Mineral diversity in wild plants: benefits and bane for moose

We studied the mineral nutrition ecology of moose, Alces alces , by a comprehensive examination of concentration levels of 18 elements in browsing plants, and in rumen and distal colon contents, respectively. The plants, in total 14 species, included deciduous and evergreen trees, shrubs, herbs, grasses and aquatic macrophytes. Our study was done in four sites in southern Norway and the plants were sampled in spring, summer, autumn and winter to document seasonal trends. The plants were generally characterized by low concentrations of major elements, very low phosphorus: calcium ratios, and the willow Salix aurita – a preferred browse – had high cadmium concentrations, up to 9 ppm (dry mass). Sodium concentrations in terrestrial plants were significantly under the dietary requirement, while levels were sufficient in aquatic plants, which, however, had high concentrations of toxic heavy metals. We suggest that the moose experience a nutritional dilemma as a strong physiological need for sodium results in an overintake of heavy metals. A selective intake of plants rich in heavy metals was corroborated by high heavy metal concentrations in rumen and distal colon. Over all, the plants were characterized by a marked mineral diversity due to element concentration levels that were highly variable between species and sites. Thus, there is a strong link between plant species diversity and mineral diversity, which has a pivotal role for herbivores. It is concluded that a diversity of plant species is a prerequisite for the mineral diversity that the moose needs to obtain essential minerals, not only in sufficient amounts, but also in physiologically balanced proportions.     

Subnetwork hierarchies of biochemical pathways

MOTIVATION: The vastness and complexity of the biochemical networks that have been mapped out by modern genomics calls for decomposition into subnetworks. Such networks can have inherent non-local features that require the global structure to be taken into account in the decomposition procedure. Furthermore, basic questions such as to what extent the network (graph theoretically) can be said to be built by distinct subnetworks are little studied. RESULTS: We present a method to decompose biochemical networks into subnetworks based on the global geometry of the network. This method enables us to analyze the full hierarchical organization of biochemical networks and is applied to 43 organisms from the WIT database. Two types of biochemical networks are considered: metabolic networks and whole-cellular networks (also including for example information processes). Conceptual and quantitative ways of describing the hierarchical ordering are discussed. The general picture of the metabolic networks arising from our study is that of a few core-clusters centred around the most highly connected substances enclosed by other substances in outer shells, and a few other well-defined subnetworks. AVAILABILITY: An implementation of our algorithm and other programs for analyzing the data is available from http://www.tp.umu.se/forskning/networks/meta/ SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.tp.umu.se/forskning/networks/meta/     

Nonsuicidal self-harm in youth: a population-based survey

Background

Nonsuicidal self-harm includes cutting, scratching, burning and minor overdosing. There have been few studies that have examined the rate of self-harm and mental-health correlates among community-based youth. We performed a population-based study to determine the prevalence of nonsuicidal self-harm, its mental-health correlates and help-seeking behaviour.

Methods

We used data from the Victoria Healthy Youth Survey, a population-based longitudinal survey of youth aged 14–21 in Victoria, British Columbia. The survey included questions about the history, method, frequency, age of onset and help-seeking for nonsuicidal self-harm. Youth were interviewed between February and June 2005. Univariable group differences were analyzed using students t test for continuous data and χ² for binary or categorical data. Multivariate analyses were conducted by use of multivariate analysis of variance and logistic regression.

Results

Ninety-six of 568 (16.9%) youth indicated that they had ever harmed themselves. Self-injuries such as cutting, scratching and self-hitting were the most common forms of nonsuicidal self-harm (83.2%). The mean age of onset was 15.2 years. Of those who reported nonsuicidal self-harm, 56% had sought help for this behaviour. Participants who reported 5 or more symptoms (out of 6) in a given symptom category were more likely than those who reported less than 5 symptoms to report nonsuicidal self-harm for the following categories: depressive mood (odds ratio [OR] 2.18, confidence interval [CI] 1.28–3.7) and problems with regulation of attention, impulsivity and activity (OR 2.24, CI 1.33–3.76).

Interpretation

We found a high lifetime prevalence of nonsuicidal self-harm. Many mental-health symptoms were associated with this behaviour, particularly those with depressive mood and attention-related problems. Just over half of youth reported seeking help for nonsuicidal self-harm. Clinicians who encounter youth should be vigilant to assess for this behaviour in youth who present with mental health issues.Nonsuicidal self-harm includes behaviours such as self-cutting, scratching and burning, done without the conscious intent to take one''s life. Onset typically occurs between 14 and 24 years of age.^1,2 The most common reasons for this type of harm are regulation of affect (e.g., to reduce tension or relieve dysphoric feelings), but reasons may also include self-punishment, interpersonal reasons, sensation seeking and anti-dissociation mechanisms.³ Factors associated with nonsuicidal self-harm include being female, awareness of self harm in peers, family members who self harm, drug misuse, depression, anxiety, impulsivity, disruptive disorders and low self-esteem.^4,5 Suicide ideation and attempts are more likely to be reported among those with repeated nonsuicidal self-harm.⁶A definition of “deliberate self-harm,” which does not distinguish between suicidal and nonsuicidal intent, has been proposed by the Child and Adolescent Self-Harm in Europe research group and has been used in several school-based surveys of adolescents.^4,7 The prevalence self-harm has been studied in school-based surveys of adolescents and young adults.^4–6,8 The results of these surveys are of limited generalizability because the samples were restricted to schools in large urban centres. Thus, we performed a population-based survey of youth in western Canada to investigate nonsuicidal self-harm. Our objectives were to determine the rate of nonsuicidal self-harm among Canadian youth; to determine the mental-health factors associated with nonsuicidal self-harm; and to examine the help-seeking patterns for this behaviour.     

Glycosaminoglycan remodeling during chondrogenic differentiation of human bone marrow−/synovial-derived mesenchymal stem/stromal cells under normoxia and hypoxia

Glycosaminoglycans (GAGs) are major components of cartilage extracellular matrix (ECM), which play an important role in tissue homeostasis not only by providing mechanical load resistance, but also as signaling mediators of key cellular processes such as adhesion, migration, proliferation and differentiation. Specific GAG types as well as their disaccharide sulfation patterns can be predictive of the tissue maturation level but also of disease states such as osteoarthritis. In this work, we used a highly sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to perform a comparative study in terms of temporal changes in GAG and disaccharide composition between tissues generated from human bone marrow- and synovial-derived mesenchymal stem/stromal cells (hBMSC/hSMSC) after chondrogenic differentiation under normoxic (21% O₂) and hypoxic (5% O₂) micromass cultures. The chondrogenic differentiation of hBMSC/hSMSC cultured under different oxygen tensions was assessed through aggregate size measurement, chondrogenic gene expression analysis and histological/immunofluorescence staining in comparison to human chondrocytes. For all the studied conditions, the compositional analysis demonstrated a notable increase in the average relative percentage of chondroitin sulfate (CS), the main GAG in cartilage composition, throughout MSC chondrogenic differentiation. Additionally, hypoxic culture conditions resulted in significantly different average GAG and CS disaccharide percentage compositions compared to the normoxic ones. However, such effect was considerably more evident for hBMSC-derived chondrogenic aggregates. In summary, the GAG profiles described here may provide new insights for the prediction of cartilage tissue differentiation/disease states and to characterize the quality of MSC-generated chondrocytes obtained under different oxygen tension culture conditions.

     

Gender differences in inflammatory proteins and pathways in seasonal allergic rhinitis

In model organisms, thousands of genes differ in expression between females and males. It is not known if differences on a similar scale are found in humans nor how this relates to disease. However, in allergic disease gender differences in the levels of both inflammatory cells and proteins have been shown. In this study, we found lower nasal fluid allergen-specific IgE in women than men with seasonal allergic rhinitis (SAR). This led to genome-wide analyses of gene expression in allergen-challenged CD4⁺ cells from patients with SAR before and after treatment with cortisone. Before treatment, 975 genes differed in expression between women and men: 337 were higher in women. After treatment only 428 genes and one pathway differed in expression. The genes that differed in expression between women and men were over-represented in 10 pathways. Five of the pathways regulated chemotaxis. All five were less active in women. One of the pathways was induced by the eosinophilic chemokine CCL4. Analysis of nasal fluid CCL4 protein confirmed lower levels in women with seasonal allergic rhinitis, before and during the pollen season. By contrast, nasal fluid CCL3 levels did not differ between the genders. In summary, this study shows gender differences in specific inflammatory pathways and proteins in patients with seasonal allergic rhinitis. Further studies are warranted to examine if such differences have diagnostic and therapeutic implications in allergic diseases.     

The applicability of recurrent neural networks for biological sequence analysis

Selection of machine learning techniques requires a certain sensitivity to the requirements of the problem. In particular, the problem can be made more tractable by deliberately using algorithms that are biased toward solutions of the requisite kind. In this paper, we argue that recurrent neural networks have a natural bias toward a problem domain of which biological sequence analysis tasks are a subset. We use experiments with synthetic data to illustrate this bias. We then demonstrate that this bias can be exploitable using a data set of protein sequences containing several classes of subcellular localization targeting peptides. The results show that, compared with feed forward, recurrent neural networks will generally perform better on sequence analysis tasks. Furthermore, as the patterns within the sequence become more ambiguous, the choice of specific recurrent architecture becomes more critical.