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PubMed2026

Systematic performance evaluation and application validation of an end-to-end NGS workstation.

Next-generation sequencing (NGS) library preparation is a core component of precision genomics, but it is commonly constrained by inefficiency, variability, and low throughput of manual protocols. To address these limitations, we developed and systematically evaluated a fully automated NGS workstations and further validated its performance across representative application scenarios. The automated system reduced total processing time from 8 to 10 to 4–6 h. At the same time, it maintained similar performance in pre-library metric, including DNA yield and fragment size, as well as post-capture sequencing metrics (Q30 > 90%, mapping rates > 95%, on-target rates 85–90%). The duplication rate was reduced to 5–8%, compared with 10–15% for manual methods, indicating increased library complexity. Bioinformatic evaluation of inter-species read mapping showed minimal cross-contamination, with a maximum contamination ratio of 0.0003%, indicating effective sample isolation in the automated workflow. High concordance in variant detection was observed between automated and manual workflows. Overall, this automated workstation provides a standardized and reproducible workflow that supports scalable precision genomics applications.

High-Throughput Nucleotide Sequencing↗
PubMedDate not supplied

Characterization of small combinatorial chemistry libraries by (1)H NMR. Quantitation with a convenient and novel internal standard.

A novel silane standard, 1,4-bis(trimethylsilyl)benzene (BTMSB), is introduced for the generic quantitation of small organic molecules in DMSO-d(6) solution by (1)H NMR. This standard is an easily weighable solid and is stable for at least 1 month in DMSO solution, and its (1)H NMR spectrum contains a strong singlet in a region usually free of signals. With a set of certified standards, concentration determination with about 2% precision and accuracy is verified after solution preparation with fully automated procedures, thus making very effective the characterization of small combinatorial chemistry libraries for identity and purity when combined with other physicochemical or biochemical tests. As an example, for a set of about 400 compounds, results of (1)H NMR characterization are compared to the more customary LC-UV-MS method. NMR and MS data agree for identity on the vast majority of cases (84% positive and 5% negative), whereas the remaining cases (11%) are marked as highly impure only after NMR spectra analysis. Most importantly, determination of concentration rather than that of relative purity appears the right choice for a correct evaluation of biochemical potency.

Chromatography, High Pressure Liquid↗
PubMed1994

Introduction of YACs into intact yeast cells by a procedure which shows low levels of recombinagenicity and co-transformation.

Yeast artificial chromosomes (YACs) enable the cloning and analysis of large segments of genomic DNA and permit the isolation of sequences which are impossible to maintain in Escherichia coli. However, the construction of genome libraries in YAC vectors is beset by a number of technical problems, not least of which is the creation of cloned fragments which are not true representatives of the donor genome. These artefactual clones arise mainly due to intra-fragment rearrangements or inter-fragment chimaera formation, both phenomena resulting from the activity of the host yeast's mitotic recombination system. We demonstrate that this system is significantly stimulated by the spheroplasting step of the standard YAC transformation system. In contrast, the transformation of intact yeast cells by either the lithium method or a new lithium-free protocol is much less recombinagenic. It is not possible to introduce high molecular weight YACs into yeast using the lithium protocol, but we find that such molecules may be introduced into pde2-mutants using the lithium-free approach. Since intact cells are transformed by this method, automation of post-transformation steps in the construction of YAC libraries is facilitated. Moreover, the frequency of cotransformation (and, therefore, chimera formation) is significantly reduced. However, these advantages do incur a penalty. Yields of YAC transformants by this simplified intact cell approach are reduced some 25- to 30-fold compared to those obtained by the spheroplast transformation route. Nevertheless, the considerable advantages of the new system recommend it for a number of applications.

Chromosomes, Artificial, Yeast↗
PubMedDate not supplied

Managing the film library: what to do until the panacea arrives.

Today's imaging departments are complex and often decentralized. Despite such growth, the film library is often overlooked and minimally planned for. The oversight may come from the anticipation of picture archiving and communications systems (PACS), considered by many to be the panacea for film management, but in reality, still only a concept, or at best, in its early stages. Since most departments do not anticipate going filmless for many years and others expect to continue hard copy imaging at a 20 to 30 percent rate, managing the film library remains an important issue. In general, film librarians' daily work remains labor intensive, despite attempts to automate some tasks. Yet when cutbacks are made, this support staff is often cut. One way to deal with service and expansion issues in the film library is to stop and evaluate the situation, assess the decline in the level of service, and determine what issues need improvement. Managers should gather information, analyze the data and listen to all interested parties to be sure they understand the overall problems, often best done by someone from outside the department. Analyzing and evaluating work processes, even observing the design of work areas, can be useful in understanding productivity inside the department. An invaluable way to gather data is to listen to those who carry out the daily tasks and those who use the services. Until their needs are understood by management, further changes will have minimal success. When a list of issues is assembled, managers should establish a team to review and prioritize them. Team members will need to understand departmental long-term plans before making recommendations. While every library's operations are unique, a key problem remains lost films. Policies and procedures for removing films must come from hospital senior administration, while managing film within the department is everyone's job. With the chaos under control, managers will be ready to face the challenge of electronic imaging.

Efficiency, Organizational↗
PubMed1996

Design, synthesis and use of binary encoded synthetic chemical libraries.

With the advent of combinatorial chemistry a new paradigm is evolving in the field of drug discovery. The approach is based on an integration of chemistry, high-throughput screening and automation engineering. The chemistry arm is usually based on solid-phase synthesis technology as the preferred approach to library construction. One of the most powerful of the solid-phase methods is encoded split synthesis, in which the reaction history experience by each polymeric bead is unambiguously recorded. This split-and-pool approach, employing chemically robust tags, was used to construct a 85,000-membered dihydrobenzopyran library.

Benzopyrans↗
PubMed2002

Automated ribotyping of vancomycin-resistant Enterococcus faecium isolates.

Vancomycin-resistant Enterococcus faecium (VREF) strains represent an important threat in hospital infections in the United States and are found at high frequencies in both the community and farm animals in Europe. We evaluated automated ribotyping for interlaboratory reproducibility by using the restriction enzymes EcoRI and BamHI and compared ribotyping to both amplification of fragment length polymorphism (AFLP) analysis and multilocus sequence typing (MLST) to assess its discriminatory power and capacity for the identification of epidemiologically important strains. Of 19 (EcoRI) and 16 (BamHI) isolates tested in duplicate in two laboratories, 18 (95%) and 16 (100%), respectively, showed reproducible ribotypes. These high reproducibility rates were obtained only after manual refinement of the automated fingerprint analysis. A group of 49 VREF strains initially selected to represent 32 distinct AFLP types were separated into 28 EcoRI ribotypes, 25 BamHI ribotypes, and 28 sequence types. Ribotyping with EcoRI and BamHI was able to discern the host-specific genogroups recently disclosed by AFLP typing and MLST and to distinguish most strains containing the esp gene, a marker specific for strains causing hospital outbreaks. An expandable ribotype identification library was created. We recommend EcoRI as the enzyme of choice for automated ribotyping of VREF strains. Given the high level of discrimination of VREF strains, the high rate of interlaboratory reproducibility, and the potential for the identification of epidemiologically important genotypes, automated ribotyping appears to be a very valuable approach for characterizing VREF strains.

Alleles↗
PubMed2002

Phage versus phagemid libraries for generation of human monoclonal antibodies.

Non-immune (naïve) phage antibody libraries have become an important source of antibodies for reagent, diagnostic, and therapeutic use. To date, reported naïve libraries have been constructed in phagemid vectors as fusions to pIII, yielding primarily single copy (monovalent) display of antibody fragments. For this work, we subcloned the single chain Fv (scFv) gene repertoire from a naïve phagemid antibody library into a true phage vector to create a multivalently displayed scFv phage library. Compared to monovalently displayed scFv, multivalent phage display resulted in improved efficiency of display as well as antibody selection. A greater number of antibodies were obtained and at earlier rounds of selection. Such increased efficiency allows the screening for binding antibodies after a single round of selection, greatly facilitating automation. Expression levels of antigen-binding scFv were also higher than from the phagemid library. In contrast, the affinities of scFv from the phage library were lower than from the phagemid library. This could be overcome by utilizing the scFv in a multivalent format, by affinity maturation, or by converting the library to monovalent display after the first round of selection.

Amino Acid Sequence↗
PubMedDate not supplied

Automated electrochemical synthesis and photoelectrochemical characterization of Zn1-xCo(x)O thin films for solar hydrogen production.

High-throughput electrochemical methods have been developed for the investigation of Zn1-xCo(x)O films for photoelectrochemical hydrogen production from water. A library of 120 samples containing 27 different compositions (0 <or= x <or= 0.068) was synthesized by automated serial electrochemical deposition. High-throughput photoelectrochemical screening revealed improved solar hydrogen production for the cobalt-doped films, with Zn0.956Co0.044O exhibiting a 4-fold improvement over pure ZnO with no external bias. Flat-band potential, bias-dependent photocurrent, and action spectra were also measured automatically with the high-throughput screening system. The 200-nm-thick films were subsequently characterized by numerous techniques, including SEM, XRD, XPS, and UV-vis, which show that the depositions are well-controlled. Zn/Co stoichiometry in the films was controlled by the ratio of the Zn and Co precursors in each deposition bath. All films exhibited the wurtzite structure typical of pure ZnO, and the Co2+ appears to substitute Zn2+, forming a single-phase solid solution. Band gaps of the solid solutions were systematically lower than the 3.2-eV band gap typical of ZnO.

Automation↗
PubMedDate not supplied

Screening of synthetic peptide libraries with radiolabeled acceptor molecules.

A method has been developed for the identification of specific acceptor molecule-binding sequences from a chemically synthesized peptide library. The peptide resin beads, each bead carrying one peptide sequence, are incubated with radiolabeled acceptor molecule and subsequently immobilized in a thin layer of agarose. Resin beads that carry acceptor molecule-specific sequences are identified by autoradiography and subjected to automated gas-phase sequencing. The method was tested by screening a synthetic pentapeptide library with an anti-beta-endorphin monoclonal antibody.

Amino Acid Sequence↗
PubMed1971

New trends in medical libraries in hospitals.

External and internal forces affecting medical library services are examined. Public Law 89-239, the Heart, Cancer and Stroke Amendments of 1965, and Public Law 89-291, the Medical Library Assistance Act of 1965 which was extended by Public Law 91-212 have an impact on medical libraries. The Veterans Administration relationships with primary beneficiaries of these laws are explained. Internally, effort has been expended through automation, networking, and extension of resources by amalgamation of books and audiovisuals to evolve responsive concepts with emphasis on independence through interdependence. The Veterans Administration Library Service plans and accomplishments in these areas are reviewed.

Information Services↗
PubMed2002

Automated colorimetric screen for apyrase inhibitors.

Apyrases are enzymes that efficiently hydrolyze ATP and ADP and may operate both inside and outside the cell. Although apyrases are important to a variety of cellular mechanisms and uses in industry, there are no available apyrase-specific inhibitors. Colorimetric assays based on the Fiske-Subbarow method for measuring inorganic phosphate are able to detect the release of inorganic phosphate from ATP and other nucleotides. We found that this type of assay could be automated and used to screen for apyrase-inhibiting compounds by assaying for a reduction in released phosphate in the presence of potential inhibitors. The automation of this assay allowed for the successful screening of a commercially available compound library. Several low molecular weight compounds were identified that, when used at micromolar concentrations, effectively inhibited apyrase activity.

Apyrase↗
PubMed1996

A cell-free, nonisotopic, high-throughput assay for inhibitors of type-I interleukin-1 receptor.

A cell-free, nonisotopic assay has been developed to discover molecules that compete with the natural ligands for binding to the active site of the Type-I interleukin-1 receptor. The key reagents are the interleukin-1 receptor antagonist, a recombinant soluble form of the receptor (sIL-1R), and a specific anti-sIL-1R nonneutralizing monoclonal antibody (MAb79). With these molecules a sensitive assay has been developed using a reversed format: the ligand is immobilized and the receptor is in solution. The ligand-bound receptor is detected using MAb79 and an enzyme-linked secondary antibody. Since no cells or cell membranes are used, the assay is very robust, with no interference from membrane-perturbing agents and high resistance to the organic solvents normally used to resuspend compounds of chemical libraries. The microplate format and colorimetric detection have allowed the complete automation of the immobilized-ligand IL-1 receptor binding assay, which has been used for high-throughput screening of synthetic compounds and natural products.

Enzyme-Linked Immunosorbent Assay↗
PubMed2005

Occurrence and ribotypes of Listeria monocytogenes in Gorgonzola cheeses.

In this study 1656 Gorgonzola cheeses, collected from October 2003 to April 2004 in the same industrial plant located in Lombardia (Italy), were analysed in order to evaluate their level of contamination with Listeria monocytogenes after packaging, as well as at the end of the shelf life. A subset of Gorgonzola isolates was submitted to automated EcoRI ribotyping to evaluate their DUP-IDs (DuPont identification library code) and their level of genetic diversity. The isolate ribotyping profiles were included in an on-line database named PathogenTracker database. The strain DUP-IDs and the similarities between Gorgonzola isolates and PathogenTracker human sporadic strains allowed to evaluate the potential virulence of Gorgonzola-associated strains. The L. monocytogenes detection rates observed in the cheese samples monitored after packaging and at the end of the shelf life were 2.1% and 4.8%, respectively. Seventy percent of the strains genotyped were classified in the same ribotype, labelled as 204 S5, indicating that L. monocytogenes population associated to Gorgonzola cheese shows a low level of genetic diversity. Ninety percent of the strains were classified in DUP-IDs belonging to the II pathogenicity lineage identified for L. monocytogenes. That lineage includes serotype 1/2a, 1/2c and 3c strains, associated to the 35% of the human sporadic isolates described in the literature as causing listeriosis. Moreover, 16.7% of Gorgonzola isolates showed a similarity >or=99% with PathogenTracker human sporadic strains. The results of this study showed that the incidence of L. monocytogenes in Gorgonzola cheeses commercialised by the plant tested was lower than that observed in other Italian blue-veined cheeses by other authors. However, it increased during cheese storage and it become double at the end of the cheese shelf life, ranging from 30 to 60 days after packaging.

Cheese↗
PubMed2003

IVR and administrative operations in healthcare and hospitals.

IVR (Interactive Voice Response) systems are effectively used in healthcare and hospitals for drug and health library information, prescription refills, history records, medical transcripts, patient information services, automated pre-admissions, patient account records, appointment scheduling and reminder, lab results notification, food services, and many other applications. Among its benefits, IVR relieves administrative staff and physicians of routine customer interactions and helps healthcare organizations increase their efficiency, productivity, and profitability.

Appointments and Schedules↗
PubMedDate not supplied

A simple and effective method for producing nonrandom peptide libraries using cotton as a carrier in continuous flow peptide synthesizers.

A method has been developed for generating nonrandom peptide libraries on cotton. Disks of cotton fabric were chemically modified to enable peptide synthesis. Incorporation of a 6-aminocaproic acid residue handle on the cellulose turned out to be advantageous. Disks were labeled with silver ink, stacked one on top of another in a continuous flow peptide synthesizer column, and simultaneously subjected to automated synthesis procedures. Depending on the sequences to be synthesized, the automatic synthesis procedure was stopped, and the disks were removed from the column, sorted, and reapplied to subsequent synthesis steps. In this way, individual peptides could be easily prepared in milligram quantities on each of the cotton disks.

Automation↗
PubMed2004

Validation of an empirical RNA-ligand scoring function for fast flexible docking using Ribodock.

We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection ('enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome.

Fluorescence Resonance Energy Transfer↗