CiteULike: Author Alper

Expanding the metabolic engineering toolbox: more options to engineer cells.

KE Tyo — 2007-04-23T17:23:53-00:00

Trends Biotechnol, Vol. 25, No. 3. (March 2007), pp. 132-137.

Metabolic engineering exploits an integrated, systems-level approach for optimizing a desired cellular property or phenotype; and great strides have been made within this scope and context during the past fifteen years. However, due to limitations in the concepts and techniques, these have relied on a focused, pathway-oriented view. Recent advances in 'omics' technologies and computational systems biology have brought the foundational systems approach of metabolic engineering into focus. At the same time, protein engineering and synthetic biology have expanded the breadth and precision of the methods available to metabolic engineers to improve strain properties. Examples are presented that illustrate this broader perspective of tools and concepts, including a recent approach for global transcriptional machinery engineering (gTME), which has demonstrated the ability to elicit multigenic transcriptional changes that have improved phenotypes compared with single-gene perturbations.

Identification of a basolateral Cl-/HCO3- exchanger specific to gastric parietal cells

Snezana Petrovic — 2008-07-31T21:11:44-00:00

Am J Physiol Gastrointest Liver Physiol, Vol. 284, No. 6. (1 June 2003), pp. G1093-1103.

The basolateral Cl[-]/HCO[IMG]img002.gif" ALT="<UP>3</UP>"> exchanger in parietal cells plays an essential role in gastric acid secretion mediated via the apical gastric H+-K+-ATPase. Here, we report the identification of a new Cl[-]/HCO[IMG]img002.gif" ALT="<UP>3</UP>"> exchanger, which shows exclusive expression in mouse stomach and kidney, with expression in the stomach limited to the basolateral membrane of gastric parietal cells. Tissue distribution studies by RT-PCR and Northern hybridizations demonstrated the exclusive expression of this transporter, also known as SLC26A7, to stomach and kidney, with the stomach expression significantly more abundant. No expression was detected in the intestine. Cellular distribution studies by RT-PCR and Northern hybridizations demonstrated predominant localization of SLC26A7 in gastric parietal cells. Immunofluorescence labeling localized this exchanger exclusively to the basolateral membrane of gastric parietal cells, and functional studies in oocytes indicated that SLC26A7 is a DIDS-sensitive Cl[-]/HCO[IMG]img002.gif" ALT="<UP>3</UP>"> exchanger that is active in both acidic and alkaline pHi. On the basis of its unique expression pattern and function, we propose that SLC26A7 is a basolateral Cl[-]/HCO[IMG]img002.gif" ALT="<UP>3</UP>"> exchanger in gastric parietal cells and plays a major role in gastric acid secretion. 10.1152/ajpgi.00454.2002

Temporal relationships between colds, upper respiratory viruses detected by polymerase chain reaction, and otitis media in young children followed through a typical cold season.

B Winther — 2008-06-17T06:05:38-00:00

Pediatrics, Vol. 119, No. 6. (June 2007), pp. 1069-1075.

INTRODUCTION: Otitis media is a frequent complication of a viral upper respiratory tract infection, and the reported co-incidence of those diseases increases with assay sensitivity and sampling density. We determined the incidence of otitis-media complications in young children when referenced to cold-like illnesses and to concurrent virus recovery from the nasopharynx. METHODS: A total of 60 children from 24 families were followed from October 2003 through April 30, 2004, by daily parental recording of illness signs, weekly pneumatic otoscopic examinations, and periodic polymerase chain reaction assay of collected nasal fluids for common viruses. RESULTS: One hundred ninety-nine cold-like illnesses were observed, but a sample for virus assay was not collected concurrent with 71 episodes. Of the remainder, 73% of cold-like illnesses were temporally related to recovery of 1 or a combination of the assayed viruses, with rhinovirus predominating. For non-cold-like illness periods, 54 (18%) of 297 assays were positive for virus, and the virus frequency distribution was similar to that for cold-like illnesses. There were 93 diagnosed otitis-media episodes; 65 (70%) of these occurred during a cold-like illness. For the 79 otitis-media episodes with available nasal samples, 61 (77%) were associated with a positive virus result. In this population, the otitis-media complication rate for a cold-like illness was 33%. CONCLUSIONS: A cold-like illness was not a prerequisite for polymerase chain reaction detection of viruses in the nose and nasopharynx of young children. Viral detection by polymerase chain reaction in the absence of a cold-like illness is associated with complications in some subjects. Otitis media is a complication of viral infection both with and without concurrent cold-like illnesses, thus downwardly biasing coincidence estimates that use cold-based illnesses as the denominator.

Data capture in bioinformatics: requirements and experiences with Pedro

Daniel Jameson — 2008-04-10T14:56:42-00:00

BMC Bioinformatics, Vol. 9, No. 1. (2008)

BACKGROUND:The systematic capture of appropriately annotated experimental data is a prerequisite for most bioinformatics analyses. Data capture is required not only for submission of data to public repositories, but also to underpin integrated analysis, archiving, and sharing - both within laboratories and in collaborative projects. The widespread requirement to capture data means that data capture and annotation are taking place at many sites, but the small scale of the literature on tools, techniques and experiences suggests that there is work to be done to identify good practice and reduce duplication of effort.RESULTS:This paper reports on experience gained in the deployment of the Pedro data capture tool in a range of representative bioinformatics applications. The paper makes explicit the requirements that have recurred when capturing data in different contexts, indicates how these requirements are addressed in Pedro, and describes case studies that illustrate where the requirements have arisen in practice. CONCLUSIONS:Data capture is a fundamental activity for bioinformatics; all biological data resources build on some form of data capture activity, and many require a blend of import, analysis and annotation. Recurring requirements in data capture suggest that model-driven architectures can be used to construct data capture infrastructures that can be rapidly configured to meet the needs of individual use cases. We have described how one such model-driven infrastructure, namely Pedro, has been deployed in representative case studies, and discussed the extent to which the model-driven approach has been effective in practice.

Daily Tympanometry for High-Resolution Measurement of the Time between Onset Of Cold-Like Illness and Middle Ear Effusion.

William Doyle — 2008-06-05T20:51:48-00:00

The Laryngoscope (18 March 2008)

BACKGROUND:: Tympanometry is a simple method to assess middle ear pressure (MEP) and the presence of middle ear effusion (MEE), a marker of otitis media (OM). OBJECTIVES:: To determine whether daily parental tympanometry and illness sign recording in their children can be used to define the time between onsets of cold-like illness (CLI) and MEE at high resolution. STUDY DESIGN:: Prospective, longitudinal, 7 month, daily follow-up on 169 children aged 1 through 8.6 years. METHODS:: Tympanograms and illness were recorded daily by a parent. Tympanograms were examined, rejected if artifactual, and MEP data were entered into a database, with "flat tympanograms" coded as -400 mm H2O = MEE. The incidence and burden of CLIs (>2 days) were calculated, and for each CLI, the presence/absence of concurrent MEE (>2 days) was determined. For each child, the average MEP for CLI and nonCLI days was calculated. Paired CLI and tympanometric results were aligned and the days between event onsets determined. Stepwise regression was used to assign risk predictors for the measured outcomes. RESULTS:: A total of 566 CLIs were recorded, and the average CLI burden/child was 16%. Age was a significant predictor of CLI incidence/child, and age, history of colds, and daily environment were predictors of CLI-burden/child. Of the 433 evaluable CLI episodes, MEE was a complication in 37%, and MEE with a CLI was predicted by age, OM history, and environment. MEP was significantly more negative during CLI episodes, and the magnitude was predicted by age, race, and OM history. The average difference in MEE-CLI onsets was 1.2 +/- 4.0 days; approximately 32% of MEEs occurred prior to CLI onset and 17% on the same day as CLI onset. CONCLUSIONS:: CLIs adversely affect the middle ear-ambient pressure balance and are frequently associated with MEE episodes. The distribution in onsets between those events suggests that chemoprophylaxis of a child with a newly identified CLI to prevent MEE would have a low expected efficiency.

Requirements and Services for Metadata Management

Paolo Missier — 2008-03-07T10:27:19-00:00

IEEE Internet Computing, Vol. 11, No. 5. (September 2007), pp. 17-25.

Feta: A Light-Weight Architecture for User Oriented Semantic Service Discovery

Phillip Lord — 2008-05-15T09:27:31-00:00

The Semantic Web: Research and Applications (2005), pp. 17-31.

Semantic Web Services offer the possibility of highly flexible web service architectures, where new services can be quickly discovered, orchestrated and composed into workflows. Most existing work has, however, focused on complex service descriptions for automated composition. In this paper, we describe the requirements from the bioinformatics domain which demand technically simpler descriptions, involving the user community at all levels. We describe our data model and light-weight semantic discovery architecture. We explain how this fits in the larger architecture of the myGrid project, which overall enables interoperability and composition across, disparate, autonomous, third-party services. Our contention is that such light-weight service discovery provides a good fit for user requirements of bioinformatics and possibly other domains.

Architectural Patterns for the Semantic Grid

Ioannis Kotsiopoulos — 2008-05-15T07:39:40-00:00

Knowledge and Data Management in GRIDs (2007), pp. 119-134.

The Semantic Grid reference architecture, S-OGSA, includessemantic provisioning servicesthat are able to produce semantic annotations of Grid resources, andsemantically aware Grid servicesthat are able to exploit those annotations in various ways. In this paper we describe the dynamic aspects of S-OGSA by presenting the typical patterns of interaction among these services. A use case for a Grid meta-scheduling service is used to illustrate how the patterns are applied in practice.

Metadata Management in S-OGSA

Oscar Corcho — 2008-05-14T16:29:57-00:00

Computational Science ICCS 2007 (2007), pp. 712-719.

Metadata-intensive applications pose strong requirements for metadata management infrastructures, which need to deal with a large amount of distributed and dynamic metadata. Among the most relevant requirements we can cite those related to access control and authorisation, lifecycle management and notification, and distribution transparency. This paper discusses such requirements and proposes a systematic approach to deal with them in the context of S-OGSA.

e-Science and the Semantic Web: A Symbiotic Relationship

Carole Goble — 2008-05-14T16:00:35-00:00

Algorithmic Learning Theory (2006), pp. 12-12.

e-Science is scientific investigation performed through distributed global collaborations between scientists and their resources, and the computing infrastructure that enables this [4]. Scientific progress increasingly depends on pooling know-how and results; making connections between ideas, people, and data; and finding and reusing knowledge and resources generated by others in perhaps unintended ways. It is about harvesting and harnessing the collective intelligence of the scientific community. The Semantic Web is an extension of the current Web in which information is given well-defined meaning to facilitate sharing and reuse, better enabling computers and people to work in cooperation [1]. Applying the Semantic Web paradigm to e-Science [3] has the potential to bring significant benefits to scientific discovery [2]. We identify the benefits of lightweight and heavyweight approaches, based on our experiences in the Life Sciences.

myGrid and UTOPIA: An Integrated Approach to Enacting and Visualising in Silico Experiments in the Life Sciences

Steve Pettifer — 2008-05-14T15:22:47-00:00

Data Integration in the Life Sciences (2007), pp. 59-70.

In silico experiments have hitherto required ad hoc collections of scripts and programs to process and visualise biological data, consuming substantial amounts of time and effort to build, and leading to tools that are difficult to use, are architecturally fragile and scale poorly. With examples of the systemgapgaps applied to real biological problems, we describe two complimentary software frameworks that address this problem in a principled manner; Grid Taverna, a workflow design and enactment environment enabling coherent experiments to be built, and UTOPIA, a flexible visualisation system to aid in examining experimental results.

Grid metadata management: Requirements and architecture

O Corcho — 2008-05-14T15:16:29-00:00

Grid Computing, 2007 8th IEEE/ACM International Conference on (2007), pp. 97-104.

Metadata annotations of grid resources can potentially be used for a number of purposes, including accurate resource allocation to jobs, discovery of services, and precise retrieval of information resources. In order to realize this potential on a large scale, various aspects of metadata must be managed. These include uniform and secure access to distributed and independently maintained metadata repositories, as well as management of metadata lifecycle. In this paper we analyze these issues and present a service-oriented architecture for metadata management, called S-OGSA, that addresses them in a systematic way.

An overview of S-OGSA: A Reference Semantic Grid Architecture

Oscar Corcho — 2007-01-02T02:02:34-00:00

Web Semantics: Science, Services and Agents on the World Wide Web, Vol. 4, No. 2. (June 2006), pp. 102-115.

The Grid's vision, of sharing diverse resources in a flexible, coordinated and secure manner through dynamic formation and disbanding of virtual communities, strongly depends on metadata. Currently, Grid metadata is generated and used in an ad hoc fashion, much of it buried in the Grid middleware's code libraries and database schemas. This ad hoc expression and use of metadata causes chronic dependency on human intervention during the operation of Grid machinery, leading to systems which are brittle when faced with frequent syntactic changes in resource coordination and sharing protocols.The Semantic Grid is an extension of the Grid in which rich resource metadata is exposed and handled explicitly, and shared and managed via Grid protocols. The layering of an explicit semantic infrastructure over the Grid Infrastructure potentially leads to increased interoperability and greater flexibility.In recent years, several projects have embraced the Semantic Grid vision. However, the Semantic Grid lacks a Reference Architecture or any kind of systematic framework for designing Semantic Grid components or applications. The Open Grid Service Architecture (OGSA) aims to define a core set of capabilities and behaviours for Grid systems. We propose a Reference Architecture that extends OGSA to support the explicit handling of semantics, and defines the associated knowledge services to support a spectrum of service capabilities. Guided by a set of design principles, Semantic-OGSA (S-OGSA) defines a model, the capabilities and the mechanisms for the Semantic Grid.We conclude by highlighting the commonalities and differences that the proposed architecture has with respect to other Grid frameworks.

Recycling workflows and services through discovery and reuse: Research Articles

Chris Wroe — 2008-05-14T14:32:02-00:00

Concurr. Comput. : Pract. Exper., Vol. 19, No. 2. (February 2007), pp. 181-194.

The myGrid ontology: bioinformatics service discovery

K Wolstencroft — 2007-12-02T18:13:39-00:00

International Journal of Bioinformatics Resesearch and Applications, Vol. 3, No. 3. (2007), pp. 303-325.

myGrid supports in silico experiments in the life sciences, enabling the design and enactment of workflows as well as providing components to assist service discovery, data and metadata management. The myGrid ontology is one component in a larger semantic discovery framework for the identification of the highly distributed and heterogeneous bioinformatics services in the public domain. From an initial model of formal OWL-DL semantics throughout, we now adopt a spectrum of expressivity and reasoning for different tasks in service annotation and discovery. Here, we discuss the development and use of the myGrid ontology and our experiences in semantic service discovery.

Identification of innate immunity genes and pathways using a comparative genomics approach

Scott Alper — 2008-05-13T06:53:25-00:00

Proceedings of the National Academy of Sciences (7 May 2008), 0802405105.

To reveal regulators of innate immunity, we used RNAi assays to monitor the immune response when genes are inhibited in Caenorhabditis elegans and mouse macrophages. Genes that altered innate immune responsiveness in C. elegans were validated in murine macrophages, resulting in the discovery of 11 genes that regulate the innate immune response in both systems and the subsequent identification of a protein interaction network with a conserved role in innate immunity regulation. We confirmed the role of four of these 11 genes in antimicrobial gene regulation using available mutants in C. elegans. Several of these genes (acy-1, tub-2, and tbc-1) also regulate susceptibility to the pathogen Pseudomonas aeruginosa. These genes may prove critical to understanding host defense and represent potential therapeutic targets for infectious and immunological diseases. 10.1073/pnas.0802405105

Drought- and salt-tolerant plants result from overexpression of the AVP1 H+-pump

Roberto Gaxiola — 2008-05-07T09:29:43-00:00

Proceedings of the National Academy of Sciences, Vol. 98, No. 20. (25 September 2001), pp. 11444-11449.

Transgenic plants overexpressing the vacuolar H+-pyrophosphatase are much more resistant to high concentrations of NaCl and to water deprivation than the isogenic wild-type strains. These transgenic plants accumulate more Na+ and K+ in their leaf tissue than the wild type. Moreover, direct measurements on isolated vacuolar membrane vesicles derived from the AVP1 transgenic plants and from wild type demonstrate that the vesicles from the transgenic plants have enhanced cation uptake. The phenotypes of the AVP1 transgenic plants suggest that increasing the vacuolar proton gradient results in increased solute accumulation and water retention. Presumably, sequestration of cations in the vacuole reduces their toxic effects. Genetically engineered drought- and salt-tolerant plants could provide an avenue to the reclamation of farmlands lost to agriculture because of salinity and a lack of rainfall. 10.1073/pnas.191389398

Communicating evidence for participatory decision making.

RM Epstein — 2008-04-22T20:57:55-00:00

JAMA : the journal of the American Medical Association, Vol. 291, No. 19. (19 May 2004), pp. 2359-2366.

CONTEXT: Informed patients are more likely to actively participate in their care, make wiser decisions, come to a common understanding with their physicians, and adhere more fully to treatment; however, currently there are no evidence-based guidelines for discussing clinical evidence with patients in the process of making medical decisions. OBJECTIVE: To identify ways to communicate evidence that improve patient understanding, involvement in decisions, and outcomes. DATA SOURCES AND STUDY SELECTION: Systematic review of MEDLINE for the period 1966-2003 and review of reference lists of retrieved articles to identify original research dealing with communication between clinicians and patients and directly addressing methods of presenting clinical evidence to patients. DATA EXTRACTION: Two investigators and a research assistant screened 367 abstracts and 2 investigators reviewed 51 full-text articles, yielding 8 potentially relevant articles. DATA SYNTHESIS: Methods for communicating clinical evidence to patients include nonquantitative general terms, numerical translation of clinical evidence, graphical representations, and decision aids. Focus-group data suggest presenting options and/or equipoise before asking patients about preferred decision-making roles or formats for presenting details. Relative risk reductions may be misleading; absolute risk is preferred. Order of information presented and time-frame of outcomes can bias patient understanding. Limited evidence supports use of human stick figure graphics or faces for single probabilities and vertical bar graphs for comparative information. Less-educated and older patients preferred proportions to percentages and did not appreciate confidence intervals. Studies of decision aids rarely addressed patient-physician communication directly. No studies addressed clinical outcomes of discussions of clinical evidence. CONCLUSIONS: There is a paucity of evidence to guide how physicians can most effectively share clinical evidence with patients facing decisions; however, basing our recommendations largely on related studies and expert opinion, we describe means of accomplishing 5 communication tasks to address in framing and communicating clinical evidence: understanding the patient's (and family members') experience and expectations; building partnership; providing evidence, including a balanced discussion of uncertainties; presenting recommendations informed by clinical judgment and patient preferences; and checking for understanding and agreement.

Tuning genetic control through promoter engineering.

Hal Alper — 2005-08-29T22:29:37-00:00

Proc Natl Acad Sci U S A (25 August 2005)

Gene function is typically evaluated by sampling the continuum of gene expression at only a few discrete points corresponding to gene knockout or overexpression. We argue that this characterization is incomplete and present a library of engineered promoters of varying strengths obtained through mutagenesis of a constitutive promoter. A multifaceted characterization of the library, especially at the single-cell level to ensure homogeneity, permitted quantitative assessment correlating the effect of gene expression levels to improved growth and product formation phenotypes in Escherichia coli. Integration of these promoters into the chromosome can allow for a quantitative accurate assessment of genetic control. To this end, we used the characterized library of promoters to assess the impact of phosphoenolpyruvate carboxylase levels on growth yield and deoxy-xylulose-P synthase levels on lycopene production. The multifaceted characterization of promoter strength enabled identification of optimal expression levels for ppc and dxs, which maximized the desired phenotype. Additionally, in a strain preengineered to produce lycopene, the response to deoxy-xylulose-P synthase levels was linear at all levels tested, indicative of a rate-limiting step, unlike the parental strain, which exhibited an optimum expression level, illustrating that optimal gene expression levels are variable and dependent on the genetic background of the strain. This promoter library concept is illustrated as being generalizable to eukaryotic organisms (Saccharomyces cerevisiae) and thus constitutes an integral platform for functional genomics, synthetic biology, and metabolic engineering endeavors.

Engineering yeast transcription machinery for improved ethanol tolerance and production.

H Alper — 2008-03-24T01:46:10-00:00

Science, Vol. 314, No. 5805. (8 December 2006), pp. 1565-1568.

Global transcription machinery engineering (gTME) is an approach for reprogramming gene transcription to elicit cellular phenotypes important for technological applications. Here we show the application of gTME to Saccharomyces cerevisiae for improved glucose/ethanol tolerance, a key trait for many biofuels programs. Mutagenesis of the transcription factor Spt15p and selection led to dominant mutations that conferred increased tolerance and more efficient glucose conversion to ethanol. The desired phenotype results from the combined effect of three separate mutations in the SPT15 gene [serine substituted for phenylalanine (Phe(177)Ser) and, similarly, Tyr(195)His, and Lys(218)Arg]. Thus, gTME can provide a route to complex phenotypes that are not readily accessible by traditional methods.

Physicians Answer More Clinical Questions and Change Clinical Decisions More Often With Synthesized Evidence: A Randomized Trial in Primary Care

Brian Alper — 2007-11-15T19:20:14-00:00

Ann Fam Med, Vol. 3, No. 6. (1 November 2005), pp. 507-513.

PURPOSE Clinicians need evidence in a format that rapidly answers their questions. DynaMed is a database of synthesized evidence. We investigated whether primary care clinicians would answer more clinical questions, change clinical decision making, and alter search time using DynaMed in addition to their usual information sources. METHODS Fifty-two primary care clinicians naive to DynaMed searched for answers to 698 of their own clinical questions using the Internet. On a per-question basis, participants were randomized to have access to DynaMed (A) or not (N) in addition to their usual information sources. Outcomes included proportions of questions answered, proportions of questions with answers that changed clinical decision making, and median search times. The statistical approach of per-participant analyses of clinicians who asked questions in both A and N states was decided before data collection. RESULTS Among 46 clinicians in per-participant analyses, 23 (50%) answered a greater proportion of questions during A than N, and 13 (28.3%) answered more questions during N than A (P = .05). Finding answers that changed clinical decision making occurred more often during A (25 clinicians, 54.3%) than during N (13 clinicians, 28.3%) (P = .01). Search times did not differ significantly. Overall, participants found answers for 263 (75.8%) of 347 A questions and 250 (71.2%) of 351 N questions. Answers changed clinical decision making for 224 (64.6%) of the A questions and 209 (59.5%) of the N questions. CONCLUSIONS Using DynaMed, primary care clinicians answered more questions and changed clinical decisions more often, without increasing overall search time. Synthesizing results of systematic evidence surveillance is a feasible method for meeting clinical information needs in primary care. 10.1370/afm.370

What Is A Newtonian System? The Failure Of Energy Conservation And Determinism In Supertasks

JS Alper — 2007-08-14T13:44:08-00:00

Synthese, Vol. 124, No. 2. (2000), pp. 281-293.

Supertasks recently discussed in the literature purport to display a failure ofenergy conservation and determinism in Newtonian mechanics. We debatewhether these supertasks are admissible as Newtonian systems, with Earmanand Norton defending the affirmative and Alper and Bridger the negative.

Knowledge Discovery for Biology with Taverna

Carole Goble — 2007-10-19T13:17:51-00:00

Semantic Web (2007), pp. 355-395.

Life Science research has extended beyond in vivo and in vitro bench-bound science to incorporate in silico knowledge discovery, using resources that have been developed over time by different teams for different purposes and in different forms. The myGrid project has developed a set of software components and a workbench, Taverna, for building, running and sharing workflows that link third party bioinformatics services, such as databases, analytic tools and applications. Intelligently discovering prior services, workflow or data is aided by a Semantic Web of annotations, as is the building of the workflows themselves. Metadata associated with the workflow experiments, the provenance of the data outcomes and the record of the experimental process need to be flexible and extensible. Semantic Web metadata technologies would seem to be well-suited to building a Semantic Web of provenance. We have the potential to integrate and aggregate workflow outcomes, and reason over provenance logs to identify new experimental insights, and to build and export a Semantic Web of experiments that contributes to Knowledge Discovery for Taverna users and for the scientific community as a whole.

Hemodynamic shear stress and its role in atherosclerosis.

AM Malek — 2005-12-01T01:15:28-00:00

JAMA, Vol. 282, No. 21. (1 December 1999), pp. 2035-2042.

Atherosclerosis, the leading cause of death in the developed world and nearly the leading cause in the developing world, is associated with systemic risk factors including hypertension, smoking, hyperlipidemia, and diabetes mellitus, among others. Nonetheless, atherosclerosis remains a geometrically focal disease, preferentially affecting the outer edges of vessel bifurcations. In these predisposed areas, hemodynamic shear stress, the frictional force acting on the endothelial cell surface as a result of blood flow, is weaker than in protected regions. Studies have identified hemodynamic shear stress as an important determinant of endothelial function and phenotype. Arterial-level shear stress (>15 dyne/cm2) induces endothelial quiescence and an atheroprotective gene expression profile, while low shear stress (<4 dyne/cm2), which is prevalent at atherosclerosis-prone sites, stimulates an atherogenic phenotype. The functional regulation of the endothelium by local hemodynamic shear stress provides a model for understanding the focal propensity of atherosclerosis in the setting of systemic factors and may help guide future therapeutic strategies.

Mutational spectrum of MYO15A: the large N-terminal extension of myosin XVA is required for hearing

Nevra Nal — 2007-09-07T08:52:37-00:00

Human Mutation, Vol. 28, No. 10. (2007), pp. 1014-1019.

Human MYO15A is located on chromosome 17p11.2, has 66 exons and encodes unconventional myosin XVA. Recessive mutations of MYO15A are associated with profound, nonsyndromic hearing loss DFNB3 in humans, and deafness and circling behavior in shaker 2 mice. In the inner ear, this motor protein is necessary for the development of hair cell stereocilia, which are actin-filled projections on the apical surface and the site of mechanotransduction of sound. The longest isoform of myosin XVA has 3,530 amino acid residues. Two isoform classes of MYO15A are distinguished by the presence or absence of 1,203 residues preceding the motor domain encoded by alternatively-spliced exon 2. It is not known whether this large N-terminal extension of myosin XVA is functionally necessary for hearing. We ascertained approximately 600 consanguineous families segregating hereditary hearing loss as a recessive trait and found evidence of linkage of markers at the DFNB3 locus to hearing loss in 38 of these families ascertained in Pakistan (n=30), India (n=6), and Turkey (n=2). In this study, we describe 16 novel recessive mutations of MYO15A associated with severe to profound hearing loss segregating in 20 of these DFNB3-linked families. Importantly, two homozygous mutant alleles - c.3313G>T (p.E1105X) and c.3334delG (p.G1112fsX1124) of MYO15A - located in exon 2 are associated with severe to profound hearing loss segregating in two families. These data demonstrate that isoform 1, containing the large N-terminal extension, is also necessary for normal hearing. Hum Mutat 28(10), 1014-1019, 2007. Published 2007 Wiley-Liss, Inc.

MDCT Angiography of the Renal Arteries in Patients with Atherosclerotic Renal Artery Stenosis: Implications for Renal Artery Stenting with Distal Protection

Adam Talenfeld — 2007-08-03T07:56:42-00:00

Am. J. Roentgenol., Vol. 188, No. 6. (1 June 2007), pp. 1652-1658.

OBJECTIVE. Use of distal protection in renal artery stenting entails overcoming challenges unique to renal artery anatomy. We used 3D image reconstruction to review high-spatial-resolution MDCT angiographic data to better characterize the anatomy of stenotic renal arteries. MATERIALS AND METHODS. A total of 218 abdominal MDCT angiograms from a single tertiary care referral center were reviewed. The subjects were 108 patients who had 127 arteries with more than 50% ostial atherosclerotic renal artery stenosis. Vessel analysis software was used to measure renal artery length, cross-sectional area, and maximum diameter. Differences between mean values for women and men and for left and right renal arteries were measured with a two-tailed Student's t test. RESULTS. Significant differences for men and women were found in average maximum cross-sectional area distal to the point of stenosis (0.3 +/- 0.19 vs 0.23 +/- 0.09 cm2, p = 0.006) and the corresponding maximum diameter (6.9 +/- 1.7 vs 6.1 +/- 1.1 cm2, p = 0.003). Average lengths of the main renal artery did not differ significantly for men and women. Differences for the left and right main renal arteries were found in minimum area (i.e., area of maximum stenosis, 0.08 +/- 0.04 vs 0.06 +/- 0.03 cm2, p = 0.03), area proximal to the bifurcation (0.26 +/- 0.11 cm2 vs 0.23 +/- 0.07 cm2, p = 0.02), and length (38.5 +/- 12.6 vs 48.7 +/- 16.2 mm, p = 0.0002). CONCLUSION. Significant anatomic differences exist between the left and right renal arteries, between the renal arteries in men and those in women, and from one person to the next. Many of these differences are relevant to the design and use of distal protection devices in stenting of the renal arteries. 10.2214/AJR.06.1255

Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets

Hal Alper — 2005-05-06T02:44:45-00:00

Nature Biotechnology, Vol. 23, No. 5. (10 April 2005), pp. 612-616.

Discrimination as a consequence of genetic testing.

PR Billings — 2007-02-20T15:36:49-00:00

Am J Hum Genet, Vol. 50, No. 3. (March 1992), pp. 476-482.

Genetic discrimination refers to discrimination directed against an individual or family based solely on an apparent or perceived genetic variation from the "normal" human genotype. We describe here the results of a case history study designed to assess whether or not genetic discrimination exists. Using the above definition of genetic discrimination and applying stringent criteria for case selection, we find that genetic discrimination exists and is manifested in many social institutions, especially in the health and life insurance industries. Stigmatization, and denial of services or entitlements to individuals who have a genetic diagnosis but who are asymptomatic or who will never become significantly impaired, is noted. Follow-up comprehensive studies on the significance and varieties of genetic discrimination are needed. In order to avoid creating a new social underclass based on genetic discrimination (the "asymptomatic ill"), existing and future genetic testing or screening programs need review by medical, scientific, legal, and social policy experts, as well as the public, and may require modification.

Individual, family, and societal dimensions of genetic discrimination: a case study analysis.

LN Geller — 2006-10-27T12:53:46-00:00

Sci Eng Ethics, Vol. 2, No. 1. (January 1996), pp. 71-88.

Identifying functionally important mutations from phenotypically diverse sequence data.

K Jensen — 2007-02-04T11:05:04-00:00

Appl Environ Microbiol, Vol. 72, No. 5. (May 2006), pp. 3696-3701.

Here we present a simple statistical method to determine the phenotypic contribution of a single mutation from libraries of mutants with diverse phenotypes in which each mutant contains a multitude of mutations. The central premise of this method is that, given M phenotypic classes, mutations that do not affect the phenotype should partition among the M classes according to a multinomial distribution. Deviations from this distribution are indicative of a link between specific mutations and phenotypes. We suggest that this method will aid the engineering of functional nucleic acids, proteins, and other biomolecules by uncovering target sites for rational mutagenesis. As a proof of the principle, we show how the method can be used to deduce the individual effects of mutations in a set of 69 P(L)-lambda promoter variants. Each of these promoters was generated by error-prone PCR and incorporated numerous mutations. The activity of the promoters was assayed using flow cytometry to measure the fluorescence of a green fluorescent protein reporter gene. Our analysis of the sequences of these mutants revealed seven positions having a statistically significant correlation with promoter activity. Using site-directed mutagenesis, we constructed point mutations for several sites, both statistically significant and insignificant, and combinations of these sites. Our results show that the statistical method correctly elucidated the phenotypic manifestations of these mutations. We suggest that this method may be useful for expediting directed evolution experiments by allowing both desired and undesired mutations to be identified and incorporated between rounds of mutagenesis.

Genetic discrimination and the law.

MR Natowicz — 2006-10-27T13:05:16-00:00

Am J Hum Genet, Vol. 50, No. 3. (March 1992), pp. 465-475.

The use of genetic tests can lead to genetic discrimination, discrimination based solely on the nature of an individual's genotype. Instances of the discriminatory uses of genetic tests by employers and insurance companies have already been reported. The recently enacted Americans with Disabilities Act of 1990 (ADA), together with other federal and state laws, can be used to combat some forms of this discrimination. In this article we define and characterize genetic discrimination, discuss the applicability of the various relevant federal and state laws, including the ADA, in the areas of employment and insurance discrimination, explore the limitations of these laws, and, finally, suggest some means of overcoming these limitations.

Reply to Hook and Lowden: the definition and implications of genetic discrimination.

PR Billings — 2006-10-27T12:54:57-00:00

Am J Hum Genet, Vol. 51, No. 4. (October 1992), pp. 903-905.

Genetic discrimination and screening for hemochromatosis.

JS Alper — 2006-10-27T12:52:36-00:00

J Public Health Policy, Vol. 15, No. 3. (1994), pp. 345-358.

Recent advances in tests for the genotype for hemochromatosis and suggestions that the tests be used in mass screening programs for the disease raise the possibility of a large increase in the incidence of discrimination against people who are found to be homozygous for hemochromatosis. This paper presents cases of genetic discrimination drawn from a study of discrimination against people with a variety of genetic conditions. The cases discussed here involve employment and several types of insurance discrimination against people diagnosed with hemochromatosis who either are currently asymptomatic or whose condition is controlled by means of phlebotomies. There is no justification for these types of discrimination since people with controlled hemochromatosis suffer no excess mortality or morbidity. Our study suggests that genetic discrimination is already a serious problem and that any proposed screening program for hemochromatosis or other genetic condition must consider and attempt to mitigate its effects.

The exceptionally small size of the scrapie agent.

T Alper — 2006-07-03T22:46:27-00:00

Biochem Biophys Res Commun, Vol. 22, No. 3. (3 February 1966), pp. 278-284.

Friedreich's ataxia.

G Alper — 2006-06-29T11:45:25-00:00

Pediatr Neurol, Vol. 28, No. 5. (May 2003), pp. 335-341.

Friedreich's ataxia, the most common hereditary ataxia, is caused by expansion of a GAA triplet located within the first intron of the frataxin gene on chromosome 9q13. There is a clear correlation between size of the expanded repeat and severity of the phenotype. Frataxin is a mitochondrial protein that plays a role in iron homeostasis. Deficiency of frataxin results in mitochondrial iron accumulation, defects in specific mitochondrial enzymes, enhanced sensitivity to oxidative stress, and eventually free-radical mediated cell death. Friedreich's ataxia is considered a nuclear encoded mitochondrial disease.This review discusses the major and rapid progress made in Friedreich's ataxia from gene mapping and identification of the gene to pathogenesis and encouraging therapeutic implications.

Genes, free will, and criminal responsibility.

JS Alper — 2006-05-15T16:41:24-00:00

Soc Sci Med, Vol. 46, No. 12. (June 1998), pp. 1599-1611.

Advances in human genetics have raised the possibility that genetic mechanisms can explain various aspects of human behavior. It has been suggested that such genetic explanations would tend to diminish responsibility for one's actions. In this paper I argue that the genetic approach adds little to our understanding of free will, determinism, and responsibility. Even though human beings are material systems obeying the laws of the physical and biological sciences, their behavior may still be unpredictable and essentially undetermined. Moreover, with few exceptions, behavior influenced by genes is no more deterministic than is behavior influenced by the environment. An analysis of the genetic and environmental influences and the complex interactions between them reveals a certain symmetry between genetic and environmental explanations of behavior. Consequently, any argument concerning the relevance of a genetic excuse to a criminal defense will be equally applicable to an environmental excuse.

Experiential curriculum improves medical students' ability to answer clinical questions using the internet.

BS Alper — 2005-11-09T18:16:14-00:00

Fam Med, Vol. 37, No. 8. (September 2005), pp. 565-569.

BACKGROUND AND OBJECTIVES: Teaching about evidence-based medicine (EBM) is widespread, yet physicians still use rapid references preferentially over EBM techniques such as literature searching and appraisal of original research. The Internet now provides rapid access to preappraised evidence. We provided clinically integrated teaching of using the Internet to answer clinical questions for third-year medical students and assessed the change in their search skills. METHODS: The curriculum included two 90-minute computer lab sessions with teaching of search skills related to clinical questions. Immediately before the first and after the second session, students recorded sites searched, time needed for searching, and answers found for three standardized questions. Pretest and posttest questions were matched and reversed with each block. RESULTS: Eighty-six students completed pretests and posttests. For two questions about conventional medical care, posttest answer quality was significantly higher, and posttest search times were significantly shorter, by 1.6 minutes for question 1 (mean pretest search time 6.3 minutes, mean posttest search time 4.7 minutes) and 1.9 minutes for question 2 (mean pretest search time 8 minutes, mean posttest search time 6.1 minutes). For a question about herbal medicine, results were similar, but there were smaller differences that did not reach statistical significance. Students used or found significantly fewer sites on the posttest than on the pretest to find answers for all three question types (absolute difference=0.3 sites for each question). CONCLUSIONS Introducing students to useful Web sites, practicing answering clinical questions, and integrating this process with clinical rotation experiences can reduce the effort that students need to find answers and improve the quality of answers they find.