bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magnetic Properties and Magnetoresistance Effect of
YMn6Sn6-x
Cr
x
(x = 0-0.8) Compounds
Authors: Zhang Li-Gang  , Li Yun-Bao  , Zhang Shao-Ying  , Yao Jin-Lei  , Shen Bao-Gen  
Published: July 2002

The magnetic properties and magnetoresistance effect of
YMn6Sn6-x
Cr
x
(x = 0-0.8) compounds have been experimentally
studied by magnetic properties and resistivity measurements in the applied
field range 0-5 T. The compound (x = 0.8) displays a ferromagnetic behaviour,
while the compounds (x = 0-0.4) display an antiferromagnetic behaviour in the
whole ordering temperature range. The compounds (x = 0.5, 0.6) experienced a
transition from an antiferromagnetic state to a ferromagnetic state with
increasing temperature. The compound with x = 0.8 is rapidly saturated in the
lower magnetic field with saturation magnetization of 35.92 emu/g. The
compounds (x = 0-0.6) display a field-induced metamagnetic transition, and the
threshold fields decrease with increasing Cr content. The cell-volume V
of compounds (x = 0-0.8) increases, and the ordering temperature decreases
with the increasing Cr content. A large magnetoresistance effect was
observed for the compounds (x = 0.4, 0.5), and the maximum absolute
value at 5 K are 32% and 24% under 5 T for x = 0.4 and x = 0.5, respectively.
MOUSE (Mitochondrial and Other Useful SEquences)
a compilation of population genetic markers
Authors: Burckhardt Florian 
Published: July 2002

Abstract
Summary: Mitochondrial and Other Useful SEquences (MOUSE) is an integrated and comprehensive compilation of mtDNA from hypervariable regions I and II and of the low recombining nuclear loci Xq13.3 from about 11 200 humans and great apes, whose geographic and if applicable, linguistic classification is stored with their aligned sequences and publication details. The goal is to provide population geneticists and genetic epidemiologists with a comprehensive and user friendly repository of sequences and population information that is usually dispersed in a variety of other sources.
Availability: http://www.gen-epi.de/mouse
Contact: florian.burckhardt@gsf.de
Supplementary Information: Documentation and detailed information on population subgroups is available on the homepage: http://www.gen-epi.de/mouse
Determining a unique defining DNA sequence for yeast species using hashing techniques
Authors: Wesselink Jan-Jaap , de la Iglesia Beatriz , James Stephen A. , Dicks Jo L. , Roberts Ian N. , Rayward-Smith Vic J. 
Published: July 2002

Abstract
Motivation: Yeasts are often still identified with physiological growth tests, which are both time consuming and unsuitable for detection of a mixture of organisms. Hence, there is a need for molecular methods to identify yeast species.
Results: A hashing technique has been developed to search for unique DNA sequences in 702 26S rRNA genes. A unique DNA sequence has been found for almost every yeast species described to date. The locations of the unique defining sequences are in accordance with the variability map of large subunit ribosomal RNA and provide detail of the evolution of the D1/D2 region. This approach will be applicable to the rapid identification of unique sequences in other DNA sequence sets.
Availability: Freely available upon request from the authors.
Supplementary information: Results are available at http://www.sys.uea.ac.uk/~jjw/project/paper
Contact: jjw@sys.uea.ac.uk
* To whom correspondence should be addressed.
About the use of protein models
Authors: Peitsch Manuel C. 
Published: July 2002

Abstract
Protein models can be of great assistance in functional genomics, as they provide the structural insights often necessary to understand protein function. Although comparative modelling is far from yielding perfect structures, this is still the most reliable method and the quality of the predictions is now well understood. Models can be classified according to their correctness and accuracy, which will impact their applicability and usefulness in functional genomics and a variety of situations.
Contact: manuel.peitsch@pharma.novartis.com; manuel.peitsch@isb-sib.ch
The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes
Authors: Lespinet Olivier , Wolf Yuri I. , Koonin Eugene V. , Aravind L. 
Published: July 2002

A computational procedure was developed for systematic detection of lineage-specific expansions (LSEs) of protein families in sequenced genomes and applied to obtain a census of LSEs in five eukaryotic species, the yeasts Saccharomyces cerevisiae andSchizosaccharomyces pombe, the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the green plant Arabidopsis thaliana. A significant fraction of the proteins encoded in each of these genomes, up to 80% in A. thaliana, belong to LSEs. Many paralogous gene families in each of the analyzed species are almost entirely comprised of LSEs, indicating that their diversification occurred after the divergence of the major lineages of the eukaryotic crown group. The LSEs show readily discernible patterns of protein functions. The functional categories most prone to LSE are structural proteins, enzymes involved in an organism's response to pathogens and environmental stress, and various components of signaling pathways responsible for specificity, including ubiquitin ligase E3 subunits and transcription factors. The functions of several previously uncharacterized, vastly expanded protein families were predicted through in-depth protein sequence analysis, for example, small-molecule kinases and methylases that are expanded independently in the fly and in the nematode. The functions of several other major LSEs remain mysterious; these protein families are attractive targets for experimental discovery of novel, lineage-specific functions in eukaryotes. LSEs seem to be one of the principal means of adaptation and one of the most important sources of organizational and regulatory diversity in crown-group eukaryotes.[Supplemental material is available online at ftp://ncbi.nlm.nih.gov/pub/aravind/expansions, and http://www.genome.org.]
Glyphosate-Resistant Goosegrass. Identification of a Mutation in the Target Enzyme 5-Enolpyruvylshikimate-3-Phosphate Synthase
Authors: Baerson Scott R. , Rodriguez Damian J. , Tran Minhtien , Feng Yongmei , Biest Nancy A. , Dill Gerald M. 
Published: July 2002

Abstract
The spontaneous occurrence of resistance to the herbicide glyphosate in weed species has been an extremely infrequent event, despite over 20 years of extensive use. Recently, a glyphosate-resistant biotype of goosegrass (Eleusine indica) was identified in Malaysia exhibiting an LD50 value approximately 2- to 4-fold greater than the sensitive biotype collected from the same region. A comparison of the inhibition of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) activity by glyphosate in extracts prepared from the resistant (R) and sensitive (S) biotypes revealed an approximately 5-fold higher IC50(glyphosate) for the (R) biotype. Sequence comparisons of the predicted EPSPS mature protein coding regions from both biotypes revealed four single-nucleotide differences, two of which result in amino acid changes. One of these changes, a proline to serine substitution at position 106 in the (R) biotype, corresponds to a substitution previously identified in a glyphosate-insensitive EPSPS enzyme from Salmonella typhimurium. Kinetic data generated for the recombinant enzymes suggests that the second substitution identified in the (R) EPSPS does not contribute significantly to its reduced glyphosate sensitivity. Escherichia coli aroA− (EPSPS deficient) strains expressing the mature EPSPS enzyme from the (R) biotype exhibited an approximately 3-fold increase in glyphosate tolerance relative to strains expressing the mature EPSPS from the (S) biotype. These results provide the first evidence for an altered EPSPS enzyme as an underlying component of evolved glyphosate resistance in any plant species.
Variation in Growth Rate between Arabidopsis Ecotypes Is Correlated with Cell Division and A-Type Cyclin-Dependent Kinase Activity
Authors: Beemster Gerrit T.S. , De Vusser Kristof , De Tavernier Evelien , De Bock Kirsten , Inzé Dirk 
Published: July 2002

Abstract
We used a kinematic analysis to investigate the growth processes responsible for variation in primary root growth between 18 ecotypes of Arabidopsis. Root elongation rate differed 4-fold between the slowest (Landsberg erecta, 71 μm h−1) and fastest growing line (Wassilewskija [Ws]; 338 μm h−1). This difference was contributed almost equally by variations in mature cortical cell length (84 μm [Landsbergerecta] to 237 μm [Ws]) and rate of cell production (0.63 cell h−1 [NW108] to 1.83 cell h−1[Ws]). Cell production, in turn, was determined by variation in cell cycle duration (19 h [Tsu] to 48 h [NW108]) and, to a lesser extent, by differences in the number of dividing cells (32 [Weiningen] to 61 [Ws]). We found no correlation between mature cell size and endoreduplication, refuting the hypothesis that the two are linked. However, there was a strong correlation between cell production rates and the activity of the cyclin-dependent kinase (CDKA). The level of the protein could explain 32% of the variation in CDKA. Therefore, it is likely that regulators of CDKA, such as cyclins and inhibitors, are also involved. These data provide a functional link between cell cycle regulation and whole-plant growth rate as affected by genetic differences.
Heterology Expression of the ArabidopsisC-Repeat/Dehydration Response Element Binding Factor 1 Gene Confers Elevated Tolerance to Chilling and Oxidative Stresses in Transgenic Tomato
Authors: Hsieh Tsai-Hung , Lee Jent-Turn , Yang Pei-Tzu , Chiu Li-Hui , Charng Yee-yung , Wang Yu-Chie , Chan Ming-Tsair 
Published: July 2002

Abstract
In an attempt to improve stress tolerance of tomato (Lycopersicon esculentum) plants, an expression vector containing an Arabidopsis C-repeat/dehydration responsive element binding factor 1 (CBF1) cDNA driven by a cauliflower mosaic virus 35S promoter was transferred into tomato plants. Transgenic expression of CBF1 was proved by northern- and western-blot analyses. The degree of chilling tolerance of transgenic T1 and T2 plants was found to be significantly greater than that of wild-type tomato plants as measured by survival rate, chlorophyll fluorescence value, and radical elongation. The transgenic tomato plants exhibited patterns of growth retardation; however, they resumed normal growth after GA3(gibberellic acid) treatment. More importantly, GA3-treated transgenic plants still exhibited a greater degree of chilling tolerance compared with wild-type plants. Subtractive hybridization was performed to isolate the responsive genes of heterologous ArabidopsisCBF1 in transgenic tomato plants.CATALASE1 (CAT1) was obtained and showed activation in transgenic tomato plants. The CAT1 gene and catalase activity were also highly induced in the transgenic tomato plants. The level of H2O2 in the transgenic plants was lower than that in the wild-type plants under either normal or cold conditions. The transgenic plants also exhibited considerable tolerance against oxidative damage induced by methyl viologen. Results from the current study suggest that heterologous CBF1expression in transgenic tomato plants may induce several oxidative-stress responsive genes to protect from chilling stress.
Analysis of the NRT2 Nitrate Transporter Family in Arabidopsis. Structure and Gene Expression
Authors: Orsel Mathilde , Krapp Anne , Daniel-Vedele Françoise 
Published: July 2002

Abstract
Nitrate is an essential element for plant growth, both as a primary nutrient in the nitrogen assimilation pathway and as an important signal for plant development. The uptake of nitrate from the soil and its translocation throughout the plant has been the subject of intensive physiological and molecular studies. Using a reverse genetic approach, the AtNRT2.1 gene has been shown to be involved in the inducible component of the high-affinity nitrate transport system in Arabidopsis. The Arabidopsis Genome Initiative has released nearly the whole genome sequence of Arabidopsis, allowing the identification of a small NRT2 multigene family in this species. Thus, we investigated the phylogenetic relationship between NRT2 proteins belonging to several kingdoms and compared the structure of the different members of the Arabidopsis family. We analyzed, by semiquantitative reverse transcriptase-polymerase chain reaction, the expression pattern of each gene depending on plant organ and development or nutritional status, and compared the relative level of each gene by real-time polymerase chain reaction. We also evaluated the significance of each paralog on the basis of the relative levels of gene expression. The results are discussed in relation with distinct roles for the individual members of the AtNRT2 family.
The family of toxin‐related ecto‐ADP‐ribosyltransferases in humans and the mouse
Authors: Glowacki Gustavo , Braren Rickmer , Firner Kathrin , Nissen Marion , Kühl Maren , Reche Pedro , Bazan Fernando , Cetkovic‐Cvrlje Marina , Leiter Edward , Haag Friedrich , Koch‐Nolte Friedrich 
Published: July 2002

AbstractADP‐ribosyltransferases including toxins secreted byVibrio cholera, Pseudomonas aerurginosa, and other pathogenic bacteria inactivate the function of human target proteins by attaching ADP‐ribose onto a critical amino acid residue. Cross‐species polymerase chain reaction (PCR) and database mining identified the orthologs of these ADP‐ribosylating toxins in humans and the mouse. The human genome contains four functional toxin‐related ADP‐ribosyltransferase genes (ARTs) and two related intron‐containing pseudogenes; the mouse has six functional orthologs. The human and mouseARTgenes map to chromosomal regions with conserved linkage synteny. The individualARTgenes reveal highly restricted expression patterns, which are largely conserved in humans and the mouse. We confirmed the predicted extracellular location of the ART proteins by expressing recombinant ARTs in insect cells. Two human and four mouse ARTs contain the active site motif (R‐S‐EXE) typical of arginine‐specific ADP‐ribosyltransferases and exhibit the predicted enzyme activities. Two other human ARTs and their murine orthologues deviate in the active site motif and lack detectable enzyme activity. Conceivably, these ARTs may have acquired a new specificity or function. The position‐sensitive iterative database search program PSI‐BLAST connected the mammalian ARTs with most known bacterial ADP‐ribosylating toxins. In contrast, no related open reading frames occur in the four completed genomes of lower eucaryotes (yeast, worm, fly, and mustard weed). Interestingly, these organisms also lack genes for ADP‐ribosylhydrolases, the enzymes that reverse protein ADP‐ribosylation. This suggests that the two enzyme families that catalyze reversible mono‐ADP‐ribosylation either were lost from the genomes of these nonchordata eucaryotes or were subject to horizontal gene transfer between kingdoms.
Electrostatic contributions to protein–protein interactions: Fast energetic filters for docking and their physical basis
Authors: Norel Raquel , Sheinerman Felix , Petrey Donald , Honig Barry 
Published: July 2002

AbstractThe methods of continuum electrostatics are used to calculate the binding free energies of a set of protein–protein complexes including experimentally determined structures as well as other orientations generated by a fast docking algorithm. In the native structures, charged groups that are deeply buried were often found to favor complex formation (relative to isosteric nonpolar groups), whereas in nonnative complexes generated by a geometric docking algorithm, they were equally likely to be stabilizing as destabilizing. These observations were used to design a new filter for screening docked conformations that was applied, in conjunction with a number of geometric filters that assess shape complementarity, to 15 antibody–antigen complexes and 14 enzyme‐inhibitor complexes. For the bound docking problem, which is the major focus of this paper, native and near‐native solutions were ranked first or second in all but two enzyme‐inhibitor complexes. Less success was encountered for antibody–antigen complexes, but in all cases studied, the more complete free energy evaluation was able to idey native and near‐native structures. A filter based on the enrichment of tyrosines and tryptophans in antibody binding sites was applied to the antibody–antigen complexes and resulted in a native and near‐native solution being ranked first and second in all cases. A clear improvement over previously reported results was obtained for the unbound antibody–antigen examples as well. The algorithm and various filters used in this work are quite efficient and are able to reduce the number of plausible docking orientations to a size small enough so that a final more complete free energy evaluation on the reduced set becomes computationally feasible.
Ideication of disulfide‐linked peptides by isotope profiles produced by peptic digestion of proteins in 50% 18O water
Authors: Wallis Tristan P. , Pitt James J. , Gorman Jeffrey J. 
Published: July 2002

AbstractDetermination of the disulfide‐bond arrangement of a protein by characterization of disulfide‐linked peptides in proteolytic digests may be complicated by resistance of the protein to specific proteases, disulfide interchange, and/or production of extremely complex mixtures by less specific proteolysis. In this study, mass spectrometry has been used to show that incorporation of 18O into peptides during peptic digestion of disulfide‐linked proteins in 50% 18O water resulted in isotope patterns and increases in average masses that facilitated ideication and characterization of disulfide‐linked peptides even in complex mixtures, without the need for reference digests in 100% 16O water. This is exemplified by analysis of peptic digests of model proteins lysozyme and ribonuclease A (RNaseA) by matrix‐assisted laser desorption/ionization–time of flight (MALDI‐TOF) and electrospray ionization (ESI) mass spectrometry (MS). Distinct isotope profiles were evident when two peptide chains were linked by disulfide bonds, provided one of the chains did not contain the C terminus of the protein. This latter class of peptide, and single‐chain peptides containing an intrachain disulfide bond, could be ideied and characterized by mass shifts produced by reduction. Reduction also served to confirm other assignments. Isotope profiling of peptic digests showed that disulfide‐linked peptides were often enriched in the high molecular weight fractions produced by size exclusion chromatography (SEC) of the digests. Applicability of these procedures to analysis of a more complex disulfide‐bond arrangement was shown with the hemagglutinin/neuraminidase of Newcastle disease virus.
Structure of the transmembrane region of the M2 protein H+ channel
Authors: Wang Junfeng , Kim Sanguk , Kovacs Frank , Cross Timothy A. 
Published: July 2002

AbstractThe transmembrane domain of the M2 protein from influenza A virus forms a nearly uniform and ideal helix in a liquid crystalline bilayer environment. The exposure of the hydrophilic backbone structure is minimized through uniform hydrogen bond geometry imposed by the low dielectric lipid environment. A high‐resolution structure of the monomer backbone and a detailed description of its orientation with respect to the bilayer were achieved using orientational restraints from solid‐state NMR. With this unique information, the tetrameric structure of this H+ channel is constrained substantially. Features of numerous published models are discussed in light of the experimental structure of the monomer and derived features of the tetrameric bundle.
Reconstitution of a native‐like SH2 domain from disordered peptide fragments examined by multidimensional heteronuclear NMR
Authors: Ojennus Deanna Dahlke , Fleissner Mark R. , Wuttke Deborah S. 
Published: July 2002

AbstractThe N‐terminal SH2 domain from the p85α subunit of phosphatidylinositol 3′ kinase is cleaved specifically into 9‐ and 5‐kD fragments by limited proteolytic digestion with trypsin. The noncovalent SH2 domain complex and its constituent tryptic peptides have been investigated using high‐resolution heteronuclear magnetic resonance (NMR). These studies have established the viability of the SH2 domain as a fragment complementation system. The individual peptide fragments are predominantly unstructured in solution. In contrast, the noncovalent 9‐kD + 5‐kD complex shows a native‐like 1H‐15N HSQC spectrum, demonstrating that the two fragments fold into a native‐like structure on binding. Chemical shift analysis of the noncovalent complex compared to the native SH2 domain reveals that the highest degree of perturbation in the structure occurs at the cleavage site within a flexible loop and along the hydrophobic interface between the two peptide fragments. Mapping of these chemical shift changes on the structure of the domain reveals changes consistent with the reduction in affinity for the target peptide ligand observed in the noncovalent complex relative to the intact protein. The 5‐kD fragment of the homologous Src protein is incapable of structurally complementing the p85 9‐kD fragment, either in complex formation or in the context of the full‐length protein. These high‐resolution structural studies of the SH2 domain fragment complementation features establish the suitability of the system for further protein‐folding and design studies.
Novel Ciprofloxacin-Resistant, Nalidixic Acid-Susceptible Mutant of
Staphylococcus aureus
Authors: Piddock Laura J. V. , Jin Yu Fang , Webber Mark A. , Everett Martin J. 
Published: July 2002

ABSTRACT

A ciprofloxacin-resistant, nalidixic acid-susceptible mutant of
Staphylococcus aureus
(F145) contained no mutations within
gyrA
,
gyrB
,
grlA
, and
grlB
or within
norA
or its promoter region. MICs and accumulation studies suggest the role of a novel multidrug efflux pump.
Neuroprotection and Reduced Proliferation of Microglia in Ribavirin-Treated Bornavirus-Infected Rats
Authors: Solbrig Marylou V. , Schlaberg Robert , Briese Thomas , Horscroft Nigel , Lipkin W. Ian 
Published: July 2002

ABSTRACTIn a rat model of Borna disease, intracerebral ribavirin caused clinical improvement without changes in virus titer or nucleic acid. Levels of microglia and infiltrating CD4 and CD8 cells were decreased, despite increases in mRNAs encoding interleukin-1β (IL-1β), IL-10, and gamma interferon in the brain. Intracerebral ribavirin may reduce morbidity through effects on microglia cell proliferation.
Tn
5406
, a New Staphylococcal Transposon Conferring Resistance to Streptogramin A and Related Compounds Including Dalfopristin
Authors: Haroche Julien , Allignet Jeanine , El Solh Névine 
Published: July 2002

ABSTRACT

We characterized a new transposon, Tn
5406
(5,467 bp), in a clinical isolate of
Staphylococcus aureus
(BM3327). It carries a variant of
vgaA
, which encodes a putative ABC protein conferring resistance to streptogramin A but not to mixtures of streptogramins A and B. It also carries three putative genes, the products of which exhibit significant similarities (61 to 73% amino acid identity) to the three transposases of the staphylococcal transposon Tn
554
. Like Tn
554
, Tn
5406
failed to generate target repeats. In BM3327, the single copy of Tn
5406
was inserted into the chromosomal
att554
site, which is the preferential insertion site of Tn
554
. In three other independent
S. aureus
clinical isolates, Tn
5406
was either present as a single plasmid copy (BM3318), as two chromosomal copies (BM3252), or both in the chromosome and on a plasmid (BM3385). The Tn
5406
-carrying plasmids also contain two other genes,
vgaB
and
vatB
. The insertion sites of Tn
5406
in BM3252 were studied: one copy was in
att554
, and one copy was in the additional
SCCmec
element. Amplification experiments revealed circular forms of Tn
5406
, indicating that this transposon might be active. To our knowledge, a transposon conferring resistance to streptogramin A and related compounds has not been previously described.