DNA barcoding for identification of cryptic species in the field and existing museum collections: a case study of Aethomys and Micaelamys (Rodentia: Muridae)

DNA barcoding has been proposed as a method for species identification. However, this method has been criticised for its over-reliance on a single mitochondrial gene. In this study, four mitochondrial gene regions and one nuclear gene region were used to investigate their different abilities to identify tissue associated with museum specimens of Aethomys chrysophilus, Aethomys ineptus and Micaelamys namaquensis. Aethomys chrysophilus and the more recently elevated A. ineptus are indistinguishable on morphological grounds; however, their ranges are largely parapatric with only one syntopic locality currently known. All of the mitochondrial gene regions were able to separate M. namaquensis from A. chrysophilus and A. ineptus, but they varied in their abilities to resolve differences between A. chrysophilus and A. ineptus. The sequence results identified a specimen from KwaZulu-Natal that was misclassified and should have been identified as A. ineptus. Seven specimens that had not been reclassified following the elevation of A. ineptus to species level were identified as A. ineptus. Individuals of A. chrysophilus from Malawi could not be classified as either A. chrysophilus or A. ineptus, and may be a hybrid or a new, distinct species. This study indicates that DNA barcoding may be used to separate M. namaquensis from A. chrysophilus and A. ineptus, and although it was not able to separate A. chrysophilus and A. ineptus, it did indicate specimens from Malawi may be a new cryptic species.     

An immunohistochemical study of various peptide-containing endocrine cells and neurones at the equine ileocaecal junction

The ileocaecal junctions of 5 horses and 2 donkeys were examined by using antisera to the following peptides: somatostatin, glucagon, gastrin, neurotensin, vasoactive intestinal peptide (VIP), peptide histidine isoleucine (PHI), calcitonin gene-related peptide (CGRP), substance P (SP) and neuropeptide Y (NPY). Antisera to somatostatin, neurotensin and NPY demonstrated endocrine cells in the ileal- and caecal parts of the ileocaecal junction, while immunoreactivity for glucagon was demonstrated in endocrine cells of the ileal part only. Nerve cell bodies showing immunoreactivity to SP, VIP, CGRP and PHI were demonstrated in the myenteric and submucosal plexuses and were associated with small blood vessels in the submucosa of all the regions tested. Ramified nerve fibres in the submucosa immunoreactive to SP, VIP, CGRP and PHI extended to the mucosa and to small blood vessels in the submucosa. Nerve fibres showing immunoreactivity to SP, VIP and PHI extended to the circular smooth muscle layer of the ileocaecal junction.     

Exploratory trials on reinforcement of veld with legumes in the south‐eastern transvaal highveld

Abstract

The feasibility and potential of reinforcing veld with legumes in the south‐eastern Transvaal highveld was assessed in a number of trials during the period 1974–84. Experience was gained with regard to methods of establishment, adaptation of legumes to the local environment, responses to fertilization, especially with lime and superphosphate, and the reaction of legumes to fire and grazing. In all, 17 legumes were involved, including the genera Coronilla, Desmodium, Glycine, Lespedeza, Lotus, Macroptilium, Medicago, Neoto‐nonia, Trifolium and Vigna. Only Coronilla varia (crownvetch) showed a satisfactory degree of persistence. However, crownvetch is slow to establish, is intolerant of waterlogging and has a relatively high requirement for lime and phosphate. Considering these features, and the probability of undesirable changes in grass species composition in reinforced veld, it is recommended that intensification be achieved through development of improved pastures for use in conjunction with veld, rather than by means of veld reinforcement.     

Early growth responses from weed control and planting larger stock of Pinus radiata are greater than that obtained from mechanical soil cultivation

Early growth of two grades ofbare-root Pinus radiata D.Don seedlingswere studied in response to four soilcultivation treatments and two weed controltreatments.Soil cultivation treatments included (i) pitsmade by hand, (ii) pits made with an auger,(iii) ripping alone, and (iv) ripping plusdisking. Weed treatments included (i) manualrelease 1 year after planting or (ii) totalweed control for 1 year involving the use ofherbicides and additional hoeing. Bare-rootseedlings were separated into either medium(4.1-mm average root-collar diameter; height25–31 cm) or small (2.8-mm average root-collardiameter; height 14–20 cm) size classes.Growth on this site was excellent and 7 yearsafter treatment, trees in the least expensivetreatment averaged 12.8 m in height. Use ofmedium seedlings and extra weed controlincreased merchantable volume by20 m³ ha^{minus 1} and 19 m³ ha^{minus 1},respectively. When combined, the increase was39 m³ ha^{minus 1}. However, none of the soilcultivation treatments caused a significantincrease in merchantable volume. Disking onthis site proved to be of no benefit. Aboundary-line analysis was used to examine themarginal returns from investing in intensivesilviculture.     

The topography and gross anatomy of the gastrointestinal tract of the Cape dune mole-rat (Bathyergus suillus)

The Cape dune mole-rat, Bathyergus suillus, is the largest truly subterranean rodent in the world and is restricted to sandy soil areas of the southern and South-western Cape Province. These animals are herbivorous, feeding mostly on the below ground portions of grass and geophytes. The present study was undertaken to explore whether there are any gross anatomical gastrointestinal adaptations associated with the herbivorous diet of the Cape dune mole-rat and to provide a basis for further investigations into the nutrition and ecology of this animal. The stomach was unilocular (simple) and the entire internal aspect displayed macroscopically visible glandular epithelium. The caecum was voluminous and arranged into a spiral of approximately one and a half turns. The tip of the caecum resembled a vermiform appendix and lay against the left lateral abdominal wall. The ascending colon consisted of proximal and distal portions, arranged in a large double loop and attached to each other by a fat-filled mesenteric fold. The looped, folded ascending colon filled the right side of the abdominal cavity, lying against the right dorsal, lateral and ventral abdominal wall. The internal structure of the ascending colon revealed a shallow groove, lined on either side by a row of papillae. The simple, glandular stomach in conjunction with a prominent caecum and a greatly enlarged ascending colon suggests that this animal is a hindgut fermenting herbivore, rather than a caecal fermenter, as is the case in most rodent species.     

Target-based and whole-worm screening approaches to anthelmintic discovery

Experimental approaches for identifying new anthelmintics include target-based and whole-worm screening methods. The former involves basic research into characterising and validating new targets, mostly proteins, followed by identification of inhibitors or agonists through the use of target-based screening assays and/or in silico drug design. The latter experimental approach uses whole-worm assays to identify anthelmintic agents with unknown modes of action, or where the primary interest lies in whether analogues are able to kill (or disable) worms rather than in measuring their direct impact on their likely target. This paper focuses initially on the intestine and external layers of nematodes as potential drug targets. Specific anthelmintic agents targeting either tissue are discussed to illustrate the impact of disruption to these structures. In both cases, the activity of these agents against insects was known, and activity against nematodes was identified using whole worm screening assays. Recent literature identifying ecdysone signalling pathway receptors in nematodes is then used to provide an example of basic research into a specific target that may lead to the development of high-throughput target-based drug screening assays. Finally, the role of whole-worm screening approaches versus target-based screening is discussed briefly.     

Tree survival and maximum density of planted forests–Observations from South African spacing studies

Background:Among the most important aspects of risk and hazard studies relating to forest ecosystems are maximum forest density and density-dependent tree survival.Methods:Long-term observations about the maximum density of unthinned Pinus patula and P.elliottii field plots based on the Correlated Curve Trend(CCT)spacing studies which were established almost 8 decades ago by O’Connor(Forest Research with Special Reference to Planting Distances and Thinning,1935)in South Africa.Three specific approaches were introduced for analysing maximum density and tree survival,namely the‘limiting line’,Nilson’s sparsity and tree survival with the Weibull function.Results:The main results are:a)Maximum densities differ greatly among the two species grown on the same site and within the same species grown on different sites;it is possible to relate these differences to site index in both species.b)The relationship between the quadratic mean diameter and the minimum average spacing of surviving trees(known as Nilson’s Sparsity)appears to be surprisingly similar in both species.c)An analysis of tree survival in response to different initial planting espacements shows that the Weibull survival function parameters can be estimated if the initial planting density is known.This result is presented for each of the eight large experiments used in this study.Conclusions:This study contributes to a better understanding of tree survival and maximum density which are the key factors required for estimating risk and uncertainty.The risk of tree mortality is not constant,but varies with tree species,planting density,tree age and growing site.For estimating that risk,therefore,continuous long-term observation on different sites and with varying planting densities,as provided by the unthinned CCT series,are essential.     

Transoceanic migration, spatial dynamics, and population linkages of white sharks

The large-scale spatial dynamics and population structure of marine top predators are poorly known. We present electronic tag and photographic identification data showing a complex suite of behavioral patterns in white sharks. These include coastal return migrations and the fastest known transoceanic return migration among swimming fauna, which provide direct evidence of a link between widely separated populations in South Africa and Australia. Transoceanic return migration involved a return to the original capture location, dives to depths of 980 meters, and the tolerance of water temperatures as low as 3.4 degrees C. These findings contradict previous ideas that female white sharks do not make transoceanic migrations, and they suggest natal homing behavior.     

Dual oxidase 2 and glutathione peroxidase gene expression are elevated in hyperimmunized sheep challenged with Haemonchus contortus

A sequential biopsy sampling method was used to investigate oxidant and antioxidant gene responses in resistant sheep challenged with Haemonchus contortus larvae or a sham saline challenge. The expression of key sheep oxidant and antioxidant producing genes were measured in sequential samples removed from the abomasums at days 0, 1, 2, 3, 5, 7 and 28 post challenge. Gene expression levels at each time point were compared to expression at day 0, and levels of the various genes were also correlated to other markers of infection including immune cell counts and cytokine gene expression. The early response to larval challenge infection in resistant animals was marked by a divergence of two groups of host oxidant producing genes: the dual oxidase group (DUOX2/DUOXA2) showing increases in expression to day 7, while members of the phagocytic NADPH oxidase (PHOX) group showed significant decreases in expression. The change in DUOX2 expression between days zero and seven, when host resistance to infection is mediated, was negatively correlated to final worm burden suggesting NADPH oxidase expression may play a role in parasite expulsion. Expression of the DUOX group oxidants was positively correlated to expression of the Th2 cytokine IL4. Changes in host antioxidant pathways between different members of the glutathione peroxidase family (intestinal and plasma GPX) and genes involved in glutathione metabolism were also observed. This first study of the putative roles of oxidant production by the dual oxidase group, antioxidant glutathione pathways, immune cell populations, and cytokine profiles, in the development of resistance to infection by hyperimmune sheep are discussed.     

The current status and outlook for insecticide,acaricide and anthelmintic resistances across the Australian ruminant livestock industries: assessing the threat these resistances pose to the livestock sector

The Australian ruminant livestock industries are faced with the need to control parasitic infectious diseases that can seriously impact the health of animals. However, increasing levels of resistance to insecticides, anthelmintics and acaricides are substantially reducing the ability to control some of these parasites. Here we review the current situation with regard to chemical resistances in parasites across the various sectors of the Australian ruminant livestock industries and assess the level of threat that these resistances pose to the sustainability of these sectors in the short to long terms. We also look at the extent to which testing for resistance occurs across the various industry sectors, and hence how well-informed these sectors are of the extent of chemical resistance. We examine on-farm management practices, breeding of parasite-resistant animals, and non-chemical therapeutics that may act as short to long term means to reduce the current reliance on chemicals for parasite control. Finally, we look at the balance between the prevalence and magnitude of current resistances and the availability and adoption rates of management, breeding and therapeutic alternatives in order to assess the parasite control outlook for the various industry sectors.