eGenomics: Cataloguing our complete genome collection III

This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS), Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS) specification (v1.1), consensus on a variety of features to be added to the Genome Catalogue (GCat), agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates) and working towards a single, global list of all public genomes and metagenomes

Ring-Exchange Interaction Effects on Magnons in Dirac Magnet CoTiO3_3

In magnetically ordered materials with localized electrons, the fundamental magnetic interactions are due to exchange of electrons [1-3]. Typically, only the interaction between pairs of electrons' spins is considered to explain the nature of the ground state and its excitations, whereas three-, four-, and six-spin interactions are ignored. When these higher order processes occur in a loop they are called cyclic or ring exchange. The ring-exchange interaction is required to explain low temperature behavior in bulk and thin films of solid $^3$He [4-8]. It also plays a crucial role in the quantum magnet La$_2$CuO$_4$ [9,10]. Here, we use a combination of time domain THz (TDTS) and magneto-Raman spectroscopies to measure the low energy magnetic excitations in CoTiO$_3$, a proposed Dirac topological magnon material [11,12] where the origin of the energy gap in the magnon spectrum at the Brillouin zone center remains unclear. We measured the magnetic field dependence of the energies of the two lowest energy magnons and determine that the gap opens due to the ring-exchange interaction between the six spins in a hexagon. This interaction also explains the selection rules of the THz magnon absorption. Finally, we clarify that topological surface magnons are not expected in CoTiO$_3$. Our study demonstrates the power of combining TDTS and Raman spectroscopies with theory to identify the microscopic origins of the magnetic excitations in quantum magnets.Comment: 7 pages, 4 figures in main text, 26 pages and 11 figures in supplemen

Spectroscopic and Mechanistic Studies of Heterodimetallic Forms of Metallo-β-lactamase NDM-1

In an effort to characterize the roles of each metal ion in metallo-β-lactamase NDM-1, heterodimetallic analogues (CoCo-, ZnCo-, and CoCd-) of the enzyme were generated and characterized. UV–vis, 1H NMR, EPR, and EXAFS spectroscopies were used to confirm the fidelity of the metal substitutions, including the presence of a homogeneous, heterodimetallic cluster, with a single-atom bridge. This marks the first preparation of a metallo-β-lactamase selectively substituted with a paramagnetic metal ion, Co(II), either in the Zn1 (CoCd-NDM-1) or in the Zn2 site (ZnCo-NDM-1), as well as both (CoCo-NDM-1). We then used these metal-substituted forms of the enzyme to probe the reaction mechanism, using steady-state and stopped-flow kinetics, stopped-flow fluorescence, and rapid-freeze-quench EPR. Both metal sites show significant effects on the kinetic constants, and both paramagnetic variants (CoCd- and ZnCo-NDM-1) showed significant structural changes on reaction with substrate. These changes are discussed in terms of a minimal kinetic mechanism that incorporates all of the data

A novel malaria vaccine candidate antigen expressed in Tetrahymena thermophila

Development of effective malaria vaccines is hampered by the problem of producing correctly folded Plasmodium proteins for use as vaccine components. We have investigated the use of a novel ciliate expression system, Tetrahymena thermophila, as a P. falciparum vaccine antigen platform. A synthetic vaccine antigen composed of N-terminal and C-terminal regions of merozoite surface protein-1 (MSP-1) was expressed in Tetrahymena thermophila. The recombinant antigen was secreted into the culture medium and purified by monoclonal antibody (mAb) affinity chromatography. The vaccine was immunogenic in MF1 mice, eliciting high antibody titers against both N- and C-terminal components. Sera from immunized animals reacted strongly with P. falciparum parasites from three antigenically different strains by immunofluorescence assays, confirming that the antibodies produced are able to recognize parasite antigens in their native form. Epitope mapping of serum reactivity with a peptide library derived from all three MSP-1 Block 2 serotypes confirmed that the MSP-1 Block 2 hybrid component of the vaccine had effectively targeted all three serotypes of this polymorphic region of MSP-1. This study has successfully demonstrated the use of Tetrahymena thermophila as a recombinant protein expression platform for the production of malaria vaccine antigens

Distinct magneto-Raman signatures of spin-flip phase transitions in CrI3_{3}

The discovery of 2-dimensional (2D) materials, such as CrI$_{3}$, that retain magnetic ordering at monolayer thickness has resulted in a surge of both pure and applied research in 2D magnetism. Here, we report a magneto-Raman spectroscopy study on multilayered CrI$_{3}$, focusing on two additional features in the spectra that appear below the magnetic ordering temperature and were previously assigned to high frequency magnons. Instead, we conclude these modes are actually zone-folded phonons. We observe a striking evolution of the Raman spectra with increasing magnetic field applied perpendicular to the atomic layers in which clear, sudden changes in intensities of the modes are attributed to the interlayer ordering changing from antiferromagnetic to ferromagnetic at a critical magnetic field. Our work highlights the sensitivity of the Raman modes to weak interlayer spin ordering in CrI$_{3}$

Distinct magneto-Raman signatures of spin-flip phase transitions in CrI3

The discovery of 2-dimensional (2D) materials, such as CrI3, that retain magnetic ordering at monolayer thickness has resulted in a surge of research in 2D magnetism from both pure and applied perspectives. Here, we report a magneto-Raman spectroscopy study on multilayered CrI3, focusing on two new features in the spectra which appear at temperatures below the magnetic ordering temperature and were previously assigned to high frequency magnons. We observe a striking evolution of the Raman spectra with increasing magnetic field in which clear, sudden changes in intensities of the modes are attributed to the interlayer ordering changing from antiferromagnetic to ferromagnetic at a critical magnetic field. Our work highlights the sensitivity of the Raman modes to weak interlayer spin ordering in CrI3. In addition, we theoretically examine potential origins for the new modes, which we deduce are unlikely single magnons

The Canine Oral Microbiome

Determining the bacterial composition of the canine oral microbiome is of interest for two primary reasons. First, while the human oral microbiome has been well studied using molecular techniques, the oral microbiomes of other mammals have not been studied in equal depth using culture independent methods. This study allows a comparison of the number of bacterial taxa, based on 16S rRNA-gene sequence comparison, shared between humans and dogs, two divergent mammalian species. Second, canine oral bacteria are of interest to veterinary and human medical communities for understanding their roles in health and infectious diseases. The bacteria involved are mostly unnamed and not linked by 16S rRNA-gene sequence identity to a taxonomic scheme. This manuscript describes the analysis of 5,958 16S rRNA-gene sequences from 65 clone libraries. Full length 16S rRNA reference sequences have been obtained for 353 canine bacterial taxa, which were placed in 14 bacterial phyla, 23 classes, 37 orders, 66 families, and 148 genera. Eighty percent of the taxa are currently unnamed. The bacterial taxa identified in dogs are markedly different from those of humans with only 16.4% of oral taxa are shared between dogs and humans based on a 98.5% 16S rRNA sequence similarity cutoff. This indicates that there is a large divergence in the bacteria comprising the oral microbiomes of divergent mammalian species. The historic practice of identifying animal associated bacteria based on phenotypic similarities to human bacteria is generally invalid. This report describes the diversity of the canine oral microbiome and provides a provisional 16S rRNA based taxonomic scheme for naming and identifying unnamed canine bacterial taxa

Telomere Lengths, Pulmonary Fibrosis and Telomerase (TERT) Mutations

mutations. mutation carriers demonstrate reduced life expectancy, with a mean age of death of 58 and 67 years for males and females, respectively. mutation have shorter telomere lengths than controls, demonstrating epigenetic inheritance of a shortened parental telomere length set-point