New insights into the long-term evolutionary history of the avian MHC

SummaryGene duplication and neofunctidnalization are important processes in the evolution of phenotypic complexity. They account for important evolutionary novelties that confer ecological adaptation, such as the major histocompatibility complex (MHC), a multigene family with a central role in vertebrates' adaptive immune system. Multigene families, which evolved in large part through duplication, represent promising systems to study the still strongly depbated relative roles of neutral and adaptive processes in the evolution of phenotypic complexity. Detailed knowledge on ecological function and a well-characterized evolutionary history place the mammals' MHC amongst ideal study systems. However mammalian MHCs usually encompass several million base pairs and hold a large number of functional and non-functional duplicate genes, which makes their study complex. Avian MHCs on the other hand are usually way more compact, but the reconstruction of. their evolutionary history has proven notoriously difficult. However, no focused attempt has been undertaken so far to study the avian MHC evolutionary history in a broad phylogenetic context and using adequate gene regions.In the present PhD, we were able to make important contributions to the understanding of the long-term evolution of the avian MHC class II Β (MHCI1B). First, we isolated and characterized MHCIIB genes in barn owl (Tyto alba?, Strigiformes, Tytonidae), a species from an avian lineage in which MHC has not been studied so far. Our results revealed that with only two functional MHCIIB genes the MHC organization of barn owl may be similar to the 'minimal essential' MHC of chicken (Gallus gallus), indicating that simple MHC organization may be ancestral to birds. Taking advantage of the sequence information from barn owl, we studied the evolution of MHCIIB genes in 13 additional species of 'typical' owls (Strigiformes, Strigidae). Phylogenetic analyses revealed that according to their function, in owls the peptide-binding region (PBR) encoding exon 2 and the non-PBR encoding exon 3 evolve by different patterns. Exon 2 exhibited an evolutionary history of positive selection and recombination, while exon 3 traced duplication history and revealed two paralogs evolving divergently from each other in owls, and in a shorebird, the great snipe {Gallinago media). The results from exon 3 were the first ever from birds to demonstrate gene orthology in species that diverged tens of millions of years ago, and strongly questioned whether the taxa studied before provided an adequate picture of avian MHC evolution. In a follow-up study, we aimed at explaining a striking pattern revealed by phylogenetic trees analyzing the owl sequences along with MHCIIB sequences from other birds: One owl paralog (termed DAB1) grouped with sequences of passerines and falcons, while the other (DAB2) grouped with wildfowl, penguins and birds of prey. This could be explained by either a duplication event preceding the evolution of these bird orders, or by convergent evolution of similar sequences in a number of orders. With extensive phylogenetic analyses we were able to show, that indeed a duplication event preceeded the major avian radiation -100 my ago, and that following this duplication, the paralogs evolved under positive selection. Furthermore, we showed that the divergently evolving amino acid residues in the MHCIIB-encoded β-chain potentially interact with the MHCI I α-chain, and that molecular coevolution of the interacting residues may have been involved in the divergent evolution of the MHCIIB paralogs.The findings of this PhD are of particular interest to the understanding of the evolutionary history of the avian MHC and, by providing essential information on long-term gene history in the avian MHC, open promising perspectives for advances in the understanding of the evolution of multigene families in general, and for avian MHC organization in particular. Amongst others I discuss the importance of including protein structure in the phylogenetic study of multigene families, and the roles of ecological versus molecular selection pressures. I conclude by providing a population genomic perspective on avian MHC, which may serve as a basis for future research to investigate the relative roles of neutral processes involving effective population size effects and of adaptation in the evolution of avian MHC diversity and organization.RésuméLa duplication de gènes et leur néo-fonctionnalisation sont des processus importants dans l'évolution de la complexité phénotypique. Ils sont impliqués dans l'apparition d'importantes nouveautés évolutives favorisant l'adaptation écologique, comme c'est le cas pour le complexe majeur d'histocompatibilité long-terme du CMH aviaire classe II Β (CMH II Β). Nous avons isolé et caractérisé les gènes CMH I IB de la chouette effraie (Tyto alba; Strigiformes, Tytonidae), une espèce appartenant à une lignée aviaire dont le CMH n'avait pas été étudié jusqu'ici. Avec uniquement deux gènes CMHIIB fonctionnels, l'organisation CMH de la chouette effraie semble être comparable à celle "minimale" du poulet (Gallus gallus), ce qui suggère qu'une organisation simple du CMH pourrait être ancestrale chez les oiseaux. En se basant sur l'information obtenue pour cette espèce, nous avons ensuite étudié l'évolution des gènes CMHIIB chez 13 espèces de chouettes "typiques" (Strigiformes, Strigidae). Les analyses phylogénétiques ont révélé que chez les chouettes, selon leur fonction, l'exon 2 codant pour la 'peptide-binding region' (PBR) et l'exon 3 ne codant pas pour la région PBR évoluent de manière distincte. L'exon 2 montre une histoire évolutive de sélection positive et recombinaison, tandis que l'exon 3 retrace l'histoire de duplication et révèle deux paralogues évoluant de façon divergente chez les chouettes, ainsi que chez un limicole, la bécassine double (Gallinago media). Les résultats découlant de l'analyse de l'exon 3 ont montré pour la première fois chez les oiseaux une orthologie de gènes chez des espèces ayant divergé il y a des dizaines de millions d'années. Dans une deuxième étude, nous avons voulu expliquer le pattern surprenant révélé par les arbres phylogénétiques lorsque les séquences CMHIIB des chouettes sont analysées avec les séquences d'autres oiseaux: un paralogue de chouette (appelé DABI) forme un groupe avec les séquences de passereaux et faucons, tandis que l'autre (DAB2) se regroupe avec les gallo-ansériformes, les manchots et les rapaces diurnes. Ceci pourrait être expliqué soit par une duplication qui a précédé l'évolution de ces ordres aviaires soit par évolution convergente dans un certain nombre d'ordres. Grâce à des analyses phylogénétiques approfondies, nous avons pu montrer qu'un événement de duplication a effectivement précédé la radiation aviaire principale d'il y a environ 100 millions d'années, et qu'après cette duplication les paralogues ont évolué sous sélection positive. De plus, les résidus d'acides aminés évoluant de façon divergente dans la chaîne β codée par le CMHIIB interagissent potentiellement avec la chaîne α codée par le CMHII, et que la coévolution moléculaire de ces résidus pourrait être à la base de l'évolution divergente des paralogues CMHIIB.Dans cette thèse sont discutés entre autres l'importance d'inclure la structure des protéines dans l'étude phylogénétique des familles multigéniques, ainsi que les rôles respectifs des pressions sélectives écologique et moléculaire. La conclusion comporte une perspective sur la génomique des populations du CMH aviaire, qui pourrait servir de base pour de futures recherches sur les rôles relatifs joués par Îes processus neutres comprenant les effets de la taille efficace des populations et l'adaptation dans l'évolution de la diversité et l'organisation du MHC aviaire.

Long-Stay Activity Report 2005

Long-Stay Activity Report 2005 This report presents data collected through a survey of long-stay units in 2005. The aim of the survey is to provide statistics on the number of beds available for long-term care, how the beds are used and the types of patients who occupy these beds. In 2004, additional information on bed types was requested for the first time in order to provide a more accurate picture of activity within this sector. This report includes analysis on long-stay beds, limited-stay beds and all beds in each table. Click here to download PDF 867kb

End-of-Life Care for Older People in Acute and Long-Stay Care Settings in Ireland

The National Council on Ageing and Older People (NCAOP) and the Irish Hospice Foundation (IHF) are pleased to present this report, End-of-Life Care for Older People in Acute and Long-Stay Care Settings in Ireland. The report details the results of research that focuses, for the first time in Ireland, on the quality oflife and quality of care at the end-of-life for older people in various care settings including acute hospitals, public extended care units, private nursing homes, voluntary nursing homes and welfare homes. The report provides a new model for care at the end-of-life which goes beyond specialist palliative care provision to embrace a compassionate approach that supports older people who are living with, or dying from, progressive, chronic and life-threatening conditions, and attends to all their needs: physical, psychological,social and spiritual. Download document here

Long Stay Activity Report for 2006

Long Stay Activity Report for 2006 This report presents data collected through a survey of long-stay units in 2006. The aim of the survey is to provide statistics on the number of beds available for long-term care, how the beds are used and the types of patients who occupy these beds. In order to present the data this report has been divided into a number of sections. This introductory section examines how data was collected and analysed and gives a summary of the results. Click here to download PDF 2mb

Report of the Interdepartmental Working Group on Long Term Care, 2006

Report of the Interdepartmental Working Group on Long Term Care, 2006 This report was finalised by the working group at the end of 2005 and submitted to Government in January 2006. While the reportâ?Ts proposals were not formally endorsed by Government, its analysis and recommendations have informed subsequent decisions, including the Fair Deal policy on Long-Term Nursing Home Care.The principles underpinning the report formed the basis for discussions about long term care with the Social Partners prior to the new national programme negotiations leading to a clear vision articulated in Towards 2016 on a number of priority actions to support older people to participate in society in a full and meaningful way. Click here to download PDF 693kb

Value for Money Report - The Efficiency and Effectiveness of Long-Stay Residential Care for Adults within the Mental Health Services

Value for Money Report – The Efficiency and Effectiveness of Long-Stay Residential Care for Adults within the Mental Health Services Executive Summary and Contents PDF 164kb Chapters 1 and 2 – Introduction and Service Objectives PDF 504kb Chapter 3 plus annexes – Service Effectiveness and Efficiency PDF 3.7mb Chapter 4 – Service Resources PDF 2.4mb Chapters 5, 6 and 7 – Future Funding and Alternative Approaches, Key Performance Indicators, Conclusions and Recommendations PDF 2.4mb Appendices 1 to 6

Electro-cortical modulations and fronto-parietal activity during motor transitions in the elderly

With aging, bimanual movements are performed with increased cerebral activity in frontal and parietal areas. In contrast, motor switching is poorly documented and is expected to engage increasing resources in the elderly. In this study, spontaneous electroencephalographic activity (EEG) was recorded while 39 young participants (YP) and 37 elderly (EP) performed motor transitions from unimanual tapping to symmetric bimanual tapping (= Activation), and opposite (= Inhibition). We measured the delay of switching using the mean and standard deviation of transition time (meanTT and sdTT). Task-related power (TRPow) in alpha frequency band (8-12Hz) was used to measure electro-cortical changes, negative values corresponding to increased cerebral activity. A balance index (BI) was computed between frontal and parietal regions, values non-significantly different from "zero" representing a comparable level of cerebral activity in these regions. The results reveal higher sdTT 1) in EP compared to YP in both transitions, 2) in Activation compared to Inhibition in both groups. TRPow tends to reach greater negative values (p=0.052) in EP compared to YP in both tapping modes and both motor transitions. Furthermore, the results show more negative TRPow 1) in both motor transitions compared to the tapping movements and 2) in frontal region for YP compared to EP during Inhibition only. BI values differ significantly from "zero" for YP in Inhibition only. In conclusion, motor transitions are more variable and tend to be resource-consuming in the elderly. Moreover, the cerebral activity spreading in EP characterized by similar level of activity between frontal and parietal regions suggest reduced capacity to recruit specialized neural mechanisms during motor inhibition.

Long Stay Activity Report for 2008

Long Stay Activity Report for 2008 Click here to download PDF 2.7mb

Long Stay Activity Report for 2007

Long Stay Activity Report for 2007 Click here to download PDF 2.5mb

Long Stay Activity Report for 2010

Long Stay Activity Report for 2010 Click here to download PDF 1.42MB

Long Stay Activity Report for 2009

Long Stay Activity Report for 2009 Click here to download PDF 2.19MB

A long, naturally presented immunodominant epitope from NY-ESO-1 tumor antigen: implications for cancer vaccine design.

The tumor antigen NY-ESO-1 is a promising cancer vaccine target. We describe here a novel HLA-B7-restricted NY-ESO-1 epitope, encompassing amino acids 60-72 (APRGPHGGAASGL), which is naturally presented by melanoma cells. The tumor epitope bound to HLA-B7 by bulging outward from the peptide-binding cleft. This bulged epitope was not an impediment to T-cell recognition, however, because four of six HLA-B7(+) melanoma patients vaccinated with NY-ESO-1 ISCOMATRIX vaccine generated a potent T-cell response to this determinant. Moreover, the response to this epitope was immunodominant in three of these patients and, unlike the T-cell responses to bulged HLA class I viral epitopes, the responding T cells possessed a remarkably broad TCR repertoire. Interestingly, HLA-B7(+) melanoma patients who did not receive the NY-ESO-1 ISCOMATRIX vaccine rarely generated a spontaneous T-cell response to this cryptic epitope, suggesting a lack of priming of such T cells in the natural anti-NY-ESO-1 response, which may be corrected by vaccination. Together, our results reveal several surprising aspects of antitumor immunity and have implications for cancer vaccine design.

Long Stay Activity Report for 2011

This report presents data collected through a survey of long-stay units in 2011. The aim of the survey is to provide statistics on the number of beds available for long-term care, how the beds are used and the types of patients who occupy these beds. In order to present the data this report has been divided into a number of sections. This introductory section examines how data was collected and analysed and gives a summary of the results.   Click here to download PDF 2.8mb  

Long-Stay Activity Statistics 2012

This report presents data collected through a survey of long-stay units in 2012. The aim of the survey is to provide statistics on the number of beds available for long-term care, how the beds are used and the types of patients who occupy these beds.In order to present the data this report has been divided into a number of sections. This introductory section examines how data was collected and analysed and gives a summary of the results. Long-Stay Activity Statistics 2012