Comparative genome-wide analysis of repetitive DNA in the genus <Emphasis Type="Italic">Populus</Emphasis> L.

Genome skimming was performed, using Illumina sequence reads, in order to obtain a detailed comparative picture of the repetitive component of the genome of Populus species. Read sets of seven Populus and two Salix species (as outgroups) were subjected to clustering using RepeatExplorer (Novák et al. BMC Bioinformatics 11:378 2010). The repetitive portion of the genome ranged from 33.8 in Populus nigra to 46.5% in Populus tremuloides. The large majority of repetitive sequences were long terminal repeat-retrotransposons. Gypsy elements were over-represented compared to Copia ones, with a mean ratio Gypsy to Copia of 6.7:1. Satellite DNAs showed a mean genome proportion of 2.2%. DNA transposons and ribosomal DNA showed genome proportions of 1.8 and 1.9%, respectively. The other repeat types accounted for less of 1% each. Long terminal repeat-retrotransposons were further characterized, identifying the lineage to which they belong and studying the proliferation times of each lineage in the different species. The most abundant lineage was Athila, which showed large differences among species. Concerning Copia lineages, similar transpositional profiles were observed among all the analysed species; by contrast, differences in transpositional peaks of Gypsy lineages were found. The genome proportions of repeats were compared in the seven species, and a phylogenetic tree was built, showing species separation according to the botanical section to which the species belongs, although significant differences could be found within sections, possibly related to the different geographical origin of the species. Overall, the data indicate that the repetitive component of the genome in the poplar genus is still rapidly evolving.     

Root Strength and Root Area Ratio of Forest Species in Lombardy (Northern Italy)

Forest vegetation is known to increase hillslope stability by reinforcing soil shear resistance and by influencing hydrologic conditions of soil. Although the importance of plant root systems for hillslope stability has received considerable attention in recent years, the quantification of such an effect needs more investigation. In this paper, we present a synthesis of the data gathered in the last 5 years for some species in different locations of the Alps and Prealps of Lombardy (Northern Italy) with the aim to increase our knowledge on root tensile strength and on Root Area Ratio distribution within the soil. Concerning root tensile strength we developed tensile strength–diameter relationships for eight species: green alder (Alnus viridis(Chaix) D.C.), beech (Fagus sylvatica L.), red willow (Salix purpurea L.), goat willow (Salix caprea L.), hazel (Corylus avellana L.), European ash (Fraxinus excelsior L.), Norway spruce (Picea abies (L.) Karst.) and European larch (Larix decidua Mill.). Results show a great variability among the different species and also for the same species. In general, however, root strength (in terms of tension) tends to decrease with diameter according to a power law, as observed by other Authors. Comparing the power law fitting curves for the considered species, it can be observed that they fall in a relatively narrow band, with the exception of hazel, which appears the most resistant. Concerning the evaluation of root distribution within the soil we estimated the Root Area Ratio (the ratio between the area occupied by roots in a unit area of soil) according to its depth for five species (beech, Norway spruce, European larch, mixed hazel and ash) in three locations of Lombardy. Results show that there is a great variability of root density for the same species well as for different points at the same locality. The general behaviour of root density, in any case, is to decrease with depth according to a gamma function for all the studied species. The results presented in this paper contribute to expanding the knowledge on root resistance behaviour and on root density distribution within the soil. The studied location have allowed the implementation of soil–root reinforcement models and the evaluation of the vegetation contribution to soil stability.     

Food, vigilance, and sperm: the role of male direct benefits in the evolution of female preference in a polygamous bird

The adaptive significance of female selection of copulationpartners remains unresolved, particularly in polygamous specieswhere males do not provide paternal care. In these species thepossibility that direct benefits other than paternal care mayplay an important role in the evolution of female choice hasreceived little attention. I tested whether direct benefitsare associated with female choice in the polygamous feral fowl,Gallus g. domesticus, where females prefer socially dominantcopulation partners and males do not care for the young butdo provide females with three commodities: food, vigilance,and sperm. I used a combination of empirical and experimentaldata to show that male propensity to offer food and vigilance,but not sperm, was positively associated with male social status,suggesting that the provision of these resources may be costlyand condition dependent in males. Copulation success was correlatedwith male status but not with the number of feedings a femalereceived from a male, indicating that a female preferred dominantpartners that in general provided any female with more food,rather than partners that provided only her with more food,consistent with the idea that females may use male resourceprovisioning as a proximate mechanism to assess male condition.Together, these results indicate that male resources provisioningis (1) tightly linked to male social status, (2) a potentialindicator of male condition and possibly genetic quality, and(3) a potential criterion for females to select dominant partners,thus playing an important role in the evolution of partner choiceeven in polygamous species lacking paternal care.     

Asymmetrical myocardial expression of natriuretic peptides in pacing-induced heart failure

High-frequency pacing of the left ventricle (LV) free wall causes a dyssynchronous pattern of contraction that leads to progressive heart failure (HF) with pronounced differences in regional contractility. Aim of this study was to evaluate possible changes in brain natriuretic peptide (BNP) and C-type natriuretic peptide (CNP) mRNA expression in the anterior/anterior lateral region (pacing site, PS) as compared to the infero-septal region (opposite site, OS) and to explore possible association between the contractiling pattern and biomarker expression. Cardiac tissue was collected from minipigs with pacing-induced HF (n = 8) and without (control, n = 6). The samples were selectively harvested from the anterior left ventricular (LV) wall, PS, and from an area remote to the pacing-site, OS. BNP and CNP mRNA expression was evaluated by semi-quantitative polymerase chain reaction (PCR). A significant difference in BNP expression was found in the PS between HF animals and controls (BNP/GAPDH: 0.65 ± 0.11 vs. 0.35 ± 0.04, p = 0.02), but not in the OS (BNP/GAPDH: 0.36 ± 0.05, ns vs. controls). CNP expression was not different compared to controls, although higher levels were observed in the PS and in the OS with respect to the controls (CNP/GAPDH: controls 0.089 ± 0.036, PS 0.289 ± 0.23, OS 0.54 ± 0.16). This finding was in tune with an increase of CNP tissue concentration (controls: 0.69 ± 0.13; PS = 1.56 ± 0.19; OS = 1.70 ± 0.42 pg/mg protein; p = 0.039 controls vs. OS). Higher BNP mRNA expression in the PS is consistent with a reduction in contractile function in this region, while higher CNP mRNA expression in the OS suggests the presence of concomitant endothelial dysfunction in the remote region.     

Biochemical investigation of the effects of human platelet releasates on human articular chondrocytes

The aim of the present study was to demonstrate the mitogenic and differentiating properties of platelet‐rich plasma releasates (PRPr) on human chondrocytes in mono‐ and three‐dimensional cultures. In order to assess if PRPr supplementation could maintain the chondrocyte phenotype or at least inhibit the cell de‐differentiation even after several days in culture, we performed a proteomic study on several cell cultures independently grown, for different periods of time, in culture medium with FCS, human serum (HS), and releasates obtained from PRP and platelet‐poor plasma (PPP). We found that PRP treatment actually induced in chondrocytes the expression of proteins (some of which novel) involved in differentiation. J. Cell. Biochem. 108: 1153–1165, 2009. © 2009 Wiley‐Liss, Inc.     

Plant physiology in theory and practice: An analysis of the WBE model for vascular plants

The theoretical model of West, Brown and Enquist (hereafter WBE) proposed the fractal geometry of the transport system as the origin of the allometric scaling laws observed in nature. The WBE model has either been criticized for some restrictive and biologically unrealistic constraints or its reliability debated on the evidence of empirical tests. In this work, we revised the structure of the WBE model for vascular plants, highlighting some critical assumptions and simplifications and discuss them with regard to empirical evidence from plant anatomy and physiology. We conclude that the WBE model had the distinct merit of shedding light on some important features such as conduit tapering. Nonetheless, it is over-simplistic and a revised model would be desirable with an ontogenetic perspective that takes some important phenomena into account, such as the transformation of the inner sapwood into heartwood and the effect of hydraulic constraints in limiting the growth in height.     

The p53-p66shc-Manganese Superoxide Dismutase (MnSOD) network: a mitochondrial intrigue to generate reactive oxygen species

Once considered as a mere by-product of respiration, mitochondrial generation of reactive oxygen species (ROS) has recently emerged as a genetically controlled phenomenon, involved in complex intracellular signal transduction cascades that directly regulate cell survival and death in responses to environmental stressors. These cascades are involved in the pathogenesis of several major age-related diseases, such as cancer and neurodegeneration, and also appear to somehow regulate the "normal" ageing process. The present short review summarizes recent discoveries on mitochondrial reactive oxygen species regulation by p53, a tumor suppressor protein and p66shc, a protein implicated in the life-span determination. It also outlines the emerging network whereby these molecules cross-talk with each other and with the mitochondrial antioxidant system, namely MnSOD (SOD2), another life-span determining protein, to regulate oxidative stress in the organelle. This molecular circuit, which comprises two genetic determinants of longevity and a major tumor suppressor gene, also provides a theoretical framework connecting senescence and cancer.     

Structures of the tumor necrosis factor α inducing protein Tipα: A novel virulence factor from Helicobacter pylori

Helicobacter pylori secretes a unique virulence factor, Tipα, that enters gastric cells and both stimulates the production of the TNF-α and activates the NF-κB pathway. The structures of a truncated version of Tipα (TipαN34) in two crystal forms are presented here. Tipα adopts a novel β₁α₁α₂β₂β₃α₃α₄ topology that can be described as a combination of three domains. A first region consists in a short flexible extension, a second displays a dodecin-like fold and a third is a helical bundle domain similar to the sterile alpha motif (SAM). Analysis of the oligomerisation states of TipαN34 in the crystals and in solution suggests that the disulfide bridges could hold together Tipα monomers during their secretion in the gastric environment.

Structured summary

MINT-7033680:TIP alpha (uniprotkb:B2UTN0) and TIP alpha (uniprotkb:B2UTN0) bind (MI:0407) by cosedimentation (MI:0027)     

8p22 MTUS1 Gene Product ATIP3 Is a Novel Anti-Mitotic Protein Underexpressed in Invasive Breast Carcinoma of Poor Prognosis

Background

Breast cancer is a heterogeneous disease that is not totally eradicated by current therapies. The classification of breast tumors into distinct molecular subtypes by gene profiling and immunodetection of surrogate markers has proven useful for tumor prognosis and prediction of effective targeted treatments. The challenge now is to identify molecular biomarkers that may be of functional relevance for personalized therapy of breast tumors with poor outcome that do not respond to available treatments. The Mitochondrial Tumor Suppressor (MTUS1) gene is an interesting candidate whose expression is reduced in colon, pancreas, ovary and oral cancers. The present study investigates the expression and functional effects of MTUS1 gene products in breast cancer.

Methods and Findings

By means of gene array analysis, real-time RT-PCR and immunohistochemistry, we show here that MTUS1/ATIP3 is significantly down-regulated in a series of 151 infiltrating breast cancer carcinomas as compared to normal breast tissue. Low levels of ATIP3 correlate with high grade of the tumor and the occurrence of distant metastasis. ATIP3 levels are also significantly reduced in triple negative (ER- PR- HER2-) breast carcinomas, a subgroup of highly proliferative tumors with poor outcome and no available targeted therapy. Functional studies indicate that silencing ATIP3 expression by siRNA increases breast cancer cell proliferation. Conversely, restoring endogenous levels of ATIP3 expression leads to reduced cancer cell proliferation, clonogenicity, anchorage-independent growth, and reduces the incidence and size of xenografts grown in vivo. We provide evidence that ATIP3 associates with the microtubule cytoskeleton and localizes at the centrosomes, mitotic spindle and intercellular bridge during cell division. Accordingly, live cell imaging indicates that ATIP3 expression alters the progression of cell division by promoting prolonged metaphase, thereby leading to a reduced number of cells ungergoing active mitosis.

Conclusions

Our results identify for the first time ATIP3 as a novel microtubule-associated protein whose expression is significantly reduced in highly proliferative breast carcinomas of poor clinical outcome. ATIP3 re-expression limits tumor cell proliferation in vitro and in vivo, suggesting that this protein may represent a novel useful biomarker and an interesting candidate for future targeted therapies of aggressive breast cancer.