The C‐terminal regions of YidC from Rhodopirellula baltica and Oceanicaulis alexandrii bind to ribosomes and partially substitute for SRP receptor function in Escherichia coli

The marine Gram‐negative bacteria Rhodopirellula baltica and Oceanicaulis alexandrii have, in contrast to Escherichia coli, membrane insertases with extended positively charged C‐terminal regions similar to the YidC homologues in mitochondria and Gram‐positive bacteria. We have found that chimeric forms of E. coli YidC fused to the C‐terminal YidC regions from the marine bacteria mediate binding of YidC to ribosomes and therefore may have a functional role for targeting a nascent protein to the membrane. Here, we show in E. coli that an extended C‐terminal region of YidC can compensate for a loss of SRP‐receptor function in vivo. Furthermore, the enhanced affinity of the ribosome to the chimeric YidC allows the isolation of a ribosome nascent chain complex together with the C‐terminally elongated YidC chimera. This complex was visualized at 8.6 Å by cryo‐electron microscopy and shows a close contact of the ribosome and a YidC monomer.     

Can monitoring data contribute to the biodiversity-ecosystem function debate? Evaluating data from a highly dynamic ecosystem

One of the most controversially discussed topics in current biodiversity-ecosystem function research is the transfer of results from experimental and theoretical studies to natural ecosystems. At the same time, monitoring data on biodiversity are requested as key indicators for the state of an ecosystem in most environmental evaluation frameworks. We analyse two monitoring data sets comprising information on abundance and biomass of macrozoobenthos communities in the German Wadden Sea in order to evaluate how much information monitoring data on biodiversity provide concerning ecosystem functioning and what implications this information (or the lack thereof) has for future monitoring programmes. Our results show a positive correlation between number of species of macrozoobenthos and its standing stock. Despite differences in overall biomass and individual size in different functional groups, this correlation remained consistent for different feeding guilds and therefore is likely to be independent of certain species traits. Moreover, functional turnover analyses indicate that increasing species richness is needed to maintain biomass levels over increasing periods of time. Whereas our data thus corroborate predictions from theory, we could not determine any causal relationships, because monitoring data commonly include only vague proxies for very few functional parameters, in our case standing biomass as a proxy for production. As to the use of diversity as an indicator for ecosystem functioning, we advise that management decisions are to be based on verified causal relationships and therefore strongly suggest the general incorporation of unambiguous proxies for functional parameters in the measuring campaigns of monitoring programmes.     

On the origin of the Norwegian lemming

The Pleistocene glacial cycles resulted in significant changes in species distributions, and it has been discussed whether this caused increased rates of population divergence and speciation. One species that is likely to have evolved during the Pleistocene is the Norwegian lemming (Lemmus lemmus). However, the origin of this species, both in terms of when and from what ancestral taxon it evolved, has been difficult to ascertain. Here, we use ancient DNA recovered from lemming remains from a series of Late Pleistocene and Holocene sites to explore the species' evolutionary history. The results revealed considerable genetic differentiation between glacial and contemporary samples. Moreover, the analyses provided strong support for a divergence time prior to the Last Glacial Maximum (LGM), therefore likely ruling out a postglacial colonization of Scandinavia. Consequently, it appears that the Norwegian lemming evolved from a small population that survived the LGM in an ice‐free Scandinavian refugium.     

Unexpected Patterns of Admixture in German Populations of Aedes japonicus japonicus (Diptera: Culicidae) Underscore the Importance of Human Intervention

The mosquito Aedes japonicus japonicus, originally restricted to temperate East Asia, is now widespread in North America and more recently has become established in Europe. To ascertain the putative number of separate introductions to Europe and examine patterns of expansion we analyzed the genetic makeup of Ae. j. japonicus populations from five cemeteries in North Rhine-Westphalia and Rhineland-Palatinate, two western German federal states, as well as of specimens from populations in Belgium, Switzerland, and Austria/Slovenia. To do so, we genotyped individual specimens at seven pre-existing polymorphic microsatellite loci and sequenced part of the nad4 mitochondrial locus. We found evidence of two different genotypic signatures associated with different nad4 mitochondrial haplotypes, indicating at least two genetically differentiated populations of Ae. j. japonicus in Europe (i.e. two distinct genotypes). Belgian, Swiss, and Austrian/Slovenian populations all share the same genotypic signature although they have become differentiated since isolation. Contrary to expectations, the German Ae. j. japonicus are not closely related to those in Belgium which are geographically nearest but are also highly inbred. German populations have a unique genotype but also evidence of mixing between the two genotypes. Also unexpectedly, the populations closest to the center of the German infestation had the highest levels of admixture indicating that separate introductions did not expand and merge but instead their expansion was driven by punctuated human-mediated transport. Critically, the resulting admixed populations have higher genetic diversity and appear invasive as indicated by their increased abundance and recent spread across western Germany.     

Coordinate Based Meta-Analysis of Functional Neuroimaging Data Using Activation Likelihood Estimation; Full Width Half Max and Group Comparisons

Coordinate based meta-analysis (CBMA) is used to find regions of consistent activation across fMRI and PET studies selected for their functional relevance to a hypothesis. Results are clusters of foci where multiple studies report in the same spatial region, indicating functional relevance. Contrast meta-analysis finds regions where there are consistent differences in activation pattern between two groups. The activation likelihood estimate methods tackle these problems, but require a specification of uncertainty in foci location: the full width half max (FWHM). Results are sensitive to FWHM. Furthermore, contrast meta-analysis requires correction for multiple statistical tests. Consequently it is sensitive only to very significant localised differences that produce very small p-values, which remain significant after correction; subtle diffuse differences between the groups can be overlooked. In this report we redefine the FWHM parameter, by analogy with a density clustering algorithm, and provide a method to estimate it. The FWHM is modified to account for the number of studies in the analysis, and represents a substantial change to the CBMA philosophy that can be applied to the current algorithms. Consequently we observe more reliable detection of clusters when there are few studies in the CBMA, and a decreasing false positive rate with larger study numbers. By contrast the standard definition (FWHM independent of the number of studies) is demonstrated to paradoxically increase the false positive rate as the number of studies increases, while reducing ability to detect true clusters for small numbers of studies. We also provide an algorithm for contrast meta-analysis, which includes a correction for multiple correlated tests that controls for the proportion of false clusters expected under the null hypothesis. Furthermore, we detail an omnibus test of difference between groups that is more sensitive than contrast meta-analysis when differences are diffuse. This test is useful where contrast meta-analysis is unrevealing.     

Black carbon accrual during 2000 years of paddy‐rice and non‐paddy cropping in the Yangtze River Delta,China

Rice straw burning has accompanied paddy management for millennia, introducing black carbon (BC) into soil as the residue of incomplete combustion. This study examined the contribution of BC to soil organic matter and the rate at which it accumulates in paddy soils as a result of prolonged paddy management. Soil depth profiles were sampled along a chronosequence of 0–2000 years of rice–wheat rotation systems and adjacent non‐paddy systems (50–700 years) in the Bay of Hangzhou (Zhejiang province, China). The soil BC content and its degree of condensation were assessed using benzene‐polycarboxylic acids (BPCAs) as geochemical markers. The results showed that despite regular long term BC input, BC only contributed 7–11% of total soil organic carbon (SOC) in the topsoil horizons. Nevertheless, along with SOC, paddy soils accumulated BC with increasing duration of management until 297 years to reach a steady‐state of 13 t BC ha^?1. This was 1.8 times more than in non‐paddy soils. The fate of BC in paddy soils (0–1 m) could be modeled revealing an average annual input of 44 kg ha^?1 yr^?1, and a mean residence time of 303 years. The subsoils contributed at least 50% to overall BC stocks, which likely derived from periods prior to land embankment and episodic burial of ancient topsoil, as also indicated by BPCA pattern changes. We conclude that there is a significant but limited accumulation of C in charred forms upon prolonged paddy management. The final contribution of BC to total SOC in paddy soils was similar to that in other aerobic ecosystems of the world.     

Serum albumin leads to false-positive results in the XTT and the MTT assay

Tetrazolium salts like 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) or sodium 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT) that form formazans after reduction are widely used to investigate cell viability. Besides cellular enzymes, some constituents of cell media and other substances reduce tetrazolium salts, thereby interfering with these assays. We describe here that different preparations of serum albumin from bovine or human origin can lead to a concentration-dependent increase in the signals of the XTT assay; therefore leading to an overestimation of cell numbers and to an underestimation of potential cytotoxic effects of compounds to be tested. The same effect was seen in the MTT assay with human serum albumin (HSA). We demonstrate that this reductive activity cannot be inactivated by proteolytic digestion, but that it is due to the free cysteine residue in albumin, and is also observed when cysteine or glutathione (GSH) are used. Binding of N-ethylmaleimide (NEM) to the free cysteine residue leads to a decrease of the albumin interference in the XTT assay.     

Differential pH-dependent cellular uptake pathways among foamy viruses elucidated using dual-colored fluorescent particles

ABSTRACT: BACKGROUND: It is thought that foamy viruses (FVs) enter host cells via endocytosis because all FV glycoproteins examined display pH-dependent fusion activities. Only the prototype FV (PFV) glycoprotein has also significant fusion activity at neutral pH, suggesting that its uptake mechanism may deviate from other FVs. To gain new insights into the uptake processes of FV in individual live host cells, we developed fluorescently labeled infectious FVs. RESULTS: N-terminal tagging of the FV envelope leader peptide domain with a fluorescent protein resulted in efficient incorporation of the fluorescently labeled glycoprotein into secreted virions without interfering with their infectivity. Double-tagged viruses consisting of an eGFP-tagged PFV capsid (Gag-eGFP) and mCherry-tagged Env (Ch-Env) from either PFV or macaque simian FV (SFVmac) were observed during early stages of the infection pathway. PFV Env, but not SFVmac Env, containing particles induced strong syncytia formation on target cells. Both virus types showed trafficking of double-tagged virions towards the cell center. Upon fusion and subsequent capsid release into the cytosol, accumulation of naked capsid proteins was observed within four hours in the perinuclear region, presumably representing the centrosomes. Interestingly, virions harboring fusion-defective glycoproteins still promoted virus attachment and uptake, but failed to show syncytia formation and perinuclear capsid accumulation. Non-fused or non-fusogenic viruses are rapidly cleared from the cells by putative lysosomal degradation. Monitoring the fraction of viruses containing both Env and capsid signals as a function of time demonstrated that PFV virions fused within the first few minutes, whereas fusion of SFVmac virions was less pronounced and observed over the entire 90 minutes measured. CONCLUSIONS: The characterized double-labeled FVs described here provide new mechanistic insights into FV early entry steps, demonstrating that productive viral fusion occurs early after target cell attachment and uptake. The analysis highlights apparent differences in the uptake pathways of individual FV species. Furthermore, the infectious double-labeled FVs promise to provide important tools for future detailed analyses on individual FV fusion events in real time using advanced imaging techniques.