Isolation and characterization of highly pathogenic avian influenza virus subtype H5N1 from donkeys

Background  

The highly pathogenic H5N1 is a major avian pathogen that crosses species barriers and seriously affects humans as well as some mammals. It mutates in an intensified manner and is considered a potential candidate for the possible next pandemic with all the catastrophic consequences.     

Genetic variation and effective population size in isolated populations of coastal cutthroat trout

Following glacial recession in southeast Alaska, waterfalls created by isostatic rebound have isolated numerous replicate populations of coastal cutthroat trout (Oncorhynchus clarkii clarkii) in short coastal streams. These replicate isolated populations offer an unusual opportunity to examine factors associated with the maintenance of genetic diversity. We used eight microsatellites to examine genetic variation within and differentiation among 12 population pairs sampled from above and below these natural migration barriers. Geological evidence indicated that the above-barrier populations have been isolated for 8,000–12,500 years. Genetic differentiation among below-barrier populations (F _ST = 0.10, 95% C.I. 0.08–0.12) was similar to a previous study of more southern populations of this species. Above-barrier populations were highly differentiated from adjacent below-barrier populations (mean pairwise F _ST = 0.28; SD 0.18) and multiple lines of evidence were consistent with asymmetric downstream gene flow that varied among streams. Each above-barrier population had reduced within-population genetic variation when compared to the adjacent below-barrier population. Within-population genetic diversity was significantly correlated with the amount of available habitat in above-barrier sites. Increased genetic differentiation of above-barrier populations with lower genetic diversity suggests that genetic drift has been the primary cause of genetic divergence. Long-term estimates of N _e based on loss of heterozygosity over the time since isolation were large (3,170; range 1,077–7,606) and established an upper limit for N _e if drift were the only evolutionary process responsible for loss of genetic diversity. However, it is likely that a combination of mutation, selection, and gene flow have also contributed to the genetic diversity of above-barrier populations. Contemporary above-barrier N _e estimates were much smaller than long-term N _e estimates, not correlated with within-population genetic diversity, and not consistent with the amount of genetic variation retained, given the approximate 10,000-year period of isolation. The populations isolated by waterfalls in this study that occur in larger stream networks have retained substantial genetic variation, which suggests that the amount of habitat in headwater streams is an important consideration for maintaining the evolutionary potential of isolated populations.     

Effects of sieving, drying and rewetting upon soil bacterial community structure and respiration rates

Soil microcosm studies often require some form of soil homogenisation, such as sieving, to provide a representative sample. Frequently, soils are also homogenised following drying and are then rewetted, yet little research has been done to understand how these methods impact upon microbial communities. Here we compared the molecular diversity and functional responses of intact cores from a Scottish grassland soil with homogenised samples prepared by drying, sieving and rewetting or freshly sieving wet soils. Results showed that there was no significant difference in total soil CO₂-C efflux between the freshly sieved and intact core treatments, however, respiration was significantly higher in the dried and rewetted microcosms. Molecular fingerprinting (T-RFLP) of bacterial communities at two different time-points showed that both homogenisation methods significantly altered bacterial community structure with the largest differences being observed after drying and rewetting. Assessments of responsive taxa in each treatment showed that intact cores were dominated by Acidobacterial peaks whereas an increased relative abundance of Alphaproteobacterial terminal restriction fragments were apparent in both homogenised treatments. However, the shift in community structure was not as large in the freshly sieved soil. Our findings suggest that if soil homogenisation must be performed, then fresh sieving of wet soil is preferable to drying and rewetting in approximating the bacterial diversity and functioning of intact cores.     

<Emphasis Type="Italic">TRAF1/C5</Emphasis>polymorphism is not associated with increased mortality in rheumatoid arthritis: two large longitudinal studies

Introduction  

Recently an association between a genetic variation in TRAF1/C5 and mortality from sepsis or cancer was found in rheumatoid arthritis (RA). The most prevalent cause of death, cardiovascular disease, may have been missed in that study, since patients were enrolled at an advanced disease stage. Therefore, we used an inception cohort of RA patients to investigate the association between TRAF1/C5 and cardiovascular mortality, and replicate the findings on all-cause mortality. As TRAF1/C5 associated mortality may not be restricted to RA, we also studied a large cohort of non-RA patients.     

Soft Tissue Modelling of Cardiac Fibres for Use in Coupled Mechano-Electric Simulations

The numerical solution of the coupled system of partial differential and ordinary differential equations that model the whole heart in three dimensions is a considerable computational challenge. As a consequence, it is not computationally practical—either in terms of memory or time—to repeat simulations on a finer computational mesh to ensure that convergence of the solution has been attained. In an attempt to avoid this problem while retaining mathematical rigour, we derive a one dimensional model of a cardiac fibre that takes account of elasticity properties in three structurally defined axes within the myocardial tissue. This model of a cardiac fibre is then coupled with an electrophysiological cell model and a model of cellular electromechanics to allow us to simulate the coupling of the electrical and mechanical activity of the heart. We demonstrate that currently used numerical methods for coupling electrical and mechanical activity do not work in this case, and identify appropriate numerical techniques that may be used when solving the governing equations. This allows us to perform a series of simulations that: (i) investigate the effect of some of the assumptions inherent in other models; and (ii) reproduce qualitatively some experimental observations.     

Metabolite cross-feeding enhances virulence in a model polymicrobial infection

Microbes within polymicrobial infections often display synergistic interactions resulting in enhanced pathogenesis; however, the molecular mechanisms governing these interactions are not well understood. Development of model systems that allow detailed mechanistic studies of polymicrobial synergy is a critical step towards a comprehensive understanding of these infections in vivo. In this study, we used a model polymicrobial infection including the opportunistic pathogen Aggregatibacter actinomycetemcomitans and the commensal Streptococcus gordonii to examine the importance of metabolite cross-feeding for establishing co-culture infections. Our results reveal that co-culture with S. gordonii enhances the pathogenesis of A. actinomycetemcomitans in a murine abscess model of infection. Interestingly, the ability of A. actinomycetemcomitans to utilize L-lactate as an energy source is essential for these co-culture benefits. Surprisingly, inactivation of L-lactate catabolism had no impact on mono-culture growth in vitro and in vivo suggesting that A. actinomycetemcomitans L-lactate catabolism is only critical for establishing co-culture infections. These results demonstrate that metabolite cross-feeding is critical for A. actinomycetemcomitans to persist in a polymicrobial infection with S. gordonii supporting the idea that the metabolic properties of commensal bacteria alter the course of pathogenesis in polymicrobial communities.     

Do "Language Rights" Serve Indigenous Interests? Some Hopi and Other Queries

While valuable, the discourse of language rights neglects language use in cultural, social, and historical contexts. This article examines some implications of that neglect, especially vis-a-vis small-scale, indigenous, "oral" societies. Drawing principally on Hopi examples, I argue that language rights discourse rests on a reflexivization of language and culture enhanced by globalism. Now reified, language becomes an allegory of ethnic identity. Preexisting sociolinguistic sensibilities get repositioned, for example, in Native Americancommunities in which language has hitherto been deployed as a technique of privacy and sovereignty, language rights ideology islogocentric and presumes a democratic, secular space of language use, conflicting with both privacy and performativity in Native linguisticvalues. And some linguistic usage reinforces social inequality, both transnationally and group-internally: Here, language rights contradict other human rights. Language rights discourse also requires anthropology to rethink its recent antipathy to the culture concept and to treat language and culture objectively. [Keywords: language rights, sociolinguistic values, sovereignty, logocentrism, globalism]     

Chromosomally located gene fusions constructed in Acinetobacter sp. ADP1 for the detection of salicylate

Acinetobacter sp. ADP1 is a common soil-associated bacterium with high natural competency, allowing it to efficiently integrate foreign DNA fragments into its chromosome. This property was exploited to engineer salicylate-inducible luxCDABE and green fluorescent protein (GFP) variants of Acinetobacter sp. ADP1. Specifically, Acinetobacter sp. ADPWH_lux displayed the higher sensitivity when comparing the two variants (minimum detection c. 0.5-1 microM salicylate) and a faster turnover of the lux marker gene, making it suitable for whole-cell luminescence assays of salicylate concentration. In contrast, the longer maturation and turnover times of the GFP protein make the Acinetobacter sp. ADPWH_gfp variant more suited to applications involving whole-cell imaging of the presence of salicylate. The sensitivity of the luxCDABE variant was demonstrated by assaying salicylate production in naphthalene-degrading cultures. Assays using ADPWH_lux specifically mapped the kinetics of salicylate production from naphthalene and were similar to that observed by high-performance liquid chromatography (HPLC) data. However, ADPWH_lux exhibited the higher sensitivity, when compared with HPLC, for detecting salicylate production during the first 24 h of naphthalene metabolism. These data demonstrate that the engineered Acinetobacter variants have significant potential for salicylate detection strategies in laboratory and field studies, especially in scenarios where genetic stability of the construct is required for in situ monitoring.     

Functional and compositional comparison of two activated sludge communities remediating coking effluent

The success of engineered microbiological systems is evident in the global application of activated sludge communities to remediate coking effluent. However, there is a lack of understanding of the microbiology underlying treatment efficiency and stability. In this study, two functionally distinct activated sludge pools, treating the same effluent and operating under the same conditions, were examined to establish a relationship between overall diversity and/or functional diversity with respect to process stability. Molecular profiling, sequencing and RNA-based stable isotope probing were used to examine the bacterial diversity, general composition and functional composition of the most abundant members of the two communities. The inferior process stability in one of the pools could not be explained by reduced total bacterial diversity or evenness. RNA-based stable isotope probing revealed that both pools harboured an abundant phenol-degrading Acidovorax species, and that the pool of inferior stability accommodated an additional closely related phenol-degrading Acidovorax species at high abundance. These results are discussed in the context of deterministic and stochastic models of microbial community assembly.