An invasive non-native mammal population conserves genetic diversity lost from its native range.

Invasive, non-native species are one of the major causes of global biodiversity loss. Although they are, by definition, successful in their non-native range, their populations generally show major reductions in their genetic diversity during the demographic bottleneck they experience during colonization. By investigating the mitochondrial genetic diversity of an invasive non-native species, the stoat Mustela erminea, in New Zealand and comparing it to diversity in the species' native range in Great Britain, we reveal the opposite effect. We demonstrate that the New Zealand stoat population contains four mitochondrial haplotypes that have not been found in the native range. Stoats in Britain rely heavily on introduced rabbits Oryctolagus cuniculus as their primary prey and were introduced to New Zealand in a misguided attempt at biological control of rabbits, which had also been introduced there. While invasive stoats have since decimated the New Zealand avifauna, native stoat populations were themselves decimated by the introduction to Britain of Myxoma virus as a control measure for rabbits. We highlight the irony that while introduced species (rabbits) and subsequent biocontrol (myxomatosis) have caused population crashes of native stoats, invasive stoats in New Zealand, which were also introduced for biological control, now contain more genetic haplotypes than their most likely native source.

Patterns of direct and indirect contact between cattle and badgers naturally infected with tuberculosis.

Tuberculosis (TB) due to infection with Mycobacterium bovis is transmitted between cattle and badgers (Meles meles) in the UK and Ireland but it is unclear where or when transmission occurs. We investigated direct and indirect interactions between badgers and cattle using automated proximity loggers on animals and at badger latrines located on pasture, in an area of south-west England with a high-density badger population. Direct contacts (interactions within 1.4 m) between badgers and cattle at pasture were very rare (four out of >500000 recorded animal-to-animal contacts) despite ample opportunity for interactions to occur. Indirect interactions (visits to badger latrines by badgers and cattle) were two orders of magnitude more frequent than direct contacts: 400 visits by badgers and 1700 visits by cattle were recorded. This suggests that indirect contacts might be more important than direct contacts in terms of disease transmission at pasture. The TB infection status of individual badgers (ascribed with 93% accuracy using three diagnostic tests) did not affect the frequency or duration of their visits to latrines located on pasture grazed by cattle. Nevertheless, there was wide variation in contact behaviour between individuals, which highlights the importance of understanding heterogeneity in contact patterns when developing strategies to control disease spread in wildlife and livestock.

Multi-state modelling reveals sex-dependent transmission, progression and severity of tuberculosis in wild badgers.

Statistical models of epidemiology in wildlife populations usually consider diseased individuals as a single class, despite knowledge that infections progress through states of severity. Bovine tuberculosis (bTB) is a serious zoonotic disease threatening the UK livestock industry, but we have limited understanding of key epidemiological processes in its wildlife reservoirs. We estimated differential survival, force of infection and progression in disease states in a population of Eurasian badgers (Meles meles), naturally infected with bTB. Our state-dependent models overturn prevailing categorizations of badger disease states, and find novel evidence for early onset of disease-induced mortality in male but not female badgers. Males also have higher risk of infection and more rapid disease progression which, coupled with state-dependent increases in mortality, could promote sex biases in the risk of transmission to cattle. Our results reveal hidden complexities in wildlife disease epidemiology, with implications for the management of TB and other zoonotic diseases.

Heterogeneity in the risk of Mycobacterium bovis infection in European badger (Meles meles) cubs.

The behaviour of certain infected individuals within socially structured populations can have a disproportionately large effect on the spatio-temporal distribution of infection. Endemic infection with Mycobacterium bovis in European badgers (Meles meles) in Great Britain and Ireland is an important source of bovine tuberculosis in cattle. Here we quantify the risk of infection in badger cubs in a high-density wild badger population, in relation to the infection status of resident adults. Over a 24-year period, we observed variation in the risk of cub infection, with those born into groups with resident infectious breeding females being over four times as likely to be detected excreting M. bovis than cubs from groups where there was no evidence of infection in adults. We discuss how our findings relate to the persistence of infection at both social group and population level, and the potential implications for disease control strategies.

Zigzag persistence for coral reef resilience using a stochastic spatial model.

A complex interplay between species governs the evolution of spatial patterns in ecology. An open problem in the biological sciences is characterizing spatio-temporal data and understanding how changes at the local scale affect global dynamics/behaviour. Here, we extend a well-studied temporal mathematical model of coral reef dynamics to include stochastic and spatial interactions and generate data to study different ecological scenarios. We present descriptors to characterize patterns in heterogeneous spatio-temporal data surpassing spatially averaged measures. We apply these descriptors to simulated coral data and demonstrate the utility of two topological data analysis techniques-persistent homology and zigzag persistence-for characterizing mechanisms of reef resilience. We show that the introduction of local competition between species leads to the appearance of coral clusters in the reef. We use our analyses to distinguish temporal dynamics stemming from different initial configurations of coral, showing that the neighbourhood composition of coral sites determines their long-term survival. Using zigzag persistence, we determine which spatial configurations protect coral from extinction in different environments. Finally, we apply this toolkit of multi-scale methods to empirical coral reef data, which distinguish spatio-temporal reef dynamics in different locations, and demonstrate the applicability to a range of datasets.

Farm-scale risk factors for bovine tuberculosis incidence in cattle herds during the Randomized Badger Culling Trial.

We analysed the incidence of cattle herd breakdowns due to bovine tuberculosis (Mycobacterium bovis) in relation to experimental badger culling, badger populations and farm characteristics during the Randomized Badger Culling Trial (RBCT). Mixed modelling and event history analysis were used to examine the individual risk factors. The interdependencies of covariates were examined using structural equation modelling. There were consistent findings among the different analyses demonstrating that during a badger culling programme farms experiencing: reactive culling, larger herd sizes, larger holdings and holdings with multiple parcels of land were all at greater risk of a herd breakdown. Proactive culling reduced risks within the culling area, but we did not assess any potential effects in the periphery of the treatment area. Badger-related variables measured prior to the start of culling (number of social groups and length of badger territorial boundaries) did not consistently point to an increase in risk, when set against a background of ongoing badger culling. This could be because (1) the collected variables were not important to risk in cattle, or (2) there were insufficient data to demonstrate their importance. Our findings highlight the difficulty in identifying simple predictors of spatial variation in transmission risks from badger populations and the consequent challenge of tailoring management actions to any such field data.

Point transect sampling along linear features.

Distance sampling is a widely used methodology for assessing animal abundance. A key requirement of distance sampling is that samplers (lines or points) are placed according to a randomized design, which ensures that samplers are positioned independently of animals. Often samplers are placed along linear features such as roads, so that bias is expected if animals are not uniformly distributed with respect to distance from the linear feature. We present an approach for analyzing distance data from a survey when the samplers are points placed along a linear feature. Based on results from a simulation study and from a survey of Irish hares in Northern Ireland conducted from roads, we conclude that large bias may result if the position of samplers is not randomized, and analysis methods fail to account for nonuniformity.

Glucocorticoid regulation of amino acid transport in anucleate rat hepatoma (HTC) cells.

The transport of alpha-aminoisobutyric acid (AIB) by rat hepatoma tissue culture (HTC) cells is rapidly and reversibly inhibited by dexamethasone and other glucocorticoids. To investigate the role of the nucleus in the regulation of transport and to determine whether steroid hormones or steroid-receptor complexes may have direct effects on cytoplasmic or membrane functions, we have examined the regulation of transport by dexamethasone in anucleate HTC cells. Cytoplasts prepared from suspension cultures of HTC cells fully retain active transport of AIB with the same kinetic properties as intact cells. However, the uptake of AIB is not inhibited by dexamethasone or other corticosteroids. Neither is the inhibited rate of transport, manifested by cytoplasts prepared from dexamethasone-treated cells, restored to normal upon removal of the hormone. Anucleate cells exhibit specific, saturable binding of [3H]dexamethasone; however, the binding is reduced compared with that of intact cells. The nucleus is thus required for the glucocorticoid regulation of amino acid transport in HTC cells.

The relationship of donor source and age on short- and long-term allograft survival in pediatric renal transplantation.

Limited pediatric data on allograft survival from advanced aged kidney donors exist. To determine the influence of donor source and age on allograft survival in pediatric renal transplant recipients, we analyzed the OPTN database. Allograft survival for 7291 pediatric renal transplants was evaluated. Up to five yr post-transplantation, graft survival was higher for LD vs. DD recipients. At seven yr, allograft survival was 71% in 18-54 yr-old LD recipients, 59.1% in >or=55 yr-old LD, and 45.1% in >or=50 yr-old DD recipients. An approximate 35% improvement in allograft survival in 18-54 yr-old LD recipients was observed. Multivariate results showed that recipients of LD 35-49 (aRR 0.66, 95% CI 0.55-0.80) and LD 50-54 (aRR 0.65, 95% CI 0.45-0.94) have a graft survival advantage over the ideal DD. In LD >or=55 yr, no improvement in graft survival was observed when compared with the 18-34 yr-old DD. In summary, we observed in a pediatric population, <55 yr-old LD kidneys afford improved long-term allograft survival when compared with DD kidney recipients. Increasing awareness of the long-term graft survival advantage for children receiving an LD kidney, even from older donors, should be a priority.

Survival advantage of pediatric recipients of a first kidney transplant among children awaiting kidney transplantation.

The mortality rate in children with ESRD is substantially lower than the rate experienced by adults. However, the risk of death while awaiting kidney transplantation and the impact of transplantation on long-term survival has not been well characterized in the pediatric population. We performed a longitudinal study of 5961 patients under age 19 who were placed on the kidney transplant waiting list in the United States. Of these, 5270 received their first kidney transplant between 1990 and 2003. Survival was assessed via a time-varying nonproportional hazards model adjusted for potential confounders. Transplanted children had a lower mortality rate (13.1 deaths/1000 patient-years) compared to patients on the waiting list (17.6 deaths/1000 patient-years). Within the first 6 months of transplant, there was no significant excess in mortality compared to patients remaining on the waiting list (adjusted Relative Risk (aRR) = 1.01; p = 0.93). After 6 months, the risk of death was significantly lower: at 6-12 months (aRR = 0.37; p < 0.001) and at 30 months (aRR 0.26; p < 0.001). Compared to children who remain on the kidney transplant waiting list, those who receive a transplant have a long-term survival advantage. With the potential for unmeasured bias in this observational data, the results of the analysis should be interpreted conservatively.

Incidence of PTLD in pediatric renal transplant recipients receiving basiliximab, calcineurin inhibitor, sirolimus and steroids.

Pediatric renal transplant recipients were enrolled in a multicenter, randomized, double-blind trial of steroid withdrawal. Subjects received basiliximab, calcineurin inhibitor, sirolimus and steroids. Of 274 subjects enrolled, 19 (6.9%) subjects developed posttransplant lymphoproliferative disorder (PTLD). The relative hazard (RH) for PTLD was 5.3-fold higher in children aged < or =5 versus those >12 years (p = 0.0017). EBV seronegative subjects had a 4.7-fold higher RH compared to EBV positive subjects (p = 0.02). Among EBV donor+/recipient- (D+/R-) subjects, the RH increased by 6.1-fold (p = 0.0001). In a multivariate model, risk factors included recipient age < or =5 years (RH 3.2, 95% CI: 1.1-9.6, p = 0.034) and EBV D+/R- status (RH 7.7, 95% CI: 1.6-35.9, p = 0.010). Of 19 patients with PTLD, 17 are alive with functioning grafts and 2 lost their grafts, 1 of whom subsequently died of recurrent PTLD. This 'robust' immunosuppression protocol was associated with low rejection rates but an unacceptably high incidence of PTLD. The combination of basiliximab, calcineurin inhibitor, sirolimus and steroids resulted in over-immunosuppression in a high-risk pediatric population and we do not recommend its use. Future studies must include routine viral monitoring to permit early identification of viral activity and a protocol driven reduction of immunosuppression aimed at avoiding complications.

Should pediatric patients wait for HLA-DR-matched renal transplants?

Graft survival rates from deceased donors aged 35 years or less among all primary pediatric kidney transplant recipients in the United States between 1996 and 2004 were retrospectively examined to determine the effect of HLA-DR mismatches on graft survival. Zero HLA-DR-mismatched kidneys had statistically comparable 5-year graft survival (71%), to 1-DR-mismatched kidneys (69%) and 2-DR-mismatched kidneys (71%). When compared to donors less than 35 years of age, the relative rate of allograft failure was 1.32 (p = 0.0326) for donor age greater than or equal to age 35. There was no statistical increase in the odds of developing a panel-reactive antibody (PRA) greater than 30% at the time of second waitlisting, based upon the degree of HLA-A, -B or -DR mismatch of the first transplant, nor was there a 'dose effect' when more HLA antigens were mismatched between the donor and recipient. Therefore, pediatric transplant programs should utilize the recently implemented Organ Procurement and Transplantation Network's (OPTN)allocation policy, which prioritizes pediatric recipients to receive kidneys from deceased donors less than 35 years of age, and should not turn down such kidney offers to wait for a better HLA-DR-matched kidney.

Urokinase is required for the pulmonary inflammatory response to Cryptococcus neoformans. A murine transgenic model.

Urokinase (uPA) is hypothesized to provide proteolytic activity enabling inflammatory cells to traverse tissues during recruitment, and it is implicated as a cytokine modulator. Definitive evaluation of these hypotheses in vivo has previously been impossible because uPA could not completely and irreversibly be eliminated. This limitation has been overcome through the development of uPA-deficient transgenic mice (uPA-/-). Using these mice, we evaluated the importance of uPA in the pulmonary inflammatory response to Cryptococcus neoformans (strain 52D). C. neoformans was inoculated into uPA-/- and control mice (uPA+/+), and cell recruitment to the lungs was quantitated. The number of CFU in lung, spleen and brain was determined to assess clearance, and survival curves were generated. By day 21 after inoculation, uPA-/- mice had markedly fewer pulmonary inflammatory (CD45+), CD4+, and CD11b/CD18+ cells compared with uPA+/+ controls (P<0.0007); pulmonary CFUs in the uPA-/- mice continued to increase, whereas CFUs diminished in uPA+/+ mice(P<0.005). In survival studies, only 3/19 uPA+/+ mice died, whereas 15/19 uPA-/- mice died (p<0.001). We have demonstrated that uPA is required for a pulmonary inflammatory response to C. neoformans. Lack of uPA results in inadequate cellular recruitment, uncontrolled infection, and death.

How well do farmers know their badgers? Relating farmer knowledge to ecological survey data.

Knowledge of badger distribution is important for the management of bovine tuberculosis. At the farm level, typically the only information on badger activity available is from the farmers themselves. This study compares how well farmer perceptions of badger activity match data obtained from ecological surveys. Farmer estimates of numbers of badger setts (burrows) surrounding their farms were generally correlated with field survey results, but tended to be underestimates. Farmers correctly recorded 50 per cent of setts recorded in surveys, with larger setts and active setts more likely to be correctly recorded. Badger visits to farm buildings and yards were also monitored using surveillance cameras. The majority of farmers were aware of badger visits to their farm buildings, but in 22 per cent of cases farmers were not aware of badger visits. At the farm level, knowledge of badger activity will be useful in informing vets and animal health professionals of the potential risks of disease transmission, and hence directing management interventions. However, the tendency to underestimate activity, combined with a lack of detailed knowledge of sett locations, means that farmer estimates of badger activity should be interpreted with caution and in isolation may not be sufficient to inform management interventions.

lncRNA/MicroRNA interactions in the vasculature.

MicroRNA (miRNA) have gained widespread attention for their role in diverse vascular processes including angiogenesis, apoptosis, proliferation, and migration. Despite great understanding of miRNA expression and function, knowledge of long noncoding RNA (lncRNA) molecular mechanisms still remains limited. The influence of miRNA on lncRNA function, and the converse, is now beginning to emerge. lncRNA may regulate miRNA function by acting as endogenous sponges to regulate gene expression and miRNA have been shown to bind and regulate lncRNA stability. A detailed understanding of the molecular and cellular effects of lncRNA-miRNA-mediated interactions in vascular pathophysiology could pave the way for new diagnostic markers and therapeutic approaches, but first there is a requirement for a more detailed understanding of the impact of such regulatory networks.

Widespread exposure to lead affects the body condition of free-living whooper swans Cygnus cygnus wintering in Britain.

Lead poisoning, through the ingestion of spent lead gunshot, is an established cause of morbidity and mortality in waterbirds globally, but the thresholds at which blood levels begin to affect the physiology of birds in the wild are less well known. Here we determine the prevalence of lead exposure in whooper swans and, for the first time, identify the level of blood lead associated with initial reductions in body condition. Blood lead elevated above background levels (i.e. >20 µg dL(-1)) was found in 41.7% (125/300) of swans tested. Blood lead was significantly negatively associated with winter body condition when levels were ≥44 µg dL(-1) (27/260 = 10%). Our findings indicating that sub-lethal impacts of lead on body condition occur at the lower end of previously established clinical thresholds and that a relatively high proportion of individuals in this population may be affected, reaffirm the importance of reducing contamination of the environment with lead shot.

The enteric immune response to shigella antigens.

Mucosal immunity to some enteropathogens occurs naturally following infection. By learning how to optimize initiation of the mucosal immune response it will be possible to develop vaccines against a wide variety of enteropathogens and their toxic products. In the past few years, we have examined stimulation of the mucosal response to Shigella antigens. We have found that the mucosal memory response to Shigella LPS can be stimulated by oral immunization with live, but not with killed Shigella. This primes specific B lymphocytes which, following rechallenge, quickly migrate from the Peyer's patches to mesenteric lymph nodes, the spleen, and back to the Peyer's patches. We have found that the uptake of S. flexneri is the initial step in developing a mucosal immune response to Shigella. Whereas there is little difference between the initial uptake of virulent and avirulent bacteria by M cells, pathogenic strains of Shigella are able to replicate following their uptake by the specialized M cells located in the follicle-associated epithelium of the gut. This likely serves as the source of the ulcerative lesions found in dysentery. Lastly, we have detected a vigorous secretory IgA response to Shiga toxin. The titer of IgA activity to Shiga toxin from these loop secretions correlated well with the ability to prevent Shiga toxin cytotoxin effects in vitro. The extremely vigorous mucosal immune response to Shiga toxin makes this an attractive alternative to cholera toxin to potentiate the secretory IgA immune response.

Steroid specificity of the glucocorticoid inhibition of amino acid transport in rat hepatoma cells.

Dexamethasone, a synthetic glucocorticoid, inhibits the initial rate of transport of the nonmetabolizable amino acid, alpha-aminoisobutyric acid, in rat hepatoma tissue culture (HTC) cells. To determine whether this inhibition is mediated by the same proximal steps as is the steroidal induction of tyrosine aminotransferase, we have examined the hormonal specificity of these two responses for various steroids previously characterized with respect to transaminase induction as agonists, partial agonists, antagonists, or inactive steroids. We conclude that the steroidal inhibition of amino acid transport, at steroid concentrations of 10(-5) M or less is mediated by the same glucocorticoid receptor mechanisms as the induction of tyrosine aminotransferase. First, the concentrations at which the full agonists, dexamethasone and cortisol, produce their half-maximal effects on phenomena are the same. Second, tetrahydrocortisol, which does not interact with the glucocorticoid receptor, neither inhibits transport nor induces transaminase. Third, the competitive interactions between partial agonists or antagonists and the full agonist dexamethasone with respect to both transport inhibition and enzyme induction are virtually identical. At concentrations greater than 10(-5)M, however, both partial agonist and antagonist steroids are capable of fully inhibiting amino acid transport. The effects of these steroids on transport, like those of dexamethasone, are reversible and are blocked by cycloheximide and actinomycin D. Furthermore, these steroids, like dexamethasone, slow the rate of efflux of alpha-aminoisobutyric acid from preloaded cells. Thus, the effects of high concentrations of partial agonist and antagonist steroids on amino acid transport do not appear to reflect a generalized toxic effect on membrane function.

Detection of HIV-1 Nucleic Acids by Southern Blotting.

Replication of the human immunodeficiency virus type 1 (HIV-1) is associated with a high degree of viral sequence variation (1) that has been shown to correlate with disease state (2-8). The genetic diversity of the viral swarm within an HIV-1 infected individual is so extensive that this entity has been termed as quasi-species. Geographic distributions of HIV-1 reveal sequence clustering into a major group M and a minor (outlier) group O. Group M HIV-Is are further divided into a growing number of subtypes (A through H at this writing). Although DNA sequence analysis is the gold standard technique for HIV-1 genetic subtyping, molecular hybridization of untyped viral sequences with subtype-specific probes is frequently used as a subtyping screen.

Detection of HIV-1 Nucleic Acids by Northern Blotting.

Northern blotting (1) is one of many tools used in understanding the human immunodeficiency virus type 1 (HIV-1). In the process of Northern blotting, RNA is first separated by size through a denaturing agarose gel and transferred onto a membrane. With this transfer or blotting, and subsequent hybridization with a DNA or RNA probe, quantitation, expression levels of the RNA, size of the RNA, and mapping of the 5'- and 3'-terminal end of the RNA can be determined from primary and cultured cells, blood, and tissue. For HIV research, Northern blotting has been utilized for determining the expression levels and splicing patterns of HIV RNA regulatory genes (2-4), HIV RNA protease gene (5), cytokine effects on the levels of spliced and genomic HIV RNA (6,7), steady-state transcriptional levels and splicing patterns of HIV RNA as a result of antiviral constructs (8), and receptor studies (9,10). In addition, Northern blotting has be utilized to answer questions on the effect on the HIV RNA level of expression of the envelope protein on calmodulin (11) and carbohydrate binding proteins (12).