On the generation of asymmetric warps in disk galaxies

The warps in many spiral galaxies are now known to asymmetric. Recent sensitive observations have revealed that asymmetry of warps may be the norm rather than exception. However there exists no generic mechanism to generate these asymmetries in warps. We have derived the dispersion relation in a compact form for the S-shaped warps(described by the m=1 mode) and the bowl-shaped distribution(described by the m=0 mode) in galactic disk embedded in a dark matter halo. We then performed the numerical modal analysis and used the linear and time-dependent superposition principle to generate asymmetric warps in the disk. On doing the modal analysis we find the frequency of the $m=0$ mode is much larger than that of the $m=1$ mode. The linear and time-dependent superposition of these modes with their unmodulated amplitudes(that is, the coefficients of superposition being unity) results in an asymmetry in warps of ~ 20 - 40 %, whereas a smaller coefficient for the m=0 mode results in a smaller asymmetry. The resulting values agree well with the recent observations. We study the dependence of the asymmetry index on the dark matter halo parameters. This approach can also naturally produce U-shaped warps and L-shaped warps. We show that a rich variety of possible asymmetries in the z-distribution of the spiral galaxies can naturally arise due to a dynamical wave interference between the first two bending modes(i.e. m=0 and m=1) in the disk. This is a simple but general method for generating asymmetric warps that is independent of how the individual modes arise in the disk.Comment: Accepted for publication in A &

The minor house dust mite allergen Der p 13 is a fatty acid binding protein and an activator of a TLR2-mediated innate immune response

Background: The house dust mite (HDM) allergen Der p 13 could be a lipid-binding protein able to activate key innate signaling pathways in the initiation of the allergic response. We investigated the IgE reactivity of recombinant Der p 13 (rDer p 13), its lipid binding activities and its capacity to stimulate airway epithelium cells. Methods: Purified rDer p 13 was characterized by mass spectrometry, circular dichroism, fluorescence-based lipid binding assays and in-silico structural prediction. IgE binding activity and allergenic potential of Der p 13 were examined by ELISA, basophil degranulation assays and in-vitro airway epithelial cell activation assays. Results: Protein modeling and biophysical analysis indicated that Der p 13 adopts a β barrel structure with a predominately apolar pocket representing a potential binding site for hydrophobic ligands. Fluorescent lipid binding assays confirmed that the protein is highly selective for ligands and that it binds a fatty acid with a dissociation constant typical of lipid transporter proteins. The low IgE binding frequency (7%, n= 224) in Thai HDM-allergic patients as well as the limited propensity to activate basophil degranulation classifies Der p 13 as a minor HDM allergen. Nevertheless, the protein with its presumptively associated lipid(s) triggered the production of IL-8 and GM-CSF in respiratory epithelial cells through a TLR2-, MyD88-, NF-kB- and MAPK-dependent signaling pathway. Conclusions: Although a minor allergen, Der p 13 may, through its lipid binding capacity, play a role in the initiation of the HDM allergic response through TLR2 activation

MyDas, an extensible Java DAS server

A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users. We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details

Consumption of the Total Western Diet Promotes Colitis and Inflammation-Associated Colorectal Cancer in Mice

Consumption of a Western type diet is a known risk factor for colorectal cancer. Our group previously developed the total Western diet (TWD) for rodents with energy and nutrient profiles that emulate a typical Western diet. In this study, we tested the hypothesis that consumption of the TWD would enhance colitis, delay recovery from gut injury and promote colon tumorigenesis. In multiple experiments using the azoxymethane + dextran sodium sulfate or ApcMin/+ mouse models of colitis-associated colorectal carcinogenesis (CAC), we determined that mice fed TWD experienced more severe and more prolonged colitis compared to their counterparts fed the standard AIN93G diet, ultimately leading to markedly enhanced colon tumorigenesis. Additionally, this increased tumor response was attributed to the micronutrient fraction of the TWD, and restoration of calcium and vitamin D to standard amounts ameliorated the tumor-promoting effects of TWD. Finally, exposure to the TWD elicited large scale, dynamic changes in mRNA signatures of colon mucosa associated with interferon (IFN) response, inflammation, innate immunity, adaptive immunity, and antigen processing pathways, among others. Taken together, these observations indicate that consumption of the TWD markedly enhanced colitis, delayed recovery from gut injury, and enhanced colon tumorigenesis likely via extensive changes in expression of immune-related genes in the colon mucosa

Uncovering the Origins of Spiral Structure by Measuring Radial Variation in Pattern Speeds

Current theories of spiral and bar structure predict a variety of pattern speed behaviors, calling for detailed, direct measurement of the radial variation of pattern speeds. Our recently developed Radial Tremaine-Weinberg (TWR) method allows this goal to be achieved for the first time. Here we present TWR spiral pattern speed estimates for M101, IC 342, NGC 3938 and NGC 3344 in order to investigate whether spiral structure is steady or winding, whether spirals are described by multiple pattern speeds, and the relation between bar and spiral speeds. Where possible, we interpret our pattern speeds estimates according to the resonance radii associated with each (established with the disk angular rotation), and compare these to previous determinations. By analyzing the high-quality HI and CO data cubes available for these galaxies, we show that it is possible to determine directly multiple pattern speeds within these systems, and hence identify the characteristic signatures of the processes that drive the spiral structure. Even this small sample of galaxies reveals a surprisingly complex taxonomy, with the first direct evidence for the presence of resonant coupling of multiple patterns found in some systems, and the measurement of a simple single pattern speed in others. Overall, this study demonstrates that we are now in a position to uncover more of the apparently complex physics that lies behind spiral structure.Comment: 15 pages in emulateapj format, 12 figures, accepted for publication in Ap

The chemical evolution of galaxies within the IGIMF theory: the [alpha/Fe] ratios and downsizing

The chemical evolution of galaxies is investigated within the framework of the star formation rate (SFR) dependent integrated galactic initial mass function (IGIMF). We study how the global chemical evolution of a galaxy and in particular how [alpha/Fe] abundance ratios are affected by the predicted steepening of the IGIMF with decreasing SFR. We use analytical and semi-analytical calculations to evaluate the mass-weighted and luminosity-weighted [alpha/Fe] ratios in early-type galaxies of different masses. The models with the variable IGIMF produce a [alpha/Fe] vs. velocity dispersion relation which has the same slope as the observations of massive galaxies, irrespective of the model parameters, provided that the star formation duration inversely correlates with the mass of the galaxy (downsizing). These models also produce steeper [alpha/Fe] vs. sigma relations in low-mass early-type galaxies and this trend is consistent with the observations. Constant IMF models are able to reproduce the [alpha/Fe] ratios in large elliptical galaxies as well, but they do not predict this change of slope for small galaxies. In order to obtain the best fit between our results and the observations, the downsizing effect (i.e. the shorter duration of the star formation in larger galaxies) must be milder than previously thought.Comment: 13 pages, 18 figures, accepted for publication in Astronomy and Astrophysic

The PrPC Cl fragment derived from the ovine A(136)R(154)R(171) PRNP allele is highly abundant in sheep brain and inhibits fibrillisation of full-length PrPC protein in vitro

AbstractExpression of the cellular prion protein (PrPC) is crucial for the development of prion diseases. Resistance to prion diseases can result from reduced availability of the prion protein or from amino acid changes in the prion protein sequence. We propose here that increased production of a natural PrP α-cleavage fragment, C1, is also associated with resistance to disease. We show, in brain tissue, that ARR homozygous sheep, associated with resistance to disease, produced PrPC comprised of 25% more C1 fragment than PrPC from the disease-susceptible ARQ homozygous and highly susceptible VRQ homozygous animals. Only the C1 fragment derived from the ARR allele inhibits in-vitro fibrillisation of other allelic PrPC variants. We propose that the increased α-cleavage of ovine ARR PrPC contributes to a dominant negative effect of this polymorphism on disease susceptibility. Furthermore, the significant reduction in PrPC β-cleavage product C2 in sheep of the ARR/ARR genotype compared to ARQ/ARQ and VRQ/VRQ genotypes, may add to the complexity of genetic determinants of prion disease susceptibility

Preliminary assessment of COVID-19 implications for the water and sanitation sector in Latin America and the Caribbean

COVID-19 has had a severe impact on human health, as well as in social and economic terms, with implications for the management and governance of the water and sanitation sector. These implications are evident in Latin America and the Caribbean due to existing challenges the region faces in accessing water and sanitation services. In spite of significant advances, around 65 million people in the LAC region currently lack appropriate access to water and soap to wash their hands—one of the most basic measures to prevent the spread of disease. Furthermore, social and economic vulnerabilities have exacerbated the effects of the pandemic in the region, particularly among those living in poverty. The COVID-19 pandemic thus requires the mobilization of frameworks such as the human rights to water and sanitation, specifically considering the region’s realities. This paper provides a review of some of the challenges currently faced in the region and advances a series of recommendations for enhancing access to water, sanitation and hygiene. The importance of effective governance, management and communication strategies in the water provisioning sector is highlighted in the context of the pandemic, and the role of science and research for adequate decision making is emphasized

Evaluating a Modeling Curriculum by Using Heuristics for Productive Disciplinary Engagement

The BIO2010 report provided a compelling argument for the need to create learning experiences for undergraduate biology students that are more authentic to modern science. The report acknowledged the need for research that could help practitioners successfully create and reform biology curricula with this goal in mind. Our objective in this article was to explore how a set of six design heuristics could be used to evaluate the potential of curricula to support productive learning experiences for science students. We drew on data collected during a long-term study of an undergraduate traineeship that introduced students to mathematical modeling in the context of modern biological problems. We present illustrative examples from this curriculum that highlight the ways in which three heuristics—instructor role-modeling, holding students to scientific norms, and providing students with opportunities to practice these norms—consistently supported learning across the curriculum. We present a more detailed comparison of two different curricular modules and explain how differences in student authority, problem structure, and access to resources contributed to differences in productive engagement by students in these modules. We hope that our analysis will help practitioners think in more concrete terms about how to achieve the goals set forth by BIO2010

PROSITE, a protein domain database for functional characterization and annotation

PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE is largely used for the annotation of domain features of UniProtKB/Swiss-Prot entries. Among the 983 (DNA-binding) domains, repeats and zinc fingers present in Swiss-Prot (release 57.8 of 22 September 2009), 696 (∼70%) are annotated with PROSITE descriptors using information from ProRule. In order to allow better functional characterization of domains, PROSITE developments focus on subfamily specific profiles and a new profile building method giving more weight to functionally important residues. Here, we describe AMSA, an annotated multiple sequence alignment format used to build a new generation of generalized profiles, the migration of ScanProsite to Vital-IT, a cluster of 633 CPUs, and the adoption of the Distributed Annotation System (DAS) to facilitate PROSITE data integration and interchange with other sources. The latest version of PROSITE (release 20.54, of 22 September 2009) contains 1308 patterns, 863 profiles and 869 ProRules. PROSITE is accessible at: http://www.expasy.org/prosite/