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PubMed2004

Uncultured soil bacteria are a reservoir of new antibiotic resistance genes.

Antibiotic resistance genes are typically isolated by cloning from cultured bacteria or by polymerase chain reaction (PCR) amplification from environmental samples. These methods do not access the potential reservoir of undiscovered antibiotic resistance genes harboured by soil bacteria because most soil bacteria are not cultured readily, and PCR detection of antibiotic resistance genes depends on primers that are based on known genes. To explore this reservoir, we isolated DNA directly from soil samples, cloned the DNA and selected for clones that expressed antibiotic resistance in Escherichia coli. We constructed four libraries that collectively contain 4.1 gigabases of cloned soil DNA. From these and two previously reported libraries, we identified nine clones expressing resistance to aminoglycoside antibiotics and one expressing tetracycline resistance. Based on the predicted amino acid sequences of the resistance genes, the resistance mechanisms include efflux of tetracycline and inactivation of aminoglycoside antibiotics by phosphorylation and acetylation. With one exception, all the sequences are considerably different from previously reported sequences. The results indicate that soil bacteria are a reservoir of antibiotic resistance genes with greater genetic diversity than previously accounted for, and that the diversity can be surveyed by a culture-independent method.

Acetyltransferases↗
PubMed2004

A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans.

Plant-parasitic nematodes are important and cosmopolitan pathogens of crops. Here, we describe the generation and analysis of 1928 expressed sequence tags (ESTs) of a splice-leader 1 (SL1) library from mixed life stages of the root-lesion nematode Pratylenchus penetrans. The ESTs were grouped into 420 clusters and classified by function using the Gene Ontology (GO) hierarchy and the Kyoto KEGG database. Approximately 80% of all translated clusters show homology to Caenorhabditis elegans proteins, and 37% of the C. elegans gene homologs had confirmed phenotypes as assessed by RNA interference tests. Use of an SL1-PCR approach, while ensuring the cloning of the 5' ends of mRNAs, has demonstrated bias toward short transcripts. Putative nematode-specific and Pratylenchus -specific genes were identified, and their implications for nematode control strategies are discussed.

Animals↗
PubMed2000

Analysis of expressed sequence tags of retinal pigment epithelium: cystatin C is an abundant transcript.

In order to identify genes that are expressed in the retinal pigment epithelium (RPE), randomly chosen clones of a cDNA library of cultured human foetal RPE cells were analyzed by sequencing. Of 164 informative expressed sequence tags (ESTs), 88 matched the sequences of 74 genes for proteins of known or presumed function. Approximately a third of these represented genes with involvement in gene/protein expression, with a major subcategory concerned with protein turnover. In particular, the gene coding for precursor cystatin C was represented by 3 independent ESTs, and plaque hybridization estimated the frequency of cystatin C clones in the library to be 1.3%. Cystatin C mRNA in cultured RPE cells was confirmed by Northern blotting and by reverse transcription polymerase chain reaction (RT-PCR) with identification of the cystatin C sequence as the product of the reaction. The survey also revealed 25 novel human sequences representing genes that are active in RPE. One of these was localized near a recently identified, new autosomal recessive retinitis pigmentosa locus. In conclusion, the findings specifically demonstrate the unexpected presence of cystatin C mRNA at fairly high abundance in cultured human RPE cells, and, more generally, serve as a model study establishing the usefulness of the EST approach for further characterizing the molecular basis of the activities of the RPE.

Cells, Cultured↗
PubMed2004

Phylogenetic screening of ribosomal RNA gene-containing clones in Bacterial Artificial Chromosome (BAC) libraries from different depths in Monterey Bay.

Marine picoplankton are central mediators of many oceanic biogeochemical processes, but much of their biology and ecology remains ill defined. One approach to better defining these environmentally significant microbes involves the acquisition of genomic data that can provide information about genome content, metabolic capabilities, and population variability in picoplankton assemblages. Previously, we constructed and phylogenetically screened a Bacterial Artificial Chromosome (BAC) library from surface water picoplankton of Monterey Bay. To further describe niche partitioning, metabolic variability, and population structure in coastal picoplankton populations, we constructed and compared several picoplankton BAC libraries recovered from different depths in Monterey Bay. To facilitate library screening, a rapid technique was developed (ITS-LH-PCR) to identify and quantify ribosomal RNA (rRNA) gene-containing BAC clones in BAC libraries. The approach exploited natural length variations in the internal transcribed spacer (ITS) located between SSU and LSU rRNA genes, as well as the presence and location of tRNA-alanine coding genes within the ITS. The correspondence between ITS-LH-PCR fragment sizes and 16S rRNA gene phylogenies facilitated rapid identification of rRNA genes in BAC clones without requiring direct DNA sequencing. Using this approach, 35 phylogenetic groups (previously identified by cultivation or PCR-based rRNA gene surveys) were detected and quantified among the BAC clones. Since the probability of recovering chimeric rRNA gene sequences in large insert BAC clones was low, we used these sequences to identify potentially chimeric sequences from previous PCR amplified clones deposited in public databases. Full-length SSU rRNA gene sequences from picoplankton BAC libraries, cultivated bacterioplankton, and nonchimeric RNA genes were then used to refine phylogenetic analyses of planktonic marine gamma Proteobacteria, Roseobacter, and Rhodospirillales species.

Bacteria↗
PubMed1992

Information excess in medicine. Overview, relevance to dermatology, and strategies for coping.

BACKGROUND: The amount of biomedical information contained in scientific journals has grown to the point that complete coverage of this material is impossible. The number of articles and journals being published has been growing at an exponential rate since 1750. Thirty-four thousand references from 4000 journals are added each month to the National Library of Medicine MEDLINE database from among the more than 100,000 scientific journals now published. This increase in scientific literature reflects not greater productivity but simply a larger number of scientists at work. Most articles written are eventually published in the medical literature, but a large number of scientific articles are of less than optimal quality, and most scientific articles that are published are never cited. Articles of higher quality and usefulness cluster in a few journals that enjoy great use in medical libraries and high scores on bibliometric scores such as the Science Citation Index. OBSERVATIONS: To assess the reading habits of dermatologic trainees and evaluate how they cope with this information excess, a survey was distributed to 36 residents in three training programs. The average number of medical journal reading hours per month was 17; the number of hours devoted to reading issues of the Archives of Dermatology, the Journal of the American Academy of Dermatology, and the Journal of Investigative Dermatology were 3.2, 5.0, and 1.4, respectively; and the average resident read seven peer-reviewed journals, two to four dermatologic tabloids, and four peer-reviewed medical journals. CONCLUSIONS: Critically and consistently reading a limited number of high-quality peer-reviewed journals as well as taking advantage of information available through computer networks and bibliographic and full-text databases is the best approach to coping with the volume of medical literature. Translating this information into a change in attitude and modification of physician behavior is best accomplished when local role models incorporate new ideas into their practice and teaching. Modifications that would, in fact, bring about truly useful changes, such as decreasing the number of new publications, melding journals already present into smaller numbers of publications rather than instituting new journals, altering the "publish-or-perish" rules, and writing more comprehensive articles rather than multiple small contributions, all await fundamental alterations in long-accepted policies in medicine.

Dermatology↗
PubMed2000

Growth and determinants of access in patient e-mail and Internet use.

OBJECTIVES: To measure the rate of access to and use of the Internet and e-mail, to determine sociodemographic predictors of access, and to measure the change in Internet and e-mail access over a 1-year interval. DESIGN: Survey study. Comparison of data with those from a similar survey from 1998. SETTING: Emergency department of a large urban pediatric teaching hospital. PARTICIPANTS: Primary caretakers of pediatric patients or the patients themselves if aged 16 years or older. MAIN OUTCOME MEASURES: Use of and access to the Internet or e-mail. RESULTS: We surveyed 214 individuals: 72.8% use or have access to the Internet, e-mail, or both, an increase from 52.2% in the 1998 survey (P<.001), and 48.5% regularly use the Internet or e-mail, compared with 43.1% in 1998 (P = .32). Outside the home, access is primarily at work (52.2%), schools (8.9%), public libraries (11.5%), and friends' and relatives' houses (16.7%). Internet use and access are linearly correlated with income (r = 0.43; P<.001). White patients are more likely to have access (odds ratio, 2.6; 95% confidence interval, 1.3-5.4; P<.001) than black or Asian patients, whereas those of Hispanic ethnicity are less likely to have access (odds ratio, 0.20; 95% confidence interval, 0.09-0.43; P<.001). However, after adjustment for race and Hispanic ethnicity, only income was a significant predictor of family access to the Internet and e-mail. CONCLUSIONS: During the past year, many patients have gained access to the Internet and e-mail, although rates of regular use have remained steady. This access is often from outside the home. Furthermore, access is directly related to income and is unevenly distributed across racial and ethnic groups.

Adolescent↗
PubMed2003

Cochrane neonatal systematic reviews: a survey of the evidence for neonatal therapies.

A survey is reported of 113 systematic reviews of therapies in neonatology, based on 559 eligible randomized trials in total. These reviews were prepared by the CNRG and were published in the Cochrane Library, Issue 3,2001. The median number of included trials per review was 3 (range 0 to 32) and participants 207 (range 0 to 5460). Among 90 reviews with a categorical primary outcome, the median number of outcome events per review was 54 (range 1 to 1284). Among reviews finding a statistically significant benefit of treatment, the effect size was large (median relative risk 0.55, range 0.09 to 0.93). Reviews of surfactant for prevention and treatment of respiratory distress syndrome were able to detect moderate-sized treatment effects (median relative risk 0.85) because of the large number and size of trials in this field. Among many reviews finding no evidence of treatment effect, large and potentially important benefits or harms could not be excluded. Most CNRG reviews were current. There is a continuing need to prepare systematic review of therapies not yet covered and to keep an increasing number of reviews up-to-date.

Bibliometrics↗
PubMed1991

Evolution of the ferric enterobactin receptor in gram-negative bacteria.

Using sodium dodecyl sulfate-polyacrylamide gel electrophoresis of iron-deficient and replete cell envelopes, 59Fe-siderophore uptake studies, and Western immunoblots and cytofluorimetric analyses with monoclonal antibodies (MAbs), we surveyed a panel of gram-negative bacteria to identify outer membrane proteins that are structurally related to the Escherichia coli K-12 ferric enterobactin receptor, FepA. Antibodies within the panel identified FepA epitopes that are conserved among the majority of the bacteria tested, as well as epitopes present in only a few of the strains. In general, epitopes of FepA that are buried in the outer membrane bilayer were more conserved among gram-negative bacteria than epitopes that are exposed on the bacterial cell surface. The surface topology and tertiary structure of FepA are quite similar in E. coli and Shigella flexneri but differ in Salmonella typhimurium. Of the 18 different genera tested, 94% of the bacteria transported ferric enterobactin, including members of the previously unrecognized genera Citrobacter, Edwardsiella, Enterobacter, Haemophilus, Hafnia, Morganella, Neisseria, Proteus, Providencia, Serratia, and Yersinia. The ferric enterobactin receptor contains at least one buried epitope, recognized by MAb 2 (C. K. Murphy, V. I. Kalve, and P. E. Klebba, J. Bacteriol. 172:2736-2746, 1990), that is conserved within the structure of an iron-regulated cell envelope protein in all the bacteria that we have surveyed. With MAb 2, we identified and determined the Mr of cell envelope antigens that are immunologically related to E. coli FepA in all the gram-negative bacteria tested. Collectively, the library of anti-FepA MAbs showed unique patterns of reactivity with the different bacteria, allowing identification and discrimination of species within the following gram-negative genera: Aeromonas, Citrobacter, Edwardsiella, Enterobacter, Escherichia, Haemophilus, Hafnia, Klebsiella, Morganella, Neisseria, Proteus, Providencia, Pseudomonas, Salmonella, Serratia, Shigella, Vibrio, and Yersinia.

Amino Acid Sequence↗
PubMed2006

The transformation of spinal curvature into spinal deformity: pathological processes and implications for treatment.

BACKGROUND: This review summarizes what is known about the pathological processes (e.g. structural and functional changes), by which spinal curvatures develop and evolve into spinal deformities. METHODS: Comprehensive review of articles (English language only) published on 'scoliosis,' whose content yielded data on the pathological changes associated with spinal curvatures. Medline, Science Citation Index and other searches yielded > 10,000 titles each of which was surveyed for content related to 'pathology' and related terms such as 'etiology,' 'inheritance,' 'pathomechanism,' 'signs and symptoms.' Additional resources included all books published on 'scoliosis' and available through the Arizona Health Sciences Library, Interlibrary Loan, or through direct contact with the authors or publishers. RESULTS: A lateral curvature of the spine-'scoliosis'-can develop in association with postural imbalance due to genetic defects and injury as well as pain and scarring from trauma or surgery. Irrespective of the factor that triggers its appearance, a sustained postural imbalance can result, over time, in establishment of a state of continuous asymmetric loading relative to the spinal axis. Recent studies support the longstanding hypothesis that spinal deformity results directly from such postural imbalance, irrespective of the primary trigger, because the dynamics of growth within vertebrae are altered by continuous asymmetric mechanical loading. These data suggest that, as long as growth potential remains, evolution of a spinal curvature into a spinal deformity can be prevented by reversing the state of continuous asymmetric loading. CONCLUSION: Spinal curvatures can routinely be diagnosed in early stages, before pathological deformity of the vertebral elements is induced in response to asymmetric loading. Current clinical approaches involve 'watching and waiting' while mild reversible spinal curvatures develop into spinal deformities with potential to cause symptoms throughout life. Research to define patient-specific mechanics of spinal loading may allow quantification of a critical threshold at which curvature establishment and progression become inevitable, and thereby yield strategies to prevent development of spinal deformity.Even within the normal spine there is considerable flexibility with the possibility of producing many types of curves that can be altered during the course of normal movements. To create these curves during normal movement simply requires an imbalance of forces along the spine and, extending this concept a little further, a scoliotic curve is produced simply by a small but sustained imbalance of forces along the spine. In fact I would argue that no matter what you believe to be the cause of AIS, ultimately the problem can be reduced to the production of an imbalance of forces along the spine 1.

Journal Article↗
PubMed1986

The Nordic contribution to the English language twin literature.

This project was inspired by the extensive contribution of Nordic researchers to the English language twin literature. The purpose of the study was to compile a source bibliography of twin literature written at Nordic institutions. The bibliography compiled as a supplement for this paper provides as complete a survey as is possible to obtain in the United States. Our search began with a Medline Computer data base. To make our survey more complete, we cross-referenced and added to this using the Index Medicus, the National Institute of Mental Health Bibliography, Excerpta Medica, specific article references, references provided by Nordic university libraries and Gedda's Estudio dei Gemelli. The full bibliography of 313 references is available at no cost from the Center for the study of multiple Birth, Rm. 476, 333 E. Superior, Chicago, Ill. 60611, U.S.A.

Bibliographies as Topic↗
PubMed2004

An online learning course in Ergonomics.

For the past two years, the Department of Occupational Therapy at the University of Haifa has offered an online course to third year occupational therapists on the topic of Ergonomics for Health Care Professionals. The development and implementation of this course was funded by the Israeli Ministry of Education. Unique teaching materials, developed and uploaded to the University's server via "High Learn", included interactive and self-directed documents containing graphics, animations, and video clips. Extensive use was made of the discussion forum and survey tools, and students submitted all assignments online. For the final topic, an expert in ergonomics from Boston University delivered a lecture via two-way videoconferencing. The course site included comprehensive library listings in which all bibliographic materials were made available online. Students accessed course materials at the University in a computer classroom and at home via modem. In an accompanying research study, the frequency of student usage of the various online tools was tracked and extensive data were collected via questionnaires documenting students' demographic background, preferred learning style, prior usage of technology, satisfaction with the course and academic achievement. This paper focuses on the results of the research study that examined how the students responded to and coped with teaching material presented and accessed in this format.

Adult↗
PubMed2006

Information literacy and library attitudes of occupational therapy students.

Information literacy, often described as a person's ability to effectively find and evaluate answers to questions using a variety of information resources, is of particular importance to health care workers. This paper presents the results of an information literacy survey presented to occupational therapy (OT) students at Thomas Jefferson University during a series of required class activities. Also described are the authors' activities with the faculty and courses at Jefferson. The survey was made available to first-, second-, third-, and fourth-year occupational therapy students along with nursing students and pharmacy students. The survey is designed to identify research habits, skills, and preferences. Results confirm some commonly held perceptions about searching skills of young adults and an interesting dichotomy in students' learning habits. The paper concludes with a discussion of recommendations to OT faculty and librarians on how to improve information literacy education. The survey can be obtained by contacting the authors.

Adult↗
PubMed2003

The role of the academic medical center library in training public librarians.

PURPOSE: This project enhanced access to and awareness of health information resources on the part of public libraries in western Pennsylvania. SETTING/PARTICIPANTS/RESOURCES: The Health Sciences Library System (HSLS), University of Pittsburgh, conducted a needs assessment and offered a series of workshops to 298 public librarians. BRIEF DESCRIPTION: The National Library of Medicine-funded project "Access to Electronic Health Information" at the HSLS, University of Pittsburgh, provided Internet health information training to public libraries and librarians in sixteen counties in western Pennsylvania. Through this project, this academic medical center library identified the challenges for public librarians in providing health-related reference service, developed a training program to address those challenges, and evaluated the impact of this training on public librarians' ability to provide health information. RESULTS/OUTCOME: The HSLS experience indicates academic medical center libraries can have a positive impact on their communities by providing health information instruction to public librarians. The success of this project--demonstrated by the number of participants, positive course evaluations, increased comfort level with health-related reference questions, and increased use of MEDLINEplus and other quality information resources--has been a catalyst for continuation of this programming, not only for public librarians but also for the public in general. EVALUATION METHOD: A training needs assessment, course evaluation, and impact training survey were used in developing the curriculum and evaluating the impact of this training on public librarians' professional activities.

Academic Medical Centers↗
PubMed2004

EST-based analysis of gene expression in the porcine brain.

Since pig is an important livestock species worldwide, its gene expression has been investigated intensively, but rarely in brain. In order to study gene expression profiles in the pig central nervous system, we sequenced and analyzed 43,122 high-quality 5' end expressed sequence tags (ESTs) from porcine cerebellum, cortex cerebrum, and brain stem cDNA libraries, involving several different prenatal and postnatal developmental stages. The initial ESTs were assembled into 16,101 clusters and compared to protein and nucleic acid databases in GenBank. Of these sequences, 30.6% clusters matched protein databases and represented function known sequences; 75.1% had significant hits to nucleic acid databases and partial represented known function; 73.3% matched known porcine ESTs; and 21.5% had no matches to any known sequences in GenBank. We used the categories defined by the Gene Ontology to survey gene expression in the porcine brain.

Animals↗
PubMed1992

Electronic data interchange in hospital materiel management.

The survey findings reported here support the continued trend toward increasing application of computer linkages in hospital operations. A majority of the hospitals surveyed already had some sort of computer linkages with their suppliers, possibly an EOE system. There were strong indications of expanding computer linkages to other health care institutions, financial institutions, business partners (i.e., insurance companies), purchasing groups, supporting agencies (i.e., libraries, research laboratories, and counseling agencies), electronic mail, and patient billing. Private hospitals, especially nonprofit hospitals, were more aggressive in the implementation of computer linkages. The initial costs of electronic linkage systems seemed to be affordable, or well justified, as indicated by the relatively large number of medium-size hospitals already linked electronically to other institutions. Top management attention was positively related to the implementation of computer linkages to suppliers but played a lesser role in establishing other types of linkages. The overall optimism concerning future expansion of computer linkages suggests an increasingly important role for electronic linkages in materiel management.

Alabama↗
PubMed2004

Serological identification of endothelial antigens predominantly recognized in Kawasaki disease patients by recombinant expression cloning.

We showed IgG immune response against endothelial antigens in sera obtained from convalescent Kawasaki disease (KD) patients after recovery from the disease during the follow-up period using serological analysis of recombinant cDNA expression library (SEREX) methodology. We identified 46 antigens represented by 69 clones by immunoscreening of a cDNA expression library from tumor necrosis factor-alpha (TNFalpha) treated human umbilical vein endothelial cells (HUVEC) with sera from 4 KD patients. They included ubiquitin pathway proteins, transcriptional factors, signal transduction molecules, metabolic enzymes, cytoskeletal proteins, an adhesion molecule, and a cell cycle protein. By serological survey using phage plaque assay, sera from 5 non-KD patients were rarely reactive with the antigens. Among the antigens, tropomyosin was most frequently isolated (18 of 69 clones). Seventeen of the 18 clones were identified using KD3 serum. The second most frequently isolated antigen was also a cytoskeletal protein, called Tplastin (3 of 69 clones).

Antibodies↗
PubMed1986

The secondary structure of salt-extracted ribosomal proteins from Escherichia coli as studied by circular dichroic spectroscopy.

Ribosomal proteins from Escherichia coli MRE600 have been obtained by a new, mild purification procedure. This involves extraction of the subunits with salt followed by chromatographic fractionation in the presence of salt. The use of urea or other denaturing agents and conditions is avoided. A survey of the secondary structure of the 30 S and 50 S proteins, as observed by circular dichroic spectroscopy, is presented. The spectra have been analysed by a new procedure which uses a library of 16 circular dichroic spectra of proteins with a known three-dimensional structure. This method provides a more reliable analysis, especially of the contribution from beta-sheet. The results show that most of the 30 S proteins have a high alpha-helix content, whereas the 50 S proteins are more diverse. The latter group shows a larger contribution from beta-sheet. The data presented here are compared with those already published for a number of proteins which were, with one exception, prepared in the presence of urea. In most cases we find higher alpha-helix and beta-sheet values for the salt-extracted proteins than for the corresponding urea-treated proteins. In those cases, however, where special care was taken to renature the urea-treated proteins agreement is found to within the expected experimental error. The results show that salt-extracted ribosomal proteins have a well-defined secondary structure with a relatively small contribution from unordered structure.

Circular Dichroism↗