∼14 000 years of geochemical and isotopic data from Lake Simcoe, Canada.

This dataset contains measurements of modern water and ancient core materials from Lake Simcoe, the fourth largest lake wholly in Ontario, Canada. These data consist of: (i) oxygen, hydrogen and carbon isotope (δ 18O, δ 2H and δ 13C) compositions for modern water samples; (ii) physical measurements of one piston core, PC-5; (iii) δ 13C and δ 18O values of ostracods collected from PC-5, and (iv) δ 13C and δ 18O values of ancient DIC and water, respectively, inferred from item (iii). Physical measurements performed on core PC-5 include magnetic susceptibility, mineralogy and grain size. Mass accumulation rates are also reported. These data will be of interest to those aiming to better characterize the timing and pathway of meltwater flow during and following deglaciation of the Laurentide Ice Sheet in the Laurentian Great Lakes region. These data will also be useful to researchers investigating the influence of deglaciation on the oxygen and carbon isotope systematics of ancient lake environments. A discussion of these data is available in "A ∼14 000-year record of environmental change from Lake Simcoe, Canada" [1].

Salmonella enterica serovar typhimurium colonizing the lumen of the chicken intestine grows slowly and upregulates a unique set of virulence and metabolism genes.

The pattern of global gene expression in Salmonella enterica serovar Typhimurium bacteria harvested from the chicken intestinal lumen (cecum) was compared with that of a late-log-phase LB broth culture using a whole-genome microarray. Levels of transcription, translation, and cell division in vivo were lower than those in vitro. S. Typhimurium appeared to be using carbon sources, such as propionate, 1,2-propanediol, and ethanolamine, in addition to melibiose and ascorbate, the latter possibly transformed to d-xylulose. Amino acid starvation appeared to be a factor during colonization. Bacteria in the lumen were non- or weakly motile and nonchemotactic but showed upregulation of a number of fimbrial and Salmonella pathogenicity island 3 (SPI-3) and 5 genes, suggesting a close physical association with the host during colonization. S. Typhimurium bacteria harvested from the cecal mucosa showed an expression profile similar to that of bacteria from the intestinal lumen, except that levels of transcription, translation, and cell division were higher and glucose may also have been used as a carbon source.

Immune response to a killed infectious bursal disease virus vaccine in inbred chicken lines with different major histocompatibility complex haplotypes.

The influence of MHC on antibody responses to killed infectious bursal disease virus (IBDV) vaccine was investigated in several MHC inbred chicken lines. We found a notable MHC haplotype effect on the specific antibody response against IBDV as measured by ELISA. Some MHC haplotypes were high responders (B201, B4, and BR5), whereas other MHC haplotypes were low responders (B19, B12 and BW3). The humoral response of 1 pair of recombinants isolated from a Red Jungle Fowl (BW3 and BW4) being identical on BF and BG, but different on BL, indicated that part of the primary vaccine response was an MHC II restricted T-cell dependent response. The humoral response in another pair of recombinant haplotypes originating in 2 different White Leghorn chickens being BF21, BL21, BG15 (BR4) and BF15, BL15, BG21 (BR5) on the MHC locus indicated that the BG locus may perform an adjuvant effect on the antibody response as well. Vaccination of chickens at different ages and in lines with different origin indicated that age and background genes also influence the specific antibody response against inactivated IBDV vaccine.

The chicken proinflammatory cytokines interleukin-1beta and interleukin-6: differences in gene structure and genetic location compared with their mammalian orthologues.

The genes encoding the chicken proinflammatory cytokines interleukin (IL)-1B and IL-6 were cloned, sequenced and mapped. The exon:intron structure of the coding region of chicken IL1B corresponds almost exactly to those of mammalian IL1B. As yet, we have no evidence for a 5'-UTR non-coding exon equivalent to that found in mammalian IL1B. The exon:intron structure of chicken IL6 differs from those of mammalian IL6, having one exon fewer (the first two exons in mammalian IL6 genes appear to be fused in the chicken gene). We were unable to clone or sequence the promoter of chicken IL1B. The chicken IL6 promoter shares a number of potential regulatory sequences similar to those found in the human IL6 promoter. These putative elements include (5'-3') a glucocorticoid response element (GRE), an AP-1 binding site, an NF-IL-6 binding site (albeit in the reverse orientation), an NF-kappaB binding site, a second AP-1 binding site and a TATAAA box. A further GRE, a cAMP response element and regions with homology to c-fos serum responsive elements or retinoblastoma control elements were absent. Promoter sequence polymorphisms were not identified in eight different inbred chicken lines. A restriction single-stranded conformational polymorphism was identified which enabled chicken IL1B to be genetically mapped to one end of chromosome 2. Chicken IL6 was mapped by fluorescent in situ hybridization also to chromosome 2, at an FLpter of 0.26.

Faecal shedding and intestinal colonization of Salmonella enterica in in-bred chickens: the effect of host-genetic background.

Considerable and reproducible differences were observed in the amount and duration of faecal excretion when in-bred lines of chickens were infected orally with S. enterica serovar Typhimurium at 6 weeks of age after being given a gut flora preparation when newly hatched. Similar but less pronounced results were observed with S. Enteritidis or S. Infantis. Differences in the viable numbers of the inoculated bacteria in caecal contents were detectable within 24 h of inoculation. No major differences were seen in Salmonella-specific serum IgA or IgG titres. Small differences were seen in the numbers of circulating heterophilic cells. Caecal contents taken from the more resistant lines immediately prior to challenge appeared to be no more inhibitory for Salmonella in vivo than contents taken from susceptible lines. The more resistant lines showed a slightly higher rate of intestinal flow, as indicated by the rate of production of faecal droppings, although there was no difference in the rate of emptying of the caeca. In an F1 generation resistance was dominant and not sex-linked. There was no MHC linkage or any association with SAL1, the gene implicated in resistance to systemic salmonellosis in chickens, or NRAMP1.

Characterisation of a resource population of pigs screened for resistance to salmonellosis.

The degree of resistance to Salmonella choleraesuis infection in a reference family purposely bred to map resistance genes was assessed. Aspects of the innate and specific immune system were studied to find a parameter that might predict the resistance of pigs to salmonellosis. The family was bred from commercial full-sister pairs of F1-gilts and four boars. One boar (G398) was identified as breeding susceptible offspring, and one boar (G402) as breeding resistant offspring on the basis of pyrexial responses and numbers of Salmonella in liver and spleen post mortem. The other two boars were classified as 'possible resistant' (Y2008) and 'unknown' (Y6101) respectively. Functional differences in immune cells (neutrophils and lymphocytes) between the offspring of G398 and G402 were detected. The most resistant piglets had a higher number of circulating neutrophils and better polymorphonuclear neutrophils (PMNs) function, but a lower mitogenic response of lymphocytes both pre- and post-infection and a lower antibody response. Between the offspring groups of Y2008 and Y6101 no differences were found in the number of viable Salmonella in liver and spleen at post mortem or in immune cell function, however, the survival rate of these offspring groups was clearly different. Twenty three percent of the Y2008-offspring and 33% of the Y6101-offspring reached the predetermined humane clinical endpoint before the end of the experiment. Our findings suggest a role for several inherited immunological traits, including PMN function and lecithin-induced mitogenic proliferation, which appear to influence resistance to salmonellosis.

Major histocompatibility complex-linked immune response of young chickens vaccinated with an attenuated live infectious bursal disease virus vaccine followed by an infection.

The influence of the MHC on infectious bursal disease virus (IBDV) vaccine response in chickens was investigated in three different chicken lines containing four different MHC haplotypes. Two MHC haplotypes were present in all three lines with one haplotype (B19) shared between the lines. Line 1 further contains the BW1 haplotype isolated from a Red Jungle Fowl. Line 131 further contains the B131 haplotype isolated from a meat-type chicken. Finally, Line 21 further contains the international B21 haplotype. The chickens were vaccinated with live attenuated commercial IBDV vaccine at 3 wk of age, followed by a challenge with virulent IBDV at 6 wk of age. In this study, we found a notable MHC haplotype effect on the specific antibody response against IBDV, as measured by ELISA. The BW1 haplotype was found to have a significantly higher serum antibody titer against IBDV (7,872) than haplotypes B19 (mean 5,243), B21 (5,570), and B131 (5,333) at 8 d postinfection. However, a virus-neutralizing antibody test did not reflect this result. Nevertheless, the MHC haplotype-associated protective immunity was further supported by the bursa of Fabricius (bursa) recovery from the disease, as measured by histological scorings of the bursa. Chickens carrying the BW1 haplotype had a significantly lower bursa lesion score (1.7) than the haplotypes B19 (mean 3.8), B21 (3.6), and B131 (4.3) 8 d postinfection. Furthermore, multiple line effects were found in other variables when comparing Day 6 with Day 8. Body weight, relative weights of the bursa and the spleen, percentage and relative number of MHC II molecules on MHC II-positive lymphocytes, percentage and relative number of CD4 molecules on CD4-positive lymphocytes, and the specific antibody response all differed significantly among lines. Line 1, with Red Jungle Fowl genes, was clearly differentiated from the other two investigated lines. These results suggest an MHC II restricted T-cell dependent secondary antibody response against IBDV.

The genes encoding E-selectin (SELE) and lymphotactin (SCYC1) lie on separate chicken chromosomes although they are closely linked in human and mouse.

Three differentially expressed selectin genes (SELE, SELP, and SELL), important in the initial stages of leukocyte extravasation, have been reported in mammals. All three genes map close to the chemokine SCYC1 (small inducible cytokine subfamily C, member 1) in a large conserved chromosomal segment that extends from RXRG (retinoic acid receptor, gamma) to TNNT2 (troponin T2) on Chromosome (Chr) 1 in both human and mouse. In the mouse, we demonstrate that Sele is flanked by Prrx1 (paired-related homeobox gene 1) and Scyc1 and define the order of, and distances between, loci as centromere-Prrx1-(0.7+/-0.7 cM)-Sele-(1.2+/-0.9 cM)-Scyc1-telomere. In the chicken, we isolated BAC clones containing PRRX1, SELE, and SCYC1 and positioned them by fluorescent in situ hybridization. SELE and PRRX1 mapped to the short arm of chicken Chr 8 and SCYC1 mapped to the region equivalent to 1q11-1q13 on the long arm of chicken Chr 1. The location of SELE on chicken Chr 8 was independently established by linkage analysis of COM0185, an (AT)16 microsatellite locus identified in a BAC clone that contained SELE. COM0185 was linked to several loci that mapped to one end of chicken Chr 8, with the order of loci, and genetic distances (in cM) between them defined as MSU0435, MSU0325-(7.8+/-3.7)-COM0185-(5.8+/-3.2)-ROS0338-(9.6+/-4.0)-ABR0322-(3.8+/-2.6)-GLUL. We have therefore positioned an evolutionary breakpoint in mammals and chickens between SELE and SCYC1. Furthermore, comparative mapping analysis of the RXRG-TNNT2 chromosomal segment that is conserved on human and mouse Chr 1 indicates that it is divided into four segments in the chicken, each of which maps to a different chromosome.

Structure and chromosomal localization of chicken CD5.

CD5 is a transmembrane glycoprotein on all T cells and on a subpopulation of B cells. Based on the analysis of chicken CD5-cDNA we have previously shown that the structure of the CD5 protein is conserved between species. Here we report the isolation and chromosomal mapping of the chicken CD5 gene. The gene spans 3.4 kb and is extremely compact with a high GC-nucleotide content. There are 10 exons and the introns are spliced out similarly to those in the human CD5 gene. Each of the three extracellular scavenger receptor cysteine-rich (SRCR) domains is encoded as an exon of its own, as is the proline-rich hinge region that separates the first two membrane-distal SRCR domains. The fluorescence in situ hybridization (FISH) technique was used to map the gene to chromosome five. This is the first report describing the organization of the CD5 gene from a nonmammalian species.

Identification, mapping, and phylogenetic analysis of three novel chicken CC chemokines.

We have identified three novel chicken CC chemokine genes among cDNA clones derived from lipopolysaccharide-stimulated cells of the chicken macrophage cell line HD11. Two of these chemokines show DNA sequence homology to the mammalian genes SCYA20 (MIP-3alpha) and SCYA5 (RANTES), while the third shows similar levels of homology to several mammalian CC chemokines. Sequencing of genomic DNA showed that all three chicken chemokines possess the three-exon structure and conserved intron positions typical of mammalian CC chemokines. Genetic mapping of the three chicken chemokines locates them in three chromosomal regions which correspond to regions containing homologous chemokines in humans. Phylogenetic analysis of the currently known chicken and human chemokines suggests that individual chicken and human chemokines derive from common ancestral genes in patterns that reflect their genomic positions, indicating that the diversity of chemokine genes pre-dated avian-mammalian divergence. Since the function of the chemokines is principally to act as intermediates between stimulated cells and specific subsets of responding immune cells, this suggests that the complex organization of the immune system and diversity of responding cells were largely in place at that time.

Localization to chicken chromosome 5 of a novel locus determining salmonellosis resistance.

Clear genetic differences in the susceptibility of chickens to visceral infection by Salmonella have been observed and it has been possible to identify resistant and susceptible lines of inbred chickens. We report here the results of experiments to map directly the gene(s) controlling this trait in chickens by examining crosses between highly susceptible and highly resistant lines. In the mapping panel, a region on chicken Chromosome (Chr) 5 was found to have a large effect on resistance, and this effect was observed in three separate resource populations. Mapping of additional marker loci in the region of the resistance gene further localized it to a region of approximately 2 cM, close to the genes for creatine kinase (CKB) and dynein (DNCH1). This region shows conserved synteny with telomeric regions of human Chr 14 and mouse Chr 12. On the basis of this conserved synteny, this resistance gene seems unlikely to correspond to the previously identified salmonellosis resistance genes Lps (located on mouse Chr 4) or Nos(2) (located on mouse Chr 11). There was no association between Nramp1 and resistance in these crosses, although this gene was shown to contribute to resistance in other crosses. The homologous human and mouse regions at present contain no likely candidate genes for this trait. Thus this appears to be a novel resistance gene, which we designate SAL1.

Measuring infectious bursal disease virus RNA in blood by multiplex real-time quantitative RT-PCR.

A quantitative reverse transcription polymerase chain reaction (RT-PCR) protocol for assessing infectious bursal disease virus (IBDV) RNA levels in blood was developed using the ABI PRISM 7700 Sequence Detection System coupled with TaqMan chemistry. To control for variations in sampling and processing between samples 28S rRNA was co-amplified in a multiplex reaction and used to quantify total RNA. Relative quantification and standardisation was achieved using a log10 dilution series of RNA extracted from IBDV stock. A linear relationship was observed between input RNA and cycle threshold values (C(T)) over 5 log10 dilutions for the IBDV-specific product and 6 log10 dilutions for the 28S rRNA-specific product. As a test of the assay it was used to determine whether differences in susceptibility to IBDV observed between inbred lines of chickens could be detected at the level of viral load in the blood. Viral RNA levels peaked 2 days post-infection when there was significantly less viral RNA in the blood of resistant line 6(1) chickens compared with the more susceptible Brown Leghorns (P = 0.01). These results demonstrate that the course of IBDV infection can be monitored by quantifying IBDV RNA extracted from blood of infected chickens using TaqMan technology.

A consensus linkage map of the chicken genome.

A consensus linkage map has been developed in the chicken that combines all of the genotyping data from the three available chicken mapping populations. Genotyping data were contributed by the laboratories that have been using the East Lansing and Compton reference populations and from the Animal Breeding and Genetics Group of the Wageningen University using the Wageningen/Euribrid population. The resulting linkage map of the chicken genome contains 1889 loci. A framework map is presented that contains 480 loci ordered on 50 linkage groups. Framework loci are defined as loci whose order relative to one another is supported by odds greater then 3. The possible positions of the remaining 1409 loci are indicated relative to these framework loci. The total map spans 3800 cM, which is considerably larger than previous estimates for the chicken genome. Furthermore, although the physical size of the chicken genome is threefold smaller then that of mammals, its genetic map is comparable in size to that of most mammals. The map contains 350 markers within expressed sequences, 235 of which represent identified genes or sequences that have significant sequence identity to known genes. This improves the contribution of the chicken linkage map to comparative gene mapping considerably and clearly shows the conservation of large syntenic regions between the human and chicken genomes. The compact physical size of the chicken genome, combined with the large size of its genetic map and the observed degree of conserved synteny, makes the chicken a valuable model organism in the genomics as well as the postgenomics era. The linkage maps, the two-point lod scores, and additional information about the loci are available at web sites in Wageningen (http://www.zod.wau.nl/vf/ research/chicken/frame_chicken.html) and East Lansing (http://poultry.mph.msu.edu/).