'Next-generation' sequencing becomes 'now-generation'

A report on the Advances in Genome Biology & Technology conference, Marco Island, USA, 2-5 February 2011

Increasing Transit Ridership: Lessons from the Most Successful Transit Systems in the 1990s, MTI Report-01-22

This study systematically examines recent trends in public transit ridership in the U.S. during the 1990s. Specifically, this analysis focuses on agencies that increased ridership during the latter half of the decade. While transit ridership increased steadily by 13 percent nationwide between 1995 and 1999, not all systems experienced ridership growth equally. While some agencies increased ridership dramatically, some did so only minimally, and still others lost riders. What sets these agencies apart from each other? What explains the uneven growth in ridership

A clustering method for repeat analysis in DNA sequences

BACKGROUND: A computational system for analysis of the repetitive structure of genomic sequences is described. The method uses suffix trees to organize and search the input sequences; this data structure has been used previously for efficient computation of exact and degenerate repeats. RESULTS: The resulting software tool collects all repeat classes and outputs summary statistics as well as a file containing multiple sequences (multi fasta), that can be used as the target of searches. Its use is demonstrated here on several complete microbial genomes, the entire Arabidopsis thaliana genome, and a large collection of rice bacterial artificial chromosome end sequences. CONCLUSIONS: We propose a new clustering method for analysis of the repeat data captured in suffix trees. This method has been incorporated into a system that can find repeats in individual genome sequences or sets of sequences, and that can organize those repeats into classes. It quickly and accurately creates repeat databases from small and large genomes. The associated software (RepeatFinder), should prove helpful in the analysis of repeat structure for both complete and partial genome sequences

Designing and Operating Safe and Secure Transit Systems: Assessing Current Practices in the United States and Abroad, MTI Report 04-05

Public transit systems around the world have for decades served as a principal venue for terrorist acts. Today, transit security is widely viewed as an important public policy issue and is a high priority at most large transit systems and at smaller systems operating in large metropolitan areas. Research on transit security in the United States has mushroomed since 9/11; this study is part of that new wave of research. This study contributes to our understanding of transit security by (1) reviewing and synthesizing nearly all previously published research on transit terrorism; (2) conducting detailed case studies of transit systems in London, Madrid, New York, Paris, Tokyo, and Washington, D.C.; (3) interviewing federal officials here in the United States responsible for overseeing transit security and transit industry representatives both here and abroad to learn about efforts to coordinate and finance transit security planning; and (4) surveying 113 of the largest transit operators in the United States. Our major findings include: (1) the threat of transit terrorism is probably not universal—most major attacks in the developed world have been on the largest systems in the largest cities; (2) this asymmetry of risk does not square with fiscal politics that seek to spread security funding among many jurisdictions; (3) transit managers are struggling to balance the costs and (uncertain) benefits of increased security against the costs and (certain) benefits of attracting passengers; (4) coordination and cooperation between security and transit agencies is improving, but far from complete; (5) enlisting passengers in surveillance has benefits, but fearful passengers may stop using public transit; (6) the role of crime prevention through environmental design in security planning is waxing; and (7) given the uncertain effectiveness of antitransit terrorism efforts, the most tangible benefits of increased attention to and spending on transit security may be a reduction in transit-related person and property crimes

Too Big Too Fast? Potential Implications of the Rapid Increase in Emergency Medicine Residency Positions

Emergency medicine (EM) has expanded rapidly since its inception in 1979. Workforce projections from current data demonstrate a rapid rise in the number of accredited EM residency programs and trainee positions. Based on these trends, the specialty may soon reach a point of saturation, particularly in urban areas. This could negatively impact future trainees entering the job market as well as the career plans of medical students. More time and resources should be devoted to obtaining accurate projections, assessing the distribution of emergency physicians in rural versus urban settings, and implementing central workforce planning to protect the future of graduating trainees.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154425/1/aet210400.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154425/2/aet210400_am.pd

How Deep Is Deep enough for RNA-Seq Profiling of Bacterial Transcriptomes?

Background: High-throughput sequencing of cDNA libraries (RNA-Seq) has proven to be a highly effective approach for studying bacterial transcriptomes. A central challenge in designing RNA-Seq-based experiments is estimating a priori the number of reads per sample needed to detect and quantify thousands of individual transcripts with a large dynamic range of abundance. Results: We have conducted a systematic examination of how changes in the number of RNA-Seq reads per sample influences both profiling of a single bacterial transcriptome and the comparison of gene expression among samples. Our findings suggest that the number of reads typically produced in a single lane of the Illumina HiSeq sequencer far exceeds the number needed to saturate the annotated transcriptomes of diverse bacteria growing in monoculture. Moreover, as sequencing depth increases, so too does the detection of cDNAs that likely correspond to spurious transcripts or genomic DNA contamination. Finally, even when dozens of barcoded individual cDNA libraries are sequenced in a single lane, the vast majority of transcripts in each sample can be detected and numerous genes differentially expressed between samples can be identified. Conclusions: Our analysis provides a guide for the many researchers seeking to determine the appropriate sequencing depth for RNA-Seq-based studies of diverse bacterial species

UCHIME improves sensitivity and speed of chimera detection

Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments

Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation

The position of a poly(A) site of eukaryotic mRNA is determined by sequence signals in pre-mRNA and a group of polyadenylation factors. To reveal rice poly(A) signals at a genome level, we constructed a dataset of 55 742 authenticated poly(A) sites and characterized the poly(A) signals. This resulted in identifying the typical tripartite cis-elements, including FUE, NUE and CE, as previously observed in Arabidopsis. The average size of the 3′-UTR was 289 nucleotides. When mapped to the genome, however, 15% of these poly(A) sites were found to be located in the currently annotated intergenic regions. Moreover, an extensive alternative polyadenylation profile was evident where 50% of the genes analyzed had more than one unique poly(A) site (excluding microheterogeneity sites), and 13% had four or more poly(A) sites. About 4% of the analyzed genes possessed alternative poly(A) sites at their introns, 5′-UTRs, or protein coding regions. The authenticity of these alternative poly(A) sites was partially confirmed using MPSS data. Analysis of nucleotide profile and signal patterns indicated that there may be a different set of poly(A) signals for those poly(A) sites found in the coding regions. Based on the features of rice poly(A) signals, an updated algorithm termed PASS-Rice was designed to predict poly(A) sites