Human children rely more on social information than chimpanzees do

Human societies are characterized by more cultural diversity than chimpanzee communities. However, it is currently unclear what mechanism might be driving this difference. Because reliance on social information is a pivotal characteristic of culture, we investigated individual and social information reliance in children and chimpanzees. We repeatedly presented subjects with a reward-retrieval task on which they had collected conflicting individual and social information of equal accuracy in counterbalanced order. While both species relied mostly on their individual information, children but not chimpanzees searched for the reward at the socially demonstrated location more than at a random location. Moreover, only children used social information adaptively when individual knowledge on the location of the reward had not yet been obtained. Social information usage determines information transmission and in conjunction with mechanisms that create cultural variants, such as innovation, it facilitates diversity. Our results may help explain why humans are more culturally diversified than chimpanzees.     

ClassyFlu: Classification of Influenza A Viruses with Discriminatively Trained Profile-HMMs

Accurate and rapid characterization of influenza A virus (IAV) hemagglutinin (HA) and neuraminidase (NA) sequences with respect to subtype and clade is at the basis of extended diagnostic services and implicit to molecular epidemiologic studies. ClassyFlu is a new tool and web service for the classification of IAV sequences of the HA and NA gene into subtypes and phylogenetic clades using discriminatively trained profile hidden Markov models (HMMs), one for each subtype or clade. ClassyFlu merely requires as input unaligned, full-length or partial HA or NA DNA sequences. It enables rapid and highly accurate assignment of HA sequences to subtypes H1–H17 but particularly focusses on the finer grained assignment of sequences of highly pathogenic avian influenza viruses of subtype H5N1 according to the cladistics proposed by the H5N1 Evolution Working Group. NA sequences are classified into subtypes N1–N10. ClassyFlu was compared to semiautomatic classification approaches using BLAST and phylogenetics and additionally for H5 sequences to the new “Highly Pathogenic H5N1 Clade Classification Tool” (IRD-CT) proposed by the Influenza Research Database. Our results show that both web tools (ClassyFlu and IRD-CT), although based on different methods, are nearly equivalent in performance and both are more accurate and faster than semiautomatic classification. A retraining of ClassyFlu to altered cladistics as well as an extension of ClassyFlu to other IAV genome segments or fragments thereof is undemanding. This is exemplified by unambiguous assignment to a distinct cluster within subtype H7 of sequences of H7N9 viruses which emerged in China early in 2013 and caused more than 130 human infections. http://bioinf.uni-greifswald.de/ClassyFlu is a free web service. For local execution, the ClassyFlu source code in PERL is freely available.     

Hepatitis C Virus Hypervariable Region 1 Variants Presented on Hepatitis B Virus Capsid-Like Particles Induce Cross-Neutralizing Antibodies

Hepatitis C virus (HCV) infection is still a serious global health burden. Despite improved therapeutic options, a preventative vaccine would be desirable especially in undeveloped countries. Traditionally, highly conserved epitopes are targets for antibody-based prophylactic vaccines. In HCV-infected patients, however, neutralizing antibodies are primarily directed against hypervariable region I (HVRI) in the envelope protein E2. HVRI is the most variable region of HCV, and this heterogeneity contributes to viral persistence and has thus far prevented the development of an effective HVRI-based vaccine. The primary goal of an antibody-based HCV vaccine should therefore be the induction of cross-reactive HVRI antibodies. In this study we approached this problem by presenting selected cross-reactive HVRI variants in a highly symmetric repeated array on capsid-like particles (CLPs). SplitCore CLPs, a novel particulate antigen presentation system derived from the HBV core protein, were used to deliberately manipulate the orientation of HVRI and therefore enable the presentation of conserved parts of HVRI. These HVRI-CLPs induced high titers of cross-reactive antibodies, including neutralizing antibodies. The combination of only four HVRI CLPs was sufficient to induce antibodies cross-reactive with 81 of 326 (24.8%) naturally occurring HVRI peptides. Most importantly, HVRI CLPs with AS03 as an adjuvant induced antibodies with a 10-fold increase in neutralizing capability. These antibodies were able to neutralize infectious HCVcc isolates and 4 of 19 (21%) patient-derived HCVpp isolates. Taken together, these results demonstrate that the induction of at least partially cross-neutralizing antibodies is possible. This approach might be useful for the development of a prophylactic HCV vaccine and should also be adaptable to other highly variable viruses.     

Urinary Calprotectin and Posttransplant Renal Allograft Injury

Objective

Current methods do not predict the acute renal allograft injury immediately after kidney transplantation. We evaluated the diagnostic performance of urinary calprotectin for predicting immediate posttransplant allograft injury.

Methods

In a multicenter, prospective-cohort study of 144 incipient renal transplant recipients, we postoperatively measured urinary calprotectin using an enzyme-linked immunosorbent assay and estimated glomerular filtration rate (eGFR) after 4 weeks, 6 months, and 12 months.

Results

We observed a significant inverse association of urinary calprotectin concentrations and eGFR 4 weeks after transplantation (Spearman r = −0.33; P<0.001). Compared to the lowest quartile, patients in the highest quartile of urinary calprotectin had an increased risk for an eGFR less than 30 mL/min/1.73 m² four weeks after transplantation (relative risk, 4.3; P<0.001; sensitivity, 0.92; 95% CI, 0.77 to 0.98; specificity, 0.48; 95% CI, 0.31 to 0.66). Higher urinary calprotectin concentrations predicted impaired kidney function 4 weeks after transplantation, as well as 6 months and 12 months after transplantation. When data were analyzed using the urinary calprotectin/creatinine-ratio similar results were obtained. Urinary calprotectin was superior to current use of absolute change of plasma creatinine to predict allograft function 12 months after transplantation. Urinary calprotectin predicted an increased risk both in transplants from living and deceased donors. Multivariate linear regression showed that higher urinary calprotectin concentrations and older donor age predicted lower eGFR four weeks, 6 months, and 12 months after transplantation.

Conclusions

Urinary calprotectin is an early, noninvasive predictor of immediate renal allograft injury after kidney transplantation.     

Biogenic methane contributes to the food web of a large,shallow lake

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Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases

We performed targeted mutagenesis of a transgene and nine endogenous soybean (Glycine max) genes using zinc-finger nucleases (ZFNs). A suite of ZFNs were engineered by the recently described context-dependent assembly platform--a rapid, open-source method for generating zinc-finger arrays. Specific ZFNs targeting dicer-like (DCL) genes and other genes involved in RNA silencing were cloned into a vector under an estrogen-inducible promoter. A hairy-root transformation system was employed to investigate the efficiency of ZFN mutagenesis at each target locus. Transgenic roots exhibited somatic mutations localized at the ZFN target sites for seven out of nine targeted genes. We next introduced a ZFN into soybean via whole-plant transformation and generated independent mutations in the paralogous genes DCL4a and DCL4b. The dcl4b mutation showed efficient heritable transmission of the ZFN-induced mutation in the subsequent generation. These findings indicate that ZFN-based mutagenesis provides an efficient method for making mutations in duplicate genes that are otherwise difficult to study due to redundancy. We also developed a publicly accessible Web-based tool to identify sites suitable for engineering context-dependent assembly ZFNs in the soybean genome.     

Shrubline but not treeline advance matches climate velocity in montane ecosystems of south‐central Alaska

Tall shrubs and trees are advancing into many tundra and wetland ecosystems but at a rate that often falls short of that predicted due to climate change. For forest, tall shrub, and tundra ecosystems in two pristine mountain ranges of Alaska, we apply a Bayesian, error‐propagated calculation of expected elevational rise (climate velocity), observed rise (biotic velocity), and their difference (biotic inertia). We show a sensitive dependence of climate velocity on lapse rate and derive biotic velocity as a rigid elevational shift. Ecosystem presence identified from recent and historic orthophotos ~50 years apart was regressed on elevation. Biotic velocity was estimated as the difference between critical point elevations of recent and historic logistic fits divided by time between imagery. For both mountain ranges, the 95% highest posterior density of climate velocity enclosed the posterior distributions of all biotic velocities. In the Kenai Mountains, mean tall shrub and climate velocities were both 2.8 m y^?1. In the better sampled Chugach Mountains, mean tundra retreat was 1.2 m y^?1 and climate velocity 1.3 m y^?1. In each mountain range, the posterior mode of tall woody vegetation velocity (the complement of tundra) matched climate velocity better than either forest or tall shrub alone, suggesting competitive compensation can be important. Forest velocity was consistently low at 0.1–1.1 m y^?1, indicating treeline is advancing slowly. We hypothesize that the high biotic inertia of forest ecosystems in south‐central Alaska may be due to competition with tall shrubs and/or more complex climate controls on the elevational limits of trees than tall shrubs. Among tall shrubs, those that disperse farthest had lowest inertia. Finally, the rapid upward advance of woody vegetation may be contributing to regional declines in Dall's sheep (Ovis dalli), a poorly dispersing alpine specialist herbivore with substantial biotic inertia due to dispersal reluctance.     

Diacylglycerol metabolism in phospholipase C-treated mammalian cells

Treatment of cultured cells with phospholipase C causes increased rates of hydrolysis of cellular phosphatidylcholine and increased rates of incorporation of choline into phosphatidylcholine. The fate of the diacylglycerol produced by the phospholipase C hydrolysis was examined in two cell lines, Chinese hamster ovary and HeLa. In the former cells, turnover of the glycerol moiety of phosphatidylcholine was not enhanced by phospholipase C treatment, indicating that the phospholipase C-generated diacylglycerol was recycled into new phosphatidylcholine. In HeLa cells, turnover of the glycerol backbone of phosphatidylcholine was enhanced by phospholipase C treatment, and the increased rate of turnover of the glycerol moiety was similar to that of the phosphate moiety. Thus, the fate of diacylglycerol generated at the plasma membrane was demonstrated to differ in these two cell lines. Incorporation of precursors of diacylglycerol into phosphatidylcholine was not enhanced by phospholipase C treatment in either cell line.     

Computational geometry assessment for morphometric analysis of the mandible

This paper presents a fully automated algorithm for geometry assessment of the mandible. Anatomical landmarks could be reliably detected and distances were statistically evaluated with principal component analysis. The method allows for the first time to generate a mean mandible shape with statistically valid geometrical variations based on a large set of 497 CT-scans of human mandibles. The data may be used in bioengineering for designing novel oral implants, for planning of computer-guided surgery, and for the improvement of biomechanical models, as it is shown that commercially available mandible replicas differ significantly from the mean of the investigated population.