Observing CMB polarisation through ice

Ice crystal clouds in the upper troposphere can generate polarisation signals at the uK level. This signal can seriously affect very sensitive ground based searches for E- and B-mode of Cosmic Microwave Background polarisation. In this paper we estimate this effect within the ClOVER experiment observing bands (97, 150 and 220 GHz) for the selected observing site (Llano de Chajnantor, Atacama desert, Chile). The results show that the polarisation signal from the clouds can be of the order of or even bigger than the CMB expected polarisation. Climatological data suggest that this signal is fairly constant over the whole year in Antarctica. On the other hand the stronger seasonal variability in Atacama allows for a 50% of clean observations during the dry season.Comment: 7 Pages, 4 figure

An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis

<p>Abstract</p> <p>Background</p> <p><it>Siraitia grosvenorii </it>(Luohanguo) is an herbaceous perennial plant native to southern China and most prevalent in Guilin city. Its fruit contains a sweet, fleshy, edible pulp that is widely used in traditional Chinese medicine. The major bioactive constituents in the fruit extract are the cucurbitane-type triterpene saponins known as mogrosides. Among them, mogroside V is nearly 300 times sweeter than sucrose. However, little is known about mogrosides biosynthesis in <it>S. grosvenorii</it>, especially the late steps of the pathway.</p> <p>Results</p> <p>In this study, a cDNA library generated from of equal amount of RNA taken from <it>S. grosvenorii </it>fruit at 50 days after flowering (DAF) and 70 DAF were sequenced using Illumina/Solexa platform. More than 48,755,516 high-quality reads from a cDNA library were generated that was assembled into 43,891 unigenes. De novo assembly and gap-filling generated 43,891 unigenes with an average sequence length of 668 base pairs. A total of 26,308 (59.9%) unique sequences were annotated and 11,476 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. cDNA sequences for all of the known enzymes involved in mogrosides backbone synthesis were identified from our library. Additionally, a total of eighty-five cytochrome P450 (CYP450) and ninety UDP-glucosyltransferase (UDPG) unigenes were identified, some of which appear to encode enzymes responsible for the conversion of the mogroside backbone into the various mogrosides. Digital gene expression profile (DGE) analysis using Solexa sequencing was performed on three important stages of fruit development, and based on their expression pattern, seven <it>CYP450</it>s and five <it>UDPG</it>s were selected as the candidates most likely to be involved in mogrosides biosynthesis.</p> <p>Conclusion</p> <p>A combination of RNA-seq and DGE analysis based on the next generation sequencing technology was shown to be a powerful method for identifying candidate genes encoding enzymes responsible for the biosynthesis of novel secondary metabolites in a non-model plant. Seven <it>CYP450</it>s and five <it>UDPG</it>s were selected as potential candidates involved in mogrosides biosynthesis. The transcriptome data from this study provides an important resource for understanding the formation of major bioactive constituents in the fruit extract from <it>S. grosvenorii</it>.</p

Quantitative Proteomic Approach Identifies Vpr Binding Protein as Novel Host Factor Supporting Influenza A Virus Infections in Human Cells

Influenza A virus infections are a major cause for respiratory disease in humans, which affects all age groups and contributes substantially to global morbidity and mortality. IAV have a large natural host reservoir in avian species. However, many avian IAV strains lack adaptation to other hosts and hardly propagate in humans. While seasonal or pandemic influenza A virus (IAV) strains replicate efficiently in permissive human cells, many avian IAV cause abortive non-productive infections in these hosts despite successful cell entry. However, the precise reasons for these differential outcomes are poorly defined. We hypothesized that the distinct course of an IAV infection with a given virus strain is determined by the differential interplay between specific host and viral factors. By using Spike-in SILAC mass spectrometry-based quantitative proteomics we characterized sets of cellular factors whose abundance is specifically up- or down-regulated in the course of permissive vs. non-permissive IAV infection, respectively. This approach allowed for the definition and quantitative comparison of about 3500 proteins in human lung epithelial cells in response to seasonal or low-pathogenic avian H3N2 IAV. Many identified proteins were similarly regulated by both virus strains, but also 16 candidates with distinct changes in permissive vs. non-permissive infection were found. RNAi-mediated knockdown of these differentially regulated host factors identified Vpr binding protein (VprBP) as pro-viral host factor since its down-regulation inhibited efficient propagation of seasonal IAV while over-expression increased viral replication of both seasonal and avian IAV. These results not only show that there are similar differences in the overall changes during permissive and non-permissive imfluenza virus infections, but also provide a basis to evaluate VprBP as novel anti-IAV drug target

Vertical Profiles Of Methanogenesis And Methanogens In Two Contrasting Acidic Peatlands In Central New York State, USA

Northern acidic peatlands are important sources ofatmospheric methane, yet the methanogens in themare poorly characterized. We examined methanogenicactivities and methanogen populations at differentdepths in two peatlands, McLean bog (MB) and Chicagobog (CB). Both have acidic (pH 3.5–4.5) peatsoils, but the pH of the deeper layers of CB is nearneutral,reflecting its previous existence as a neutralpHfen. Acetotrophic and hydrogenotrophic methanogenesiscould be stimulated in upper samples fromboth bogs, and phylotypes of methanogens using H2/CO2 (Methanomicrobiales) or acetate (Methanosarcinales) were identified in 16S rRNA gene clone librariesand by terminal restriction fragment lengthpolymorphism (T-RFLP) analyses using a novelprimer/restriction enzyme set that we developed. Particularlydominant in the upper layers was a clade intheMethanomicrobiales, called E2 here and the R10or fen group elsewhere, estimated by quantitativepolymerase chain reaction to be present at~108cellsper gram of dry peat. Methanogenic activity was considerablylower in deeper samples from both bogs.The methanogen populations detected by T-RFLP indeeper portions of MB were mainly E2 and the unculturedeuryarchaeal rice cluster (RC)-II group, whereaspopulations in the less acidic CB deep layers wereconsiderably different, and included aMethanomicrobialesclade we call E1-E1¢, as well as RC-I, RC-II,marine benthic group D, and a new cluster that we callthe subaqueous cluster. E2 was barely detectable inthe deeper samples from CB, further evidence for theassociations of most organisms in this group withacidic habitat

Effect of genetic variability in 20 pharmacogenes on concentrations of tamoxifen and its metabolites

Background: Tamoxifen, as a treatment of estrogen receptor positive (ER+) breast cancer, is a weak anti-estrogen that requires metabolic activation to form metabolites with higher anti-estrogenic activity. Endoxifen is the most-studied active tamoxifen metabolite, and endoxifen concentrations are highly associated with CYP2D6 activity. Associations of tamoxifen efficacy with measured or CYP2D6-predicted endoxifen concentrations have been inconclusive. Another active metabolite, 4-OHtam, and other, less active metabolites, Z-4′-endoxifen and Z-4′-OHtam, have also been reported to be associated with tamoxifen efficacy. Method: Genotype for 20 pharmacogenes was determined by VeriDose® Core Panel and VeriDose®CYP2D6 CNV Panel, followed by translation to metabolic activity phenotype following standard activity scoring. Concentrations of tamoxifen and seven metabolites were measured by UPLC-MS/MS in serum samples collected from patients receiving 20 mg tamoxifen per day. Metabolic activity was tested for association with tamoxifen and its metabolites using linear regression with adjustment for upstream metabolites to identify genes associated with each step in the tamoxifen metabolism pathway. Results: A total of 187 patients with genetic and tamoxifen concentration data were included in the analysis. CYP2D6 was the primary gene associated with the tamoxifen metabolism pathway, especially the conversion of tamoxifen to endoxifen. CYP3A4 and CYP2C9 were also responsible for the metabolism of tamoxifen. CYP2C9 especially impacted the hydroxylation to 4-OHtam, and this involved the OATP1B1 (SLCO1B1) transporter. Conclusion: Multiple genes are involved in tamoxifen metabolism and multi-gene panels could be useful to predict active metabolite concentrations and guide tamoxifen dosing.publishedVersio

Functional associations and resilience in microbial communities.

Microbial communities have inherently high levels of metabolic flexibility and functional redundancy, yet the structure of microbial communities can change rapidly with environmental perturbation. To understand whether such changes observed at the taxonomic level translate into differences at the functional level, we analyzed the structure of taxonomic and functional gene distribution across Arctic and Antarctic locations. Taxonomic diversity (in terms of alpha diversity and species richness) differed significantly with location. However, we found that functional genes distributed evenly across bacterial networks and that this functional distribution was also even across different geographic locations. For example, on average 15% of the functional genes were related to carbon cycling across all bacterial networks, slightly over 21% of the genes were stress-related and only 0.5% of the genes were linked to carbon degradation functions. In such a distribution, each bacterial network includes all of the functional groups distributed following the same proportions. However, the total number of functional genes that is included in each bacterial network differs, with some clusters including many more genes than others. We found that the proportion of times a specific gene must occur to be linked to a specific cluster is 8%, meaning the relationship between the total number of genes in the cluster and the number of genes per function follows a linear pattern: smaller clusters require a gene to appear less frequently to get fixed within the cluster, while larger clusters require higher gene frequencies. We suggest that this mechanism of functional association between equally rare or equally abundant genes could have implications for ecological resilience, as non-dominant genes also associate in fully functioning ecological networks, potentially suggesting that there are always pre-existing functional networks available to exploit new ecological niches (where they can become dominant) as they emerge; for example, in the case of rapid or sudden environmental change. Furthermore, this pattern did not correlate with taxonomic distribution, suggesting that bacteria associate based on functionality and this is independent of its taxonomic position. Our analyses based on ecological networks also showed no clear evidence of recent environmental impact on polar marine microbial communities at the functional level, unless all communities analyzed have changed exactly in the same direction and intensity, which is unlikely given we are comparing areas changing at different rates

Key roles for freshwater Actinobacteria revealed by deep metagenomics sequencing

Freshwater ecosystems are critical but fragile environments directly affecting society and its welfare. However, our understanding of genuinely freshwater microbial communities, constrained by our capacity to manipulate its prokaryotic participants in axenic cultures, remains very rudimentary. Even the most abundant components, freshwater Actinobacteria, remain largely unknown. Here, applying deep metagenomic sequencing to the microbial community of a freshwater reservoir, we were able to circumvent this traditional bottleneck and reconstruct de novo seven distinct streamlined actinobacterial genomes. These genomes represent three new groups of photoheterotrophic, planktonic Actinobacteria. We describe for the first time genomes of two novel clades, acMicro (Micrococcineae, related to Luna2,) and acAMD (Actinomycetales, related to acTH1). Besides, an aggregate of contigs belonged to a new branch of the Acidimicrobiales. All are estimated to have small genomes (approximately 1.2 Mb), and their GC content varied from 40 to 61%. One of the Micrococcineae genomes encodes a proteorhodopsin, a rhodopsin type reported for the first time in Actinobacteria. The remarkable potential capacity of some of these genomes to transform recalcitrant plant detrital material, particularly lignin-derived compounds, suggests close linkages between the terrestrial and aquatic realms. Moreover, abundances of Actinobacteria correlate inversely to those of Cyanobacteria that are responsible for prolonged and frequently irretrievable damage to freshwater ecosystems. This suggests that they might serve as sentinels of impending ecological catastrophes.This work was funded by the Spanish Ministerio de Ciencia e Innovacion/ Programa CONSOLIDER-INGENIO (Grants CSD2009-00006)This work was funded by the Generalitat Valenciana PROMETEO (Grants II/2014/012

Mycosporine-Like Amino Acids: Relevant Secondary Metabolites. Chemical and Ecological Aspects

Taxonomically diverse marine, freshwater and terrestrial organisms have evolved the capacity to synthesize, accumulate and metabolize a variety of UV-absorbing substances called mycosporine-like amino acids (MAAs) as part of an overall strategy to diminish the direct and indirect damaging effects of environmental ultraviolet radiation (UVR). Whereas the enzymatic machinery to synthesize MAAs was probably inherited from cyanobacteria ancestors via the endosymbionts hypothesis, metazoans lack this biochemical pathway, but can acquire and metabolize these compounds by trophic transference, symbiotic or bacterial association. In this review we describe the structure and physicochemical properties of MAAs, including the recently discovered compounds and the modern methods used for their isolation and identification, updating previous reviews. On this basis, we review the metabolism and distribution of this unique class of metabolites among marine organism

Diversity in gut bacterial community of school-age children in Asia

10.1038/srep08397Scientific Reports

Microbiologia molecular na aquacultura: em busca de uma comunidade microbiana saudável

The microbial communities of aquaculture systems are involved in maintaining the health and growth of farmed organisms. They participate in nutrient cycling, nutrition, disease control and water quality of the system and effluents. We use DGGE fingerprint techniques and high-throughput sequencing analyzes to access the semi-intensive and intensive aquaculture microbiota. First, we investigated the composition of the bacterioplankton communities of a recirculating aquaculture system (RAS) used for the production of juveniles sole (Solea senegalensis). The most abundant orders detected in the aquaculture of sole were: Alteromonadales, Rhodobacterales, Oceanospirillales, Vibrionales and Flavobacteriales. OTUs related to potential fish pathogens in aquaculture systems were detected, as well as naturally occurring probiotic bacteria. These may have played a role in suppressing potential pathogens of fish, keeping the aquaculture free from disease. In an aquaculture of adult sole, the presence of fish was described as the main factor influencing bacterial composition. Here, supply water served as an important seed bank for the colonization of bacterial populations in the hatchery RAS tanks, mainly related to probiotic bacteria. The importance of this compartment for the maintenance of a healthy aquaculture and its importance in the development of strategies for microbial manipulation/management of aquaculture was reinforced. Subsequently, we describe the seasonal dynamics and potential interactions of bacterial and microeukaryotic plankton communities in a semi-intensive aquaculture for European sea bass (Dicentrarchus labrax) over a year. The most abundant bacterial classes were Gammaproteobacteria, Flavobacteriia and Alphaproteobacteria; while the microeukaryotic communities were dominated by the Ochrophyta, Chlorophyta and Ciliophora groups. Here, in addition to the potential effects of abiotic parameters on microbial plankton, there was a correlation between bacterial and microeukaryote populations which may be an indication of trophic and / or metabolic interdependence between these two domains. These studies allowed us to describe the normal microbiota of aquaculture systems, their ecological interactions and the impacts exerted by environmental factors in order to support the development of strategies for the maintenance of a productive and healthy environment.As comunidades microbianas dos sistemas de aquacultura estão envolvidas na manutenção da saúde e crescimento dos organismos cultivados. Participam no ciclo dos nutrientes, nutrição, controle de doenças e qualidade da água do sistema e efluentes. Neste trabalho foram utilizadas técnicas independentes de cultivo (Denaturing Gradient Gel Electrophoresis e sequenciação) para caracterizar o microbioma da água de um sistema semi-intensivo e um sistema intensivo de aquacultura de peixes. Primeiro, investigamos a composição das comunidades bacterioplânctonicas de um sistema de aquacultura recirculante (SRA) utilizado para a produção de juvenis de linguado (Solea senegalensis). As ordens mais abundantes detectadas nas aquaculturas de liguado foram: Alteromonadales, Rhodobacterales, Oceanospirillales, Vibrionales e Flavobacteriales. Foram detetadas sequências com similaridade a espécies potencialmente patogénicas, assim como sequências com similaridade a grupos previamente descritos como probióticos. É discutido o papel destas ultimas na supressão dos potenciais patógenos de peixes e manutenção de um ambiente saudável (sem surtos de doenças). Numa aquacultura de adultos de linguados, a presença dos peixes foi descrita como um dos principais fatores determinantes na composição das comunidades bacterianas. Aqui, a água atuou como um importante banco de sementes para a colonização de populações bacterianas nos tanques do SRA, principalmente das relacionadas às bactérias probióticas. Este trabalho demonstra que a origem da água pode ter um papel relevante na manutenção de uma comunidade microbiana saudável, reforçando a sua importância em possíveis estratégias de manipulação/gestão microbiana das aquaculturas. Posteriormente, descrevemos a dinâmica sazonal e potenciais interações das comunidades de plâncton bacteriano e microeucariótico em uma aquicultura semi-intensiva para robalo (Dicentrarchus labrax) durante um ano. As classes bacterianas mais abundantes foram Gammaproteobacteria, Flavobacteriia e Alphaproteobacteria; enquanto a comunidades microeucariotica foi dominada pelos grupos Ochrophyta, Chlorophyta e Ciliophora. Aqui, além dos efeitos potenciais dos parâmetros abióticos no plâncton microbiano, houve correlação entre as populações de bactérias e microeucariotos o que pode ser uma indicação de interdependência trófica e / ou metabólica entre estes dois domínios. Estes estudos permitiram-nos descrever o microbioma normal de sistemas de aquacultura, suas interações ecológicas e os impactos exercidos pelos fatores ambientais com o intuito de fundamentar o desenvolvimento de estratégias para a manutenção de um ambiente produtivo e saudável.Programa Doutoral em Biologi