Calculations of the Far-Wing Line Profiles of Sodium and Potassium in the Atmospheres of Substellar-Mass Objects

At the low temperatures achieved in cool brown dwarf and hot giant planet atmospheres, the less refractory neutral alkali metals assume an uncharacteristically prominent role in spectrum formation. In particular, the wings of the Na-D (5890 \AA) and K I (7700 \AA) resonance lines come to define the continuum and dominate the spectrum of T dwarfs from 0.4 to 1.0 \mic. Whereas in standard stellar atmospheres the strengths and shapes of the wings of atomic spectral lines are rarely needed beyond 25 \AA of a line center, in brown dwarfs the far wings of the Na and K resonance lines out to 1000's of \AA detunings are important. Using standard quantum chemical codes and the Unified Franck-Condon model for line profiles in the quasi-static limit, we calculate the interaction potentials and the wing line shapes for the dominant Na and K resonance lines in H$_2$- and helium-rich atmospheres. Our theory has natural absorption profile cutoffs, has no free parameters, and is readily adapted to spectral synthesis calculations for stars, brown dwarfs, and planets with effective temperatures below 2000 Kelvin.Comment: 14 pages, Latex, 7 figures in JPEG format, accepted for publication in the Astrophysical Journa

A Collaborative Filtering Approach for Protein-Protein Docking Scoring Functions

A protein-protein docking procedure traditionally consists in two successive tasks: a search algorithm generates a large number of candidate conformations mimicking the complex existing in vivo between two proteins, and a scoring function is used to rank them in order to extract a native-like one. We have already shown that using Voronoi constructions and a well chosen set of parameters, an accurate scoring function could be designed and optimized. However to be able to perform large-scale in silico exploration of the interactome, a near-native solution has to be found in the ten best-ranked solutions. This cannot yet be guaranteed by any of the existing scoring functions

Knowledge to Serve the City: Insights from an Emerging Knowledge-Action Network to Address Vulnerability and Sustainability in San Juan, Puerto Rico

This paper presents initial efforts to establish the San Juan Urban Long-Term Research Area Exploratory (ULTRA-Ex), a long-term program aimed at developing transdisciplinary social-ecological system (SES) research to address vulnerability and sustainability for the municipality of San Juan. Transdisciplinary approaches involve the collaborations between researchers, stakeholders, and citizens to produce socially-relevant knowledge and support decision-making. We characterize the transdisciplinary arrangement emerging in San Juan ULTRA-Ex as a knowledge-action network composed of multiple formal and informal actors (e.g., scientists, policymakers, civic organizations and other stakeholders) where knowledge, ideas, and strategies for sustainability are being produced, evaluated, and validated. We describe in this paper the on-the-ground social practices and dynamics that emerged from developing a knowledge-action network in our local context. Specifically, we present six social practices that were crucial to the development of our knowledge-action network: 1) understanding local framings; 2) analyzing existing knowledge-action systems in the city; 3) framing the social-ecological research agenda; 4) collaborative knowledge production and integration; 5) boundary objects and practices; and 6) synthesis, application, and adaptation. We discuss key challenges and ways to move forward in building knowledge-action networks for sustainability. Our hope is that the insights learned from this process will stimulate broader discussions on how to develop knowledge for urban sustainability, especially in tropical cities where these issues are under-explored

A novel transport mechanism for MOMP in Chlamydophila pneumoniae and its putative role in immune-therapy

Major outer membrane proteins (MOMPs) of Gram negative bacteria are one of the most intensively studied membrane proteins. MOMPs are essential for maintaining the structural integrity of bacterial outer membranes and in adaptation of parasites to their hosts. There is evidence to suggest a role for purified MOMP from Chlamydophila pneumoniae and corresponding MOMP-derived peptides in immune-modulation, leading to a reduced atherosclerotic phenotype in apoE−/− mice via a characteristic dampening of MHC class II activity. The work reported herein tests this hypothesis by employing a combination of homology modelling and docking to examine the detailed molecular interactions that may be responsible. A three-dimensional homology model of the C. pneumoniae MOMP was constructed based on the 14 transmembrane β-barrel crystal structure of the fatty acid transporter from Escherichia coli, which provides a plausible transport mechanism for MOMP. Ligand docking experiments were used to provide details of the possible molecular interactions driving the binding of MOMP-derived peptides to MHC class II alleles known to be strongly associated with inflammation. The docking experiments were corroborated by predictions from conventional immuno-informatic algorithms. This work supports further the use of MOMP in C. pneumoniae as a possible vaccine target and the role of MOMP-derived peptides as vaccine candidates for immune-therapy in chronic inflammation that can result in cardiovascular events

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

Transposable elements (TEs) are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. Using this approach, about half of the human genome has been previously identified as TEs and low-complexity repeats. We recently developed a highly sensitive alternative de novo strategy, P-clouds, that instead searches for clusters of high-abundance oligonucleotides that are related in sequence space (oligo “clouds”). We show here that P-clouds predicts >840 Mbp of additional repetitive sequences in the human genome, thus suggesting that 66%–69% of the human genome is repetitive or repeat-derived. To investigate this remarkable difference, we conducted detailed analyses of the ability of both P-clouds and a commonly used conventional approach, RepeatMasker (RM), to detect different sized fragments of the highly abundant human Alu and MIR SINEs. RM can have surprisingly low sensitivity for even moderately long fragments, in contrast to P-clouds, which has good sensitivity down to small fragment sizes (∼25 bp). Although short fragments have a high intrinsic probability of being false positives, we performed a probabilistic annotation that reflects this fact. We further developed “element-specific” P-clouds (ESPs) to identify novel Alu and MIR SINE elements, and using it we identified ∼100 Mb of previously unannotated human elements. ESP estimates of new MIR sequences are in good agreement with RM-based predictions of the amount that RM missed. These results highlight the need for combined, probabilistic genome annotation approaches and suggest that the human genome consists of substantially more repetitive sequence than previously believed

Secondary Metabolites of Marine Microbes: From Natural Products Chemistry to Chemical Ecology

Marine natural products (MNPs) exhibit a wide range of pharmaceutically relevant bioactivities, including antibiotic, antiviral, anticancer, or anti-inflammatory properties. Besides marine macroorganisms such as sponges, algae, or corals, specifically marine bacteria and fungi have shown to produce novel secondary metabolites (SMs) with unique and diverse chemical structures that may hold the key for the development of novel drugs or drug leads. Apart from highlighting their potential benefit to humankind, this review is focusing on the manifold functions of SMs in the marine ecosystem. For example, potent MNPs have the ability to exile predators and competing organisms, act as attractants for mating purposes, or serve as dye for the expulsion or attraction of other organisms. A large compilation of literature on the role of MNPs in marine ecology is available, and several reviews evaluated the function of MNPs for the aforementioned topics. Therefore, we focused the second part of this review on the importance of bioactive compounds from crustose coralline algae (CCA) and their role during coral settlement, a topic that has received less attention. It has been shown that certain SMs derived from CCA and their associated bacteria are able to induce attachment and/or metamorphosis of many benthic invertebrate larvae, including globally threatened reef-building scleractinian corals. This review provides an overview on bioactivities of MNPs from marine microbes and their potential use in medicine as well as on the latest findings of the chemical ecology and settlement process of scleractinian corals and other invertebrate larvae