Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders

Merino sheep are a breed of choice across the world, popularly kept for their wool and mutton value. They are often reared as a pure breed or used in crossbreeding and are a common component in synthetic breed development. This study evaluated genetic diversity, population structure, and breed divergence in 279 animals of Merino and Merino-based sheep breeds in South Africa using the Illumina Ovine SNP 50K BeadChip. The sheep breeds analysed included the three Merino-derived breeds of Dohne Merino (n = 50); Meatmaster (n = 47); and Afrino (n = 52) and five presumed ancestral populations of Merinos (Merino (n = 46); South African Merino (n = 10); and South African Mutton Merino (n = 8)); and the non-Merino founding breeds of Damara (n = 20); Ronderib Afrikaner (n = 17); and Nguni (n = 29). Highest genetic diversity values were observed in the Dohne Merino (DM), with H _o = 0.39 ± 0.01, followed by the Meatmaster and South African Merino (SAM), with H _o = 0.37 ± 0.03. The level of inbreeding ranged from 0.0 ± 0.02 (DM) to 0.27 ± 0.05 (Nguni). Analysis of molecular variance (AMOVA) showed high within-population variance (>80%) across all population categories. The first principal component (PC1) separated the Merino, South African Mutton Merino (SAMM), DM, and Afrino (AFR) from the Meatmaster, Damara, Nguni, and Ronderib Afrikaner (RDA). PC2 aligned each Merino-derived breed with its presumed ancestors and separated the SAMM from the Merino and SAM. The iHS analysis yielded selection sweeps across the AFR (12 sweeps), Meatmaster (four sweeps), and DM (29 sweeps). Hair/wool trait genes such as FGF12; metabolic genes of ICA1, NXPH1, and GPR171; and immune response genes of IL22, IL26, IFNAR1, and IL10RB were reported. Other genes include HMGA, which was observed as selection signatures in other populations; WNT5A, important in the development of the skeleton and mammary glands; ANTXR2, associated with adaptation to variation in climatic conditions; and BMP2, which has been reported as strongly selected in both fat-tailed and thin-tailed sheep. The DM vs. SAMM shared all six sweep regions on chromosomes 1, 10, and 11 with AFR vs. SAMM. Genes such as FGF12 on OAR 1:191.3-194.7 Mb and MAP2K4 on OAR 11:28.6-31.3 Mb were observed. The selection sweep on chromosome 10 region 28.6-30.3 Mb harbouring the RXFP2 for polledness was shared between the DM vs. Merino, the Meatmaster vs. Merino, and the Meatmaster vs. Nguni. The DM vs. Merino and the Meatmaster vs. Merino also shared an Rsb-based selection sweep on chromosome 1 region 268.5-269.9 Mb associated with the Calpain gene, CAPN7. The study demonstrated some genetic similarities between the Merino and Merino-derived breeds emanating from common founding populations and some divergence driven by breed-specific selection goals. Overall, information regarding the evolution of these composite breeds from their founding population will guide future breed improvement programs and management and conservation efforts.

Factor XIII-A Val34Leu and Tyr204Phe variants influence clot kinetics in a cohort of South African type 2 diabetes mellitus patients

Factor XIII, a transglutaminase that plays a crucial role in clot formation, consists of subunits A and B. Single nucleotide polymorphisms in Factor XIII-A have been linked to thrombotic risk. In Type 2 Diabetes mellitus (T2DM), a hypercoagulable state is thought to contribute to the high mortality rate associated with thrombotic diseases. Due to the lack of prevalence data of FXIII-A single nucleotide polymorphisms (SNPs) in T2DM in a South African cohort, this study assessed the prevalence FXIII-A Val34Leu (rs5985) and Tyr204Phe (rs3024477) SNP's and the effect on clot kinetics in T2DM.

MATERIALS AND METHODS

A cohort of T2DM patients (n = 100) and race, age and gender matched healthy controls (n = 101) were recruited following ethical approval. Thromboelastography® (TEG®) was used to assess the viscoelastic properties in platelet poor plasma (PPP) in controls (n = 91) and T2DM patients (n = 91) younger than 50 years old. Genomic DNA was isolated from whole blood using the Quick-DNA™ Miniprep Plus Kit and PCR-RFLP was used to genotype each sample for FXIII-A rs5985 and rs3024477 SNPs.

RESULTS

TEG® analyses indicated a longer R-time (p < 0.0001) and higher TMRTG (p < 0.0001) in PPP of T2DM patients. Control and T2DM genotype distribution conformed to Hardy-Weinberg equilibrium (p > 0.05). There was a higher prevalence of the wildtype genotype of FXIII-A Tyr204Phe (rs3024477) SNP in T2DM (OR = 0.23, 95% CI = 0.12-0.42, p < 0.0001). The 204Phe variant was more frequent in the Caucasians (OR = 0.39, 95% CI = 0.05-0.33, p < 0.0001). The presence of the 204Phe variant in T2DM affected TMRTG (p = 0.0207). The variant affected R time (p = 0.0432) and TMRTG (p = 0.0209 and p = 0.0207) in controls and T2DM, respectively.

CONCLUSION

An inverse association with T2DM and FXIII-A Tyr204Phe was found. A hypo coagulable PPP clot profile was observed in T2DM. A shorter reaction time was observed and but faster rate at which the clot reached maximum strength in both controls and T2DM in the presence of the 204Phe variant.

Relationship between population genomic structure and growth profiles of South African goats under different production systems

Goats play a major role in poor marginalized communities of South Africa for food security and socio-economic purposes. Majority of the goats are raised in villages with poor infrastructure and resources, therefore facing challenges that affect growth performance which leads to low mature weights. Investigating growth profiles will shed light on growth performances and will aid in goat improvement and selection. This study investigated the growth profiles and genomic structure of SA indigenous breeds raised in different production systems to unravel the genetic potential of indigenous goat populations. Live weights and morphological body measurements were collected from a total of 83 kids representing the commercial meat-producing SA Boer (n = 14); the indigenous veld goats (IVG) of NC Skilder (n = 14), Mbuzi (n = 13), and Xhosa lob (n = 14) raised under intensive systems; and nondescript village goat populations (n = 14) raised in intensive and others (n = 14) raised in extensive production systems. The remaining 72 of 83 phenotyped goats were genotyped using the Illumina Caprine SNP50K BeadChip. The SA Boer had a higher weight (28.96 ± 0.30 kg) gain as compared to other populations. The Mbuzi population was the smallest (14.83 ± 0.33 kg), while the village goats raised in Pella Village were relatively smaller (17.55 ± 0.37 kg) than those raised on the research farm (19.55 ± 0.36 kg). The study concluded that both genetics and management systems can lead to improved growth performance in goat production. The outputs of this study can be used to identify suitable breeds and potential genotypes for optimal growth and establish optimal goat management systems suitable for communal farmers for improved productivity.

The stabilizing effect of an oligomeric proanthocyanidin on red blood cell membrane structure of poorly controlled Type II diabetes

Type II diabetes (T2D) is a pandemic characterized by pathological circulating inflammatory markers, high-glucose levels and oxidative stress. The hematological system is especially vulnerable to these aberrant circulating molecules, and erythrocytes (RBCs) show aberrant rheology properties, owing to the direct contact with these molecules. Pathological levels of circulating inflammatory markers in T2D therefore have a direct effect on the molecular and cellular structure of RBCs. Previous research has suggested that antioxidants may reduce oxidative stress that results from the pathological inflammatory markers. Particularly, polyphenol antioxidants like oligomeric proanthocyanidins (OPCs) may act as a hydroxyl mopping agent, and may have a positive effect on the deformability and membrane protein structure of RBCs from T2D. In this paper, we look at the effect of one such agent, Pinus massoniana bark extract (standardized to 95% oligomeric proanthicyanidins), on the RBC membrane structures and RBC shape changes of T2D, after laboratory exposure at physiological levels. Our methods of choice were atomic force microscopy and scanning electron microscopy to study RBC elasticity and ultrastructure. Results showed that in our hands, this OPC could change both the eryptotic nature of the RBCs, as viewed with scanning electron microscopy, as well as the elasticity. We found a significant difference in variation between the elasticity measurement values between the RBCs before and after OPC exposure (P-value <0.0001). In conclusion, the data from both these techniques therefore suggest that OPC usage might contribute to the improvement of RBC functioning.

Providing clinicians with information on laboratory test costs leads to reduction in hospital expenditure

OBJECTIVES

We aimed to ascertain the efficacy of an intervention in which laboratory test costs were provided to clinicians as a pocket-sized brochure, in reducing laboratory test costs over a 4-month period.

METHODS

This was a non-randomised intervention study in the Internal Medicine wards at Steve Biko Academic Hospital, Pretoria, in which the intervention was laboratory test costs provided to clinicians as a pocket-sized brochure. The intervention period was the winter months of May - August 2008 and the pre-intervention period was the same months of the preceding year. In the two 4-month periods (2007 and 2008), the number of days in hospital and the laboratory tests ordered were computed for each patient admitted. For the intervention and control groups, pre- and post-intervention cost and days in hospital were estimated.

RESULTS

The mean cost per patient admitted in the intervention group decreased from R2 864.09 to R2 097.47 - a 27% reduction. The mean cost per day in the intervention group as a whole also decreased, from R442.90 to R284.14 - a 36% reduction.

CONCLUSION

Displaying the charges for diagnostic tests on the laboratory request form may significantly reduce both the number and cost of tests ordered, and by doing so bring about considerable in-hospital cost savings.

Right leg swelling as primary presentation of metastatic Merkel cell carcinoma

Merkel cell carcinoma (MCC) is a rare malignant cutaneous neuroendocrine tumour with an aggressive behaviour and frequent regional lymph node and distant metastases. It mostly occurs in old patients and the commonest sites are the skin of the head, neck and the extremities. Typically, the primary tumour presents as a fast-growing, painless, reddish nodule with an iceberg-like effect, broadening in the depth. Although the pathogenesis of MCC remains largely unknown, ultraviolet radiation and immunosuppression are likely to play a significant pathogenetic role. The authors describe an unusual case of MCC clinically presenting as lymphedema on the right leg due to an inguinal lymphonodal metastasis. Although extensive investigations were performed the authors were unable to discover the cutaneous primary tumor. The authors examine the etiopathogenesis and hypothesis of this rare tumour and describe the clinical differential diagnosis. They suggest that clinical features together with imaging studies and morphological and immuno-histochemical findings are important for the correct diagnosis.

The positive predictive value of myocardial perfusion imaging in screening patients for suspected coronary artery disease

BACKGROUND

In patients with known or suspected coronary artery disease, diagnosis and risk stratification can be aided by non-invasive tests for myocardial ischaemia. The main indications for the use of radionuclide perfusion imaging (sestamibi) rather than exercise electrocardiography include complete left bundle branch block, inconclusive stress electrocardiography and an inability to exercise. The published data on myocardial perfusion imaging is limited to eight studies of only 628 patients with widely varying ranges of sensitivities and specificities and the major problem being the bias created when patients with positive test results are referred far more frequently for coronary angiography than those with negative results. Furthermore, certain categories of patients are postulated to have a high number of false positives, especially obese patients and women, but this hypothesis has not been tested.

METHODS AND RESULTS

A retrospective descriptional study on patients with positive sestamibi scans, who had coronary angiography within six months of each other, was performed. The study population consisted of 132 patients, 53.8% of whom were male and 44.7% had a body mass index of less than 28. The overall positive predictive value of the sestamibi scan in predicting significant coronary angiographic stenosis was 63.6%. This value increased significantly to 80.3% in males (p = 0.000). The positive predictive value did not differ in the different age categories, nor did it change with the different indications for sestamibi scanning.

CONCLUSIONS

The sestamibi scan remains a useful screening test for coronary artery disease in patients who are exercise intolerant or those with inconclusive stress electrocardiography. The test is highly predictive in males rather than females.

Unsuspected glucose abnormalities in patients with coronary artery disease

OBJECTIVES

To compare the ability of fasting glucose, glycosylated haemoglobin ( HbA(1c)), the American Diabetic Association (ADA) score and measures of the metabolic syndrome (waist circumference, high-density lipoprotein (HDL), and triglycerides) in predicting an initial diagnosis of diabetes mellitus or abnormal glucose tolerance based on the World Health Organization (WHO) criteria.

DESIGN

A cross-sectional, diagnostic study was undertaken of 120 patients admitted to the cardiology wards of Pretoria Academic Hospital for elective coronary angiographic studies.

MAIN OUTCOME MEASURES

All subjects underwent a modified glucose tolerance test whereby fasting and 2-hour post glucose (75 g) plasma glucose levels were measured. Using the revised WHO criteria, the overall incidence of diabetes was found to be 11.7% (95% confidence interval (CI): 6.5 - 19) and the overall incidence of abnormal glucose tolerance was 46% (CI: 37 - 55).

RESULTS

In univariate analysis for the diagnosis of diabetes, HbA(1c) (p < 0.05) yielded the largest area (0.76) under the receiver operating characteristic (ROC) curve, with a sensitivity of 21%, specificity of 99%, positive predictive value (PPV) of 75% and negative predictive value (NPV) of 91%. For the prediction of abnormal glucose tolerance, applying multivariate analysis using a logistic regression model, the combination of age, ethnic group, serum HDL, serum triglycerides and HbA(1c) yielded an area under the ROC curve of 0.79, sensitivity of 66%, specificity of 80%, PPV of 76% and a NPV of 71%.

CONCLUSION

Most subjects with diabetes mellitus (9 of 14) would not have been detected if a 2-hour oral glucose tolerance test had not been done. Addition of either HbA(1c) or lipid parameters to the model of age and ethnic group were similar in predicting abnormal glucose tolerance.

Self-detected cutaneous melanomas in Italian patients

Self-detection of suspicious pigmented skin lesion combined with rapid referral to dermatologic centres is the key strategy in the fight against melanoma. The investigation of factors associated with pattern of detection of melanoma (self- vs. nonself-detection) may be useful to refine educational strategies for the future. We investigated the frequency of melanoma self-detection in a Mediterranean population at intermediate melanoma risk. A multicentric survey identified 816 consecutive cases of cutaneous melanoma in the period January to December 2001 in 11 Italian clinical centres belonging to the Italian Multidisciplinary Group on Melanoma. All patients filled a standardized questionnaire and were clinically examined by expert dermatologists. Self-detected melanomas were 40.6%, while the remaining lesions were detected by a dermatologist (18.5%), the family physician (15.2%), other specialists (5%), the spouse (12.5%), a friend or someone else (8.2%). Variables associated with self-detected melanomas were female sex, young age, absence of atypical nevi, knowledge of the ABCD rule, habit of performing skin self-examination. Self-detected melanomas did not differ from nonself-detected tumours in term of lesion thickness; however, patients with self-detected melanomas waited a longer period before having a diagnostic confirmation (patient's delay) (> 3 months: odds ratio, 3.89; 95% confidence interval, 2.74-5.53). In order to reduce the patients' delays, educational messages should adequately stress the need for a prompt referral to a physician once a suspicious pigmented lesion is self-detected.