Ecology of marine turtles across the eastern Mediterranean and the Middle East

Marine turtles are wide-ranging, long-lived, iteroparous species of conservation concern. From indirect threats, such as development at their breeding grounds and negative fisheries interactions, to direct take of eggs meat and shells, they are impacted at all stages of their life-cycle by the activities of Man. A better understanding of their reproductive and spatial ecology together with knowledge of population status can inform conservation and management actions for their protection. This thesis presents a collection of chapters covering three species of marine turtle, from four countries in two regions where major knowledge gaps existed on marine turtle biology and ecology. In Oman we identify plasticity in adult loggerhead turtle (Caretta caretta) internesting behaviour combined with globally-atypical, predominantly oceanic habitat use and we raise concerns over potential bias derived from temporally-restricted tracking studies. Conversely, we show that adult female individuals of the principally oceanic olive ridley turtle (Lepidochelys olivacea) remain in neritic waters outside of the breeding season, with some local turtles unusually utilising the same location both during and after the breeding period. We also show that green turtles (Chelonia mydas) nesting on Masirah Island are long distance migrators, travelling 2000 km or more into the Red Sea. Together with our tracking data for the other species in Oman we highlight the threat that fisheries interaction, in a region with poor fisheries regulation, is likely to have on these populations. We describe the recent status of green turtle populations in Kuwait and Syria. In Kuwait nesting habitats have recently been halved through development of one of the two critical nesting areas and with the remaining nesting population estimated at no more than 5 females per year. For Syria, we describe the discovery of a regionally important nesting aggregation located south of Latakia city, with 30 individuals estimated nesting in 2004. Using satellite telemetry we identify potentially important foraging locations for individuals from both locations. Results from Syria further highlight the importance of neritic habitats off north Africa for adult turtles in the Mediterranean and results from Kuwait revealed the potential threat from the use of the unselective coastal fish traps locally known as a ‘hadra’. Lastly, in Greece we investigate the status of turtles in a neritic coastal habitat through a boat-based mark-recapture study. Combining flipper tagging, satellite telemetry and genetic research we verify that Amvrakikos Gulf hosts regionally important numbers of 3 loggerhead turtles (300 individuals identified from 67 days fieldwork) that establish distinct home ranges and maintain long-term associations to the area. A male-biased sex ratio was revealed in the area. These turtles are predominantly derived from local breeding stocks, especially from Zakynthos Island, and we hypothesise that a combination of environmental and biological factors specific to Zakynthos Island are the cause of this bias. The results presented here, generated from a range of techniques including field surveys, satellite telemetry and genetic analysis, contribute to our knowledge of the status of several under-reported or previously unknown sea turtle populations, including evidence of their spatial footprint, and demonstrate the utility in adopting a variety of methods to corroborate results on migrations and linkages at individual and population levels

A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads

Downstream analyses of short-reads from next-generation sequencing platforms are often preceded by a pre-processing step that removes uncalled and wrongly called bases. Standard approaches rely on their associated base quality scores to retain the read or a portion of it when the score is above a predefined threshold. It is difficult to differentiate sequencing error from biological variation without a reference using a quality score. The effects of quality score based trimming have not been systematically studied in de novo transcriptome assembly. Using RNA-Seq data produced from Illumina,we teased out the effects of quality score based filtering or trimming on de novo transcriptome reconstruction. We showed that assemblies produced from reads subjected to different quality score thresholds contain truncated and missing transfrags when compared to those from untrimmed reads. Our data supports the fact that de novo assembling of untrimmed data is challenging for de Bruijn graph assemblers. However, our results indicates that comparing the assemblies from untrimmed and trimmed read subsets can suggest appropriate filtering parameters and enables election of the optimum de novo transcriptome assembly in non-model organisms.South African Research Chair Initiative National Research Foundation of South Afric

Metabolic Analysis of Bovine Nucleus Pulposus Cells with Constant and Variable Glucose Supply

There is no standardized method for culture of intervertebral disc (IVD) cells when monitoring metabolic processes. We hypothesize that the metabolic rates of cells that are crucial to experiment designs depend on the cell culture method used. The glycolytic pathway and the tricarboxylic acid (TCA) cycle are the pathways through which metabolites are processed into energy for cellular functions in the form of ATP. Imbalances in these pathways are linked to degeneration of the IVD. Key metabolites monitored through this pathway include glucose, lactate, citrate, and non-essential amino acids. Changes in the presence of these metabolites may provide insight into cellular stress, disease, and metabolic demand from different cells. A fluidized bed bioreactor was used to control glucose concentration, allowing metabolic analysis of bovine nucleus pulposus cells. An increase in central metabolic pathways, such as glycolysis and the TCA cycle, was observed in the constant glucose cell culture compared to the standard cyclic feeding method

On Extremal k-Graphs Without Repeated Copies of 2-Intersecting Edges

The problem of determining extremal hypergraphs containing at most r isomorphic copies of some element of a given hypergraph family was first studied by Boros et al. in 2001. There are not many hypergraph families for which exact results are known concerning the size of the corresponding extremal hypergraphs, except for those equivalent to the classical Turan numbers. In this paper, we determine the size of extremal k-uniform hypergraphs containing at most one pair of 2-intersecting edges for k in {3,4}. We give a complete solution when k=3 and an almost complete solution (with eleven exceptions) when k=4.Comment: 17 pages, 5 figure

Optimization and Simulation of an Evolving Kidney Paired Donation (KPD) Program

The old concept of barter exchange has extended to the modern area of living-donor kidney transplantation, where one incompatible donor-candidate pair is matched to another pair with a complementary incompatibility, such that the donor from one pair gives an organ to a compatible candidate in the other pair and vice versa. Kidney paired donation (KPD) programs provide a unique and important platform for living incompatible donor-candidate pairs to exchange organs in order to achieve mutual benefit. We propose a novel approach to organizing kidney exchanges in an evolving KPD program with advantages, including (i) it allows for a more exible utility-based evaluation of potential kidney transplants; (ii) it takes into consideration stochastic features in managing a KPD program; and (iii) it exploits possible alternative exchanges when the originally planed allocation cannot be fully executed. Another primary contribution of this work is rooted in the development of a comprehensive microsimulation system for simulating and studying various aspects of an evolving KPD program. Various allocations can be obtained using integer programming (IP) techniques and microsimulation models can allow tracking of the evolving KPD over a series of match runs to evaluate different allocation strategies. Simulation studies are provided to illustrate the proposed method

Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map

Determining the position and order of contigs and scaffolds from a genome assembly within an organism’s genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies for DNA sequencing. We developed a strategy for whole genome single nucleotide polymorphism sequencing allowing the positioning of sequence contigs onto a linkage map using the bin mapping method. The strategy was tested on a draft genome of the fungal pathogen Venturia inaequalis, the causal agent of apple scab, and further validated using sequence contigs derived from the diploid plant genome Fragaria vesca. Using our novel method we were able to anchor 70% and 92% of sequences assemblies for V. inaequalis and F. vesca, respectively, to genetic linkage maps. We demonstrated the utility of this approach by accurately determining the bin map positions of the majority of the large sequence contigs from each genome sequence and validated our method by mapping single sequence repeat markers derived from sequence contigs on a full mapping population.Deciduous Fruit Producers Trust THRIP Program National Research Foundation Claude Harris Leon FoundationWeb of Scienc

El uso de marcadores de ADN mitocondrial en tortuga boba (Caretta caretta) (Testudines: Cheloniidae) nidificando en la bahía de Kyparissia, Grecia, confirma la unidad de Grecia oriental y la estructuración regional

Genetic markers have been widely used in marine turtles to assess population structuring and origin of individuals in common feeding grounds, which are key elements for understanding their ecology and for developing conservation strategies. However, these analyses are very sensitive to missing information, especially from abundant nesting sites. Kyparissia Bay (western Greece) hosts the second largest Mediterranean nesting aggregation of the loggerhead turtle (Caretta caretta), but the genetic profile of this nesting site has not, as yet, been described using the extended version of the historically used mitochondrial DNA (mtDNA) marker. This marker was genotyped for 36 individuals nesting at Kyparissia Bay and haplotype frequencies obtained were compared with published data from other Mediterranean nesting sites. The results confirmed the connection between Kyparissia and other western Greek nesting sites and the isolation of this western Greek group from other Mediterranean nesting areas. As a consequence of this isolation, this abundant group of nesting aggregations (almost 30% of the Mediterranean stock) is not likely to significantly contribute to the recovery of other declining Mediterranean units.El uso de marcadores genéticos ha sido muy extendido en tortugas marinas con el fin de determinar la estructura poblacional y el origen de individuos en zonas comunes de alimentación; elementos clave para entender su ecología y desarrollar estrategias efectivas de conservación. Sin embargo, este tipo de análisis es muy sensible a la falta de información de ciertas zonas de nidificación, especialmente de aquellas muy abundantes. El perfil genético de las tortugas nidificantes de la bahía de Kyparissia (Grecia occidental) todavía no ha sido descrito usando la versión extendida del marcador mitocondrial (mtDNA) usado históricamente en esta especie, a pesar de ser la segunda zona de nidificación más abundante de todo el Mediterráneo. Con el fin de cubrir este vacío de información, se secuenciaron 36 individuos nidificantes de la bahía de Kyparissia y se compararon las frecuencias de haplotipos obtenidas con datos publicados de otras zonas de nidificación del Mediterráneo. Los resultados confirmaron la conexión entre Kyparissia y otras zonas de nidificación de Grecia así como el aislamiento de este grupo de Grecia occidental con el resto de zonas de nidificación del Mediterráneo. Como consecuencia de este aislamiento, todo parece indicar que este abundante grupo de zonas de nidificación (casi el 30% de la producción del Mediterráneo) no podría contribuir de forma significativa a la recuperación del número de hembras nidificantes en otras poblaciones en declive del Mediterráneo

Decision making in kidney paired donation programs with altruistic donors

In recent years, kidney paired donation has been extended to include living non-directed or altruistic donors, in which an altruistic donor donates to the candidate of an incompatible donor candidate pair with the understanding that the donor in that pair will further donate to the candidate of a second pair, and so on; such a process continues and thus forms an altruistic donor-initiated chain. In this paper, we propose a novel strategy to sequentially allocate the altruistic donor (or bridge donor) so as to maximize the expected utility; analogous to the way a computer plays chess, the idea is to evaluate different allocations for each altruistic donor (or bridge donor) by looking several moves ahead in a derived look-ahead search tree. Simulation studies are provided to illustrate and evaluate our proposed method