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At least 1,657 records · Page 92Linked to original sources
PubMed2002

Development of a murine hematopoietic progenitor complementary DNA microarray using a subtracted complementary DNA library.

With the goal of creating a resource for in-depth study of myelopoiesis, we have executed a 2-pronged strategy to obtain a complementary DNA (cDNA) clone set enriched in hematopoietic genes. One aspect is a library subtraction to enrich for underrepresented transcripts present at early stages of hematopoiesis. For this, a hematopoietic cDNA library from primary murine bone marrow cells enriched for primitive progenitors was used as tester. The subtraction used 10 000 known genes and expressed sequence tags (ESTs) as driver. The 2304 randomly picked clones from the subtracted cDNA libraries represent 1255 distinct genes, of which 622 (50%) are named genes, 386 (30%) match uncharacterized ESTs, and 247 (20%) are novel. The second aspect of our strategy was to complement this subtracted library with genes known to be involved in myeloid cell differentiation and function. The resulting cDNAs were arrayed on polylysine-coated glass slides. The microarrays were used to analyze gene expression in primary and cultured murine bone marrow-derived progenitors. We found expression of various types of genes, including regulatory cytokines and their receptors, signal transduction genes, and transcription factors. To assess gene expression during myeloid differentiation, we examined patterns of change during induced differentiation of EML cells. Several hundred of the genes underwent fluctuations in expression level during myeloid cell differentiation. The complete database, accessible on the World Wide Web at http://yale130132115135.med.yale.edu/, allows for retrieval of information regarding these genes. Our microarray allows for genomewide expression analysis of myeloid stem cells, which will help in defining the regulatory mechanisms of stem cell differentiation.

Animals↗
PubMed2001

FastGroup: a program to dereplicate libraries of 16S rDNA sequences.

BACKGROUND: Ribosomal 16S DNA sequences are an essential tool for identifying and classifying microbes. High-throughput DNA sequencing now makes it economically possible to produce very large datasets of 16S rDNA sequences in short time periods, necessitating new computer tools for analyses. Here we describe FastGroup, a Java program designed to dereplicate libraries of 16S rDNA sequences. By dereplication we mean to: 1) compare all the sequences in a data set to each other, 2) group similar sequences together, and 3) output a representative sequence from each group. In this way, duplicate sequences are removed from a library. RESULTS: FastGroup was tested using a library of single-pass, bacterial 16S rDNA sequences cloned from coral-associated bacteria. We found that the optimal strategy for dereplicating these sequences was to: 1) trim ambiguous bases from the 5' end of the sequences and all sequence 3' of the conserved Bact517 site, 2) match the sequences from the 3' end, and 3) group sequences > or =97% identical to each other. CONCLUSIONS: The FastGroup program simplifies the dereplication of 16S rDNA sequence libraries and prepares the raw sequences for subsequent analyses.

Algorithms↗
PubMed2006

Construction of a 7-fold BAC library and cytogenetic mapping of 10 genes in the giant panda (Ailuropoda melanoleuca).

BACKGROUND: The giant panda, one of the most primitive carnivores, is an endangered animal. Although it has been the subject of many interesting studies during recent years, little is known about its genome. In order to promote research on this genome, a bacterial artificial chromosome (BAC) library of the giant panda was constructed in this study. RESULTS: This BAC library contains 198,844 clones with an average insert size of 108 kb, which represents approximately seven equivalents of the giant panda haploid genome. Screening the library with 15 genes and 8 microsatellite markers demonstrates that it is representative and has good genome coverage. Furthermore, ten BAC clones harbouring AGXT, GHR, FSHR, IRBP, SOX14, TTR, BDNF, NT-4, LH and ZFX1 were mapped to 8 pairs of giant panda chromosomes by fluorescence in situ hybridization (FISH). CONCLUSION: This is the first large-insert genomic DNA library for the giant panda, and will contribute to understanding this endangered species in the areas of genome sequencing, physical mapping, gene cloning and comparative genomic studies. We also identified the physical locations of ten genes on their relative chromosomes by FISH, providing a preliminary framework for further development of a high resolution cytogenetic map of the giant panda.

Animals↗
PubMed2006

Whitefly (Bemisia tabaci) genome project: analysis of sequenced clones from egg, instar, and adult (viruliferous and non-viruliferous) cDNA libraries.

BACKGROUND: The past three decades have witnessed a dramatic increase in interest in the whitefly Bemisia tabaci, owing to its nature as a taxonomically cryptic species, the damage it causes to a large number of herbaceous plants because of its specialized feeding in the phloem, and to its ability to serve as a vector of plant viruses. Among the most important plant viruses to be transmitted by B. tabaci are those in the genus Begomovirus (family, Geminiviridae). Surprisingly, little is known about the genome of this whitefly. The haploid genome size for male B. tabaci has been estimated to be approximately one billion bp by flow cytometry analysis, about five times the size of the fruitfly Drosophila melanogaster. The genes involved in whitefly development, in host range plasticity, and in begomovirus vector specificity and competency, are unknown. RESULTS: To address this general shortage of genomic sequence information, we have constructed three cDNA libraries from non-viruliferous whiteflies (eggs, immature instars, and adults) and two from adult insects that fed on tomato plants infected by two geminiviruses: Tomato yellow leaf curl virus (TYLCV) and Tomato mottle virus (ToMoV). In total, the sequence of 18,976 clones was determined. After quality control, and removal of 5,542 clones of mitochondrial origin 9,110 sequences remained which included 3,843 singletons and 1,017 contigs. Comparisons with public databases indicated that the libraries contained genes involved in cellular and developmental processes. In addition, approximately 1,000 bases aligned with the genome of the B. tabaci endosymbiotic bacterium Candidatus Portiera aleyrodidarum, originating primarily from the egg and instar libraries. Apart from the mitochondrial sequences, the longest and most abundant sequence encodes vitellogenin, which originated from whitefly adult libraries, indicating that much of the gene expression in this insect is directed toward the production of eggs. CONCLUSION: This is the first functional genomics project involving a hemipteran (Homopteran) insect from the subtropics/tropics. The B. tabaci sequence database now provides an important tool to initiate identification of whitefly genes involved in development, behaviour, and B. tabaci-mediated begomovirus transmission.

Amino Acid Sequence↗
PubMed2005

Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics.

BACKGROUND: The lycophytes are an ancient lineage of vascular plants that diverged from the seed plant lineage about 400 Myr ago. Although the lycophytes occupy an important phylogenetic position for understanding the evolution of plants and their genomes, no genomic resources exist for this group of plants. RESULTS: Here we describe the construction of a large-insert bacterial artificial chromosome (BAC) library from the lycophyte Selaginella moellendorffii. Based on cell flow cytometry, this species has the smallest genome size among the different lycophytes tested, including Huperzia lucidula, Diphaiastrum digita, Isoetes engelmanii and S. kraussiana. The arrayed BAC library consists of 9126 clones; the average insert size is estimated to be 122 kb. Inserts of chloroplast origin account for 2.3% of the clones. The BAC library contains an estimated ten genome-equivalents based on DNA hybridizations using five single-copy and two duplicated S. moellendorffii genes as probes. CONCLUSION: The S. moellenforffii BAC library, the first to be constructed from a lycophyte, will be useful to the scientific community as a resource for comparative plant genomics and evolution.

Chromosomes, Artificial, Bacterial↗
PubMed2004

Multi-line split DNA synthesis: a novel combinatorial method to make high quality peptide libraries.

BACKGROUND: We developed a method to make a various high quality random peptide libraries for evolutionary protein engineering based on a combinatorial DNA synthesis. RESULTS: A split synthesis in codon units was performed with mixtures of bases optimally designed by using a Genetic Algorithm program. It required only standard DNA synthetic reagents and standard DNA synthesizers in three lines. This multi-line split DNA synthesis (MLSDS) is simply realized by adding a mix-and-split process to normal DNA synthesis protocol. Superiority of MLSDS method over other methods was shown. We demonstrated the synthesis of oligonucleotide libraries with 1016 diversity, and the construction of a library with random sequence coding 120 amino acids containing few stop codons. CONCLUSIONS: Owing to the flexibility of the MLSDS method, it will be able to design various "rational" libraries by using bioinformatics databases.

Amino Acid Sequence↗
PubMed2025

Large-scale screening of genes responsible for silique length and seed size in Brassica Napus via pooled CRISPR library.

BACKGROUND: Enhancing rapeseed (Brassica napus, B. napus) yield is critical for ensuring global vegetable oil security. However, yield is heavily influenced by silique development and seed size, the enhancement of which is limited by scarce genetic resources. The CRISPR/Cas9 system has emerged as a powerful tool for constructing genome-wide mutant libraries, even in polyploid crops with complex genomes. RESULTS: The transcriptome-wide association study (TWAS) data, tissue-specific expression profiles data and reported genes were integrated to identify candidate genes regulating silique development and seed size. We constructed a sgRNA library targeting these genes and generated a CRISPR/Cas9 editing mutant library through genetic transformation. Specifically, 6124 sgRNAs were designed for 1739 candidate genes with ≦ 4 orthologues. 681 T0 plants were obtained through genetic transformation, which harbor 453 sgRNAs. Of 408 T0 plants analyzed, 151 (37.00%) exhibited successful gene editing events, targeting 84 candidate genes. Ten homozygous mutant plants were isolated and preliminary phenotypic analysis was performed in mutants targeting the BnaHRDs. The results suggest that mutations in BnaHRD.A03 and BnaHRD.C03 may modulate plant height (PH), main inflorescence length (MIL), silique length (SL), effective silique number per plant (ENS), seed number per silique (SNPS), and thousand-seed weight (TSW). CONCLUSIONS: This study harnessed the CRISPR/Cas9 technology to establish a preliminary library of gene-edited mutants in B. napus, thereby laying a robust foundation for the future screening of candidate genes pertaining to silique development and seed size. Furthermore, this study provides a methodological framework for rapid functional gene discovery in B. napus through CRISPR-based approaches.

Brassica napus↗
PubMedDate not supplied

Creating a pediatric digital library for pediatric health care providers and families: using literature and data to define common pediatric problems.

The goal of this study was to complete a literature-based needs assessment with regard to common pediatric problems encountered by pediatric health care providers (PHCPs) and families, and to develop a problem-based pediatric digital library to meet those needs. The needs assessment yielded 65 information sources. Common problems were identified and categorized, and the Internet was manually searched for authoritative Web sites. The created pediatric digital library (www.generalpediatrics.com) used a problem-based interface and was deployed in November 1999. From November 1999 to November 2000, the number of hyperlinks and authoritative Web sites increased 51.1 and 32.2 percent, respectively. Over the same time, visitors increased by 57.3 percent and overall usage increased by 255 percent. A pediatric digital library has been created that begins to bring order to general pediatric resources on the Internet. This pediatric digital library provides current, authoritative, easily accessed pediatric information whenever and wherever the PHCPs and families want assistance.

Computer Systems↗
PubMed1981

For parents and children only: a parent-child educational library.

A Parent-Child Education Library was developed at a children's hospital to help fill the gap in communication between staff and families. The written materials supplement the staff's verbal explanations. Materials include both medical and other child-related, educational topics. The library was approved by the medical staff and is funded by donations. Counseling has become an appropriate adjunct to the library, as parents and/or children share their problems and feelings. The library is a service provided by the Child Life Program.

Adult↗
PubMed2001

Thyroid peroxidase autoantibodies obtained from random single chain FV libraries contain the same heavy/light chain combinations as occur in vivo.

Three combinatorial libraries were constructed from unpurified, CD19(+), and antithyroid peroxidase (anti-TPO) B cells extracted from thyroid tissue of Graves' disease patients. Fifteen of the 41 randomly derived anti-TPO single chain variable region fragments (scFvs), showed VH1-3/V lambda 1-51 or VH1-69/V lambda 1-40 heavy/light chain pairing similar to that obtained with TPO-specific scFv derived from an in-cell library. One VH1-3/V lambda 1-51 scFv, A16, showed exactly the same nucleotide sequence as in-cell scFv ICB7, demonstrating that in vivo rearrangement can be obtained from a random combinatorial library. The majority of the scFvs used a heavy chain gene derived from the VH1-3 gene segment, whereas the light chain gene segments used were more heterogeneous, with dominance of the V kappa 1-39 and V lambda 1-51 gene segments. The anti-TPO scFvs showed high affinities to TPO, with values between 0.77 and 12.3 nM, and defined seven antigenic regions on the TPO molecule. The anti-TPO fragments, particularly VH1-3/V lambda 1-51 randomly associated scFv B4, which mimic natural H/L pairing, and VH1-3/V lambda 1-40 in-cell-derived scFv ICA5, efficiently displaced the TPO binding of serum autoantibodies from 20 Graves' disease patients. Our study directly demonstrates that antibodies derived from combinatorial libraries are likely to represent in vivo pairing, leading to high affinity antibody fragments mimicking the binding of serum autoantibodies to TPO.

Adult↗
PubMed2001

Construction of a BAC library derived from the inbred Hd-rR strain of the teleost fish, Oryzias latipes.

A large insert genomic bacterial artificial chromosome (BAC) library was constructed from the inbred Hd-rR strain of the medaka, Oryzias latipes. Approximately 92,000 clones were gridded on high-density replica filters. Insert analysis of randomly selected clones indicated a mean insert size of 210 kb and predicted a 24 times coverage of the medaka genome. The library was hybridized with a single locus DNA fragment, and the resulting positive clones were characterized and shown to be compatible with a 24-fold redundant library. This first large insert genomic library of the medaka should increase the speed of genomic analyses for this fish species.

Animals↗
PubMed2002

Construction of BAC libraries derived from the ascidian Ciona intestinalis.

Large insert genomic bacterial artificial chromosome (BAC) libraries were constructed from a basal chordate, the ascidian Ciona intestinalis. Insert analyses of randomly selected clones indicated that in the first library the mean insert size was 135 kb and predicted a 15-fold coverage of the Ciona genome, and in the second library the mean insert size was 165 kb and predicted a 5-fold coverage of the genome. These first large insert genomic libraries of the ascidian should increase the speed of genomic analyses of basal chordates.

Animals↗
PubMed1986

Standards for reference services in health sciences libraries: the reference product.

Standards for reference services were prepared by a committee of the Oregon Health Sciences Libraries Association (OHSLA). The standards are qualitative and address the following: quality control, appropriateness, accuracy, documentation, timeliness, accessibility, confidentiality, and evaluation. The standards are components of minimally competent reference service as reflected in the reference product. A discussion of concerns and prescriptive measures accompanies the statement of each standard. While prepared specifically for health sciences libraries, the standards are applicable to all types of libraries and may be used as guidelines in evaluating the reference product, in upgrading library service, and in writing policies and procedures.

Information Services↗
PubMed1986

Hospital libraries in West Germany: an overview of reference services.

This article presents a study on reference services in German hospital libraries. Information for the study was obtained through personal interviews conducted at four libraries in Stuttgart, West Germany in August 1985. A detailed questionnaire covering services provided, staff training, and use of computers was used during the interviews. While reference services are minimal at the libraries in the study, the commitment to patient library services in Germany is exceptional.

Data Collection↗
PubMed1996

The hospital library as provider of consumer health information.

The health care environment of the 1990s demands that hospital libraries develop creative strategies for providing consumer health information (CHI). Librarians at the Reuben L. Sharp Health Sciences Library at Cooper Hospital/University Medical Center have developed a multifaceted approach to the problem. Using a combination of institutional resources, private funding, and cooperative arrangements with public libraries, the Sharp Library helps to serve the consumer health information needs of the southern New Jersey community.

Community Participation↗
PubMed1999

Security and crime in health sciences libraries in the southern United States.

Crime is a part of life that has become more evident in libraries through reports in journals, newspapers, television, and other media. As the result of a sharing session, a survey was conducted of the libraries composing the South Central Chapter of the Medical Library Association. This survey looked at the incidence of major and minor crimes in the libraries and their institutions; security measures, regulations, or policies that were in effect prior to these or having been initiated since; and the effect the crimes and/or security measures have had on the institution and its employees.

Arkansas↗
PubMed2000

One small community hospital library's successful outsourcing of document delivery: an ongoing study.

When DOCLINE was implemented in 1985, community hospital librarians were beginning to feel the economic pressures of the changing health care arena. However, staff and resources were often sufficient or plentiful. Now, fifteen years after the creation of DOCLINE, many existing small hospitals either no longer have a librarian, an assistant is managing the library, the librarian is managing one or more libraries of an integrated system, or the number of librarians has been reduced. A system that is heavily staff dependent is no longer feasible. In addition, as the role of the community hospital librarian evolves into one of instructor and patient education liaison, a system that does not permit the librarian to expand such services will be detrimental to the entire library program. Following is a discussion of one small community hospital's decision to outsource document delivery services as a result of staffing changes and the expansion of additional library programs.

Baltimore↗
PubMed2004

The library as finals resting place: expanding service to health sciences students during final exams.

To increase services to health sciences students during their final exam period, and to demonstrate to campus administration that the library is in tune with the students' fluctuating needs, the Kornhauser Health Sciences Library, University of Louisville, increased its hours of operation; created an inviting, comfortable environment; and offered free snacks and drinks for the students. The event, coined the "Finals Resting Place," was a positive public relations tool that strengthened the library's relationship with its students. Moreover, it reinforced the library's role and mission to the campus administration, particularly that of the dental and medical schools.

Allied Health Personnel↗