Direct searches for dark matter: Recent results

There is abundant evidence for large amounts of unseen matter in the universe. This dark matter, by its very nature, couples feebly to ordinary matter and is correspondingly difficult to detect. Nonetheless, several experiments are now underway with the sensitivity required to detect directly galactic halo dark matter through their interactions with matter and radiation. These experiments divide into two broad classes: searches for weakly interacting massive particles (WIMPs) and searches for axions. There exists a very strong theoretical bias for supposing that supersymmetry (SUSY) is a correct description of nature. WIMPs are predicted by this SUSY theory and have the required properties to be dark matter. These WIMPs are detected from the byproducts of their occasional recoil against nucleons. There are efforts around the world to detect these rare recoils. The WIMP part of this overview focuses on the cryogenic dark matter search (CDMS) underway in California. Axions, another favored dark matter candidate, are predicted to arise from a minimal extension of the standard model that explains the absence of the expected large CP violating effects in strong interactions. Axions can, in the presence of a large magnetic field, turn into microwave photons. It is the slight excess of photons above noise that signals the axion. Axion searches are underway in California and Japan. The axion part of this overview focuses on the California effort. Brevity does not allow me to discuss other WIMP and axion searches, likewise for accelerator and satellite based searches; I apologize for their omission.

Stationary-phase mutation in the bacterial chromosome: Recombination protein and DNA polymerase IV dependence

Several microbial systems have been shown to yield advantageous mutations in slowly growing or nongrowing cultures. In one assay system, the stationary-phase mutation mechanism differs from growth-dependent mutation, demonstrating that the two are different processes. This system assays reversion of a lac frameshift allele on an F′ plasmid in Escherichia coli. The stationary-phase mutation mechanism at lac requires recombination proteins of the RecBCD double-strand-break repair system and the inducible error-prone DNA polymerase IV, and the mutations are mostly −1 deletions in small mononucleotide repeats. This mutation mechanism is proposed to occur by DNA polymerase errors made during replication primed by recombinational double-strand-break repair. It has been suggested that this mechanism is confined to the F plasmid. However, the cells that acquire the adaptive mutations show hypermutation of unrelated chromosomal genes, suggesting that chromosomal sites also might experience recombination protein-dependent stationary-phase mutation. Here we test directly whether the stationary-phase mutations in the bacterial chromosome also occur via a recombination protein- and pol IV-dependent mechanism. We describe an assay for chromosomal mutation in cells carrying the F′ lac. We show that the chromosomal mutation is recombination protein- and pol IV-dependent and also is associated with general hypermutation. The data indicate that, at least in these male cells, recombination protein-dependent stationary-phase mutation is a mechanism of general inducible genetic change capable of affecting genes in the bacterial chromosome.

Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome c1 precursor.

Since most of the examples of "exon shuffling" are between vertebrate genes, the view is often expressed that exon shuffling is limited to the evolutionarily recent lineage of vertebrates. Although exon shuffling in plants has been inferred from the analysis of intron phases of plant genes [Long, M., Rosenberg, C. & Gilbert, W. (1995) Proc. Natl. Acad. Sci. USA 92, 12495-12499] and from the comparison of two functionally unknown sunflower genes [Domon, C. & Steinmetz, A. (1994) Mol. Gen. Genet. 244, 312-317], clear cases of exon shuffling in plant genes remain to be uncovered. Here, we report an example of exon shuffling in two important nucleus-encoded plant genes: cytosolic glyceraldehyde-3-phosphate dehydrogenase (cytosolic GAPDH or GapC) and cytochrome c1 precursor. The intron-exon structures of the shuffled region indicate that the shuffling event took place at the DNA sequence level. In this case, we can establish a donor-recipient relationship for the exon shuffling. Three amino terminal exons of GapC have been donated to cytochrome c1, where, in a new protein environment, they serve as a source of the mitochondrial targeting function. This finding throws light upon an old important but unsolved question in gene evolution: the origin of presequences or transit peptides that generally exist in nucleus-encoded organelle genes.

Adaptive mutation sequences reproduced by mismatch repair deficiency.

Adaptive reversions of a lac frameshift mutation in Escherichia coli are -1 deletions in small mononucleotide repeats, whereas growth-dependent reversions are heterogeneous. The adaptive mutations resemble instability of simple repeats, which, in hereditary colon cancer, in yeast, and in E. coli occurs in the absence of mismatch repair. The postulate that mismatch repair is disabled transiently during adaptive mutation in E. coli is supported here by the demonstration that the growth-dependent mutation spectrum can be made indistinguishable from adaptive mutations by disallowing mismatch repair during growth. Physiologically induced mismatch repair deficiency could be an important mutagenic mechanism in cancers and in evolution.

Intron phase correlations and the evolution of the intron/exon structure of genes.

Two issues in the evolution of the intron/exon structure of genes are the role of exon shuffling and the origin of introns. Using a large data base of eukaryotic intron-containing genes, we have found that there are correlations between intron phases leading to an excess of symmetric exons and symmetric exon sets. We interpret these excesses as manifestations of exon shuffling and make a conservative estimate that at least 19% of the exons in the data base were involved in exon shuffling, suggesting an important role for exon shuffling in evolution. Furthermore, these excesses of symmetric exons appear also in those regions of eukaryotic genes that are homologous to prokaryotic genes: the ancient conserved regions. This last fact cannot be explained in terms of the insertional theory of introns but rather supports the concept that some of the introns were ancient, the exon theory of genes.

Fluidity of the lipid domain of cell wall from Mycobacterium chelonae.

The mycobacterial cell wall contains large amounts of unusual lipids, including mycolic acids that are covalently linked to the underlying arabinogalactan-peptidoglycan complex. Hydrocarbon chains of much of these lipids have been shown to be packed in a direction perpendicular to the plane of the cell surface. In this study, we examined the dynamic properties of the organized lipid domains in the cell wall isolated from Mycobacterium chelonae grown at 30 degrees C. Differential scanning calorimetry showed that much of the lipids underwent major thermal transitions between 30 degree C and 65 degrees C, that is at temperatures above the growth temperature, a result suggesting that a significant portion of the lipids existed in a structure of extremely low fluidity in the growing cells. Spin-labeled fatty acid probes were successfully inserted into the more fluid part of the cell wall. Our model of the cell wall suggests that this domain corresponds to the outermost leaflet, a conclusion reinforced by the observation that labeling of intact cells produced electron spin resonance spectra similar to those of the isolated cell wall. Use of stearate labeled at different positions showed that the fluidity within the outer leaflet increased only slightly as the nitroxide group was placed farther away from the surface. These results are consistent with the model of mycobacterial cell wall containing an asymmetric lipid bilayer, with an internal, less fluid mycolic acid leaflet and an external, more fluid leaflet composed of lipids containing shorter chain fatty acids. The presence of the low-fluidity layer will lower the permeability of the cell wall to lipophilic antibiotics and chemotherapeutic agents and may contribute to the well-known intrinsic resistance of mycobacteria to such compounds.

TRPC1, a human homolog of a Drosophila store-operated channel.

In many vertebrate and invertebrate cells, inositol 1,4,5-trisphospate production induces a biphasic Ca2+ signal. Mobilization of Ca2+ from internal stores drives the initial burst. The second phase, referred to as store-operated Ca2+ entry (formerly capacitative Ca2+ entry), occurs when depletion of intracellular Ca2+ pools activates a non-voltage-sensitive plasma membrane Ca2+ conductance. Despite the prevalence of store-operated Ca2+ entry, no vertebrate channel responsible for store-operated Ca2+ entry has been reported. trp (transient receptor potential), a Drosophila gene required in phototransduction, encodes the only known candidate for such a channel throughout phylogeny. In this report, we describe the molecular characterization of a human homolog of trp, TRPC1. TRPC1 (transient receptor potential channel-related protein 1) was 40% identical to Drosophila TRP over most of the protein and lacked the charged residues in the S4 transmembrane region proposed to be required for the voltage sensor in many voltage-gated ion channels. TRPC1 was expressed at the highest levels in the fetal brain and in the adult heart, brain, testis, and ovaries. Evidence is also presented that TRPC1 represents the archetype of a family of related human proteins.

Human von Willebrand factor gene sequences target expression to a subpopulation of endothelial cells in transgenic mice.

The present study was undertaken to define the 5' and 3' regulatory sequences of human von Willebrand factor gene that confer tissue-specific expression in vivo. Transgenic mice were generated bearing a chimeric construct that included 487 bp of 5' flanking sequence and the first exon fused in-frame to the Escherichia coli lacZ gene. In situ histochemical analyses in independent lines demonstrated that the von Willebrand factor promoter targeted expression of LacZ to a subpopulation of endothelial cells in the yolk sac and adult brain. LacZ activity was absent in the vascular beds of the spleen, lung, liver, kidney, testes, heart, and aorta, as well as in megakaryocytes. In contrast, in mice containing the lacZ gene targeted to the thrombomodulin locus, the 5-bromo-4-chloro-3-indolyl beta-D-galactopyranoside reaction product was detected throughout the vascular tree. These data highlight the existence of regional differences in endothelial cell gene regulation and suggest that the 733-bp von Willebrand factor promoter may be useful as a molecular marker to investigate endothelial cell diversity.

O cérebro sócio-musical: estudo de uma experiência de educação musical

A prática musical tem efeitos positivos no desenvolvimento humano, envolvendo aspectos cognitivos, emocionais, motivacionais e sociais, que implicam em alterações no processamento cerebral. O número de Programas de Educação Musical (PEMs) com enfoque em populações jovens em vulnerabilidade social tem crescido no Brasil e no mundo. Dessa maneira, torna-se importante a realização de estudos que verifiquem os efeitos de PEMs no desenvolvimento destas populações. O objetivo do presente estudo é investigar os impactos de uma experiência de um PEM sobre os aspectos psicológicos de seus estudantes, mais especificamente a autoestima, as habilidades sociais e o funcionamento executivo. A coleta de dados foi realizada em um PEM da cidade de Ribeirão Preto SP e em duas escolas regulares de ensino, uma particular e outra da rede pública. Participaram do estudo 69 crianças e adolescentes com idades entre 10 e 17 anos, divididos em três grupos, a saber: Grupo Iniciante (GI), composto por alunos com até 12 meses de matrícula no PEM; Grupo Experiente (GE), composto por alunos com mais de 24 meses de matrícula no PEM; e Grupo Controle (GC), constituído por participantes sem qualquer envolvimento com aprendizado musical. Cada grupo foi composto por 23 estudantes. Os três grupos de participantes responderam aos seguintes testes psicológicos: Escala de Autoestima de Rosenberg (EAR), Matson Evaluation of Social Skills with Youngsters (MESSY) e Teste de Stroop. Também foram realizadas entrevistas semi-estruturadas com todos os estudantes dos grupos GI e GE, dez estudantes do PEM que não compuseram nenhum grupo por não possuírem o pré-requisito de tempo de matrícula exigido, seis responsáveis legais dos estudantes e doze profissionais do PEM. As entrevistas tiveram a função de fornecerem relatos verbais a respeito dos impactos percebidos nos estudantes pelo envolvimento com o PEM. Os dados dos testes psicológicos foram analisados através dos testes estatísticos ANOVA, Mann-Whitney e t de Student e as entrevistas foram analisadas através da investigação qualitativa em educação. As análises dos testes psicológicos mostraram que os GI e GE não possuem diferenças entre si para nenhuma das variáveis de estudo. O GC apresentou escores inferiores aos GI e GE para a Autoestima e escores superiores para Solidão e Ansiedade Social, indicando que o envolvimento com o PEM pode acarretar em ganhos nessas habilidades. A partir da análise das entrevistas foram construídas três categorias de codificação relacionadas a impactos comportamentais do envolvimento com o PEM, a saber: relacionamento interpessoal, desenvolvimento de habilidades intrapessoais e envolvimento com música e desenvolvimento humano na perspectiva de profissionais e responsáveis legais. A análise das entrevistas indicou que a participação no PEM está relacionada a impactos positivos na autoestima, habilidades sociais e funcionamento executivo dos participantes. Os resultados foram discutidos buscando interrelaciona-los de maneira a integrar os dados colhidos por meio dos testes psicológicos e através das entrevistas. Conclui-se que a participação em PEMs com enfoque no resgate social de populações vulneráveis possui influência no desenvolvimento de crianças e adolescentes, indicando que o uso da educação musical caracteriza uma importante estratégia de intervenção social.

Molecular Genetic Basis of Opposite Gene by Environment Interactions in Reading Disability and Attention Deficit/Hyperactivity Disorder

The goal of this study is to better understand the genetic basis of Reading Disability (RD) and Attention Deficit Hyperactivity Disorder (ADHD) by examining molecular G x E interactions with parental education for each disorder. Research indicates that despite sharing genetic risk factors, RD and ADHD are influenced by different types of G x E interactions with parental education - a diathesis stress interaction in the case of ADHD and a bioecological interaction in RD. In order to resolve this apparent paradox, we conducted a preliminary study using behavioral genetic methods to test for G x E interactions in RD and the inattentive subtype of ADHD (ADHD-I) in the same sample of monozygotic and dizygotic Colorado Learning Disabilities Research Center same-sex twin pairs (DeFries et al., 1997), and our findings were consistent with the literature. We posited a genetic hypothesis for this opposite pattern of interactions, which suggests that only genes specific to each disorder enter into these opposite interactions, not the shared genes underlying their comorbidity. This study sought to further investigate this paradox using molecular genetics methods. We examined multiple candidate genes identified for RD or related language phenotypes and those identified for ADHD for G x E interactions with parental education. The specific aims of this study were as follows: 1) partition known risk alleles for RD and/or related language phenotypes and ADHD-I into those which are pleiotropic and non-pleiotropic by testing each risk allele for association with both RD and ADHD-I, 2) explore the main effects of parental education on both RD and ADHD-I, 3) address G-E correlations, and 4) conduct exploratory G x E interaction analyses in order to test the genetic hypothesis. Analyses suggested a number of pleiotropic genes that influence both RD and ADHD; however, results did not remain after correcting for multiple comparisons. Although exploratory G x E interaction findings were not significant after multiple comparison correction, results suggested a G x E interaction in the bioecological direction with KIAA0319, parental education, and ADHD-I. Given the limited power in the current study, replication of these findings with larger samples is necessary.

Post-Conflict Maternal Communication, Children's Understandings, and Child Functioning in Violent and Non-Violent Families

The last two decades have been marked by a growing public awareness of family violence. Research by social scientists has suggested that family violence is widespread (Gelles and Straus, 1988). It is estimated that every year 1.8 to 4 million women are physically abused by their partners (Novello, 1992). In fact, more women are abused by their husbands or boyfriends than are injured in car accidents, muggings, or rapes (Jaffe, Wolfe, and Wilson, 1990). A recent prevalence study by Fantuzzo, Boruch, Beriama, Atkins, and Marcus (1997) found that children were disproportionately present in households where there was a substantial incident of adult female assault. Experts estimate that 3.3 to 10 million children are exposed to marital violence each year (Carlson, 1984; Straus, 1991). Until recently, most researchers did not consider the impact of parental conflict on the children who witness this violence. The early literature in this field primarily focused on the incidence of violence against women and the inadequate response of community agencies (Jaffe et al, 1990). The needs of children were rarely considered. However, researchers have become increasingly aware that children exposed to marital violence are victims of a range of psychological maltreatment (e.g., terrorizing, isolation;Hart, Brassared & Karlson, 1996) and are at serious risk for the development of psychological problems (Fantuzzo, DePaola, Lambert, Martino, Anderson, and Sutton, 1991). Jouriles, Murphy and O'Leary (1989) found that children of battered women were four times more likely to exhibit psychopathology as were children living in non-violent homes. Further, researchers have found associations between childhood exposure to parental violence and the expression of violence in adulthood (Carlson, 1990). Existing research suggests that children who have witnessed marital violence manifest numerous emotional, social, and behavioral problems (Sternberg et al., 1993; Fantuzzo et al., 1991; Jaffe et al, 1990). Studies have found that children of battered women exhibit more internalizing and externalizing behavior problems than non-witnesschildren (Hughes and Fantuzzo, 1994; McCloskey, Figueredo, and Koss, 1995). In addition, children exposed to marital violence have been found to exhibit difficulties with social problem-solving, and have lower levels of social competence than nonwitnesses (Rosenberg, 1987; Moore, Pepler, Weinberg, Hammond, Waddell, & Weiser, 1990). Other reported difficulties include low self esteem (Hughes, 1988), poor school performance (Moore et al., 1990) and problems with aggression (Holden & Ritchie, 1991; Jaffe, Wolfe, Wilson, & Zak, 1986). Further, within the last decade, researchers have found that some children are traumatized by the witnessing experience, showing elevated levels of posttraumatic stress symptoms (Devoe & Graham-Bermann, 1997; Rossman, Bingham, & Emde, 1996; Kilpatrick, Litt, & Williams, 1997). These findings corroborate clinical reports that describe many exposed children as experiencing trauma reactions. It appears that the negative effects of witnessing marital violence are numerous and varied, ranging from mild emotional and behavioral problems to clinically significant levels of posttraumatic stress symptoms. These incidence figures and research findings indicate that children's exposure to violence is a significant problem in our nation today and has serious implications for the future.

THE NEW WALLS AND FENCES: CONSEQUENCES FOR ISRAEL AND PALESTINE. CEPS Middle East Working Paper No. 9, June 2003

Good fences make good neighbours’ wrote the poet Robert Frost. Israel and Palestine are certainly not good neighbours and the question that arises is will a fence between Israel and Palestine turn them into ‘good neighbours’. This paper deals with the Israeli decision to construct a fence that will divide Israel and the West Bank. Almost all public debate of the wall in Israel has been limited to the security aspects. In light of the success enjoyed so far by the wall or fence around the Gaza Strip in preventing suicide bombers from getting through, the defence for needing a similar wall around the West Bank seems like an easy task. One of the main proponents of the wall concept in Israel is Dan Scheuftan, whose book on the subject has served as a guide for policy-makers. The paper provides a critique of Scheuftan’s book. The paper addresses various aspects of the wall and focuses on the different consequences of building a barrier between the two entities. Significant attention is paid to the economic consequences of the wall. The paper also looks at other issues such as the impact the wall will have on future attempts of peace-making. The paper attempts to show that the prevention of Palestinian access to Israel – the main goal of the wall – may not really have the hoped for effect of enhancing Israel’s security