10.1128/jcm.32.11.2660-2666.1994

Several PCR assays which identify the genus Brucella but do not discriminate among species have been reported. We describe a PCR assay that comprises five oligonucleotide primers which can identify selected biovars of four species of Brucella. Individual biovars within a species are not differentiated. The assay can identify three biovars (1, 2, and 4) of B. abortus, all three biovars of B. melitensis, biovar 1 of B. suis, and all B. ovis biovars. These biovars include all of the Brucella species typically isolated from cattle in the United States, a goal of the present research. The assay exploits the polymorphism arising from species-specific localization of the genetic element IS711 in the Brucella chromosome. Identity is determined by the size(s) of the product(s) amplified from primers hybridizing at various distances from the element. The performance of the assay with U.S. field isolates was highly effective. When 107 field isolates were screened by the described method, there was 100% agreement with the identifications made by conventional methods. Six closely related bacteria (Agrobacterium radiobacter, Agrobacterium rhizogenes, Ochrobactrum anthropi, Rhizobium leguminosarum, Rhizobium meliloti, and Rhodospirillum rubrum) and two control bacteria (Bordetella bronchiseptica and Escherichia coli) tested negative by the assay.

Segregation of Bovine Viral Diarrhea Virus into Genotypes
Julia F. Ridpath, Steven R. Bolin, Edward J. Dubovi
1994· Virology561doi:10.1006/viro.1994.1620

Isolates of bovine viral diarrhea virus (BVDV) were segregated into two groups based on comparison of sequences from the 5' untranslated region (UTR) of the viral genome. Phylogenic analysis suggested that these groups, termed BVDV I and BVDV II, are as different from each other as reference BVDV (BVDV-NADL, BVDV-SD-1, BVDV-Osloss) are from hog cholera virus. Polymerase chain reaction (PCR) tests, based on the 5' untranslated region and the genomic region coding for the p125 polypeptide, were designed to differentiate between BVDV I and BVDV II. Using these tests, 76 of 140 isolates of BVDV were identified as BVDV II. Antigenic and pathologic differences were noted between BVDV I and BVDV II viruses. Among BVDV I were viruses commonly used in vaccine production, diagnostic tests, and research. BVDV II was isolated predominantly from fetal bovine sera, persistently infected calves born to dams vaccinated against BVDV, and cattle that had died from an acute form of BVDV termed hemorrhagic syndrome.

Open reading frame 2 of porcine circovirus type 2 encodes a major capsid protein
Porntippa Nawagitgul, Igor Morozov, Steven R. Bolin, Perry Harms +2 more
2000· Journal of General Virology537doi:10.1099/0022-1317-81-9-2281

Porcine circovirus 2 (PCV2), a single-stranded DNA virus associated with post-weaning multisystemic wasting syndrome of swine, has two potential open reading frames, ORF1 and ORF2, greater than 600 nucleotides in length. ORF1 is predicted to encode a replication-associated protein (Rep) essential for replication of viral DNA, while ORF2 contains a conserved basic amino acid sequence at the N terminus resembling that of the major structural protein of chicken anaemia virus. Thus far, the structural protein(s) of PCV2 have not been identified. In this study, a viral structural protein of 30 kDa was identified in purified PCV2 particles. ORF2 of PCV2 was cloned into a baculovirus expression vector and the gene product was expressed in insect cells. The expressed ORF2 gene product had a molecular mass of 30 kDa, similar to that detected in purified virus particles. The recombinant ORF2 protein self-assembled to form capsid-like particles when viewed by electron microscopy. Antibodies against the ORF2 protein were detected in samples of sera obtained from pigs as early as 3 weeks after experimental infection with PCV2. These results show that the major structural protein of PCV2 is encoded by ORF2 and has a molecular mass of 30 kDa.

Alterations in bovine neutrophil function during the periparturient period
Marcus E. Kehrli, Brian J. Nonnecke, James A. Roth
1989· American Journal of Veterinary Research483doi:10.2460/ajvr.1989.50.02.207

Neutrophils from 8 Holstein heifers were evaluated for function during the periparturient period. Random migration, ingestion of bacteria, superoxide anion production, native (nonenhanced) chemiluminescence, iodination, and antibody-dependent, cell-mediated cytotoxicity by neutrophils were determined. Foremilk samples were evaluated for bacteria. Significant (P less than 0.05) increases in random migration of neutrophils, iodination, and chemiluminescence were evident 2 weeks before parturition and then decreased dramatically by the first week after parturition. These impairments of neutrophil function after parturition may be manifested as a severe cumulative deficit in the native defenses afforded by the neutrophil.

The Leptospiral Major Outer Membrane Protein LipL32 Is a Lipoprotein Expressed during Mammalian Infection
David A. Haake, G Chao, Richard L. Zuerner, Jeanne K. Barnett +4 more
2000· Infection and Immunity481doi:10.1128/iai.68.4.2276-2285.2000

We report the cloning of the gene encoding the 32-kDa lipoprotein, designated LipL32, the most prominent protein in the leptospiral protein profile. We obtained the N-terminal amino acid sequence of a staphylococcal V8 proteolytic-digest fragment to design an oligonucleotide probe. A Lambda-Zap II library containing EcoRI fragments of Leptospira kirschneri DNA was screened, and a 5.0-kb DNA fragment which contained the entire structural lipL32 gene was identified. Several lines of evidence indicate that LipL32 is lipid modified in a manner similar to that of other procaryotic lipoproteins. The deduced amino acid sequence of LipL32 would encode a 272-amino-acid polypeptide with a 19-amino-acid signal peptide, followed by a lipoprotein signal peptidase cleavage site. LipL32 is intrinsically labeled during incubation of L. kirschneri in media containing [(3)H]palmitate. The linkage of palmitate and the amino-terminal cysteine of LipL32 is acid labile. LipL32 is completely solubilized by Triton X-114 extraction of L. kirschneri; phase separation results in partitioning of LipL32 exclusively into the hydrophobic, detergent phase, indicating that it is a component of the leptospiral outer membrane. CaCl(2) (20 mM) must be present during phase separation for recovery of LipL32. LipL32 is expressed not only during cultivation but also during mammalian infection. Immunohistochemistry demonstrated intense LipL32 reactivity with L. kirschneri infecting proximal tubules of hamster kidneys. LipL32 is also a prominent immunogen during human leptospirosis. The sequence and expression of LipL32 is highly conserved among pathogenic Leptospira species. These findings indicate that LipL32 may be important in the pathogenesis, diagnosis, and prevention of leptospirosis.

The complete genome sequence of<i>Mycobacterium avium</i>subspecies<i>paratuberculosis</i>
Lingling Li, John P. Bannantine, Qing Zhang, Alongkorn Amonsin +4 more
2005· Proceedings of the National Academy of Sciences448doi:10.1073/pnas.0505662102

We describe here the complete genome sequence of a common clone of Mycobacterium avium subspecies paratuberculosis (Map) strain K-10, the causative agent of Johne's disease in cattle and other ruminants. The K-10 genome is a single circular chromosome of 4,829,781 base pairs and encodes 4,350 predicted ORFs, 45 tRNAs, and one rRNA operon. In silico analysis identified >3,000 genes with homologs to the human pathogen, M. tuberculosis (Mtb), and 161 unique genomic regions that encode 39 previously unknown Map genes. Analysis of nucleotide substitution rates with Mtb homologs suggest overall strong selection for a vast majority of these shared mycobacterial genes, with only 68 ORFs with a synonymous to nonsynonymous substitution ratio of >2. Comparative sequence analysis reveals several noteworthy features of the K-10 genome including: a relative paucity of the PE/PPE family of sequences that are implicated as virulence factors and known to be immunostimulatory during Mtb infection; truncation in the EntE domain of a salicyl-AMP ligase (MbtA), the first gene in the mycobactin biosynthesis gene cluster, providing a possible explanation for mycobactin dependence of Map; and Map-specific sequences that are likely to serve as potential targets for sensitive and specific molecular and immunologic diagnostic tests. Taken together, the availability of the complete genome sequence offers a foundation for the study of the genetic basis for virulence and physiology in Map and enables the development of new generations of diagnostic tests for bovine Johne's disease.

Isolation and Characterization of Porcine Epidemic Diarrhea Viruses Associated with the 2013 Disease Outbreak among Swine in the United States
Qi Chen, Ganwu Li, Judith Stasko, Joseph T. Thomas +4 more
2013· Journal of Clinical Microbiology433doi:10.1128/jcm.02820-13

Porcine epidemic diarrhea virus (PEDV) was detected in May 2013 for the first time in U.S. swine and has since caused significant economic loss. Obtaining a U.S. PEDV isolate that can grow efficiently in cell culture is critical for investigating pathogenesis and developing diagnostic assays and for vaccine development. An additional objective was to determine which gene(s) of PEDV is most suitable for studying the genetic relatedness of the virus. Here we describe two PEDV isolates (ISU13-19338E and ISU13-22038) successfully obtained from the small intestines of piglets from sow farms in Indiana and Iowa, respectively. The two isolates have been serially propagated in cell culture for over 30 passages and were characterized for the first 10 passages. Virus production in cell culture was confirmed by PEDV-specific real-time reverse-transcription PCR (RT-PCR), immunofluorescence assays, and electron microscopy. The infectious titers of the viruses during the first 10 passages ranged from 6 × 10(2) to 2 × 10(5) 50% tissue culture infective doses (TCID50)/ml. In addition, the full-length genome sequences of six viruses (ISU13-19338E homogenate, P3, and P9; ISU13-22038 homogenate, P3, and P9) were determined. Genetically, the two PEDV isolates were relatively stable during the first 10 passages in cell culture. Sequences were also compared to those of 4 additional U.S. PEDV strains and 23 non-U.S. strains. All U.S. PEDV strains were genetically closely related to each other (≥99.7% nucleotide identity) and were most genetically similar to Chinese strains reported in 2011 to 2012. Phylogenetic analyses using different genes of PEDV suggested that the full-length spike gene or the S1 portion is appropriate for sequencing to study the genetic relatedness of these viruses.

Experimental infection of calves and adult cattle with Escherichia coli O157:H7
William C. Cray, Harley W. Moon
1995· Applied and Environmental Microbiology409doi:10.1128/aem.61.4.1586-1590.1995

Preweaned calves and adult cattle were inoculated with 10(10) CFU of Escherichia coli O157:H7 strain 3081, a calf isolate which produces Shiga-like toxin, to define the magnitude and duration of fecal shedding of E. coli O157:H7 for each age group. Fecal samples of eight of eight, eight of eight, three of eight, and two of eight calves were positive at 2, 7, 14, and 20 weeks, respectively. In contrast, nine of nine, two of nine, and one of nine steers were positive at 2, 7, and 14 weeks, respectively. The magnitude of shedding (CFU per gram) by individual animals at any one time postinoculation varied widely within each age group but was greater for calves as a group. The differences in shedding patterns between adults and calves were statistically significant. After inoculation, 25 of 29 animals remained healthy and 4 of 17 calves had transient diarrhea. Histologic sections of the brain, kidney, jejunum, ileum, cecum, and colon taken at necropsy from nine calves either 3, 14, or 18 days postinoculation or three adults either 2, 3, or 4 days postinoculation were normal. E. coli O157:H7 was recovered from the alimentary tracts of all of the animals necropsied, and there was no evidence of spread to the liver, spleen, or kidneys. Four calves that had ceased shedding were reinfected when inoculated again with the same strain. E. coli O157:H7 was recovered from none of five and two of five adults inoculated with 10(4) and 10(7) CFU, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project
Leif Andersson, Alan Archibald, C. D. K. Bottema, Rüdiger Bräuning +4 more
2015· Genome Biology402doi:10.1186/s13059-015-0622-4

We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.

Detection of Heat-Labile <i>Escherichia coli</i> Enterotoxin with the Use of Adrenal Cells in Tissue Culture
Sam T. Donta, Harley W. Moon, S. C. Whipp
1974· Science393doi:10.1126/science.183.4122.334

Cell-free culture filtrates of heat-labile enterotoxin-producing strains of Escherichia coli are capable of inducing morphological changes and steroidogenesis in monolayer cultures of adrenal cells. These tissue culture changes are simiar to those induced by cholera enterotoxin and cannot be effected by culture filtrates of other enterotoxigenic or enteropathogenic types of bacteria. The results of the tissue culture studies correlated well with those done in the standard intestinal-loop systems and suggest that this tissue culture system could be used to significantly aid epidemiological and molecular studies with heat-labile Escherichia coli enterotoxin.

Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations
Torey Looft, Heather K. Allen, Brandi L. Cantarel, Uri Y. Levine +4 more
2014· The ISME Journal383doi:10.1038/ismej.2014.12

Disturbance of the beneficial gut microbial community is a potential collateral effect of antibiotics, which have many uses in animal agriculture (disease treatment or prevention and feed efficiency improvement). Understanding antibiotic effects on bacterial communities at different intestinal locations is essential to realize the full benefits and consequences of in-feed antibiotics. In this study, we defined the lumenal and mucosal bacterial communities from the small intestine (ileum) and large intestine (cecum and colon) plus feces, and characterized the effects of in-feed antibiotics (chlortetracycline, sulfamethazine and penicillin (ASP250)) on these communities. 16S rRNA gene sequence and metagenomic analyses of bacterial membership and functions revealed dramatic differences between small and large intestinal locations, including enrichment of Firmicutes and phage-encoding genes in the ileum. The large intestinal microbiota encoded numerous genes to degrade plant cell wall components, and these genes were lacking in the ileum. The mucosa-associated ileal microbiota harbored greater bacterial diversity than the lumen but similar membership to the mucosa of the large intestine, suggesting that most gut microbes can associate with the mucosa and might serve as an inoculum for the lumen. The collateral effects on the microbiota of antibiotic-fed animals caused divergence from that of control animals, with notable changes being increases in Escherichia coli populations in the ileum, Lachnobacterium spp. in all gut locations, and resistance genes to antibiotics not administered. Characterizing the differential metabolic capacities and response to perturbation at distinct intestinal locations will inform strategies to improve gut health and food safety.

Influenza Research Database: An integrated bioinformatics resource for influenza virus research
Yun Zhang, Brian D. Aevermann, Tavis K. Anderson, David F. Burke +4 more
2016· Nucleic Acids Research373doi:10.1093/nar/gkw857

The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics and therapeutics against influenza virus by providing a comprehensive collection of influenza-related data integrated from various sources, a growing suite of analysis and visualization tools for data mining and hypothesis generation, personal workbench spaces for data storage and sharing, and active user community support. Here, we describe the recent improvements in IRD including the use of cloud and high performance computing resources, analysis and visualization of user-provided sequence data with associated metadata, predictions of novel variant proteins, annotations of phenotype-associated sequence markers and their predicted phenotypic effects, hemagglutinin (HA) clade classifications, an automated tool for HA subtype numbering conversion, linkouts to disease event data and the addition of host factor and antiviral drug components. All data and tools are freely available without restriction from the IRD website at https://www.fludb.org.

Comparison of Fumonisin Concentrations in Kernels of Transgenic Bt Maize Hybrids and Nontransgenic Hybrids
Gary P. Munkvold, Richard L. Hellmich, L. G. Rice
1999· Plant Disease371doi:10.1094/pdis.1999.83.2.130

Maize hybrids genetically engineered with genes from the bacterium Bacillus thuringiensis (Bt maize) express CryIA(b) and other Cry proteins that are toxic to certain insects, particularly the European corn borer (Ostrinia nubilalis). Maize kernel feeding by O. nubilalis often leads to infection by fungi in the genus Fusarium, including the fumonisin-producing species F. verticillioides and F. proliferatum. In field experiments in 1995, 1996, and 1997, transgenic maize hybrids and near-isogenic, nontransgenic hybrids were manually infested with neonatal European corn borer larvae. Manual infestation increased Fusarium ear rot severity and fumonisin concentrations in kernels of nontransgenic hybrids. Transgenic hybrids with kernel expression of CryIA(b) consistently experienced less insect feeding on kernels and less Fusarium ear rot than their nontransgenic counterparts. In manually infested treatments, these hybrids also exhibited lower concentrations of fumonisins in kernels compared with their nontransgenic counterparts. In manually infested treatments in 1995, mean fumonisin B 1 concentrations were 8.8 μg/g in the nontransgenic hybrid and 6.7 or 3.0 μg/g in transgenic hybrids. In 1996, mean fumonisin B 1 concentrations in manually infested treatments were 4.9 μg/g (range 2.3 to 8.8) for nontransgenic and 1.2 μg/g (range 1.0 to 1.3) for transgenic hybrids with kernel expression. Mean total fumonisin concentrations (fumonisin B1 + B2 + B3) were 7.0 μg/g (range 3.0 to 12.2) for nontransgenic and 1.7 μg/g (range 1.5 to 1.9) for transgenic hybrids with kernel expression. In 1997, mean fumonisin B 1 concentrations in manually infested treatments were 11.8 μg/g (range 7.6 to 17.3) for nontransgenic and 1.3 μg/g (range 0.8 to 2.2) for transgenic hybrids with kernel expression of CryIA(b) or Cry9C. Mean total fumonisin concentrations were 16.5 μg/g (range 10.7 to 24.0) for nontransgenic and 2.1 μg/g (range 1.5 to 3.1) for transgenic hybrids with kernel expression. Transgenic hybrids that do not express CryIA(b) or Cry9C in kernels did not consistently have fumonisin concentrations different from the nontransgenic hybrids. Higher fumonisin concentrations in nontransgenic hybrids were associated with high European corn borer populations during the early reproductive stages of the maize plants. These results indicate that under some conditions, genetic engineering of maize for insect resistance may enhance its safety for animal and human consumption.