Birds of a feather flock together:a dataset for Clock and Adcyap1 genes from migration genetics studies

Birds in seasonal habitats rely on intricate strategies for optimal timing of migrations. This is governed by environmental cues, including photoperiod. Genetic factors affecting intrinsic timekeeping mechanisms, such as circadian clock genes, have been explored, yielding inconsistent findings with potential lineage-dependency. To clarify this evidence, a systematic review and phylogenetic reanalysis was done. This descriptor outlines the methodology for sourcing, screening, and processing relevant literature and data. PRISMA guidelines were followed, ultimately including 66 studies, with 34 focusing on candidate genes at the genotype-phenotype interface. Studies were clustered using bibliographic coupling and citation network analysis, alongside scientometric analyses by publication year and location. Data was retrieved for allele data from databases, article supplements, and direct author communications. The dataset, version 1.0.2, encompasses data from 52 species, with 46 species for the Clock gene and 43 for the Adcyap1 gene. This dataset, featuring data from over 8000 birds, constitutes the most extensive cross-species collection for these candidate genes, used in studies investigating gene polymorphisms and seasonal bird migration.</p

Molecular screening for specific causative mutations in the South African malignant hyperthermia population

Thesis (M.Sc. (Biochemistry))--North-West University, Potchefstroom Campus, 2005Malignant hyperthermia (MH) is an autosomal dominant, pharmacogenetic disorder. MH susceptible (MHS) patients appear clinically normal, but may present with a hypermetabolic crisis and muscle contracture when exposed to triggering substances which elicit excessive release of calcium ions from the sarcoplasmic reticulum. The underlying cause of MH has emerged as biochemical abnormalities that occur in skeletal muscle. Presymptomatic diagnosis of MH susceptibility is currently made via the in vitro contracture test. The phenotypically similar porcine MH model led to the identification of the chromosomal region bearing the underlying defect. The first human MHS locus, MHS-1, has been mapped to chromosome 19q13. MH is mainly due to mutations in the skeletal muscle ryanodine receptor gene (RYRI). To date the RYRI gene has been associated with an MH phenotype in approximately 50% of MH families. However, the disorder is genetically heterogeneous, as six other loci have to date been associated with MHS. The aim of the molecular investigation presented here was to determine if 24 recently reported causative mutations in the RYRI gene are present in any of the 45 South African MHS probands investigated. Furthermore, eight mutations of the RYRI gene and the Arg1086His mutation of the CACNAIS that have already been analysed in previous phases of the research programme were investigated. One alteration, Thr482611e was detected for the first time in a single South African MH family, contributing to the description of the aetiology of MHS in South Africa. None of the remaining alterations were detected in any South African MH probands analysed. The absence of the majority of reported mutations in all probands included in this study could indicate that the mutations either represent family-specific alterations or could be attributed to the fact that these mutations do not play a role in MHS in the South African population.Master

Screening of the RYR1 gene in malignant hyperthermia probands from South Africa indicates towards a novel epigenetic eatiology in this population

Thesis (Ph.D. (Biochemistry))--North-West University, Potchefstroom Campus, 2008.Malignant hyperthermia (MH) is an autosomal dominant, potentially lethal pharmacogenetic disorder of skeletal muscle, which is elicited by exposure to volatile anaesthetics and depolarising muscle relaxants. Susceptible individuals appear clinically normal, but may present with a hypermetabolic crisis and muscle contracture when exposed to triggering substances that elicit excessive release of calcium ions from the sarcoplasmic reticulum. Diagnosis of MH susceptibility is currently made via the in vitro contracture test. Genetically, in more than 50% of the affected families, MH occurs due to alterations in the skeletal muscle ryanodine receptor gene (RYR1) on chromosome 19q13.1. However, the disorder is genetically heterogeneous, as six other loci have to date been associated with MH susceptibility (MHS). Thus far, molecular tests have focused on three mutation hotspots of the RYR1 gene, which refer to regions that are more frequently mutated. Screening the entire RYR1 has led to a higher detection rate in a variety of populations. In this study the entire coding region of the RYR1 gene was screened via sequencing for novel or reported alterations for the first time in 15 South African probands. Eight different RYR1 alterations were observed in seven MHS South African probands, six of which were previously reported and two of which were novel. Compound heterozygous alterations and alterations outside the mutation hotspots were detected. Screening of the entire coding region of the RYR1 gene is crucial for genetic investigations into MHS. It was postulated that MH in the South African population is due to multifactorial inheritance in which a network of several genetic, environmental and epigenetic factors interact and cumulatively result in the development of the MH phenotype. Data generated in this study highlight the complexity of this disorder, further supporting a novel epigenetic aetiology for MH in the South African population.Doctora

Comparison of four TLR polymorphisms between 10 <i>in situ</i> African penguins and other birds species.

<p>Comparison of four TLR polymorphisms between 10 <i>in situ</i> African penguins and other birds species.</p

Map indicating the respective sampling localities of this study of <i>in situ</i> African penguins in Southern Africa.

<p>Map indicating the respective sampling localities of this study of <i>in situ</i> African penguins in Southern Africa.</p

Schematic representation of the structure of the targeted TLR genes (adapted from Temperley <i>et al</i>., 2008; Alcaide and Edwards, 2011).

<p>Exons are represented by boxes. Arrow heads denote the position of the primers used in this study. Coloured areas designate coding regions, whereas white areas are non-coding regions. The gene regions that code for conserved domains of the protein are represented by different colours [Green, leucine-rich repeat (LRR) domains; dark blue, C-terminal LRR domains; light blue, transmembrane region; teal, cytoplasmic Toll/interleukin I resistance (TIR) domain].</p

Polymorphisms in African penguin TLRs.

<p>Synonymous SNPs indicated outside of parentheses and non-synonymous SNPs in the coding regions indicated in parentheses.</p

Observed (H_o), expected heterozygosity (H_e) and unbiased heterozygosity (H_z) estimates and polymorphism statistics at four TLR genotyped in African penguins.

<p>Observed (H_o), expected heterozygosity (H_e) and unbiased heterozygosity (H_z) estimates and polymorphism statistics at four TLR genotyped in African penguins.</p

Combined neighbour-joining phylogenetic analysis of the <i>TLR1LA</i>, <i>TLR1LB</i>, <i>TLR2</i> and <i>TLR5</i> genes of the African penguin (<i>Spheniscus demersus</i>).

<p>Supplementary sequences from other bird species are specified. Bootstrap values are indicated at each branch point.</p