Molecular characterization and genetic structure of the Nero Siciliano pig breed

Nero Siciliano is an autochthonous pig breed that is reared mainly in semi-extensive systems in northeastern Sicily. Despite its economic importance and well-appreciated meat products, this breed is currently endangered. Consequently, an analysis of intra-breed variability is a fundamental step in preserving this genetic resource and its breeding system. In this work, we used 25 microsatellite markers to examine the genetic composition of 147 unrelated Nero Siciliano pigs. The total number of alleles detected (249, 9.96 per locus) and the expected heterozygosity (0.708) indicated that this breed had a high level of genetic variability. Bayesian cluster analysis showed that the most likely number of groups into which the sample could be partitioned was nine. Based on the proportion of each individuals genome derived from ancestry, pigs with at least 70% of their genome belonging to one cluster were assigned to that cluster. The cluster size ranged from 7 to 17 (n = 108). Genetic variability in this sub-population was slightly lower than in the whole sample, genetic differentiation among clusters was moderate (F(ST) 0.125) and the F(IS) value was 0.011. NeighborNet and correspondence analysis revealed two clusters as the most divergent. Molecular coancestry analysis confirmed the good within-breed variability and highlighted the clusters that retained the highest genetic diversity.     

Rock weathering creates oases of life in a High Arctic desert

During primary colonization of rock substrates by plants, mineral weathering is strongly accelerated under plant roots, but little is known on how it affects soil ecosystem development before plant establishment. Here we show that rock mineral weathering mediated by chemolithoautotrophic bacteria is associated to plant community formation in sites recently released by permanent glacier ice cover in the Midtre Lovénbreen glacier moraine (78°53′N), Svalbard. Increased soil fertility fosters growth of prokaryotes and plants at the boundary between sites of intense bacterial mediated chemolithotrophic iron‐sulfur oxidation and pH decrease, and the common moraine substrate where carbon and nitrogen are fixed by cyanobacteria. Microbial iron oxidizing activity determines acidity and corresponding fertility gradients, where water retention, cation exchange capacity and nutrient availability are increased. This fertilization is enabled by abundant mineral nutrients and reduced forms of iron and sulfur in pyrite minerals within a conglomerate type of moraine rock. Such an interaction between microorganisms and moraine minerals determines a peculiar, not yet described model for soil genesis and plant ecosystem formation with potential past and present analogues in other harsh environments with similar geochemical settings.     

Multidistrict human mesenchymal vascular cells: pluripotency and stemness characteristics

Background aimsThe presence of ectopic tissues in the pathologic artery wall raises the issue of whether multipotent stem cells may reside in the vasculature itself. Recently mesenchymal stromal cells (MSC) have been isolated from different human vascular segments (VW MSC), belying the previous view that the vessel wall is a relatively quiescent tissue.MethodsResident multipotent cells were recovered from fresh arterial segments (aortic arches, thoracic and femoral arteries) collected in a tissue-banking facility and used to establish an in situ and in vitro study of the stemness features and multipotency of these multidistrict MSC populations.ResultsNotch-1⁺, Stro-1⁺, Sca-1⁺ and Oct-4⁺ cells were distributed along an arterial wall vasculogenic niche. Multidistrict VW MSC homogeneously expressed markers of stemness (Stro-1, Notch-1 and Oct-4) and MSC lineages (CD44, CD90, CD105, CD73, CD29 and CD166) whilst they were negative for hematopoietic and endothelial markers (CD34, CD45, CD31 and vWF). Each VW MSC population had characteristics of stem cells, i.e. a high efflux capability for Hoechst 33342 dye and the ability to form spheroids when grown in suspension and generate colonies when seeded at low density. Again, VW MSC cultured in induction media exhibited adipogenic, chondrogenic and leiomyogenic potential but less propensity to osteogenic differentiation, as documented by histochemical, immunohistochemical, molecular and electron microscopy analysis.ConclusionsOverall, these findings may enlighten the physiopathologic mechanisms of vascular wall diseases as well as having potential implications for cellular, genetic and tissue engineering approaches to treating vascular pathologies when these are unresponsive to medical and surgical therapies.     

Learning gene regulatory networks from only positive and unlabeled data

Background  

Recently, supervised learning methods have been exploited to reconstruct gene regulatory networks from gene expression data. The reconstruction of a network is modeled as a binary classification problem for each pair of genes. A statistical classifier is trained to recognize the relationships between the activation profiles of gene pairs. This approach has been proven to outperform previous unsupervised methods. However, the supervised approach raises open questions. In particular, although known regulatory connections can safely be assumed to be positive training examples, obtaining negative examples is not straightforward, because definite knowledge is typically not available that a given pair of genes do not interact.     

The 3D path of body centre of mass during adult human walking on force treadmill

Three-dimensional (3D) path of the body centre of mass (CM) over an entire stride was computed from ground reaction forces during walking at constant average speed on a treadmill mounted on 3D force sensors. Data were obtained from 18 healthy adults at speeds ranging from 0.30 to 1.40 m s^?1, in 0.1 m s^?1 increments. Six subsequent strides were analyzed for each subject and speed (total strides=1296). The test session lasted about 30 min (10 min for walking). The CM path had an upward concave figure-of-eight shape that was highly consistent within and across subjects. Vertical displacement of the CM increased monotonically as a function of walking speed. The forward and particularly lateral displacements of the CM showed a U-shaped relationship to speed. The same held for the total 3D displacement (25.6–16.0 cm, depending on the speed). The results provide normative benchmarks and suggest hypotheses for further physiologic and clinical research. The familiar inverted pendulum model might be expanded to gyroscopic, “spin-and-turn” models. Abnormalities of the 3D path might flag motor impairments and recovery.     

The dynamic interaction of AMBRA1 with the dynein motor complex regulates mammalian autophagy

Autophagy is an evolutionary conserved catabolic process involved in several physiological and pathological processes such as cancer and neurodegeneration. Autophagy initiation signaling requires both the ULK1 kinase and the BECLIN 1-VPS34 core complex to generate autophagosomes, double-membraned vesicles that transfer cellular contents to lysosomes. In this study, we show that the BECLIN 1-VPS34 complex is tethered to the cytoskeleton through an interaction between the BECLIN 1-interacting protein AMBRA1 and dynein light chains 1/2. When autophagy is induced, ULK1 phosphorylates AMBRA1, releasing the autophagy core complex from dynein. Its subsequent relocalization to the endoplasmic reticulum enables autophagosome nucleation. Therefore, AMBRA1 constitutes a direct regulatory link between ULK1 and BECLIN 1-VPS34, which is required for core complex positioning and activity within the cell. Moreover, our results demonstrate that in addition to a function for microtubules in mediating autophagosome transport, there is a strict and regulatory relationship between cytoskeleton dynamics and autophagosome formation.     

Imaging of cell trafficking in Crohn's disease

Inflammatory bowel diseases are represented by ulcerative colitis and Crohn's disease, both consisting of a chronic, uncontrolled inflammation of the intestinal mucosa of any part of the gastrointestinal tract with patchy or continuous inflammation. Ileo‐colonoscopy is considered the current gold standard imaging technique for the diagnosis. However, as the majority of patients need a long‐term follow‐up it would be ideal to rely on a non‐invasive technique with good compliance. This review focuses on nuclear medicine imaging techniques in Crohn's disease. Different scintigraphic methods of imaging cells involved in the pathogenesis are described. The radiopharmaceuticals can be divided into non‐specific radiopharmaceuticals for inflammation and specific radiopharmaceuticals that directly image lymphocytes involved in the process. This non‐invasive molecular imaging approach can be useful also because it images the small bowel or other areas––where colonoscopy is not useful—and that it may play a role for constant follow‐up, because relapses are frequent. Finally, an update on other imaging modalities, and particularly MRI, in the evaluation of Crohn's disease activity, is provided. Although MRI cannot directly detect inflammatory cells, it has shown a high sensitivity in detecting the macroscopic signs of inflammation at the level of the intestinal wall affected by Crohn's disease and Ulcerative colitis. The current diagnostic value of MRI in the detection of inflamed bowel segment and in the assessment of CD activity, as well the potentials MR spectroscopy, MR diffusion imaging and MR molecular imaging, is briefly discussed. J. Cell. Physiol. 223:562–571, 2010. © 2010 Wiley‐Liss, Inc.     

PTPD1 supports receptor stability and mitogenic signaling in bladder cancer cells

PTPD1, a cytosolic non-receptor protein-tyrosine phosphatase, stimulates the Src-EGF transduction pathway. Localization of PTPD1 at actin cytoskeleton and adhesion sites is required for cell scattering and migration. Here, we show that during EGF stimulation, PTPD1 is rapidly recruited to endocytic vesicles containing the EGF receptor. Endosomal localization of PTPD1 is mediated by interaction with KIF16B, an endosomal kinesin that modulates receptor recycling at the plasma membrane. Silencing of PTPD1 promotes degradation of EGF receptor and inhibits downstream ERK signaling. We also found that PTPD1 is markedly increased in bladder cancer tissue samples. PTPD1 levels positively correlated with the grading and invasiveness potential of these tumors. Transgenic expression of an inactive PTPD1 mutant or genetic knockdown of the endogenous PTPD1 severely inhibited both growth and motility of human bladder cancer cells. These findings identify PTPD1 as a novel component of the endocytic machinery that impacts on EGF receptor stability and on growth and motility of bladder cancer cells.     

Convergence and divergence in organization of phytoplankton communities under various regimes of physical and biological control

The hypothesis that physical constraints may be as important, if not more important, than biological ones in shaping the structure of phytoplankton assemblage was tested by analyzing long-term (11–29 years) phytoplankton series in eight lakes and nine sites located along a latitudinal gradient in the Northern hemisphere. Phytoplankton biomass was used and similarity of assemblages in same months of the annual data sets was then calculated by subtracting the Bray–Curtis dissimilarity index from 1. The extent of biological and physical forcing was partly based on “expert evaluation”: the importance of four physical (light availability, temperature, conductivity, and sediment stirring up) and five biological variables (basic nutrients [SRP-, DIN-, SRSi-availability] as estimators of competition straight, importance of grazing, and importance of parasitism) was evaluated month by month by arbitrarily scaling from 1 to 5 the intensity of each variable and then summing them in the appropriate subgroup. Since the number of physical variables is less than that of the biological ones, the latter was rescaled to reach the same maximum attainable value of physical variables. The results showed an extremely high variability, making evident that each lake, although showing the same metabolic processes, behaves as an individual with regard to its phytoplankton structure. More generally, it was possible to highlight a largely more important role of physical constraints in shaping both biomass and composition of phytoplankton. This is especially true in winter. In addition, the results were compared to the outcomes of the PEG model, since a plasticity in the structure of phytoplankton much greater than that reported in this widely acknowledged model has been recorded in the data set used. This high variability found in this study in relation to physical constraints might also explain the different patterns of phytoplankton growth observed from Northern temperate to Mediterranean lakes as well as those occurring in shallow and deep lakes.     

Vitamin D deficiency in rheumatoid arthritis: prevalence,determinants and associations with disease activity and disability

Introduction  

The aim of this study was to estimate the prevalence and determinants of vitamin D deficiency in patients with rheumatoid arthritis (RA) as compared to healthy controls and to analyze the association between 25-hydroxyvitamin D (25(OH)D) with disease activity and disability.