Mathias Weber

All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing

BackgroundDNA-based methods like PCR efficiently identify and quantify the taxon composition of complex biological materials, but are limited to detecting species targeted by the choice of the primer assay. We show here how untargeted deep sequencing of foodstuff total genomic DNA, followed by bioinformatic analysis of sequence reads, facilitates highly accurate identification of species from all kingdoms of life, at the same time enabling quantitative measurement of the main ingredients and detection of unanticipated food components.ResultsSequence data simulation and real-case Illumina sequencing of DNA from reference sausages composed of mammalian (pig, cow, horse, sheep) and avian (chicken, turkey) species are able to quantify material correctly at the 1% discrimination level via a read counting approach. An additional metagenomic step facilitates identification of traces from animal, plant and microbial DNA including unexpected species, which is prospectively important for the detection of allergens and pathogens.ConclusionsOur data suggest that deep sequencing of total genomic DNA from samples of heterogeneous taxon composition promises to be a valuable screening tool for reference species identification and quantification in biosurveillance applications like food testing, potentially alleviating some of the problems in taxon representation and quantification associated with targeted PCR-based approaches.

Phylogenetic analyses of endoparasitic Acanthocephala based on mitochondrial genomes suggest secondary loss of sensory organs

The metazoan taxon Syndermata (Monogononta, Bdelloidea, Seisonidea, Acanthocephala) comprises species with vastly different lifestyles. The focus of this study is on the phylogeny within the syndermatan subtaxon Acanthocephala (thorny-headed worms, obligate endoparasites). In order to investigate the controversially discussed phylogenetic relationships of acanthocephalan subtaxa we have sequenced the mitochondrial (mt) genomes of Echinorhynchus truttae (Palaeacanthocephala), Paratenuisentis ambiguus (Eoacanthocephala), Macracanthorhynchus hirudinaceus (Archiacanthocephala), and Philodina citrina (Bdelloidea). In doing so, we present the largest molecular phylogenetic dataset so far for this question comprising all major subgroups of Acanthocephala. Alongside with publicly available mt genome data of four additional syndermatans as well as 18 other lophotrochozoan (spiralian) taxa and one outgroup representative, the derived protein-coding sequences were used for Maximum Likelihood as well as Bayesian phylogenetic analyses. We achieved entirely congruent results, whereupon monophyletic Archiacanthocephala represent the sister taxon of a clade comprising Eoacanthocephala and monophyletic Palaeacanthocephala (Echinorhynchida). This topology suggests the secondary loss of lateral sensory organs (sensory pores) within Palaeacanthocephala and is further in line with the emergence of apical sensory organs in the stem lineage of Archiacanthocephala.

Biocompatibility of Alginates for Grafting: Impact of Alginate Molecular Weight

Optimising microencapsulation technology towards the effective clinical transplantation has created the need for highly biocompatible alginates. Therefore, in this study the biocompatibility of different beads prepared from alginates with varying average molecular weight was examined. In some experiments the beads were covered with a multilayer membrane surrounded by an alginate layer. First of all, we found that beads made of a lower weight average alginate elicted a much stronger fibrotic response compared to beads made of a higher weight average alginate (LV‐alginate > MV‐alginate). The results were confirmed by the observation that the extent of tissue fibrosis was significantly increased in multilayer capsules made of an alginate with a lower weight average (core and surface LV‐alginate, Mw 0.7–1*106 g/mol, viscosity of a 0.1% solution 1–2.5 mPa s− 1) compared to multilayer capsules made of an alginate with a higher weight average (core and surface MV‐alginate; Mw 1.2–1.3*106 g/mol, viscosity of a 0.1% solution 5–7 mPa s− 1). It should be stressed, that the pro‐fibrotic effect of the LV‐alginate alginate in the core was only partially reversed by a MV‐alginate on the surface of the multilayer capsules. On the basis of the raised data, it can be assumed that the molecular weight average of the alginates have an decisive effect on the biocompatibility. Therefore, it seems to be recommendable to reduce the low molecular weight fractions of the alginate during the purification process to improve the biocompatibility.

Between Usefulness and Legitimacy Media Coverage of Governmental Intervention during the Financial Crisis and Selected Effects

We argue that during the financial crisis, economic news served as a dominant source of information for the public and as an influential factor in legitimating economic policy. We analyze (1) how German news broadcasts treated governmental intervention during the crisis and (2) selected effects on public opinion. Drawing on results from a content analysis of television news broadcasts (n = 980), we show that governmental intervention was covered substantially, focusing on fiscal measures. To investigate possible effects of the news coverage, we conducted an online experiment with subjects differing in their degree of involvement with the consequences of the crisis (n = 293). A news article treating governmental debt guarantees within a supportive frame induced subjects to approve of governmental intervention, as contrasted with an adverse version of the article. However, the effects of the media coverage were partially moderated by subjects’ involvement.

Transcriptome analysis of the spalax hypoxia survival response includes suppression of apoptosis and tight control of angiogenesis

BackgroundThe development of complex responses to hypoxia has played a key role in the evolution of mammals, as inadequate response to this condition is frequently associated with cardiovascular diseases, developmental disorders, and cancers. Though numerous studies have used mice and rats in order to explore mechanisms that contribute to hypoxia tolerance, these studies are limited due to the high sensitivity of most rodents to severe hypoxia. The blind subterranean mole rat Spalax is a hypoxia tolerant rodent, which exhibits unique longevity and therefore has invaluable potential in hypoxia and cancer research.ResultsUsing microarrays, transcript abundance was measured in brain and muscle tissues from Spalax and rat individuals exposed to acute and chronic hypoxia for varying durations. We found that Spalax global gene expression response to hypoxia differs from that of rat and is characterized by the activation of functional groups of genes that have not been strongly associated with the response to hypoxia in hypoxia sensitive mammals. Using functional enrichment analysis of Spalax hypoxia induced genes we found highly significant overrepresentation of groups of genes involved in anti apoptosis, cancer, embryonic/sexual development, epidermal growth factor receptor binding, coordinated suppression and activation of distinct groups of transcription factors and membrane receptors, in addition to angiogenic related processes. We also detected hypoxia induced increases of different critical Spalax hub gene transcripts, including antiangiogenic genes associated with cancer tolerance in Down syndrome human individuals.ConclusionsThis is the most comprehensive study of Spalax large scale gene expression response to hypoxia to date, and the first to use custom Spalax microarrays. Our work presents novel patterns that may underlie mechanisms with critical importance to the evolution of hypoxia tolerance, with special relevance to medical research.

The dynamics of online news discussions: effects of news articles and reader comments on users’ involvement, willingness to participate, and the civility of their contributions*

ABSTRACT This study investigates when and why news website visitors write civil or uncivil comments in response to news articles or related user comments. In an experiment, we manipulated the news value of news articles and the presence of ‘deliberative’ or ‘detrimental’ elements of comments to compare their impact on participants’ involvement, willingness to comment, and the comments they posted. News factors and comment characteristics increased participants’ willingness to comment via cognitive and affective involvement. Cognitive involvement made it less likely and affective involvement more likely that participants wrote uncivil comments. Additionally, involvement with previous comments increased participants’ willingness to comment on articles and vice versa. Results imply that news articles and comments dynamically shape the discussion value of online news.

Six amino acids define a minimal dimerization sequence and stabilize a transmembrane helix dimer by close packing and hydrogen bonding

Distinct amino acid sequences have been described to mediate oligomerization of transmembrane α‐helices. However, as the sequence context is crucial to determine specificity in transmembrane helix–helix interaction, the question arises how small a sequence can be without losing specificity. In the present analysis, six amino acids have been identified in the PsbF transmembrane helix dimer, which form the contact region of two interacting helices and are directly involved in helix–helix interactions. However, individual amino acids within the complex sequence pattern only together ensure sequence specificity of the analyzed transmembrane helix–helix interactions by mediating close packing and inter‐helical hydrogen bonding.

That Man Behind the Curtain: Investigating the Sexual Online Dating Behavior of Men Who Have Sex With Men but Hide Their Same-Sex Sexual Attraction in Offline Surroundings

ABSTRACT This study investigates how men who have sex with men (MSM) use chat and dating sites based on theories of stigma-related offline behavior and online self-disclosure. We hypothesize that hidden MSM (those who self-label as heterosexual or who hide their same-sex sexual attraction from family, friends, acquaintances, or a female romantic partner) differ from open MSM in how they behave on gay chat and dating sites and in offline gay venues. Drawing on a survey of 12,002 MSM, we show that hidden MSM tend to mask their identity on gay chat and dating sites while avoiding offline gay venues. They also focus more strongly on online sexual activities (e.g., masturbating during online chats) when using gay chat and dating sites. However, they spend the same amount of time on these sites, and they use them to initiate offline sexual encounters as often and as fast as open MSM.

AFS: identification and quantification of species composition by metagenomic sequencing

DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions. Using Illumina data from a reference sausage comprising four species, we reveal that AFS is independent of the sequencing assay and library preparation protocol. Cost-saving short (50-bp) single-end reads and Nextera® library preparation yield reliable results. AVAILABILITY AND IMPLEMENTATION Datasets, binaries and usage instructions are available under http://all-food-seq.sourceforge.net Raw data is available at NCBIs SRA with accession number PRJNA271645. CONTACT hankeln@uni-mainz.deSupplementary information: Supplementary data are available at Bioinformatics online.Summary: DNA‐based methods to detect and quantify taxon composition in biological materials are often based on species‐specific polymerase chain reaction, limited to detecting species targeted by the assay. Next‐generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions. Using Illumina data from a reference sausage comprising four species, we reveal that AFS is independent of the sequencing assay and library preparation protocol. Cost‐saving short (50‐bp) single‐end reads and Nextera® library preparation yield reliable results. Availability and Implementation: Datasets, binaries and usage instructions are available under http://all‐food‐seq.sourceforge.net. Raw data is available at NCBIs SRA with accession number PRJNA271645. Contact: hankeln@uni‐mainz.de Supplementary information: Supplementary data are available at Bioinformatics online.

Insights Into Aspects Behind Internet-Related Disorders in Adolescents: The Interplay of Personality and Symptoms of Adjustment Disorders

PURPOSE Problematic Internet use (PIU) that has recently been referred to as Internet-related disorder is a growing health concern. Yet, it is unclear why some adolescents are developing problematic use, whereas others sustain control. Based on previous research, we hypothesize that personality traits (low conscientiousness and high neuroticism) act as predispositions for PIU. We further hypothesize that PIU can be understood as a maladaptive reaction toward critical life events and that these maladaptive reactions are exacerbated by dysfunctional personality traits. METHODS The study investigates the prevalence of distinct subtypes of PIU among a sample of adolescents (n = 1,489; 10-17 years). Personality traits (Big Five Inventory-10 [BFI-10]), perceived stress (Perceived Stress Scale 4 [PSS-4]), and their relations to PIU (Scale for the Assessment of Internet and Computer Game Addiction [AICA-S]) were examined. As novel research questions, associations between PIU and adjustment disorders (Adjustment Disorder-New Module [ADNM]-6) and the mediating role of personality were investigated. RESULTS The prevalence of PIU was 2.5%; girls (3.0%) were more often affected than boys (1.9%). Social networking sites in girls and online games in boys were most often associated with PIU. Low conscientiousness and high neuroticism generally predicted PIU. Significantly more adolescents with PIU (70%) reported critical life events compared with those without PIU (42%). PIU was related to heightened stress and higher adjustment disorder symptoms. These associations were exacerbated by conscientiousness and neuroticism. CONCLUSIONS Although the overall prevalence for PIU is in line with previous studies, it appeared unexpectedly that girls were affected more often than boys. Adjustment disorders and stress showed strong associations with PIU. This bears implications for adapting etiopathological assumptions and early intervention strategies.