Community Next Steps for Making Globally Unique Identifiers Work for Biocollections Data

Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets. For data associated with biocollections, the biodiversity community has long recognized that an essential part of establishing and preserving linkages is to apply globally unique identifiers at the point when data are generated in the field and to persist these identifiers downstream, but this is seldom implemented in practice. There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses. In order to further progress towards a broader community consensus, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks. The workshop participants divided into four groups focusing on: identifier practice in current field biocollections; identifier application for legacy biocollections; identifiers as applied to biodiversity data records as they are published and made available in semantically marked-up publications; and cross-cutting identifier solutions that bridge across these domains. The main outcome was consensus on key issues, including recognition of differences between legacy and new biocollections processes, the need for identifier metadata profiles that can report information on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier. Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided.     

Association between oral health, cognitive impairment and oral health-related quality of life

doi: 10.1111/j.1741‐2358.2011.00542.x
Association between oral health, cognitive impairment and oral health–related quality of life Objective: Investigating oral health–related quality of life’s (OH‐QoL) relationship with cognitive state. Background: Oral health affects OH‐QoL and is poor in institutionalised and cognitively impaired people. Material and Methods: This was a cross‐sectional study involving 215 institutionalised elderly (82.9 mean age), who were interviewed, examined and cognitively screened using the Pfeiffer test. Results: Mean GOHAI score was 53.1; only 43.7% of the participants reported having a good OH‐QoL. Needing help with dressing or washing (OR 2.14; p = 0.004), having one to nine teeth (OR 4.65; p ≥ 0.001), eight or less occluding pairs (OR 2.74; p = 0.002), one to three caries (OR 1.85; p = 0.005) and being cognitive impaired (OR 0.54; p = 0.034) were significantly associated with altered OH‐QoL in bi‐variate analysis. Being edentulous (OR 3.18; p = 0.0046), having 1–9 teeth (OR 2.62; p = 0.056) and presenting mild cognitive impairment (MCI) (OR 0.32; p = 0.016) appeared as predictive variables in logistic regression for having an altered OH‐QoL. Conclusions: Participants having MCI had significantly better GOHAI score than cognitively normal residents. Performing cognitive screening parallel to applying any OH‐QoL instrument would make the results more reliable and would benefit cognitively impaired people.     

Meiosis in autologous ectopic transplants of immature testicular tissue grafted to Callithrix jacchus

Grafting of immature testicular tissue provides a tool to examine testicular development and may offer a perspective for preservation of fertility in prepubertal patients. Successful xenografting in mice, resulting in mature spermatids, has been performed in several species but has failed with testicular tissues from the common marmoset, Callithrix jacchus. Previous data indicate that the hormonal milieu provided by the mouse host might cause this failure. We conducted autologous ectopic transplantation of testicular fragments under the back skin in newborn marmoset monkeys. Seventeen months after transplantation, we found viable transplants in 2 out of the 4 grafted animals. In the transplants, tubules developed up to a state intermediate between the pregraft situation and adult controls. Dividing spermatogonia and primary spermatocytes were present. Boule-like positivity and CDC25A negativity indicated that spermatogenesis was arrested at early meiosis. Immunohistochemistry revealed normal maturation of Sertoli cells, Leydig cells, and peritubular cells. Serum testosterone values were not restored to the normal range and bioactive chorionic gonadotropin levels increased to castrate levels. Meiotic arrest could have occurred in the grafts because of lack of sufficient testosterone or because of hyperthermia caused by the ectopic position of the grafts. We conclude that autologous transplants of immature testicular tissues in the marmoset can mature up to meiosis but that normal serum testosterone levels are not restored. Further studies have to be performed to overcome the meiotic arrest to explore the model further and to develop therapeutic options.     

Discovery of a novel class of 2-mercaptohexanoic acid derivatives as highly active PPARα agonists

A novel and robust scaffold for highly active PPARα agonists based on the 2-mercaptohexanoic acid substructure is presented. Systematic structural variation of the substitution pattern of the phenolic backbone yielded detailed SAR especially of ortho and meta substituents. We corroborated the importance of the sulfur atom as well as of the n-butyl chain for PPARα activity in the 2-mercaptohexanoic acid head group by preparation of carbon analogs and α-unsubstituted derivatives. Compound 10 represents a low nano molar active PPARα activator with excellent selectivity towards PPARγ.     

First evidence for adoption in California sea lions

Demographic parameters such as birth and death rates determine the persistence of populations. Understanding the mechanisms that influence these rates is essential to developing effective management strategies. Alloparental behavior, or the care of non-filial young, has been documented in many species and has been shown to influence offspring survival. However, the role of alloparental behavior in maintaining population viability has not been previously studied. Here, we provide the first evidence for adoption in California sea lions and show that adoption potentially works to maintain a high survival rate of young and may ultimately contribute to population persistence. Alloparental behavior should have a positive effect on the population growth rate when the sum of the effects on fitness for the alloparent and beneficiary is positive.     

Genome-scale identification of membrane-associated human mRNAs

The subcellular localization of proteins is critical to their biological roles. Moreover, whether a protein is membrane-bound, secreted, or intracellular affects the usefulness of, and the strategies for, using a protein as a diagnostic marker or a target for therapy. We employed a rapid and efficient experimental approach to classify thousands of human gene products as either "membrane-associated/secreted" (MS) or "cytosolic/nuclear" (CN). Using subcellular fractionation methods, we separated mRNAs associated with membranes from those associated with the soluble cytosolic fraction and analyzed these two pools by comparative hybridization to DNA microarrays. Analysis of 11 different human cell lines, representing lymphoid, myeloid, breast, ovarian, hepatic, colon, and prostate tissues, identified more than 5,000 previously uncharacterized MS and more than 6,400 putative CN genes at high confidence levels. The experimentally determined localizations correlated well with in silico predictions of signal peptides and transmembrane domains, but also significantly increased the number of human genes that could be cataloged as encoding either MS or CN proteins. Using gene expression data from a variety of primary human malignancies and normal tissues, we rationally identified hundreds of MS gene products that are significantly overexpressed in tumors compared to normal tissues and thus represent candidates for serum diagnostic tests or monoclonal antibody-based therapies. Finally, we used the catalog of CN gene products to generate sets of candidate markers of organ-specific tissue injury. The large-scale annotation of subcellular localization reported here will serve as a reference database and will aid in the rational design of diagnostic tests and molecular therapies for diverse diseases.     

Phosphoproteomic analysis of STRIPAK mutants identifies a conserved serine phosphorylation site in PAK kinase CLA4 to be important in fungal sexual development and polarized growth

The highly conserved striatin-interacting phosphatases and kinases (STRIPAK) complex regulates phosphorylation/dephosphorylation of developmental proteins in eukaryotic microorganisms, animals and humans. To first identify potential targets of STRIPAK, we performed extensive isobaric tags for relative and absolute quantification-based proteomic and phosphoproteomic analyses in the filamentous fungus Sordaria macrospora. In total, we identified 4,193 proteins and 2,489 phosphoproteins, which are represented by 10,635 phosphopeptides. By comparing phosphorylation data from wild type and mutants, we identified 228 phosphoproteins to be regulated in all three STRIPAK mutants, thus representing potential targets of STRIPAK. To provide an exemplarily functional analysis of a STRIPAK-dependent phosphorylated protein, we selected CLA4, a member of the conserved p21-activated kinase family. Functional characterization of the ∆cla4 deletion strain showed that CLA4 controls sexual development and polarized growth. To determine the functional relevance of CLA4 phosphorylation and the impact of specific phosphorylation sites on development, we next generated phosphomimetic and -deficient variants of CLA4. This analysis identified (de)phosphorylation of a highly conserved serine (S685) residue in the catalytic domain of CLA4 as being important for fungal cellular development. Collectively, these analyses significantly contribute to the understanding of the mechanistic function of STRIPAK as a phosphatase and kinase signaling complex.     

Sur la structure des parois de l'appareil circulatoire dePhoronis psammophila Cori (Phoronida,Lophophorata)

Resume Trois types de parois ont été décrits dans l'appareil circulatoire du tronc dePhoronis psammophila. La succession des diverses couches de chaque type est la suivante: 1. cellules péritonéales — lame basale — rares cellules endothéliales; 2. cellules myoépithéliales — lame basale — rares cellules endothéliales; 3. une couche de muscles circukires, puis une de muscles longitudinaux — épaisse lame basale — endothélium continu.

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On the wall structure of the circulatory system inPhoronis psammophila Cori (Phoronida, Lophophorata)

Summary Three types of wall structure of blood vessels have been described. It consists of the following distinct layers, from exterior to interior: 1. peritoneal cells — thin basal lamina — some endothelial cells; 2. myoepithelial cells resting on a basal lamina — some endothelial cells; 3. circular and longitudinal muscle layers of myoepithelial cells — thick basal lamina — continuous endothelial lining.

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Abréviations C capillaire - ce cavité coelomique - ce cellule endothéliale - cm cellule myoépithé'liale - cp cellule péritonéale - fc fibre musculaire circulaire - fl fibre musculaire longitudinale - gs globule sanguin - lb lame basale - m myofibrille - mf myofilament - tvp tissu vasopéritonéal - V vaisseau sanguin