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At least 649 records · Page 36Linked to original sources
PubMed2006

TreeDyn: towards dynamic graphics and annotations for analyses of trees.

BACKGROUND: Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptions or gene functions that can hardly be encoded within the tree itself (if using popular tree formats). Consequently, a tedious manual analysis and post-processing of the tree graphics are required if one needs to use external information for displaying or investigating trees. RESULTS: We have developed TreeDyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees. CONCLUSION: TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections.

Computer Graphics↗
PubMed2007

Pyrosequencing of phage display libraries for the identification of cell-specific targeting ligands.

High combinatorial phage display libraries have become an important tool in the search for ligand-receptor interactions. The advantage this approach offers is the ability to screen large repertoires of peptides, displayed on the coat proteins of bacteriophages, against a target at the same time. In addition, no prior knowledge is required of the target or the ligand. However, to characterize the peptides of interest a short length of the bacteriophage genome that encodes the peptide sequence requires DNA sequencing. The number of candidate bacteriophages can be large and so sequencing is expensive, time-consuming, and laborious. Therefore, a methodology using Pyrosequencing has been developed where 96-phage displaying a seven amino acid peptide can be analyzed simultaneously within 45 min and at a fraction of the cost associated with traditional automated Sanger sequencing.

Bacteriophages↗
PubMed1986

The use of jargon in medical school libraries.

The public services divisions of forty-seven medical school libraries participated in a survey to document jargon used by library staff and users in referring to information sources in the health sciences. The survey yielded 624 unique instances of jargon, 54% of which were acronyms of initialisms. Examples of problems created by the use of jargon are given and the importance of the librarian as a facilitator of communication, even in the presence of automated information systems, is discussed. Implications of the study for novice librarians are suggested. The body of jargon appears to serve as an effective cross-professions communications device.

Catalogs, Library↗
PubMed2005

Connecting health departments and providers: syndromic surveillance's last mile.

INTRODUCTION: A critical need exists for mechanisms to identify and report acute illness clusters to health departments. The Massachusetts Department of Public Health (MDPH) works with partner organizations to conduct syndromic surveillance. This effort is based on CDC's Health Alert Network program and includes automated generation and notification of signals and a mechanism to obtain detailed clinical information when needed. METHODS: Syndromic surveillance partners collect emergency department and ambulatory care data. The principal communications platform between syndromic surveillance partners and MDPH is the Massachusetts Homeland and Health Alert Network (HHAN). This Internet-based application serves as a portal for communication and collaboration and alerts predefined groups of users involved in emergency response. Syndromic surveillance partners' systems report to HHAN by using Public Health Information Network Messaging System events that meet thresholds selected by MDPH. Cluster summaries are automatically posted into a document library. HHAN notifies users by electronic mail, alphanumeric pager, facsimile, or voice communications; users decide how they want to be notified for each level of alert. Discussion threads permit real-time communication among all parties. RESULTS: This automated alert system became operational in July 2004. During July-December 2004, HHAN facilitated communication and streamlined investigation of 15 alerts. CONCLUSION: The system allows rapid, efficient alerting and bidirectional communication among public health and private-sector partners and might be applicable to other public health agencies.

Disaster Planning↗
PubMed2006

Development and application of automatic high-resolution light microscopy for cell-based screens.

Large-scale microscopy-based screens offer compelling advantages for assessing the effects of genetic and pharmacological modulations on a wide variety of cellular features. However, development of such assays is often confronted by an apparent conflict between the need for high throughput, which usually provides limited information on a large number of samples, and a high-content approach, providing detailed information on each sample. This chapter describes a novel high-resolution screening (HRS) platform that is able to acquire large sets of data at a high rate and light microscope resolution using specific "reporter cells," cultured in multiwell plates. To harvest extensive morphological and molecular information in these automated screens, we have constructed a general analysis pipeline that is capable of assigning scores to multiparameter-based comparisons between treated cells and controls. This chapter demonstrates the structure of this system and its application for several research projects, including screening of chemical compound libraries for their effect on cell adhesion, discovery of novel cytoskeletal genes, discovery of cell migration-related genes, and a siRNA screen for perturbation of cell adhesion.

Automation↗
PubMed1987

A comparison of interlibrary loan requests received by the National Library of Medicine: 1959 and 1984.

In 1962, an analysis of interlibrary loan requests for serials filled by NLM in 1959 was published. In the twenty-five years following 1959, important changes occurred in the biomedical library community, which had a significant impact on interlibrary loan activities, including the development of MEDLARS and online searching, the Regional Medical Library (RML) network, and union listing for serials. To describe NLM's current interlibrary loan request traffic for serials and to identify any significant changes in traffic between 1959 and 1984, a comparative analysis of 1984 serial loan requests was performed, primarily by manipulation of automated request records. The changes in request traffic strongly suggest that the efforts to strengthen regional document delivery through the RML program have been successful and that NLM's collection is now used primarily as a last resort.

Interlibrary Loans↗
PubMed2003

From EST to IHC: human antibody pipeline for target research.

We have developed a method for the high-level expression of expressed sequence tags (ESTs) as inclusion bodies in Escherichia coli by C-terminal fusion to the N1-domain of g3p of filamentous phage M13. Soluble fusion protein is obtained by an efficient refolding procedure. We have applied such protein preparations to the selection of human antibody fragments from phage-displayed HuCAL libraries. For all fusion proteins tested in this study, HuCAL antibodies could be generated which specifically detect, e.g. in immunohistochemistry, the maternal full-length protein corresponding to the protein fragment. This expression technology, in combination with the automated HuCAL antibody generation (AutoCAL), has proven to be useful for the rapid, high-throughput generation of high-quality human antibodies against EST-encoded protein fragments for target research.

Animals↗
PubMed1997

All in one: a highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination.

BACKGROUND: About a decade ago, the concept of rotamer libraries was introduced to model sidechains given known mainchain coordinates. Since then, several groups have developed methods to handle the challenging combinatorial problem that is faced when searching rotamer libraries. To avoid a combinatorial explosion, the dead-end elimination method detects and eliminates rotamers that cannot be members of the global minimum energy conformation (GMEC). Several groups have applied and further developed this method in the fields of homology modelling and protein design. RESULTS: This work addresses at the same time increased prediction accuracy and calculation speed improvements. The proposed enhancements allow the elimination of more than one-third of the possible rotameric states before applying the dead-end elimination method. This is achieved by using a highly detailed rotamer library allowing the safe application of an energy-based rejection criterion without risking the elimination of a GMEC rotamer. As a result, we gain both in modelling accuracy and in computational speed. Being completely automated, the current implementation of the dead-end elimination prediction of protein sidechains can be applied to the modelling of sidechains of proteins of any size on the high-end computer systems currently used in molecular modelling. The improved accuracy is highlighted in a comparative study on a collection of proteins of varying size for which score results have previously been published by multiple groups. Furthermore, we propose a new validation method for the scoring of the modelled structure versus the experimental data based upon the volume overlap of the predicted and observed sidechains. This overlap criterion is discussed in relation to the classic RMSD and the frequently used +/- 40 degrees window in comparing chi 1 and chi 2 angles. CONCLUSIONS: We have shown that a very detailed library allows the introduction of a safe energy threshold rejection criterion, thereby increasing both the execution speed and the accuracy of the modelling program. We speculate that the current method will allow the sidechain prediction of medium-sized proteins and complex protein interfaces involving up to 150 residues on low-end desktop computers.

Algorithms↗
PubMed2007

Automated multiple ligand screening by frontal affinity chromatography-mass spectrometry (FAC-MS).

High-throughput screening (HTS) efforts to discover "hits" typically rely on the large-scale parallel screening of individual compounds with attempts to screen mixtures of compounds typically and, unfortunately, giving rise to false positives and false negatives due to the nature of the HTS readout (% inhibition/activation above a defined threshold) that makes deconvolution virtually intractable. Bioaffinity screening methods have emerged as an alternative or orthogonal method to classic HTS. One of these methods, frontal affinity chromatography coupled to mass spectrometry detection (FAC-MS), although still a relatively new technique, is turning out to be a viable screening tool. However, to push FAC-MS more to the forefront as a moderate primary HTS system (or a secondary screening assay), automation needs to be addressed. An automated FAC-MS system is described using 2 columns containing immobilized hERbeta, whereby while 1 column is being regenerated, the other is being used. The authors are extrapolating that in a continuous 24-h operation, the number of ligands screened could potentially approach 10,000. In addition, preliminary structure-activity relationship binding information (typically not seen in early primary HTS) can be obtained by observing the rank order of the library members in the various mixtures.

Amino Acid Sequence↗
PubMed2001

Fast generic-gradient reversed-phase high-performance liquid chromatography using short narrow-bore columns packed with small nonporous silica particles for the analysis of combinatorial libraries.

The extremely large number of samples generated for the quality control analysis of combinatorial libraries that are developed in the pharmaceutical research for drug discovery requires fast generic methods such as rapid-gradient reversed-phase high-performance liquid chromatography (HPLC). These methods are necessary as standard procedures to produce up to several hundreds of analytical results per day and should be optimized in order to be applied to library products of widely differing polarities. This work presents an optimized generic method using a narrow-bore column packed with 1.5-microm nonporous particles and a completely automated HPLC workstation configured for the best efficiency, throughput, and robustness with this column. A test mix of 12 compounds with a wide polarity range is separated within 1.5 min with a cycle time of 3.5 min. The throughput is further enhanced using a Gilson 233XL dual-injection sampler to feed two parallel HPLC systems in order to perform 34 analyses per hour.

Chemistry, Pharmaceutical↗
PubMed2005

Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

BACKGROUND: Cluster analyses are used to analyze microarray time-course data for gene discovery and pattern recognition. However, in general, these methods do not take advantage of the fact that time is a continuous variable, and existing clustering methods often group biologically unrelated genes together. RESULTS: We propose a quadratic regression method for identification of differentially expressed genes and classification of genes based on their temporal expression profiles for non-cyclic short time-course microarray data. This method treats time as a continuous variable, therefore preserves actual time information. We applied this method to a microarray time-course study of gene expression at short time intervals following deafferentation of olfactory receptor neurons. Nine regression patterns have been identified and shown to fit gene expression profiles better than k-means clusters. EASE analysis identified over-represented functional groups in each regression pattern and each k-means cluster, which further demonstrated that the regression method provided more biologically meaningful classifications of gene expression profiles than the k-means clustering method. Comparison with Peddada et al.'s order-restricted inference method showed that our method provides a different perspective on the temporal gene profiles. Reliability study indicates that regression patterns have the highest reliabilities. CONCLUSION: Our results demonstrate that the proposed quadratic regression method improves gene discovery and pattern recognition for non-cyclic short time-course microarray data. With a freely accessible Excel macro, investigators can readily apply this method to their microarray data.

Algorithms↗
PubMed2006

A longitudinal study of Salmonella and Campylobacter jejuni isolates from day of hatch through processing by automated ribotyping.

Comparisons of bacterial populations over long periods of time allow researchers to identify clonal populations, perhaps those responsible for contamination of farms or humans. Salmonella and Campylobacter can cause human illness, and our objective was to use a library typing system to track strains that persist in the poultry house and through the processing plant. Two farms, over four consecutive flocks, were studied. Multiple samples were taken of the poultry house environment, feed mill, transport crates, and carcasses in the processing plant. Sample collection on the farm took place on chick placement day, midgrowout, and the day of harvest. This study found that 80.3% of isolates belonged to a single strain of Salmonella Kentucky that persisted in several environmental samples for all flocks at both farms, from chick placement day to the final product at the plant. Surgical shoe covers produced most isolates (n = 26), and processing day yielded the highest recovery (n = 68). Additional serotypes were recovered, but the Salmonella Kentucky-positive eggshells and chick mortality appeared to be the source of the organism for both farms. All Campylobacter isolates recovered were identified as C. jejuni. Most Campylobacter isolates (90.1%) belonged to one of three core strains. C. jejuni was not recovered on chick placement day. Cecal droppings yielded all nine strains. Most isolates (98.2%) were from one farm. Cluster analysis grouped C. jejuni and Salmonella isolates into four and six distinct clusters, respectively, on the basis of a similarity level of 80%.

Animal Husbandry↗
PubMed2000

Gene expression profile and identification of differentially expressed transcripts during human intrathymic T-cell development by cDNA sequencing analysis.

The development of immature thymocytes to mature T-lymphocytes is a central process for establishing a functional immune system. The gene regulatory events involved in this process are of outstanding interest in understanding the generation of the T-cell repertoire as well as the differentiation of lineage-specific cells, such as CD4(+) helper T-cells or CD8(+) cytotoxic T-lymphocytes. While some essential genes involved in lineage decision and thymocyte differentiation have been already identified, the exact regulatory mechanisms and differential gene expressions are still unknown. The present study was performed to analyze the gene expression profile during T-cell development, in particular, during the differentiation of immature thymocytes into CD4(+) mature T-cells by analyses of expressed sequence tags (ESTs), and to elucidate novel human genes involved in this process. Based on distinct developmental stages, three PCR-based cDNA libraries from immature CD3(-),4(-),8(-) triple-negative, CD4(+),8(+) double-positive, and mature CD4(+),8(-) single-positive thymocytes were constructed. A total of 1477 randomly selected clones were analyzed by automated single-pass sequencing, and the assembly of ESTs resulted in 1027 different species of contig sequences. Among them, 392 contig sequences were matched to known genes, and several novel transcripts were discovered. The matched clones were classified into seven categories according to their functional aspects, and the gene expression profiles of the three thymocyte subsets were compared. The information obtained in current study will serve as a valuable resource for elucidating the molecular mechanism of intrathymic T-cell development.

Cell Differentiation↗
PubMed1997

Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances.

Comparative genomic hybridization (CGH) to metaphase chromosomes has been widely used for the genome-wide screening of genomic imbalances in tumor cells. Substitution of the chromosome targets by a matrix consisting of an ordered set of defined nucleic acid target sequences would greatly enhance the resolution and simplify the analysis procedure, both of which are prerequisites for a broad application of CGH as a diagnostic tool. However, hybridization of whole genomic human DNA to immobilized single-copy DNA fragments with complexities below the megabase pair level has been hampered by the low probability of specific binding because of the high probe complexity. We developed a protocol that allows CGH to chips consisting of glass slides with immobilized target DNAs arrayed in small spots. High-copy-number amplifications contained in tumor cells were rapidly scored by use of target DNAs as small as a cosmid. Low-copy-number gains and losses were identified reliably by their ratios by use of chromosome-specific DNA libraries or genomic fragments as small as 75 kb cloned in PI or PAC vectors as targets, thus greatly improving the resolution achievable by chromosomal CGH. The ratios obtained for the same chromosomal imbalance by matrix CGH and by chromosomal CGH corresponded very well. The new matrix CGH protocol provides a basis for the development of automated diagnostic procedures with biochips designed to meet clinical needs.

Chromosome Aberrations↗
PubMed2005

Ribosome display: next-generation display technologies for production of antibodies in vitro.

Antibodies represent an important and growing class of biologic research reagents and biopharmaceutical products. They can be used as therapeutics in a variety of diseases. With the rapid expansion of proteomic studies and biomarker discovery, there is a need for the generation of highly specific binding reagents to study the vast number of proteins encoded by the genome. Display technologies provide powerful tools for obtaining antibodies. Aside from the preservation of natural antibody repertoires, they are capable of exploiting diversity by DNA recombination to create very large libraries for selection of novel molecules. In contrast to in vivo immunization processes, display technologies allow selection of antibodies under in vitro-defined selection condition(s), resulting in enrichment of antibodies with desired properties from large populations. In addition, in vitro selection enables the isolation of antibodies against difficult antigens including self-antigens, and this can be applied to the generation of human antibodies against human targets. Display technologies can also be combined with DNA mutagenesis for antibody evolution in vitro. Some methods are amenable to automation, permitting high-throughput generation of antibodies. Ribosome display is considered as representative of the next generation of display technologies since it overcomes the limitations of cell-based display methods by using a cell-free system, offering advantages of screening larger libraries and continuously expanding new diversity during selection. Production of display-derived antibodies can be achieved by choosing one of a variety of prokaryotic and eukaryotic cell-based expression systems. In the near future, cell-free protein synthesis may be developed as an alternative for large-scale generation of antibodies.

Antibodies↗
PubMed1993

Characterization of porcine bone sialoprotein: primary structure and cellular expression.

Bone sialoprotein (BSP) is a highly glycosylated and sulphated phosphoprotein that is a major non-collagenous protein of bone. To further characterize the porcine protein and to study its expression during bone formation BSP cDNA clones were isolated from a porcine bone cDNA library. The primary sequence of the protein was derived from the nucleotide sequence of the largest cDNA insert and from the amino-terminal amino acid sequence determined by the automated Edman degradation procedure. When compared with sequences obtained from the human and rat BSPs 74% and 64% of the amino acids, respectively, were identical and a further 11% and 17%, respectively, were conservative replacements. Moreover, 60% of the amino acids in a concensus sequence derived from the primary sequences of mammalian BSPs were conserved with 16% conservative replacements. The two stretches of polyglutamic acid, through which the protein is capable of binding to hydroxyapatite, and an RGD motif that mediates cell attachment are retained in conserved sequences as are a number of potential sites of serine, threonine and tyrosine phosphorylation, glycosylation and tyrosine sulphation. Secondary structure prediction and hydrophilicity analysis indicate that the nascent BSP has an open flexible structure with the potential to form significant amounts of alpha-helix and some beta-sheet. In situ hybridization of fetal porcine bone with cRNA probes to porcine BSP mRNA shows that BSP is specifically expressed in differentiated osteoblasts on the surface of newly-forming bone trabeculae with especially high levels of hybridization at sites of de novo bone formation. The highly conserved features of BSP and its restricted distribution indicate an important role for this sialoprotein in the formation of bone.

Amino Acid Sequence↗
PubMed1982

Clostridium perfringens type A enterotoxin: characterization of the amino-terminal region.

The amino-terminal region of the enterotoxin of Clostridium perfringens was investigated by automated sequence analysis. The primary structure results revealed that the enterotoxin is composed of a single polypeptide amino acid sequence. Computer comparison of a 20-residue sequence with a sequence library of reported proteins revealed no significant chemical similarities, indicating that the enterotoxin represents a unique polypeptide primary structure.

Amino Acid Sequence↗
PubMed2005

Rapid forensic analysis and identification of ''lilac'' architectural finishes using Raman spectroscopy.

The potential of Raman spectroscopy to discriminate between architectural finishes (household paint) has been investigated using a test set of 51 ''lilac'' paints and three different excitation wavelengths. The spectra obtained with visible excitation typically displayed a series of intense Raman bands on a featureless fluorescence background but the spectra of all the paints studied had essentially identical bands. With 785 nm excitation, although the same bands that dominated the 514 nm spectra were still observed, other bands with comparable intensity also appeared. The two strongest scattering constituents were identified as a dioxazine dye, Violet 23 and beta-Cu(phthalocyanine). A scatter plot of the intensities of marker bands for these constituents (normalized to the strong rutile bands that were always present) showed that, despite the fact that the sample set spanned a wide range of rutile : dioxazine dye : phthalo- cyanine ratios, many of the samples had very similar ratios and could not be discriminated. However, all the samples (even those with similar relative proportions of the main constituents) could be discriminated on the basis of their minor constituents, either by manually measuring band intensities or through the creation and searching of spectral libraries.

Architecture↗