Short Courses: Flexible Learning Opportunities in Informatics

In today’s fast-paced, data-driven world, researchers need to have a good foundation in informatics to store, organize, process, and analyze growing amounts of data. However, not all degree programs offer such training. Obtaining training in informatics on your own can be a daunting task for both new and established researchers who have little informatics experience. Providing educational opportunities appropriate for various skill levels and that mesh with a full-time schedule can remove barriers and foster a collaborative, informatics-savvy community that is better equipped to push science forward. To enhance informatics education in bioinformatics, VCUs Wright Center for Clinical and Translational Research of- fers a complementary series of seminars and workshops. These short course offerings introduce attendees to bioinformatics concepts and applications, and provide hands-on experience using online Bioinformatics databases. Bioinformatics 101 (B101) is an 8-week long series of 1-hour seminars focused on introducing topics in bioinformatics related to Next Generation Sequencing (NGS). Lectures are application focused and include overviews of NGS technology, practical bioinformatics pipelines, and examples of how the technology can influence downstream bioinformatics analyses. Bioinformatics 102 (B102) is a 5-day, 2 hours per day workshop developed in collaboration with VCU Libraries that provides attendees with hands-on experience accessing and using public data repositories. Sessions include a brief lecture followed by hands-on exercises. A Certificate of Completion is awarded upon meeting certain criteria for either the 101 or 102 courses. Bioinformatics 101 has been offered 3 times with a combined total of 246 registrants, and Bioinformatics 102 has been offered twice with a total of 78 registrants (limited to 30 per session per day). From course surveys, 82% (n=108) and 95% (n=47) of respondents gave B101 and B102 a positive rating, respectively. In addition, 89% of B101 respondents indicated their knowledge was improved, with 100% of B102 respondents indicating the same. A total of 84 and 33 certificates have been awarded for B101 and B102, respectively. The Bioinformatics 101 and 102 courses have become highly anticipated across the university, and have gained the external attention of surrounding businesses and colleges. Registrants have diverse backgrounds including biological, clinical, computational, administrative, librarian, business, and others with a total of 77 departments across VCU and VCU Health represented. Due to this interest, Bioinformatics 101 began offering live online attendance to accommodate those who were unable to travel across campus, or who are attending from outside VCU. This past year, 50% of attendance was online indicating a growing need for flexible education opportunities in informatics. Increasing researcher knowledge of Bioinformatics along with awareness of university resources for informatics support fosters an informatics-savvy research community that is empowered to take advantage of existing and new data sources in the pursuit of new insights and scientific discoveries for the betterment of human health. Future work will include the development of a more comprehensive educational framework by creating new and flexible learning opportunities that will make informatics education easy and convenient for our dedicated researchers

Providing Hands-on Training with Bioinformatics Databases: A Collaboration Between VCU Libraries & Wright Center for Clinical and Translational Research

BackgroundWith the goal of increasing specialized services for researchers, Virginia Commonwealth University (VCU) Libraries sent its basic science librarians to an intensive training on bioinformatics databases, “A Librarian’s Guide to NCBI.” VCU’s Wright Center for Clinical and Translational Research (Wright CCTR) was expanding the educational component of its bioinformatics support around the same time. This year, the librarians partnered with the Wright CCTR to offer an introductory bioinformatics database workshop introducing researchers to genetic/genomic databases. MethodsFor one week in June, sessions were conducted introducing up to 30 faculty and staff to The Cancer Genome Atlas and NCBI’s Gene, BLAST, Variation Viewer and Gene Expression Omnibus. Librarians taught resources they learned in the NCBI training, and Wright CCTR staff taught resources they use often. Each day’s 1.5 hour session included presentations, demonstrations, and hands-on assignment time. Certificates were awarded to participants who completed 4 out of 5 assignments. ResultsRegistration for the workshop was full in under a week with a waiting list. All survey respondents (n=27) evaluated the overall quality of the workshop as good or excellent and indicated that they would recommend the workshop to a colleague or student. ConclusionsThis successful partnership between VCU Libraries and the Wright CCTR allowed for a broader range of bioinformatics topics to be covered, in addition to easing the planning and teaching workload for each group. The strong interest in this series across a variety of disciplines from both VCU and VCU Health indicates a need for staff and faculty-oriented bioinformatics training within the university

`NMR Crystallization': in-situ NMR techniques for time-resolved monitoring of crystallization processes

Solid-state NMR spectroscopy is a well-established and versatile technique for studying structural and dynamic properties of solids, and there is considerable potential to exploit the power and versatility of solid-state NMR for in-situ studies of chemical processes. However, a number of technical challenges are associated with adapting this technique for in-situ studies, depending on the process of interest. Recently, an in-situ solid-state NMR strategy for monitoring the evolution of crystallization processes has been developed and has proven to be a promising approach for identifying the sequence of distinct solid forms present as a function of time during crystallization from solution, and for the discovery of new polymorphs. The latest development of this technique, called “CLASSIC” NMR, allows simultaneous measurement of both liquid-state and solid-state NMR spectra as a function of time, thus yielding complementary information on the evolution of both the liquid phase and the solid phase during crystallization from solution. This article gives an overview of the range of NMR strategies that are currently available for in-situ studies of crystallization processes, with examples of applications that highlight the potential of these strategies to deepen our understanding of crystallization phenomena

X-ray Birefringence Imaging and other fundamental aspects of solid organic inclusion compounds

This thesis presents new experimental techniques and utilizes these strategies in the analysis of solid organic inclusion compounds. This thesis also reports the production of a new series of co-crystals and examines their crystal structures. Chapter 1 acts as an introduction to the materials studied in this research. It explains the properties of inclusion compounds and lists the chemical materials used for these experiments. Chapter 2 explains the experimental techniques used in this research. Specifically it explains X-ray diffraction, X-ray birefringence and in-situ solid-state NMR. Chapter 3 presents a new technique for spatially resolved mapping of specific bond orientations in anisotropic solid materials using wide beam linearly polarized X-rays and an area detector. Earlier work with a focussed beam and a point detector showed the sensitivity of X-ray Birefringence to the orientation of specific energy-matching bonds inside a material, but these experiments only probed a small section of the crystal. Our wide beam imaging technique (X-ray Birefringence Imaging) shows similar sensitivity but allows us to investigate the full crystal simultaneously, which allows us to identify different domains within a single crystal. We apply this technique to a model material (1 bromocyclohexane/thiourea) which undergoes a low temperature phase transition and serves to demonstrate the usefulness of imaging techniques - in the high temperature phase the relevant C−Br bonds are isotropically disordered and no birefringence is observed, in the low temperature phase the relevant C−Br bonds are ordered but there are three possible orientations for the bromocyclohexane molecule so different regions of the crystal exhibit different birefringent signal. This behaviour is very clear on an imaging technique, but can appear highly confusing when using point-detector techniques. Chapter 4 utilizes X-ray Birefringence Imaging to investigate the dynamic rotational properties of guest molecules in a different set of solid organic inclusion compounds. By studying the known structures of 1,10-dibromodecane/urea and 1,8-dibromooctance/urea we have determined that XBI is a time-averaged and space-averaged technique. Additionally this chapter utilizes a Ge(555) analyzer instead of the Si(555) analyzer, which results in better spatial resolution and a different beam shape on the final images. Chapter 5 utilizes solid-state in-situ NMR to monitor crystallization processes as they occur and gain insight on competitive uptake of different guest molecules within the inclusion compound. These experiments use alkane and α,ω-dibromoalkane guest molecules inside urea inclusion compounds where the urea host structure (created in-situ) acts like a one-dimensional tunnel confining the guest. Every position within the urea tunnel is equivalent (a property of the incommensurate structure) which serves to simply the solid-state NMR spectra and means that for a given atom at the end of an alkane chain the only difference in NMR site comes from the neighbour molecule along the tunnel. This means in the solid phase we can observe peak splitting on certain atoms based on neighbour environment (e.g. the -CH3 in undecane will give a slightly different chemical shift if the neighbouring guest molecule is another undecane compared to if the neighbouring guest molecule is 1,8-dibromooctane) which in turn allows us to extract some information about the ordering within the inclusion compound. In these experiments we can also clearly distinguish between the same molecules in different phases, so as crystallization occurs we observe the loss of solution signal alongside the gain of solid signal. Additionally these experiments show no evidence of any intermediate structures or transition states. Chapter 6 describes a new set of organic co-crystals formed by reacting thiourea with α,ω-diiodoalkane chains and examines the crystal structures of these materials. Chapter 7 details further work and potential applications of this research. Digital data includes animated videos of the X-ray birefringence imaging data obtained in Chapter 3 and CIF files of the structures determined in Chapter 6

Phenotypic indicators to identify methionine rich European grain legumes and the correlation of grain methionine contents with the sulphur supply

Home grown legumes are a valuable protein source for pure on-farm diets for livestock in organic farming. Whereas protein of Glycine max naturally has higher contents of methionine nand also lysine typical European grain legumes (Pisum sativum L., Vicia faba L., Lupinus angustifolius L.) used in organic farms as component of animal food are relatively low in those amino acids

Limits on the Dipole Moments of the τ\tau-Lepton via the Process $e^{+}e^{-}\to \tau^+ \tau^- \gamma in a Left-Right Symmetric Model

Limits on the anomalous magnetic moment and the electric dipole moment of the $\tau$ lepton are calculated through the reaction $e^{+}e^{-}\to \tau^+ \tau^- \gamma$ at the $Z_1$-pole and in the framework of a left-right symmetric model. The results are based on the recent data reported by the L3 Collaboration at CERN LEP. Due to the stringent limit of the model mixing angle $\phi$, the effect of this angle on the dipole moments is quite small.Comment: 15 pages, 3 figure

Templeting of Thin Films Induced by Dewetting on Patterned Surfaces

The instability, dynamics and morphological transitions of patterns in thin liquid films on periodic striped surfaces (consisting of alternating less and more wettable stripes) are investigated based on 3-D nonlinear simulations that account for the inter-site hydrodynamic and surface-energetic interactions. The film breakup is suppressed on some potentially destabilizing nonwettable sites when their spacing is below a characteristic lengthscale of the instability, the upper bound for which is close to the spinodal lengthscale. The thin film pattern replicates the substrate surface energy pattern closely only when, (a) the periodicity of substrate pattern matches closely with the characteristic lengthscale, and (b) the stripe-width is within a range bounded by a lower critical length, below which no heterogeneous rupture occurs, and an upper transition length above which complex morphological features bearing little resemblance to the substrate pattern are formed.Comment: 5 pages TeX (REVTeX 4), other comments: submitted to Phys. Rev.Let