Inactivation of Omi/HtrA2 protease leads to the deregulation of mitochondrial Mulan E3 ubiquitin ligase and increased mitophagy

Omi/HtrA2 is a nuclear encoded mitochondrial serine protease with dual and opposite functions that depend entirely on its subcellular localization. During apoptosis, Omi/HtrA2 is released into the cytoplasm where it participates in cell death. While confined in the inter-membrane space of the mitochondria, Omi/HtrA2 has a pro-survival function that may involve the regulation of protein quality control (PQC) and mitochondrial homeostasis. Loss of Omi/HtrA2's protease activity causes the neuromuscular disorder of the mnd2 (motor neuron degeneration 2) mutant mice. These mice develop multiple defects including neurodegeneration with parkinsonian features. Loss of Omi/HtrA2 in non-neuronal tissues has also been shown to cause premature aging. The normal function of Omi/HtrA2 in the mitochondria and how its deregulation causes neurodegeneration or premature aging are unknown. Here we report that the mitochondrial Mulan E3 ubiquitin ligase is a specific substrate of Omi/HtrA2. During exposure to H₂O₂, Omi/HtrA2 degrades Mulan, and this regulation is lost in cells that carry the inactive protease. Furthermore, we show accumulation of Mulan protein in various tissues of mnd2 mice as well as in Omi/HtrA2(−/−) mouse embryonic fibroblasts (MEFs). This causes a significant decrease of mitofusin 2 (Mfn2) protein, and increased mitophagy. Our work describes a new stress-signaling pathway that is initiated in the mitochondria and involves the regulation of Mulan by Omi/HtrA2 protease. Deregulation of this pathway, as it occurs in mnd2 mutant mice, causes mitochondrial dysfunction and mitophagy, and could be responsible for the motor neuron disease and the premature aging phenotype observed in these animals.     

Effects of long‐term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach

To understand the fine‐scale effects of changes in nutrient availability on eukaryotic soil microorganisms communities, a multiple barcoding approach was used to analyse soil samples from four different treatments in a long‐term fertilization experiment. We performed PCR amplification on soil DNA with primer pairs specifically targeting the 18S rRNA genes of all eukaryotes and three protist groups (Cercozoa, Chrysophyceae‐Synurophyceae and Kinetoplastida) as well as the ITS gene of fungi and the 23S plastid rRNA gene of photoautotrophic microorganisms. Amplicons were pyrosequenced, and a total of 88 706 quality filtered reads were clustered into 1232 operational taxonomic units (OTU) across the six data sets. Comparisons of the taxonomic coverage achieved based on overlapping assignment of OTUs revealed that half of the eukaryotic taxa identified were missed by the universal eukaryotic barcoding marker. There were only little differences in OTU richness observed between organic‐ (farmyard manure), mineral‐ and nonfertilized soils. However, the community compositions appeared to be strongly structured by organic fertilization in all data sets other than that generated using the universal eukaryotic 18S rRNA gene primers, whereas mineral fertilization had only a minor effect. In addition, a co‐occurrence based network analysis revealed complex potential interaction patterns between OTUs from different trophic levels, for example between fungivorous flagellates and fungi. Our results demonstrate that changes in pH, moisture and organic nutrients availability caused shifts in the composition of eukaryotic microbial communities at multiple trophic levels.     

T17b murine embryonal endothelial progenitor cells can be induced towards both proliferation and differentiation in a fibrin matrix

Endothelial progenitor cells (EPC) may enhance blood vessel formation in a variety of clinical settings such as ischaemia and tumour angiogenesis as well as in tissue-engineered matrices. In the present study, we cultured a murine endothelial progenitor cell line, T17b, in vitro in cell culture as well as in an FDA-approved fibrin matrix and investigated cell proliferation, differentiation and secretion patterns of the angiogenic growth factor VEGF under hypoxia and differentiation. We show that T17b EPC remain viable for at least 8 days in the fibrin matrix where they proliferate and form clusters including lumen-like structures. Proliferation in fibrin clots overlayed with basal medium (BM) was confirmed morphologically and immunohistochemically by positive Ki67 staining, indicating mitotic activity. Significant cell proliferation and Ki-67 expression were absent when cells were incubated with dibutyryl-cAMP and retinoic acid (RA). Incubation with dibutyryl-cAMP and RA stimulated the expression of the EPC differentiation markers von Willebrand Factor (vWF) and VEGF receptor 2 (VEGFR-2), indicating successful differentiation in the fibrin clot. EPC differentiation induced by dibutyryl-cAMP and RA was confirmed in 2-D chamber slide cultures by positive vWF immunostaining, which was absent in BM controls. EPC chamber slides also displayed positive vWF staining when exposed to hypoxia under BM conditions, indicating EPC activation and differentiation could also be induced by hypoxia. Taken together, T17b EPC secrete increased levels of VEGF when submitted to either hypoxia or differentiation and can be differentiated into mature endothelial cells not only in cell and matrigel cultures but also in a fibrin matrix that is FDA approved for clinical application.     

分布区扩张的群体遗传学后果:类型与过程,以栎瘿蜂为模型系统（英）

生物入侵是不均衡世界的一个永恒话题,尤其是当人类有意或无意地引入物种后,很多引入显然是无害的,但另外一些则有着严重的后果,会给入侵地的生物以至于整个生物群落造成影响,本文总结了分布区扩张的常见模式,概述了它们对遗传多样性和种群结构式样所造成的影响,描述了如何根据以一批遗传标记所得到的遗传多样性式样来推断入侵途径,来揭示伴随扩张选择和嘌变在形成种群遗传样式中的作用,本文对日益增多的群体遗传学方法进行了总结,这些技术可以用来在不同的时间尺度上推断种群规模所发生的巨大变化（瓶颈效应及种群扩张）,最后,我们以欧洲栎瘿蜂（膜翅目,瘿蜂科,瘿蜂族）一系列入侵的数据为例对一些方法进行了说明,从500-10000年的时间尺度上,多态的等位酶位点上等位基因频率的数据表明：1）遗传多样性沿入侵路线呈不断下降的趋势,支持了冰河期避难所作为遗传多样性中心的作用;2）入侵地区的种群与该物种原产地的种群相比,遗传上的分化更为强烈,这种种群结构在空间上的变异可能是被栎瘿蜂开发的资源尤其是栎树寄主在斑块上出现变异的反映。     

Cryptic serpulid-microbialite bioconstructions in the Kakoskali submarine cave (Cyprus,Eastern Mediterranean)

The biostalactites from the Kakoskali cave in Cyprus represent a new example of the complex biotic relationships between skeletal organisms and microbial communities in building bioconstructions of cryptic marine environments. Biostalactites are mainly constituted of polychaetes of the family Serpulidae and, to a lesser degree, foraminifers and bryozoans. Within the skeletal framework of these organisms, two types of microcrystalline calcite (micrite) have been recognized: autochthonous and detrital micrite. The autochthonous fraction is syndepositionally lithified and occurs as clotted peloidal and, subordinately, aphanitic (structureless) textures, suggesting the presence of heterotrophic microbial activities thriving on decaying metazoan organic matter. This fraction is limited to the protected portions of the bioconstructions, especially in the inner and lower parts. The presence of iron and manganesiferous oxidizing bacteria is suggested by the deposition of ferromanganesiferous crusts and Frutexites-like structures. These microbial-induced biomineralizations are the main evidence of carbonatogenetic and Fe–Mn, autotrophic and chemoheterotrophic, bacterial activities. The Kakoskali cave is frequently visited by divers who, during their immersions, resuspend the fine bottom sediment, which later covers the surface of the bioconstructions, disturbing the delicate equilibrium of the biotic association. This perturbation, which is also caused by strong waves and currents, during winter months, reflects on the bioconstruction morphologies, community composition, and colonization pattern. Bioconstructions exhibit an upper smooth surface, produced by few taxa (e.g., polychaetes, foraminifers), hosting a low number of living individuals, and a lower comparably rough surface, colonized by a more abundant community showing a higher species richness. The ratio surface roughness/smoothness is related to micrite sediment type: the upper part is mainly characterized by loose detrital micrite while the internal and lower parts by syndepositional cemented autochthonous micrite.     

Evidence for genetic differentiation and variable recombination rates among Dutch populations of the opportunistic human pathogen Aspergillus fumigatus

As the frequency of antifungal drug resistance continues to increase, understanding the genetic structure of fungal populations, where resistant isolates have emerged and spread, is of major importance. Aspergillus fumigatus is an ubiquitously distributed fungus and the primary causative agent of invasive aspergillosis (IA), a potentially lethal infection in immunocompromised individuals. In the last few years, an increasing number of A. fumigatus isolates has evolved resistance to triazoles, the primary drugs for treating IA infections. In most isolates, this multiple-triazole-resistance (MTR) phenotype is caused by mutations in the cyp51A gene, which encodes the protein targeted by the triazoles. We investigated the genetic differentiation and reproductive mode of A. fumigatus in the Netherlands, the country where the MTR phenotype probably originated, to determine their role in facilitating the emergence and distribution of resistance genotypes. Using 20 genome-wide neutral markers, we genotyped 255 Dutch isolates including 25 isolates with the MTR phenotype. In contrast to previous reports, our results show that Dutch A. fumigatus genotypes are genetically differentiated into five distinct populations. Four of the five populations show significant linkage disequilibrium, indicative of an asexual reproductive mode, whereas the fifth population is in linkage equilibrium, indicative of a sexual reproductive mode. Notably, the observed genetic differentiation among Dutch isolates does not correlate with geography, although all isolates with the MTR phenotype nest within a single, predominantly asexual, population. These results suggest that both reproductive mode and genetic differentiation contribute to the structure of Dutch A. fumigatus populations and are probably shaping the evolutionary dynamics of drug resistance in this potentially deadly pathogen.     

Discriminating between rival biochemical network models: three approaches to optimal experiment design

Background  

The success of molecular systems biology hinges on the ability to use computational models to design predictive experiments, and ultimately unravel underlying biological mechanisms. A problem commonly encountered in the computational modelling of biological networks is that alternative, structurally different models of similar complexity fit a set of experimental data equally well. In this case, more than one molecular mechanism can explain available data. In order to rule out the incorrect mechanisms, one needs to invalidate incorrect models. At this point, new experiments maximizing the difference between the measured values of alternative models should be proposed and conducted. Such experiments should be optimally designed to produce data that are most likely to invalidate incorrect model structures.