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At least 613 records · Page 34Linked to original sources
PubMed2006

Challenging the spliceosome machine.

BACKGROUND: Using cDNA copies of transcripts and corresponding genomic sequences from the Berkeley Drosophila Genome Project, a set of 24,753 donor and acceptor splice sites were computed with a scanning algorithm that tested for single nucleotide insertion, deletion and substitution polymorphisms. Using this dataset, we developed a progressive partitioning approach to examining the effects of challenging the spliceosome system. RESULTS: Our analysis shows that information content increases near splice sites flanking progressively longer introns and exons, suggesting that longer splice elements require stronger binding of spliceosome components. Information also increases at splice sites near very short introns and exons, suggesting that short splice elements have crowding problems. We observe that the information found at individual splice sites depends upon a balance of splice element lengths in the vicinity, including both flanking and non-adjacent introns and exons. CONCLUSION: These results suggest an interdependence of multiple splicing events along the pre-mRNA, which may have implications for how the macromolecular spliceosome machine processes sets of neighboring splice sites.

Animals↗
PubMed2006

PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification.

The Berkeley Phylogenomics Group presents PhyloFacts, a structural phylogenomic encyclopedia containing almost 10,000 'books' for protein families and domains, with pre-calculated structural, functional and evolutionary analyses. PhyloFacts enables biologists to avoid the systematic errors associated with function prediction by homology through the integration of a variety of experimental data and bioinformatics methods in an evolutionary framework. Users can submit sequences for classification to families and functional subfamilies. PhyloFacts is available as a worldwide web resource from http://phylogenomics.berkeley.edu/phylofacts.

Animals↗
PubMed2003

A successful educational collaboration between scientists and educators: microscopic explorations.

The teacher's guide, Microscopic Explorations: A GEMS Festival Guide (Brady and Willard, 1998), is the result of a partnership between Great Explorations in Math and Science (GEMS), a program of the Lawrence Hall of Science (LHS), the public science and curriculum development center of the University of California, Berkeley, and the Microscopy Society of America (MSA). Microscopic Exploration supports the MSA's low-cost national outreach program and, also, reaches a very large educational community as part of the GEMS series. Some of the lessons learned through the extremely successful MSA/LHS collaboration are summarized here in hopes that they may be instructive to other scientists and educators as they launch their own partnerships and collaborations.

Cooperative Behavior↗
PubMed2006

Progress of epidemiological and molecular epidemiological studies on benzene in China.

Benzene is an organic solvent that has been used in industry for about 100 years throughout the world. Since 1973, a series of toxicological and molecular epidemiological studies on benzene were conducted by researchers at the Chinese Academy of Preventive Medicine (CAPM) (1973-1986) and subsequently by a collaboration between the CAPM and the National Cancer Institute (NCI) in the United States that began in 1986, which was joined by investigators from the University of California at Berkeley, the University of North Carolina at Chapel Hill, and New York University. The findings demonstrated that the risk of leukemia and lymphoma among benzene-exposed workers was significantly increased, with elevated risks for leukemia present not only at higher exposure but also among workers exposed to under 10 ppm. Therefore, the benzene permissible level was decreased to 1.8 ppm (6 mg/m(3)) and benzene-induced leukemia is treated as an occupational cancer in China. The benzene permissible level is 1.0 in the United States and in several other developed countries and it has been suggested to be decreased to 0.5 ppm (ACGIH). A number of potential biomarkers are related to benzene exposure and poisoning. Some of these are benzene oxide-protein adducts, chromosome aberration of lymphocytes, and GPA mutations in erythrocytes, a decrease in B cell and CD4(-)T cell counts in peripheral blood, and altered expression of CXCL16, ZNF331, JUN, and PF4 in lymphocytes. Variation in multiple benzene metabolizing genes may be associated with risk of benzene hematotoxicity, including CYP2E1, MPO, NQO1, and GSTT1.

Benzene↗
PubMed2003

Longitudinal hierarchical linear modeling analyses of California Psychological Inventory data from age 33 to 75: an examination of stability and change in adult personality.

Twenty aspects of personality assessed via the California Psychological Inventory (CPI; Gough & Bradley, 1996) from age 33 to 75 were examined in a sample of 279 individuals. Oakland Growth Study and Berkeley Guidance Study members completed the CPI a maximum of 4 times. We used longitudinal hierarchical linear modeling (HLM) to ask the following: Which personality characteristics change and which do not? Five CPI scales showed uniform lack of change, 2 showed heterogeneous change giving an averaged lack of change, 4 showed linear increases with age, 2 showed linear decreases with age, 4 showed gender or sample differences in linear change, 1 showed a quadratic peak, and 2 showed a quadratic nadir. The utility of HLM becomes apparent in portraying the complexity of personality change and stability.

Adult↗
PubMed1984

Stereotactic heavy-ion Bragg peak radiosurgery for intra-cranial vascular disorders: method for treatment of deep arteriovenous malformations.

The present paper represents the first clinical report of the use of stereotactically-directed narrow beams of helium ions from the 184-inch Synchrocyclotron at the Lawrence Berkeley Laboratory for the radiosurgical treatment of life-threatening vascular disorders of the brain, including inoperable or inaccessible deep arteriovenous malformations (AVMs) and carotid artery-cavernous sinus fistulas ( CCFs ). We describe the methods developed for stereotactic neuroradiological imaging and stereotactic helium-ion Bragg peak radiosurgery in the evaluation and treatment of the first 55 patients with deep AVMs in a clinical research protocol. We discuss the diagnosis and epidemiological characteristics of the diseases, the neurosurgical and radiosurgical methods of treatment available and the initial experience of stereotactic helium-ion Bragg peak radiosurgery , including stereotactic neuroradiological evaluation, treatment planning, heavy-ion beams, patient treatment protocol, early clinical results, patient evaluation and follow-up studies planned, and conclusions thus far obtained.

Adult↗
PubMed1997

Silica-induced apoptosis in alveolar and granulomatous cells in vivo.

Silica is a toxicant that can stimulate cells to produce various cellular products such as free radicals, cytokines, and growth factors. Silica and its induced substances may induce apoptosis to regulate the evolution of silica-induced inflammation and fibrosis. To examine this hypothesis, groups of Wistar male rats were intratracheally instilled with different doses of Min-U-Sil 5 silica (Silica, Berkeley Springs, WV). Ten days after the instillation, we obtained cells by bronchoalveolar lavage and placed them on slides by cytospin preparation. The slides were stained with Diff-Quik (Lab Aids, Sydney, NSW, Australia) and examined under oil immersion. A substantial number of cells with apoptotic features were identified in all silica-instilled rats and the apoptosis was confirmed by agarose gel electrophoresis. The number of apoptotic cells was clearly related to silica dosage. Engulfment of apoptotic cells by macrophages was also noted. Neutrophil influx in silica-instilled rats could be saturated with the increase of silica dosage and the number of macrophages in different dose groups changed in parallel with the proportion of apoptotic cells. Fifty-six days after instillation, morphologically apoptotic cells could be identified in granulomatous cells of lung tissue from silica-instilled rats. We conclude that intratracheal instillation of silica could induce apoptosis in both alveolar and granulomatous cells, and the apoptotic change and subsequent engulfment by macrophages might play a role in the evolution of silica-induced effects.

Administration, Inhalation↗
PubMed1998

A case study in innovative outreach--combining training, research, and technology transfer to address real-world problems.

Outreach, training, technology transfer, and research are often treated as programmatically distinct activities. The interdisciplinary and applied aspects of the Superfund Basic Research Program offer an opportunity to explore different models. A case study is presented that describes a collaborative outreach effort that combines all of the above. It involves the University of California's Davis and Berkeley program projects, the University of California Systemwide Toxic Substances Research and Teaching Program, the U.S. Navy's civilian workforce at the former Mare Island Naval Shipyard, Vallejo, California (MINSY), a Department of Defense (DoD) Environmental Education Demonstration Grant program, and the Private Industry Council of Napa and Sonoma counties in California. The effort applied a Superfund-developed technology to a combined waste, radium and polychlorinated biphenyl contamination, stemming from a problematic removal action at an installation/restoration site at MINSY. The effort demonstrates that opportunities for similar collaborations are possible at DoD installations.

California↗
PubMed1999

Exposures of children to organophosphate pesticides and their potential adverse health effects.

Recent studies show that young children can be exposed to pesticides during normal oral exploration of their environment and their level of dermal contact with floors and other surfaces. Children living in agricultural areas may be exposed to higher pesticide levels than other children because of pesticides tracked into their homes by household members, by pesticide drift, by breast milk from their farmworker mother, or by playing in nearby fields. Nevertheless, few studies have assessed the extent of children's pesticide exposure, and no studies have examined whether there are adverse health effects of chronic exposure. There is substantial toxicologic evidence that repeated low-level exposure to organophosphate (OP) pesticides may affect neurodevelopment and growth in developing animals. For example, animal studies have reported neurobehavorial effects such as impairment on maze performance, locomotion, and balance in neonates exposed (italic)in utero(/italic) and during early postnatal life. Possible mechanisms for these effects include inhibition of brain acetylcholinesterase, downregulation of muscarinic receptors, decreased brain DNA synthesis, and reduced brain weight in offspring. Research findings also suggest that it is biologically plausible that OP exposure may be related to respiratory disease in children through dysregulation of the autonomic nervous system. The University of California Berkeley Center for Children's Environmental Health Research is working to build a community-university partnership to study the environmental health of rural children. This Center for the Health Assessment of Mothers and Children of Salinas, or CHAMACOS in Monterey County, California, will assess (italic)in utero(/italic) and postnatal OP pesticide exposure and the relationship of exposure to neurodevelopment, growth, and symptoms of respiratory illness in children. The ultimate goal of the center is to translate research findings into a reduction of children's exposure to pesticides and other environmental agents, and thereby reduce the incidence of environmentally related disease.

Adult↗
PubMed2001

Cloning and expression of Drosophila melanogaster UDP-GlcNAc:alpha-3-D-mannoside beta1,2-N-acetylglucosaminyltransferase I.

A TBLASTN search of the Drosophila melanogaster expressed sequence tag (EST) database with the amino acid sequence of human UDP-N-acetylglucosamine:alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I (GnT I, EC 2.4.1.101) as probe yielded a clone (GM01211) with 56% identity over 36 carboxy-terminal amino acids. A 550 base pair (bp) probe derived from the EST clone was used to screen a Drosophila cDNA library in lambda-ZAP II and two cDNAs lacking a start ATG codon were obtained. 5'-Rapid amplification of cDNA ends (5'-RACE) yielded a 2828 bp cDNA containing a full-length 1368 bp open reading frame encoding a 456 amino acid protein with putative N-terminal cytoplasmic (5 residues) and hydrophobic transmembrane (20 residues) domains. The protein showed 52% amino acid sequence identity to human GnT I. This cDNA, truncated to remove the N-terminal hydrophobic domain, was expressed in the baculovirus/Sf9 system as a secreted protein containing an N-terminal (His)6 tag. Protein purified by adsorption to and elution from nickel beads converted Man alpha1-6(Man alpha1-3)Man beta-octyl (M3-octyl) to Man alpha1-6(GlcNAc beta1-2Man alpha1-3)Man beta-octyl. The Km values (0.7 and 0.03 mM for M3-octyl and UDP-GlcNAc respectively), temperature optimum (37 degrees C), pH optimum (pH 5 to 6) and divalent cation requirements (Mn > Fe, Mg, Ni > Ba, Ca, Cd, Cu) were similar to mammalian GnT I. TBLASTN searches of the Berkeley Drosophila Genome Project database with the Drosophila GnT I cDNA sequence as probe allowed localization of the gene to chromosomal region 2R; 57A9. Comparison of the cDNA and genomic DNA sequences allowed the assignment of seven exons and six introns; all introns showed GT-AG splice site consensus sequences. This is the first insect GnT I gene to be cloned and expressed.

Amino Acid Sequence↗
PubMed2003

Does heavy drinking affect academic performance in college? Findings from a prospective study of high achievers.

OBJECTIVE: This study examined the effects of heavy drinking, alcohol-related problems and drinking opportunities on academic performance (grade point average [GPA]) in a prospective cohort of college students attending the University of California at Berkeley. METHOD: Several waves of survey data were collected from 465 students beginning in the summer prior to their freshman year. Cross-sectional and regression analyses were conducted to determine whether heavy alcohol use, alcohol-related problems and drinking opportunities were associated with college GPA before and after controlling for demographics and high school GPA. RESULTS: Cross-sectional analyses generally revealed modest and nonsignificant associations between college GPA and measures of heavy alcohol use, alcohol-related problems and drinking opportunities in the first year of college. High school GPA was modestly associated with both heavy alcohol use and college GPA. Only a summative measure of alcohol-related academic problems was significantly associated with college GPA, but this relationship did not persist in a regression model that included high school GPA and student demographic characteristics as control variables. CONCLUSIONS: Heavy alcohol use, alcohol-related problems and drinking opportunities do not appear to have an important effect on students' academic performance, but additional research with longitudinal data from representative student samples is needed to confirm these findings.

Adolescent↗
PubMed2004

The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes.

The Berkeley Drosophila Genome Project (BDGP) strives to disrupt each Drosophila gene by the insertion of a single transposable element. As part of this effort, transposons in >30,000 fly strains were localized and analyzed relative to predicted Drosophila gene structures. Approximately 6300 lines that maximize genomic coverage were selected to be sent to the Bloomington Stock Center for public distribution, bringing the size of the BDGP gene disruption collection to 7140 lines. It now includes individual lines predicted to disrupt 5362 of the 13,666 currently annotated Drosophila genes (39%). Other lines contain an insertion at least 2 kb from others in the collection and likely mutate additional incompletely annotated or uncharacterized genes and chromosomal regulatory elements. The remaining strains contain insertions likely to disrupt alternative gene promoters or to allow gene misexpression. The expanded BDGP gene disruption collection provides a public resource that will facilitate the application of Drosophila genetics to diverse biological problems. Finally, the project reveals new insight into how transposons interact with a eukaryotic genome and helps define optimal strategies for using insertional mutagenesis as a genomic tool.

Animals↗
PubMed2006

Molecular characterization of teflon, a gene required for meiotic autosome segregation in male Drosophila melanogaster.

Drosophila melanogaster males lack recombination and have evolved a mechanism of meiotic chromosome segregation that is independent of both the chiasmatic and achiasmatic segregation systems of females. The teflon (tef) gene is specifically required in males for proper segregation of autosomes and provides a genetic tool for understanding recombination-independent mechanisms of pairing and segregation as well as differences in sex chromosome vs. autosome segregation. Here we report on the cloning of the tef gene and the molecular characterization of tef mutations. Rescue experiments using a GAL4-driven pUAS transgene demonstrate that tef corresponds to predicted Berkeley Drosophila Genome Project (BDGP) gene CG8961 and that tef expression is required in the male germ line prior to spermatocyte stage S4. Consistent with this early prophase requirement, expression of tef was found to be independent of regulators of meiotic M phase initiation or progression. The predicted Tef protein contains three C2H2 zinc-finger motifs, one at the amino terminus and two in tandem at the carboxyl terminus. In addition to the zinc-finger motifs, a 44- to 45-bp repeat is conserved in three related Drosophila species. On the basis of these findings, we propose a role for Tef as a bridging molecule that holds autosome bivalents together via heterochromatic connections.

Amino Acid Sequence↗
PubMed2004

Farmers' perceptions, knowledge, and management of coffee pests and diseases and their natural enemies in Chiapas, Mexico.

Small farmers' perceptions of coffee Coffea arabica L. herbivores and their natural enemies, how those perceptions relate to field infestation levels, and pest management practices being implemented by members from two organic and nonorganic coffee grower organizations in the Soconusco region, southeastern Mexico, were analyzed through an interview survey, diagnostic workshops, and field sampling. The terms pest, disease, and damage were commonly used as synonyms. The major phytophagous species, as perceived by the interviewees, were Hypothenemus hampei (Ferrari), and to a lesser extent the fungi Corticium koleroga Cooke (Höhnel) and Hemileia vastatrix Berkeley & Broome. Among the nonorganic farmers, other nonpest-related constraints were regarded as more important. Awareness of the existence of natural enemies was low, despite more organic farmers have used the ectoparasitoid bethylid Cephalonomia stephanoderis Betrem against H. hampei. Labor supplied by household members was most frequent for pest control; only organic farmers exchanged labor for this purpose. The levels of infestation by H. hampei, Leucoptera coffeella Guérin-Méneville, and C. koleroga were lower within the organic coffee stands. However, a low effectiveness for pest control was commonly perceived, probably due to a feeling, among the organic farmers, of a low impact of their pest management extension service, whereas a lack of motivation was prevalent among the nonorganic farmers, shown by a concern with their low coffee yields and the emigration of youth. The importance of understanding farmers' perceptions and knowledge of pests and their natural enemies and the need for participatory pest management approaches, are discussed.

Agriculture↗
PubMed1978

Health services needs of children in day care centers.

In order to assess health services needs of children in day care centers, interviews were carried out with health coordinators or directors of 52 licensed day care centers in Berkeley, California. Over one-third of the centers lacked a designated health coordinator; one-fourth of the centers lacked written health guidelines and/or emergency guidelines; almost one-half lacked nutrition education services; and over two-thirds lacked a dental health education program. Only one out of five centers was willing to admit mildly ill children. Health coordinators and directors showed strong preference for care of mildly ill children at home by a trained worker. The presence of a designated health coordinator and of state funds was highly associated with the content and scope of health services provided.

Administrative Personnel↗
PubMed2004

Creation of a minimal tiling path of genomic clones for Drosophila: provision of a common resource.

On the basis of shotgun subclone libraries used in the sequencing of the Drosophila melanogaster genome, a minimal tiling path of subclones across much of the genome was determined. About 320,000 shotgun clones for chromosomes X(12-20), 2R, 2L, 3R, and 4 were available from the Berkeley Drosophila Genome Project. The clone inserts have an average length of 3.4 kb and are amenable to standard PCR amplification. The resulting tiling path covers 86.2% of chromosome X(12-20), 86.2% of chromosomal arm 2R, 79.0% of 2L, 89.6% of 3R, and 80.5% of chromosome 4. In total, the 25,135 clones represent 76.7 Mb--equivalent to about 67% of the genome--and would be suitable for producing a microarray on a single slide.

Animals↗
PubMed2003

The discovery of epidepride and its analogs as high-affinity radioligands for imaging extrastriatal dopamine D(2) receptors in human brain.

[(123)I]Epidepride, [(18)F]fallypride, and [(76)Br]isoremoxipride (FLB-457) and their corresponding [(11)C]labeled derivatives belong to a class of high-affinity radioligands for SPECT or PET imaging of dopamine D(2) receptors in the human brain. In contrast to previously used imaging agents, these ligands are capable of identifying extrastriatal dopamine D(2) receptors. The design of these substituted benzamides derive its origin from the atypical antipsychotic agent, remoxipride. Starting in the late 1970's, halogenated analogs of (S)-sulpiride were evaluated in binding assays and behavioral studies, leading to the discovery of remoxipride. Remoxipride was 10 times weaker than sulpiride in vitro but 50 times more potent in vivo. Search for a putative active metabolite of remoxipride led to the discovery of raclopride and eticlopride, the former becoming a useful radioligand as tritium or carbon-11 labeled form for receptor binding and PET studies, respectively. In the US, the mono-iodine analog of raclopride, [(123)I]iodobenzamide (IBZM), was found to have moderate putamen-to-cerebellum ratio in rat and human brain. Continued search for metabolites of remoxipride led to the discovery of its 3,6-dihydroxy derivative, NCQ-344, with an extremely potent in vivo activity in the rat. SAR studies of the metabolites of remoxipride led to the discovery of the 3-methoxy isomer, isoremoxipride (FLB-457) and its corresponding 6-hydroxy analog, FLB-463, both having affinities for the dopamine D(2) receptor in the 20-30 pM range. Later, the 5-[(123)I]iodo analog of FLB-463, [(123)I]ioxipride ([(123)I]NCQ-298), became a potential SPECT imaging agent. In the mean time, the deshydroxy analog of IBZM, [(125)I]iodopride, showed binding potential in the rat similar to [(125)I]IBZM. Epidepride was designed by combining the structure of isoremoxipride with that of iodopride. In 1988, epidepride was independently prepared and radiolabeled in three separate laboratories in Stockholm, Berkeley, and Nashville. Evaluation of seven [(125)I]iodine substituted analogs of raclopride, including IBZM, revealed the unusual high striatum-to-cerebellum ratio of 234 of [(125)I]epidepride in the rat. Subsequent SPECT images with [(123)I]epidepride demonstrated its ability to identify extrastriatal dopamine D(2) receptors in the human brain. Exploration of the structure of epidepride confirmed its exceptional properties, to be exceeded only by its N-allyl homolog, [(125)I]nalepride. The design by others of a series of potent 5-(3-[(18)F]fluoropropyl) substituted analogs of epidepride for PET imaging, lead to the discovery of [(18)F]fallypride. By elucidating the role of lipophilicity in the substituted benzamides, the excellent imaging characteristics of [(11)C]/[(123)I]epidepride, [(11)C]/[(76)Br]isoremoxipride and [(18)F]fallypride, could not only be explained but predicted with remarkable accuracy. By using the inverse product of the receptor affinity (K(D)), and the apparent partition constant of the radioligand (P((7.4))), estimates of maximal binding potential of any radioligand for imaging of any neurotransmitter receptor or transporter site seem possible.

Animals↗
PubMed1997

"Looking back, what period of your life brought you the most satisfaction".

Common myths hold that old persons are fixated on childhood memories, that they believe that youth is the best part of life, and that old age contains few satisfactions. Berkeley Older Generation Study members, when asked on two occasions during old age (M ages = 69.8 and 82.7) to name the periods of their lives that brought them the most and the least satisfaction, dispelled these myths. The thirties and forties were popular choices for periods of great satisfaction, but childhood and adolescence were quite unpopular for these old persons. "Right now" was named more often than any other life period as most satisfactory. Men and women did not differ in life periods nominated, but they did differ in the reasons given for their choices. Each period provided its own pattern of satisfactions and disappointments, and strong individual differences were apparent.

Aged↗