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PubMed2005

Ionization potentials of small lithium clusters (Lin) and hydrogenated lithium clusters (LinH).

We present accurate ionization potentials (IPs) for small lithium clusters and hydrogenated lithium clusters (n=1-4), computed using coupled-cluster singles and doubles theory augmented with a perturbative correction for connected triple excitations [CCSD(T)] with the correlation-consistent weighted core-valence quadruple-zeta basis set (cc-pwCVQZ). In some cases the full CCSDT method has been used. Comparison of computed binding energies with experiment for the pure cationic lithium clusters reveals excellent agreement, demonstrating that previous discrepancies between computed and experimentally derived atomization energies for the corresponding neutral clusters are due to the use of an inaccurate experimental IP for Li(4). The experimental IP for Li(4) falls 0.43 eV below our theoretical adiabatic value of 4.74 eV, which should be a lower bound to the measured IP. Our recommended zero-point corrected adiabatic IPs for Li, Li(2), Li(3), Li(4), LiH, Li(2)H, Li(3)H, and Li(4)H are 5.39, 5.14, 4.11, 4.74, 7.69, 3.98, 4.69, and 4.05 eV, respectively. Zero-point vibrationally corrected CCSD(T) atomization energies per atom for Li(2) (+), Li(3) (+), Li(4) (+), LiH(+), Li(2)H(+), Li(3)H(+), and Li(4)H(+) are 0.64, 0.96, 0.90, 0.056, 1.62, 1.40, and 1.40 eV, respectively.

Journal Article↗
PubMed2005

Vibrational predissociation spectroscopy of the (H2O)(6-21)- clusters in the OH stretching region: evolution of the excess electron-binding signature into the intermediate cluster size regime.

We report vibrational predissociation spectra of the (H2O)n- cluster ions in the OH stretching region to determine whether the spectral signature of the electron-binding motif identified in the smaller clusters [Hammer et al. Science 306, 675 (2004)] continues to be important in the intermediate size regime (n = 7-21). This signature consists of a redshifted doublet that dominates the OH stretching region, and has been traced primarily to the excitation of a single water molecule residing in a double H-bond acceptor (AA) binding site, oriented with both of its H atoms pointing toward the excess electron cloud. Strong absorption near the characteristic AA doublet is found to persist in the spectra of the larger clusters, but the pattern evolves into a broadened triplet around n = 11. A single free OH feature associated with dangling hydrogen atoms on the cluster surface is observed to emerge for n > or = 15, in sharp contrast to the multiplet pattern of unbonded OH stretches displayed by the H+(H2O)n clusters throughout the n = 2-29 range. We also explore the vibration-electronic coupling associated with normal-mode displacements of the AA molecule that most strongly interact with the excess electron. Specifically, electronic structure calculations on the hexamer anion indicate that displacement along the -OH2 symmetric stretching mode dramatically distorts the excess electron cloud, thus accounting for the anomalously large oscillator strength of the AA water stretching vibrations. We also discuss these vibronic interactions in the context of a possible relaxation mechanism for the excited electronic states involving the excess electron.

Journal Article↗
PubMed2002

Iron-sulfur cluster biosynthesis. Thermatoga maritima IscU is a structured iron-sulfur cluster assembly protein.

Genetic evidence has indicated that Isc proteins play an important role in iron-sulfur cluster biogenesis. In particular, IscU is believed to serve as a scaffold for the assembly of a nascent iron-sulfur cluster that is subsequently delivered to target iron-sulfur apoproteins. We report the characterization of an IscU from Thermatoga maritima, an evolutionarily ancient hyperthermophilic bacterium. The stabilizing influence of a D40A substitution allowed characterization of the holoprotein. Mössbauer (delta = 0.29 +/- 0.03 mm/s, DeltaE(Q) = 0.58 +/- 0.03 mm/s), UV-visible absorption, and circular dichroism studies of the D40A protein show that T. maritima IscU coordinates a [2Fe-2S]2+ cluster. Thermal denaturation experiments demonstrate that T. maritima IscU is a thermally stable protein with a thermally unstable cluster. This is also the first IscU type domain that is demonstrated to possess a high degree of secondary and tertiary structure. CD spectra indicate 36.7% alpha-helix, 13.1% antiparallel beta-sheet, 11.3% parallel beta-sheet, 20.2% beta-turn, and 19.1% other at 20 degrees C, with negligible spectral change observed at 70 degrees C. Cluster coordination also has no effect on the secondary structure of the protein. The dispersion of signals in 1H-15N heteronuclear single quantum correlation NMR spectra of wild type and D40A IscU supports the presence of significant tertiary structure for the apoprotein, consistent with a scaffolding role, and is in marked contrast to other low molecular weight Fe-S proteins where cofactor coordination is found to be necessary for proper protein folding. Consistent with the observed sequence homology and proposed conservation of function for IscU-type proteins, we demonstrate T. maritima IscU-mediated reconstitution of human apoferredoxin.

Amino Acid Sequence↗
PubMed2003

Small nucleolar RNA clusters in trypanosomatid Leptomonas collosoma. Genome organization, expression studies, and the potential role of sequences present upstream from the first repeated cluster.

Trypanosomatid small nucleolar RNA (snoRNA) genes are clustered in the genome. snoRNAs are transcribed polycistronically and processed into mature RNAs. In this study, we characterized four snoRNA clusters in Leptomonas collosoma. All of the clusters analyzed carry both C/D and H/ACA RNAs. The H/ACA RNAs are composed of a single hairpin, a structure typical to trypanosome and archaea guide RNAs. Using deletion and mutational analysis of a tagged C/D snoRNA situated within the snoRNA cluster, we identified 10-nucleotide flanking sequences that are essential for processing snoRNA from its precursor. Chromosome walk was performed on a snoRNA cluster, and a sequence of 700 bp was identified between the first repeat and the upstream open reading frame. Cloning of this sequence in an episome vector enhanced the expression of a tagged snoRNA gene in an orientation-dependent manner. However, continuous transcript spanning of this region was detected in steady-state RNA, suggesting that snoRNA transcription also originates from an upstream-long polycistronic transcriptional unit. The 700-bp fragment may therefore represent an example of many more elements to be discovered that enhance transcription along the chromosome, especially when transcription from the upstream gene is reduced or when enhanced transcription is needed.

Amino Acid Sequence↗
PubMed1974

Macrophage-lymphocyte clusters in the immune response to soluble protein antigen in vitro. II. Ultrastructure of clusters formed during the early response.

Macrophage-lymphocyte clusters are formed when lymph node cells and autologous peritoneal exudate cells from guinea pigs immunized with tubercle bacilli are cultured in the presence of purified protein derivative of tuberculin (PPD) for 20 h. We have studied the ultrastructure of these clusters employing transmission and scanning electron microscopy. The most simple macrophage-lymphocyte cluster consisted of one macrophage, one large central lymphocyte with a blastoid appearance attached to the macrophage with a broad area of contact, and from a few to more than 20 small peripheral lymphocytes attached to the central lymphocyte by their uropods. Some clusters were of more complex type, containing two or three macrophages or one macrophage with more than one central lymphocyte attached to the surface, but even in these clusters each peripheral lymphocyte was attached only to one central lymphocyte. By morphological criteria the peripheral lymphocytes were T lymphocytes.

Animals↗
PubMedDate not supplied

Xanthomonas campestris contains a cluster of hrp genes related to the larger hrp cluster of Pseudomonas solanacearum.

All Xanthomonas campestris pathovars tested contain DNA which hybridizes to the large hrp gene cluster of Pseudomonas solanacearum (C.A. Boucher, F. Van Gijsegem, P.A. Barberis, M. Arlat, and C. Zischek, J. Bacteriol. 169:5626-5632, 1987). Clones carrying these sequences were isolated from genomic libraries of X. campestris pvs. campestris and vitians. Mutagenesis of the corresponding genomic regions of both pathovars gave strains defective in both pathogenicity and hypersensitive response induction. X. c. pv. campestris contained a hrp gene cluster covering about 25 kb, which was homologous and colinear over a continuous 19-kb DNA region with the P. solanacearum hrp cluster. Cross-complementation showed that X. c. pv. vitians and X. c. pv. campestris hrp sequences are functionally interchangeable, but the source of the hrp genes did not determine the compatibility-incompatibility of the host-pathogen interaction. One X. c. pv. campestris Hrp- mutant was "complemented" by specific subclones of the P. solanacearum hrp cluster, suggesting the existence of some functional homology between the clusters of the two species. Expression of hrp genes (studied by lacZ fusions) was repressed in rich medium, and in minimal medium the level of expression depended on the carbon source supplied to the cells. Transcription of hrp genes was not regulated by genes that control the synthesis of extracellular enzymes, which are required for pathogenicity. In addition X. campestris Hrp- mutants produced wild-type levels of these extracellular enzyme activities. These results suggest the existence of two independent sets of pathogenicity genes that are regulated differently.

Chromosome Mapping↗
PubMed1998

Transcriptional analysis of essential genes of the Escherichia coli fatty acid biosynthesis gene cluster by functional replacement with the analogous Salmonella typhimurium gene cluster.

The genes encoding several key fatty acid biosynthetic enzymes (called the fab cluster) are clustered in the order plsX-fabH-fabD-fabG-acpP-fabF at min 24 of the Escherichia coli chromosome. A difficulty in analysis of the fab cluster by the polar allele duplication approach (Y. Zhang and J. E. Cronan, Jr., J. Bacteriol. 178:3614-3620, 1996) is that several of these genes are essential for the growth of E. coli. We overcame this complication by use of the fab gene cluster of Salmonella typhimurium, a close relative of E. coli, to provide functions necessary for growth. The S. typhimurium fab cluster was isolated by complementation of an E. coli fabD mutant and was found to encode proteins with > 94% homology to those of E. coli. However, the S. typhimurium sequences cannot recombine with the E. coli sequences required to direct polar allele duplication via homologous recombination. Using this approach, we found that although approximately 60% of the plsX transcripts initiate at promoters located far upstream and include the upstream rpmF ribosomal protein gene, a promoter located upstream of the plsX coding sequence (probably within the upstream gene, rpmF) is sufficient for normal growth. We have also found that the fabG gene is obligatorily cotranscribed with upstream genes. Insertion of a transcription terminator cassette (omega-Cm cassette) between the fabD and fabG genes of the E. coli chromosome abolished fabG transcription and blocked cell growth, thus providing the first indication that fabG is an essential gene. Insertion of the omega-Cm cassette between fabH and fabD caused greatly decreased transcription of the fabD and fabG genes and slower cellular growth, indicating that fabD has only a weak promoter(s).

Bacterial Proteins↗
PubMed2006

Gene clusters for beta-lactam antibiotics and control of their expression: why have clusters evolved, and from where did they originate?

While beta-lactam compounds were discovered in filamentous fungi, actinomycetes and gram-negative bacteria are also known to produce different types of beta-lactams. All beta-lactam compounds contain a four-membered beta-lactam ring. The structure of their second ring allows these compounds to be classified into penicillins, cephalosporins, clavams, carbapenens or monobactams. Most beta-lactams inhibits bacterial cell wall biosynthesis but others behave as beta-lactamase inhibitors (e.g., clavulanic acid) and even as antifungal agents (e.g., some clavams). Due to the nature of the second ring in beta-lactam molecules, the precursors and biosynthetic pathways of clavams, carbapenems and monobactams differ from those of penicillins and cephalosporins. These last two groups, including cephamycins and cephabacins, are formed from three precursor amino acids that are linked into the alpha-aminoadipyl-L-cysteinyl-D-valine tripeptide. The first two steps of their biosynthetic pathways are common. The intermediates of these pathways, the characteristics of the enzymes involved, the lack of introns in the genes and bioinformatic analysis suggest that all of them should have evolved from an ancestral gene cluster of bacterial origin, which was surely transferred horizontally in the soil from producer to non-producer microorganisms. The receptor strains acquired fragments of the original bacterial cluster and occasionally inserted new genes into the clusters, which once modified, acquired new functions and gave rise to the final compounds that we know. When the order of genes in the Streptomyces genome is analyzed, the antibiotic gene clusters are highlighted as gene islands in the genome. Nonetheless, the assemblage of the ancestral beta-lactam gene cluster remains a matter of speculation.

Anti-Bacterial Agents↗
PubMed1979

The high potential iron-sulfur cluster of aconitase is a binuclear iron-sulfur cluster.

It has been reported (Ruzicka, F.J., and Beinert, H. (1978) J. Biol. Chem. 253, 2514-2517) that aconitase in the oxidized state, as isolated, shows an electron paramagnetic resonance signal centered at g = 2.01, typical of high potential iron-sulfur proteins. Since the magnetic state corresponding to this signal has thus far only been found in tetranuclear iron-sulfur clusters in model compounds and proteins, it could be expected that aconitase also contains a [4Fe-4S] cluster. We show here that core extrusion, in the presence of hexamethylphosphoramide and o-xylyl-alpha,alpha'-dithiol and subsequent ligand exchange with p-trifluoromethylbenzenethiol yield absorption spectra typical of binuclear iron-sulfur clusters. According to the absorbance measured, the concentration of the extruded [2Fe-2S] cluster quantitatively accounts for the iron-sulfur content of the preparations examined. Preliminary studies of the 19F nuclear magnetic resonance spectrum obtained on extrusion with p-trifluoromethylbenzenethiol confirm the presence of a binuclear cluster in aconitase.

Aconitate Hydratase↗
PubMed1996

Population-averaged and cluster-specific models for clustered ordinal response data.

We compare population-averaged and cluster-specific models for clustered ordinal data. We consider generalized estimating equations and constrained equations maximum likelihood estimation of population-averaged cumulative logit regression models, and mixed effects estimation of cluster-specific cumulative logit regression models. A previously reported relationship between population-averaged and cluster-specific parameters for the binary logistic link appears to hold for analogous parameters under the cumulative logit link. We address these issues in the context of data from two cross-over clinical trials.

Chi-Square Distribution↗
PubMed1994

Assessment of cancer clusters using limited cohort data with spreadsheets: application to a leukemia cluster among rubber workers.

This paper presents methods for initial investigation of occupational cancer clusters using limited data. Phase 1 of the methods developed uses basic data from the cluster of cases, but with cohort data limited to the size of the workforce at the plant. Phase 2 of the methods requires knowledge of the number of workers entering and leaving the workforce in each year. In the absence of data concerning age, the spreadsheet programs explore a variety of worker age distributions in synthetic cohort analyses. The methods were used to assess a cluster of six cases of leukemia with an average duration of work of 11 years in a tire manufacturing plant. It was concluded that the relative risk for the age range 30-50 was at least 7, providing further evidence for the association of leukemia with work in tire manufacture. The use of spreadsheet programs can provide a valuable first step assessment of apparent workplace cancer clusters.

Adult↗
PubMed1992

Clusters galore: insights about environmental clusters from probability theory.

The posterior probability of a causal explanation given that an environmental cancer cluster is statistically significant depends on the prior probability of an environmentally caused cluster, the sensitivity of the statistical test and its specificity. The prior probability is low, because it is rare to have enough carcinogen in the general environment to cause a relative risk of cancer high enough to achieve statistical significance in a small geographic area. The sensitivity and specificity are not great. The likelihood that a census tract escapes statistically significant elevations in all 80 types of cancer can be calculated. Many of the thousands of census tracts will, by chance alone, have at least one type of cancer whose elevation is statistically significant. Actual observation from a large cancer registry confirms this probabilistic prediction. Applying the principles of Bayes' Theorem would suggest that most statistically significant environmental cancer clusters are not due to environmental carcinogens. One would have to investigate hundreds of environmental cancer clusters to find one with a true environmental cause.

Bayes Theorem↗
PubMed2003

A memetic-aided approach to hierarchical clustering from distance matrices: application to gene expression clustering and phylogeny.

We propose a heuristic approach to hierarchical clustering from distance matrices based on the use of memetic algorithms (MAs). By using MAs to solve some variants of the Minimum Weight Hamiltonian Path Problem on the input matrix, a sequence of the individual elements to be clustered (referred to as patterns) is first obtained. While this problem is also NP-hard, a probably optimal sequence is easy to find with the current advances for this problem and helps to prune the space of possible solutions and/or to guide the search performed by an actual clustering algorithm. This technique has been successfully applied to both a Branch-and-Bound algorithm, and to evolutionary algorithms and MAs. Experimental results are given in the context of phylogenetic inference and in the hierarchical clustering of gene expression data.

Algorithms↗
PubMed1999

Clusters and clustering of childhood cancer: a review.

Methodological considerations in the study of clusters and clustering of childhood cancer are reviewed briefly. A selection of 11 studies of individual clusters of childhood leukaemia which are either particularly notable or recent and have been reported in peer review journals is then considered. Focus is placed on sources of alerts, descriptive studies, field-work studies, conclusions and communication management. Some of these studies are probably essential but they are unlikely to yield firm conclusions; studies of large data sets are recommended. No causal factor has been identified which can explain a single cluster of childhood leukaemia.

Adolescent↗
PubMed2002

Valsalva-induced cluster: a new subtype of cluster headache.

We report the case of a man who suffered from Valsalva-induced cluster headaches. The headaches deviated from classic cluster in that they were solely induced by activity involving the Valsalva maneuver, such as coughing and sneezing, and never occurred spontaneously. The attacks were prevented by treatment with indomethacin. This may be the first reported case of cluster that only occurs after a defined trigger and never spontaneously. It also may be the first cluster headache subtype that is indomethacin responsive.

Aged↗
PubMed2003

Robust cluster analysis of microarray gene expression data with the number of clusters determined biologically.

MOTIVATION: The success of each method of cluster analysis depends on how well its underlying model describes the patterns of expression. Outlier-resistant and distribution-insensitive clustering of genes are robust against violations of model assumptions. RESULTS: A measure of dissimilarity that combines advantages of the Euclidean distance and the correlation coefficient is introduced. The measure can be made robust using a rank order correlation coefficient. A robust graphical method of summarizing the results of cluster analysis and a biological method of determining the number of clusters are also presented. These methods are applied to a public data set, showing that rank-based methods perform better than log-based methods. AVAILABILITY: Software is available from http://www.davidbickel.com.

Algorithms↗
PubMed2004

An integrated tool for microarray data clustering and cluster validity assessment.

UNLABELLED: In this paper we present a data mining system, which allows the application of different clustering and cluster validity algorithms for DNA microarray data. This tool may improve the quality of the data analysis results, and may support the prediction of the number of relevant clusters in the microarray datasets. This systematic evaluation approach may significantly aid genome expression analyses for knowledge discovery applications. The developed software system may be effectively used for clustering and validating not only DNA microarray expression analysis applications but also other biomedical and physical data with no limitations. AVAILABILITY: The program is freely available for non-profit use on request at http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.html CONTACT: Nadia.Bolshakova@cs.tcd.ie.

Algorithms↗
PubMed2003

Cluster-Buster: Finding dense clusters of motifs in DNA sequences.

The signals that determine activation and repression of specific genes in response to appropriate stimuli are one of the most important, but least understood, types of information encoded in genomic DNA. The nucleotide sequence patterns, or motifs, preferentially bound by various transcription factors have been collected in databases. However, these motifs appear to be individually too short and degenerate to enable detection of functional enhancer and silencer elements within a large genome. Several groups have proposed that dense clusters of motifs may diagnose regulatory regions more accurately. Cluster-Buster is the third incarnation of our software for finding clusters of pre-specified motifs in DNA sequences. We offer a Cluster-Buster web server at http://zlab.bu.edu/cluster-buster/.

Binding Sites↗