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The human striatum has been implicated in processing reward-related information. More recently, activity in the striatum, particularly the caudate nucleus, has been observed when a contingency between behavior and reward exists, suggesting a role for the caudate in reinforcement-based learning. Using a gambling paradigm, in which affective feedback (reward and punishment) followed simple, random guesses on a trial by trial basis, we sought to investigate the role of the caudate nucleus as reward-related learning progressed. Participants were instructed to make a guess regarding the value of a presented card (if the value of the card was higher or lower than 5). They were told that five different cues would be presented prior to making a guess, and that each cue indicated the probability that the card would be high or low. The goal was to learn the contingencies and maximize the reward attained. Accuracy, as measured by participant's choices, improved throughout the experiment for cues that strongly predicted reward, while no change was observed for unpredictable cues. Event-related fMRI revealed that activity in the caudate nucleus was more robust during the early phases of learning, irrespective of contingencies, suggesting involvement of this region during the initial stages of trial and error learning. Further, the reward feedback signal in the caudate nucleus for well-learned cues decreased as learning progressed, suggesting an evolving adaptation of reward feedback expectancy as a behavior–outcome contingency becomes more predictable.

Bovine herpesvirus-1 (BoHV-1) causes significant disease in cattle. Control programs in North America incorporate vaccination with modified live viral (MLV) or killed (KV) vaccine. BoHV-1 strains are isolated from diseased animals or fetuses after vaccination. There are markers for differentiating MLV from field strains using whole-genome sequencing and analysis identifying single nucleotide polymorphisms (SNPs). Using multiple primer sets and sequencing of products permits association of BoHV-1 isolates with vaccines. To determine association between vaccine virus and strains isolated from clinical cases following vaccination, we analyzed 12 BoHV-1 isolates from animals with various clinical syndromes; 9 corresponded to BoHV-1.1 respiratory group. The remaining three corresponded to BoHV-1.2b, typically found in genital tracts of cattle. Four BoHV-1 isolates were identical to a vaccine strain; three were from post-vaccination abortion episodes with typical herpetic lesions whose dams had received MLV vaccine during pregnancy, and one from a heifer given a related MLV vaccine; Sequences of two respiratory isolates perfectly matched mutations characterizing RLB106 strain, a temperature sensitive mutant used in intranasal and parenteral vaccines. The last three respiratory strains clearly appeared related to a group of MLV vaccines. Previously the MLV vaccines were grouped into four groups based on SNPs patterns. In contrast with above-mentioned isolates that closely matched SNP patterns of their respective MLV vaccine virus, these 3 strains both lacked some and possessed a number of additional mutations compared to a group of MLV vaccine viral genome. Finding BoHV-1.2b in respiratory cases indicates focus should be given BoHV-1.2b as an emerging virus or a virus not recognized nor fully characterized in BRD.

The recent publication of the chicken genome sequence along with the extensive single nucleotide polymorphism and physical map open exciting avenues for defining gene function and for understanding the genotypic basis of phenotypic variation in the chicken. The number of genes identified on the sequence map is growing rapidly. Genetically uniform lines and crosses derived from them will allow identification of gene function and gene interactions that contribute to traits such as immunity, disease resistance, growth, production, and behavior. Selected, inbred, and congenic lines will continue to be essential in defining the genetics of many traits. Although dwindling under budgetary pressures, a number of well characterized lines and genetic strains remain. If preserved, these can be used to address questions regarding newly mapped candidate genes defining their importance in a variety of problems in basic, biomedical, and applied avian biology. If lost, years of breeding and selection will be required to replace them.

Telomeres are the specialized ends of chromosomes consisting of highly conserved repeat (5'-TTAGGG-3')(n) sequences. Lack of information regarding the existence of an in vivo telomere clock function in birds, conflicting data regarding telomere array length in the chicken model, and the paucity of molecular telomere information for other avian species led us to study telomere array organization within and among 18 species and subspecies of birds. Most of the species contained between 2% and 4% telomere sequence per diploid genome. Arrays spanning 0.5-10 kb (Class I) and 10-40 kb (Class II) were observed in all of the species studied. Extremely long arrays, ranging from hundreds of kilobases to 1-2 Mb (Class III) were observed in all except two raptor species, the northern goshawk and American bald eagle. In chicken, there was evidence for shortening of the Class II arrays in vivo, based on intraindividual comparisons of somatic versus germline tissues in birds of different ages; terminally differentiated erythrocyte arrays were, on average, 2.3 kb shorter than sperm (germline) arrays. This study provides the first evidence for the existence of telomere arrays significantly larger than have been described for any vertebrate species to date and for developmentally programmed in vivo telomere shortening in the Aves taxa. The novel finding of megabase-sized telomere arrays may be an important feature of avian karyotypes that contain a large number of very small genetic units, the microchromosomes.

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome—composed of approximately one billion base pairs of sequence and an estimated 20,000–23,000 genes—provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

The chicken major histocompatibility complex ( MHC) genes are organized into two genetically independent clusters which both possess class I and class IIbeta genes: the classical B complex and the Restriction fragment pattern- Y ( Rfp-Y) complex. In this study, we have examined the role of Rfp-Y genes in transplantation immunity. For this we used three sublines, B19H1, B19H2 and B19H3, derived from a line fixed for B19. Southern blots, PCR-SSCP assays using primers specific for Rfp-Y genes, and Rfp-Y class I allele-specific sequencing show that the polymorphisms observed in B19H1, B19H2 and B19H3 are due to the presence of three different Rfp-Y haplotypes. The Rfp-Y class I ( YF) alleles in these three haplotypes are highly polymorphic, and RT-PCR shows that at least two YF loci are expressed in each subline. The three sublines show Rfp-Y-directed alloreactivity in that Rfp-Y-incompatible skin grafts are rejected within 15 days, a rate intermediate between that seen in B-incompatible rejection (7 days) and that observed for grafts within the sublines (20 days). We conclude that Rfp-Y has an intermediate role in allograft rejection, likely to be attributable to polymorphism at the class I loci within this region.

Rhythmic movements, such as peristaltic contraction, are initiated by output from central pattern generator (CPG) networks in the CNS. These oscillatory networks elicit locomotion in the absence of external sensory or descending inputs, but CPG circuits produce more directed and behaviorally relevant movement via peripheral nervous system (PNS) input. Drosophila melanogaster larval locomotion results from patterned muscle contractions moving stereotypically along the body segments, but without PNS feedback, contraction of body segments is uncoordinated. We have dissected the role of a subset of mechanosensory neurons in the larval PNS, the chordotonal organs (chos), in providing sensory feedback to the locomotor CPG circuit with Dias (Dynamic Image Analysis System) software. We analyzed mutants carrying cho mutations including atonal, a cho proneural gene, beethoven, a cho cilia class mutant, smetana and touch-insensitive larva B, two axonemal mutants, and 5D10, a weak cho mutant. All cho mutants have defects in gross path morphology compared to controls. These mutants exhibit increased frequency and duration of turning (decision-making) and reduced duration of linear locomotion. Furthermore, cho mutants affect locomotor parameters, including reduced average speed, direction change, and persistence. DIAS analysis of peristaltic waves indicates that mutants exhibit reduced average speed, positive flow and negative flow, and increased stride period. Thus, cho sensilla are major proprioceptive components that underlie touch sensitivity, locomotion, and peristaltic contraction by providing sensory feedback to the locomotor CPG circuit in larvae.

Many of the genes that comprise the vertebrate adaptive immune system are conserved across wide evolutionary time scales. Most notably, homologs of the mammalian MHC gene family have been found in virtually all jawed vertebrates, including sharks, bony fishes, reptiles, and birds. The CD1 family of antigen-presenting molecules are related to the MHC class I family but have evolved to bind and present lipid antigens to T cells. Here, we describe two highly divergent nonclassical MHC class I genes found in the chicken (Gallus gallus) that have sequence homology to the mammalian CD1 family of proteins. One of the chicken CD1 genes expresses a full-length transcript, whereas the other has multiple splice variants. Both Southern blot and single nucleotide polymorphism analysis indicates that chicken CD1 is relatively nonpolymorphic. Moreover, cross-hybridizing bands are present in other bird species, suggesting broad conservation in the avian class. Northern analysis of chicken tissue shows a high level of CD1 expression in the bursa and spleen. In addition, molecular modeling predicts that the potential antigen-binding pocket is probably hydrophobic, a universal characteristic of CD1 molecules. Genomic analysis indicates that the CD1 genes are located on chicken chromosome 16 and maps to within 200 kb of the chicken MHC B locus, suggesting that CD1 genes diverged from classical MHC genes while still linked to the major histocompatibility complex locus. The existence of CD1 genes in an avian species suggests that the origin of CD1 extends deep into the evolutionary history of terrestrial vertebrates.

Chicken infectious anemia virus (CIAV) is a resistant and ubiquitous virus of chickens causing disease in young chickens and immunosuppression in all birds. This paper reviews the current knowledge of CIAV with a focus on new findings indicating that immunosuppressive effects have not been fully appreciated, especially as they relate to the development of antigen-specific cytotoxic T cells. A more complete understanding of the immunosuppressive effects of CIAV emphasizes the need for better vaccines, especially for the broiler industry. In addition, a new model is proposed for the control of viral replication in the reproductive tract of specific-pathogen-free chickens, which may be latently infected. This model suggests that virus transcription is controlled by viral enhancer and repressor elements, which are regulated by different hormones. As a consequence, CIAV has a well-adapted relationship with its host, avoiding immune detection, ensuring passage of virus to the next generation, and eliciting limited pathology to the host.

Shifting political alliances and new environmental challenges are prompting debate over processes of sub-regionalisation and whether the interplay between multiple scales of governance leads to positive synergistic outcomes or negative institutional disruption. Regional management of tuna fisheries in the Western and Central Pacific Ocean is an example where a web of treaties, conventions and institutional frameworks underlie international cooperation. Through examining the interplay between the regional Western and Central Pacific Fisheries Commission and sub-regional Parties to the Nauru Agreement, this paper explores the extent to which the PNA and WCPFC interact in the management of regional tuna fisheries. The results demonstrate that for contested marine resources such as fisheries, international sub-regions can go beyond functional units to also present wider opportunities to shift power relations in favour of small island states. Additionally, the presence of sub-regional groups like the PNA has served to challenge the performance of the WCPFC, stimulating greater debate and progress within the regional body. The paper concludes that the combined work of the PNA and the WCPFC puts them ahead on many issues and may represent a testing ground for a functional multilateralism utilising both regional and sub-regional governance platforms for the management of shared resources.