A Genomic map of positive selection in Sardinia

The recent production of population-scale genomic data offers an unprecedented opportunity to understand how natural selection has shaped human phenotypic variation within populations. To identify signatures of recent positive selection in Sardinia, we used 23 million single nucleotide polymorphisms from low-coverage whole genomes of 3,514 Sardinians along with data from the 1000 Genomes project. Using single-population (iHS, nSL) and cross-population (Fst, PBS, XP-EHH) based statistics, we found many genetic regions showing evidence of positive selection. We found that selection statistics computed for outlier variants cannot be explained by neutral forces alone. By intersecting genome-wide association study data for hundreds of traits measured in Sardinians with publicy available functional genomic databases, we found that autoimmunity-related genes are enriched for these putatively adaptive variants. Taken together, these results illustrate the importance of characterizing the phenotypic variation within a population, and especially the utility of whole-genome-sequence data, when proposing and interpreting genetic signatures of positive selection

Failure to achieve lupus low disease activity state (LLDAS) six months after diagnosis is associated with early damage accrual in Caucasian patients with systemic lupus erythematosus

Background: The aim was to assess the attainability and outcome of the lupus low disease activity state (LLDAS) in the early stages of systemic lupus erythematosus (SLE). Methods: LLDAS prevalence was evaluated at 6 (T1) and 18 (T2) months after diagnosis and treatment initiation (T0) in a monocentric cohort of 107 (median disease duration 9.7 months) prospectively followed Caucasian patients with SLE. Reasons for failure to achieve LLDAS were also investigated. Multivariate models were built to identify factors associated with lack of LLDAS achievement and to investigate the relationship between LLDAS and Systemic Lupus International Collaboration Clinics (SLICC)/Damage Index (SDI) accrual. Results: There were 47 (43.9%) patients in LLDAS at T1 and 48 (44.9%) at T2. The most frequent unmet LLDAS criterion was prednisolone dose >7.5 mg/day (83% of patients with no LLDAS at T1). Disease manifestations with the lowest remission rate during follow up were increased anti-double-stranded DNA (persistently present in 85.7% and 67.5% of cases at T1 and T2, respectively), low serum complement fractions (73.2% and 66.3%) and renal abnormalities (46.4% and 28.6%). Renal involvement at T0 was significantly associated with failure to achieve LLDAS both at T1 (OR 7.8, 95% CI 1.4-43.4; p = 0.019) and T2 (OR 3.9, 95% CI 1.4-10.6; p = 0.008). Presence of any organ damage (SDI â\u89¥1) at T2 was significantly associated with lack of LLDAS at T1 (OR 5.0, 95% CI 1.5-16.6; p = 0.009) and older age at diagnosis (OR 1.05 per year, 95% CI 1.01-1.09; p = 0.020). Conclusion: LLDAS is a promising treatment target in the early stages of SLE, being attainable and negatively associated with damage accrual, but it fit poorly to patients with renal involvement

Splice-mediated Variants of Proteins (SpliVaP) – data and characterization of changes in signatures among protein isoforms due to alternative splicing

<p>Abstract</p> <p>Background</p> <p>It is often the case that mammalian genes are alternatively spliced; the resulting alternate transcripts often encode protein isoforms that differ in amino acid sequences. Changes among the protein isoforms can alter the cellular properties of proteins. The effect can range from a subtle modulation to a complete loss of function.</p> <p>Results</p> <p>(i) We examined human splice-mediated protein isoforms (as extracted from a manually curated data set, and from a computationally predicted data set) for differences in the annotation for protein signatures (Pfam domains and PRINTS fingerprints) and we characterized the differences & their effects on protein functionalities. An important question addressed relates to the extent of protein isoforms that may lack any known function in the cell. (ii) We present a database that reports differences in protein signatures among human splice-mediated protein isoform sequences.</p> <p>Conclusion</p> <p>(i) Characterization: The work points to distinct sets of alternatively spliced genes with varying degrees of annotation for the splice-mediated protein isoforms. Protein molecular functions seen to be often affected are those that relate to: binding, catalytic, transcription regulation, structural molecule, transporter, motor, and antioxidant; and the processes that are often affected are nucleic acid binding, signal transduction, and protein-protein interactions. Signatures are often included/excluded and truncated in length among protein isoforms; truncation is seen as the predominant type of change. Analysis points to the following novel aspects: (a) Analysis using data from the manually curated Vega indicates that one in 8.9 genes can lead to a protein isoform of no "known" function; and one in 18 expressed protein isoforms can be such an "orphan" isoform; the corresponding numbers as seen with computationally predicted ASD data set are: one in 4.9 genes and one in 9.8 isoforms. (b) When swapping of signatures occurs, it is often between those of same functional classifications. (c) Pfam domains can occur in varying lengths, and PRINTS fingerprints can occur with varying number of constituent motifs among isoforms – since such a variation is seen in large number of genes, it could be a general mechanism to modulate protein function. (ii) Data: The reported resource (at <url>http://www.bioinformatica.crs4.org/tools/dbs/splivap/</url>) provides the community ability to access data on splice-mediated protein isoforms (with value-added annotation such as association with diseases) through changes in protein signatures.</p

MMsPred: a bioactivity and toxicology predictive system

In the last decade, the development and use of new methods in combinatorial chemistry and high-throughput screening has dramatically increased the number of known biologically active compounds. Paradoxically, the number of drugs reaching the market has not followed the same trend, often because many of the candidate drugs present poor qualities in absorption, distribution, metabolism, excretion, and toxicological properties (ADME-Tox). The ability to recognize and discard bad candidates early in the drug discovery steps would save lost investments in time and money. Machine learning techniques could provide solutions to this problem.&#xd;&#xa;The goal of my research is to develop classifiers that accurately discriminate between active and inactive molecules for a specific target. To this end, I am comparing the effectiveness of the application of different machine learning techniques to this problem.&#x9;As a source of data we have selected a set of PubChem&#x27;s public BioAssays1. In addition, with the objective of realizing a real-time query service with our predictors, we aim to keep the features describing the chemical compounds relatively simple.&#xd;&#xa;At the end of this process, we should better understand how to build statistical models that are able to recognize molecules active in a specific bioassay, including how to select the most appropriate classification technique, and how to describe compounds in such a way that is not excessively resource-consuming to generate, yet contains sufficient information for the classification. We see immediate applications of such technology to recognize compounds with high-risk of toxicity, and also to suggest likely metabolic pathways that would process it

Thermoelasticity of Fe2+-bearing bridgmanite

We present LDA+U calculations of high temperature elastic properties of bridgmanite with composition (Mg$_{(1-x)}$Fe$_{x}^{2+}$)SiO$_3$ for $0\le{x}\le0.125$. Results of elastic moduli and acoustic velocities for the Mg-end member (x=0) agree very well with the latest high pressure and high temperature experimental measurements. In the iron-bearing system, we focus particularly on the change in thermoelastic parameters across the state change that occurs in ferrous iron above $\sim$30 GPa, often attributed to a high-spin (HS) to intermediate spin (IS) crossover but explained by first principles calculations as a lateral displacement of substitutional iron in the perovskite cage. We show that the measured effect of this change on the equation of state of this system can be explained by the lateral displacement of substitutional iron, not by the HS to IS crossover. The calculated elastic properties of (Mg$_{0.875}$Fe$_{0.125}^{2+}$)SiO$_3$ along an adiabatic mantle geotherm, somewhat overestimate longitudinal velocities but produce densities and shear velocities quite consistent with Preliminary Reference Earth Model data throughout most of the lower mantle.Comment: Accepted for Geophysical Research Letters (DOI: 10.1002/2014GL062888

Dissecting the dynamics of dysregulation of cellular processes in mouse mammary gland tumor

<p>Abstract</p> <p>Background</p> <p>Elucidating the sequence of molecular events underlying breast cancer formation is of enormous value for understanding this disease and for design of an effective treatment. Gene expression measurements have enabled the study of transcriptome-wide changes involved in tumorigenesis. This usually occurs through identification of differentially expressed genes or pathways.</p> <p>Results</p> <p>We propose a novel approach that is able to delineate new cancer-related cellular processes and the nature of their involvement in tumorigenesis. First, we define modules as densely interconnected and functionally enriched areas of a Protein Interaction Network. Second, 'differential expression' and 'differential co-expression' analyses are applied to the genes in these network modules, allowing for identification of processes that are up- or down-regulated, as well as processes disrupted (low co-expression) or invoked (high co-expression) in different tumor stages. Finally, we propose a strategy to identify regulatory miRNAs potentially responsible for the observed changes in module activities. We demonstrate the potential of this analysis on expression data from a mouse model of mammary gland tumor, monitored over three stages of tumorigenesis. Network modules enriched in adhesion and metabolic processes were found to be inactivated in tumor cells through the combination of dysregulation and down-regulation, whereas the activation of the integrin complex and immune system response modules is achieved through increased co-regulation and up-regulation. Additionally, we confirmed a known miRNA involved in mammary gland tumorigenesis, and present several new candidates for this function.</p> <p>Conclusions</p> <p>Understanding complex diseases requires studying them by integrative approaches that combine data sources and different analysis methods. The integration of methods and data sources proposed here yields a sensitive tool, able to pinpoint new processes with a role in cancer, dissect modulation of their activity and detect the varying assignments of genes to functional modules over the course of a disease.</p

Magnetic Energy Landscape of Dimolybdenum Tetraacetate on a Bulk Insulator Surface

The magnetic states and the magnetic anisotropy barrier of a transition metal molecular complex, dimolybdenum tetraacetate, are investigated via density functional theory (DFT). Calculations are performed in the gas phase and on a calcite (10.4) bulk insulating surface, using the Generalized-Gradient Approximation (GGA)-PBE and the Hubbard-corrected DFT + U and DFT + U + V functionals. The molecular complex (denoted MoMo) contains two central metallic molybdenum atoms, embedded in a square cage of acetate groups. Recently, MoMo was observed to form locally regular networks of immobile molecules on calcite (10.4), at room conditions. As this is the first example of a metal-coordinated molecule strongly anchored to an insulator surface at room temperature, we explore here its magnetic properties with the aim to understand whether the system could be assigned features of a single molecule magnet (SMM) and could represent the basis to realize stable magnetic networks on insulators. After an introductory review on SMMs, we show that, while the uncorrected GGA-PBE functional stabilizes MoMo in a nonmagnetic state, the DFT + U and DFT + U + V approaches stabilize an antiferromagnetic ground state and several meta-stable ferromagnetic and ferrimagnetic states. Importantly, the energy landscape of magnetic states remains almost unaltered on the insulating surface. Finally, via a noncollinear magnetic formalism and a newly introduced algorithm, we calculate the magnetic anisotropy barrier, whose value indicates the stability of the molecule’s magnetic moment

Severe neuropsychiatric systemic lupus erythematosus successfully treated with rituximab: An alternative to standard of care

Demyelinating syndrome secondary to systemic lupus erythematosus (DS-SLE) is a rare encephalomyelitis burden with a high risk of disability and death. We report on a 49-year-old Caucasian woman with systemic lupus erythematosus (SLE) complicated by severe cognitive dysfunction, brainstem disease, cranial nerve palsies, weakness and numbness in limbs and multiple discrete magnetic resonance imaging (MRI) areas of damage within the white matter of semioval centers, temporal lobe, external capsule, claustrum, subinsular regions and midbrain. She also had multiple mononeuritis diagnosed through sensory and motor nerve conduction study. She was diagnosed with severe DS-SLE prominently involving the brain and was treated with 500 mg methylprednisolone (PRE) pulses for 3 consecutive days, followed by one single pulse of 500 mg cyclophosphamide, and 1 g rituximab, which was then repeated 14 days later. PRE 25 mg/day, rapidly tapered to 7.5 mg/day in 6 months, and mycophenolate mofetil 1 g/day were prescribed as maintenance therapy. She had progressive and sustained improvement in neurological symptoms with almost complete resolution of brain MRI lesions after 1 year. B-cell depleting therapy could be considered as a possible alternative to standard of care in the management of severe inflammatory neuropsychiatric SLE but it should be associated with a conventional immunosuppressant as maintenance treatment to reduce the risk of flare and reduce corticosteroids dose