Time‐shift experiments and patterns of adaptation across time and space

Time‐shift experiments provide measures of the mean fitness of a population in environments of different points in time. Here, we show how to use this type of data to decompose mean fitness into (1) the effect of the environment in which the population is transplanted, (2) the effect of the genetic composition of the population and (3) ‘temporal adaptation’, which measures how the population fits the environment at that time. We derive analytical results for the pattern of ‘temporal adaptation’ and show that it is in general maximal in the recent past. The link between ‘temporal adaptation’ and ‘local adaptation’ is discussed, and we show when patterns of adaptation in time and space are expected to be similar. Finally, we illustrate the potential use of this approach using a data set measuring the adaptation of HIV to the immune response of several recently infected patients.     

Assessing community functional attributes during substrate colonization: a field experiment using stream insects

Initial colonists of empty habitats tend to differ from those arriving later in terms of species identity and traits. We evaluated the dynamics of the functional attributes in aquatic insect communities during a colonization experiment under natural conditions. We tested whether the late stages of colonization show higher functional richness, diversity and specialization than early successional stages. We used 60 artificial slate samplers that were removed after 1, 3, 5, 10, 15 and 30 days of colonization. We considered five traits (with a total of 17 trait categories): feeding habits, dispersal medium, body size, body shape and locomotion. With these traits, we computed a global specialization index at the community level. Large shredders with a cylindrical body shape and fly dispersal while flying were prominent in late colonization. In contrast, early colonists tended to have flattened body and to disperse through water. Functional diversity and functional richness significantly increased in late colonization, resulting in a more specialized community. Our results suggest that any interference during the processes involved in stream insect colonization can be reflected in the community through the decrease or even lack of functional attributes.

     

The DNA binding mechanism of a SSB protein from Lactococcus lactis siphophage p2

Virulent lactococcal phages of the Siphoviridae family are responsible for the industrial milk fermentation failures worldwide. Lactococcus lactis, a Gram-positive bacterium widely used for the manufacture of fermented dairy products, is subjected to infections by virulent phages, predominantly those of the 936 group, including phage p2. Among the proteins coded by lactococcal phage genomes, of special interest are those expressed early, which are crucial to efficiently carry out the phage lytic cycle. We previously identified and solved the 3D structure of lactococcal phage p2 ORF34, a single stranded DNA binding protein (SSBp2). Here we investigated the molecular basis of ORF34 binding mechanism to DNA. DNA docking on SSBp2 and Molecular Dynamics simulations of the resulting complex identified R15 as a crucial residue for ssDNA binding. Electrophoretic Mobility Shift Assays (EMSA) and Atomic Force Microscopy (AFM) imaging revealed the inability of the Arg15Ala mutant to bind ssDNA, as compared to the native protein. Since R15 is highly conserved among lactococcal SSBs, we propose that its role in the SSBp2/DNA complex stabilization might be extended to all the members of this protein family.     

Perceptions of Health,Health Care and Community-Oriented Health Interventions in Poor Urban Communities of Kinshasa,Democratic Republic of Congo

In Democratic Republic of Congo access to health care is limited because of many geographical and financial barriers, while quality of care is often low. Global health donors assist the country with a number of community-oriented interventions such as free distribution of bednets, antihelminthic drugs, vitamin A supplementation and vaccination campaigns, but uptake of these interventions is not always optimal. The aim of this study was to explore the perceptions of poor urban communities of the capital Kinshasa with regard to health issues in general as well as their experiences and expectations concerning facility-based health services and community-oriented health interventions. Applying an approach rooted in the grounded theory framework, focus group discussions were conducted in eight neighborhoods of poor urban areas in the city of Kinshasa in July 2011. Study participants were easily able to evoke the city’s major health problems, with the notable exceptions of malnutrition and HIV/AIDS. They perceive the high out-of-pocket cost of health services as the major obstacle when seeking access to quality care. Knowledge of ongoing community-oriented health interventions seems good. Still, while the study participants agree that those interventions are beneficial; their acceptability seems to be problematic. This is chiefly put down to a lack of information and government communication about the programs and their interventions. Furthermore, the study participants referred to rumors and the deterring effect of stories about alleged harmful consequences of those interventions. Along with improving the provision and quality of general health care, the government and international actors must improve their efforts in informing the communities about disease control programs, their rationale and benefit/risk ratio. Directly engaging community members in a dialogue might be beneficial in terms of improving acceptability and overall access to health services and interventions. Novel ways of reducing the high out-of-pocket expenditure should also be explored.     

Multi-channel surface EMG classification using support vector machines and signal-based wavelet optimization

The study proposes a method for supervised classification of multi-channel surface electromyographic signals with the aim of controlling myoelectric prostheses. The representation space is based on the discrete wavelet transform (DWT) of each recorded EMG signal using unconstrained parameterization of the mother wavelet. The classification is performed with a support vector machine (SVM) approach in a multi-channel representation space. The mother wavelet is optimized with the criterion of minimum classification error, as estimated from the learning signal set. The method was applied to the classification of six hand movements with recording of the surface EMG from eight locations over the forearm. Misclassification rate in six subjects using the eight channels was (mean ± S.D.) 4.7 ± 3.7% with the proposed approach while it was 11.1 ± 10.0% without wavelet optimization (Daubechies wavelet). The DWT and SVM can be implemented with fast algorithms, thus, the method is suitable for real-time implementation.     

Plio‐Pleistocene diversification and genetic population structure of an endangered lizard (the Blue Mountains water skink,Eulamprus leuraensis) in south‐eastern Australia

Aim Although climatic fluctuations occurred world‐wide during the Pleistocene, the severity of glacial and drought events – and hence their influence on animal and plant biogeography – differed among regions. Many Holarctic species were forced to warmer‐climate refugia during glacial periods, leaving the genetic signature of recent expansion and gene flow among modern‐day populations. Montane south‐eastern Australia experienced less extreme glaciation, but the effects of drier and colder climatic conditions over this period on biotic distributions, and hence on the present‐day genetic structure of animal and plant populations, are poorly known. Location South‐eastern Australia. Methods The endangered Blue Mountains water skink (Eulamprus leuraensis) is a viviparous lizard known from fewer than 40 isolated small swamps at 560–1060 m elevation in south‐eastern Australia. We conducted molecular phylogenetic, dating and population genetics analyses using the mitochondrial NADH dehydrogenase 4 (ND4) of 224 individuals of E. leuraensis sampled across the species’ distribution. Results Ancient divergences in haplotype groups between lizards from the Blue Mountains and the Newnes Plateau, and strong genetic differences, even between swamps separated by only a few kilometres, suggest that the species has persisted as a series of relatively isolated populations within its current distribution for about a million years. Presumably, habitat patches similar to current‐day swamps persisted throughout glacial–interglacial cycles in this region, allowing the development of high levels of genetic structuring within and among present‐day populations. Main conclusions Our results suggest that less extreme glacial conditions occurred in the Southern Hemisphere compared with the Northern Hemisphere, allowing cold‐adapted species (such as E. leuraensis) to persist in montane areas. However, additional studies are needed before we can assemble a comprehensive view of the impact of Pleistocene climatic variation on the phylogeography of Southern Hemisphere taxa.     

Exonuclease Domain of the Lassa Virus Nucleoprotein Is Critical To Avoid RIG-I Signaling and To Inhibit the Innate Immune Response

Lassa virus (LASV), which causes a viral hemorrhagic fever, inhibits the innate immune response. The exonuclease (ExoN) domain of its nucleoprotein (NP) is implicated in the suppression of retinoic acid-inducible gene I (RIG-I) signaling. We show here that a LASV in which ExoN function has been abolished strongly activates innate immunity and that this effect is dependent on RIG-I signaling. These results highlight the key role of NP ExoN function in the immune evasion that occurs during LASV infection.