Parallels,nonparallels, and plasticity in population differentiation of threespine stickleback within a lake

The frequent occurrence of parallel phenotypic divergence in similar habitats is often evoked when emphasizing the role of ecology in adaptive radiation and speciation. However, because phenotypic plasticity can contribute to the observed pattern of divergence, confirmation of divergence at loci underlying phenotypic traits is important for confirming adaptive divergence. In the present study, we examine parallel morphological, neutral, and potentially adaptive genetic divergence of threespine stickleback inhabiting different habitats within a lake. Three genetic clusters best explained the neutral genetic structure within the lake; however, morphological differences were only weakly connected to genetic clusters and there was considerable phenotypic variation within clusters. Among the factors that could contribute to the observed pattern of morphological and genetic divergence are phenotypic plasticity, selective mortality of hybrids, and habitat choice based on morphology. Several loci are identified as outliers indicating divergent selection between the morphs and some parallels in morphological and adaptive genetic divergence are found in stickleback spawning at two lava sites. However, neutral genetic structure indicates considerable genetic connectivity among the two lava sites, and the parallels in morphology may therefore represent selective distribution of phenotypes rather than parallel divergence. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 803–813.     

Genetic structure of Anogeissus dhofarica (Combretaceae) populations endemic to the monsoonal fog oases of the southern Arabian Peninsula

Anogeissus dhofarica (Combretaceae) is an endemic tree of the monsoon affected coastal mountains of the southern Arabian Peninsula, being the character species of the Hybantho durae–Anogeissetum dhofaricae association, a drought deciduous, monsoon forest community found only in the Dhofar region of southern Oman and the eastern Al‐Mahra region of south‐east Yemen. Due to the steep precipitation gradient from the centre to the edges in this monsoon affected area, A. dhofarica is found in two different habitat types: in continuous woodland belts of the Hawf and Dhofar mountains, and in isolated, scattered woodland patches, as found especially in the Fartak Mts (south‐east Yemen). Fifteen populations (212 individuals) from across the whole distribution area of the species were analysed using amplified fragment length polymorphism fingerprinting to: (1) evaluate the consequences of population fragmentation on the genetic diversity harboured in isolated patches versus cohering stands of the species and (2) to reconstruct the phylogeographical pattern of A. dhofarica as a consequence of oscillations in the monsoon activity during the Pleistocene and Holocene. The analysis of among‐population genetic differentiation and within‐population genetic diversity in A. dhofarica populations resulted in a lack of genetic pauperization and genetic differentiation of populations of the distinctly isolated patches of the Fartak Mts compared to the more luxurious forests of the Hawf and Dhofar regions. This is considered to be due to the high buffer capacity against the loss of genetic diversity caused by the long‐lived life‐form of the species combined with the capability to propagate clonally and the relatively recent fragmentation of Anogeissus forests into the described patches rather than due to high values of gene flow among remnant populations caused by bee pollination and anemochorical and hydrochorical diaspore dispersal. The phylogeographical pattern of the species argues for a quite recent fragmentation of a once continuous forest belt of A. dhofarica that is rather connected with climate changes in the Holocene than triggered by aridity–humidity oscillations reported for the Pleistocene. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97 , 40–51.     

Xiphograptus and the evolution of virgella‐bearing graptoloids

Abstract: The virgellar spine is one of the most consistent features of the graptolite sicula. It is present in a large number of graptoloid groups, but evolved separately and independently in these as it is seen from the presence of the spine in either ventral (Axonophora) or dorsal (Phyllograptus, Xiphograptus) position. The evolution of the virgellar spine in the Pan‐Bireclinata in the Upper Dapingian to Lower Darriwilian time interval is known to follow four main steps, from a simple rutellum, through a lamelliform rutellum and a lanceolate virgella to the true virgellar spine. For the xiphograptids and in Phyllograptus, the origin and early development is less well documented, but appears to follow a similar path. However, the individual stages are condensed, and a true virgellar spine emerges already in the Floian time interval. A virgellar spine was found in Didymograptellus bifidus, necessitating a revision of the diagnosis of the genus Didymograptellus. A number of species of the virgellate genera Xiphograptus, Yutagraptus and Didymograptellus are described from isolated material for the first time. The species are useful for the biostratigraphic correlation of endemic mid‐continent North American faunas with the Pacific Type faunal realm. Xiphograptus artus sp. nov., Didymograptellus primus sp. nov. and Didymograptellus cowheadensis sp. nov. from the Cow Head Group of western Newfoundland are described as new.     

Negative Role of RIG-I Serine 8 Phosphorylation in the Regulation of Interferon-�� Production

RIG-I (retinoic acid-inducible gene I) and TRIM25 (tripartite motif protein 25) have emerged as key regulatory factors to induce interferon (IFN)-mediated innate immune responses to limit viral replication. Upon recognition of viral RNA, TRIM25 E3 ligase binds the first caspase recruitment domain (CARD) of RIG-I and subsequently induces lysine 172 ubiquitination of the second CARD of RIG-I, which is essential for the interaction with downstream MAVS/IPS-1/CARDIF/VISA and, thereby, IFN-β mRNA production. Although ubiquitination has emerged as a major factor involved in RIG-I activation, the potential contribution of other post-translational modifications, such as phosphorylation, to the regulation of RIG-I activity has not been addressed. Here, we report the identification of serine 8 phosphorylation at the first CARD of RIG-I as a negative regulatory mechanism of RIG-I-mediated IFN-β production. Immunoblot analysis with a phosphospecific antibody showed that RIG-I serine 8 phosphorylation steady-state levels were decreased upon stimulation of cells with IFN-β or virus infection. Substitution of serine 8 in the CARD RIG-I functional domain with phosphomimetic aspartate or glutamate results in decreased TRIM25 binding, RIG-I ubiquitination, MAVS binding, and downstream signaling. Finally, sequence comparison reveals that only primate species carry serine 8, whereas other animal species carry an asparagine, indicating that serine 8 phosphorylation may represent a primate-specific regulation of RIG-I activation. Collectively, these data suggest that the phosphorylation of RIG-I serine 8 operates as a negative switch of RIG-I activation by suppressing TRIM25 interaction, further underscoring the importance of RIG-I and TRIM25 connection in type I IFN signal transduction.     

Obtaining valid laboratory data in clinical trials conducted in resource diverse settings: lessons learned from a microbicide phase III clinical trial

Background

Over the last decade several phase III microbicides trials have been conducted in developing countries. However, laboratories in resource constrained settings do not always have the experience, infrastructure, and the capacity to deliver laboratory data meeting the high standards of clinical trials. This paper describes the design and outcomes of a laboratory quality assurance program which was implemented during a phase III clinical trial evaluating the efficacy of the candidate microbicide Cellulose Sulfate 6% (CS) [1].

Methodology

In order to assess the effectiveness of CS for HIV and STI prevention, a phase III clinical trial was conducted in 5 sites: 3 in Africa and 2 in India. The trial sponsor identified an International Central Reference Laboratory (ICRL), responsible for the design and management of a quality assurance program, which would guarantee the reliability of laboratory data. The ICRL provided advice on the tests, assessed local laboratories, organized trainings, conducted supervision visits, performed re-tests, and prepared control panels. Local laboratories were provided with control panels for HIV rapid tests and Chlamydia trachomatis/Neisseria gonorrhoeae (CT/NG) amplification technique. Aliquots from respective control panels were tested by local laboratories and were compared with results obtained at the ICRL.

Results

Overall, good results were observed. However, discordances between the ICRL and site laboratories were identified for HIV and CT/NG results. One particular site experienced difficulties with HIV rapid testing shortly after study initiation. At all sites, DNA contamination was identified as a cause of invalid CT/NG results. Both problems were timely detected and solved. Through immediate feedback, guidance and repeated training of laboratory staff, additional inaccuracies were prevented.

Conclusions

Quality control guidelines when applied in field laboratories ensured the reliability and validity of final study data. It is essential that sponsors provide adequate resources for implementation of such comprehensive technical assessment and monitoring systems.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00153777","term_id":"NCT00153777"}}NCT00153777 and Current Controlled Trials ISRCTN95638385     

Characterization of novel microsatellite loci for red clover (Trifolium pratense L.) from enriched genomic libraries

Twenty‐seven polymorphic microsatellite markers were isolated from red clover (Trifolium pratense). Allelic variability and cross‐species amplification were assessed on 24 red clover and eight white clover (Trifolium repens) genotypes. The number of alleles detected in red clover ranged from two to 25. Observed and expected heterozygosities were high with average values of 0.71 and 0.88, respectively. Five of the 27 loci were also successfully amplified from white clover, where two to 13 alleles were detected. These highly polymorphic microsatellite loci provide powerful tools for population genetic studies as well as for marker‐assisted selection in this important forage legume species.     

In Vitro Studies on the Biosynthesis of the Surface Glycoprotein of Trypanosoma congolense1,2

Tritiated leucine, glucosamine, mannose, and galactose were incorporated into the variant specific surface glycoprotein (VSG) of Trypanosoma congolense in vitro. The uptake of the precursors is shown by SDS-polyacrylamide electrophoresis and fluorography, by assay of the radioactivity in immunoprecipitates obtained with specific antisera, and by the isolation of the labeled antigens by affinity chromatography on concanavalin A-sepharose and isoelectric focusing. The in vitro labeled VSG exhibits the same degree of microheterogeneity as that observed in the VSG isolated from trypanosomes grown in animals. Analysis of the incorporated sugars after hydrolysis of the glycoprotein showed that glucosamine and mannose were utilized in biosynthesis of the carbohydrate moiety directly whereas galactose was converted possibly to other intermediates before being incorporated into the antigen. Tunicamycin completely prevented the incorporation of the radiolabeled sugars into the surface glycoprotein. The unglycosylated VSG with a molecular weight of 47 kDa had completely lost its size heterogeneity.