A multi-layer method to study genome-scale positions of nucleosomes

The basic unit of eukaryotic chromatin is the nucleosome, consisting of about 150 bp of DNA wrapped around a protein core made of histone proteins. Nucleosomes position is modulated in vivo to regulate fundamental nuclear processes. To measure nucleosome positions on a genomic scale both theoretical and experimental approaches have been recently reported. We have developed a new method, Multi-Layer Model (MLM), for the analysis of nucleosome position data obtained with microarray-based approach. The MLM is a feature extraction method in which the input data is processed by a classifier to distinguish between several kinds of patterns. We applied our method to simulated-synthetic and experimental nucleosome position data and found that besides a high nucleosome recognition and a strong agreement with standard statistical methods, the MLM can identify distinct classes of nucleosomes, making it an important tool for the genome wide analysis of nucleosome position and function. In conclusion, the MLM allows a better representation of nucleosome position data and a significant reduction in computational time.     

A Preliminary Study of the Temporal and Spatial Biomass Patterns of Herbaceous Vegetation Consumed by Mountain Gorillas in an Afromontane Rain Forest

Although many animal species consume herbaceous vegetation found in African tropical forests, little is known of the temporal and spatial availability of these plants. From September 2004 to August 2005 we conducted a study that quantified the temporal and spatial biomass availability of 20 species of herbs frequently consumed by endangered mountain gorillas at two locations (Buhoma and Ruhija) in Bwindi Impenetrable National Park, Uganda. In general, the biomass of herbs varied over the study period, but these changes were relatively small. For 12 of 18 and nine of 11 species in Buhoma and Ruhija, respectively, herb biomass differed significantly among habitat types. Of the nine species found in both locations, seven species had a higher biomass at Ruhija, one species had a higher biomass at Buhoma, and one species showed no difference. These results demonstrate that herb biomass varied little temporally but spatial differences in herb biomass were more pronounced. Future studies should investigate the variables that may influence herb phenological patterns such as rainfall, light, soil quality, previous disturbance regimes, and animal foraging and trampling damage.     

Fibrogenic Potential of Human Multipotent Mesenchymal Stromal Cells in Injured Liver

Multipotent mesenchymal stromal cells (MSC) are currently investigated clinically as cellular therapy for a variety of diseases. Differentiation of MSC toward endodermal lineages, including hepatocytes and their therapeutic effect on fibrosis has been described but remains controversial. Recent evidence attributed a fibrotic potential to MSC. As differentiation potential might be dependent of donor age, we studied MSC derived from adult and pediatric human bone marrow and their potential to differentiate into hepatocytes or myofibroblasts in vitro and in vivo. Following characterization, expanded adult and pediatric MSC were co-cultured with a human hepatoma cell line, Huh-7, in a hepatogenic differentiation medium containing Hepatocyte growth factor, Fibroblast growth factor 4 and oncostatin M. In vivo, MSC were transplanted into spleen or liver of NOD/SCID mice undergoing partial hepatectomy and retrorsine treatment. Expression of mesenchymal and hepatic markers was analyzed by RT-PCR, Western blot and immunohistochemistry. In vitro, adult and pediatric MSC expressed characteristic surface antigens of MSC. Expansion capacity of pediatric MSC was significantly higher when compared to adult MSC. In co-culture with Huh-7 cells in hepatogenic differentiation medium, albumin expression was more frequently detected in pediatric MSC (5/8 experiments) when compared to adult MSC (2/10 experiments). However, in such condition pediatric MSC expressed alpha smooth muscle more strongly than adult MSC. Stable engraftment in the liver was not achieved after intrasplenic injection of pediatric or adult MSC. After intrahepatic injection, MSC permanently remained in liver tissue, kept a mesenchymal morphology and expressed vimentin and alpha smooth muscle actin, but no hepatic markers. Further, MSC localization merges with collagen deposition in transplanted liver and no difference was observed using adult or pediatric MSC. In conclusion, when transplanted into an injured or regenerating liver, MSC differentiated into myofibroblasts with development of fibrous tissue, regardless of donor age. These results indicate that MSC in certain circumstances might be harmful due to their fibrogenic potential and this should be considered before potential use of MSC for cell therapy.     

Effects of flaxseed dietary supplementation on sperm quality and on lipid composition of sperm subfractions and prostatic granules in rabbit

Lipids are the main structural/functional components of the sperm, and their composition may undergo a series of modifications in relation to either physiologic events (capacitation and acrosome reaction) and/or diet. The goals of the current study were (1) to investigate whether a flaxseed (FS) dietary supplementation could affect the lipid and fatty acid profile of sperm subfractions and of prostatic granules (PGs) and (2) to evaluate the effects of dietary FS on rabbit buck semen quality. Accordingly, 20 adult New Zealand White rabbits were fed ad libitum a control diet (CO) or a diet supplemented with 5% extruded FS. Integration of diet with FS, as a consequence of the linolenic acid (C18:3n-3; LNA; 56%), increased the dietary n-3/n-6 ratio and resulted in a substantial rearrangement of sperm fatty acid composition at the subcellular level, mainly of polyunsaturated fatty acid (PUFA)n-3 (8.3% vs. 14.3%, P < 0.05). The lipid and fatty acid profiles of sperm tail membrane were the most affected, undergoing the following significant changes: (1) a reduction by half of linoleic acid (C18:2n-6; LA) and docosapentaenoic acid (22:5n-6; DPA), and a reduction of cholesterol (−70%); (2) a concomitant increase of LNA (+65%), docosahexaenoic acid (22:6n-3; DHA; +83%), and of oleic acid (C18:1n-9, +61%). As a consequence, the sperm of FS-fed rabbits had a twice higher n-3/n-6 ratio and phospholipid/cholesterol ratio compared with the control sperm. These changes might have been on the basis of the higher responsiveness to hypo-osmotic solution and, hence, the higher sperm track speed observed for the FS group. Also, the membrane integrity and viability of the LNA-enriched sperm were both improved. On the other hand, the presence of lignans in FS might have accounted for the reduction of sperm cholesterol in the semen of FS-treated rabbits. The responsiveness of sperm to acrosome reaction was not affected by the dietary treatment probably due to supranutritional level of vitamin E and to the higher number of PGs, which are known to play a key role in sperm capacitation. In conclusion, our data showed for the first time that the integration of FS into the rabbit diet may improve sperm quality by modifying the sperm lipid composition and that the sperm subfractions and the PGs respond differently to the FS-induced lipid manipulation.     

<Emphasis Type="Italic">In vitro</Emphasis> antioxidant activity of the prostatic secretory granules in rabbit semen after exposure to organic peroxides

Background  

The prostate gland of rabbits produces numerous granules, which are specifically implicated in the inhibition of sperm capacitation during the first hours after mating. These granules are rich in vitamin E, but their role in the antioxidant protection of rabbit sperm has not been studied.     

Covert shift of attention modulates the ongoing neural activity in a reaching area of the macaque dorsomedial visual stream

Background

Attention is used to enhance neural processing of selected parts of a visual scene. It increases neural responses to stimuli near target locations and is usually coupled to eye movements. Covert attention shifts, however, decouple the attentional focus from gaze, allowing to direct the attention to a peripheral location without moving the eyes. We tested whether covert attention shifts modulate ongoing neuronal activity in cortical area V6A, an area that provides a bridge between visual signals and arm-motor control.

Methodology/Principal Findings

We performed single cell recordings from 3 Macaca Fascicularis trained to fixate straight-head, while shifting attention outward to a peripheral cue and inward again to the fixation point. We found that neurons in V6A are influenced by spatial attention. The attentional modulation occurs without gaze shifts and cannot be explained by visual stimulations. Visual, motor, and attentional responses can occur in combination in single neurons.

Conclusions/Significance

This modulation in an area primarily involved in visuo-motor transformation for reaching may form a neural basis for coupling attention to the preparation of reaching movements. Our results show that cortical processes of attention are related not only to eye-movements, as many studies have shown, but also to arm movements, a finding that has been suggested by some previous behavioral findings. Therefore, the widely-held view that spatial attention is tightly intertwined with—and perhaps directly derived from—motor preparatory processes should be extended to a broader spectrum of motor processes than just eye movements.     

An Improved Strategy for Generating Forces in Steered Molecular Dynamics: The Mechanical Unfolding of Titin,e2lip3 and Ubiquitin

One of the applications of Molecular Dynamics (MD) simulations is to explore the energetic barriers to mechanical unfolding of proteins such as occurs in response to the mechanical pulling of single molecules in Atomic Force Microscopy (AFM) experiments. Although Steered Molecular Dynamics simulations have provided microscopic details of the unfolding process during the pulling, the simulated forces required for unfolding are typically far in excess of the measured values. To rectify this, we have developed the Pulsed Unconstrained Fluctuating Forces (PUFF) method, which induces constant-momentum motions by applying forces directly to the instantaneous velocity of selected atoms in a protein system. The driving forces are applied in pulses, which allows the system to relax between pulses, resulting in more accurate unfolding force estimations than in previous methods. In the cases of titin, ubiquitin and e2lip3, the PUFF trajectories produce force fluctuations that agree quantitatively with AFM experiments. Another useful property of PUFF is that simulations get trapped if the target momentum is too low, simplifying the discovery and analysis of unfolding intermediates.     

Human Bone Marrow Mesenchymal Stem Cells Display Anti-Cancer Activity in SCID Mice Bearing Disseminated Non-Hodgkin's Lymphoma Xenografts

Background

Although multimodality treatment can induce high rate of remission in many subtypes of non-Hodgkin''s lymphoma (NHL), significant proportions of patients relapse with incurable disease. The effect of human bone marrow (BM) mesenchymal stem cells (MSC) on tumor cell growth is controversial, and no specific information is available on the effect of BM-MSC on NHL.

Methodology/Principal Findings

The effect of BM-MSC was analyzed in two in vivo models of disseminated non-Hodgkin''s lymphomas with an indolent (EBV⁻ Burkitt-type BJAB, median survival = 46 days) and an aggressive (EBV⁺ B lymphoblastoid SKW6.4, median survival = 27 days) behavior in nude-SCID mice. Intra-peritoneal (i.p.) injection of MSC (4 days after i.p. injection of lymphoma cells) significantly increased the overall survival at an optimal MSC∶lymphoma ratio of 1∶10 in both xenograft models (BJAB+MSC, median survival = 58.5 days; SKW6.4+MSC, median survival = 40 days). Upon MSC injection, i.p. tumor masses developed more slowly and, at the histopathological observation, exhibited a massive stromal infiltration coupled to extensive intra-tumor necrosis. In in vitro experiments, we found that: i) MSC/lymphoma co-cultures modestly affected lymphoma cell survival and were characterized by increased release of pro-angiogenic cytokines with respect to the MSC, or lymphoma, cultures; ii) MSC induce the migration of endothelial cells in transwell assays, but promoted endothelial cell apoptosis in direct MSC/endothelial cell co-cultures.

Conclusions/Significance

Our data demonstrate that BM-MSC exhibit anti-lymphoma activity in two distinct xenograft SCID mouse models of disseminated NHL.     

Deterioration of cichlid habitat by increased sedimentation in the rocky littoral zone of Lake Malawi

Lake Malawi has been affected by soil erosion across the catchment area. We experimentally investigated habitat preferences of cichlids in the rocky littoral zone to examine the influence of increased sedimentation on bottom-dwelling cichlids. Numbers of individuals and species, as well as the feeding rate of some of these cichlids, increased following the clearing of sediment. The results showed that these cichlids preferred sediment-free bottom and that the sedimentation causes deterioration of their habitats. Studies on the consequences of the habitat deterioration caused by increased sedimentation are needed in the management of these most diverse freshwater fish communities.