Introduced or glacial relict? Phylogeography of the cryptogenic tunicate Molgula manhattensis (Ascidiacea,Pleurogona)

Aim The tunicate Molgula manhattensis has a disjunct amphi‐Atlantic distribution and a recent history of world‐wide introductions. Its distribution could be the result of regional extinctions followed by post‐glacial recolonization, or anthropogenic dispersal. To determine whether the North Atlantic distribution of M. manhattensis is natural or human‐mediated, we analysed mtDNA cytochrome c oxidase subunit I (COI) sequence variation in individuals from cryptogenic and introduced ranges. Location North Atlantic Europe and America; Black Sea; San Francisco Bay; Osaka Bay. Methods Nuclear 18S rDNA sequences were used to resolve phylogenetic relationships and mtDNA COI sequences for phylogeographic analyses. Results Phylogenetic analyses confirmed that M. manhattensis and M. socialis, which are frequently confused, are distinct species. MtDNA haplotype diversity was nearly three times higher with deeper relationships among haplotypes on the North‐east American coast than in Europe. Diversity declined from south to north in America but not in Europe. In areas of known introductions (Black Sea, Japan, San Francisco Bay), M. manhattensis showed variable levels of haplotype diversity. Medium‐to‐high‐frequency haplotypes originating from the North‐west Atlantic were present in two locations of known introductions, but not in Europe. Private haplotypes were found on both sides of the Atlantic and in introduced populations. The mismatch distribution for the North‐east Atlantic coast indicates a recent expansion. Main conclusions Molgula manhattensis is native in North‐east America. However, whether it was introduced or is native to Europe remains equivocal. Additional sampling might or might not reveal the presence of putative private European haplotypes in America. The low European diversity may be explained by low effective population size and a recent expansion, or by low propagule pressure of anthropogenic introduction. Absence of medium‐to‐high‐frequency American haplotypes in Europe may be the result of exclusive transport from southern ports, or long‐term residence. These arguments are ambiguous, and M. manhattensis remains cryptogenic in Europe.     

A statistical model of the international spread of wild poliovirus in Africa used to predict and prevent outbreaks

Background

Outbreaks of poliomyelitis in African countries that were previously free of wild-type poliovirus cost the Global Polio Eradication Initiative US$850 million during 2003–2009, and have limited the ability of the program to focus on endemic countries. A quantitative understanding of the factors that predict the distribution and timing of outbreaks will enable their prevention and facilitate the completion of global eradication.

Methods and Findings

Children with poliomyelitis in Africa from 1 January 2003 to 31 December 2010 were identified through routine surveillance of cases of acute flaccid paralysis, and separate outbreaks associated with importation of wild-type poliovirus were defined using the genetic relatedness of these viruses in the VP1/2A region. Potential explanatory variables were examined for their association with the number, size, and duration of poliomyelitis outbreaks in 6-mo periods using multivariable regression analysis. The predictive ability of 6-mo-ahead forecasts of poliomyelitis outbreaks in each country based on the regression model was assessed. A total of 142 genetically distinct outbreaks of poliomyelitis were recorded in 25 African countries, resulting in 1–228 cases (median of two cases). The estimated number of people arriving from infected countries and <5-y childhood mortality were independently associated with the number of outbreaks. Immunisation coverage based on the reported vaccination history of children with non-polio acute flaccid paralysis was associated with the duration and size of each outbreak, as well as the number of outbreaks. Six-month-ahead forecasts of the number of outbreaks in a country or region changed over time and had a predictive ability of 82%.

Conclusions

Outbreaks of poliomyelitis resulted primarily from continued transmission in Nigeria and the poor immunisation status of populations in neighbouring countries. From 1 January 2010 to 30 June 2011, reduced transmission in Nigeria and increased incidence in reinfected countries in west and central Africa have changed the geographical risk of polio outbreaks, and will require careful immunisation planning to limit onward spread. Please see later in the article for the Editors'' Summary     

High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis Endosperm

Genomic imprinting is an epigenetic phenomenon leading to parent-of-origin specific differential expression of maternally and paternally inherited alleles. In plants, genomic imprinting has mainly been observed in the endosperm, an ephemeral triploid tissue derived after fertilization of the diploid central cell with a haploid sperm cell. In an effort to identify novel imprinted genes in Arabidopsis thaliana, we generated deep sequencing RNA profiles of F1 hybrid seeds derived after reciprocal crosses of Arabidopsis Col-0 and Bur-0 accessions. Using polymorphic sites to quantify allele-specific expression levels, we could identify more than 60 genes with potential parent-of-origin specific expression. By analyzing the distribution of DNA methylation and epigenetic marks established by Polycomb group (PcG) proteins using publicly available datasets, we suggest that for maternally expressed genes (MEGs) repression of the paternally inherited alleles largely depends on DNA methylation or PcG-mediated repression, whereas repression of the maternal alleles of paternally expressed genes (PEGs) predominantly depends on PcG proteins. While maternal alleles of MEGs are also targeted by PcG proteins, such targeting does not cause complete repression. Candidate MEGs and PEGs are enriched for cis-proximal transposons, suggesting that transposons might be a driving force for the evolution of imprinted genes in Arabidopsis. In addition, we find that MEGs and PEGs are significantly faster evolving when compared to other genes in the genome. In contrast to the predominant location of mammalian imprinted genes in clusters, cluster formation was only detected for few MEGs and PEGs, suggesting that clustering is not a major requirement for imprinted gene regulation in Arabidopsis.     

Yeast thioredoxin peroxidase expression enhances the resistance of Escherichia coli to oxidative stress induced by singlet oxygen

Abstract

Singlet oxygen (¹O₂) is a highly reactive form of molecular oxygen that may harm living systems by oxidizing critical cellular macromolecules. A soluble protein from Saccharomyces cerevisiae specifically provides protection against a thiol-containing metal-catalyzed oxidation system (thiol/Fe³⁺/O₂) but not against an oxidation system without thiol. This 25 kDa protein acts as a peroxidase but requires the NADPH-dependent thioredoxin system or a thiol-containing intermediate, and was named thioredoxin peroxidase (TPx). The role of TPx in the cellular defense against oxidative stress induced by singlet oxygen was investigated in Escherichia coli containing an expression vector with a yeast genomic DNA fragment that encodes TPx and mutant in which the catalytically essential amino acid cysteine (Cys-47) has been replaced with alanine by a site-directed mutagenesis. Upon exposure to methylene blue and visible light, which generates singlet oxygen, there was a distinct difference between the two strains in regard to growth kinetics, viability, the accumulation of oxidized proteins and lipids, and modulation of activities of superoxide dismutase and catalase. The results suggest that TPx may play an important protective role in a singlet oxygen-mediated cellular damage.     

Marine bioactivity in Irish waters

In 2009, the Marine Biodiscovery Laboratory was set-up at the Marine Institute with funds from the Marine Institute and the Beaufort Marine Biodiscovery Research Programme. The Marine Biodiscovery Laboratory has already processed over 130 marine specimens from coastal zones and from the Deep Sea (≤3,000 m) within the Marine Irish Exclusive Economic Zone. Beaufort Biodiscovery funded taxonomists are involved in species identification and elucidation of evolutionary relationships. The project approach links sampling, systematics, extraction, microbial metagenomics and biomaterials. The Laboratory consists of approximately 56 m² including an extraction and a bioassay suite. The Laboratory samples and assesses marine biological diversity geared towards developing natural products for drug discovery, advanced material applications and bio-medical devices. Samples are tracked from sample log-into right through to extraction and bioassay using a customised Marine Biodiscovery Database. The extraction procedure is described along with the anti-bacterial bioassay selected for routine use. The Marine Biodiscovery Database manages the data generated and links the data collected by the project’s stakeholders to existing biodiversity, genetic and chemical resources. The system uses in-house developed software tools to merge biodiscovery data collected with other MI resources and external databases and for the data mining and visualisation of biogeographical, genetic and chemical information aimed at the identification of potential biodiversity and bioactivity “hotspots”.     

温度植被干旱指数在蒙古高原干旱监测中的应用

以蒙古高原为研究区,选择2000—2019年植物生长季的MODIS归一化植被指数(NDVI)和陆地表面温度(LST)构建NDVI-LST特征空间,由该特征空间计算蒙古高原温度植被干旱指数(TVDI);利用Theil-Sen Median趋势分析、Mann-Kendall检验及Hurst指数方法分析蒙古高原TVDI的时空变化特征和未来的变化趋势,利用偏相关分析法探究气象因子与蒙古高原TVDI之间的关系。结果表明: 2000—2019年,蒙古高原TVDI以0.0001·a^-1呈增大趋势,期间,蒙古高原的干旱情况小幅加重,其中,草甸草原和典型草原干旱情况逐渐减轻,而荒漠草原和高山草地干旱情况加重。蒙古高原TVDI的Hurst指数均值为0.45,小于0.5的地区面积占比为71.5%,说明大部分地区2000—2019年的TVDI变化趋势与过去相反。中部的荒漠草原地区和东部的草甸草原地区未来干旱情况可能加重;典型草原的大部分地区以及内蒙古境内的荒漠草原未来干旱可能减轻;高山草地地区的干旱变化无法确定。蒙古高原有33.6%的地区TVDI与气温呈显著正相关,34.8%的地区TVDI与降水量呈显著负相关,其中,典型草原受气象因子的影响最显著。     

Human epidermal Langerhans cells replenish skin xenografts and are depleted by alloreactive T cells in vivo

Epidermal Langerhans cells (LC) are potent APCs surveying the skin. They are crucial regulators of T cell activation in the context of inflammatory skin disease and graft-versus-host disease (GVHD). In contrast to other dendritic cell subtypes, murine LC are able to reconstitute after local depletion without the need of peripheral blood-derived precursors. In this study, we introduce an experimental model of human skin grafted to NOD-SCID IL2Rγ(null) mice. In this model, we demonstrate that xenografting leads to the transient loss of LC from the human skin grafts. Despite the lack of a human hematopoietic system, human LC repopulated the xenografts 6 to 9 wk after transplantation. By staining of LC with the proliferation marker Ki67, we show that one third of the replenishing LC exhibit proliferative activity in vivo. We further used the skin xenograft as an in vivo model for human GVHD. HLA-disparate third-party T cells stimulated with skin donor-derived dendritic cells were injected intravenously into NOD-SCID IL2Rγ(null) mice that had been transplanted with human skin. The application of alloreactive T cells led to erythema and was associated with histological signs of GVHD limited to the transplanted human skin. The inflammation also led to the depletion of LC from the epidermis. In summary, we provide evidence that human LC are able to repopulate the skin independent of blood-derived precursor cells and that this at least partly relates to their proliferative capacity. Our data also propose xeno-transplantation of human skin as a model system for studying the role of skin dendritic cells in the efferent arm of GVHD.     

湖北房县下寒武统西蒿坪段钉形骨片化石

本文对采自湖北房县三座庵剖面下寒武统西蒿坪段的钉形骨片(nail-shaped)化石进行了研究,系统厘定和描述了2属2种,分别为Parazhijinites guizhouensis和Cambroclavus angxianensis;其中以C.fangxianensis骨片化石最为丰富,由三种类型的骨片组成,它们可能...     

Association mapping for partial resistance to Phytophthora sojae in soybean (Glycine max (L.) Merr.)

Association mapping is a powerful high-resolution mapping tool for complex traits. The objective of this study was to identify QTLs for partial resistance to Phytophthora sojae. In this study, we evaluated a total of 214 soybean accessions by the hypocotyl inoculation method, and 175 were susceptible. The 175 susceptible accessions were then evaluated for P. sojae partial resistance using slant board assays. The 175 accessions were screened with 138 SSR markers that generated 730 SSR alleles. A subset of 495 SSR loci with minor allele frequency (MAF) ≥ 0.05 was used for association mapping by the Tassel general linear model (GLM) and mixed linear model (MLM) program. This soybean population could be divided into two subpopulations and no or weak relatedness was detected between pairwise accessions. Four SSR alleles, Satt634-133, Satt634-149, Sat_222-168 and Satt301-190, associated with partial resistance to P. sojae were detected by both GLM and MLM methods. Of these identified markers, one marker, Satt301, was located in regions where P. sojae resistance QTL have been previously mapped using linkage analysis. The identified markers will help to understand the genetic basis of partial resistance, and facilitate future marker-assistant selection aimed to improve resistance to P. sojae and reduce disease-related mortality in soybean.     

Proteomic Changes of Alveolar Lining Fluid in Illnesses Associated with Exposure to Inhaled Non-Infectious Microbial Particles

Background

Hyperresponsiveness to inhaled non-infectious microbial particles (NIMPs) has been associated with illnesses in the airways. Hypersensitivity pneumonitis (HP) is considered to be the prototype for these NIMPs-related diseases; however, there is no consensus on the definitions or diagnostic criteria for HP and the spectrum of related illnesses.

Methods and Findings

In order to identify the possible diagnostic markers for illnesses associated with NIMPs in alveolar lining fluid, we performed a proteomic analysis using a two-dimensional difference gel electrophoresis on bronchoalveolar lavage (BAL) fluid from patients with exposure to NIMPs in the context of damp building-related illness (DBRI) or conditions on the borderline to acute HP, designated here as agricultural type of microbial exposure (AME). Samples from patients with HP and sarcoidosis (SARC) were included for reference. Results were compared to results of healthy subjects (CTR). Western blot was used for validation of potential marker proteins from BAL fluid and plasma. Protein expression patterns suggest a close similarity between AME and HP, while DBRI was similar to CTR. However, in DBRI the levels of the inflammation associated molecules galectin-3 and alpha-1-antitrypsin were increased. A novel finding emerging from this study was the increases of semenogelin levels in BAL fluid from patients with AME, HP and SARC. Histone 4 levels were increased in AME, HP and SARC. Elevated plasma levels of histone 2B were detected in HP and SARC, suggesting it to be a potential blood indicator for inflammatory diseases of the lungs.

Conclusions

In this study, the proteomic changes in bronchoalveolar lavage of DBRI patients were distinct from other NIMP exposure associated lung diseases, while changes in AME overlapped those observed for HP patient samples. Some of the proteins identified in this study, semenogelin and histone 4, could function as diagnostic markers for differential diagnosis between DBRI and HP-like conditions.