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

Orientation Effects in the Development of Linear Object Tracking in Early Infancy

Infants' oculomotor tracking develops rapidly but is poorer when there are horizontal and vertical movement components. Additionally, persistence of objects moving through occlusion emerges at 4 months but initially is absent for objects moving obliquely. In two experiments we recorded eye movements of 32 4-month-old and 32 6-month-old infants (mainly Caucasian-White) tracking horizontal, vertical, and oblique trajectories. Infants tracked oblique trajectories less accurately, but six-month-olds tracked more accurately, such that they tracked oblique trajectories as accurately as 4-month-olds tracked horizontal and vertical trajectories. Similar results emerged when the object was temporarily occluded. Thus, 4-month-olds’ tracking of oblique trajectories may be insufficient to support object persistence, whereas 6-month-olds may track sufficiently accurately to perceive object persistence for all trajectory orientations

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