Latitudinal variation in thermal performance of the common coral, Pocillopora spp

Understanding how tropical corals respond to temperatures is important to evaluating their capacity to persist in a warmer future. We studied the common Pacific coral Pocillopora over 44° of latitude, and used populations at three islands with different thermal regimes to compare their responses to temperature using thermal performance curves (TPCs) for respiration and gross photosynthesis. Corals were sampled in the local autumn from Moorea, Guam, and Okinawa where mean (± s.d.) annual seawater temperature is 28.0±0.9°C, 28.9±0.7°C, and 25.1±3.4°C, respectively. TPCs for respiration were similar among latitudes, the thermal optimum (Topt) was above the local maximum temperature at all three islands, and maximum respiration was lowest at Okinawa. TPCs for gross photosynthesis were wider, implying greater thermal eurytopy, with a higher Topt in Moorea versus Guam and Okinawa. Topt was above the maximum temperature in Moorea, but was similar to daily temperatures over 13% of the year in Okinawa, and 53% of the year in Guam. There was greater annual variation in daily temperatures in Okinawa than Guam or Moorea, which translated to large variation in the supply of metabolic energy and photosynthetically fixed carbon at higher latitudes. Despite these trends, the differences in TPCs for Pocillopora were not profoundly different across latitudes, reducing the likelihood that populations of these corals could better match their phenotypes to future more extreme temperatures through migration. Any such response would place a premium on high metabolic plasticity and tolerance of large seasonal variations in energy budgets.

Fluctuating selection and global change: a synthesis and review on disentangling the roles of climate amplitude, predictability and novelty

A formidable challenge for global change biologists is to predict how natural populations will respond to the emergence of conditions not observed at present, termed novel climates. Popular approaches to predict population vulnerability are based on the expected degree of novelty relative to the amplitude of historical climate fluctuations experienced by a population. Here, we argue that predictions focused on amplitude may be inaccurate because they ignore the predictability of environmental fluctuations in driving patterns of evolution and responses to climate change. To address this disconnect, we review major findings of evolutionary theory demonstrating the conditions under which phenotypic plasticity is likely to evolve in natural populations, and how plasticity decreases population vulnerability to novel environments. We outline key criteria that experimental studies should aim for to effectively test theoretical predictions, while controlling for the degree of climate novelty. We show that such targeted tests of evolutionary theory are rare, with marine systems being overall underrepresented in this venture despite exhibiting unique opportunities to test theory. We conclude that with more robust experimental designs that manipulate both the amplitude and predictability of fluctuations, while controlling for the degree of novelty, we may better predict population vulnerability to climate change.

Multi-modal locomotion: from animal to application

The majority of robotic vehicles that can be found today are bound to operations within a single media (i.e. land, air or water). This is very rarely the case when considering locomotive capabilities in natural systems. Utility for small robots often reflects the exact same problem domain as small animals, hence providing numerous avenues for biological inspiration. This paper begins to investigate the various modes of locomotion adopted by different genus groups in multiple media as an initial attempt to determine the compromise in ability adopted by the animals when achieving multi-modal locomotion. A review of current biologically inspired multi-modal robots is also presented. The primary aim of this research is to lay the foundation for a generation of vehicles capable of multi-modal locomotion, allowing ambulatory abilities in more than one media, surpassing current capabilities. By identifying and understanding when natural systems use specific locomotion mechanisms, when they opt for disparate mechanisms for each mode of locomotion rather than using a synergized singular mechanism, and how this affects their capability in each medium, similar combinations can be used as inspiration for future multi-modal biologically inspired robotic platforms.

Development of a parametric kinematic model of the human hand and a novel robotic exoskeleton

This paper reports the integration of a kinematic model of the human hand during cylindrical grasping, with specific focus on the accurate mapping of thumb movement during grasping motions, and a novel, multi-degree-of-freedom assistive exoskeleton mechanism based on this model. The model includes thumb maximum hyper-extension for grasping large objects (~> 50 mm). The exoskeleton includes a novel four-bar mechanism designed to reproduce natural thumb opposition and a novel synchro-motion pulley mechanism for coordinated finger motion. A computer aided design environment is used to allow the exoskeleton to be rapidly customized to the hand dimensions of a specific patient. Trials comparing the kinematic model to observed data of hand movement show the model to be capable of mapping thumb and finger joint flexion angles during grasping motions. Simulations show the exoskeleton to be capable of reproducing the complex motion of the thumb to oppose the fingers during cylindrical and pinch grip motions.

Functional modelling of an equine bronchoalveolar lavage fluid proteome provides experimental confirmation and functional annotation of equine genome sequences

The equine genome sequence enables the use of high-throughput genomic technologies in equine research, but accurate identification of expressed gene products and interpreting their biological relevance require additional structural and functional genome annotation. Here, we employ the equine genome sequence to identify predicted and known proteins using proteomics and model these proteins into biological pathways, identifying 582 proteins in normal cell-free equine bronchoalveolar lavage fluid (BALF). We improved structural and functional annotation by directly confirming the in vivo expression of 558 (96%) proteins, which were computationally predicted previously, and adding Gene Ontology (GO) annotations for 174 proteins, 108 of which lacked functional annotation. Bronchoalveolar lavage is commonly used to investigate equine respiratory disease, leading us to model the associated proteome and its biological functions. Modelling of protein functions using Ingenuity Pathway Analysis identified carbohydrate metabolism, cell-to-cell signalling, cellular function, inflammatory response, organ morphology, lipid metabolism and cellular movement as key biological processes in normal equine BALF. Comparative modelling of protein functions in normal cell-free bronchoalveolar lavage proteomes from horse, human, and mouse, performed by grouping GO terms sharing common ancestor terms, confirms conservation of functions across species. Ninety-one of 92 human GO categories and 105 of 109 mouse GO categories were conserved in the horse. Our approach confirms the utility of the equine genome sequence to characterize protein networks without antibodies or mRNA quantification, highlights the need for continued structural and functional annotation of the equine genome and provides a framework for equine researchers to aid in the annotation effort.

Uncoupling hypoxia signaling from oxygen sensing in the liver results in hypoketotic hypoglycemic death

As the ultimate electron acceptor in oxidative phosphorylation, oxygen plays a critical role in metabolism. When oxygen levels drop, heterodimeric hypoxia-inducible factor (Hif) transcription factors become active and facilitate adaptation to hypoxia. Hif regulation by oxygen requires the protein von Hippel-Lindau (pVhl) and pVhl disruption results in constitutive Hif activation. The liver is a critical organ for metabolic homeostasis, and Vhl inactivation in hepatocytes results in a Hif-dependent shortening in life span. While albumin-Cre;Vhl^F/F mice develop hepatic steatosis and impaired fatty acid oxidation, the variable penetrance and unpredictable life expectancy has made the cause of death elusive. Using a system in which Vhl is acutely disrupted and a combination of ex vivo liver perfusion studies and in vivo oxygen measurements, we demonstrate that Vhl is essential for mitochondrial respiration in vivo. Adenovirus-Cre mediated acute Vhl disruption in the liver caused death within days. Deprived of pVhl, livers accumulated tryglicerides and circulating ketone and glucose levels dropped. The phenotype was reminiscent of inborn defects in fatty acid oxidation and of fasted PPARα-deficient mice and while death was unaffected by pharmacologic PPARα activation, it was delayed by glucose administration. Ex vivo liver perfusion analyses and acylcarnitine profiles showed mitochondrial impairment and a profound inhibition of liver ketone and glucose production. By contrast, other mitochondrial functions, such as ureagenesis, were unaffected. Oxygen consumption studies revealed a marked suppression of mitochondrial respiration, which, as determined by magnetic resonance oximetry in live mice, was accompanied by a corresponding increase in liver pO₂. Importantly, simultaneous inactivation of Hif-1β suppressed liver steatosis and rescued the mice from death. These data demonstrate that constitutive Hif activation in mice is sufficient to suppress mitochondrial respiration in vivo and that no other pathway exists in the liver that can allow oxygen utilization when Hif is active precluding thereby metabolic collapse.

The neoplastically transformed (CD30hi) Marek's disease lymphoma cell phenotype most closely resembles T-regulatory cells

INTRODUCTION

Marek's disease (MD), a herpesvirus-induced lymphoma of chickens is a unique natural model of CD30-overexpressing (CD30hi) lymphoma. We have previously proposed that the CD30hi neoplastically transformed CD4+ T cells in MD lymphomas have a phenotype antagonistic to cell mediated immunity. Here were test the hypothesis that the CD30hi neoplastically transformed MD lymphoma cells have a phenotype more closely resembling T-helper (Th)-2 or regulatory T (T-reg) cells.

MATERIALS AND METHODS

We separated ex vivo-derived CD30hi, from the CD30lo/- (non-transformed), MD lymphoma cells and then quantified the relative amounts of mRNA and proteins for cytokines and other genes that define CD4+ Th-1, Th-2 or T-reg phenotypes.

RESULTS AND DISCUSSION

Gene Ontology-based modeling of our data shows that the CD30hi MD lymphoma cells having a phenotype more similar to T-reg. Sequences that could be bound by the MD virus putative oncoprotein Meq in each of these genes' promoters suggests that the MD herpesvirus may play a direct role in maintaining this T-reg-like phenotype.

Functional genomics of the chicken--a model organism

Since the sequencing of the genome and the development of high-throughput tools for the exploration of functional elements of the genome, the chicken has reached model organism status. Functional genomics focuses on understanding the function and regulation of genes and gene products on a global or genome-wide scale. Systems biology attempts to integrate functional information derived from multiple high-content data sets into a holistic view of all biological processes within a cell or organism. Generation of a large collection ( approximately 600K) of chicken expressed sequence tags, representing most tissues and developmental stages, has enabled the construction of high-density microarrays for transcriptional profiling. Comprehensive analysis of this large expressed sequence tag collection and a set of approximately 20K full-length cDNA sequences indicate that the transcriptome of the chicken represents approximately 20,000 genes. Furthermore, comparative analyses of these sequences have facilitated functional annotation of the genome and the creation of several bioinformatic resources for the chicken. Recently, about 20 papers have been published on transcriptional profiling with DNA microarrays in chicken tissues under various conditions. Proteomics is another powerful high-throughput tool currently used for examining the dynamics of protein expression in chicken tissues and fluids. Computational analyses of the chicken genome are providing new insight into the evolution of gene families in birds and other organisms. Abundant functional genomic resources now support large-scale analyses in the chicken and will facilitate identification of transcriptional mechanisms, gene networks, and metabolic or regulatory pathways that will ultimately determine the phenotype of the bird. New technologies such as marker-assisted selection, transgenics, and RNA interference offer the opportunity to modify the phenotype of the chicken to fit defined production goals. This review focuses on functional genomics in the chicken and provides a road map for large-scale exploration of the chicken genome.

Bovine germinal vesicle oocyte and cumulus cell proteomics

Germinal vesicle (GV) breakdown is fundamental for maturation of fully grown, developmentally competent, mammalian oocytes. Bidirectional communication between oocytes and surrounding cumulus cells (CC) is essential for maturation of a competent oocyte. However, neither the factors involved in this communication nor the mechanisms of their actions are well defined. Here, we define the proteomes of GV oocytes and their surrounding CC, including membrane proteins, using proteomics in a bovine model. We found that 4395 proteins were expressed in the CC and 1092 proteins were expressed in oocytes. Further, 858 proteins were common to both the CC and the oocytes. This first comprehensive proteome analysis of bovine oocytes and CC not only provides a foundation for signaling and cell physiology at the GV stage of oocyte development, but are also valuable for comparative studies of other stages of oocyte development at the molecular level. Furthermore, some of these proteins may represent molecular biomarkers for developmental potential of oocytes.

GOing from functional genomics to biological significance

The chicken genome is sequenced and this, together with microarray and other functional genomics technologies, makes post-genomic research possible in the chicken. At this time, however, such research is hindered by a lack of genomic structural and functional annotations. Bio-ontologies have been developed for different annotation requirements, as well as to facilitate data sharing and computational analysis, but these are not yet optimally utilized in the chicken. Here we discuss genomic annotation and bio-ontologies. We focus specifically on the Gene Ontology (GO), chicken GO annotations and how these can facilitate functional genomics in the chicken. The GO is the most developed and widely used bio-ontology. It is the de facto standard for functional annotation. Despite its critical importance in analyzing microarray and other functional genomics data, relatively few chicken gene products have any GO annotation. When these are available, the average quality of chicken gene products annotations (defined using evidence code weight and annotation depth) is much less than in mouse. Moreover, tools allowing chicken researchers to easily and rapidly use the GO are either lacking or hard to use. To address all of these problems we developed ChickGO and AgBase. Chicken GO annotations are provided by complementary work at MSU-AgBase and EBI-GOA. The GO tools pipeline at AgBase uses GO to derive functional and biological significance from microarray and other functional genomics data. Not only will improved genomic annotation and tools to use these annotations benefit the chicken research community but they will also facilitate research in other avian species and comparative genomics.

Protein expression ofpectoralis majormuscle in chickens in response to dietary methionine status

The present study evaluated the effect of dietary methionine on breast-meat accretion and protein expression in skeletal muscle of broiler chickensin vivo. All broilers received a common pre-test diet up to 21d of age, and were subsequently fed either a methionine-deficient (MD) or -adequate (MA) diet (3·1V. 4·5g/kg diet) from age 21 to 42d. Dietary cystine levels were 3·7V. 3·6g/kg diet for the MD and MA diet, respectively. Detrimental effects on carcass yield (P=0·004), abdominal fat percentage (P=0·001), and breast-meat weight (P=0·001), yield (P=0·001), and uniformity (P=0·002) were observed and validated in birds fed MD diets. Via tandem MS, a total of 190 individual proteins were identified frompectoralis major(PM) muscle tissue. From the former composite, peptides from three proteins were observed to be present exclusively in breast muscle from those chickens fed the MD diet (pyruvate kinase, myosin alkali light chain-1, ribosomal-protein-L-29). No proteins were observed to be uniquely expressed in chickens fed MA diets. Research is warranted to further explore the possibility of the proteins pyruate kinase, myosin alkali light chain-1, or ribosomal protein L-29, as potential biological indicators of differences in protein expression of PM of chickens in response to a dietary methionine deficiency.

Maternal antibody transfer from dams to their egg yolks, egg whites, and chicks in meat lines of chickens

Maternal antibodies are transferred from hens to the chicks via the egg. To gain insight into maternal antibody transfer and endogenous production of antibodies in broiler chicks, total IgY, IgA, IgM, as well as anti-Newcastle disease virus (NDV) and anti-infectious bronchitis (IBV) antibody levels were examined in the dams' plasma, egg yolks, egg whites, and chicks' plasma on d 3, 7, 14, and 21. Blood was collected from 39-wk-old breeder hens (line 1, n = 17; line 2, n = 21). Fertile eggs were used for antibody extraction from the egg yolks and egg whites (4 to 5 eggs/dam) and for hatching. Unvaccinated chicks (4 to 5 chicks/dam) were reared in a HEPA-filtered room and were bled on d 3, 7, 14 and 21. Based on ELISA methods, plasma levels of IgY and IgM were higher (P < 0.0001), and those of IgA were similar (P = 0.31), in line 2 compared with line 1. Egg yolk IgY and IgA, as well as egg white IgY, IgA, and IgM levels were higher in line 2 compared with line 1 (P < 0.0001). Independent of line of chicken, the percentage dam-to-chick (3 d) plasma transfer of IgY was estimated to be approximately 30%, with that for IgM and IgA less than 1%. Chicks synthesized IgM first, followed by IgA and IgY. Anti-NDV and anti-IBV antibodies were detected in the dams' plasma, egg yolks, and in the chicks' plasma on d 3 and 7, with line 2 having higher anti-IBV and lower anti-NDV levels than line 1 in all samples (P < 0.0001). In summary, IgY levels, total or antigen-specific, in the dams' plasma or eggs were found to be a direct indicator of maternal antibody transfer to the chicks' circulation, with an expected percentage transfer of approximately 30%. This knowledge, together with the observed time course of endogenous antibody production in broiler chicks, may find direct application in formulating strategies for protecting chicks, especially during the first few weeks of age when their immune system is not yet fully functional.

In ovo DNA immunisation followed by a recombinant fowlpox boost is fully protective to challenge with virulent IBDV

The aim of this study was to investigate the potential use of DNA vaccination delivered in ovo for protecting against challenge with infectious bursal disease virus (IBDV). Using a plasmid expressing the beta-galactosidase gene, DNA was successfully delivered to the embryo after in ovo injection and localises to the proventriculus and thymus. The coding sequence for the immunogenic IBDV protein, VP2, was cloned into pCI-neo, creating pCI-Vp2. Complete protection against IBDV was obtained by priming in ovo with pCI-Vp2, followed by boosting with the fowlpox recombinant, fpIBD1, also expressing the VP2 gene. This complete protection was not evident with either of the experimental vaccines on their own. An antibody response was not detected after the prime-boost vaccination, even after chicks had been challenged with IBDV, implying that the DNA prime delivered in ovo stimulated a protective cellular immune response.

Hematopoietic prostaglandin D2 synthase in the chicken Harderian gland

The Harderian gland (HG), a sero-mucous secreting organ in the eye orbit, has long been recognized as immunologically important in chickens. During experimentation to characterize immune components of the gland, proteomics analysis revealed the presence of hematopoietic prostaglandin D synthase (H-PGDS). Extraction of total RNA followed by RT-PCR produced cDNA of 597 base pairs. DNA sequencing revealed nucleic acid and predicted amino acid sequences that were 99% aligned with the one published sequence for chicken H-PGDS of the spleen. Alignment with murine, rat, and human H-PGDS were 69, 69, and 66%, respectively. Ocular vaccination of chickens with a Newcastle Disease/Infectious Bronchitis vaccine (Mass.-Ark. Strain) induced an increase in H-PGDS expression determined by real-time PCR. Furthermore, immunohistochemistry of frozen HG sections showed positive stained cells for both H-PGDS and mast cell tryptase in the sub-epithelial cell layers of the HG ducts. Based on the potent vasoactive role of PGD(2), it appears that the chicken HG is a site of active mucosal immunity partially mediated by PGD(2) synthesized by H-PGDS in the gland.

Assessment of dietary amino acid scarcity on growth and blood plasma proteome status of broiler chickens

Dietary Lys needs for chicks were studied. A titration diet consisting of progressive amounts of dietary Lys from 0.95% up to 1.40% was fed to broiler chicks from 0 to 18 d of age. Optimal dietary Lys level was calculated using regression analysis. Body weight gain and feed conversion were maximized at Lys levels of 1.24% (1.10% digestible) and 1.27% (1.13% digestible) of diet, respectively. Blood samples were then collected from 2 groups: birds fed the lowest Lys level and birds fed dietary Lys nearest the determined requirement level (1.25% Lys). Plasma was analyzed for protein spectra via mass spectrometry and then classified by their functional characteristics. The number of proteins was similar between the 2 samples, but there was a tendency toward increased peptides for specific proteins in plasma from chicks fed adequate Lys levels. Furthermore, after these proteins were classified, more muscle-related proteins were found in plasma samples of birds fed Lys-adequate diets. It would appear that an individual dietary amino acid deficiency does not necessarily translate into decreasing protein synthesis proportionate to body weight, but rather significant changes may be occurring within the types of proteins undergoing anabolism. In conclusion, results herein illustrate the potential for using functional genomics in nutritionally related responses of poultry.

Placental immunopathology and pregnancy failure in the FIV-infected cat

Placental HIV infections frequently result in infected babies or miscarriage. Aberrant placental cytokine expression during HIV infections may facilitate transplacental viral transmission or pregnancy perturbation. The feline immunodeficiency virus (FIV)-infected cat is a model for HIV infections due to similarities in biology and clinical disease. The purpose of this study was to evaluate placental immunomodulator expression and reproductive outcome using the FIV-infected cat model. Kittens were cesarean delivered from FIV-B-2542-infected and control queens near term; placental and fetal tissues were collected. Real-time RT-PCR was used to measure expression of representative placental Th1 cytokines, interleukin-1beta (IL-1beta) and interferon-gamma (IFN-gamma), a Th2 cytokine, IL-10, and chemokine receptor CXCR4. On average, control queens delivered 3.8 kittens/litter; 1 of 31 kittens (3.2%) was non-viable. FIV-infected queens produced 2.7 kittens/litter; 15 of 25 concepti (60%) were non-viable. FIV was detected in 14 of 15 placentas (93%) and 21 of 22 fetuses (95%) using PCR. Placental immunomodulator expression did not differ significantly when placentas from infected cats were compared to those of control cats. However, elevated expression of Th1 cytokines and increased Th1/Th2 ratios (IL-1beta/IL-10) occurred in placentas from resorptions. Therefore, increased placental Th1 cytokine expression was associated with pregnancy failure in the FIV-infected cat.

Isoleucine needs of thirty- to forty-day-old female chickens: immunity

Broilers fed diets with reduced amino acid levels may be limiting in isoleucine. Because research addressing daily Ile needs for broiler immunity is sparse, Ile responses for immunity in female broilers were evaluated in 2 experiments in broilers from 30 to 42 d of age. Cellular and humoral immunity were evaluated in diets limiting in Ile and diets varying in Ile from deficient to adequate. Pen was the experimental unit in both experiments. Treatments in experiment 1 consisted of 2 levels of Ile (0.42 vs. 0.72% total of diet) and 3 strains of broilers, Arbor Acres+, Ross 508, Ross 708 (6 treatments; 5 pens each). In experiment 1, measurements consisted of: a cutaneous basophil hypersensitivity test to phytohemagglutinin-P (PHA-P) on d 37 and 38; cell quantification of CD4+, CD8+, and BU-1+ lymphocytes at d 41 and 42; and relative immune organ weights at 42 d. No Ile x strain interaction occurred. Feeding an Ile-deficient diet to broilers suppressed the cell mediated response to PHA-P, and reduced thymus weight and the percentage of CD8+ T cells. There were no significant differences between strains. In experiment 2, gradations of Ile (0.42, 0.50, 0.58, 0.66, 0.74, and 0.82% total of diet) were fed to one strain (Ross 508) of female broilers (7 pens per diet). A control diet containing 0.70% Ile (6 pens) was compared with an Ile surfeit concentration. Measurements in experiment 2 consisted of a hypersensitivity test to PHA-P on d 35 and 36; a primary antibody response to SRBC from 35 to 42 d; cell quantification of CD8+ alpha, beta, and T cell receptor (TCR)-1 (delta/gamma) lymphocytes on d 41 and 42; and immune organ weights at 42 d. Immunity measurements in birds fed surfeit Ile in the titration diets were equal to birds fed the control diet. A linear response to increasing Ile was obtained for relative bursa, but no Ile quadratic responses were noted for other measurements in experiment 2. Although feeding broilers a diet deficient in Ile suppressed some immune criteria, it does not appear that a marginal Ile deficiency will compromise immunity in growing female broilers.

Marek's disease is a natural model for lymphomas overexpressing Hodgkin's disease antigen (CD30)

Animal models are essential for elucidating the molecular mechanisms of carcinogenesis. Hodgkin's and many diverse non-Hodgkin's lymphomas overexpress the Hodgkin's disease antigen CD30 (CD30(hi)), a tumor necrosis factor receptor II family member. Here we show that chicken Marek's disease (MD) lymphoma cells are also CD30(hi) and are a unique natural model for CD30(hi) lymphoma. Chicken CD30 resembles an ancestral form, and we identify a previously undescribed potential cytoplasmic signaling domain conserved in chicken, human, and mouse CD30. Our phylogeneic analysis defines a relationship between the structures of human and mouse CD30 and confirms that mouse CD30 represents the ancestral mammalian gene structure. CD30 expression by MD virus (MDV)-transformed lymphocytes correlates with expression of the MDV Meq putative oncogene (a c-Jun homologue) in vivo. The chicken CD30 promoter has 15 predicted high-stringency Meq-binding transcription factor recognition motifs, and Meq enhances transcription from the CD30 promoter in vitro. Plasma proteomics identified a soluble form of CD30. CD30 overexpression is evolutionarily conserved and defines one class of neoplastic transformation events, regardless of etiology. We propose that CD30 is a component of a critical intracellular signaling pathway perturbed in neoplastic transformation. Specific anti-CD30 Igs occurred after infection of genetically MD-resistant chickens with oncogenic MDV, suggesting immunity to CD30 could play a role in MD lymphoma regression.

Proteomics in the chicken: tools for understanding immune responses to avian diseases

The entire chicken genome sequence will be available by the time this review is in press. Chickens will be the first production animal species to enter the "postgenomic era." This fundamental structural genomics achievement allows, for the first time, complete functional genomics approaches for understanding the molecular basis of chicken normo- and pathophysiology. The functional genomics paradigm, which contrasts with classical functional genetic investigations of one gene (or few) in isolation, is the systematic holistic genetic analyses of biological systems in defined contexts. Context-dependent gene interactions are the fundamental mechanics of all life. Functional genomics uses high-throughput large-scale experimental methods combined with statistical and computational analyses. Projects with expressed sequence tags in chickens have already allowed the creation of cDNA microarrays for large-scale context-dependant mRNA analysis (transcriptomics). However, proteins are the functional units of almost all biological processes, and protein expression very often bears no correlation to mRNA expression. Proteomics, a discipline within functional genomics, is the context-defined analysis of complete complements of proteins. Proteomics bridges the "sequence-to-phenotype gap;" it complements structural and other functional genomics approaches. Proteomics requires high capital investment but has ubiquitous biological applications. Although currently the fastest-growing human biomedical discipline, new paradigms may need to be established for production animal proteomics research. The prospective promise and potential pitfalls of using proteomics approaches to improve poultry pathogen control will be specifically highlighted. The first stage of our recently established proteomics program is global protein profiling to identify differentially expressed proteins in the context of the commercially important pathogens. Our trials and tribulations in establishing our proteomics program, as well some of our initial data to understand chicken immune system function, will be discussed.

NMR indirect detection of glutamate to measure citric acid cycle flux in the isolated perfused mouse heart

(13)C-edited proton nuclear magnetic resonance (NMR) spectroscopy was used to follow enrichment of glutamate C3 and C4 with a temporal resolution of approximately 20 s in mouse hearts perfused with (13)C-enriched substrates. A fit of the NMR data to a kinetic model of the tricarboxylic acid (TCA) cycle and related exchange reactions yielded TCA cycle (V(tca)) and exchange (V(x)) fluxes between alpha-ketoglutarate and glutamate. These fluxes were substrate-dependent and decreased in the order acetate (V(tca)=14.1 micromol g(-1) min(-1); V(x)=26.5 micromol g(-1) min(-1))>octanoate (V(tca)=6.0 micromol g(-1) min(-1); V(x)=16.1 micromol g(-1) min(-1))>lactate (V(tca)=4.2 micromol g(-1) min(-1); V(x)=6.3 micromol g(-1) min(-1)).

Resistance to Marek's disease herpesvirus-induced lymphoma is multiphasic and dependent on host genotype

Genotype-dependent differences in Marek's disease (MD) susceptibility were identified using 14-day-old line N and 6(1) (resistant) and 151 and 7(2) (susceptible) inbred chickens infected with HPRS-16 MD virus (MDV). All line 72 chickens developed progressive MD. Line 15I had fluctuating MD-specific clinical signs and individuals recovered. A novel histologic scoring system enabled indices to be calculated for lymphocyte infiltration into nonlymphoid organs. All genotypes had increased mean lesion scores (MLSs) and mean total lesion scores after MDV infection. These differed quantitatively and qualitatively between the genotypes. Lines 6(1) and 7(2) had a similar MLS distribution in the cytolytic phase, although scores were greater in line 7(2). At the time lymphomas were visible in line 7(2), histologic lesions in line 6(1) were regressing. AV37+ cells were present in similar numbers in all genotypes in the cytolytic phase, suggesting that neoplastically transformed cells were present in all genotypes regardless of MD susceptibility. After the cytolytic phase, AV37+ cell numbers increased in lines 7(2) and 15I but decreased in lines 6(1) and N. In the cytolytic and latent phases, in all genotypes, most infiltrating cells were CD4+. After this time, line 7(2) and 15I lesions increased in size and most cells were CD4+; line 6(1) and N lesions decreased in size and most cells were CD8+. In all genotypes, AV37 immunostaining was weak in lesions with many CD8+ cells, suggesting that AV37 antigen expression or AV37+ cells were controlled by CD8+ cells. The rank order, determined by clinical signs and pathology, for MD susceptibility (highest to lowest) was 7(2) > 15I > 6(1) > N.

13C isotopomer analysis of glutamate by J-resolved heteronuclear single quantum coherence spectroscopy

13C NMR isotopomer analysis is a powerful method for measuring metabolic fluxes through pathways intersecting in the tricarboxylic acid cycle. However, the inherent insensitivity of 13C NMR spectroscopy makes application of isotopomer analysis to small tissue samples (mouse tissue, human biopsies, or cells grown in tissue culture) problematic. (1)H NMR is intrinsically more sensitive than 13C NMR and can potentially supply the same information via indirect detection of 13C providing that isotopomer information can be preserved. We report here the use of J-resolved HSQC (J-HSQC) for 13C isotopomer analysis of tissue samples. We show that J-HSQC reports isotopomer multiplet patterns identical to those reported by direct 13C detection but with improved sensitivity.

A quantitative duplex PCR technique for measuring amounts of cell-associated Marek's disease virus: differences in two populations of lymphoma cells

A duplex polymerase chain reaction (PCR) was developed to measure Marek's disease virus (MDV) load in two subpopulations of Marek's disease (MD) lymphoma cells from chickens. PCR primers were designed using the sequence of the MDV-ICP4 gene and the chicken IFNgamma gene. Each set of primers was present in the same reaction tube so that the 327 bp ICP4 product and the 420 bp IFNgamma product were co-amplified. Two different fluorescent dyes were used to 5'-end label one PCR primer of each pair to distinguish the IFNgamma and ICP4 products by colour. The IFNgamma PCR product was used as an internal standard enabling comparisons of MDV-ICP4 products between different samples. Neither duplex PCR product was preferentially amplified and both reactions were in their exponential phases when stopped. The products could be distinguished by both size and colour. MD lymphoma cells were taken ex vivo and separated on the basis of expressing a novel host surface antigen recognised by the monoclonal antibody AV37. AV37 + lymphoma cells had greater MDV-loads than AV37 lymphoma cells. The principles used here should be applicable to any cell phenotype and/or cell-associated DNA virus.

Counting absolute numbers of specific leukocyte subpopulations in avian whole blood using a single-step flow cytometric technique: comparison of two inbred lines of chickens

A novel flow cytometric technique was developed to determine the absolute numbers of leukocytes of specific phenotypes in whole blood from two lines of inbred chickens (line 7(2) and line 6(1)). This single step method is rapid, accurate, repeatable, can be used in the presence of nucleated erythrocytes and addresses the problems encountered when electronically counting the numbers of leukocytes in specific subpopulations in the blood of non-mammalian species. It is superior to previous methods in that (1) peripheral blood leukocytes (PBL) do not need to be separated by density gradient centrifugation, (2) erythrocyte lysis is not necessary and (3) absolute numbers of specific phenotypes of cells are determined directly. A standard volume of diluted whole blood was added to a standard number of fluorescent beads before incubation with fluorescently-conjugated monoclonal antibodies recognising specific PBL surface antigens. Samples were analysed by flow cytometry and electronic gates were set to count a standard number of beads and the concomitant fluorescently-labelled cells. Absolute numbers of B, CD4+ and CD8+ PBL were determined. Since the bead fluorescence is constant, it was also possible to measure relative MHC class I expression using fluorescence intensity. In both lines of chickens absolute numbers of all of the phenotypes of PBL measured increased with age. Although line 7(2) chickens had greater numbers of B, CD4+, and CD8+ PBL than line 6(1) chickens, there was no significant difference in the CD4+:CD8+ PBL ratios, the T:B PBL ratios or relative MHC class I expression between the two lines. Relative MHC class I expression increased with age in both lines.

Marek's disease virus EcoRI-Q gene (meq) and a small RNA antisense to ICP4 are abundantly expressed in CD4+ cells and cells carrying a novel lymphoid marker, AV37, in Marek's disease lymphomas

Mature lymphomas produced in Rhode Island Red (RIR) chickens infected with the RB1B strain of Marek's disease virus (MDV) were examined for the presence of viral DNA and RNA and expression of viral antigens. In situ hybridization showed that all tumours examined contained viral DNA in areas of lymphoid infiltration. In 3/5 tumours, there was a correlation between the number and distribution of cells expressing the Marek's disease EcoRI-Q gene (meq) and those that carried the lymphoid cell marker AV37. Expression of the MDV-specific phosphoprotein pp38 was infrequent in lymphomas but abundant in a splenic tumour which also expressed the viral glycoprotein gB. Northern blot analysis of lymphocyte fractions purified by immunoaffinity showed that CD4+ and AV37+ fractions from lymphomas expressed meq and the small RNA antisense to ICP4 (SAR). The results are consistent with the notion that transformed cells are CD4+ cells, carrying the AV37 marker and expressing meq and SAR.