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Article

JAZZ: A whole genome shotgun assembler

LBL Publications (2002)

We present, JAZZ, a new graphical algorithm for whole genome assembly that self-consistently treats paired-end constraints. The algorithm is designed to be scalable for application to large animal and plant genome sequencing projects. To aid in the development and validation of assemblies, we have also developed a suite of graphical tools for examining and manipulating large layouts. JAZZ has been used at the JGI to put together then genomes of many microbes, a fungal genome, and the genomes of two chordates, the sea squirt Ciona intestinalis and the putter fish Fugu ruripes; long, highly accurate scaffolds are recovered that are excellent substrates for annotation. We discuss the challenges faced in assembling these genomes, and strategies for future sequencing projects.

Cover page: JAZZ: A whole genome shotgun assembler

Article
Peer Reviewed

A review of East Asian reports of aurorae and comets circa AD 775

UC Berkeley Previously Published Works (2015)

Given that a strong 14C variation in AD 775 has recently been suggested to be due to the largest solar flare ever recorded in history, it is relevant to investigate whether celestial events observed around that time may have been aurorae, possibly even very strong aurorae, or otherwise related to the 14C variation (e.g. a suggested comet impact with Earth's atmosphere). We critically review several celestial observations from AD 757 to the end of the 770s, most of which were previously considered to be true, and in some cases, strong aurorae; we discuss in detail the East Asian records and their wording. We conclude that probably none among the events after AD 770 was actually an aurora, including the event in AD 776 Jan, which was misdated for AD 774 or 775; the observed white qi phenomenon that happened above the moon in the south-east was most probably a halo effect near the full Moon - too late in any case to be related to the 14C variation in AD 774/5. There is another report of a similar (or identical) white qi phenomenon above the moon, reported just before a comet observation and dated to AD 776 Jan; the reported comet observed by the Chinese was misdated to AD 776, but actually sighted in AD 767. Our critical review of East Asian reports of aurorae circa AD 775 shows some very likely true Chinese auroral displays observed and reported for AD 762; there were also several events prior to AD 771 that may have been aurorae but are questionable.

Cover page: A review of East Asian reports of aurorae and comets circa AD 775

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Peer Reviewed

β-carotene treatment of cervical intraepithelial neoplasia: A phase II study

UC Irvine Previously Published Works (1996)

The use of Papanicolaou smears for cervical cancer screening has led to an increased detection of preinvasive conditions of the cervix, cervical intraepithelial neoplasia (CIN). Epidemiological studies have shown an association between low levels of dietary β-carotene and CIN. In this Phase II study, we have explored the effect of p.o. β-carotene administration on CIN I and II. Patients with documented CIN I or II were treated with 30 mg daily of β-carotene for 6 months. Response rates were determined at 0, 3, 6, and 12 months with cytology, colposcopy, and/or biopsies. Levels of β- carotene and vitamin E were determined at the same time intervals in vaginal mucosa cells and serum. Response rates were 18 of 30 (60%), 21 of 30 (70%), and 10 of 30 (33%) at 3, 6, and 12 months, respectively. Significant changes occurred in the serum β-carotene levels over time. Median levels over 2200 mg/ml were found at 3 and 6 months versus a baseline median level of 111 (P < 0.0001). Significant increases were also noted in the β-carotene levels of the vaginal mucosa compared to baseline (P = 0.01) and a significant correlation was noted between serum and vaginal β-carotene levels as well (P < 0.0001). This study indicates that a large percentage of patients with CIN I and II will respond clinically to p.o. β-carotene supplementation. There is a positive relationship between serum and tissue levels of β-carotene which suggests that serum levels can be used for monitoring purposes. Because of these encouraging results, prospective randomized studies are ongoing comparing the efficacy of β-carotene against an untreated control arm.

Cover page: β-carotene treatment of cervical intraepithelial neoplasia: A phase II study

Creative Commons 'BY' version 4.0 license

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A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis

UC Berkeley Previously Published Works (2017)

PRDM9 binding localizes almost all meiotic recombination sites in humans and mice. However, most PRDM9-bound loci do not become recombination hotspots. To explore factors that affect binding and subsequent recombination outcomes, we mapped human PRDM9 binding sites in a transfected human cell line and measured PRDM9-induced histone modifications. These data reveal varied DNA-binding modalities of PRDM9. We also find that human PRDM9 frequently binds promoters, despite their low recombination rates, and it can activate expression of a small number of genes including CTCFL and VCX. Furthermore, we identify specific sequence motifs that predict consistent, localized meiotic recombination suppression around a subset of PRDM9 binding sites. These motifs strongly associate with KRAB-ZNF protein binding, TRIM28 recruitment, and specific histone modifications. Finally, we demonstrate that, in addition to binding DNA, PRDM9's zinc fingers also mediate its multimerization, and we show that a pair of highly diverged alleles preferentially form homo-multimers.

Cover page: A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis

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Peer Reviewed

A randomized, double blind, Phase III trial using oral beta-carotene supplementation for women with high-grade cervical intraepithelial neoplasia.

UC Irvine Previously Published Works (2001)

To evaluate the effect of daily beta-carotene (30 mg) versus placebo over a 2-year period on cervical intraepithelial neoplasia (CIN) 2 and 3 lesions. Human papillomavirus (HPV) typing was done to determine whether lesion regression was related to HPV. Micronutrient levels were measured to determine whether levels were predictive of regression. Variables that influence the risk of HPV infection and CIN, such as cigarette smoking and sexual behavior, were evaluated. Women were randomized to beta-carotene or placebo, with cytology and colposcopy every 3 months. Cervical biopsies were performed before treatment and after 6 and 24 months to evaluate response. Persistence of or progression to CIN 3 resulted in removal from the study, whereas treatment continued for 2 years on all others. The presence and type of HPV was determined by PCR. Response was defined as an improvement in CIN by 2 grades. Mantel-Haenszel chi(2) test was used to analyze response to treatment. Fisher's exact test was used to determine the effect of HPV and CIN grade on response Wilcoxon's rank-sum tests were used to compare micronutrient levels between groups. Twenty-one of 124 enrolled women were not randomized because they either moved, became pregnant, voluntarily withdrew, or the pathological review of their initial cervical biopsies did not confirm CIN 2 or 3. Of the remaining 103 women, 33 experienced lesion regression, 45 had persistent or progressive disease, and 25 women did not complete the study and were considered nonresponders in the final analysis. The overall regression rate (32%) was similar between treatment arms and when stratified for CIN grade. Data on 99 women with HPV typing showed that 77% were HPV-positive and 23% HPV-negative at enrollment. HPV-positive lesions were subdivided into indeterminate-, low-, and high-risk categories; the response rate was highest for women with no HPV detected (61%), lower for indeterminate/low-risk (30%), and lowest for high-risk (18%; P =.001). CIN regression was negatively correlated with retinol levels. In conclusion, beta-carotene does not enhance the regression of high-grade CIN, especially in HPV-positive subjects.

Cover page: A randomized, double blind, Phase III trial using oral beta-carotene supplementation for women with high-grade cervical intraepithelial neoplasia.

Article

The genome of the sea squirt Ciona Intestinalis: The seeds of vertebrate innovation

LBL Publications (2002)

The first chordates appeared over a half a billion years ago, providing the ancestral stock from which modern vertebrates emerged. To shed some light on the chordate origins, we have sequenced the genome of Ciona intestinalis, a sea squirt whose lineage split from that of vertebrates in the mid Cambrian. Ciona has long been a popular model system for the study of development, featuring world-wide and year-round availability, easily visualized cells and morphogenetic processes, simple methods for transient transgene expression, and a growing genomic infrastructure including extensive EST and cDNA collections. A comparison of the assembled Ciona genome sequence and gene complement with available invertebrate and vertebrate sequences provides insight into the origins and development of a chordate and vertebrate systems including the nervous systems, muscular, immune and endocrine systems, as well as the evolution of the chordate body plan. The Ciona genome provides a foundation for a genome-scale analyses of regulatory networks through chordate development.

Cover page: The genome of the sea squirt Ciona Intestinalis: The seeds of vertebrate innovation

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Peer Reviewed

Status of the LUX Dark Matter Search

UC Berkeley Previously Published Works (2010)

The Large Underground Xenon (LUX) dark matter search experiment is currently being deployed at the Homestake Laboratory in South Dakota. We will highlight the main elements of design which make the experiment a very strong competitor in the field of direct detection, as well as an easily scalable concept. We will also present its potential reach for supersymmetric dark matter detection, within various timeframes ranging from 1 year to 5 years or more. © 2010 American Institute of Physics.

Cover page: Status of the LUX Dark Matter Search

Article

Search for Nonminimal Neutral Bosons from Z-Boson Decays

LBL Publications (1990)

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Measurement of the B0-meson lifetime.

UC Irvine Previously Published Works (1990)

We report a measurement of the lifetime of the B0 meson based upon 29-GeV e+e- annihilation data taken with the Mark II detector at the SLAC storage ring PEP. The B0 mesons are tagged by their decays into D*- and D*+, where the D*- is tagged by its decay into -D 0. We reconstruct the decay vertices of 15 B0-meson candidates and measure the B0 lifetime to be 1.20-0.360.14+0.52+0.16 psec. © 1990 The American Physical Society.

Cover page: Measurement of the B0-meson lifetime.

Article

Measurement of the b{ovr b} Fraction in Hadronic Z{sup 0} Decays with Precision Vertex Detectors

LBL Publications (1991)