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Blackburn MB, Farrar RR, Sparks ME, Kuhar D, Mowery JD, Mitchell A, Gundersen-Rindal DE. Chromobacterium paludis sp. nov., a novel bacterium isolated from a Chesapeake Bay marsh. Int J Syst Evol Microbiol 2020; 70:6142-6146. [PMID: 33054903 DOI: 10.1099/ijsem.0.004509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two isolates of Gram-reaction-negative, motile, violet-pigmented bacteria were isolated from a small pool in marshland near the mouth of the Nanticoke River in Maryland, USA. The isolates IIBBL 257-1T and IIBBL 257-2 had identical 16S rRNA gene sequences as determined by PCR, and highly similar fatty acid and biochemical profiles. The 16S rRNA gene sequences indicated the isolates belonged to the genus Chromobacterium. Genomic sequencing of IIBBL 257-1T revealed a genome of 4.27 Mb, with a G+C content of 63.6 %. Whole genome comparisons with other members of the Chromobacterium using JSpecies and the genome blast distance phylogeny approach indicated that among described species, IIBBL 257-1T was most closely related to C. amazonense and C. phragmitis. Comparison of the IIBBL 257-1T genome with those of type strains of these species resulted in ANIb and dDDH values of ca. 85 and 30 %, respectively, for both. These results demonstrate that IIBBL 257-1T and IIBBL 257-2 represent a new taxon within the genus Chromobacterium. We propose the name Chromobacterium paludis sp. nov. for this taxon; the type strain is IIBBL 257-1T (=NRRL B-65555T=JCM 33770T).
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Affiliation(s)
- Michael B Blackburn
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Robert R Farrar
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Michael E Sparks
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Daniel Kuhar
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Joseph D Mowery
- Electron and Confocal Microscopy Unit, USDA-ARS, Beltsville, MD 20705, USA
| | - Ashaki Mitchell
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
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Blackburn MB, Farrar RR, Sparks ME, Kuhar D, Mowery JD, Mitchell A, Gundersen-Rindal DE. Chromobacterium phragmitis sp. nov., isolated from estuarine marshes. Int J Syst Evol Microbiol 2019; 69:2681-2686. [PMID: 31199223 DOI: 10.1099/ijsem.0.003508] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Thirteen isolates of Gram-stain-negative, motile, violet-pigmented bacteria were isolated from marshes along tidal portions of the Potomac and James rivers in Maryland and Virginia, USA, respectively. 16S rRNA gene sequences and fatty acid analysis revealed a high degree of relatedness among the isolates, and genomic sequencing of two isolates, IIBBL 112-1T and IIBBL 274-1 (from the Potomac and James rivers, respectively), revealed highly similar genomic sequences, with a blast-based average nucleotide identity (ANIb) of ca. 98.7 %. Phylogenetic analysis of 16S rRNA gene sequences suggested that the species most highly related to IIBBL 112-1T were Chromobacterium amazonense, Chromobacterium subtsugae and Chromobacterium sphagni. However, deletion of a 25-nucleotide sequence that may have been horizontally acquired by both IIBBL 112-1T and C. amazonense resulted in a substantially different analysis; in the latter case, the species nearest IIBBL 112-1T were Chromobacterium violaceum, Chromobacterium vaccinii and Chromobacterium piscinae. Whole-genome alignments between either IIBBL 112-1T or IIBBL 274-1 and the type strains of C. vaccinii or C. violaceum resulted in ANIb values in the range of ca. 87 %, while alignment with C. amazonense CBMAI 310T resulted in an ANIb of ca. 83 %. Collectively, these data demonstrate that IIBBL 112-1T and IIBBL 274-1 represent a new taxon within the genus Chromobacterium. We propose the name Chromobacterium phragmitis sp. nov. for this taxon; the type strain is IIBBL 112-1T (=NRRL B-67132T=JCM 31884T).
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Affiliation(s)
- Michael B Blackburn
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Robert R Farrar
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Michael E Sparks
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Daniel Kuhar
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Joseph D Mowery
- Electron and Confocal Microscopy Unit, USDA-ARS, Beltsville, MD 20705, USA
| | - Ashaki Mitchell
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
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Bredlau JP, Kuhar D, Gundersen-Rindal DE, Kester KM. The Parasitic Wasp, Cotesia congregata (Say), Consists of Two Incipient Species Isolated by Asymmetric Reproductive Incompatibility and Hybrid Inability to Overcome Host Defenses. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Blackburn MB, Farrar RR, Sparks ME, Kuhar D, Mitchell A, Gundersen-Rindal DE. Chromobacterium sphagni sp. nov., an insecticidal bacterium isolated from Sphagnum bogs. Int J Syst Evol Microbiol 2017; 67:3417-3422. [PMID: 28829025 DOI: 10.1099/ijsem.0.002127] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sixteen isolates of Gram-reaction-negative, motile, violet-pigmented bacteria were isolated from Sphagnum bogs in West Virginia and Maine, USA. 16S rRNA gene sequences and fatty acid analysis revealed a high degree of relatedness among the isolates, and genome sequencing of two isolates, IIBBL 14B-1T and IIBBL 37-2 (from West Virginia and Maine, respectively), revealed highly similar genomic sequences. The average nucleotide identity (gANI) calculated for these two isolates was found to be in excess of 99 %, but did not exceed 88 % when comparing either isolate with genomic sequences of Chromobacterium violaceum ATCC 12472T, C. haemolyticum DSM 19808T, C. piscinae ND17, C. subtsugae PRAA4-1T, C. vaccinii MWU205T or C. amazonense CBMAI 310T. Collectively, gANI and 16S rRNA gene sequence comparisons suggested that isolates IIBBL 14B-1T and IIBBL 37-2 were most closely related to C. subtsugae, but represented a distinct species. We propose the name Chromobacterium sphagni sp. nov. for this taxon; the type strain is IIBBL 14B-1T (=NRRL B-67130T=JCM 31882T).
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Affiliation(s)
- Michael B Blackburn
- Invasive Insect Biocontrol and Behavior Laboratory, USDA, ARS, Bldg 007, Rm 301, BARC-West, Beltsville, MD 20705, USA
| | - Robert R Farrar
- Invasive Insect Biocontrol and Behavior Laboratory, USDA, ARS, Bldg 007, Rm 301, BARC-West, Beltsville, MD 20705, USA
| | - Michael E Sparks
- Invasive Insect Biocontrol and Behavior Laboratory, USDA, ARS, Bldg 007, Rm 301, BARC-West, Beltsville, MD 20705, USA
| | - Daniel Kuhar
- Invasive Insect Biocontrol and Behavior Laboratory, USDA, ARS, Bldg 007, Rm 301, BARC-West, Beltsville, MD 20705, USA
| | - Ashaki Mitchell
- Invasive Insect Biocontrol and Behavior Laboratory, USDA, ARS, Bldg 007, Rm 301, BARC-West, Beltsville, MD 20705, USA
| | - Dawn E Gundersen-Rindal
- Invasive Insect Biocontrol and Behavior Laboratory, USDA, ARS, Bldg 007, Rm 301, BARC-West, Beltsville, MD 20705, USA
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Sparks ME, Shelby KS, Kuhar D, Gundersen-Rindal DE. Transcriptome of the invasive brown marmorated stink bug, Halyomorpha halys (Stål) (Heteroptera: Pentatomidae). PLoS One 2014; 9:e111646. [PMID: 25386688 PMCID: PMC4227672 DOI: 10.1371/journal.pone.0111646] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/03/2014] [Indexed: 01/29/2023] Open
Abstract
Halyomorpha halys (Stål) (Heteroptera: Pentatomidae), the brown marmorated stink bug, is an invasive agricultural and nuisance pest rapidly expanding its incidence in North America. This voracious pest poses a significant threat to rural and urban agriculture, especially to specialty crops such as apples, grapes and ornamentals, as well as staple crops including soybean and corn. The object of this study was to generate transcript sequence resources for H. halys. RNA-seq libraries derived from distinct developmental stages and sexes were sequenced and assembled into 248,569 putatively unique transcripts (PUTs). PUTs were segmented into three disjoint tiers of varying reliability, with 4,794 classified as gold tier (highest quality), 16,878 as silver, and 14,357 as bronze. The gold-tier PUTs associated with 2,580 distinct non-redundant protein sequences from the NCBI NR database--1,785 of these (69%) mapped to annotated UniProtKB database proteins, from which 1,273 unique Pfam families and 459 unique Molecular Function GO terms were encountered. Of the silver tier's 6,527 PUTs associated with unique proteins, 4,193 mapped to UniProtKB (64%), from which 1,941 and 640 unique Pfam and Molecular Function GO terms were extracted. H. halys PUTs related to important life processes like immunity, endocrinology, reproduction, development, behavior, neurotransmission, neurotoxicity, olfaction, and small RNA pathways were validated through quantitative Real-Time PCR (qRT-PCR) for differential expression during distinct life stages (eggs, 2nd instar nymphs, 4th instar nymphs, female adults, male adults). PUTs similar to hypothetical proteins identified in symbiont microbes, including Pantoea and Nosema species, were more abundantly expressed in adults versus nymphs. These comprehensive H. halys transcriptomic resources can be utilized to aid development of novel control methodologies to disrupt life processes; to conduct reverse genetic screens to determine host gene function; and to design environmentally unobtrusive means to control host populations or target specific H. halys life stages, such as molecular biopesticides.
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Affiliation(s)
- Michael E. Sparks
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
| | - Kent S. Shelby
- USDA-ARS Biological Control of Insects Research Laboratory, Columbia, Missouri, United States of America
| | - Daniel Kuhar
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
| | - Dawn E. Gundersen-Rindal
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
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Blackburn MB, Martin PAW, Kuhar D, Farrar RR, Gundersen-Rindal DE. Crystalliferous Bacillus cereus group bacteria from a Maryland hardwood forest are dominated by psychrotolerant strains. Microbiologyopen 2014; 3:578-84. [PMID: 24985699 PMCID: PMC4287184 DOI: 10.1002/mbo3.189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 05/09/2014] [Accepted: 05/26/2014] [Indexed: 11/17/2022] Open
Abstract
Crystal-forming bacteria of the Bacillus cereus group were isolated from soil samples collected at different elevations within a mixed hardwood forest in central Maryland, and their phylogenetic relationships determined by multilocus sequence analysis. The vast majority of isolates obtained were associated with two phylogenetic groups known to be psychrotolerant, with very few isolates representing phylogenetic groups more typically associated with Bacillus thuringiensis. Isolates from the psychrotolerant groups were found to grow on solid media at 7°C. Isolates of 11 highly related, novel sequence types (STs) from the psychrotolerant group that includes Bacillus weihenstephanensis were generally found at higher elevations, and were not associated with soils near streams. Isolates of two related STs from the second psychrotolerant group were nearly always found at the bottoms of ravines near streams, in areas abundant in earthworm castings.
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Affiliation(s)
- Michael B Blackburn
- Invasive Insect Biocontrol and Behavior Laboratory, USDA/ARS, Beltsville, Maryland, 20705
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Sparks ME, Blackburn MB, Kuhar D, Gundersen-Rindal DE. Transcriptome of the Lymantria dispar (gypsy moth) larval midgut in response to infection by Bacillus thuringiensis. PLoS One 2013; 8:e61190. [PMID: 23658687 PMCID: PMC3641027 DOI: 10.1371/journal.pone.0061190] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Accepted: 03/07/2013] [Indexed: 11/23/2022] Open
Abstract
Transcriptomic profiles of the serious lepidopteran insect pest Lymantria dispar (gypsy moth) were characterized in the larval midgut in response to infection by Bacillus thuringiensis kurstaki, a biopesticide commonly used for its control. RNA-Seq approaches were used to define a set of 49,613 assembled transcript sequences, of which 838, 1,248 and 3,305 were respectively partitioned into high-, mid- and low-quality tiers on the basis of homology information. Digital gene expression profiles suggested genes differentially expressed at 24 hours post infection, and qRT-PCR analyses were performed for verification. The differentially expressed genes primarily associated with digestive function, including α-amylase, lipase and carboxypeptidase; immune response, including C-type lectin 4; developmental genes such as arylphorin; as well as a variety of binding proteins: cellular retinoic acid binding protein (lipid-binding), insulin-related peptide binding protein (protein-binding) and ovary C/EBPg transcription factor (nucleic acid-binding). This is the first study conducted to specifically investigate gypsy moth response to a bacterial infection challenge using large-scale sequencing technologies, and the results highlight important genes that could be involved in biopesticide resistance development or could serve as targets for biologically-based control mechanisms of this insect pest.
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Affiliation(s)
- Michael E. Sparks
- United States Department of Agriculture -ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
| | - Michael B. Blackburn
- United States Department of Agriculture -ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
| | - Daniel Kuhar
- United States Department of Agriculture -ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
| | - Dawn E. Gundersen-Rindal
- United States Department of Agriculture -ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
- * E-mail:
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Wysocki M, Chen H, Steibel JP, Kuhar D, Petry D, Bates J, Johnson R, Ernst CW, Lunney JK. Identifying putative candidate genes and pathways involved in immune responses to porcine reproductive and respiratory syndrome virus (PRRSV) infection. Anim Genet 2011; 43:328-32. [PMID: 22486506 DOI: 10.1111/j.1365-2052.2011.02251.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Differences in gene expression were compared between RNAs from lungs of high (HR) and low (LR) porcine reproductive and respiratory syndrome virus (PRRSV) burden pigs using the swine protein-annotated long oligonucleotide microarray, the Pigoligoarray. Pathway analyses were carried out to determine biological processes, pathways and networks that differ between the LR and HR responses. Differences existed between HR and LR pigs for 16 signalling pathways [P < 0.01/-log (P-value) >1.96]. Top canonical pathways included acute phase response signalling, crosstalk between dendritic cells and natural killer cells and tight junction signalling, with numerous immune response genes that were upregulated (SOCS1, SOD2, RBP4, HLA-B, HLA-G, PPP2R1A and TAP1) or downregulated (IL18, TF, C4BPA, C1QA, C1QB and TYROBP). One mechanism, regulation of complement activation, may have been blocked in HR (PRRSV-susceptible) pigs and could account for the poor clearance of PRRSV by infected macrophages. Multiple inhibiting signals may have prevented effective immune responses in susceptible HR pigs, although some protective genes were upregulated in these pigs. It is likely that in HR pigs, expression of genes associated with protection was delayed, so that the immune response was not stimulated early; thus, PRRSV infection prevented protective immune responses.
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Affiliation(s)
- M Wysocki
- Animal Parasitic Diseases Laboratory, ANRI, ARS, USDA, BARC-East, Beltsville, MD 20705, USA
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Blackburn MB, Martin PAW, Kuhar D, Farrar RR, Gundersen-Rindal DE. The occurrence of photorhabdus-like toxin complexes in Bacillus thuringiensis. PLoS One 2011; 6:e18122. [PMID: 21464948 PMCID: PMC3064592 DOI: 10.1371/journal.pone.0018122] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 02/21/2011] [Indexed: 11/18/2022] Open
Abstract
Recently, genomic sequencing of a Bacillus thuringiensis (Bt) isolate from our collection revealed the presence of an apparent operon encoding an insecticidal toxin complex (Tca) similar to that first described from the entomopathogen Photorhabdus luminescens. To determine whether these genes are widespread among Bt strains, we screened isolates from the collection for the presence of tccC, one of the genes needed for the expression of fully functional toxin complexes. Among 81 isolates chosen to represent commonly encountered biochemical phenotypes, 17 were found to possess a tccC. Phylogenetic analysis of the 81 isolates by multilocus sequence typing revealed that all the isolates possessing a tccC gene were restricted to two sequence types related to Bt varieties morrisoni, tenebrionis, israelensis and toumanoffi. Sequencing of the ∼17 kb tca operon from two isolates representing each of the two sequence types revealed >99% sequence identity. Optical mapping of DNA from Bt isolates representing each of the sequence types revealed nearly identical plasmids of ca. 333 and 338 kbp, respectively. Selected isolates were found to be toxic to gypsy moth larvae, but were not as effective as a commercial strain of Bt kurstaki. Some isolates were found to inhibit growth of Colorado potato beetle. Custom Taqman® relative quantitative real-time PCR assays for Tc-encoding Bt revealed both tcaA and tcaB genes were expressed within infected gypsy moth larvae.
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Affiliation(s)
- Michael B Blackburn
- Invasive Insect Biocontrol and Behavior Laboratory, Agricultural Research Service, United States Department of Agriculture, Henry A Wallace Beltsville Agricultural Research Center, Beltsville, Maryland, United States of America.
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Tuggle CK, Bearson SMD, Uthe JJ, Huang TH, Couture OP, Wang YF, Kuhar D, Lunney JK, Honavar V. Methods for transcriptomic analyses of the porcine host immune response: application to Salmonella infection using microarrays. Vet Immunol Immunopathol 2010; 138:280-91. [PMID: 21036404 DOI: 10.1016/j.vetimm.2010.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Technological developments in both the collection and analysis of molecular genetic data over the past few years have provided new opportunities for an improved understanding of the global response to pathogen exposure. Such developments are particularly dramatic for scientists studying the pig, where tools to measure the expression of tens of thousands of transcripts, as well as unprecedented data on the porcine genome sequence, have combined to expand our abilities to elucidate the porcine immune system. In this review, we describe these recent developments in the context of our work using primarily microarrays to explore gene expression changes during infection of pigs by Salmonella. Thus while the focus is not a comprehensive review of all possible approaches, we provide links and information on both the tools we use as well as alternatives commonly available for transcriptomic data collection and analysis of porcine immune responses. Through this review, we expect readers will gain an appreciation for the necessary steps to plan, conduct, analyze and interpret the data from transcriptomic analyses directly applicable to their research interests.
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Affiliation(s)
- C K Tuggle
- Department of Animal Science, and Center for Integrated Animal Genomics, 2255 Kildee Hall, Iowa State University, Ames, IA 50010, United States.
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Lunney JK, Fritz ER, Reecy JM, Kuhar D, Prucnal E, Molina R, Christopher-Hennings J, Zimmerman J, Rowland RRR. Interleukin-8, interleukin-1beta, and interferon-gamma levels are linked to PRRS virus clearance. Viral Immunol 2010; 23:127-34. [PMID: 20373993 DOI: 10.1089/vim.2009.0087] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Infection with porcine reproductive and respiratory syndrome virus (PRRSV) results in a weak antiviral immune response that leads to a persistent infection in a subset of pigs. We investigated the intensity and timing of the early cytokine responses to PRRSV infection to determine their utility as a predictor of persistence. As part of the "Big Pig" project, we evaluated cytokine gene expression in lymphoid tissues collected from pigs for up 202 days post-infection (dpi); serum samples were collected biweekly. Cytokine mRNA levels were compared between pigs that cleared the viral infection from serum and tissues (non-persistent [NP] pigs) to those of persistent (P) pigs, that had viral RNA in their serum for up to 126 dpi. The gene expression studies in the tracheobronchial lymph nodes (TBLN) of all the pigs showed upregulation of interferon-gamma (IFN-gamma)-associated T-helper 1 (Th-1) markers from 14-84 dpi, and of T-regulatory interleukin-10 (IL-10), but no upregulation of innate markers (IFN-A, IL-1B, and IL-8). At later time points (>112 dpi) these genes were no longer differentially expressed and thus were uninformative for persistence studies. Statistical analyses of serum cytokine levels indicated that innate cytokine (IL-1beta and IL-8) levels were upregulated early after infection. Interestingly, serum IL-8 levels in NP pigs were significantly higher than in P pigs at 14 dpi. When analyzed together, variations in all three of the serum cytokines tested (IL-8, IL-1beta, and IFN-gamma) was significantly correlated with virus level, accounting for approximately 84% of the variations observed. These results indicate that while each cytokine individually has minor effects on the length of virus replication, the combination of cytokine activities should be considered when understanding the role of immunity in persistence.
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Affiliation(s)
- Joan K Lunney
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland 20705, USA.
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Opriessnig T, Patterson AR, Madson DM, Pal N, Rothschild M, Kuhar D, Lunney JK, Juhan NM, Meng XJ, Halbur PG. Difference in severity of porcine circovirus type two-induced pathological lesions between Landrace and Pietrain pigs. J Anim Sci 2009; 87:1582-90. [PMID: 19181769 DOI: 10.2527/jas.2008-1390] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Anecdotal information from the field suggests that there are host genetic differences in susceptibility to porcine circovirus type 2 (PCV2) associated disease among Landrace and Pietrain breeds. The objective of this study was to determine if a difference exists in PCV2 susceptibility between Landrace and Pietrain pigs under experimental conditions. Thirty-nine Landrace pigs and 39 Pietrain pigs were blocked by breed, sire, dam, and litter and randomly divided into the following 4 groups: Landrace noninoculated negative control (Landrace-NEG; n = 13), Pietrain noninoculated negative control (Pietrain-NEG; n = 13), Landrace-PCV2 (n = 26; Landrace), and Pietrain-PCV2 (n = 26; Pietrain). After waning of passively acquired anti-PCV2 antibodies, Landrace-PCV2 and Pietrain-PCV2 groups were inoculated with PCV2 isolate ISU-40895. The Landrace-NEG and Pietrain-NEG groups were housed in a separate room, remained noninoculated, and served as negative controls. All pigs in all groups were necropsied at 21 d post PCV2-inoculation. Onset of seroconversion and concentrations of anti-PCV2-IgM, anti-PCV2-IgG, and anti-PCV2 neutralizing antibodies were similar in Landrace-PCV2 and Pietrain-PCV2 groups. Furthermore, the amount of PCV2 DNA and cytokine concentrations in serum and plasma samples were not different between the 2 PCV2-inoculated groups. The severity of PCV2-associated microscopic lesions was different between Landrace and Pietrain pigs; Landrace-PCV2 pigs had significantly (P < 0.05) more severe lymphoid lesions than the Pietrain-PCV2 pigs. Although the pigs originated from the same farm where their dams were commingled, passively acquired anti-PCV2-antibodies waned in Pietrain pigs by approximately 12 wk of age, whereas the majority of the Landrace pigs remained PCV2 seropositive until 18 wk of age and beyond. The results from this study indicate that a genetic difference exists between these 2 breeds of pigs in susceptibility to PCV2-associated lesions.
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Affiliation(s)
- T Opriessnig
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames 50011, USA.
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Wang Y, Couture OP, Qu L, Uthe JJ, Bearson SMD, Kuhar D, Lunney JK, Nettleton D, Dekkers JCM, Tuggle CK. Analysis of porcine transcriptional response to Salmonella enterica serovar Choleraesuis suggests novel targets of NFkappaB are activated in the mesenteric lymph node. BMC Genomics 2008; 9:437. [PMID: 18811943 PMCID: PMC2570369 DOI: 10.1186/1471-2164-9-437] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Accepted: 09/23/2008] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Specific knowledge of the molecular pathways controlling host-pathogen interactions can increase our understanding of immune response biology as well as provide targets for drug development and genetic improvement of disease resistance. Toward this end, we have characterized the porcine transcriptional response to Salmonella enterica serovar Choleraesuis (S. Choleraesuis), a Salmonella serovar that predominately colonizes swine, yet can cause serious infections in human patients. Affymetrix technology was used to screen for differentially expressed genes in pig mesenteric lymph nodes (MLN) responding to infection with S. Choleraesuis at acute (8 hours (h), 24 h and 48 h post-inoculation (pi)) and chronic stages (21 days (d) pi). RESULTS Analysis of variance with false discovery rate control identified 1,853 genes with significant changes in expression level (p-value < 0.01, q-value < 0.26, and fold change (FC) > 2) during infection as compared to un-inoculated control pigs. Down-regulation of translation-related genes at 8 hpi and 24 hpi implied that S. Choleraesuis repressed host protein translation. Genes involved in the Th1, innate immune/inflammation response and apoptosis pathways were induced significantly. However, antigen presentation/dendritic cell (DC) function pathways were not affected significantly during infection. A strong NFkappaB-dependent response was observed, as 58 known NFkappaB target genes were induced at 8, 24 and/or 48 hpi. Quantitative-PCR analyses confirmed the microarray data for 21 of 22 genes tested. Based on expression patterns, these target genes can be classified as an "Early" group (induced at either 8 or 24 hpi) and a "Late" group (induced only at 48 hpi). Cytokine activity or chemokine activity were enriched within the Early group genes GO annotations, while the Late group was predominantly composed of signal transduction and cell metabolism annotated genes. Regulatory motif analysis of the human orthologous promoters for both Early and Late genes revealed that 241 gene promoters were predicted to contain NFkappaB binding sites, and that of these, 51 Early and 145 Late genes were previously not known to be NFkappaB targets. CONCLUSION Our study provides novel genome-wide transcriptional profiling data on the porcine response to S. Choleraesuis and expands the understanding of NFkappaB signaling in response to Salmonella infection. Comparison of the magnitude and timing of porcine MLN transcriptional response to different Salmonella serovars, S. Choleraesuis and S. Typhimurium, clearly showed a larger but later transcriptional response to S. Choleraesuis. Both microarray and QPCR data provided evidence of a strong NFkappaB-dependent host transcriptional response during S. Choleraesuis infection. Our data indicate that a lack of strong DC-mediated antigen presentation in the MLN may cause S. Choleraesuis infected pigs to develop a systemic infection, and our analysis predicts nearly 200 novel NFkappaB target genes which may be applicable across mammalian species.
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Affiliation(s)
- Yanfang Wang
- Department of Animal Science, and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, IA 50010, USA.
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Opriessnig T, Madson DM, Prickett JR, Kuhar D, Lunney JK, Elsener J, Halbur PG. Effect of porcine circovirus type 2 (PCV2) vaccination on porcine reproductive and respiratory syndrome virus (PRRSV) and PCV2 coinfection. Vet Microbiol 2008; 131:103-14. [PMID: 18430525 DOI: 10.1016/j.vetmic.2008.03.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 03/03/2008] [Accepted: 03/06/2008] [Indexed: 01/21/2023]
Abstract
The objectives were to determine if PCV2 vaccination is effective in reducing disease and lesions associated with PRRSV and PCV2 coinfection and if there is a difference between intradermal (ID) and intramuscular (IM) route of PCV2 vaccination. Seventy-four, 21-day-old pigs were randomly allocated into one of six groups. On day 0, pigs were vaccinated with 2ml Suvaxyn PCV2 One Dose (Fort Dodge Animal Health, Inc.) by intramuscular (VAC-M-COINF) or intradermal (VAC-D-COINF) routes. On day 28, pigs were either singularly (PRRSV-only, PCV2-only) or coinfected (COINF) with PRRSV and PCV2. All pigs in all groups were necropsied on day 42. All vaccinated pigs seroconverted (IgM, IgG, and neutralizing antibodies) to PCV2 between 14 and 28 days post-vaccination. After challenge, all groups inoculated with PRRSV had reduced average daily gain compared to CONTROLS and PCV2-only (P<0.001). COINF pigs had significantly (P<0.05) reduced anti-PCV2-IgG antibody levels and neutralizing antibody levels compared to both vaccinated groups. COINF pigs had more severe lung lesions compared to VAC-M-COINF (P<0.05). COINF pigs had higher amounts of PCV2 DNA in serum samples and feces (P<0.05) and increased amounts of PCV2 in lymphoid tissues (P<0.05) compared to both vaccinated groups. In summary, PCV2 vaccination was effective at inducing a neutralizing antibody response and significantly reducing PCV2-associated lesions and PCV2 viremia in pigs coinfected with PCV2 and PRRSV. Differences between intradermal and intramuscular routes of vaccine administration were not observed.
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Affiliation(s)
- T Opriessnig
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA.
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Petry DB, Lunney J, Boyd P, Kuhar D, Blankenship E, Johnson RK. Differential immunity in pigs with high and low responses to porcine reproductive and respiratory syndrome virus infection1,2. J Anim Sci 2007; 85:2075-92. [PMID: 17468430 DOI: 10.2527/jas.2006-721] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
One hundred Hampshire x Duroc cross-bred pigs (HD) and 100 NE Index line (I) pigs were infected with porcine reproductive and respiratory syndrome (PRRS) virus and evaluated for resistance/susceptibility. Controls (100/line) were uninfected littermates to the infected pigs. Viremia, change in weight (WTdelta), and rectal temperature at 0, 4, 7, and 14 d postinfection were recorded. Lung, bronchial lymph node (BLN), and blood tissue were collected at necropsy (14 d postinfection). The first principal component from principal component analyses of all variables was used to rank the pigs for phenotypic response to PRRS virus. Low responders (low PRRS burden) had high WTdelta, low viremia, and few lung lesions; high responders (high PRRS burden) had low WTdelta, high viremia, and many lesions. The RNA was extracted from lung and BLN tissue of the 7 highest and 7 lowest responders per line and from each of their littermates. Expression of 11 innate and T helper 1 immune markers was evaluated with cDNA in a 2 x 2 x 2 factorial design. Significant upregulation in lung, lymph, or both of infected pigs relative to controls occurred for all but one gene. Expression differences were greater in HD than I pigs. Significant downregulation for certain immune genes in low pigs, relative to littermate controls, was detected in lung and BLN, particularly in line I. Serum levels of the immune cytokines affirmed the gene expression differences. High preinfection serum levels of IL 8 were significantly associated with PRRS virus-resistant, low pigs. After infection, low expression of interferon gamma in cDNA and in serum was also correlated with PRRS virus resistance. Important genetic associations were revealed for fine mapping of candidate genes for PRRS virus resistance and determining the causative alleles.
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Affiliation(s)
- D B Petry
- Department of Animal Science, University of Nebraska, Lincoln 68583-0908, USA
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Wang Y, Qu L, Uthe JJ, Bearson SMD, Kuhar D, Lunney JK, Couture OP, Nettleton D, Dekkers JCM, Tuggle CK. Global transcriptional response of porcine mesenteric lymph nodes to Salmonella enterica serovar Typhimurium. Genomics 2007; 90:72-84. [PMID: 17499962 DOI: 10.1016/j.ygeno.2007.03.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Revised: 03/20/2007] [Accepted: 03/23/2007] [Indexed: 10/23/2022]
Abstract
To elucidate the host transcriptional response to Salmonella enterica serovar Typhimurium, Affymetrix porcine GeneChip analysis of pig mesenteric lymph nodes was used to identify 848 genes showing differential expression across different times after inoculation or when compared to non-inoculated controls. Annotation analyses showed that a high proportion of these differentially expressed (DE) genes are involved in immune and inflammatory responses. T helper 1, innate/inflammatory, and antigen-processing pathways were induced at 24 h post-inoculation (hpi) and/or 48 hpi, while apoptosis and antigen presentation/dendritic cell function pathways were downregulated at 8 hpi. Cluster analyses revealed that most DE genes annotated as NFkappaB targets were grouped into a specific induced subcluster, while many translation-related DE genes were found in a repressed subcluster. Quantitative polymerase chain reaction analyses confirmed the Affymetrix results, revealing transcriptional induction of NFkappaB target genes at 24 hpi and suppression of the NFkappaB pathway from 24 to 48 hpi. We propose that such NFkappaB suppression in antigen-presenting cells may be the mechanism by which S. Typhimurium eludes a strong inflammatory response to establish a carrier status in pigs.
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Affiliation(s)
- Yanfang Wang
- Department of Animal Science and Center for Integrated Animal Genomics Iowa State University, Ames, IA 50010, USA
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Lunney JK, Rowland R, Nelson E, Molina R, Hermann J, Kuhar D, Christopher-Hennings J, Leathers V, Zimmerman J. Do immune genes influence which pigs will have persistent Porcine Reproductive and Respiratory Syndrome virus (PRRSV) infections? (45.5). The Journal of Immunology 2007. [DOI: 10.4049/jimmunol.178.supp.45.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
This study, a part of the “Big Pig” project, was aimed at highlighting differences in immune responses between control pigs and pigs with PRRSV infections, from early times post inoculation (pi), 14 dpi, to long term persistent infections (as evidenced by viral RNA in tissues). Our goal is to identify immunological or virological correlates of persistent infection. Two-week old pigs (n=109) were inoculated with PRRSV ATCC VR-2332 and 56 age-matched animals served as uninoculated controls. Sets of PRRSV infected and control pigs were euthanized at 2 week intervals through 203 dpi; blood and tissues were collected. RNA and cDNA was prepared from respiratory and regional mucosal tissues [lung, tracheobronchial lymph nodes (TBLN), tonsil] and assayed for expression of a panel of 23 immune markers, representing innate, T helper and regulatory genes. As expected, only low levels of interferon-gamma and certain innate immune genes were expressed by infected pigs early after inoculation. Our studies are aimed at determining whether there is a pattern of cytokine expression that might help predict which pigs will clear virus, and distinguish them from those that remain persistently infected. To date no pattern has been found with lung or TBLN; tests are continuing with tonsils and sera cytokine levels. We hope to identify regulatory pathways that would stimulate PRRSV immunity.
Supported by USDA ARS and NRI PRRS CAP1 funds.
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Affiliation(s)
- Joan K. Lunney
- 1USDA ARS BARC, Bldg 1040, Rm 103, Beltsville, MD, 20705,
| | - Raymond Rowland
- 2Kansas State Univ., 1800 Denison Ave, Manhattan, KS, 66506,
| | - Eric Nelson
- 3SD State Univ, Veterinary Science Dept., Brookings, SD, 57007,
| | - Ramon Molina
- 4Iowa State Univ., 2655 Veterinary Diagnostic Lab, Ames, Iowa, 50011,
| | - Joseph Hermann
- 4Iowa State Univ., 2655 Veterinary Diagnostic Lab, Ames, Iowa, 50011,
| | - Daniel Kuhar
- 1USDA ARS BARC, Bldg 1040, Rm 103, Beltsville, MD, 20705,
| | | | - Valerie Leathers
- 5IDEXX Laboratories, Inc., One IDEXX Drive, Westbrook, ME, 04092
| | - Jeff Zimmerman
- 4Iowa State Univ., 2655 Veterinary Diagnostic Lab, Ames, Iowa, 50011,
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Zhao SH, Kuhar D, Lunney JK, Dawson H, Guidry C, Uthe JJ, Bearson SMD, Recknor J, Nettleton D, Tuggle CK. Gene expression profiling in Salmonella Choleraesuis-infected porcine lung using a long oligonucleotide microarray. Mamm Genome 2006; 17:777-89. [PMID: 16845603 DOI: 10.1007/s00335-005-0155-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Accepted: 03/07/2006] [Indexed: 12/19/2022]
Abstract
Understanding the transcriptional response to pathogenic bacterial infection within food animals is of fundamental and applied interest. To determine the transcriptional response to Salmonella enterica serovar Choleraesuis (SC) infection, a 13,297-oligonucleotide swine array was used to analyze RNA from control, 24-h postinoculation (hpi), and 48-hpi porcine lung tissue from pigs infected with SC. In total, 57 genes showed differential expression (p < 0.001; false discovery rate = 12%). Quantitative real-time PCR (qRT-PCR) of 61 genes was used to confirm the microarray results and to identify pathways responding to infection. Of the 33 genes identified by microarray analysis as differentially expressed, 23 were confirmed by qRT-PCR results. A novel finding was that two transglutaminase family genes (TGM1 and TGM3) showed dramatic increases in expression postinoculation; combined with several other apoptotic genes, they indicated the induction of apoptotic pathways during SC infection. A predominant T helper 1-type immune response occurred during infection, with interferon gamma (IFNG) significantly increased at 48 hpi. Genes induced by IFNs (GBP1, GBP2, C1S, C1R, MHC2TA, PSMB8, TAP1, TAP2) showed increased expression during porcine lung infection. These data represent the first thorough investigation of gene regulation pathways that control an important porcine respiratory and foodborne bacterial infection.
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Affiliation(s)
- Shu-Hong Zhao
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, 50011, USA
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Zhao SH, Recknor J, Lunney JK, Nettleton D, Kuhar D, Orley S, Tuggle CK. Validation of a first-generation long-oligonucleotide microarray for transcriptional profiling in the pig. Genomics 2005; 86:618-25. [PMID: 16216716 DOI: 10.1016/j.ygeno.2005.08.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2005] [Revised: 07/27/2005] [Accepted: 08/01/2005] [Indexed: 10/25/2022]
Abstract
A first-generation porcine oligonucleotide set, representing 13,297 cDNAs and ESTs, has been designed by Qiagen-Operon for transcriptional profiling. To validate this set, microarrays containing each 70-mer oligonucleotide, referred to as the Qiagen-NRSP8 array, were hybridized with targets from porcine adult liver, lung, muscle, or small intestine. Transcriptome analyses showed that 11,328 of the oligonucleotides demonstrated expression in at least one tissue. Statistical analyses revealed that 1810 genes showed differential expression among tissues (Bonferroni adjusted p < 0.05). Biological pathways identified by DAVID/EASE analysis using a list of 423 tissue-selective genes matched archetypal pathways in the corresponding human or mouse tissue. Real-time quantitative PCR confirmed expression patterns for 9 of 11 genes tested. Our results demonstrate that this first-generation porcine oligonucleotide array is informative and the specificity is high. This is essential validation for investigators using the Qiagen-NRSP8 array for porcine functional genomics and for using the pig in modeling important physiological problems.
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Affiliation(s)
- Shu-Hong Zhao
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011, USA
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20
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Dawson HD, Royaee AR, Nishi S, Kuhar D, Schnitzlein WM, Zuckermann F, Urban J, Lunney JK. Identification of key immune mediators regulating T helper 1 responses in swine. Vet Immunol Immunopathol 2004; 100:105-11. [PMID: 15183000 DOI: 10.1016/j.vetimm.2004.03.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2003] [Revised: 03/01/2004] [Accepted: 03/10/2004] [Indexed: 11/23/2022]
Abstract
This publication describes the cloning of full or partial length sequences for pig TBX21 (T-bet), MYD88, ICSBP1, CD8A (CD8alpha), CD8B (CD8beta), and CD28 cDNAs. Real-time PCR assays have been developed for the relative quantitation of these products as well as previously characterized transcripts that encode exon A-containing CD45, HLX1, IRF1, STAT1 and RPL32. When used for examining temporal immune gene expression in the liver of Toxoplasma gondii infected pigs, the positive regulators of Th1 responses, IRF1, MYD88, and STAT1, were found to be expressed prior to the simultaneous upregulation of interferon gamma (IFNG), HLX1 and TBX21 gene expression. In contrast, in the mesenteric lymph node (MLN), only expression of IRF1 and IFNG was significantly upregulated. Based on their demonstrated utility in establishing an immune response pathway, these PCR assays should be valuable additions to our swine immune toolkit.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Animals
- Antigens, Differentiation/genetics
- Antigens, Differentiation/immunology
- Base Sequence
- CD28 Antigens/genetics
- CD28 Antigens/immunology
- CD8 Antigens/genetics
- CD8 Antigens/immunology
- Molecular Sequence Data
- Myeloid Differentiation Factor 88
- RNA, Protozoan/chemistry
- RNA, Protozoan/genetics
- Receptors, Immunologic/genetics
- Receptors, Immunologic/immunology
- Repressor Proteins/genetics
- Repressor Proteins/immunology
- Reverse Transcriptase Polymerase Chain Reaction/veterinary
- Sequence Analysis, DNA
- Swine
- Swine Diseases/immunology
- Swine Diseases/parasitology
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/immunology
- Th1 Cells/immunology
- Toxoplasma/genetics
- Toxoplasma/immunology
- Toxoplasmosis, Animal/immunology
- Toxoplasmosis, Animal/parasitology
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Affiliation(s)
- Harry D Dawson
- Nutrient Requirements and Functions Laboratory, Beltsville Human Nutrition Research Center, USDA, Bldg. 307C, Room 213, BARC-East, Beltsville, MD 20705, USA
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