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PubMed2004

Identification of drought-inducible genes and differentially expressed sequence tags in barley.

Drought limits cereal yields in several regions of the world and plant water status plays an important role in tolerance to drought. To investigate and understand the genetic and physiological basis of drought tolerance in barley, differentially expressed sequence tags (dESTs) and candidate genes for the drought response were mapped in a population of 167 F8 recombinant inbred lines derived from a cross between "Tadmor" (drought tolerant) and "Er/Apm" (adapted only to specific dry environments). One hundred sequenced probes from two cDNA libraries previously constructed from drought-stressed barley (Hordeum vulgare L., var. Tokak) plants and 12 candidate genes were surveyed for polymorphism, and 33 loci were added to a previously published map. Composite interval mapping was used to identify quantitative trait loci (QTL) associated with drought tolerance including leaf relative water content, leaf osmotic potential, osmotic potential at full turgor, water-soluble carbohydrate concentration, osmotic adjustment, and carbon isotope discrimination. A total of 68 QTLs with a limit of detection score > or =2.5 were detected for the traits evaluated under two water treatments and the two traits calculated from both treatments. The number of QTLs identified for each trait varied from one to 12, indicating that the genome contains multiple genes affecting different traits. Two candidate genes and ten differentially expressed sequences were associated with QTLs for drought tolerance traits.

Chromosome Mapping↗
PubMed2007

Characterization of the prokaryotic diversity in cold saline perennial springs of the Canadian high Arctic.

The springs at Gypsum Hill and Colour Peak on Axel Heiberg Island in the Canadian Arctic originate from deep salt aquifers and are among the few known examples of cold springs in thick permafrost on Earth. The springs discharge cold anoxic brines (7.5 to 15.8% salts), with a mean oxidoreduction potential of -325 mV, and contain high concentrations of sulfate and sulfide. We surveyed the microbial diversity in the sediments of seven springs by denaturing gradient gel electrophoresis (DGGE) and analyzing clone libraries of 16S rRNA genes amplified with Bacteria and Archaea-specific primers. Dendrogram analysis of the DGGE banding patterns divided the springs into two clusters based on their geographic origin. Bacterial 16S rRNA clone sequences from the Gypsum Hill library (spring GH-4) were classified into seven phyla (Actinobacteria, Bacteroidetes, Firmicutes, Gemmatimonadetes, Proteobacteria, Spirochaetes, and Verrucomicrobia); Deltaproteobacteria and Gammaproteobacteria sequences represented half of the clone library. Sequences related to Proteobacteria (82%), Firmicutes (9%), and Bacteroidetes (6%) constituted 97% of the bacterial clone library from Colour Peak (spring CP-1). Most GH-4 archaeal clone sequences (79%) were related to the Crenarchaeota while half of the CP-1 sequences were related to orders Halobacteriales and Methanosarcinales of the Euryarchaeota. Sequences related to the sulfur-oxidizing bacterium Thiomicrospira psychrophila dominated both the GH-4 (19%) and CP-1 (45%) bacterial libraries, and 56 to 76% of the bacterial sequences were from potential sulfur-metabolizing bacteria. These results suggest that the utilization and cycling of sulfur compounds may play a major role in the energy production and maintenance of microbial communities in these unique, cold environments.

Archaea↗
PubMed1991

DNA sequences for the specific detection of Cryptosporidium parvum by the polymerase chain reaction.

The objective of this project was to construct specific and sensitive molecular probes and amplification primers for Cryptosporidium parvum that could be used in diagnosis, retrospective tissue studies, and in epidemiologic surveys. Whole genomic DNA was extracted from oocysts of C. parvum purified from human and bovine feces. A genomic library was constructed in plasmid pUC18 and propagated in Escherichia coli DH5 alpha. Transformants were screened by colony hybridization and autoradiography. The 2.3-kilobase segment in plasmid pHC1, a clone specific for C. parvum, was sequenced by the Sanger method. Computer analysis gave a G+C content of 35%. A 400-base region (bases 470-870) was selected as an amplification target because it contained a unique restriction endonuclease site that could serve as a useful marker. Primers of 26 nucleotides each were synthesized. Sensitive and specific amplification of the target sequence was demonstrated both by ethidium bromide staining of agarose and acrylamide gels, and by hybridization with chemiluminescence-labeled synthetic oligonucleotide probes.

Animals↗
PubMed2002

Preschool and school age activities: comparison of urban and suburban populations.

The objective of this study was to compare urban and suburban preschool and school age activities. A prospective survey using a convenience sample was conducted at one urban and one suburban primary care pediatric office. Questionnaires were completed for 66 urban preschool children, 70 suburban preschool children, 57 urban school age children and 61 suburban school age children during the school year. Also, questionniaires were completed for 63 suburban school age children during the summer. The suburban preschool children spent more time outdoors, were read to more frequently, visited the library more frequently and more often attended summer camp. The suburban school age children spent more time outdoors, more frequently participated in a community sport league and more often attended summer camp. The urban school age children watched more television or videos. During the summer, suburban school age children spent more time outdoors, while during the school year, suburban school age children used the library more frequently. Important differences exist between the activities of urban and suburban children in two practices in the New York metropolitan area. Pediatricians caring for urban children may have an important opportunity to promote participation in sports and educational activities.

Camping↗
PubMed2000

Preliminary profile of the Cryptosporidium parvum genome: an expressed sequence tag and genome survey sequence analysis.

Cryptosporidium parvum is a protozoan enteropathogen that infects humans and animals and causes a pronounced diarrheal disease that can be life-threatening in immunocompromised hosts. No specific chemo- or immunotherapies exist to treat cryptosporidiosis and little molecular information is available to guide development of such therapies. To accelerate gene discovery and identify genes encoding potential drug and vaccine targets we constructed sporozoite cDNA and genomic DNA sequencing libraries from the Iowa isolate of C. parvum and determined approximately 2000 sequence tags by single-pass sequencing of random clones. Together, the 567 expressed sequence tags (ESTs) and 1507 genome survey sequences (GSSs) totaled one megabase (1 mb) of unique genomic sequence indicating that approximately 10% of the 10.4 mb C. parvum genome has been sequence tagged in this gene discovery expedition. The tags were used to search the public nucleic acid and protein databases via BLAST analyses, and 180 ESTs (32%) and 277 GSSs (18%) exhibited similarity with database sequences at smallest sum probabilities P(N)< or =10(-8). Some tags encoded proteins with clear therapeutic potential including S-adenosylhomocysteine hydrolase, histone deacetylase, polyketide/fatty-acid synthases, various cyclophilins, thrombospondin-related cysteine-rich protein and ATP-binding-cassette transporters. Several anonymous ESTs encoded proteins predicted to contain signal peptides or multiple transmembrane spanning segments suggesting they were destined for membrane-bound compartments, the cell surface or extracellular secretion. One-hundred four simple sequence repeats were identified within the nonredundant sequence tag collection with (TAA)(> or =6)/(TTA)(> or =6) and (TA)(> or = 10)/(AT)(> or =10 ) being the most prevalent, occurring 40 and 15 times, respectively. Various cellular RNAs and their genes were also identified including the small and large ribosomal RNAs, five tRNAs, the U2 small nuclear RNA, and the small and large virus-like, double-stranded RNAs. This investigation has demonstrated that survey sequencing is an efficient procedure for gene discovery and genome characterization and has identified and sequence tagged many C. parvum genes encoding potential therapeutic targets.

Amino Acid Sequence↗
PubMed1988

A study of benefits offered volunteer clinical faculty.

The School of Health Related Professions (HRP) at State University of New York at Buffalo offers its volunteer clinical faculty (VCF) a number of benefits and privileges. These VCF are professionals who train students but do not receive monetary compensation for doing so. A study was conducted to determine what benefits/privileges are valued and used most, the impact and use of tuition waivers (TWs), and other benefits the VCF would desire. A survey was sent to 383 VCF, and 233 (61%) responded. The results showed that VCF valued, in order of priority: TWs, University library privileges, faculty parking, photocopying service, clinical faculty awards, use of recreational facilities, and faculty discounts. The data revealed that 42% of the respondents had used TWs, and the study demonstrated that TWs promote the University's graduate programs. The data supported the contention that TWs play a significant role in recruiting and rewarding VCF. As a result, University financial support for TWs was not eliminated. The feasibility and cost of implementing other incentives for VCF participation, suggested by the VCF, will be investigated by the School of HRP in the future.

Allied Health Personnel↗
PubMed2002

Designing a curriculum on Internet health resources for deaf high school students.

PURPOSE: This paper examines the integration of instruction about quality health resources on the Internet into the health curriculum of a specialized high school for students with hearing disabilities. SETTING/PARTICIPANTS/RESOURCES: The Health Sciences Library System (HSLS) at the University of Pittsburgh has formed a partnership with the Western Pennsylvania School for the Deaf (WPSD). BRIEF DESCRIPTION: This project was partially funded through a subcontract with the National Library of Medicine. As one component of its Health Information for the Public project, HSLS formed a partnership with the WPSD. This partnership allowed for a librarian to provide instruction to health education and learning center teachers and students at WPSD about health resources on the Internet. This paper describes the planning process, curriculum development, and challenges encountered. These challenges include student knowledge of English as a second language, the need for a sign language interpreter, students' third-to-fourth-grade reading levels, and the need for appropriate visual presentations to accompany the audio counterpart. RESULTS/OUTCOME: The partnership formed between HSLS and WPSD improved deaf high school students' ability to locate quality health information on the Internet. EVALUATION METHOD: A pre-class survey and post-class survey were used to determine the impact of the instruction.

Adolescent↗
PubMed1997

Library and information services to support the education and development of nurses: the management of co-operation and change--a clash of two cultures?

This paper reports on the findings of research conducted by the Department of Information and Library Management and the Information Services Department at the University of Northumbria at Newcastle on behalf of the LINC Health Panel. It aims to investigate the organization and funding of library and information services to the nursing profession since the move of nurse education into higher education. The paper focuses on the lack of co-operation and communication between the National Health Service and higher education cultures in the provision of services to nurses. A brief review of the literature includes the views of experts in the field on library and information services and education for nurses as they are now, and ideas for possible developments for the future. This is followed by a description of the main research findings and the five key issues identified by information professionals in a questionnaire survey as vital for future consideration and action. Finally, the conclusions drawn from the findings have been developed into recommendations for the direction of the future discussion, research and action which is needed to further improve library and information services for all nurses.

Education, Nursing, Continuing↗
PubMed2006

Semirational design of Jun-Fos coiled coils with increased affinity: Universal implications for leucine zipper prediction and design.

Activator protein-1 (AP-1) is a crucial transcription factor implicated in numerous cancers. For this reason, nine homologues of the AP-1 leucine zipper region have been characterized: Fos (c-Fos, FosB, Fra1, and Fra2), Jun (c-Jun, JunB, and JunD), and semirational library-designed winning peptides FosW and JunW. The latter two were designed to specifically target c-Fos or c-Jun. They have been identified by using protein-fragment complementation assays combined with growth competition. This assay removes nonspecific, unstable, and protease susceptible library members from the pool, leaving winners with excellent drug potential. Thermal melts of all 45 possible dimeric interactions have been surveyed, with the FosW-c-Jun complex displaying a melting temperature (T(m)) of 63 degrees C, compared to only 16 degrees C for wild-type c-Fos-c-Jun interaction. This impressive 70,000-fold K(D) decrease is largely due to optimized core packing, alpha-helical propensity, and electrostatics. Contrastingly, due to a poor c-Fos core, c-Fos-JunW dimerizes with lower affinity. However the T(m) far exceeds wild-type c-Fos-c-Jun and averaged JunW and c-Fos, indicating a preference over either homodimer. Finally, and with wider implications, we have compiled a method for predicting interaction of parallel, dimeric coiled coils, using our T(m) data as a training set, and applying it to 59 bZIP proteins previously reported. Our algorithm, unlike others to date, accounts for helix propensity, which is found to be integral in coiled coil stability. Indeed, in applying the algorithm to these 59(2) bZIP interactions, we were able to correctly identify 92% of all strong interactions and 92% of all noninteracting pairs.

Amino Acid Sequence↗
PubMed2004

Impact of an evidence-based medicine curriculum on medical students' attitudes and skills.

PURPOSE: This evaluation study sought to assess the impact of an evidence-based medicine (EBM) course on students' self-perception of EBM skills, determine their use of EBM skills, and measure their performance in applying EBM skills in a simulated case scenario. METHODS: Pre- and post-surveys and skills tests were developed to measure students' attitudes toward and proficiency in EBM skills. Third-year students completed the voluntary survey and skills test at the beginning and completion of a twelve-week clerkship in internal medicine (IM) co-taught by medical and library faculty. Data were analyzed using the Mann-Whitney U test for a two-tailed test. RESULTS: A statistically significant increase was found in the students' self-assessment of skills. Students reported using the journal literature significantly more frequently during the clerkship than before, although textbooks remained their number one resource. A majority of students reported frequent use of EBM skills during the clerkship. Statistically significant improvement in student performance was also found on the posttest, although the level of improvement was more modest than that found on the post-surveys. CONCLUSION: The introduction of EBM skills to students during a clinical clerkship provides students an opportunity to practice EBM skills and reinforces the use of evidence in making patient-care decisions.

Clinical Clerkship↗
PubMed2005

Development of a multi-target screening analysis for 301 drugs using a QTrap liquid chromatography/tandem mass spectrometry system and automated library searching.

A new multi-target screening (MTS) procedure for drugs in blood and urine for toxicological analysis has been developed using a hybrid triple-quadrupole linear ion trap mass spectrometer (QTrap) for the fast detection and identification of 301 forensically important drugs, e.g. tranquilizers (benzodiazepines), hypnotics, drugs of abuse (opiates, cocaine, amphetamines, cannabinoids), antidepressants, neuroleptics, and some cardiac drugs, in one single liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis. Samples were extracted either with liquid-liquid extraction or solid-phase extraction. A multiple reaction monitoring (MRM) as survey scan and an enhanced product ion (EPI) scan as dependent scan were performed in an information-dependent acquisition (IDA) experiment. Finally, drug identification was carried out by library search with a newly developed MS/MS library based on EPI spectra at three different collision energies in positive mode. The advantage of this newly developed method is the possibility to detect and identify 301 drugs in one single LC/MS/MS run.

Automation↗
PubMed2003

[History of arthroplasty for finger joints].

The history of joint prostheses does not begin before the end of the 19th century. Prior to that, resection arthroplasty of functionally impaired joints was attempted with results sometimes allowing flexion or straightening of a previously immobile joint. These operative methods developed into interposition arthroplasty, which in its turn represents the predecessor of joint implantation. Lower extremity joint implantation is nowadays a well established and rewarding strong hold of orthopaedic and trauma surgeons. Due to certain obstacles specific to the hand, a similar success story for prostheses of the finger joints is still awaited. Although there have been many different designs of finger joint prostheses over the last 50 years, there is still no implant which offers satisfactory and reliable long-term results such as those that we have become accustomed to expect from lower extremity joint allo-arthroplasty. Only recently are we able to speak of an acknowledged standard of PIP-joint allo-arthroplasty. Using the library of the German historical museum of orthopaedic surgery as well as the relevant sources of international medical literature, a survey of the development of finger joint implantation is made.

Arthroplasty↗
PubMed1995

Identification and expression cloning of a leptin receptor, OB-R.

The ob gene product, leptin, is an important circulating signal for the regulation of body weight. To identify high affinity leptin-binding sites, we generated a series of leptin-alkaline phosphatase (AP) fusion proteins as well as [125I]leptin. After a binding survey of cell lines and tissues, we identified leptin-binding sites in the mouse choroid plexus. A cDNA expression library was prepared from mouse choroid plexus and screened with a leptin-AP fusion protein to identify a leptin receptor (OB-R). OB-R is a single membrane-spanning receptor most related to the gp130 signal-transducing component of the IL-6 receptor, the G-CSF receptor, and the LIF receptor. OB-R mRNA is expressed not only in choroid plexus, but also in several other tissues, including hypothalamus. Genetic mapping of the gene encoding OB-R shows that it is within the 5.1 cM interval of mouse chromosome 4 that contains the db locus.

Amino Acid Sequence↗
PubMed2006

Gene expression patterns in Euglena gracilis: insights into the cellular response to environmental stress.

To better understand Euglena gracilis gene expression under different stress conditions (Chromium, Streptomycin or darkness), we undertook a survey of the E. gracilis transcriptome by cDNA sequencing and microarray analysis. First, we constructed a non-normalized cDNA library from the E. gracilis UTEX strain and sequenced a total of 1000 cDNAs. Six hundred and ten of these ESTs were similar to either Plantae or Protistae genes (e-value<e(-10)). Second, microarrays were built by spotting all the ESTs onto mirror slides. Microarray expression analysis indicated that 90 out of those 610 ESTs changed their expression level in response to different stress treatments (p<0.05). In addition, we detected 10 ESTs that changed expression levels irrespective of the tested stress. These may be considered as part of a larger set of stress-related genes in E. gracilis. Finally, we identified 23 unknown ESTs (U-ESTs) following the expression profiles of these putative stress-related genes suggesting that they could be related to the cellular mechanism of stress response.

Animals↗
PubMed2003

Expressed sequence tag analysis of Sarcoptes scabiei.

Sarcoptes scabiei is an important parasitic mite in both man and animals. Little is known about the molecular interactions between this pathogen and its host. This is in part explained by the paucity of mite-derived material, including antigens. To extend the knowledge of the molecular repertoire in S. scabiei, we have performed a gene survey by an expressed sequence tag (EST) analysis. A total of 1020 ESTs were generated from an S. scabiei cDNA library. The average sequence read was 510 bp after editing and the overall sequencing success was 89%. Clustering of the sequences resulted in 76 clusters, comprising 36% of the ESTs. Sequence similarity searches showed that almost half of the S. scabiei ESTs could be assigned a putative identity. Many of these transcripts shared similarity with genes involved in basic metabolism and cellular organization. In the data set we also identified several proteases and other types of potential allergens implicated in various disease mechanisms. A relatively large fraction of the ESTs coded for different proteins carrying protease inhibitor-like domains. The clones with no similarity to previously identified genes constituted 11% of our transcripts. The EST data generated in this study will be a valuable resource in further studies of the biology of S. scabiei and in the identification of genes that can serve as potential targets in the control of the parasite.

Animals↗
PubMed1995

Implications of the UNNDERPIN study at St George's Hospital, Morpeth, Northumberland.

UNNDERPIN (University of Northumbria at Newcastle DEvelopment of and Research into the Provision of Information to Nurses and nurse educators) was an 8-month research project at St George's Hospital, Morpeth, Northumberland. The general aim of the project has been to undertake an examination of library and information services in a climate of change where user information needs are changing and demanding changed services to be provided to meet those needs in order to support patient care and clinical developments. The paper gives an overview of the project describing its background and presenting a summary of the research findings, conclusions and wider implications of the work.

Community Health Services↗
PubMed2000

The information needs of doctors-in-training: case study from the Cairns Library, University of Oxford.

The objective of this study was to find out more about the information needs of doctors-in-training and to identify their preferred sources of information. The methodology included interviews with consultants and administrators, a focus group discussion with library staff and a postal questionnaire sent to 347 doctors-in-training (there was a 43% return). The shortcomings of a questionnaire primarily composed of closed questions were addressed by the inclusion of one-to-one interviews which offered the opportunity for more in-depth commentary on specific issues highlighted in the questionnaire. Results indicated the frequency with which various types of information sources were consulted and how this related to the 'ease of access' of each information source. There was also the opportunity to comment on future information needs. It was clear from the interviews as well as comments made on the questionnaire that the two most important requirements for doctors-in-training were 'more time to find and obtain information' and 'better access to information sources when and where they are needed'. The results, although not surprising, included specific suggestions that have been used for the strategic planning of the library service to deliver the best possible support to users within the current framework of evidence-based medicine.

Education, Medical↗