Genetic Landscape of Joubert syndrome in French Canadians

Le syndrome de Joubert est une maladie récessive caractérisée par une malformation congénitale distincte du tronc cérébral et du cervelet, associée à une anomalie des mouvements oculaires (apraxie oculomotrice), une respiration irrégulière, un retard de développement, et une ataxie à la démarche. Au cours de la dernière décennie, plus de 20 gènes responsables ont été identifiés, tous ayant un rôle important dans la structure et la fonction des cils primaires. Ainsi, le syndrome de Joubert est considéré une ciliopathie. Bien que le Syndrome de Joubert ait été décrit pour la première fois dans une famille canadienne-française en 1969, le(s) gène(s) causal demeurait inconnu dans presque tous les cas de syndrome de Joubert recensés en 2010 dans la population canadienne-française, soit début de mon projet doctoral. Nous avons identifié un total de 43 individus canadiens-français (35 familles) atteints du syndrome de Joubert. Il y avait un regroupement de familles dans la région du Bas-Saint-Laurent de la province de Québec, suggérant la présence d'un effet fondateur. L’objectif de ce projet était de caractériser la génétique du syndrome de Joubert dans la population canadienne-française. Notre hypothèse était qu’il existait un effet fondateur impliquant au moins un nouveau gène JBTS. Ainsi, dans un premier temps, nous avons utilisé une approche de cartographie par homozygotie. Cependant, nous n’avons pas identifié de région d’homozygotie partagée parmi les individus atteints, suggérant la présence d’une hétérogénéité génétique ou allélique. Nous avons donc utilisé le séquençage exomique chez nos patients, ce qui représente une approche plus puissante pour l’étude de conditions génétiquement hétérogènes. Nos travaux ont permis l’identification de deux nouveaux gènes responsables du syndrome de Joubert: C5orf42 et TMEM231. Bien que la localisation cellulaire et la fonction de C5orf42 soient inconnus au moment de cette découverte, nos résultats génétiques combinés avec des études ultérieures ont établi un rôle important de C5orf42 dans la structure et la fonction ciliaire, en particulier dans la zone de transition, qui est une zone de transition entre le cil et le reste de la cellule. TMEM231 avait déjà un rôle établi dans la zone de transition ciliaire et son interaction avec d’autres protéines impliquées dans le syndrome de Joubert était connu. Nos études ont également identifié des variants rares délétères chez un patient JBTS dans le gène ciliaire CEP104. Nous proposons donc CEP104 comme un gène candidat JBTS. Nous avons identifié des mutations causales dans 10 gènes, y compris des mutations dans CC2D2A dans 9 familles et NPHP1 dans 3 familles. Au total, nous avons identifié les mutations causales définitives chez 32 des 35 familles étudiées (91% des cas). Nous avons documenté un effet fondateur complexe dans la population canadienne-française avec de multiples mutations récurrentes dans quatre gènes différents (C5orf42, CC2D2A, TMEM231, NPHP1). Au début de ce projet de recherche, l’étiologie génétique était inconnue chez les 35 familles touchées du syndrome de Joubert. Maintenant, un diagnostique moléculaire définitif est identifié chez 32 familles, et probable chez les 3 autres. Nos travaux ont abouti à la caractérisation génétique du syndrome de Joubert dans la population canadienne-française grâce au séquençage exomique, et révèlent la présence d'un effet fondateur complexe avec une l'hétérogénéité allélique et intralocus importante. Ces découvertes ont éclairé la physiologie de cette maladie. Finalement, l’identification des gènes responsables ouvre de nouvelles perspectives diagnostiques ante-natales, et de conseils génétique, très précieuses pour les familles.

International Initiatives for Regulating Access to Genetic Resources

In light of the various international instruments and international agencies that are actively engaged in resolving the issue of ABS, the present work tries to find an answer to the larger question how far the above agencies have succeeded in regulating access and make sure of benefit sharing. In this process, the work comprehensively analyses the work of different agencies involved in the process. It tries to find out the major obstacles that stand in the way of fulfilment of the benefit sharing objective and proposes the ways and means to tackle them. The study first traces the legal foundations of the concept of property in GRs and associated TK.For this, it starts with analysis of the nature of property and the questions related to ownership in GRs as contained in the CBD as well as in various State legislations. It further examines the notion of property before and after the enactment of the CBD and establishes that the CBD contains strong private property jurisprudence.Based on the theoretical foundation of private property right,Chapter 3 analyses the benefit sharing mechanism of the CBD, i.e. the Nagoya Protocol. It searches for a theoretical convergence of the notion of property as reflected in the two instruments and successfully establishes the same. It makes an appraisal of the Nagoya regime to find out how far it has gone beyond the CBD in ensuring the task of benefit sharing and the impediments in its way.Realizing that the ITPGRFA forms part of the CBD system, Chapter 4 analyses the benefit sharing structure of ITPGRFA as revealed through its multilateral system. This gives the work the benefit of comparing two different benefit sharing models operating on the same philosophy of property. This chapter tries to find out whether there is conceptual coherence in the notion of property when the benefit sharing model changes. It alsocompares the merits and demerits of both the systems and tries to locate the hurdles in achieving benefit sharing. Aware of the legal impediments caused by IPRs in the process of ABS, Chapter 5 tries to explore the linkages between IPRs and GRs and associated TK and assesses why contract-based CBD system fails before the monopoly rights under TRIPS. Chapter 6 analyses the different solutions suggested by the international community at the TRIPS Council as well as the WIPO (World Intellectual property Organisation) and examines their effectiveness. Chapter 7 concludes that considering the inability of the present IP system to understand the grass root realities of the indigenous communities as well as the varying situations of the country of origin, the best possible way to recognise the CBD goals in the TRIPS could be better achieved through linking the two instruments by means of the triple disclosure requirement in Article 29 as suggested by the Disclosure Group during the TRIPS Council deliberations. It also recommends that considering the nature of property in GR, a new section/chapter in the TRIPS dealing with GRs would be another workable solution.

Studies on genetic polymorphism in Santalum Album L.

Loss of natural sandal populations due to illicit felling, forest encroachment and spike disease have an adverse effect on genetic diversity of the species. To initiate any genetic improvement programme in sandal, a precise understanding of the population genetic diversity structure is essential. The concern over the loss of genetic variability in sandal is particularly critical, as there is hardly any information regarding the diversity status of the natural populations. Identifying fast growing, disease resistant, oil rich sandal trees through breeding and their mass multiplication for afforestation are the best method for ensuring sustainable supply of superior sandalwood. The healthy sandal trees existing in heavily spike diseased area can be used as a promising starting point for any such breeding programme (Venkatesh, 1978). So far, no genetic information is available regarding the resistant nature of spike disease evaded trees left in heavily infected patches. The high rate of depletion of the superior trees in South Indian sandal reserves due to illegal felling and spike disease has necessitated an urgent need for conservation of the surviving trees.Widespread occurrence of spike disease in Marayoor forest reserve was reported in 1981 (Ghosh and Balasundaran, 1995). Because of the high density of trees and varying intensity of spike disease, Marayoor sandal population was found to be ideal for experimental studies in sandal (Ghosh et al., 1985). Fifteen trees of reserve 51 of Marayoor range had been selected as candidate plus trees for growth and spike disease evasion . These trees have been selected for mass multiplication through tissue culture technique.

Design of a Compact Genetic Microstrip Antenna with improved performance

In this paper the design issues of compact genetic microstrip antennas for mobile applications has been investigated. The antennas designed using Genetic Algorithms (GA) have an arbitrary shape and occupies less area (compact) compared to the traditionally designed antenna for the same frequency but with poor performance. An attempt has been made to improve the performance of the genetic microstrip antenna by optimizing the ground plane (GP) to have a fish bone like structure. The genetic antenna with the GP optimized is even better compared to the traditional and the genetic antenna.

Genetic divergence in lobsters (Crustacea: Palinuridae and Scyllaridae) from the Indian EEZ

The management of exploited species requires the identification of demographically isolated populations that can be considered as independent management units (MUs), failuring in which can lead to over -fishing and depletion of less productive stocks. By characterizing the distribution of genetic variation, population sub structuring can be detected and the degree of connectivity among populations can be estimated. The genetic variation can be observed using identified molecular markers of both nuclear and mitochondrial origin. Hence, the present work was undertaken to study the genetic diversity and population/stock structure in P. homarus homarus and T. unimaculatus from different landing centres along the Indian coast using nuclear (RAPD) and mitochondrial DNA marker tools which will help towards developing management strategies for management and conservation of these declining resources.To make consistent conservation and fisheries management decisions, accurate species identifications are needed. It is also suggested that it is not always desirable to rely on a single sequence for taxonomic identification. Thus, the feasibility of using partial sequences of additional mitochondrial genes like 16SrRNA, 12SrRNA and nuclear 18SrRNA has also been explored in our study. Phylogenies provide a sound foundation for establishing taxonomy. The present work also attempts to reconstruct the phylogeny of eleven species of commercially important lobsters from the Indian EEZ using molecular markers

Plant genetic diversity, irrigation and nutrient cycling in traditional mountain oases of northern Oman

Little is known about plant biodiversity, irrigation management and nutrient fluxes as criteria to assess the sustainability of traditional irrigation agriculture in eastern Arabia. Therefore interdisciplinary studies were conducted over 4 yrs on flood-irrigated fields dominated by wheat (Triticum spp.), alfalfa (Medicago sativa L.) and date palm (Phoenix dactylifera L.) in two mountain oases of northern Oman. In both oases wheat landraces consisted of varietal mixtures comprising T. aestivum and T. durum of which at least two botanical varieties were new to science. During irrigation cycles of 6-9 days on an alfalfa-planted soil, volumetric water contents ranged from 30-13%. For cropland, partial oasis balances (comprising inputs of manure, mineral fertilizers, N2-fixation and irrigation water, and outputs of harvested products) were similar for both oases, with per hectare annual surpluses of 131 kg N, 37 kg P and 84 kg K at Balad Seet and of 136 kg N, 16 kg P and 66 kg K at Maqta. Respective palm grove surpluses, in contrast were with 303 kg N, 38 kg P, and 173 kg K ha^-1 yr^-1 much higher at Balad Seet than with 84 kg N, 14 kg P and 91 kg K ha^-1 yr^-1 at Maqta. The results show that the sustainability of these irrigated landuse systems depends on a high quality of the irrigation water with low Na but high CaCO3, intensive recycling of manure and an elaborate terrace structure with a well tailored water management system that allows adequate drainage.

Enlarging a training set for genomic selction by imputation of un-genotyped animals in populations of varying genetic architecture

Background: The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped. ----- Methods: Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets. ----- Results: Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams. ----- Conclusions: Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited.

From Genetic Algorithms to Efficient Organization

The work described in this thesis began as an inquiry into the nature and use of optimization programs based on "genetic algorithms." That inquiry led, eventually, to three powerful heuristics that are broadly applicable in gradient-ascent programs: First, remember the locations of local maxima and restart the optimization program at a place distant from previously located local maxima. Second, adjust the size of probing steps to suit the local nature of the terrain, shrinking when probes do poorly and growing when probes do well. And third, keep track of the directions of recent successes, so as to probe preferentially in the direction of most rapid ascent. These algorithms lie at the core of a novel optimization program that illustrates the power to be had from deploying them together. The efficacy of this program is demonstrated on several test problems selected from a variety of fields, including De Jong's famous test-problem suite, the traveling salesman problem, the problem of coordinate registration for image guided surgery, the energy minimization problem for determining the shape of organic molecules, and the problem of assessing the structure of sedimentary deposits using seismic data.

Evidence for an apartheid-like social structure in early Anglo-Saxon England

The role of migration in the Anglo-Saxon transition in England remains controversial. Archaeological and historical evidence is inconclusive, but current estimates of the contribution of migrants to the English population range from less than 10 000 to as many as 200 000. In contrast, recent studies based on Y-chromosome variation posit a considerably higher contribution to the modern English gene pool (50-100%). Historical evidence suggests that following the Anglo-Saxon transition, people of indigenous ethnicity were at an economic and legal disadvantage compared to those having Anglo-Saxon ethnicity. It is likely that such a disadvantage would lead to differential reproductive success. We examine the effect of differential reproductive success, coupled with limited intermarriage between distinct ethnic groups, on the spread of genetic variants. Computer simulations indicate that a social structure limiting intermarriage between indigenous Britons and an initially small Anglo-Saxon immigrant population provide a plausible explanation of the high degree of Continental male-line ancestry in England.

Statistical methods for examining genetic influences of resistance to anti-epileptic drugs

It is generally accepted that genetics may be an important factor in explaining the variation between patients’ responses to certain drugs. However, identification and confirmation of the responsible genetic variants is proving to be a challenge in many cases. A number of difficulties that maybe encountered in pursuit of these variants, such as non-replication of a true effect, population structure and selection bias, can be mitigated or at least reduced by appropriate statistical methodology. Another major statistical challenge facing pharmacogenetics studies is trying to detect possibly small polygenic effects using large volumes of genetic data, while controlling the number of false positive signals. Here we review statistical design and analysis options available for investigations of genetic resistance to anti-epileptic drugs.

Population genetic diversity of the endemic Sardinian newt Euproctus platycephalus: implications for conservation

The Sardinian mountain newt Euproctus platycephalus, endemic to the island of Sardinia, (Italy), is considered a rare and threatened species and is classed as critically endangered by IUCN. It inhabits streams, small lakes and pools on the main mountain systems of the island. Threats from climatic and anthropogenic factors have raised concerns for the long-term survival of newt populations on the island. MtDNA sequencing was used to investigate the genetic population structure and phylogeography of this endemic species. Patterns of genetic variation were assessed by sequencing the complete Dloop region and part of the 12SrRNA, from 74 individuals representing four different populations. Analyses of molecular variance suggest that populations are significantly differentiated, and the distribution of haplotypes across the island shows strong geographical structuring. However, phylogenetic analyses also suggest that the Sardinian population consists of two distinct mtDNA groups, which may reflect ancient isolation and expansion events. Population structure, evolutionary history of the species and implications for the conservation of newt populations are discussed.

Recent developments in genetic data analysis: what can they tell us about human demographic history?

Over the last decade, a number of new methods of population genetic analysis based on likelihood have been introduced. This review describes and explains the general statistical techniques that have recently been used, and discusses the underlying population genetic models. Experimental papers that use these methods to infer human demographic and phylogeographic history are reviewed. It appears that the use of likelihood has hitherto had little impact in the field of human population genetics, which is still primarily driven by more traditional approaches. However, with the current uncertainty about the effects of natural selection, population structure and ascertainment of single-nucleotide polymorphism markers, it is suggested that likelihood-based methods may have a greater impact in the future.

Use of a novel Hill-climbing genetic algorithm in protein folding simulations

We have developed a novel Hill-climbing genetic algorithm (GA) for simulation of protein folding. The program (written in C) builds a set of Cartesian points to represent an unfolded polypeptide's backbone. The dihedral angles determining the chain's configuration are stored in an array of chromosome structures that is copied and then mutated. The fitness of the mutated chain's configuration is determined by its radius of gyration. A four-helix bundle was used to optimise simulation conditions, and the program was compared with other, larger, genetic algorithms on a variety of structures. The program ran 50% faster than other GA programs. Overall, tests on 100 non-redundant structures gave comparable results to other genetic algorithms, with the Hill-climbing program running from between 20 and 50% faster. Examples including crambin, cytochrome c, cytochrome B and hemerythrin gave good secondary structure fits with overall alpha carbon atom rms deviations of between 5 and 5.6 Angstrom with an optimised hydrophobic term in the fitness function. (C) 2003 Elsevier Ltd. All rights reserved.

Structure and biogenesis of the capsular F1 antigen from Yersinia pestis: Preserved folding energy drives fiber formation

Most gram-negative pathogens express fibrous adhesive virulence organelles that mediate targeting to the sites of infection. The F1 capsular antigen from the plague pathogen Yersinia pestis consists of linear fibers of a single subunit (Caf1) and serves as a prototype for nonpilus organelles assembled via the chaperone/usher pathway. Genetic data together with high-resolution X-ray structures corresponding to snapshots of the assembly process reveal the structural basis of fiber formation. Comparison of chaperone bound Caf1 subunit with the subunit in the fiber reveals a novel type of conformational change involving the entire hydrophobic core of the protein. The observed conformational change suggests that the chaperone traps a high-energy folding intermediate of Caf1. A model is proposed in which release of the subunit allows folding to be completed, driving fiber formation.

Escherichia coli isolates from extraintestinal organs of livestock animals harbour diverse virulence genes and belong to multiple genetic lineages

Escherichia coli, the most common cause of bacteraemia in humans in the UK, can also cause serious diseases in animals. However the population structure, virulence and antimicrobial resistance genes of those from extraintestinal organs of livestock animals are poorly characterised. The aims of this study were to investigate the diversity of these isolates from livestock animals and to understand if there was any correlation between the virulence and antimicrobial resistance genes and the genetic backbone of the bacteria and if these isolates were similar to those isolated from humans. Here 39 E. coli isolates from liver (n=31), spleen (n=5) and blood (n=3) of cattle (n=34), sheep (n=3), chicken (n=1) and pig (n=1) were assigned to 19 serogroups with O8 being the most common (n=7), followed by O101, O20 (both n=3) and O153 (n=2). They belong to 29 multi-locus sequence types, 20 clonal complexes with ST23 (n=7), ST10 (n=6), ST117 and ST155 (both n=3) being most common and were distributed among phylogenetic group A (n=16), B1 (n=12), B2 (n=2) and D (n=9). The pattern of a subset of putative virulence genes was different in almost all isolates. No correlation between serogroups, animal hosts, MLST types, virulence and antimicrobial resistance genes was identified. The distributions of clonal complexes and virulence genes were similar to other extraintestinal or commensal E. coli from humans and other animals, suggesting a zoonotic potential. The diverse and various combinations of virulence genes implied that the infections were caused by different mechanisms and infection control will be challenging.