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PubMed2002

Manic-depression genes and the new millennium: poised for discovery.

Manic-depressive illness is a common psychiatric disorder with complex etiology that likely involves multiple genes and non-genetic influences. The uncertain path to gene discovery has spurred considerable debate over genetic findings and gene-finding strategies. In this article, I review the main findings, with a focus on: (1) putative linked loci on chromosomes 1q31-32, 4p16, 6pter-p24, 10p14, 10q21-26, 12q23-24, 13q31-32, 18p11, 18q21-23, 21q22, 22q11-13, and Xq24-28; and (2) association studies with candidate genes, dynamic mutations, mitochondrial mutations, and chromosomal aberrations. Although no gene has been identified, promising findings are emerging. I then discuss the challenges and opportunities ahead, with special emphasis on gene-finding methods-in particular, questions pertaining to phenotype definition, linkage and association mapping, gene markers, sampling, study population, multigene systems, lessons from other disorders, animal models, and bioinformatics. The progress to date, together with rapid advances in genomics, analytical and computational methods, and bioinformatics, holds promise for new insights into the genetics of manic-depression, in the new millennium.

Bipolar Disorder↗
PubMed2000

JAK-STAT signaling activated by Abl oncogenes.

The Abl oncoproteins v-Abl and BCR-Abl can activate member of the signal transducers and activators of transcription (STAT) family of signaling proteins. The mechanisms by which these oncoproteins activate STATs appear to differ. In cells transformed by v-Abl, Janus kinase (JAK) tyrosine kinases are constitutively activated. In these cells, the v-Abl oncoprotein and the JAK kinases physically associate. Mapping of the JAK interaction domain in v-Abl demonstrates that amino acids within the carboxyl terminal region of v-Abl bind JAKs through a direct interaction. A mutant of v-Abl lacking this region does not bind or activate JAK 1 in vivo, fails to activate STAT proteins, does not induce cellular proliferation, and is less efficient in cellular transformation. Kinase inactive mutants of JAK 1 inhibit the ability of v-Abl to activate STATs, to induce cytokine-independent proliferation, and to transform bone marrow cells. Interestingly, these effects correlate with defects in the activation of several pathways by v-Abl including Akt, PI3-kinase, STATs, and Ras. These data suggest that Jak kinases may play an important role in v-Abl induced transformation. Oncogene (2000).

Animals↗
PubMed2004

Functions of NF-kappaB1 and NF-kappaB2 in immune cell biology.

Two members of the NF-kappaB (nuclear factor kappaB)/Rel transcription factor family, NF-kappaB1 and NF-kappaB2, are produced as precursor proteins, NF-kappaB1 p105 and NF-kappaB2 p100 respectively. These are proteolytically processed by the proteasome to produce the mature transcription factors NF-kappaB1 p50 and NF-kappaB2 p52. p105 and p100 are known to function additionally as IkappaBs (inhibitors of NF-kappaB), which retain associated NF-kappaB subunits in the cytoplasm of unstimulated cells. The present review focuses on the latest advances in research on the function of NF-kappaB1 and NF-kappaB2 in immune cells. NF-kappaB2 p100 processing has recently been shown to be stimulated by a subset of NF-kappaB inducers, including lymphotoxin-beta, B-cell activating factor and CD40 ligand, via a novel signalling pathway. This promotes the nuclear translocation of p52-containing NF-kappaB dimers, which regulate peripheral lymphoid organogenesis and B-lymphocyte differentiation. Increased p100 processing also contributes to the malignant phenotype of certain T- and B-cell lymphomas. NF-kappaB1 has a distinct function from NF-kappaB2, and is important in controlling lymphocyte and macrophage function in immune and inflammatory responses. In contrast with p100, p105 is constitutively processed to p50. However, after stimulation with agonists, such as tumour necrosis factor-alpha and lipopolysaccharide, p105 is completely degraded by the proteasome. This releases associated p50, which translocates into the nucleus to modulate target gene expression. p105 degradation also liberates the p105-associated MAP kinase (mitogen-activated protein kinase) kinase kinase TPL-2 (tumour progression locus-2), which can then activate the ERK (extracellular-signal-regulated kinase)/MAP kinase cascade. Thus, in addition to its role in NF-kappaB activation, p105 functions as a regulator of MAP kinase signalling.

Animals↗
PubMed2005

Diversity and divergence among the tribal populations of India.

Tribal populations of the Indian subcontinent have been of longstanding interest to anthropologists and human geneticists. To investigate the relationship of Indian tribes to Indian castes and continental populations, we analyzed 45 unlinked autosomal STR loci in 9 tribal groups, 8 castes, and 18 populations from Africa, Europe and East Asia. South Indian tribal populations demonstrate low within-population heterozygosity (range: 0.54 - 0.69), while tribal populations sampled further north and east have higher heterozygosity (range: 0.69 - 0.74). Genetic distance estimates show that tribal Indians are more closely related to caste Indians than to other major groups. Between-tribe differentiation is high and exceeds that for eight sub-Saharan African populations (4.8% vs. 3.7%). Telugu-speaking populations are less differentiated than non-Telugu speakers (F(ST): 0.029 vs. 0.079), but geographic distance was not predictive of genetic affinity between tribes. South Indian tribes show significant population structure, and individuals can be clustered statistically into groups that correspond with their tribal affiliation. These results are consistent with high levels of genetic drift and isolation in Indian tribal populations, particularly those of South India, and they imply that these populations may be potential candidates for linkage disequilibrium and association mapping.

Asia↗
PubMed1997

On invariant manifolds attached to oscillating boundaries in Stokes flows.

Consider a steady Stokes flow bounded by a flat wall to which a separatrix, not tangent to the wall, is attached at point S. If the wall is made to slowly oscillate periodically with small amplitude in a longitudinal direction, then the Poincare map associated with this perturbed flow has a fixed point on the wall near S with an invariant manifold. This result also holds for flows bounded by a cylindrical wall and flows in which the small periodic perturbation is not due to the oscillation of the wall. This result is applied to several flow geometries in the literature. (c) 1997 American Institute of Physics.

Journal Article↗
PubMed2005

Random walks, diffusion limited aggregation in a wedge, and average conformal maps.

We investigate diffusion-limited aggregation (DLA) in a wedge geometry. Arneodo and collaborators have suggested that the ensemble average of DLA cluster density should be close to the noise-free selected Saffman-Taylor finger. We show that a different, but related, ensemble average, that of the conformal maps associated with random clusters, yields a nontrivial shape which is also not far from the Saffman-Taylor finger. However, we have previously demonstrated that the same average of DLA in a channel geometry is not the Saffman-Taylor finger. This casts doubt on the idea that the average of noisy diffusion-limited growth is governed by a simple transcription of noise-free results.

Cluster Analysis↗
PubMed2005

Prospects for identifying functional variation across the genome.

The genetic factors contributing to complex trait variation may reside in regulatory, rather than protein-coding portions of the genome. Within noncoding regions, SNPs in regulatory elements are more likely to contribute to phenotypic variation than those in nonregulatory regions. Thus, it is important to be able to identify and annotate noncoding regulatory elements. DNA conservation among diverged species successfully identifies noncoding regulatory regions. However, because rapidly evolving regulatory regions will not generally be conserved across species, these will not detected by using purely conservation-based methods. Here we describe additional approaches that can be used to identify putative regulatory elements via signatures of nonneutral evolution. An examination of the pattern of polymorphism both within and between populations of Drosophila melanogaster, as well as divergence with its sibling species Drosophila simulans, across 24.2 kb of noncoding DNA identifies several nonneutrally evolving regions not identified by conservation. Because different methods tag different regions, it appears that the methods are complementary. Patterns of variation at different elements are consistent with the action of selective sweeps, balancing selection, or population differentiation. Together with regions conserved between D. melanogaster and Drosophila pseudoobscura, we tag 5.3 kb of noncoding DNA as potentially regulatory. Ninety-seven of the 408 common noncoding SNPs surveyed are within putatively regulatory regions. If these methods collectively identify the majority of functional noncoding polymorphisms, genotyping only these SNPs in an association mapping framework would reduce genotyping effort for noncoding regions 4-fold.

Animals↗
PubMed2006

Long-range multilocus haplotype phasing of the MHC.

Haplotypes are a powerful tool for identifying the genetic basis of common complex diseases. Disease-association mapping requires molecular methods for haplotyping biallelic SNP variation and highly complex polymorphisms. We developed a method for phasing HLA-A, HLA-B, and HLA-DRB1 alleles on chromosome 6 in unrelated individuals. This method uses the highly polymorphic HLA-B locus to discriminate the two HLA haplotypes in heterozygous individuals and its ideal location 1.4 Mbp telomeric to HLA-DRB1 and 1.2 Mbp centromeric to HLA-A to capture 2-Mbp-long genomic DNA. Genomic DNA representing a single HLA-B-captured haplotype is genotyped for HLA-A and HLA-DRB1 alleles and linkage to HLA-B is established. Proof of principle was established in a large blinded study of phase-known samples. Availability of an efficient method for MHC haplotype phase determination will facilitate the mapping of causative MHC-resident genes in many human diseases and has the potential to be broadened to other polymorphic gene complexes.

Genes, MHC Class I↗
PubMed2003

Association of the Mediator complex with enhancers of active genes.

The multiprotein Mediator complex has been shown to interact with gene-specific regulatory proteins and RNA polymerase II in vitro. Here, we use chromatin immunoprecipitation to analyze the recruitment of Mediator to GAL genes of yeast in vivo. We find that Mediator associates exclusively with transcriptionally active and not inactive GAL genes. This association maps to the upstream activating sequence, rather than the core promoter, and is independent of RNA polymerase II, general transcription factors, and core promoter sequences. These findings support the idea of Mediator as a primary conduit of regulatory information from enhancers to promoters in eukaryotic cells.

Enhancer Elements, Genetic↗
PubMed1992

Structure of the histidine-containing phosphocarrier protein HPr from Bacillus subtilis at 2.0-A resolution.

The crystal structure of the histidine-containing phosphocarrier protein (HPr) of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) from Bacillus subtilis has been determined at 2.0-A resolution and refined to a crystallographic residual error R-factor of 0.150. The secondary-structure folding topology of the molecule is that of an open-face beta-sandwich formed by four antiparallel beta-strands packed against three alpha-helices. The active-site histidine, His-15, caps the N terminus of the first helix, suggesting that the helix dipole plays a role in stabilizing the phosphorylated state of the histidine. A sulfate anion located between His-15 and the neighboring Arg-17 has been identified in the electron-density map. Association of this negatively charged species with the two key catalytic residues implies that the crystal structure resembles the phosphorylated state of the protein. A model of the phosphorylated form of the molecule is proposed, in which the negatively charged phosphoryl group interacts with two main-chain nitrogen atoms of the following helix and with the guanidinium group of Arg-17. It is also proposed that the phosphoryl transfer from HPr to the IIA domain of the glucose permease involves Arg-17 switching between two salt bridges: one with the phosphorylated histidyl of HPr and the other with two aspartyl residues associated with the active site of the IIA domain of glucose permease, which are accessible upon complex formation.

Amino Acid Sequence↗
PubMed2003

Locus-specific genetic differentiation at Rw among warfarin-resistant rat (Rattus norvegicus) populations.

Populations may diverge at fitness-related genes as a result of adaptation to local conditions. The ability to detect this divergence by marker-based genomic scans depends on the relative magnitudes of selection, recombination, and migration. We survey rat (Rattus norvegicus) populations to assess the effect that local selection with anticoagulant rodenticides has had on microsatellite marker variation and differentiation at the warfarin resistance gene (Rw) relative to the effect on the genomic background. Initially, using a small sample of 16 rats, we demonstrate tight linkage of microsatellite D1Rat219 to Rw by association mapping of genotypes expressing an anticoagulant-rodenticide-insensitive vitamin K 2,3-epoxide reductase (VKOR). Then, using allele frequencies at D1Rat219, we show that predicted and observed resistance levels in 27 populations correspond, suggesting intense and recent selection for resistance. A contrast of F(ST) values between D1Rat219 and the genomic background revealed that rodenticide selection has overwhelmed drift-mediated population structure only at Rw. A case-controlled design distinguished these locus-specific effects of selection at Rw from background levels of differentiation more effectively than a population-controlled approach. Our results support the notion that an analysis of locus-specific population genetic structure may assist the discovery and mapping of novel candidate loci that are the object of selection or may provide supporting evidence for previously identified loci.

Animals↗
PubMed2005

Current understanding of the genetic aetiology of rheumatoid arthritis and likely future developments.

Most of the work described herein was performed by the North American Rheumatoid Arthritis Consortium (NARAC). After a brief description of the NARAC and the multiplex family resource that has been developed by this consortium, we will summarize the current status of genome-wide screens using this valuable family collection. Next, we describe work that is under way to further delineate the genes on chromosome 18q that demonstrate linkage to rheumatoid arthritis (RA), including an analysis of candidate genes in the region and results of dense association mapping. We also describe an extensive analysis of functional single-nucleotide polymorphisms (SNPs) that is under way in collaboration with Celera Diagnostics, as well as studies designed to further dissect the phenotypic and genotypic heterogeneity of RA. We conclude by briefly summarizing our future plans to elucidate the genetic aetiology of RA.

Arthritis, Rheumatoid↗
PubMedDate not supplied

Allele frequency determination of publicly available cSNPs in the Korean population.

PURPOSE: As a first step toward the construction of a single-nucleotide polymorphism (SNP) database of the Korean population, the authors determined the allele frequencies of 406 cSNPs selected from the public database. METHODS: A pooled DNA sequencing approach was used to determine the allele frequencies of 406 cSNPs selected from 120 genes in 24 individuals. RESULTS: Of 406 cSNPs, 53% were monomorphic in the Korean samples. Among tested SNPs, 292 SNPs (72%) were uncommon (minor allele < 20%) and 114 SNPs (28%) were common (minor allele > or = 20%) in our population. CONCLUSION: An extensive SNP characterization would be necessary, and the ethnic and population-based differences should be considered in the selection of SNPs for the study of complex diseases with association mapping methods.

Female↗
PubMed2003

Emerging trends in the search for genetic variants predisposing to human obesity.

PURPOSE OF REVIEW: The models currently proposed for the genetic architecture of obesity are critically reviewed in the light of recent developments in the search for genetic causes of this condition. RECENT FINDINGS: As for many other 'complex' diseases, most of the genetic variants predisposing to human obesity have not yet been identified. To date, investigation of the genetic contribution to obesity has been conducted according to two main hypotheses. The common disease/common variant hypothesis proposes that the genetic architecture of complex diseases (including obesity) is likely to consist of a limited number of alleles, each conferring a small increase in risk to the individual. Alternatively, it has also been proposed that complex diseases such as obesity may instead result from the effects of a large number of rare variants, with substantial allelic heterogeneity at disease-causing loci. These two hypotheses have shaped strategies for the identification of disease genes, including the use of linkage analysis, association studies and the systematic sequencing of candidate genes. Linkage studies have recently been very successful in identifying new genes in which mutations cause rare monogenic syndromes of obesity. In common obesity, numerous linkage and association studies have suggested that an increasing number of genetic loci could be involved. Overall, however, these studies have failed to identify the causal genetic variants. In contrast, the direct sequencing of well-chosen candidate genes has led to the identification of numerous rare alleles causing both syndromic and common obesity, which are less severe forms of the condition in humans. SUMMARY: The genetic architecture of obesity is still a matter of debate. The previously accepted hypothesis of a small number of common variants has been undermined by the low reproducibility of association studies and inconsistencies among genome scans for obesity. While high-throughput association mapping of candidate regions holds some promise for the identification of common susceptibility alleles, it must also be considered that the genetic predisposition to obesity may instead result from multiple rare variants in a large number of genes.

Alleles↗
PubMed2006

Classical momentum diffusion in double-delta-kicked particles.

We investigate the classical chaotic diffusion of atoms subjected to pairs of closely spaced pulses ("kicks") from standing waves of light (the 2delta-KP ). Recent experimental studies with cold atoms implied an underlying classical diffusion of a type very different from the well-known paradigm of Hamiltonian chaos, the standard map. The kicks in each pair are separated by a small time interval E<<1, which together with the kick strength K, characterizes the transport. Phase space for the 2delta-KP is partitioned into momentum "cells" partially separated by momentum-trapping regions where diffusion is slow. We present here an analytical derivation of the classical diffusion for a 2delta-KP including all important correlations which were used to analyze the experimental data. We find an asymptotic (t-->infinity) regime of "hindered" diffusion: while for the standard map the diffusion rate, for K>>1 , D approximately K(2)/2[1-2J(2)(K)...] oscillates about the uncorrelated rate D(0)=K(2)/2, we find analytically, that the 2delta-KP can equal, but never diffuses faster than, a random walk rate. We argue this is due to the destruction of the important classical "accelerator modes" of the standard map. We analyze the experimental regime 0.1 less or approximately KE less or approximately 1 , where quantum localization lengths L approximately Planck's (-0.75) are affected by fractal cell boundaries. We find an approximate asymptotic diffusion rate D proportional to K(3)E, in correspondence to a D proportional to K(3) regime in the standard map associated with the "golden-ratio" cantori.

Journal Article↗
PubMed2006

Polymer property prediction and optimization using neural networks.

Prediction and optimization of polymer properties is a complex and highly nonlinear problem with no easy method to predict polymer properties directly and accurately. The problem is especially complicated with high molecular weight polymers such as engineering plastics which have the greatest use in industry. The effect of modifying a monomer (polymer repeat unit) on polymerization and the resulting polymer properties is not easy to investigate experimentally given the large number of possible changes. This severely curtails the design of new polymers with specific end-use properties. In this paper, we show how properties of modified monomers can be predicted using neural networks. We utilize a database of polymer properties and employ a variety of networks ranging from backpropagation networks to unsupervised self-associating maps. We select particular networks that accurately predict specific polymer properties. These networks are classified into groups that range from those that provide quick training to those that provide excellent generalization. We also show how the available polymer database can be used to accurately predict and optimize polymer properties.

Forecasting↗
PubMed2004

Assessment of tracheal intubating conditions in children using remifentanil and propofol without muscle relaxant.

BACKGROUND: Tracheal intubation in children can be achieved by deep inhalational anaesthesia or an intravenous anaesthetic and a muscle relaxant, suxamethonium being widely used despite several side-effects. Studies have shown that oral intubation can be facilitated safely and effectively in children after induction of anaesthesia with propofol and alfentanil without a muscle relaxant. Remifentanil is a new, ultra-short acting, selective mu-receptor agonist that is 20-30 times more potent than alfentanil. This clinical study was designed to assess whether combination of propofol and remifentanil could be used without a muscle relaxant to facilitate tracheal intubation in children. METHODS: Forty children (5-10 years) admitted for adenotonsillectomy were randomly allocated to one of two groups to receive remifentanil 2 microg.kg(-1) (Gp I) or remifentanil 3 microg.kg(-1) (Gp II) before the induction of anaesthesia with i.v. propofol 3 mg.kg(-1). No neuromuscular blocking agent was administered. Intubating conditions were assessed using a four-point scoring system based on ease of laryngoscopy, jaw relaxation, position of vocal cords, degree of coughing and limb movement. Mean arterial pressure (MAP) and heart rate (HR) measured noninvasively before induction of anaesthesia to 5 min after intubation (seven time points). RESULTS: Tracheal intubation was successful in all patients without requiring neuromuscular blocking agent. Intubating conditions were clinically acceptable in 10 of 20 patients (50%) in Gp I compared with 18 of 20 patients (90%) in Gp II (P < 0.05). MAP and HR decreased in both groups after induction of anaesthesia (P < 0.01). Both HR and MAP were significantly lower in Gp II compared with Gp I after tracheal intubation (P < 0.01). No patient in the present study developed bradycardia or hypotension. CONCLUSIONS: We conclude that remifentanil (3 microg.kg(-1)), administered before propofol (3 mg.kg(-1)) provides acceptable tracheal intubating conditions in children, and completely inhibited the increase in HR and MAP associated with intubation.

Adenoidectomy↗