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PubMed1995

A collection of tri- and tetranucleotide repeat markers used to generate high quality, high resolution human genome-wide linkage maps.

We report a collection of tri- and tetranucleotide repeat sequence polymorphic markers used to construct genome-wide human linkage maps. Using a strategy of marker selection to create libraries highly enriched for the presence of specific tandem repeat elements, we have developed over 2000 high heterozygosity, easy-to-use tri- and tetranucleotide short tandem repeat polymorphisms (STRPs). To date, over 1300 of these markers have been genotyped on the CEPH reference families. Additional STRPs were assigned to chromosomes using human monochromosomal somatic cell hybrids. The linkage maps constructed with these markers have been integrated with other CEPH genotypes into a comprehensive high density linkage map. These STRPs have been shown to be robust for genotyping in a variety of laboratories using a variety of methods. The high quality of these STRPs makes them ideal candidates for use in genome-wide linkage searches. The integration of these markers with physical mapping reagents and other genetic markers will create a resource for moving from genome-wide linkage searches to rapid sublocalization of disease loci.

Base Sequence↗

PubMed1998

Internet access in the libraries of the National Network of Libraries of Medicine.

As the National Library of Medicine expands access to its products and services by making them available on the Internet, more accurate information about current and future access in medical libraries is needed. The National Network Office of the National Library of Medicine conducted a survey of all network member libraries to determine the extent of connectivity and the barriers preventing 100% connectivity. Respondents called a toll-free number and, using interactive voice technology, answered questions concerning Internet access in their library. Seventy-eight percent of the network member libraries responded. Four percent of academic libraries, 27% of hospital libraries, and 10% of "other" libraries reported that they were not connected. Computer cost, lack of in-house expertise, and lack of management support were the highest ranked barriers to connecting. The National Library of Medicine and the Regional Medical Libraries will use information from this survey to develop strategies to help all member libraries achieve full connectivity.

Computer Communication Networks↗

PubMed2002

Exploring ligand-DNA space using type IIS restriction enzymes.

Investigating ligand-DNA interactions using type IIS restriction enzymes (IISRE) as footprinting reagents is reviewed and contemplated. Ligand binding at a IISRE's cleavage but not sequence recognition site protects DNA from strand scission. This spatial arrangement has been exploited in the development of qualitative (combinatorial) and quantitative ligand-DNA investigative methods collectively termed Type IIS Restriction Enzyme Footprinting (cIISREF and qIISREF respectively). In cIISREF, the consensus binding sequence of a ligand is sought by using a IISRE to segregate combinatorial library members that are bound by ligand from those that are not. A PCR is performed following the segregation step to enrich the library in ligand binding (i.e. uncut) sequences. It might be possible that diversities approaching 10(30) unique sequences could be simultaneously searched using this homogeneous and biologically relevant method. For qIISREF, a ligand-DNA equilibrium constant is measured by quantifying the amounts of target and control DNA IISRE cleavage products as a function of ligand concentration. The control sequence is engineered to not bind ligand. Along with illustrating these methods by reviewing published works, current concerns and future prospects for IISREF are discussed.

Base Sequence↗

PubMed1997

User support for a library-managed online database search service: the BMA Library free MEDLINE service.

This paper discusses user support in the context of a library-managed online database search service. Experience is drawn from the British Medical Association (BMA) Library's Free MEDLINE Service. More than 9,600 BMA members, who are largely unfamiliar with computer communications and database searching, have registered as users of the service. User support has played a significant role in the development of the service and has comprised four main aspects: an information pack, a help desk, online help, and MEDLINE courses. The paper includes an analysis of help desk usage statistics collected from January 1996 through June 1996, and highlights other relevant research. Plans for further service enhancements and their implications in terms of future user support are discussed.

Computer User Training↗

PubMed2003

Assessing the information needs of psychiatric residents.

OBJECTIVE: Staff at the Western Psychiatric Institute and Clinic Library conducted a survey of residents and fellows to determine their informational needs and their interest in an orientation to the library's resources. METHODS: A brief questionnaire was distributed to the facility's 59 psychiatric residents and fellows to determine their awareness of 12 library resources and services (e.g., online databases and database searches conducted by librarians), their interest in an orientation to these resources and services, their self-rated level of skill in using them, whether they would attend training sessions, and, if so, when the best time for such sessions might be. RESULTS: A total of 28 questionnaires were returned. Respondents favored an orientation (82%) and indicated that a 1-hour session would be appropriate, although the best time to hold it was less clear. Fifty percent or more were aware of each of the six resources they would be most likely to use in their work. Nearly all had used MEDLINE, but most respondents had not used most of the other resources and services. CONCLUSIONS: Instruction on the use of information resources can be useful to psychiatric residents and fellows. On the basis of the survey results, a library orientation session was developed to address the information needs indicated by respondents and to enhance their skills in retrieving pertinent literature for clinical care and research. A post-orientation questionnaire indicated that the session was useful and well received.

Adult↗

PubMed2026

Establishment of a CRISPR-Cas9 Library for Indica Rice and Identification of OsOPR5 (LOC_Os06g11210) as a Regulator of Root Architecture.

Functional characterization of a large number of rice genes remains a major challenge despite the availability of genome sequences and large-scale transcriptomic datasets. CRISPR-Cas9 library is a powerful approach for high-throughput targeted mutagenesis; however, its application in indica rice cultivars remains limited due to low transformation and regeneration efficiencies. In this study, we developed a CRISPR-Cas9 library targeting 12,000 rice genes and evaluated its utility for functional genomics in the indica cultivar MTU-1010. Sanger sequencing and NGS analysis of the plasmid library revealed high sgRNA coverage and more than 80% accuracy. Transformation of the developed library into the indica cultivar MTU-1010 resulted in a high target editing efficiency, with 90% of analyzed transgenic plants carrying mutations at the intended target site. Functional analysis of one homozygous mutant identified a previously uncharacterized role for OsOPR5 (LOC_Os06g11210), a member of the 12-oxophytodienoate reductase family in root architecture. The opr5 mutants exhibited significant reductions in lateral root number, seminal and crown root number, and root length, demonstrating that OsOPR5 positively regulates root system architecture in rice. Notably, endogenous jasmonic acid (JA) and JA-isoleucine levels were not significantly altered in the mutant, suggesting potential functional specialization or redundancy among rice OPR family members for JA accumulation. The root system architecture is a key determinant of water and nutrient acquisition; our results suggest that OsOPR5 may play an important role in adaptation under adverse environmental conditions. Collectively, this study establishes an efficient genome-editing platform for indica rice and identifies OsOPR5 as a novel regulator of root development.

Oryza↗

PubMed1995

Using scientific evidence to improve information practice.

The recent policy statement of the Medical Library Association (MLA) takes the position that scientific evidence is the basis for improving the quality of library and information sciences now and in the future. Research activity is seen as the foundation of an evolving knowledge base for the profession--a knowledge base that will set health sciences librarians apart from others in an increasingly competitive world of information service providers. The statement represents the culmination of many years of activity by association members, during which the role of research in health information practice has been debated. Over a similar time period, the quality movement, with its increasing demand for the collection and use of data, has been growing. Developments such as total quality management (TQM) and continuous quality improvement (CQI) reinforce the centrality of research with its increasing demand for the collection and use of data, has been growing. Developments such as total quality management (TQM) and continuous quality improvement (CQI) reinforce the centrality of research and its relationship to efficient and effective information practice as envisioned in the MLA policy statement.

Artificial Intelligence↗

PubMed2026

Identification of genes promoting fitness of a plant-associated Salmonella Choleraesuis strain on alfalfa sprouts during cold storage.

Consumption of sprouted seeds, such as alfalfa sprouts, has increased in recent years due to their nutritional value and antioxidant content. However, these products have repeatedly been implicated in outbreaks of foodborne pathogens, including Salmonella enterica. Although host-adapted Salmonella serovars are less frequently associated with foodborne illness, infections caused by these serovars often result in invasive and severe outcomes, highlighting the importance of understanding their persistence in food production systems. Moreover, the variability among Salmonella serovars requires characterization beyond the most prevalent types to support the development of precision food safety strategies effective across the diversity of serovars capable of contaminating fresh produce. Here, a plant-internalized Salmonella Choleraesuis strain was used as a model to investigate persistence mechanisms on alfalfa sprouts. A bar-coded transposon mutant library comprising approximately 33,000 unique insertions was generated, along with a collection of individual insertion mutants. These resources were used to identify genetic determinants contributing to strain fitness on sprouts under abusive cold storage (8°C) simulating commercial shelf-life environments. Genome-wide analyses identified negative selection for mutants with insertions in eda, fabF, lpp1_2, pnp, stpA, SCHChr_03621, and two intergenic regions. Competition assays confirmed fitness defects associated with eda, encoding a key enzyme of the Entner-Doudoroff pathway; mnmG, encoding a tRNA modification enzyme involved in translational fidelity; and fabF, involved in fatty acid biogenesis. These findings provide a genome-wide perspective on mechanisms enabling persistence on sprouts of a plant-associated, host-adapted Salmonella strain during cold storage and inform risk assessment and intervention design within precision food safety frameworks.IMPORTANCEFood safety strategies are frequently based on knowledge derived from well-studied, epidemiologically relevant Salmonella serovars, yet many less frequent types still pose a risk to consumers and may contaminate fresh produce. Different Salmonella serovars may vary in the relative contribution of persistence mechanisms. Recognizing these differences is essential for improving precision food safety efforts, particularly for foods such as sprouts that are repeatedly linked to outbreaks. This study highlights that less-studied serovars can rely on both shared survival strategies and unique traits that might otherwise not be captured by current control approaches. By demonstrating that strain diversity influences persistence on fresh produce, this work supports the development of precision food safety strategies that address a broader spectrum of Salmonella, thereby improving risk assessment and helping to better protect public health.

food safety↗

PubMed1996

Parallel Processing in Genome Mapping and Sequencing

Conventional genome mapping and sequencing involves the analysis and processing of individual samples and pieces of experimental data. Although these methods work, it is quite clear that more efficient and less expensive methods are needed. Our top down physical mapping experiments have focused on the parallel processing of information from multiple samples at one time. This approach has aided the construction of genomic restriction maps and allowed us to assess the degree of large-scale conservation across wide regions of the human genome. The principles of parallel processing were applied in top down experiments that ordered an overlapping cosmid library from the 14-Mb Schizosaccharomyces pombe genome. This approach produced an eight-fold increase in efficiency in clone ordering over similar efforts. Recently, we have developed an enhanced sequencing by hybridization protocol that allows DNA sequence information to be collected on a large number of samples at once. Our current research focuses on applying parallel processing principles to make genome-wide comparisons between pairs of samples for analyzing disease states.

Journal Article↗

PubMed2001

The NIEHS Xenopus maternal EST project: interim analysis of the first 13,879 ESTs from unfertilized eggs.

The sequencing of expressed sequence tags (ESTs) from Xenopus laevis has lagged behind efforts on many other common experimental organisms and man, partly because of the pseudotetraploid nature of the Xenopus genome. Nonetheless, large collections of Xenopus ESTs would be useful in gene discovery, oligonucleotide-based knockout studies, gene chip analyses of normal and perturbed development, mapping studies in the related diploid frog X. tropicalis, and for other reasons. We have created a normalized library of cDNAs from unfertilized Xenopus eggs. These cells contain all of the information necessary for the first several cell divisions in the early embryo, as well as much of the information needed for embryonic pattern formation and cell fate determination. To date, we have successfully sequenced 13,879 ESTs out of 16,607 attempts (83.6% success rate), with an average sequence read length of 508 bp. Using a fragment assembly program, these ESTs were assembled into 8,985 'contigs' comprised of up to 11 ESTs each. When these contigs were used to search publicly available databases, 46.2% bore no relationship to protein or DNA sequences in the database at the significance level of 1e-6. Examination of a sample of 100 of the assembled contigs revealed that most ( approximately 87%) were comprised of two apparent allelic variants. Expression profiles of 16 of the most prominent contigs showed that 12 exhibited some degree of zygotic expression. These findings have implications for sequence-specific applications for Xenopus ESTs, particularly the use of allele-specific oligonucleotides for knockout studies, differential hybridization techniques such as gene chip analysis, and the establishment of accurate nomenclature and databases for this species.

Alleles↗

PubMed1983

The Foundation. The occupational therapy library: a professional resource.

For the first time, much of the significant literature on occupational therapy has been gathered in one place so that clinicians, students, and scholars can use the collection for study, research, or browsing. The initial efforts have provided a rich resource on the history and evaluation of occupational therapy. Occupational therapy practitioners, educators, and researchers are encouraged to make use of library resources and to support the continued development of the library through donations of old and new materials. Interested persons may write or call the Occupational Therapy Library through the Association address or telephone number.

Foundations↗

PubMed2002

Development of new transformation-competent artificial chromosome vectors and rice genomic libraries for efficient gene cloning.

The transformation-competent artificial chromosome vector (TAC) system has been shown to be very useful for efficient gene isolation in Arabidopsis thaliana (Proc. Natl. Acad. Sci. USA 96 (1998) 6535). To adapt the vector system for gene isolation in crops, two new TAC vectors and rice genomic libraries were developed. The new vectors pYLTAC17 and pYLTAC27 use the Bar gene and Hpt gene driven by the rice Act1 promoter as the plant selectable markers, respectively, and are suitable for transformation of rice and other grasses. Two representative genomic libraries (I and II) of an Indica rice variety Minghui63, a fertility restorer line for hybrid rice, were constructed with pYLTAC17 using different size classes of partially digested DNA fragments. Library I and library II consisted of 34,560 and 1.2 x 10(5) clones, with average insert sizes of approximately 77 and 39 kb, respectively. The genome coverage of the libraries I and II was estimated to be about 5 and 11 haploid genome equivalents, respectively. Clones of the library I were stored individually in ninety 384-well plates, and those of the library II were collected as bulked pools each containing 30-50 clones and stored in eight 384-well plates. A number of probes were used to hybridize high-density colony filters of the library I prepared by an improved replicating method and each detected 2-9 positive clones. A method for rapid screening of the library II by pooled colony hybridization was developed. A TAC clone having an 80 kb rice DNA insert was successfully transferred into rice genome via Agrobacterium-mediated transformation. The new vectors and the genomic libraries should be useful for gene cloning and genetic engineering in rice and other crops.

Base Sequence↗

PubMed2026

Structure-based drug design of small-molecule c-Myc G-quadruplex binders.

The c-Myc oncogene is crucial in tumorigenesis. Although it is a promising therapeutic target, its protein lacks a conventional drug-binding pocket, making it traditionally "undruggable". Recent studies show that the c-Myc promoter can form a G-quadruplex (G4) structure, which suppresses transcription and offers a new strategy for indirect inhibition. In this study, structure-based virtual screening was performed using the c-Myc G4 crystal structure to screen the ChemDiv compound library, aiming to identify small molecules that bind to the G4 structure. Candidate compounds were evaluated in preliminary in vitro assays for biological activity. The results showed that Y502-3888 binds to the c-Myc G4 and downregulates c-Myc expression at both mRNA and protein levels. Collectively, these findings support the potential of Y502-3888 as a c-Myc G4 binder for the treatment of multiple myeloma (MM), providing a foundation for future development of anticancer agents targeting the c-Myc G4.

G-Quadruplexes↗

PubMed2003

Susceptibility of oral bacteria to an antimicrobial decapeptide.

Naturally occurring antimicrobial peptides have emerged as alternative classes of antimicrobials. In general, these antimicrobial peptides exhibit selectivity for prokaryotes and minimize the problems of engendering microbial resistance. As an alternative method to search for more effective broad-spectrum peptide antimicrobials, investigators have developed peptide libraries by using synthetic combinatorial technology. A novel decapeptide, KKVVFKVKFK (KSL), has been identified that shows a broad range of antibacterial activity. The purpose of this study was to test the efficacy of this antimicrobial peptide in killing selected strains of oral pathogens and resident saliva bacteria collected from human subjects. Cytotoxic activity of KSL against mammalian cells and the structural features of this decapeptide were also investigated, the latter by using two-dimensional NMR in aqueous and DMSO solutions. MICs of KSL for the majority of oral bacteria tested in vitro ranged from 3 to 100 microg ml(-1). Minimal bactericidal concentrations of KSL were, in general, within one to two dilutions of the MICs. KSL exhibited an ED(99) (the dose at which 99 % killing was observed after 15 min at 37 degrees C) of 6.25 microg ml(-1) against selected strains of Lactobacillus salivarius, Streptococcus mutans, Streptococcus gordonii and Actinobacillus actinomycetemcomitans. In addition, KSL damaged bacterial cell membranes and caused 1.05 log units reduction of viability counts of saliva bacteria. In vitro toxicity studies showed that KSL, at concentrations up to 1 mg ml(-1), did not induce cell death or compromise the membrane integrity of human gingival fibroblasts. NMR studies suggest that KSL adopts an alpha-helical structure in DMSO solution, which mimics the polar aprotic membrane environment, whereas it remains unstructured in aqueous medium. This study shows that KSL may be a useful antimicrobial agent for inhibiting the growth of oral bacteria that are associated with caries development and early plaque formation.

Aggregatibacter actinomycetemcomitans↗

PubMed2026

Genomic Tracking of Market-Derived Bull Shark Fins Back to Source Population of Origin.

International trade of shark fins remains difficult to monitor because products are rarely labelled to species and are often highly processed, resulting in severely degraded DNA. For several shark species listed under Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), this limits external verification of source populations supplying global trade hubs. Here, we assess whether nuclear genomic approaches can be applied to market-derived bull shark (Carcharhinus leucas) fins to determine their population of origin. We analysed dried fin trimmings collected from retail vendors in Hong Kong SAR, one of the world's largest dried shark fin trade hubs, using a targeted DArTcap single nucleotide polymorphism (SNP) panel, originally developed for population genomic studies of this species. Despite substantial DNA degradation, genomic libraries were successfully obtained for most samples, yielding sufficient SNP data to perform robust provenance and sex assignment. Using a Bayesian mixed-stock analysis, most fin samples were assigned to the Indo-West Pacific (71.4%), with smaller contributions from the western Atlantic (22.6%) and eastern Pacific (3.0%). Genetic sex assignment revealed twice as many males as females, although results indicated a conservative bias towards male assignment due to the limited number of X-linked markers available in degraded samples. Our results demonstrate that genome-wide targeted approaches can be effectively applied to highly processed shark fin products to infer population sources and sex composition. This study provides proof-of-concept for integrating genomics into shark trade monitoring, highlighting its potential to improve traceability, support CITES implementation and inform conservation and fisheries management, particularly for species with well-resolved population structure.

Animals↗

PubMed1994

Information needs of rural health care practitioners in Hawaii.

Rural health care workers need a wide range of specialized information but have difficulties locating and accessing information resources. The information needs of Hawaii's rural health care practitioners and their methods of accessing information were studied through interviews and mailed questionnaires. The following barriers to information access were identified: lack of funds, inadequate hardware, infrastructure problems, and insufficient knowledge about information sources and how to use them. Although many (85%) reported having computers, only a minority (30%) have modems, and even fewer use online resources or the free electronic databases at public and university libraries. Most reported that journal articles were the information source that best met their needs and that personal files or a colleague's collection were the most common places for accessing needed materials. Recommendations for solving some of the information problems include development of a State of Hawaii rural health information clearinghouse; better identification, training, and use of available services; and, most importantly, the establishment of rural health care information agents (modeled on agriculture extension agents) on each major island.

Hawaii↗

PubMed2002

A first class knowledge service: developing the National electronic Library for Health.

With the introduction of clinical governance and the move towards evidence-based practice, there is a growing need to provide health professionals and patients, and the public, with high quality information. Developments in the health service have added weight and urgency to this need. The National electronic Library for Health (NeLH) has a key role to play in providing health professionals with a core knowledge base of accredited and evaluated information. The Pilot NeLH was launched in November and this article outlines the progress and achievements made during this time. The NeLH is based around a central website featuring core resources and links to commissioned specialist collections. Over 70 information resources, including bibliographic databases and full text publications, are accessible via the NeLH, which aims to act as a one-stop shop to support evidence-based decision-making. Much work has been undertaken on national procurement and licensing, particularly in partnership with National Health Service (NHS) libraries. Partnerships as a whole are crucial to ensure true seamless access for health professionals. Key partners include NHS libraries, NHS Direct Online and the electronic Library for Social Care. A short glossary is included for those readers less familiar with current health service developments in the UK.

Cooperative Behavior↗

PubMed1995

A handy database for culture collections worldwide: CCINFO-PC.

Culture collections are reservoirs of cultivable microbes, cell lines and gene libraries. Their role and duty are to supply biological resources to biomedical communities; nevertheless, their visibility from the public is low because most culture collections still have poor accesses via the Internet. Therefore the WFCC World Data Center on Micro-organisms (WDCM) developed a database that runs on IBM PCs and compatibles, which are the most popular computer and will be as powerful as workstations. The database includes various information: activities of 484 culture collections from 58 countries; an integrated list of their holdings of bacteria, fungi and yeast; and data entry system for culture collections.

Bacteria↗