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PubMed1999

The interferon gene cluster: a candidate region for MS predisposition? Multiple Sclerosis Study Group.

The clinical benefits of interferon (IFN) beta therapy in some multiple sclerosis (MS) patients are still unexplained, raising the question whether polymorphism within the IFNB gene itself would provide an explanation. Screening the IFNB gene by single strand conformation polymorphism (SSCP) analysis and sequencing, a single nucleotide polymorphism was identified. Both alleles were distributed with similar frequencies in MS patients and controls. Significant linkage disequilibrium (LD) between the IFN allele [153C] and allele [02] of the previously analyzed IFNA microsatellite (Epplen et al. Ann Neurol 1997; 41: 341-352) was observed in MS patients only, indicating a disease related haplotype. On the other hand an increased risk (RR = 12.41; Pc < 8 x 10(-5)) was observed for allele [07]. Hence the study was extended to neighbouring genes. Functionally relevant polymorphisms, i.e., premature stop codons in the IFNA10 [Cys20Stop] and IFNA17 [58Stop] genes and an aminoacid (aa) substitution [ile 184Arg] in the IFNA17 gene were analyzed. Patients carrying a non-functional IFNA17 allele bear an increased risk to develop MS (RR = 25.68; Pc < 0.06). In addition, LD analysis between IFNA10 [Cys20Stop], IFNA17 [58Stop] and the IFNA microsatellite alleles provides evidence for IFNA14, IFNA16 or IFNA5 as additional, most likely candidate genes. The present study excludes the IFNB gene as a candidate for MS predisposition but provides first evidence for predisposing IFNA genes.

Alleles↗

PubMed2006

Multiple structural transformations in Lennard-Jones clusters: generic versus size-specific behavior.

The size-temperature "phase diagram" for Lennard-Jones clusters LJn with sizes up to n=147 is constructed based on the analysis of the heat capacities and orientational bond order parameter distributions computed by the exchange Monte Carlo method. Two distinct types of "phase transitions" accompanied by peaks in the heat capacities are proven to be generic. Clusters with Mackay atom packing in the overlayer undergo a lower-temperature melting (or Mackay-anti-Mackay) transition that occurs within the overlayer. All clusters undergo a higher-temperature transition, which for the three-layer clusters is proven to be the 55-atom-core-melting transition. For the two-layer clusters, the core/overlayer subdivision is ambiguous, so the higher-temperature transition is better characterized as the breaking of the local icosahedral coordination symmetry. A pronounced size-specific behavior can typically be observed at low temperatures and often occurs in clusters with highly symmetric global minima. An example of such behavior is LJ135, which undergoes a low-temperature solid-solid transition, besides the two generic transitions, i.e., the overlayer reconstruction and the core melting.

Journal Article↗

PubMed2001

Differential gene expression in premalignant human epidermis revealed by cluster analysis of serial analysis of gene expression (SAGE) libraries.

Serial analysis of gene expression (SAGE) has been used for quantitative analysis of gene expression. We applied cluster analysis on multiple SAGE libraries derived from premalignant epidermal tissue (actinic keratosis), normal human epidermis, and cultured keratinocytes. The samples were obtained from skin biopsies without contamination by dermal tissue or blood. A total of 60,000 transcripts (tags) were analyzed. Two-way cluster analysis was applied to both the transcripts and the tissues, resulting in separation of the cultured cells from the epidermal samples, and clustering of many, presumably coregulated, genes. Two clusters of genes, strongly up-regulated in the tumor tissue compared with normal epidermis, were investigated in more detail. The differential expression of genes could be confirmed in actinic keratosis from four patients. Several of these genes have been previously associated with carcinogenesis or are likely to be important on the basis of their presumed function. Automated literature search tools show that a subgroup of these genes is coexpressed in other tissues and is part of an epidermal differentiation gene cluster on chromosome 1q21. We conclude that cluster analysis on large data sets uncovers clear partitions and correlations that could be confirmed by independent methods. We predict that these partitions will lead to biological interpretations that can be relevant for understanding the processes of carcinogenesis and tumor progression.

Blotting, Northern↗

PubMed1992

Multiple transcripts encoded by the ilvGMEDA gene cluster of Escherichia coli K-12.

We report here that, using Northern (RNA) blots, we identified two relatively stable transcripts of 4.6 and 1.1 kb that correspond to the products of the ilvEDA and ilvE genes and two relatively unstable transcripts of 6.7 and 3.6 kb that correspond to the products of the ilvGMEDA and ilvDA genes. The transcripts were identified by the use of eight probes derived from segments of the ilvGMEDA cluster. In addition, we used two strains with deletions of ilvG or ilvDA and observed the expected decrease in transcript size in Northern blots. Primer extension with reverse transcriptase generated a 169-nucleotide product corresponding to a 5' end within the ilvED intercistronic region, 37 nucleotides from the AUG codon of the ilvD gene. This primer extension product presumably indicates the 5' end of the ilvDA transcript that we detected in Northern blots. The stability of the transcripts was monitored, and RNase E was found to play a major role in ilv transcript degradation. Transcript levels varied in response to growth in the presence of the end product amino acids and in response to the presence of the polar frameshift site in ilvG. Although there have been speculations about the identities and numbers of transcripts derived from the ilvGMEDA cluster on the basis of the identification of some of the sites of transcription initiation and termination, this is the first report of the use of Northern blots to determine the actual sizes and distribution of mRNAs present in vivo.

Escherichia coli↗

PubMed1987

Do genetic factors play a role in Berger's disease?

The epidemiology of Berger's disease is poorly defined. We know that the disease occurs worldwide and that there may be an increased occurrence in certain ethnic groups. Whether secondary mesangial IgA deposits should be considered part of the same disease process is unknown. The association of certain HLA antigens with the occurrence of Berger's disease has been demonstrated by several groups. The multiple occurrence of Berger's disease or of Berger's disease and Henoch-Schönlein purpura in the same family has been reported. The preliminary results of a French collaborative study show 43 such families. However, these facts do not demonstrate a familial clustering since the multiple occurrence of cases in a family may occur by chance. The study of affected siblings (sib pair method) from different families may be used nevertheless, in order to understand the possible inheritance of the disease. Previously reported data on HLA haplotypes of affected siblings are combined with unpublished cases. There is an excess of HLA-identical siblings but it is possible that there might have been some bias towards publishing HLA-identical pairs. Further systematic studies on a large number of HLA-typed affected sibling pairs are needed before concluding a linkage between HLA and the disease.

Glomerulonephritis, IGA↗

PubMed2001

HIV infection in families of HIV-positive and 'at-risk' HIV-negative women.

Research of HIV infection within the family has focused upon sexual partners and vertical transmission. The scope of the problem of multiple infections and clustering of HIV among family members has, thus far, been less extensively explored. The objectives of this study are to investigate HIV infection in family members of HIV-seropositive and HIV-seronegative high-risk women and to consider the impact of multiple HIV infections within the family. Baseline data were evaluated from a prospective observational cohort of 871 HIV-seropositive and 439 seronegative at-risk women who are participants in a longitudinal study of HIV in women at four sites in the USA (Montefiore, Bronx, NY; Johns Hopkins University, Baltimore, MD; Brown University, Providence, RI; Wayne State University, Detroit, MI). Women were asked if anyone close to them had HIV/AIDS or had died from HIV/AIDS. Responses which included HIV-positive family members were analyzed. In the seropositive cohort, 35% (307/871) of the women had a family member with HIV infection. Of these 307 women, 38% reported having a sibling, 24% a husband and 27% had more than one family member with HIV/AIDS. Forty-nine per cent of Latina women, 34% of black women, and 21% of white women reported having a family member with HIV/AIDS. Using logistic regression analysis, we found that Latina and black women were significantly more likely than white women to have a sibling, extended family member or more than one family member with HIV/AIDS. Compared to seropositive women, seronegative high-risk women enrolled in this study appear equally likely to have an HIV-infected family member. In this study of HIV-positive women and high-risk seronegative women, a third reported having multiple family members with HIV infection, most often in a sibling. The high prevalence of HIV within families, particularly in the families of Latina and black women, mandates attention in planning both prevention and care.

Black or African American↗

PubMed1995

[Coping pattern and adjustment in multiple sclerosis].

A questionnaire (FKV/LIS) was used to study the coping process in 210 patients with multiple sclerosis. By cluster analysis of five coping modes, patients could be divided into two groups of approximately the same size: cluster 1 presented with higher values for "active coping; self-affirmation; religiousness" and lower values for "depression" and "trivialization". In cluster 2, on the other hand, values were higher for "depression" and "trivialization" whereas values were lower for "active coping; self-affirmation; religiousness". Patients in cluster 1 were significantly more contented with life. Mean age and mean duration of illness were higher in cluster 1, suggesting a time-dependent change in the coping process with improvement in adaptation in the course of the disease. The extent of social support was higher in cluster 1. The consequences for psychological intervention are discussed.

Adaptation, Psychological↗

PubMed1992

A cluster of CpG islands at D10S94, near the locus responsible for multiple endocrine neoplasia type 2A (MEN2A).

We report the characterization of a dense cluster of CpG islands at D10S94 in proximal 10q11.2. D10S94 is tightly linked to the gene responsible for multiple endocrine neoplasia type 2A (MEN 2A), a dominantly inherited tumor syndrome characterized by medullary thyroid carcinoma (MTC), pheochromocytoma, and/or parathyroid adenoma. To date, no recombinants between D10S94 and MEN2A have been identified. The gene(s) responsible for two additional dominantly inherited disorders involving cancer of the medullary thyroid, MEN 2B (MEN2B), and dominantly inherited MTC without additional clinical features (MTC1), also map to this region. The gene or genes responsible for these disorders may be located at or near the D10S94 locus. A 570-kb long-range restriction map has been generated by pulsed-field gel electrophoresis using probes developed during a 160-kb bidirectional cosmid walk at D10S94. Six CpG islands are clustered within a 180-kb region; five fall within a 145-kb NotI restriction fragment that is contained in its entirety in our cosmid contig. The SacII, SfiI, and NotI restriction maps for lymphoblast and cloned DNA are concordant. These CpG islands may represent the 5' ends of candidate genes for MEN2A, MEN2B, and/or MTC1. One gene designated mcs94-1, which is associated with one of the CpG islands in this cluster, has been isolated and characterized in detail.

Base Sequence↗

PubMedDate not supplied

Micro-switch clusters to enhance hand responses and appropriate head position in two children with multiple disabilities.

This study evaluated the use of micro-switch clusters to improve response activity and posture with two children with multiple disabilities. The children were first taught a hand response and then required to combine this response with appropriate head position. The micro-switch clusters adopted for this purpose consisted of a pressure or mercury micro-switch for the hand response combined with a mercury micro-switch for the head position. Both children had an increase in the frequency of the hand response and in the percentage of times this occurred in combination with appropriate head position. These changes were maintained at a 2-month post-intervention check.

Child↗

PubMed2005

Clusters of mutations from transient hypermutability.

Collections of mutants usually contain more mutants bearing multiple mutations than expected from the mutant frequency and a random distribution of mutations. This excess is seen in a variety of organisms and also after DNA synthesis in vitro. The excess is unlikely to originate in mutator mutants but rather from transient hypermutability resulting from a perturbation of one of the many transactions that maintain genetic fidelity. The multiple mutations are sometimes clustered and sometimes randomly distributed. We model some spectra as populations comprising a majority with a low mutation frequency and a minority with a high mutation frequency. In the case of mutants produced in vitro by a bacteriophage RB69 mutator DNA polymerase, mutants with two mutations are in approximately 10-fold excess and mutants with three mutations are in even greater excess. However, phenotypically undetectable mutations seen only as hitchhikers with detectable mutations are approximately 5-fold more frequent than mutants bearing detectable mutations, indicating that they arose in a subpopulation with a higher mutation frequency. Excess multiple mutations may contribute critically to carcinogenesis and to adaptive mutation, including the adaptations of pathogens as they move from host to host. In the case of the rapidly mutating riboviruses, the viral population appears to be composed of a majority with a mutation frequency substantially lower than the average and a minority with a huge mutational load.

Animals↗

PubMed2004

Nerve-independent formation of a topologically complex postsynaptic apparatus.

As the mammalian neuromuscular junction matures, its acetylcholine receptor (AChR)-rich postsynaptic apparatus is transformed from an oval plaque into a pretzel-shaped array of branches that precisely mirrors the branching pattern of the motor nerve terminal. Although the nerve has been believed to direct postsynaptic maturation, we report here that myotubes cultured aneurally on matrix-coated substrates form elaborately branched AChR-rich domains remarkably similar to those seen in vivo. These domains share several characteristics with the mature postsynaptic apparatus, including colocalization of multiple postsynaptic markers, clustering of subjacent myonuclei, and dependence on the muscle-specific kinase and rapsyn for their formation. Time-lapse imaging showed that branched structures arise from plaques by formation and fusion of AChR-poor perforations through a series of steps mirroring that seen in vivo. Multiple fluorophore imaging showed that growth occurs by circumferential, asymmetric addition of AChRs. Analysis in vivo revealed similar patterns of AChR addition during normal development. These results reveal the sequence of steps by which a topologically complex domain forms on a cell and suggest an unexpected nerve-independent role for the postsynaptic cell in generating this topological complexity.

Animals↗

PubMed2006

The mitochondrial ATP-binding cassette transporter Abcb7 is essential in mice and participates in cytosolic iron-sulfur cluster biogenesis.

Proteins with iron-sulfur (Fe-S) clusters participate in multiple metabolic pathways throughout the cell. The mitochondrial ABC half-transporter Abcb7, which is mutated in X-linked sideroblastic anemia with ataxia in humans, is a functional ortholog of yeast Atm1p and is predicted to export a mitochondrially derived metabolite required for cytosolic Fe-S cluster assembly. Using an inducible Cre/loxP system to delete exons 9 and 10 of the Abcb7 gene, we examined the phenotype of mice deficient in Abcb7. We found that Abcb7 was essential in extra-embryonic tissues early in gestation and that the mutant allele exhibits an X-linked parent-of-origin lethality effect. Furthermore, using X-chromosome inactivation assays and tissue-specific deletions, Abcb7 was found to be essential for the development and function of numerous other cell types and tissues. A notable exception to this was liver, where loss of Abcb7 impaired cytosolic Fe-S cluster assembly but was not lethal. In this situation, control of iron regulatory protein 1, a key cytosolic modulator of iron metabolism, which is responsive to the availability of cytosolic Fe-S clusters, was impaired and contributed to the dysregulation of hepatocyte iron metabolism. Altogether, these studies demonstrate the essential nature of Abcb7 in mammals and further substantiate a central role for mitochondria in the biogenesis of cytosolic Fe-S proteins.

ATP-Binding Cassette Transporters↗

PubMed2006

Statistical methods for the detection of spatial clustering in case-control data.

In this paper, I develop new approaches for the detection of spatial clustering in case-control data. One method is based upon drawing Thiessen polygons around each control. It is unnecessary to actually draw or compute the boundaries of the polygons; it is sufficient to count, for each control, the number of cases that are closer to that control than to any other control. A second method is similar to the Cuzick-Edwards method, which is based on counts of cases that are among the k-nearest neighbours of cases, but is instead based upon the number of cases within a specified distance of cases. These first two methods are global methods in the sense that they provide a single statistic that measures the degree of spatial clustering. The third method suggests a local statistic, for tests of the null hypothesis of no spatial clustering around a prespecified focus. The method is based upon the cumulative chi2 test, which is typically used to test whether cases are more prevalent than expected around a prespecified location. This is also extended to the case where all observational locations are considered as potential cluster locations and multiple testing is carried out. Each of the new methods is illustrated using data on childhood leukaemia and lymphoma cases in North Humberside.

Bayes Theorem↗

PubMed1996

Comparison of lantibiotic gene clusters and encoded proteins.

Lantibiotics form a group of modified peptides with unique structures, containing post-translationally modified amino acids such as dehydrated and lanthionine residues. In the gram-positive bacteria that secrete these lantibiotics, the gene clusters flanking the structural genes for various linear (type A) lantibiotics have recently been characterized. The best studied representatives are those of nisin (nis), subtilin (spa), epidermin (epi), Pep5 (pep), cytolysin (cyl), lactocin S (las) and lacticin 481 (lct). Comparison of the lantibiotic gene clusters shows that they contain conserved genes that probably encode similar functions. The nis, spa, epi and pep clusters contain lanB and lanC genes that are presumed to code for two types of enzymes that have been implicated in the modification reactions characteristic of all lantibiotics, i.e. dehydration and thio-ether ring formation. The cyl, las and lct gene clusters have no homologue of the lanB gene, but they do contain a much larger lanM gene that is the lanC gene homologue. Most lantibiotic gene clusters contain a lanP gene encoding a serine protease that is presumably involved in the proteolytic processing of the prelantibiotics. All clusters contain a lanT gene encoding an ABC transporter likely to be involved in the export of (precursors of) the lantibiotics. The lanE, lanF and lanG genes in the nis, spa and epi clusters encode another transport system that is possibly involved in self-protection. In the nisin and subtilin gene clusters two tandem genes, lanR and lanK, have been located that code for a two-component regulatory system. Finally, non-homologous genes are found in some lantibiotic gene clusters. The nisI and spaI genes encode lipoproteins that are involved in immunity, the pepI gene encodes a membrane-located immunity protein, and epiD encodes an enzyme involved in a post-translational modification found only in the C-terminus of epidermin. Several genes of unknown function are also found in the las gene cluster. A database has been assembled for all putative gene products of type A lantibiotic gene clusters. Database searches, multiple sequence alignment and secondary structure prediction have been used to identify conserved sequence segments in the LanB, LanC, LanE, LanF, LanG, LanK, LanM, LanP, LanR and LanT gene products that may be essential for structure and function. This database allows for a rapid screening of newly determined sequences in lantibiotic gene clusters.

ATP-Binding Cassette Transporters↗

PubMed2026

Lineage-specific adaptation and resistance in Candida albicans.

Candida albicans exhibits substantial phenotypic and ecological diversity; however, the exact relationship between its population structure, adaptation to specific niches, and antifungal resistance remains incompletely understood. To investigate these evolutionary dynamics, we analyzed the whole-genome sequences from 591 publicly available isolates, integrating nuclear and mitochondrial phylogenomics with ecological and resistance-associated genomic analyses. Phylogenomic analyses resolved 18 core nuclear clusters together with multiple admixed lineages. Strong cytonuclear concordance was noted in the majority of the central lineages, contrasting with a higher discordance among the admixed groups, consistent with recurrent genetic exchange. The analysis revealed that geographic origin explains a larger fraction of genetic variance than anatomical niche, supporting a predominantly generalist population structure. A notable exception was Cluster N16 (Candida africana), which presented a strict genital origin in our dataset (n = 34). Additionally, although the mitochondrial genome exhibits strong purifying selection, candidate residues under diversifying selection correlated with specific niches (e.g., bloodstream) have been identified. Analysis of five resistance-associated genes (ERG11, UPC2, FKS1, TAC1 and FUR1) revealed that resistance-associated variants were generally rare but exhibited distinct gene-specific patterns. In case of ERG11 and FUR1 they were concentrated in a specific clade (N11, N17, and their admixed Group A) and exhibit gene-dependent zygosity patterns. In summary, the evolution of C. albicans appears to be driven by a predominantly clonal model punctuated by episodic genetic exchange, where both ecological adaptation and antifungal resistance mutations exhibit genomic signatures marked by lineage specificity.

Antifungal resistance↗

PubMed2005

Electronic and infrared spectroscopy of [benzene-(methanol)(n)](+) (n = 1-6).

The microsolvation structure of the [benzene-(methanol)(n)](+) (n = 1-6) clusters was analyzed by electronic and infrared spectroscopy. For the n = 1 and 2 clusters, further spectroscopic investigation was carried out by Ar atom attachment, which has been know as a useful technique for discriminating isomers of the clusters. The coexistence of multiple isomers was confirmed for the n = 1 and 2 clusters, and remarkably, preferential production of the specific isomers occurred in the Ar attachment. The most stable isomer of the n = 1 cluster was suggested to be of the "on-ring" structure where the nonbonding electrons of the methanol moiety directly interact with the pi orbital of the benzene cation moiety. This is a sharp contrast to [benzene-(H(2)O)(1)](+), exhibiting the "side" structure, where the water moiety is bound to the C-H sites of the benzene cation moiety. The structure of the n = 2 cluster was discussed with the help of density functional theory calculations. Spectral signatures of the intracluster proton-transfer reaction were found for n > or = 5. The intracluster electron-transfer reaction leading to the (methanol)(m)()(+) fragment was also seen upon vibrational and electronic excitation of n > or = 4.

Journal Article↗

PubMed2003

Quantifying double-strand breaks and clustered damages in DNA by single-molecule laser fluorescence sizing.

Fluorescence from a single DNA molecule passing through a laser beam is proportional to the size (contour length) of the molecule, and molecules of different sizes can be counted with equal efficiencies. Single-molecule fluorescence can thus determine the average length of the molecules in a sample and hence the frequency of double-strand breaks induced by various treatments. Ionizing radiation-induced frank double-strand breaks can thus be quantified by single-molecule sizing. Moreover, multiple classes of clustered damages involving damaged bases and abasic sites, alone or in combination with frank single-strand breaks, can be quantified by converting them to double-strand breaks by chemical or enzymatic treatments. For a given size range of DNA molecules, single-molecule sizing is as or more sensitive than gel electrophoresis, and requires several orders-of-magnitude less DNA to determine damage levels.

Bacteriophage T7↗

PubMed2005

Admission to hospital following head injury in England: incidence and socio-economic associations.

BACKGROUND: Head injury in England is common. Evidence suggests that socio-economic factors may cause variation in incidence, and this variation may affect planning for services to meet the needs of those who have sustained a head injury. METHODS: Socio-economic data were obtained from the UK Office for National Statistics and merged with Hospital Episodes Statistics obtained from the Department of Health. All patients admitted for head injury with ICD-10 codes S00.0-S09.9 during 2001-2 and 2002-3 were included and collated at the level of the extant Health Authorities (HA) for 2002, and Primary Care Trust (PCT) for 2003. Incidence was determined, and cluster analysis and multiple regression analysis were used to look at patterns and associations. RESULTS: 112,718 patients were admitted during 2001-2 giving a hospitalised incidence rate for England of 229 per 100,000. This rate varied across the English HA's ranging from 91-419 per 100,000. The rate remained unchanged for 2002-3 with a similar magnitude of variation across PCT's. Three clusters of HA's were identified from the 2001-2 data; those typical of London, those of the Shire counties, and those of Other Urban authorities. Socio-economic factors were found to account for a high proportion of the variance in incidence for 2001-2. The same pattern emerged for 2002-3 at the PCT level. The use of public transport for travel to work is associated with a decreased incidence and lifestyle indicators, such as the numbers of young unemployed, increase the incidence. CONCLUSION: Head injury incidence in England varies by a factor of 4.6 across HA's and PCT's. Planning head injury related services at the local level thus needs to be based on local incidence figures rather than regional or national estimates. Socio-economic factors are shown to be associated with admission, including travel to work patterns and lifestyle indicators, which suggests that incidence is amenable to policy initiatives at the macro level as well as preventive programmes targeted at key groups.

Adolescent↗