Stable Composition of the Nano- and Picoplankton Community during the Ocean Iron Fertilization Experiment LOHAFEX

The iron fertilization experiment LOHAFEX was conducted in a cold-core eddy in the Southern Atlantic Ocean during austral summer. Within a few days after fertilization, a phytoplankton bloom developed dominated by nano- and picoplankton groups. Unlike previously reported for other iron fertilization experiments, a diatom bloom was prevented by iron and silicate co-limitation. We used 18S rRNA gene tag pyrosequencing to investigate the diversity of these morphologically similar cell types within the nano- and picoplankton and microscopically enumerated dominant clades after catalyzed reported deposition fluorescence in situ hybridization (CARD-FISH) with specific oligonucleotide probes. In addition to Phaeocystis, members of Syndiniales group II, clade 10–11, and the Micromonas clades ABC and E made up a major fraction of the tag sequences of the nano- and picoplankton community within the fertilized patch. However, the same clades were also dominant before the bloom and outside the fertilized patch. Furthermore, only little changes in diversity could be observed over the course of the experiment. These results were corroborated by CARD-FISH analysis which confirmed the presence of a stable nano- and picoplankton community dominated by Phaeocystis and Micromonas during the entire course of the experiment. Interestingly, although Syndiniales dominated the tag sequences, they could hardly be detected by CARD-FISH, possibly due to the intracellular parasitic life style of this clade. The remarkable stability of the nano- and picoplankton community points to a tight coupling of the different trophic levels within the microbial food web during LOHAFEX.     

Amniotic fluid stem cells to study mTOR signaling in differentiation

The protein kinase mTOR is the central player within a pathway, which is known to be involved in the regulation of e.g., cell size, cell cycle, apoptosis, autophagy, aging and differentiation. mTOR activity responds to many signals, including cellular stress, oxygen, nutrient availability, energy status and growth factors. Deregulation of this enzyme is causatively involved in the molecular development of monogenic human diseases, cancer, obesity, type 2 diabetes or neurodegeneration. Recently, mTOR has also been demonstrated to control stem cell homeostasis. A more detailed investigation of this new mTOR function will be of highest relevance to provide more explicit insights into stem cell regulation in the near future. Different cellular tools, including adult stem cells, embryonic stem cells or induced pluripotent stem cells could be used to investigate the role of mTOR in mammalian stem cell biology. Here we discuss the potential of amniotic fluid stem cells to become a promising cellular model to study the role of signaling cascades in stem cell homeostasis.     

One plus one makes three (for social networks)

Members of social network platforms often choose to reveal private information, and thus sacrifice some of their privacy, in exchange for the manifold opportunities and amenities offered by such platforms. In this article, we show that the seemingly innocuous combination of knowledge of confirmed contacts between members on the one hand and their email contacts to non-members on the other hand provides enough information to deduce a substantial proportion of relationships between non-members. Using machine learning we achieve an area under the (receiver operating characteristic) curve (AUC) of at least 0.85 for predicting whether two non-members known by the same member are connected or not, even for conservative estimates of the overall proportion of members, and the proportion of members disclosing their contacts.     

Contribution to the molecular phylogenetic analysis of extant holocephalan fishes (Holocephali, Chimaeriformes)

Much attention has been paid to the molecular phylogeny of holocephalan fishes during recent years, but sampling was very low and not all genera were examined. This study offers an extended sampling of species from all known genera to clarify their phylogeny and to provide an estimate of the time of origin of extant holocephalan taxa. Three mitochondrial genes (cytochrome b, 12S rRNA, and 16S rRNA) were sequenced and analysed using a variety of phylogenetic methods (Bayes, maximum likelihood, and maximum parsimony). Callorhinchidae diverged from Rhinochimaeridae and Chimaeridae about 187?Ma ago. Chimaeridae and Rhinochimaeridae diverged from each other about 159?Ma ago. Within Rhinochimaeridae, Neoharriotta is the sister genus to the closely related Harriotta and Rhinochimaera. Eight species of the family Chimaeridae, belonging to the genera Hydrolagus and Chimaera, were examined. They probably had a common ancestor about 107?Ma ago and appear paraphyletic. These results indicate that the traditional morphological generic definition of the families Rhinochimaeridae and Chimaeridae has to be reinvestigated.     

How to narrow down chromosomal breakpoints in small and large derivative chromosomes – a new probe set

Here a new fluorescence in situ hybridization (FISH-) based probe set is presented and its possible applications are highlighted in 34 exemplary clinical cases. The so-called pericentric-ladder-FISH (PCL-FISH) probe set enables a characterization of chromosomal breakpoints especially in small supernumerary marker chromosomes (sSMC), but can also be applied successfully in large inborn or acquired derivative chromosomes. PCL-FISH was established as 24 different chromosome-specific probe sets and can be used in two- up multicolor-FISH approaches. PCL-FISH enables the determination of a chromosomal breakpoint with a resolution between 1 and ～10 megabasepairs and is based on locus-specific bacterial artificial chromosome (BAC) probes. Results obtained on 29 sSMC cases and five larger derivative chromosomes are presented and discussed. To confirm the reliability of PCL-FISH, eight of the 29 sSMC cases were studied by array-comparative genomic hybridization (aCGH); the used sSMC-specific DNA was obtained by glass-needle based microdissection and DOP-PCR-amplification. Overall, PCL-FISH leads to a better resolution than most FISH-banding approaches and is a good tool to narrow down chromosomal breakpoints.     

Secretome analysis of Clostridium difficile strains

Clostridium difficile causes infections ranging from mild C. difficile-associated diarrhea to severe pseudomembranous colitis. Since 2003 new hypervirulent C. difficile strains (PCR ribotype 027) emerged characterized by a dramatically increased mortality. The secretomes of the three C. difficile strains CDR20291, CD196, and CD630 were analyzed and compared. Proteins were separated and analyzed by means of SDS--PAGE and LC-MS. MS data were analyzed using Mascot and proteins were checked for export signals with SecretomeP and SignalP. LC-MS analysis revealed 158 different proteins in the supernatant of C. difficile. Most of the identified proteins originate from the cytoplasm. Thirty-two proteins in CDR20291, 36 in CD196 and 26 in CD630 were identified to be secreted by C. difficile strains. Those were mainly S-layer proteins, substrate-binding proteins of ABC-transporters, cell wall hydrolases, pilin and unknown hypothetical proteins. Toxin A and toxin B were identified after growth in brain heart infusion medium using immunological techniques. The ADP-ribosyltransferase-binding component protein, which is a part of the binary toxin CDT, was only identified in the hypervirulent ribotype 027 strains. Further proteins that are secreted specifically by hypervirulent strains were identified.     

Weight loss due to a very low calorie diet differentially affects insulin sensitivity and interleukin-6 serum levels in nondiabetic obese human subjects

Inflammatory mechanisms are involved in the pathogenesis of type 2 diabetes with interleukin (IL)-6 being particularly important. While long term exercise has been shown to be associated with reduction in IL-6 serum levels in several reports, the discussion on the effect of dietary intervention on IL-6 serum levels is controversial. In the present study, we aimed to investigate the effect of weight loss due to a very low calorie diet (VLCD) on insulin sensitivity and IL-6 serum levels in nondiabetic obese human individuals. 10 patients with obesity were examined during 12 weeks of a VLCD (800 kcal/d). Body composition was measured by impedance analysis. Blood samples were taken before, during, and after the dietary intervention. Leptin, adiponectin, and IL-6 serum levels were measured by ELISA. The body weight decreased significantly from 123.9±6.2-103.5±5.6 kg with a significant reduction in body fat content (43.2±2.3-36.1±3.1%). Leptin levels exhibited a significant decrease from 56.8±5.6-27.9±5.6 ng/ml while adiponectin levels increased significantly from 7.5±0.9-10.6±1.1 μg/ml. Thereby the leptin-to-adiponectin ratio, a novel marker for insulin sensitivity, significantly improved. Mean IL-6 serum concentrations were within the normal range (3.2±0.8 pg/ml) before the study and were not significantly altered by the nutritional therapy. Despite improvement of insulin sensitivity, IL-6 serum levels did not change throughout the study period, suggesting that in nondiabetic obese human subjects IL-6 might have only a minor role in the impairment of insulin sensitivity.     

A combined DPA1~DPB1 amino acid epitope is the primary unit of selection on the HLA-DP heterodimer

Here, we present results for DPA1 and DPB1 four-digit allele-level typing in a large (n = 5,944) sample of unrelated European American stem cell donors previously characterized for other class I and class II loci. Examination of genetic data for both chains of the DP heterodimer in the largest cohort to date, at the amino acid epitope, allele, genotype, and haplotype level, allows new insights into the functional units of selection and association for the DP heterodimer. The data in this study suggest that for the DPA1-DPB1 heterodimer, the unit of selection is the combined amino acid epitope contributed by both the DPA1 and DPB1 genes, rather than the allele, and that patterns of LD are driven primarily by dimer stability and conformation of the P1 pocket. This may help explain the differential pattern of allele frequency distribution observed for this locus relative to the other class II loci. These findings further support the notion that allele-level associations in disease and transplantation may not be the most important unit of analysis, and that they should be considered instead in the molecular context.