Ten years of barcoding at the African Centre for DNA Barcoding.

The African Centre for DNA Barcoding (ACDB) was established in 2005 as part of a global initiative to accurately and rapidly survey biodiversity using short DNA sequences. The mitochondrial cytochrome c oxidase 1 gene (CO1) was rapidly adopted as the de facto barcode for animals. Following the evaluation of several candidate loci for plants, the Plant Working Group of the Consortium for the Barcoding of Life in 2009 recommended that two plastid genes, rbcLa and matK, be adopted as core DNA barcodes for terrestrial plants. To date, numerous studies continue to test the discriminatory power of these markers across various plant lineages. Over the past decade, we at the ACDB have used these core DNA barcodes to generate a barcode library for southern Africa. To date, the ACDB has contributed more than 21 000 plant barcodes and over 3000 CO1 barcodes for animals to the Barcode of Life Database (BOLD). Building upon this effort, we at the ACDB have addressed questions related to community assembly, biogeography, phylogenetic diversification, and invasion biology. Collectively, our work demonstrates the diverse applications of DNA barcoding in ecology, systematics, evolutionary biology, and conservation.

Exposing the illegal trade in cycad species (Cycadophyta: Encephalartos) at two traditional medicine markets in South Africa using DNA barcoding.

Species in the cycad genus Encephalartos are listed in CITES Appendix I and as Threatened or Protected Species in terms of South Africa's National Environmental Management: Biodiversity Act (NEM:BA) of 2004. Despite regulations, illegal plant harvesting for medicinal trade has continued in South Africa and resulted in declines in cycad populations and even complete loss of sub-populations. Encephalartos is traded at traditional medicine markets in South Africa in the form of bark strips and stem sections; thus, determining the species traded presents a major challenge due to a lack of characteristic plant parts. Here, a case study is presented on the use of DNA barcoding to identify cycads sold at the Faraday and Warwick traditional medicine markets in Johannesburg and Durban, respectively. Market samples were sequenced for the core DNA barcodes (rbcLa and matK) as well as two additional regions: nrITS and trnH-psbA. The barcoding database for cycads at the University of Johannesburg was utilized to assign query samples to known species. Three approaches were followed: tree-based, similarity-based, and character-based (BRONX) methods. Market samples identified were Encephalartos ferox (Near Threatened), Encephalartos lebomboensis (Endangered), Encephalartos natalensis (Near Threatened), Encephalartos senticosus (Vulnerable), and Encephalartos villosus (Least Concern). Results from this study are crucial for making appropriate assessments and decisions on how to manage these markets.

Isozyme and allozyme markers distinguishing two morphologically similar, medically important Mastomys species (Rodentia: Muridae).

BACKGROUND: Two common southern African mice species, Mastomys coucha and M. natalensis, are widely distributed throughout the subregion and overlap in many areas. They also share a high degree of morphological similarity, making them impossible to distinguish in the field at present. These multimammate mice are documented carriers of serious disease vectors causing Lassa fever, plague and encephalomyocarditis, which coupled to their cohabitation with humans in many areas, could pose a significant health risk. A preliminary study reported the presence of isozyme markers at three loci (GPI-2, PT-2, -3) in one population each of M. coucha and M. natalensis. Two additional populations (from the Vaal Dam and Richards Bay) were sampled to determine the reliability of these markers, and to seek additional genetic markers. RESULTS: Fifteen proteins or enzymes provided interpretable results at a total of 39 loci. Additional fixed allele differences between the species were detected at AAT-1, ADH, EST-1, PGD-1, Hb-1 and -2. Average heterozygosities for M. coucha and M. natalensis were calculated as 0.018 and 0.032 respectively, with a mean genetic distance between the species of 0.26. CONCLUSIONS: The confirmation of the isozyme and the detection of the additional allozyme markers are important contributions to the identification of these two medical and agricultural pest species.

Persistent organochlorine pesticides detected in blood and tissue samples of vultures from different localities in South Africa.

Gas chromatography was used to establish the presence of quantifiable residues of 14 persistent chlorinated hydrocarbon pollutants in whole blood, clotted blood, heart, kidney, liver and muscle samples obtained from individual African whitebacked (Pseudogyps africanus), Cape griffon (Gyps coprotheres) and Lappetfaced (Torgos tracheliotos) vultures from different localities in South Africa. The levels of pesticides measured in whole blood samples of live specimens were compared between nestlings from two natural breeding colonies, adults from a wildlife area and birds held in captivity. Statistically significant (P<0.05) differences between populations were detected in geometric means calculated for gamma-BHC (lindane), alpha(cis)-chlordane and alpha-endosulfan. Five of the organochlorine contaminants displayed significant variations between concentrations detected in the clotted blood, organs and muscles excised from vulture carcasses. This includes residues of gamma-BHC, alpha-chlordane, dieldrin, beta-endosulfan and heptachlor epoxide. Values of the respective biocides measured in vulture samples were generally low in comparison to results documented for a number of avian species. Although no threat is posed by any of the organochloride pesticides, continual monitoring of especially breeding colonies is recommended. Furthermore, the suitability of African whitebacked vulture nestlings as basic bioindicators is highly advocated.

A review of the use of allozyme electrophoresis in plant systematics.

The role of electrophoretic data is discussed as it applies to plant taxonomy and systematic studies. Nei's (Am. Nat. 106 (1972) 283-292; Genetics 89 (1978) 583-590) genetic distances calculated for a large number of populations, species and genera were taken from published data. The relation between Nei's genetic identity measures and taxonomic rank (populations, species and genera) are shown graphically. The graphs obtained in this way (from 3021 pairs of plant taxa) differ substantially from previous graphs published by Thorpe (Ann. Rev. Ecol. Syst. 13 (1982) 139-168; in: G.S. Oxford, D. Rollinson (Eds.), Protein Polymorphism: Adaptive and Taxonomic Significance, Academic Press, London, 1983, pp. 131-152) and Thorpe and Solé-Cava (Zool. Scripta 23 (1994) 3-18). These authors suggested that the divergence between the different taxonomic ranks is roughly similar across a wide range of taxa. The latter was based on values for 2664 (Thorpe, 1982) and 8060 (Thorpe, 1983) pairs of animal and plant taxa, but the plant data contributed little to the total. For any given taxonomic rank, we found that plants are genetically more closely related than animals (possibly with the exception of birds). This result is important because the empirical relationships of genetic distance measures, to different levels of taxonomic separation, is often used for distinguishing and identifying cryptic or sibling species where conventional methods are unable to resolve systematic problems.

Allozyme variation in four populations of African whitebacked vultures (Gyps africanus) and phylogenetic relationships between four vulture species from southern Africa.

Genetic variation detected by protein electrophoresis at 41 presumptive gene loci was assayed in four populations of Gyps africanus and compared to values previously obtained for Gyps coprotheres. Values calculated for percentage of polymorphic loci (P=34.15%, 0.99 criterion) and average heterozygosity (&Hmacr;=0.108, +/-0.032) in G. africanus, confirm low levels of genetic variation as reported for G. coprotheres. Allele frequency data, assessed at 19 loci, were obtained to evaluate genetic differentiation among four vulture species. Six (31.58%) of the 19 shared loci were polymorphic. Values of 1.26 (+/-0.1), 26.32% and 0.076 (+/-0.047) for G. africanus, 1.21 (+/-0.1), 21.05% and 0.097 (+/-0.045) for Torgos tracheliotus, 1.11 (+/-0.7), 21.05% and 0.053 (+/-0.053) for Neophron percnopterus and 1.05 (+/-0.5), 5.26% and 0.044 (+/-0.047) for G. coprotheres were obtained for the mean number of alleles per locus, P and &Hmacr;, respectively. An average between-population fixation index (F(ST)) value of 0.322 was obtained, which is indicative of significant (P<0.01) differentiation between the four accipitrid species studied. Considerable concordance was obtained between dendograms produced from different analyses, pointing to the distinctiveness of N. percnopterus, which has evolved along a separate lineage as G. africanus, G. coprotheres and T. tracheliotus. Along the latter lineage G. africanus is clustered together with G. coprotheres which is consistent with the morphological similarities of these species.

Allozyme and DNA sequence comparisons of nine species of Encephalartos (Zamiaceae).

Phylogenetic relationships between Encephalartos altensteinii Lehmann, E. arenarius R.A. Dyer, E. horridus (Jacquin) Lehmann, E. latifrons Lehmann, E. lehmannii Lehmann, E. longifolius (Jacquin) Lehmann, E. princeps R.A. Dyer and E. trispinosus (Hooker) R.A. Dyer were studied, using E. ferox Bertoloni f. as outgroup. Three continuous and one discontinuous buffer systems were used and gene products of 14 enzyme coding loci were examined by horizontal starch gel-electrophoresis. Genetic variation was studied in a cultivated population of E. lehmannii and the average heterozygosity value for this population is 13.5%, which falls within the range reported for other cycad species. Fixed allele differences between the species studied was not found at any of the loci studied, which suggest that these species are closely related. DNA sequence analysis of rbcL and ITS 1 & 2 genes (1428 and 895 basepairs, respectively) confirmed the close genetic relationships between these taxa. According to ITS and rbcL sequences E. altensteinii and E. princeps are sibling taxa which form a sister group to E. arenarius, E. horridus, E. latifrons, E. lehmannii, E. longifolius, and E. trispinosus. The genetic distances between both groups were 0.12-0.47% for ITS and 0.08-0.16% for rbcL DNA. The results indicate recent (probably pleistocenic) speciation for this group of cycads, and the relationships are discussed with reference to affinities based on morphology and distribution.

Biochemical genetic markers to identify two morphologically similar South African Mastomys species (Rodentia: Muridae).

The two common southern African mice species (Mastomys coucha and M. natalensis) are morphologically almost identical, making field identification impossible at present. Specimens from two localities were collected and tissue and blood samples taken. The habitat type of each locality was studied, and a distribution map compiled. A definite correlation between biome-type and species range was found to be present. Three isozyme markers were identified: glucose phosphate isomerase in liver, and two general (non-specific) protein coding loci in muscle. In addition, we also identified species characteristic haemoglobin components in both species. This is the first study to report genetic variation within, and differentiation between these species. Our results are of medical importance because Mastomys coucha carries bubonic plague and M. natalensis carries Lassa Fever.

Effects of antibiotics on the endothelium of fresh and cryopreserved canine saphenous veins.

To determine if antibiotic solutions for potential use in antimicrobial treatment of tissues were detrimental to cell viability, canine saphenous veins were exposed to three different antibiotic solutions at 37 degrees C for 12 h. Viability was determined by tissue culture, utilizing a limiting dilution assay. The antibiotic series included two formulations currently used for the preservation of heart valves and a new formulation containing imipenem, a broad spectrum beta-lactam. Currently used antibiotic regimes and imipenem with gentamicin resulted in a decrease of 30 to 50% of the viable endothelial cells within 12 h. Exposure of the saphenous veins to imipenem or imipenem combined with amphotericin B had no adverse effects on the viability of the endothelial cells with 12 h exposure. However, veins exposed to amphotericin B were more susceptible to subsequent damage during freezing and thawing than veins frozen after incubation with either imipenem alone or imipenem combined with flucytosine. These studies indicate that imipenem combined with flucytosine is suitable for use with vein grafts.

Intellectual capacity of subjects exposed to methimazole or propylthiouracil in utero.

Antithyroid drugs, considered the treatment of choice for hyperthyroidism during pregnancy, may have an adverse effect on intellectual development of the offspring. We examined the intellectual capacity of 31 subjects aged 4-23 years, born to women with Graves disease who received antithyroid drugs throughout pregnancy. Methimazole 40-140 mg/week (n = 15) or propylthiouracil 250-1400 mg/week (n = 16) was given. I.Q. was assessed using the Wechsler test appropriate for age. Twenty-five unexposed siblings served as controls. The exposed and unexposed groups did not differ with respect to the total I.Q. Both groups scored equally in verbal and performance skills and in each of six main subcategories of the tests. There was no difference between exposure to methimazole and propylthiouracil or between the higher (greater than 40 mg/week and greater than 600 mg/week, respectively) and lower dosages. All children were euthyroid at birth and none had goitre. We conclude that exposure to methimazole or propylthiouracil during pregnancy in doses sufficient to control maternal hyperthyroidism does not pose any threat to intellectual capacity of the offspring.

The determination of the central static visual acuity.

In identical experimental situations we tested 22 adults with our proposed Landolt C wall-chart and the so-called TNO Landolt-C chart. Contrary to theoretical expectations, it appeared that there was only a slight difference in the measured visual acuities. Further study will show whether this is an incidental or a structural occurrence.

Transplantation of cryopreserved canine venous allografts.

Local vascular reconstructions frequently require the use of vein grafts to bridge arterial or venous defects. Most previous studies on the use of cryopreserved veins have used relatively large caliber vessels. There have been few studies on the effectiveness of cryopreserved micro- or small-venous allografts. Here, we tested two types of cryopreserved venous allografts: (1) 1.5- to 1.9-mm diameter microvenous grafts (MVG); and (2) 4- to 5-mm diameter small venous grafts (SVG). Cryopreserved MVG allografts were placed into saphenous arteries of six experimental dogs and SVG cryopreserved allografts were placed into femoral arteries of six experimental dogs for 3 to 6 weeks. Two fresh MVG autografts were also transplanted into experimental dogs as controls and autografts were transferred to the contralateral side in SVG dogs as controls. None of the six cryopreserved MVG grafts retained patency but three/six cryopreserved SVG allografts were patent at harvest. Histological examination of grfts revealed control autografts were undergoing arterialization with an intact intima. Experimental cryopreserved allografts showed extensive medial fibrosis, significant lymphocytic infiltrates, and sporadic areas of intact intima for both patent and nonpatent grafts.

Bactericidal effectiveness of modulated UV light.

Studies were designed to evaluate the effectiveness of pulsed modulated UV light waveforms for killing bacteria. Exposure of five strains of bacteria to the modulated information encoded in the light decreased the colony population from a confluent lawn to less than 20 colonies. However, approximately 2,000 colonies survived treatment with the same intensity and time of exposure to UV light lacking the modulated information.

Freeze-dried microarterial replacement allografts in rabbits.

Microvascular techniques offer important alternatives for reconstructive head and neck surgery. To test the viability of freeze-dried allografts, a pilot experimental study was performed using the rabbit model. Freeze-dried preserved arterial allografts were implanted into femoral artery defects in eight subjects. After 6 weeks, all grafts were harvested and prepared for histological and electron microscopic analysis. Immediate patency was 100%. One subject was excluded on the third postoperative day. Of the seven remaining grafts, three (43%) were patent at 6 weeks. These results are comparable to previous data obtained using freeze-dried arterial allografts in the same animal model. Although further investigation is required, this pilot study suggests possible future application of cryopreserved vascular micrografts.

Parameters for evaluation of viability assays: accuracy, precision, specificity, sensitivity, and standardization.

The selection of appropriate viability assays is critical in evaluating the efficacy of any cryopreservation procedure. The appropriateness of a given assay depends on the specific tissue and the function which is being optimized. Although a broad range of "viability" assays have been used, these assays can be classified in seven principle groups: (i) Morphological procedures, including routine histology, surface antigen localization, and transmission electron or scanning microscopy; (ii) proliferation studies; (iii) metabolic assays; (iv) implantation; (v) mechanical assays; (vi) motility; and (vii) DNA or RNA synthetic assays. Regardless of the class of assay, each assay may be further characterized as qualitative, quantitative, or quantal and each type may vary in the degree of subjectivity. In selecting a specific viability assay, biological variability, assay bias, and the statistical probability of both Type I and Type II errors should be considered crucial. Here we discuss a number of critical factors involved in validating viability assays, including accuracy, precision, standardization, specificity, sensitivity, selection of statistical methodology, and range of the assay.

Power analysis of statistical methods for comparing treatment differences from limiting dilution assays.

Six different statistical methods for comparing limiting dilution assays were evaluated, using both real data and a power analysis of simulated data. Simulated data consisted of a series of 12 dilutions for two treatment groups with 24 cultures per dilution and 1,000 independent replications of each experiment. Data within each replication were generated by Monte Carlo simulation, based on a probability model of the experiment. Analyses of the simulated data revealed that the type I error rates for the six methods differed substantially, with only likelihood ratio and Taswell's weighted mean methods approximating the nominal 5% significance level. Of the six methods, likelihood ratio and Taswell's minimum Chi-square exhibited the best power (least probability of type II errors). Taswell's weighted mean test yielded acceptable type I and type II error rates, whereas the regression method was judged unacceptable for scientific work.