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PubMed2004

Theoretical study of the electronic states of Nb4, Nb5 clusters and their anions (Nb4-,Nb5-).

Geometries and energy separations of the various low-lying electronic states of Nb(n) and Nb(n) (-) (n=4,5) clusters with various structural arrangements have been investigated. The complete active space multiconfiguration self-consistent field method followed by multireference singles and doubles configuration interaction (MRSDCI) calculations that included up to 52x10(6) configuration spin functions have been used to compute several electronic states of these clusters. The ground states of both Nb(4) ((1)A('), pyramidal) and Nb(4) (-) ((2)B(3g), rhombus) are low-spin states at the MRSDCI level. The ground state of Nb(5) cluster is a doublet with a distorted trigonal bipyramid (DTB) structure. The anionic cluster of Nb(5) has two competitive ground states with singlet and triplet multiplicities (DTB). The low-lying electronic states of these clusters have been found to be distorted due to Jahn-Teller effect. On the basis of the energy separations of our computed electronic states of Nb(4) and Nb(5), we have assigned the observed photoelectron spectrum of Nb(n) (-) (n=4,5) clusters. We have also compared our MRSDCI results with density functional calculations. The electron affinity, ionization potential, dissociation and atomization energies of Nb(4) and Nb(5) have been calculated and the results have been found to be in excellent agreement with the experiment.

Journal Article↗
PubMed2006

Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa.

BACKGROUND: The Gram-negative, xylem-limited phytopathogenic bacterium Xylella fastidiosa is responsible for causing economically important diseases in grapevine, citrus and many other plant species. Despite its economic impact, relatively little is known about the genomic variations among strains isolated from different hosts and their influence on the population genetics of this pathogen. With the availability of genome sequence information for four strains, it is now possible to perform genome-wide analyses to identify and categorize such DNA variations and to understand their influence on strain functional divergence. RESULTS: There are 1,579 genes and 194 non-coding homologous sequences present in the genomes of all four strains, representing a 76. 2% conservation of the sequenced genome. About 60% of the X. fastidiosa unique sequences exist as tandem gene clusters of 6 or more genes. Multiple alignments identified 12,754 SNPs and 14,449 INDELs in the 1528 common genes and 20,779 SNPs and 10,075 INDELs in the 194 non-coding sequences. The average SNP frequency was 1.08 x 10(-2) per base pair of DNA and the average INDEL frequency was 2.06 x 10(-2) per base pair of DNA. On an average, 60.33% of the SNPs were synonymous type while 39.67% were non-synonymous type. The mutation frequency, primarily in the form of external INDELs was the main type of sequence variation. The relative similarity between the strains was discussed according to the INDEL and SNP differences. The number of genes unique to each strain were 60 (9a5c), 54 (Dixon), 83 (Ann1) and 9 (Temecula-1). A sub-set of the strain specific genes showed significant differences in terms of their codon usage and GC composition from the native genes suggesting their xenologous origin. Tandem repeat analysis of the genomic sequences of the four strains identified associations of repeat sequences with hypothetical and phage related functions. CONCLUSION: INDELs and strain specific genes have been identified as the main source of variations among strains, with individual strains showing different rates of genome evolution. Based on these genome comparisons, it appears that the Pierce's disease strain Temecula-1 genome represents the ancestral genome of the X. fastidiosa. Results of this analysis are publicly available in the form of a web database.

Analysis of Variance↗
PubMed2004

Impact on genetic networks in human macrophages by a CCR5 strain of human immunodeficiency virus type 1.

Human immunodeficiency virus type 1 (HIV-1) impacts multiple lineages of hematopoietic cells, including lymphocytes and macrophages, either by direct infection or indirectly by perturbations of cell networks, leading to generalized immune deficiency. We designed a study to discover, in primary human macrophages, sentinel genetic targets that are impacted during replication over the course of 7 days by a CCR5-using virus. Expression of mRNA and proteins in virus- or mock-treated macrophages from multiple donors was evaluated. Hierarchical agglomerative cluster analysis grouped into distinct temporal expression patterns >900 known human genes that were induced or repressed at least fourfold by virus. Expression of more than one-third of the genes was induced rapidly by day 2 of infection, while other genes were induced at intermediate (day 4) or late (day 7) time points. More than 200 genes were expressed exclusively in either virus- or mock-treated macrophage cultures, independent of the donor, providing an unequivocal basis to distinguish an effect by virus. HIV-1 altered levels of mRNA and/or protein for diverse cellular programs in macrophages, including multiple genes that can contribute to a transition in the cell cycle from G(1) to G(2)/M, in contrast to expression in mock-treated macrophages of genes that maintain G(0)/G(1). Virus treatment activated mediators of cell cycling, including PP2A, which is impacted by Vpr, as well as GADD45 and BRCA1, potentially novel targets for HIV-1. The results identify interrelated programs conducive to optimal HIV-1 replication and expression of genes that can contribute to macrophage dysfunction.

CDC2 Protein Kinase↗
PubMed2006

Multiple valence superatoms.

We recently demonstrated that, in gas phase clusters containing aluminum and iodine atoms, an Al(13) cluster behaves like a halogen atom, whereas an Al(14) cluster exhibits properties analogous to an alkaline earth atom. These observations, together with our findings that Al(13)(-) is inert like a rare gas atom, have reinforced the idea that chosen clusters can exhibit chemical behaviors reminiscent of atoms in the periodic table, offering the exciting prospect of a new dimension of the periodic table formed by cluster elements, called superatoms. As the behavior of clusters can be controlled by size and composition, the superatoms offer the potential to create unique compounds with tailored properties. In this article, we provide evidence of an additional class of superatoms, namely Al(7)(-), that exhibit multiple valences, like some of the elements in the periodic table, and hence have the potential to form stable compounds when combined with other atoms. These findings support the contention that there should be no limitation in finding clusters, which mimic virtually all members of the periodic table.

Journal Article↗
PubMed2005

Dynamics of charge-transfer-to-solvent precursor states in I- (water)n (n = 3-10) clusters studied with photoelectron imaging.

The dynamics of charge-transfer-to-solvent states are studied in I- (H2O)(n=3-10) clusters and their deuterated counterparts using time-resolved photoelectron imaging. The photoelectron spectra for clusters with n > or = 5 reveal multiple time scales for dynamics after their electronic excitation. An increase in the vertical detachment energy (VDE) by several hundred millielectronvolts on a time scale of approximately 1 ps is attributed to stabilization of the excess electron, primarily through rearrangement of the solvent molecules, but a contribution to this stabilization from motion of the I atom cannot be ruled out. The VDE drops by approximately 50 meV on a time scale of tens of picoseconds; this is attributed to loss of the neutral iodine atom. Finally, the pump-probe signal decays with a time constant of 60 ps-3 ns, increasing with cluster size. This decay is commensurate with the growth of very slow electrons and is attributed to autodetachment. Smaller clusters (n = 3, 4) display simpler dynamics. Anisotropy parameters are reported for clusters n = 4-9.

Journal Article↗
PubMed2003

[60]fullerene--metal cluster complexes: novel bonding modes and electronic communication.

[60]Fullerene can bind a variety of metal clusters via eta(2)-C(60), mu-eta(2):eta(2)-C(60), and mu(3)-eta(2):eta(2):eta(2)-C(60) pi-type bonding modes. Multiple C(60) additions to a single cluster core have also been demonstrated. Modification of the coordination sphere of cluster moieties has resulted in novel transformation of the coordination mode of the C(60) ligand between pi and sigma (mu(3)-eta(1):eta(1):eta(2)-C(60) and mu(3)-eta(1):eta(2):eta(1)-C(60)) types as well as reversible interconversion between mu(3)-eta(2):eta(2):eta(2)-C(60) and mu-eta(2):eta(2)-C(60). The mu(3)-eta(2):eta(2):eta(2)-C(60) metal cluster complexes show remarkable electrochemical stability and an unusually strong electronic communication between C(60) and metal cluster centers.

Journal Article↗
PubMedDate not supplied

Identification of a diversity segment of human T-cell receptor beta-chain, and comparison with the analogous murine element.

The humoral immune system antigen-binding proteins (immunoglobulins) are disulphide-linked heterodimers of light and heavy chains. The gene for the variable region which determines antigen specificity is assembled when one member from each of the dispersed clusters of variable (V) gene segments, diversity (D) elements (for the heavy chains only) and joining (J) segments rearrange and fuse during B-cell development (reviewed in ref. 1). Short recognition sequences adjacent to these elements appear to be involved in the recombination process. The cellular immune system antigen recognition proteins are receptors on the surface of T cells, which are composed of disulphide-linked alpha-chains and beta-chains, each of which has a variable and constant region. Recently, cDNA clones of the beta-chain mRNA have been isolated; the genomic arrangement is very similar to immunoglobulin genes with multiple V beta genes, and two clusters of J beta segments, each of which is upstream from a constant-region gene segment. The V beta and J beta segments have adjacent recombinational recognition sequences like the immunoglobulin elements. However, approximately 10 nucleotides of the cDNA clones between the V beta and J beta regions were not present in the corresponding genomic elements and may have been due to intervening D beta segments. Here we describe a diversity element (D beta 1.1) in a region of high human-mouse homology about 650 bases 5' to the first J beta cluster. Two transcripts which include sequences upstream of D beta 1.1 are found in the human thymus. This region may have some other function besides providing the beta-chain with a diversity segment.

Amino Acid Sequence↗
PubMed1995

Prognostic relevance of a histologic classification system applied in bone marrow biopsies from patients with multiple myeloma: a histopathological evaluation of biopsies from 153 untreated patients.

A total of 153 diagnostic bone marrow biopsies from patients with advanced stages of multiple myeloma corresponding to stages II and III according to the Durie/Salmon classification were evaluated prior to any treatment in a prospective therapy trial of the German Myeloma Treatment Group. Histologic sections were analyzed according to a pre-defined system of criteria microscopically by 2 observers, determining three criteria: 1) grading by histopathology, regarding the cytologic differentiation of neoplastic cells and quantifying the percentage of plasmacytic, pleomorphic, and plasmablastic myeloma cells distributed within the sections; 2) the volume of infiltration; and 3) the pattern of neoplastic growth. Furthermore, four other criteria, namely hematopoiesis, fiber increase, osteomalacia, and micro-osteo-lesions, were evaluated. A cluster analysis using the three histological criteria revealed three groups of patients with significantly different survival times based on histological criteria only; the three criteria were mentioned above. It is concluded from these results that bone marrow biopsies, when evaluated histologically by grading and staging according to the three criteria, provide most valuable prognostic parameters in myeloma patients.

Bone Marrow↗
PubMed2005

Multiple loop conformations of peptides predicted by molecular dynamics simulations are compatible with nuclear magnetic resonance.

The affinity and selectivity of protein-protein interactions can be fine-tuned by varying the size, flexibility, and amino acid composition of involved surface loops. As a model for such surface loops, we study the conformational landscape of an octapeptide, whose flexibility is chemically steered by a covalent ring closure integrating an azobenzene dye into and by a disulfide bridge additionally constraining the peptide backbone. Because the covalently integrated azobenzene dyes can be switched by light between a bent cis state and an elongated trans state, six cyclic peptide models of strongly different flexibilities are obtained. The conformational states of these peptide models are sampled by NMR and by unconstrained molecular dynamics (MD) simulations. Prototypical conformations and the free-energy landscapes in the high-dimensional space spanned by the phi/psi angles at the peptide backbone are obtained by clustering techniques from the MD trajectories. Multiple open-loop conformations are shown to be predicted by MD particularly in the very flexible cases and are shown to comply with the NMR data despite the fact that such open-loop conformations are missing in the refined NMR structures.

Aminobenzoates↗
PubMed2005

Clinical and molecular characteristics of hereditary non-polyposis colorectal cancer families in Southeast Asia.

Lee S-C, Guo J-Y, Lim R, Soo R, Koay E, Salto-Tellez M, Leong A, Goh B-C. Clinical and molecular characteristics of hereditary non-polyposis colorectal cancer families in Southeast Asia. Hereditary non-polyposis colorectal cancer (HNPCC), predominantly due to germline MLH1/MSH2 mutations, is the commonest form of hereditary colorectal cancer (CRC), but data in Asians are sparse. We sequenced the MLH1/MSH2 coding and promoter core regions in CRC patients diagnosed below age 40, and/or with multiple primary cancers or familial cancer clustering suggestive of HNPCC, and correlated deleterious mutations with clinical and tumour features. Forty-six Chinese, Malay and Indian kindreds participated. Of the 153 cancers reported in the 46 kindreds, stomach (14%) and urogenital cancers (13%) were the most common extracolonic cancers, whereas endometrial cancer comprised only 7%. Eleven different MLH1 and 12 MSH2 mutations were identified, including nine novel and four recurring mutations in the Chinese. One Indian was a compound heterozygote for an MLH1 and MSH2 mutation. The MLH1/MSH2 mutation data in the Malays and the Indians represents the first in these ethnic groups. Factors strongly associated with deleterious mutations were the Amsterdam criteria, family history of stomach or multiple primary cancers, and MSI-high tumours, whereas family history of endometrial cancer and young cancer age alone correlated poorly. Distinct clinical and molecular characteristics were identified among Asian HNPCC kindreds and may have important clinical implications.

Adaptor Proteins, Signal Transducing↗
PubMedDate not supplied

Sorting variables for each case: a new algorithm to calculate injury severity score (ISS) using SPSS-PC.

One of the more often used measures of multiple injuries is the injury severity score (ISS). Determination of the ISS is based on the abbreviated injury scale (AIS). This paper suggests a new algorithm to sort the AISs for each case and calculate ISS. The program uses unsorted abbreviated injury scale (AIS) levels for each case and rearranges them in descending order. The first three sorted AISs representing the three most severe injuries of a person are then used to calculate injury severity score (ISS). This algorithm should be useful for analyses of clusters of injuries especially when more patients have multiple injuries.

Abbreviated Injury Scale↗
PubMed2006

Molecular characterization of Coxiella burnetii isolates by infrequent restriction site-PCR and MLVA typing.

BACKGROUND: Coxiella burnetii, the causative agent of Q fever, has a wide host range. Few epidemiological tools are available, and they are often expensive or not easily standardized across laboratories. In this work, C. burnetii isolates from livestock and ticks were typed using infrequent restriction site-PCR (IRS-PCR) and multiple loci variable number of tandem repeats (VNTR) analysis (MLVA). RESULTS: By applying IRS-PCR, 14 C. burnetii isolates could be divided into six groups containing up to five different isolates. Clustering as deduced from MLVA typing with 17 markers provided an increased resolution with an excellent agreement to IRS-PCR, and with the plasmid type of each strain. MLVA was then applied to 28 additional C. burnetii isolates of different origin and 36 different genotypes were identified among the 42 isolates investigated. The clustering obtained is in agreement with published Multiple Locus Sequence Typing (MLST) data. Two panels of markers are proposed, panel 1 which can be confidently typed on agarose gel at a lower cost and in any laboratory setting (10 minisatellite markers with a repeat unit larger than 9 bp), and panel 2 which comprises 7 microsatellites and provides a higher discriminatory power. CONCLUSION: Our analyses demonstrate that MLVA is a powerful and promising molecular typing tool with a high resolution and of low costs. The consistency of the results with independent methods suggests that MLVA can be applied for epidemiological studies. The resulting data can be queried on a dedicated MLVA genotyping Web service.

Animals↗
PubMed1990

Multiplication of the class I alcohol dehydrogenase locus in mammalian evolution.

Chromosomal DNA samples derived from various primates and other mammals (horse, sheep, rabbit, and mouse) were digested with restriction endonuclease and hybridized with a probe of the sixth exon of the human ADH gene, which is highly conserved in the class I alcohol dehydrogenase of these mammalian species. The copy number of the class I ADH gene in each species was estimated from the number of hybridized bands. Primate DNA samples showed three distinct bands in the blots of PstI digest and DraI digest. Moreover, most of the bands from primate DNA showed a similarity in size so as to allow us to assign the ADH1, ADH2, and ADH3 homologues in each species. In contrast, mouse has only one gene, and rabbit, sheep, and horse seem to have only two genes, for the class I ADH, which showed divergent hybridization bands. These results are consistent with the view that the human class I ADH gene cluster has been generated through gene multiplication events which occurred before the Catarrhini branch point in the course of primate evolution.

Alcohol Dehydrogenase↗
PubMed1996

Long-range disruption of gene expression by a selectable marker cassette.

Recent studies have suggested that the retention of selectable marker cassettes (like PGK-Neo, in which a hybrid gene consisting of the phosphoglycerate kinase I promoter drives the neomycin phosphotransferase gene) in targeted loci can cause unexpected phenotypes in "knockout" mice due to disruption of expression of neighboring genes within a locus. We have studied targeted mutations in two multigene clusters, the granzyme B locus and the beta-like globin gene cluster. The insertion of PGK-Neo into the granzyme B gene, the most 5' gene in the granzyme B gene cluster, severely reduced the normal expression of multiple genes within the locus, even at distances greater than 100 kb from the mutation. Similarly, the insertion of a PGK-Neo cassette into the beta-globin locus control region (LCR) abrogates the expression of multiple globin genes downstream from the cassette. In contrast, a targeted mutation of the promyelocyte-specific cathepsin G gene (which lies just 3' to the granzyme genes in the same cluster) had minimal effects on upstream granzyme gene expression. Although the mechanism of these-long distance effects are unknown, the expression of PGK-Neo can be "captured" by the regulatory domain into which it is inserted. These results suggest that the PGK-Neo cassette can interact productively with locus control regions and thereby disrupt normal interactions between local and long-distance regulatory regions within a tissue-specific domain.

Animals↗
PubMed2005

Complex histories of genes encoding 3-hydroxy-3-methylglutaryl-CoenzymeA reductase.

The mevalonate pathway for the synthesis of isoprenoids can be found in organisms from all domains of life. It has been previously demonstrated that the first gene specific to that pathway, which encodes the enzyme 3-hydroxy-3-methylglutaryl-CoenzymeA reductase (HMGR), has been transferred between domains by lateral gene transfer on several occasions. Here we look within the domain Bacteria at lateral acquisition of HMGR, whether as a single gene or as part of a mevalonate pathway cluster. We observe a complex history of multiple transfer events probably reflecting the fact that HMGR could be beneficial in a variety of physiological and genetic contexts. We demonstrate that even in Vibrio species, where HMGR is not clustered with other genes to form an operon or a metabolic cluster, it is under strong purifying selection.

Bacteria↗
PubMed2004

Elevated levels of ferrimagnetic metals in foodchains supporting the Guam cluster of neurodegeneration: do metal nucleated crystal contaminants [corrected] evoke magnetic fields that initiate the progressive pathogenesis of neurodegeneration?

Elevated levels of aluminium (Al), strontium (Sr), barium (Ba), iron (Fe), manganese (Mn) cations - combined with deficiencies of magnesium (Mg)/calcium (Ca) - have been observed in the foodchains that traditionally support the Chamorro populations affected by high incidence clusters of Alzheimer (AD), Parkinson-like (PD), motor neurone diseases and multiple sclerosis on the island of Guam. Soils drawn from the cluster region demonstrated an excessive fivefold increase in 'magnetic susceptibility' readings in relation to soils from disease free adjoining regions. A multifactorial aetiological hypothesis is proposed that pivots upon the combined exposure to high levels of natural/industrial sources of ferrimagnetic/ferroelectric compounds incorporating Al, Fe, Mn, Sr, Ba (e.g., via yam/seafood consumption or exposure to world war 2 (WW2) munitions) and to low levels of Mg/Ca in all S. Pacific locations where these clusters of neurodegenerative disease have simultaneously erupted. Once gut/blood brain barrier permeability is impaired, the increased uptake of Al, Fe, Sr, Ba, or Mn into the Mg/Ca depleted brain leads to rogue metal substitutions at the Mg/Ca vacated binding domains on various enzyme/proteoglycan groups, causing a broad ranging disruption in Mg/Ca dependent systems - such as the glutamine synthetase which prevents the accumulation of neurotoxic glutamate. The rogue metals chelate sulphate, disrupting sulphated-proteoglycan mediated inhibition of crystal proliferation, as well as its regulation of the Fibroblast growth factor receptor complex which disturbs the molecular conformation of those receptors and their regulation of transphosphorylation between intracellular kinase domains; ultimately collapsing proteoglycan mediated cell-cell signalling pathways which maintain the growth and structural integrity of the neuronal networks. The depression of Mg/Ca dependent systems in conjunction with the progressive ferrimagnetisation of the CNS due to an overload of rogue ferroelectric/ferrimagnetic metal contaminants, enables 'seeding' of metal-protein crystalline arrays that can proliferate in the proteoglycan depleted brain. The resulting magnetic field emissions initiate a free radical mediated progressive pathogenesis of neurodegeneration. The co-clustering of these various types of disease in select geographical pockets around the world suggests that all of these conditions share a common early life exposure to ferromagnetic metal nucleating agents in their multifactorial aetiology. Factors such as individual genetics, the species of metal involved, etc., dictate which specific class of disease will emerge as a delayed neurotoxic response to these environmental insults.

Amyotrophic Lateral Sclerosis↗
PubMed1987

Glucose-6-phosphate dehydrogenase and malate dehydrogenase enzyme electrophoretic patterns amongst strains of Bacteroides fragilis.

Fifty-two strains of Bacteroides fragilis were examined for their enzyme electrophoretic patterns of glucose-6-phosphate dehydrogenase (G6PDH) and malate dehydrogenase (MDH). All strains tested possessed high levels of both enzymes but the G6PDH reduced NADP whereas MDH was NAD-dependent. Twenty-seven strains produced single bands of both G6PDH and MDH. In all cases G6PDH migrated faster than MDH. Strains clustered by a single linkage algorithm were recovered in eight clusters at the 77% similarity level. The remaining 25 strains produced multiple bands of one or both enzymes. These were recovered in six clusters at the 72% similarity level using the same algorithm. The results of this study revealed considerable heterogeneity of enzyme patterns within B. fragilis.

Bacteroides fragilis↗
PubMed1997

Avoidable morbidity in infants. A classification based on diagnoses in administrative databases.

OBJECTIVES: A hierarchical classification for avoidable morbidity in infants was developed based on a conceptual model for causes of morbidity. Experts rated the impact of risk factors and health services on diseases coded according to the International Classification of Diseases, 9th Revision, Classification Modification (ICD-9-CM). An etiologic framework was chosen for the classification because knowledge of etiology often suggests strategies for prevention. Causes of morbidity that cluster on the basis of similar risk factors might be avoided using similar strategies. METHODS: Diseases (346 different diagnoses) were rated by 16 general pediatricians; 12 attributes were considered, including the impact on disease occurrence and on severity of five risk factors, preventive health services, and medical treatment. Raters evaluated the impact of health services, constitutional risk factors, and environmental risk factors without regard for service site (eg, inpatient, emergency department, primary care office). Environmental risk factors categories, including family, social, and physical environments, were rated separately. The impact of health services was rated on prevention, treatment, and complications of care. RESULTS: Only ratings indicating that the impact of a risk factor category was substantial were used for the final classification of 275 diagnoses. Consistent with the multifactorial etiology of many diseases, many diagnoses had ratings indicating substantial impact of multiple risk factors. Five mutually exclusive clusters were derived from the 12 ratings based on factor analysis and recognized strategies for prevention. Ordered by level of avoidability, these clusters were termed vaccine-preventable, health-care quality indicators, environmental, environmental/constitutional, and constitutional. CONCLUSIONS: The usefulness of this classification for policy-oriented epidemiologic and health services research is grounded in the premise that prevention is the cardinal objective of child health policy. Cluster-specific hospitalization rates, ie, rates aggregated for all diagnoses falling in a cluster, might be used for allocating resources to interventions directed at environmental or health service determinants of morbidity. Widespread use of ICD-9-CM codes in hospital discharge and ambulatory databases suggests many potential applications for this classification of morbidity burden in population groups.

Databases, Factual↗