Shane C Burgess

PMID: 19391180;Abstract:

Experimental identification of expressed proteins by proteomics constitutes the most reliable approach to identify genomic location and structure of protein-coding genes and substantially complements computational genome annotation. Channel catfish herpesvirus (CCV) is a simple comparative model for understanding herpesvirus biology and the evolution of the Herpesviridae. The canonical CCV genome has 76 predicted ORF and only 12 of these have been confirmed experimentally. We describe a modification of a statistical method, which assigns significance measures, q-values, to peptide identifications based on 2-D LC ESI MS/MS, real-decoy database searches and SEQUEST XCorr and DCn scores. We used this approach to identify CCV proteins expressed during its replication in cell culture, to determine protein composition of mature virions and, consequently, to refine the canonical CCVgenome annotation. To complement trypsin, we used partial proteinase K digestion, which yielded greater proteome coverage. At FDR 5%, for peptide identifications, we identified 25/76 previously predicted ORF using trypsin and 31/76 using proteinase K. Furthermore, we identified 17 novel protein-coding regions (7 potential ATG-initiated ORF). Most of these novel ORF encode small proteins (100 amino acids). Directed, strand-specific reverse transcription real-time PCR confirmed RNA expression from 6/7 novel ATG-initiated ORF investigated. © 2009 Wiley-VCH Verlag GmbH & Co. KGaA.

PMID: 17990261;Abstract:

Non-electrophoretic methods based on two-dimensional liquid chromatography followed directly by tandem mass spectrometry (2D-LC/MS²) have become the preferred method for high-throughput expression proteomics and are widely applied to fresh tissues. Pre-fractionation techniques are also used in combination with 2D-LC/MS² to both increase the proteome size and to assign cellular locations. Data from such experiments have become central to systems biology analyses. Here we apply a differential detergent (pre)fractionation (DDF) followed by 2D-LC/MS² to frozen archival tissues. Our results show that by using frozen archival tissues, we do not lose proteome coverage or the ability to assign proteins to cellular compartments. In addition, we were able to assign 'biological process' Gene Ontology (GO) annotations, which will facilitate systems biological modeling of our proteomics data. Copyright © 2007 John Wiley & Sons, Ltd.

PMID: 13679597;Abstract:

Marek's disease virus (MDV) is classified as an oncogenic lymphotropic herpesvirus of chickens. MDV productively and cytolytically infects B, αβT and γδT lymphocytes and latently infects T-helper lymphocytes. The aims of this study were to identify whether MDV infects macrophages in vivo and, if so, whether quantitative differences in macrophage infection are associated with MDV strain virulence. Chickens were infected with either virulent MDV (HPRS-16) or 'hypervirulent' MDV (C12/130). Flow cytometry with monoclonal antibodies recognizing MDV pp38 antigen and leukocyte antigens was used to identify MDV lytically infected cells. Macrophages from HPRS-16- and C12/130-infected chickens were pp38⁺. It is demonstrated that macrophages are pp38⁺ because they are infected and not because they have phagocytosed MDV antigens, as assessed by confocal microscopy using antibodies recognizing MDV antigens of the three herpesvirus kinetic classes: infected cell protein 4 (ICP4, immediate early), pp38 (early) and glycoprotein B (gB, late). Spleen macrophages from MDV-infected chickens were ICP4⁺, pp38⁺ and gB⁺, and ICP4 had nuclear localization denoting infection. Finally, MDV pp38⁺ macrophages had high inherent death rates, confirming cytolytic MDV infection, although production of virus particles has not been detected yet. These results have two fundamental implications for understanding MDV pathogenesis: (i) MDV evolved to perturb innate, in addition to acquired, immunity and (ii) macrophages are excellent candidates for transporting MDV to primary lymphoid organs during the earliest stages of pathogenesis.

PMID: 16675515;Abstract:

Chlorpyrifos (CPS), a known neurotoxicant, is a widely used agricultural organophosphorus insecticide. The effects of postnatal exposure to CPS on the expression of mRNA for two factors critical to brain development, nerve growth factor (NGF) and reelin, were investigated in the forebrain of rats. In addition, the expression of mRNA for the muscarinic acetylcholine receptor (mAChR) M1 subtype and cell-specific markers for developing neurons (β-III tubulin), astrocytes (glial fibrillary acidic protein, GFAP), and oligodendrocytes (myelin-associated glycoprotein, MAG) was also investigated. Oral administration of CPS (1.5 or 3.0 mg/kg) or the corn oil vehicle was performed daily from postnatal days (PNDs) 1 through 6. No signs of overt toxicity or of cholinergic hyperstimulation were observed after CPS administration. Body weight was significantly different from controls on PND7 in both males and females exposed to 3.0 mg/kg CPS. Quantitative PCR was performed on the forebrain. The expression of NGF, reelin, and M1 mAChR mRNA was significantly reduced with both dosages of CPS in both sexes. β-III Tubulin mRNA expression remained unchanged after exposure, whereas MAG mRNA expression was significantly decreased with both dosages of CPS in both sexes, suggesting effects on the developing oligodendrocytes. In contrast, GFAP mRNA levels were significantly increased with both dosages of CPS in both sexes, suggesting increased astrocyte reactivity. Our findings indicate that dosages of CPS which cause significant cholinesterase inhibition but do not exert overt toxicity can adversely affect the expression levels of critical genes involved in brain development during the early postnatal period in the rat. © 2006 Oxford University Press.

Abstract:

The effect of dietary protein on growth, carcass traits and some specific intestinal intestinal peptide and amino acid transporters in broiler chickens was studied. Birds received a common pre-test diet, and were subsequently fed either a standard positive control diet (PC) or a reduced CP diet (RCP) from 21 to 42 d of age. Growth was negatively impacted with feeding of RCP as manifested by an increase in feed consumption and feed conversion ratio. Carcass traits also showed evidence of negative effects of feeding the RCP diet, leading to a reduction in carcass and breast meat yield and an increase in abdominal fat percentage. Blood plasma total protein was reduced when the broilers were fed the RCP diet. Expression of mRNA for one peptide (PepT1) and four AA intestinal transporters (b°,+AT; CAT2; y+LAT2; EAAT3) was measured from the jejunum. Quantified mRNA for the AA transporters y+LAT2 and EAAT3 showed that they were upregulated in chickens fed the RCP-diet. The transport systems PepT1, b°,+AT, and CAT2, were not affected by the dietary treatment imposed. The live and processing data validated the in vivo portion of the study and elucidated the negative impact of feeding the RCP diet, while the responses observed with the expression of the various transporters may help provide some insight on the physiological consequences and adaptations that birds endure when provided diets too low in CP for abnormally extended periods of time.