Restricting SBH Ambiguity via Restriction Enzymes

Abstract. The expected number of n-base long sequences consistent with a given SBH spectrum grows exponentially with n, which severely limits the potential range of applicability of SBH even in an error-free setting. Restriction enzymes (RE) recognize specific patterns and cut the DNA molecule at all locations of that pattern. The output of a restriction assay is the set of lengths of the resulting fragments. By augmenting the SBH spectrum with the target string’s RE spectrum, we can eliminate much of the ambiguity of SBH. In this paper, we build on [20] to enhance the resolving power of restriction enzymes. We give a hardness result for the SBH+RE problem, and supply improved heuristics for the existing backtracking algorithm. We prove a lower bound on the number restric-tion enzymes required for unique reconstruction, and show experimental results that are not far from this bound.

Global expression mapping of mammalian genomes

he aim of genome projects is to decipher all the information contained within the DNA of an organism and to study the way this information is processed in physiological processes. It is believed that more than 95% of the information content of the mammalian genome is represented in the protein coding sequences that make up only approximately 2% of the DNA sequence. Consequently much effort is being invested in the study of coding sequences in the form of cDNA analysis. This thesis is concerned with the development of a new strategy for a highly parallel approach to analyse entire cDNA libraries. The strategy is based upon generating sufficient sequence information to identify uniquely more than 100,000 cDNA clones by hybridisation with short oligonucleotides, typically 7 - 10 mers. Each oligonucleotide is hybridised to all cDNA clones in parallel and under stringent conditions positively identifies a subset (3 - 10%) of clones. Oligonucleotides are designed in such a way that each will positively identify a different subset of clones and statistical simulations estimate that approximately 200 such hybridisation events are required to identify uniquely upto 100,000 cDNA sequences. Such a fingerprint can be generated from many cDNA libraries constructed from different tissue mRNAs and will not only lead to the identification of most sequecnes expressed from the genome but also indicate the level of expression by determining the number of times any given sequence is represented across different cDNA libraries. A human foetal brain cDNA library has been constructed and 100,000 clones arrayed into microtitre plates and on nylon membranes. All the required technological developments have been carried out successfully and are presented. In excess of 200 oligonucleotide hybridisations have been performed on a subset of 32,000 cDNA clones and 1,000 sequenced control clones. A detailed analysis of the data on the control clones is presented and the implications for cDNA fingerprinting discussed

Patterns of injury and violence in Yaoundé Cameroon: an analysis of hospital data.

BackgroundInjuries are quickly becoming a leading cause of death globally, disproportionately affecting sub-Saharan Africa, where reports on the epidemiology of injuries are extremely limited. Reports on the patterns and frequency of injuries are available from Cameroon are also scarce. This study explores the patterns of trauma seen at the emergency ward of the busiest trauma center in Cameroon's capital city.Materials and methodsAdministrative records from January 1, 2007, through December 31, 2007, were retrospectively reviewed; information on age, gender, mechanism of injury, and outcome was abstracted for all trauma patients presenting to the emergency ward. Univariate analysis was performed to assess patterns of injuries in terms of mechanism, date, age, and gender. Bivariate analysis was used to explore potential relationships between demographic variables and mechanism of injury.ResultsA total of 6,234 injured people were seen at the Central Hospital of Yaoundé's emergency ward during the year 2007. Males comprised 71% of those injured, and the mean age of injured patients was 29 years (SD = 14.9). Nearly 60% of the injuries were due to road traffic accidents, 46% of which involved a pedestrian. Intentional injuries were the second most common mechanism of injury (22.5%), 55% of which involved unarmed assault. Patients injured in falls were more likely to be admitted to the hospital (p < 0.001), whereas patients suffering intentional injuries and bites were less likely to be hospitalized (p < 0.001). Males were significantly more likely to be admitted than females (p < 0.001)DiscussionPatterns in terms of age, gender, and mechanism of injury are similar to reports from other countries from the same geographic region, but the magnitude of cases reported is high for a single institution in an African city the size of Yaoundé. As the burden of disease is predicted to increase dramatically in sub-Saharan Africa, immediate efforts in prevention and treatment in Cameroon are strongly warranted

Federal Register

Daily publication of the U.S. Office of the Federal Register contains rules and regulations, proposed legislation and rule changes, and other notices, including "Presidential proclamations and Executive Orders, Federal agency documents having general applicability and legal effect, documents required to be published by act of Congress, and other Federal agency documents of public interest" (p. ii). Table of Contents starts on page iii

Identification of left ventricular mass QTL in the stroke-prone spontaneously hypertensive rat

Left ventricular hypertrophy (LVH) is accepted as an important independent predictor of adverse cardiovascular outcome; the aetiology includes a number of well-recognized causes but there is considerable interest in the genetics underlying cardiac hypertrophy. Data from several twin studies indicates that left ventricular mass index (LVMI) has a significant genetic basis that is most likely polygenic. Given the heterogeneity of the human condition, there has been little progress made towards identification of the genes involved, in this now common disease state. As an adjuvant to current human studies, inbred animal models have been developed which in turn have led to the identification of quantitative trait loci (QTL), via investigation using a genome wide strategy. This generally involves high fidelity phenotyping of large segregating F2 populations, derived by crossing inbred strains of sufficiently differing phenotype and subsequent genotyping using a wide selection of polymorphic microsatellite markers spread across the entire rat genome. The research described in this thesis incorporated an improved analysis of a previous genome wide scan, to confirm and identify QTL containing determinants of left ventricular hypertrophy in the Glasgow SHRSP x WKY F2 cross. This genome wide scan was carried out in 134 F2 hybrids (male: female = 65:69). Systolic and diastolic blood pressure was measured by radio-telemetry at baseline and after a 3 week 1% salt challenge in addition to heart rate, motor activity and pulse pressure. Other phenotype data included body weight, heart and LV weight and plasma renin activity. QTL affecting a given phenotype were mapped relative to an improved genetic linkage map for rat chromosome 14, with the aid of JoinMap 3.0, MapManager QTXb and Windows QTL Cartographer software. The original method of single marker analysis was used initially to test previous and newly acquired genotype data and confirm the cited LVMI QTL on rat chromosome 14. More stringent and complex statistical approaches were integrated in analysis resulting in detection of a second QTL for LVMI at marker D14Got23 and a single QTL for cardiac mass at marker D14Woxl4. The identification of QTL, although a fundamental process, is only the initial step towards the end objective of gene identification. The next logical step is the physical capture and confirmation of QTL with the production of congenic strains and substrains. In this thesis, the process of verifying the chromosome 14 QTL began with the generation of congenic strains, using a marker assisted 'speed' congenic strategy, previously validated in rats by our group. This was achieved by backcross breeding two inbred rat strains (SHRSP X WKY) and introgression of marker delineated regions of chromosome 14, from one background into the recipient genome and vice versa. Complete homozygosity of the background genetic markers (n=168) was achieved after 4 backcross generations. In the time line allowed, it was not possible to achieve a fixed congenic line however based on data provided from QTL analysis it was possible to generate and analyse preliminary phenotype data from backcross 4 males on the SHRSP background. The initial readings from this pilot study provide physical evidence that substituting a portion of WKY chromosome 14 with SHRSP results in a reduced LVMI, despite equivalent systolic blood pressure. (Abstract shortened by ProQuest.)

Federal Register

Daily publication of the U.S. Office of the Federal Register contains rules and regulations, proposed legislation and rule changes, and other notices, including "Presidential proclamations and Executive Orders, Federal agency documents having general applicability and legal effect, documents required to be published by act of Congress, and other Federal agency documents of public interest" (p. ii). Table of Contents starts on page iii

Bowdoin Orient v.137, no.1-25 (2007-2008)

https://digitalcommons.bowdoin.edu/bowdoinorient-2000s/1008/thumbnail.jp

2009 Annual Progress Report: DOE Hydrogen Program

This report summarizes the hydrogen and fuel cell R&D activities and accomplishments of the DOE Hydrogen Program for FY2009. It covers the program areas of hydrogen production and delivery; fuel cells; manufacturing; technology validation; safety, codes and standards; education; and systems analysis