Molecular crystal global phase diagrams. II. Reference lattices

In the first part of this series [Keith et al. (2004). Cryst. Growth Des. 4, 1009-1012; Mettes et al. (2004). Acta Cryst. A60, 621-636], a method was developed for constructing global phase diagrams (GPDs) for molecular crystals in which crystal structure is presented as a function of intermolecular potential parameters. In that work, a face-centered-cubic center-of-mass lattice was arbitrarily adopted as a reference state. In part two of the series, experimental crystal structures composed of tetrahedral point group molecules are classified to determine what fraction of structures are amenable to inclusion in the GPDs and the number of reference lattices necessary to span the observed structures. It is found that 60% of crystal structures composed of molecules with T_d point-group symmetry are amenable and that eight reference lattices are sufficient to span the observed structures. Similar results are expected for other cubic point groups

Molecular crystal global phase diagrams. III. Sufficient parameter space determination

In previous parts of this series [Mettes et al. (2004). Acta Cryst. A60, 621-636; McClurg & Keith (2010). Acta Cryst. A66, 38-49] a method for constructing global phase diagrams (GPDs) for molecular crystals was developed and the method was applied to single-component ordered crystal structures of tetrahedral molecules. GPDs are useful for visualizing what types of crystal structures a given molecule may assume depending on molecular form/interaction. Their construction uses group-theoretical methods which enumerate all possible symmetry breakings during a statistical mechanical high-to-low temperature search. In this work these results are expanded upon by outlining a method to determine a sufficiently rich parameter space to represent the experimentally observed crystal structures in a data set derived from the Cambridge Structural Database. This is significant because previous work (Mettes et al., 2004) did not specify the number of parameters needed for GPDs. Although there are suggestions in the literature that thousands of parameters are required to adequately describe tetrahedral molecule intermolecular potentials, it is found that 15 parameters are sufficient to represent the structures of the test data. The origin of this difference and its implications for determining GPD parameter values from a more detailed intermolecular potential and for interpreting GPD parameter values are discussed

Linearized self-forces for branes

We compute the regularized force density and renormalized action due to fields of external origin coupled to a brane of arbitrary dimension in a spacetime of any dimension. Specifically, we consider forces generated by gravitational, dilatonic and generalized antisymmetric form-fields. The force density is regularized using a recently developed gradient operator. For the case of a Nambu--Goto brane, we show that the regularization leads to a renormalization of the tension, which is seen to be the same in both approaches. We discuss the specific couplings which lead to cancellation of the self-force in this case.Comment: 15 page

Intragenic alternative splicing coordination is essential for Caenorhabditis elegans slo-1 gene function

Alternative splicing is critical for diversifying eukaryotic proteomes, but the rules governing and coordinating splicing events among multiple alternate splice sites within individual genes are not well understood. We developed a quantitative PCR-based strategy to quantify the expression of the 12 transcripts encoded by the Caenorhabditis elegans slo-1 gene, containing three alternate splice sites. Using conditional probability-based models, we show that splicing events are coordinated across these sites. Further, we identify a point mutation in an intron adjacent to one alternate splice site that disrupts alternative splicing at all three sites. This mutation leads to aberrant synaptic transmission at the neuromuscular junction. In a genomic survey, we found that a UAAAUC element disrupted by this mutation is enriched in introns flanking alternate exons in genes with multiple alternate splice sites. These results establish that proper coordination of intragenic alternative splicing is essential for normal physiology of slo-1 in vivo and identify putative specialized cis-regulatory elements that regulate the coordination of intragenic alternative splicing

Characterization of the Mutagenic Spectrum of 4-Nitroquinoline 1-Oxide (4-NQO) in Aspergillus nidulans by Whole Genome Sequencing

4-Nitroquinoline 1-oxide (4-NQO) is a highly carcinogenic chemical that induces mutations in bacteria, fungi, and animals through the formation of bulky purine adducts. 4-NQO has been used as a mutagen for genetic screens and in both the study of DNA damage and DNA repair. In the model eukaryote Aspergillus nidulans, 4-NQO−based genetic screens have been used to study diverse processes, including gene regulation, mitosis, metabolism, organelle transport, and septation. Early work during the 1970s using bacterial and yeast mutation tester strains concluded that 4-NQO was a guanine-specific mutagen. However, these strains were limited in their ability to determine full mutagenic potential, as they could not identify mutations at multiple sites, unlinked suppressor mutations, or G:C to C:G transversions. We have now used a whole genome resequencing approach with mutant strains generated from two independent genetic screens to determine the full mutagenic spectrum of 4-NQO in A. nidulans. Analysis of 3994 mutations from 38 mutant strains reveals that 4-NQO induces substitutions in both guanine and adenine residues, although with a 19-fold preference for guanine. We found no association between mutation load and mutagen dose and observed no sequence bias in the residues flanking the mutated purine base. The mutations were distributed randomly throughout most of the genome. Our data provide new evidence that 4-NQO can potentially target all base pairs. Furthermore, we predict that current practices for 4-NQO−induced mutagenesis are sufficient to reach gene saturation for genetic screens with feasible identification of causative mutations via whole genome resequencing

Development and validation of a novel molecular biomarker diagnostic test for the early detection of sepsis

Introduction: Sepsis is a complex immunological response to infection characterized by early hyper-inflammation followed by severe and protracted immunosuppression, suggesting that a multi-marker approach has the greatest clinical utility for early detection, within a clinical environment focused on Systemic Inflammatory Response Syndrome (SIRS) differentiation. Pre-clinical research using an equine sepsis model identified a panel of gene expression biomarkers that define the early aberrant immune activation. Thus, the primary objective was to apply these gene expression biomarkers to distinguish patients with sepsis from those who had undergone major open surgery and had clinical outcomes consistent with systemic inflammation due to physical trauma and wound healing

Lethal Injection, Politics, and the Future of the Death Penalty

“Welcome and Keynote:” Stephen Bright, Harvey Karp Visiting Lecturer at Yale Law School, and President and Senior Counsel with the Southern Center for Human Rights. (9:00 a.m. - 9:45 a.m.) “The Death Penalty Today: Lethal Injection Issues:” Panel 1 featured Deborah W. Denno, Arthur A. McGivney Professor of Law at Fordham University School of Law; Joel Zivot, Assistant Professor of Anesthesiology and Surgery at Emory University School of Medicine, and Medical Director of the Cardiothoracic Intensive Care Unit at Emory University Hospital; Eric Berger, Associate Professor of Law at Nebraska College of Law; and Frank Green, Reporter for the Richmond Times-Dispatch. Jim Gibson, Associate Dean for Student Affairs and Professor of Law at the University of Richmond School of Law, served as moderator. (10:00 a.m. -11:30 a.m.) “The Shifting Politics of the Death Penalty:” Panel 2 featured Mark Earley, former Attorney General of Virginia; Richard B. Roper, Partner with Thompson & Knight LLP, Corinna Barrett Lain, Associate Dean for Faculty Development and Professor of Law at the University of Richmond School of Law; and Stephen Smith, Professor of Law at Notre Dame Law School. Henry L. Chambers, Professor of Law at the University of Richmond School of Law, served as moderator. (1:00 p.m. - 2:30 p.m.) “The Future of the Death Penalty:” Panel 3 featured John Douglass, Professor of Law at the University of Richmond School of Law; Brandon L. Garrett, Professor of Law at the University of Virginia School of Law; and Richard Dieter, Executive Director of the Death Penalty Information Center. Mary Kelly Tate, Professor of Law at the University of Richmond School of Law, served as moderator. (2:45 p.m. - 4:15 p.m.

Porewater Geochemical Assessment of Seismic Indications for Gas Hydrate Presence and Absence: Mahia Slope, East of New Zealand’s North Island

We compare sediment vertical methane flux off the Mahia Peninsula, on the Hikurangi Margin, east of New Zealand’s North Island, with a combination of geochemical, multichannel seismic and sub-bottom profiler data. Stable carbon isotope data provided an overview of methane contributions to shallow sediment carbon pools. Methane varied considerably in concentration and vertical flux across stations in close proximities. At two Mahia transects, methane profiles correlated well with integrated seismic and TOPAS data for predicting vertical methane migration rates from deep to shallow sediment. However, at our “control site”, where no seismic blanking or indications of vertical gas migration were observed, geochemical data were similar to the two Mahia transect lines. This apparent mismatch between seismic and geochemistry data suggests a potential to underestimate gas hydrate volumes based on standard seismic data interpretations. To accurately assess global gas hydrate deposits, multiple approaches for initial assessment, e.g., seismic data interpretation, heatflow profiling and controlled-source electromagnetics, should be compared to geochemical sediment and porewater profiles. A more thorough data matrix will provide better accuracy in gas hydrate volume for modeling climate change and potential available energy content

Sperm DNA methylation mediates the association of male age on reproductive outcomes among couples undergoing infertility treatment

Parental age at time of offspring conception is increasing in developed countries. Advanced male age is associated with decreased reproductive success and increased risk of adverse neurodevelopmental outcomes in offspring. Mechanisms for these male age effects remain unclear, but changes in sperm DNA methylation over time is one potential explanation. We assessed genome-wide methylation of sperm DNA from 47 semen samples collected from male participants of couples seeking infertility treatment. We report that higher male age was associated with lower likelihood of fertilization and live birth, and poor embryo development (p \u3c 0.05). Furthermore, our multivariable linear models showed male age was associated with alterations in sperm methylation at 1698 CpGs and 1146 regions (q \u3c 0.05), which were associated with \u3e 750 genes enriched in embryonic development, behavior and neurodevelopment among others. High dimensional mediation analyses identified four genes (DEFB126, TPI1P3, PLCH2 and DLGAP2) with age-related sperm differential methylation that accounted for 64% (95% CI 0.42–0.86%; p \u3c 0.05) of the effect of male age on lower fertilization rate. Our findings from this modest IVF population provide evidence for sperm methylation as a mechanism of age-induced poor reproductive outcomes and identifies possible candidate genes for mediating these effects