Impact of apolipoprotein E genetic polymorphisms on liver disease: An essential review.

Cirrhosis is an advanced stage of liver disease, compromising liver function with systemic health implications and poor quality of life. Hepatitis C virus (HCV) infection and alcoholic liver disease are the main causes of this pathology. However, since genetic factors may play a large role in the progression and severity of liver disease, and as apolipoprotein E (apoE) has been recognised to be mainly synthesised in the liver, apoE polymorphism studies are important to better understand the causal mechanisms in liver diseases. In this review, we summarise up-to-date studies addressing how apoE polymorphisms influence liver cirrhosis and liver transplantation outcomes and potential protective mechanisms. Although more clinical studies are needed to support these findings, the apoE ɛ4 allele seems to be protective against the progression of liver cirrhosis in the majority of aetiologies and the postoperative serum apoE phenotype of the transplanted subject receptors was converted to that of the donor, indicating that >90% of apoE in plasma is synthesised in the hepatic system.

Differences in timing of migration and response to sexual signalling drive asymmetric hybridization across a migratory divide.

Ecological traits and sexual signals may both contribute to the process of ecological speciation. Here we investigate the roles of an ecological trait, seasonal migratory behaviour and a sexual trait, song, in restricting or directing gene flow across a migratory divide in the Swainson's thrush (Catharus ustulatus). We show that short-distance migratory ecotypes wintering in Central America arrive earlier at the breeding grounds than long-distance migratory ecotypes wintering primarily in South America, providing the potential for some premating isolation. Playback experiments suggest that early- and late-arriving forms recognize each other as competitors, but that the early-arriving form responds more aggressively to a broader spectrum of stimuli. Genetic analysis suggests that hybridization occurs more often between males of the early-arriving ecotype and females of the late-arriving ecotype. Together our results suggest that differences in arrival times may reduce the temporal coincidence of mate choice, but asymmetry in response to heterotypic song may hinder complete divergence. These data provide further insight into the roles of ecological traits and sexual signals during the incipient stages of speciation.

Assessing the power of informative subsets of loci for population assignment: standard methods are upwardly biased.

It is well known that statistical classification procedures should be assessed using data that are separate from those used to train the classifier. This principle is commonly overlooked when the classification procedure in question is population assignment using a set of genetic markers that were chosen specifically on the basis of their allele frequencies from amongst a larger number of candidate markers. This oversight leads to a systematic upward bias in the predicted accuracy of the chosen set of markers for population assignment. Three widely used software programs for selecting markers informative for population assignment suffer from this bias. The extent of this bias is documented through a small set of simulations. The relative effect of the bias is largest when screening many candidate loci from poorly differentiated populations. Simple unbiased methods are presented and their use encouraged.

Rev: beyond nuclear export.

Rev remains a hot topic. In this review, we revisit the insights that have been gained into the control of gene expression by the retroviral protein Rev and speculate on where current research is leading. We outline what is known about the role of Rev in translation and encapsidation and how these are linked to its more traditional role of nuclear export, underlining the multifaceted nature of this small viral protein. We discuss what more is to be learned in these fields and why continuing research on these 116 amino acids and understanding their function is still important in devising methods to combat AIDS.

The influence of family groups on inferences made with the program Structure.

Unsupervised clustering algorithms, like the program Structure, are increasingly used to infer the presence of population structure from a sample of genotyped individuals. We evaluate the extent to which the presence of related individuals can lead such algorithms to the false inference that there is population structure. First, we demonstrate this problem using a real data set from a rainbow trout (Oncorhynchus mykiss) population. Then we perform an extensive series of simulations involving the program Structure. Our simulations encompass both a simple scenario with fixed numbers of full- and half-siblings in the sample, and a more complicated scenario in which we investigate 360 combinations of population divergence, fraction of population sampled, variance in family size, mating system and number of loci. We find that the inclusion of family members in a sample may produce very strong evidence of population structure, even when population structure is absent. This problem becomes more pronounced when more loci are genotyped, and it is particularly likely in studies of monogamous species, especially if variance in family size is high and a large fraction of a small population has been sampled. Researchers working in such situations should test observed clusters for the presence of family members to distinguish family-induced structure from real population structure. Additionally, this work shows that Structure's ability to estimate the number of subpopulations may be influenced by a number of factors, and therefore should be interpreted guardedly.

An investigation into the source and spread of foot and mouth disease virus from a wildlife conservancy in Zimbabwe.

African buffalo were introduced into a wildlife conservancy in the southeast of Zimbabwe in an effortto increase the conservancy's economic viability, which is primarily based on eco-tourism. The buffalo were infected with SAT serotypes (SAT-1, SAT-2 and SAT-3) of foot and mouth disease (FMD) virus, and in order to isolate the conservancy and prevent the transmission of FMD to adjacent populations of domestic livestock, the conservancy was surrounded by a double-fence system, 1.8 m in height. The intention was to prevent the movement of both wildlife and domestic animals across the perimeter. However, two years after the buffalo were introduced, FMD occurred in cattle farmed just outside of the conservancy. Using serological and molecular diagnostic tests, epidemiological investigations showed that it was most likely that antelope (impala or kudu), infected through contact with the buffalo herd within the conservancy, had jumped over the fence and transmitted the virus to the cattle.

A model-based method for identifying species hybrids using multilocus genetic data.

We present a statistical method for identifying species hybrids using data on multiple, unlinked markers. The method does not require that allele frequencies be known in the parental species nor that separate, pure samples of the parental species be available. The method is suitable for both markers with fixed allelic differences between the species and markers without fixed differences. The probability model used is one in which parentals and various classes of hybrids (F(1)'s, F(2)'s, and various backcrosses) form a mixture from which the sample is drawn. Using the framework of Bayesian model-based clustering allows us to compute, by Markov chain Monte Carlo, the posterior probability that each individual belongs to each of the distinct hybrid classes. We demonstrate the method on allozyme data from two species of hybridizing trout, as well as on two simulated data sets.

Genetic heterogeneity of SAT-1 type foot-and-mouth disease viruses in southern Africa.

Genetic relationships of 50 SAT-1 type foot-and-mouth disease viruses were determined by phylogenetic analysis of an homologous 417 nucleotide region encoding the C-terminal half of the VP1 gene and part of the 2A segment. Viruses obtained from persistently-infected African buffalo populations were selected in order to assess the regional genetic variation within the host species and compared with ten viruses recovered from recent and historical cases of clinical infection. Phylogenetic reconstructions identified three independently evolving buffalo virus lineages within southern Africa, that correspond with the following discrete geographic localities: (1) South Africa and southern Zimbabwe, (2) Namibia, Botswana and western Zimbabwe, and (3) Zambia, Malawi and northern Zimbabwe. This strict geographic grouping of viruses derived from buffalo was shown to be useful for determining the origin of recent SAT-1 epizootics in livestock. The percentage of conserved amino acid sites across the 50 SAT-1 viruses compared in this study was 50%. Most mutations were clustered within three discrete hypervariable regions, which coincide with the immunogenic G-H loop, H-1 loop and C-terminus region of the protein. Despite the high levels of variation within the primary sequence, secondary structural features appear to be conserved.

Monte Carlo evaluation of the likelihood for N(e) from temporally spaced samples.

A population's effective size is an important quantity for conservation and management. The effective size may be estimated from the change of allele frequencies observed in temporally spaced genetic samples taken from the population. Though moment-based estimators exist, recently Williamson and Slatkin demonstrated the advantages of a maximum-likelihood approach that they applied to data on diallelic genetic markers. Their computational methods, however, do not extend to data on multiallelic markers, because in such cases exact evaluation of the likelihood is impossible, requiring an intractable sum over latent variables. We present a Monte Carlo approach to compute the likelihood with data on multiallelic markers. So as to be computationally efficient, our approach relies on an importance-sampling distribution constructed by a forward-backward method. We describe the Monte Carlo formulation and the importance-sampling function and then demonstrate their use on both simulated and real datasets.

The foot-and-mouth disease risk posed by African buffalo within wildlife conservancies to the cattle industry of Zimbabwe.

Quantification of the risk that African buffalo (Syncerus caffer) (isolated within wildlife conservancies in Zimbabwe by a double fencing system) would infect cattle outside the conservancies with foot-and-mouth disease (FMD) virus was assessed by scenario-pathway analysis. Of the five scenarios considered, the greatest annual risk (1:5000) for cattle would be from antelope jumping over the outer perimeter fence of the conservancy and infecting cattle on the outside. The other transmission scenarios (including air-borne transmission) had a FMD risk that was low to very low. Risk management would include means to prevent the escape of antelope from the conservancies and restriction of cattle density in the proximity of the perimeter fence.

Typing of pestiviruses from eland in Zimbabwe.

Pestiviruses were isolated from three eland (Taurotragus oryx) in Zimbabwe. The viruses were characterised by typing with monoclonal antibodies and by partial genetic sequencing. All were similar to bovine viral diarrhea viruses commonly isolated from cattle. This suggests that bovine viral diarrhea virus can spread from cattle to eland.

Susceptibility and carrier status of impala, sable, and tsessebe for Cowdria ruminantium infection (heartwater).

Three species of wild African ruminants, impala (Aepyceros melampus), sable (Hippotragus equinus), and tsessebe (Damaliscus lunatus), were experimentally inoculated with in vitro culture-derived Cowdria ruminantium organisms, the tick-borne causative agent of heartwater in domestic ruminants, to determine their susceptibility to infection. No clinical disease was observed in any of the ruminants. However, C. ruminantium was detected in the sable by the transmission of heartwater to susceptible sheep, through the tick vector Amblyomma hebraeum, at 10 and 37 days postinfection (PI). Attempts to detect infection in the impala and tsessebe by tick transmission at 54 days PI failed. The impala and tsessebe were reinoculated with C. ruminantium organisms at 146 days after the first inoculation; however, a tick transmission attempt at 66 days after the reinoculation also failed. Seroconversion, as detected by immunoblotting, was demonstrated in the sable and the tsessebe but not in the impala. The results demonstrate that sable can be carriers of C. ruminantium. The susceptibility of tsessebe and impala, however, remains undetermined.

The prevalence of antibody to the viruses of bovine virus diarrhoea, bovine herpes virus 1, rift valley fever, ephemeral fever and bluetongue and to Leptospira sp in free-ranging wildlife in Zimbabwe.

The prevalence of antibody to the viruses of bovine virus diarrhoea (BVD), bovine herpes virus typel (BHV1), rift valley fever (RVF), bovine ephemeral fever (BEF) and bluetongue (BT) and to Leptospira sp. was determined in wildlife populations in Zimbabwe. Evidence of infection with BVD virus was found in 14 of the 16 species examined but was greatest in eland Taurotragus oryx, nyala Tragelaphus angasi and bushbuck Tragelaphus scriptus. Persistent infection with BVD virus was found in 1 of 303 antibody-free eland but not in the smaller sample of 102 antibody-free buffalo Syncerus caffer. Antibody to BHV1 was widespread, being found in 10 of 16 species with the highest prevalence being in buffalo and eland. Antibody to RVF was most prevalent in black rhino Diceros bicornis and white rhino Ceratotherium simum, buffalo and waterbuck Kobus ellipsiprymnus. Both BEF and BT were widespread in all the species examined. Evidence of infection with Leptospira sp. was found in 7 species. Infections were due to up to 3 of 8 different serovars.

Demonstration of a carrier state for Cowdria ruminantium in wild ruminants from Africa.

Four wild African ruminants, eland (Taurotragus oryx), giraffe (Giraffa camelopardalis), kudu (Tragephalus strepsiceros strepsiceros), and blue wildebeest (Connochaetes taurinus), were experimentally infected with the rickettsia Cowdria ruminantium, the tickborne agent causing heartwater in domestic ruminants. The infections were established, and C. ruminantium was transmitted to naive small ruminants by the vector Amblyomma hebraeum when transmission attempts were made at days 128 (eland and wildebeest), 85 (giraffe), and 24 (kudu) post infection. These wild ruminants, which are natural hosts for the tick vector, and which commonly occur within heartwater-endemic areas of Africa, are likely to play important roles in the epidemiology of heartwater as reservoirs of C. ruminantium infection. These findings also demonstrate that considerable risks are associated with the translocation of wild ruminants from heartwater-endemic areas to heartwater-free areas such as the northern and southern American mainlands, which have large populations of susceptible domestic and wild ruminant hosts and tick species that are capable of transmitting the disease.

African swine fever virus infection of the bushpig (Potamochoerus porcus) and its significance in the epidemiology of the disease.

Warthog (Phacochoerus aethiopicus), giant forest hog (Hylochoerus meinertzhageni) and bushpig (Potamochoerus porcus) are known to be susceptible to infection with African swine fever (ASF) virus. Little however, is known about the ecology of the disease in the bushpig. This study has shown that the bushpig remains viraemic for between 35 and 91 days following infection during which time it is able to infect the tick vector O. moubata. These ticks were able to transmit the disease to pigs. The virus persists in the lymphatic tissues for less than 34 weeks. Bushpigs infected with LIL 20/l virus but not VIC T90/l virus transmitted infection to in-contact pigs. Infected domestic pigs did not transmit the infection to in-contact bushpigs. ASF virus was able to replicate in in vitro cultures of bushpig leucocytes and endothelial cells. Recovered bushpigs could be reinfected with some strains of virus but not others. While it has been demonstrated that bushpigs remain carriers of ASFV following infection a complete understanding of their significance in the epidemiology of the disease awaits further investigations of their association with O. moubata.

Growth of Cowdria ruminantium in tissue culture endothelial cell lines from wild African mammals.

Endothelial cell cultures were established from several wild African mammalian species. Long-term cultures were established from three ruminants, stable antelope (Hippotragus niger), buffalo (Syncerus caffer), and eland (Tragelaphus oryx), and from an omnivore, the bushpig (Potamochoerus porcus). Cowdria ruminanntium was isolated from plasma of clinically affected animals in these four cell lines and in bovine endothelial cells used routinely for C. ruminantium propagation. Nineteen different strains of C. ruminantium from Africa and the Caribbean region were grown and maintained in these cell lines and their growth was comparable with growth in the bovine endothelial cells. The role of sable antelope, eland, and bushpigs in the epidemiology of heartwater is unknown. However, these results extend the number of cell lines that can be used to isolate and grow C. ruminantium.

A differential screen for ligand-regulated genes: identification of HoxA10 as a target of vitamin D3 induction in myeloid leukemic cells.

1,25-Dihydroxyvitamin D3 [1,25(OH)2D3], the hormonal ligand for vitamin D3, is a potent inducer of myeloid-leukemic-cell differentiation. Such cells differentiate exclusively into monocytes/macrophages in response to this ligand. Since 1,25(OH)2D3 transduces its hormone signal through the vitamin D3 receptor (VDR), a ligand-modulated transcription factor and member of the nuclear hormone receptor superfamily, we sought to identify direct VDR target genes induced during this differentiation process. To do so, we applied a modified differential screen with a nascent-RNA purification strategy using biases for immediate-early-response genes induced by 1,25(OH)2D3 in the myelomonocytic cell line U937. Using this screen, we had previously identified p21Waf1/Cip1 as a gene transcriptionally induced by 1,25(OH)2D3 and demonstrated that this induction facilitates the differentiation of U937 cells into monocytes/macrophages (24). Here, we describe in detail our differential screen strategy and the identification and isolation of 20 1,25(OH)2D3-inducible genes or unknown cDNAs by means of this screen. One gene newly identified as a target of VDR regulation in myeloid cells is the homeobox HoxA10 gene. HoxA10 protein may act as a general regulator of cell growth, since overexpression of HoxA10 facilitated the differentiation of U937 cells into monocytes/macrophages independent of 1,25(OH)2D3 and acted to strongly inhibit the growth of the breast cancer cell line MCF-7 by arresting these cells in G1.

Jejunal phlebectasia presenting with massive gastrointestinal hemorrhage.

Our case report illustrates the clinicopathologic features of this rare vascular lesion and highlights that phlebectasia should be considered as a cause of gastrointestinal bleeding of undetermined etiology in adult patients.