841 research outputs found
Description of Maribacter forsetii sp nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of the genus Maribacter
Three rod-shaped, Gram-negative, chemo-organotrophic, heterotrophic, strictly aerobic, gliding bacterial strains, KT02ds18-4, KT02ds18-5 and KT02ds18-6T, were isolated from North Sea surface waters near the island of Helgoland, Germany. Their taxonomic position was investigated by a polyphasic approach. The three strains were light yellow, oxidase- and catalase-positive, and grew optimally at 25 degrees C, at pH 7.5, and in the presence of 2.5 % (w/v) NaCl. The Chargaff's coefficient was 34.2-34.4 mol%. The three strains shared >90 % DNA-DNA relatedness and an identical 16S rRNA gene sequence. Comparative 16S rRNA gene sequence analysis allocated the three strains to the genus Maribacter in the family Flavobacteriaceae, with similarities of 97.0-97.4 % to five of the recognized Maribacter species. Their low level of DNA-DNA relatedness (<20 %) with these species and differentiating phenotypic characteristics demonstrated that they constitute a new Maribacter species for which the name Maribacter forsetii sp. nov. is proposed. Strain KT02ds18-6T (=CIP 109504T=DSM 18668T) is the type strain. An emended description of the genus Maribacter is also proposed
Off-axis electron holography of bacterial cells and magnetic nanoparticles in liquid
The mapping of electrostatic potentials and magnetic fields in liquids usingelectron holography has been considered to be unrealistic. Here, we showthat hydrated cells ofMagnetospirillum magneticumstrain AMB-1 and assem-blies of magnetic nanoparticles can be studied using off-axis electronholography in a fluid cell specimen holder within the transmission electronmicroscope. Considering that the holographic object and reference waveboth pass through liquid, the recorded electron holograms show sufficientinterference fringe contrast to permit reconstruction of the phase shift ofthe electron wave and mapping of the magnetic induction from bacterialmagnetite nanocrystals. We assess the challenges of performingin situmagne-tization reversal experiments using a fluid cell specimen holder, discussapproaches for improving spatial resolution and specimen stability, and outlinefuture perspectives for studying scientific phenomena, ranging from interpar-ticle interactions in liquids and electrical double layers at solid–liquidinterfaces to biomineralization and the mapping of electrostatic potentialsassociated with protein aggregation and folding
INFLUENCES OF WATERSHED URBANIZATION AND INSTREAM HABITAT ON MACROINVERTEBRATES IN COLD WATER STREAMS 1
We analyzed data from riffle and snag habitats for 39 small cold water streams with different levels of watershed urbanization in Wisconsin and Minnesota to evaluate the influences of urban land use and instream habitat on macroinvertebrate communities. Multivariate analysis indicated that stream temperature and amount of urban land use in the watersheds were the most influential factors determining macroinvertebrate assemblages. The amount of watershed urbanization was nonlinearly and negatively correlated with percentages of Ephemeroptera-Plecoptera-Trichoptera (EPT) abundance, EPT taxa, filterers, and scrapers and positively correlated with Hilsenhoff biotic index. High quality macroinvertebrate index values were possible if effective imperviousness was less than 7 percent of the watershed area. Beyond this level of imperviousness, index values tended to be consistently poor. Land uses in the riparian area were equal or more influential relative to land use elsewhere in the watershed, although riparian area consisted of only a small portion of the entire watershed area. Our study implies that it is extremely important to restrict watershed impervious land use and protect stream riparian areas for reducing human degradation on stream quality in low level urbanizing watersheds. Stream temperature may be one of the major factors through which human activities degrade cold-water streams, and management efforts that can maintain a natural thermal regime will help preserve stream quality.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72139/1/j.1752-1688.2003.tb03701.x.pd
Four small puzzles that Rosetta doesn't solve
A complete macromolecule modeling package must be able to solve the simplest
structure prediction problems. Despite recent successes in high resolution
structure modeling and design, the Rosetta software suite fares poorly on
deceptively small protein and RNA puzzles, some as small as four residues. To
illustrate these problems, this manuscript presents extensive Rosetta results
for four well-defined test cases: the 20-residue mini-protein Trp cage, an even
smaller disulfide-stabilized conotoxin, the reactive loop of a serine protease
inhibitor, and a UUCG RNA tetraloop. In contrast to previous Rosetta studies,
several lines of evidence indicate that conformational sampling is not the
major bottleneck in modeling these small systems. Instead, approximations and
omissions in the Rosetta all-atom energy function currently preclude
discriminating experimentally observed conformations from de novo models at
atomic resolution. These molecular "puzzles" should serve as useful model
systems for developers wishing to make foundational improvements to this
powerful modeling suite.Comment: Published in PLoS One as a manuscript for the RosettaCon 2010 Special
Collectio
Evidence for a vector charmonium-like state in
We report the measurement of via
initial-state radiation using a data sample of an integrated luminosity of
921.9 fb collected with the Belle detector at the and
nearby. We find evidence for an enhancement with a 3.4 significance in
the invariant mass of The measured mass and width
are
and ,
respectively. The mass, width, and quantum numbers of this enhancement are
consistent with the charmonium-like state at 4626 MeV/ recently reported
by Belle in The product of the cross section and the branching fraction of
is measured from
threshold to 5.6 GeV.Comment: 9 pages, 4 figure
Measurement of the CKM Matrix Element from at Belle
We present a new measurement of the CKM matrix element from decays, reconstructed with the full Belle data set
of integrated luminosity. Two form factor
parameterizations, originally conceived by the Caprini-Lellouch-Neubert (CLN)
and the Boyd, Grinstein and Lebed (BGL) groups, are used to extract the product
and the decay form factors, where
is the normalization factor and is a small
electroweak correction. In the CLN parameterization we find
, , , . For the BGL parameterization we
obtain , which is consistent with the World Average when correcting for
. The branching fraction of is measured to be . We also present a new
test of lepton flavor universality violation in semileptonic decays,
. The errors correspond to the statistical and
systematic uncertainties respectively. This is the most precise measurement of
and form factors to date and the first
experimental study of the BGL form factor parameterization in an experimental
measurement
A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry
We present here a review of the fundamental topics of Hartree-Fock theory in
Quantum Chemistry. From the molecular Hamiltonian, using and discussing the
Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock
equations for the electronic problem. Special emphasis is placed in the most
relevant mathematical aspects of the theoretical derivation of the final
equations, as well as in the results regarding the existence and uniqueness of
their solutions. All Hartree-Fock versions with different spin restrictions are
systematically extracted from the general case, thus providing a unifying
framework. Then, the discretization of the one-electron orbitals space is
reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition
of the basic underlying concepts related to the construction and selection of
Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we
close the review with a section in which the most relevant modern developments
(specially those related to the design of linear-scaling methods) are commented
and linked to the issues discussed. The whole work is intentionally
introductory and rather self-contained, so that it may be useful for non
experts that aim to use quantum chemical methods in interdisciplinary
applications. Moreover, much material that is found scattered in the literature
has been put together here to facilitate comprehension and to serve as a handy
reference.Comment: 64 pages, 3 figures, tMPH2e.cls style file, doublesp, mathbbol and
subeqn package
Structural basis for UFM1 transfer from UBA5 to UFC1
This is the final version. Available on open access from Nature Research via the DOI in this recordData availability:
Atomic coordinates and structure factors were deposited in the RCSB PDB (https://www.rcsb.org/) with the accession codes 7NW1, 7NVK, and 7NVJ for UFC1-UBA5 (389–404), UBA5(347-404)-UFC1, and UFC1(Y110A and F121A), respectively. NMR assignments for UFC1 were taken from the BMRB entry 6546. Previously published crystal structures used in this study are available from the RCSB PDB under the accession codes: 3TGD; 1J7D; 1U9A; 1×23; 1Y6L; 4Q5E; 4YII; 1Y8X; 1WZW; 6CYO; 1FZY; 1YLA; 2YBF; 2C4P; 5LBN; 3FN1; 2CYX; 2Z5D; 2F4W; 5BNB; 1YH2; 1YRV; 2Z6P; 2Z6O; 1JBB; 4Q5H; 1WZV; 3RZ3; 2DYT; 6H77. The coordinates of the structural models generated by in silico docking are provided as Supplementary Data 1–3. Source data are provided with this paper.Ufmylation is a post-translational modification essential for regulating key cellular processes. A three-enzyme cascade involving E1, E2 and E3 is required for UFM1 attachment to target proteins. How UBA5 (E1) and UFC1 (E2) cooperatively activate and transfer UFM1 is still unclear. Here, we present the crystal structure of UFC1 bound to the C-terminus of UBA5, revealing how UBA5 interacts with UFC1 via a short linear sequence, not observed in other E1-E2 complexes. We find that UBA5 has a region outside the adenylation domain that is dispensable for UFC1 binding but critical for UFM1 transfer. This region moves next to UFC1’s active site Cys and compensates for a missing loop in UFC1, which exists in other E2s and is needed for the transfer. Overall, our findings advance the understanding of UFM1’s conjugation machinery and may serve as a basis for the development of ufmylation inhibitors.Israel Science FoundationIsrael Cancer Research FundUS-Israel Binational Science Foundatio
Capturing complex tumour biology in vitro: Histological and molecular characterisation of precision cut slices
Precision-cut slices of in vivo tumours permit interrogation in vitro of heterogeneous cells from solid tumours together with their native microenvironment. They offer a low throughput but high content in vitro experimental platform. Using mouse models as surrogates for three common human solid tumours, we describe a standardised workflow for systematic comparison of tumour slice cultivation methods and a tissue microarray-based method to archive them. Cultivated slices were compared to their in vivo source tissue using immunohistochemical and transcriptional biomarkers, particularly of cellular stress. Mechanical slicing induced minimal stress. Cultivation of tumour slices required organotypic support materials and atmospheric oxygen for maintenance of integrity and was associated with significant temporal and loco-regional changes in protein expression, for example HIF-1α. We recommend adherence to the robust workflow described, with recognition of temporal-spatial changes in protein expression before interrogation of tumour slices by pharmacological or other means
- …