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PubMed2006

Single-chain antibodies against DNA aptamers for use as adapter molecules on DNA tile arrays in nanoscale materials organization.

Complex DNA nanostructures have been developed as structural components for the construction of nanoscale objects. Recent advances have enabled self-assembly of organized DNA nanolattices and their use in patterning functional bio-macromolecules and other nanomaterials. Adapter molecules that bind specifically to both DNA lattices and nanomaterials would be useful components in a molecular construction kit for patterned nanodevices. Herein we describe the selection from phage display libraries of single-chain antibodies (scFv) for binding to a specific DNA aptamer and their development as adapter molecules for nanoscale construction. We demonstrate the decoration of various DNA tile structures with aptamers and show binding of the selected single-chain antibody as well as the self-assembly of mixed DNA-protein biomolecular lattices.

Antibodies↗

PubMed2006

The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks.

The SBML ODE Solver Library (SOSlib) is a programming library for symbolic and numerical analysis of chemical reaction network models encoded in the Systems Biology Markup Language (SBML). It is written in ISO C and distributed under the open source LGPL license. The package employs libSBML structures for formula representation and associated functions to construct a system of ordinary differential equations, their Jacobian matrix and other derivatives. SUNDIALS' CVODES is incorporated for numerical integration and sensitivity analysis. Preliminary benchmarking results give a rough overview on the behavior of different tools and are discussed in the Supplementary Material. The native application program interface provides fine-grained interfaces to all internal data structures, symbolic operations and numerical routines, enabling the construction of very efficient analytic applications and hybrid or multi-scale solvers with interfaces to SBML and non SBML data sources. Optional modules based on XMGrace and Graphviz allow quick inspection of structure and dynamics.

Algorithms↗

PubMed1998

Immunotherapy of cancer with dendritic-cell-based vaccines.

Animal studies have shown that vaccination with genetically modified tumor cells or with dendritic cells (DC) pulsed with tumor antigens are potent strategies to elicit protective immunity in tumor-bearing animals, more potent than "conventional" strategies that have been tested in clinical settings with limited success. While both vaccination strategies are forms of cell therapy requiring complex and costly ex vivo manipulations of the patient's cells, current protocols using dendritic cells are considerably simpler and would be more widely available. Vaccination with defined tumor antigens presented by DC has obvious appeal. However, in view of the expected emergence of antigen-loss variants as well as natural immunovariation, effective vaccine formulations must contain mixtures of commonly, if not universally, expressed tumor antigens. When, or even if, such common tumor antigens will be identified cannot be, predicted, however. Thus, for the foreseeable future, vaccination with total-tumor-derived material as source of tumor antigens may be preferable to using defined tumor antigens. Vaccination with undefined tumor-derived antigens will be limited, however, by the availability of sufficient tumor tissue for antigen preparation. Because the mRNA content of single cells can be amplified, tumor mRNA, or corresponding cDNA libraries, offer an unlimited source of tumor antigens. DC transfected with tumor RNA were shown to engender potent antitumor immunity in animal studies. Thus, immunotherapy using autologous DC loaded with unfractionated tumor-derived antigens in the form of RNA emerges as a potentially powerful and broadly useful vaccination strategy for cancer patients.

Animals↗

PubMed1999

Induction and persistence of chromosomal exchanges in mouse bone marrow cells following whole-body exposure to X-rays.

PURPOSE: To investigate the induction and persistence of chromosome aberrations in mouse bone marrow cells after X-ray exposure and to detect differential involvement of individual chromosomes in translocations. MATERIALS AND METHODS: Male and female Swiss mice were exposed to 1 and 3 Gy of X-rays. Chromosome aberrations in bone marrow cells were analysed at 1, 7, 21 and 100 days following irradiation by means of fluorescence in situ hybridization (FISH) with mouse chromosome-specific DNA libraries (#1,13; #2,8; #6,15 and X,Y). In total, 38% of mouse genome was painted and examined. RESULTS: Pooled data indicate that the frequencies of dicentrics and fragments decreased with time and reached to the control level at day 21 after exposure. Following exposure to 1 Gy of X-rays, the frequencies of translocations were not significantly lower between days 7 and 100 than observed at day 1. However, the frequencies of translocations for the 3 Gy group were significantly (about 40%) lower at day 7, then remained constant up to day 100. After exposure to 3Gy of X-rays, the frequencies of non-reciprocal translocations decreased with time, whereas reciprocal translocations between days 7 and 100 were not significantly less frequent than at day 1. A comparison of observed and expected numbers of translocations involving individual chromosomes showed that at day 1 after irradiation, distribution of X-ray-induced translocations among the painted chromosomes was proportional to their DNA content. However, at day 100 after exposure, the observed translocations involving chromosome 2 were more frequent than expected, those involving chromosomes 8 and 15 were less frequent than expected, while chromosomes 1, 6, X and Y were involved as frequently as expected. CONCLUSION: Among induced translocations, non-reciprocal translocations are relatively unstable, especially after exposure to high-dose X-rays. While the initial distribution of X-ray-induced translocations is proportional among the painted chromosomes, the persistence of these translocations is heterogeneous.

Aneuploidy↗

PubMedDate not supplied

Three-dimensional ultrasound and magnetic resonance imaging of pelvic anatomy: potential for complications from minimally invasive procedures.

OBJECTIVE: Several new minimally invasive therapies have recently been popularized for both malignant and benign prostate disorders, including interstitial implantation of radioactive seeds and high-radiofrequency wires, cryoablation, transurethral thermotherapy, and laser prostatectomy. Complications can be incurred during the various procedures, often as a result of injury to adjacent anatomic structures. Some of the complications are inadvertent, whereas others are inherent in the particular treatment process. We hope to increase awareness and understanding of some of the potential complications. METHODS AND MATERIALS: Magnetic resonance (MR) and three-dimensional transrectal ultrasonography (TRUS) imaging were utilized to illustrate the relevant pelvic anatomy in, respectively, a healthy volunteer and four patients undergoing evaluation for prostate symptoms. In addition, data from the Visible Human dataset (the Visible Human Project is part of the National Library of Medicine 1986 Long-Range Plan) were used. RESULTS: The potential complications relating to urinary sphincter and anal sphincter control, sexual function, pelvic musculature, and pelvic nerve physiology could be explained on the basis of the MR and TRUS findings using cryoablation for illustrative purposes. CONCLUSION: A clear understanding of the relevant anatomy and physiology is essential for the physician to provide patient counseling preoperatively regarding anticipated sequelae and to avoid preventable intraoperative complications related to minimally invasive therapeutic procedures for the prostate.

Adult↗

PubMed2025

NRG-P0074 Viral Sample RU1 from Unclassified Mosigvirus Genomic Characterization and Host Range Analysis.

BACKGROUND: Machine learning models for phage-host range prediction and design require comprehensive training data on phage genomes and host ranges to predict phage-host interactions effectively. MATERIALS AND METHODS: This study characterizes phage sample NRG-P0074 viral sample RU1 from unclassified Mosigvirus, originally isolated by the Betty Kutter. The complete genome of NRG-P0074 was sequenced, annotated, and analyzed using various bioinformatic tools. Host range analysis was conducted using the Escherichia coli Reference (ECOR) Library and nine Escherichia coli (E. coli) K12 strains (Keio Knockout Collection) with single nonessential gene deletions. RESULTS: The genome of NRG-P0074 spans 168,357 base pairs with a guanine-cytosine (GC) content of 37.5%. NRG-P0074 exhibited permissiveness in 15.28% of the ECOR isolates and all 9 Keio knockout strains. Comparative genomic analysis revealed that NRG-P0074 is closely related to E. coli phage a20. Its genome is comprised of 270 coding sequences, 153 known genes, 16 terminators, 3 ribosomal-binding sites, 0 tRNAs, and 117 hypothetical proteins. CONCLUSIONS: This research provides valuable data for developing machine learning models to predict phage-host interactions, aiding the development of targeted phage therapies against antibiotic-resistant bacteria.

ECOR Library↗

PubMed1998

Library use and information-seeking behavior of veterinary medical students revisited in the electronic environment.

Veterinary medical students at Iowa State University were surveyed in January of 1997 to determine their general use of the Veterinary Medical Library and how they sought information in an electronic environment. Comparisons were made between this study and one conducted a decade ago to determine the effect of the growth in electronic resources on student library use and information-seeking behavior. The basic patterns of student activities in the library, resources used to find current information, and resources anticipated for future education needs remained unchanged. The 1997 students used the library most frequently for photocopying, office supplies, and studying coursework; they preferred textbooks and handouts as sources of current information. However, when these students went beyond textbooks and handouts to seek current information, a major shift was seen from the use of print indexes and abstracts in 1987 towards the use of computerized indexes and other electronic resources in 1997. Almost 60% of the students reported using the Internet for locating current information. Overall use of electronic materials was highest among a group of students receiving the problem-based learning method of instruction. Most of the students surveyed in 1997 indicated that electronic resources would have some degree of importance to them for future education needs. The electronic environment has provided new opportunities for information professionals to help prepare future veterinarians, some of whom will be practicing in remote geographical locations, to access the wealth of information and services available on the Internet and Web.

Computer Literacy↗

PubMed2000

High stereochemical diversity and applications for the synthesis of marine natural products: a library of carbohydrate mimics and polyketide segments

We have developed a powerful concept for the rapid assembly of a series of twenty-four homochiral building blocks from simple racemic trans-2,4-dimethyl-8-oxabicyclo[3.2.1]oct-6-en-3-one. The series comprises eight stereochemical pentades of anomeric [3.3.1]lactone acetals, eight stereochemical tetrades of anomeric carbohydrate mimics, and eight stereotetrades of acyclic polypropionate units. The utility of these enantiopure materials (average 94% ee) in natural product synthesis is demonstrated and shown to complement the popular aldol method.

Journal Article↗

PubMed1978

Family planning training: a network program and sample instructional materials.

Because of the absence of educational programs for family planning service providers, there is an ongoing need for staff training. In Connecticut, this training is provided statewide by a training network that develops and teaches courses to meet the training needs identified by family planning clinics and related health and social service agencies. This training is offered at the times and locations most convenient to the staff to be trained. A library of courses is being developed for use in the training network -- currently included are Basic Family Planning, Reproductive Health Care, Counseling Skills, Human Sexuality, Pregnancy Counselling, Common Medical Problems in Family Planning, Training Parents as Sex Educators, Family Planning for the Mentally Retarded, Values Clarification, Natural Family Planning, and Medical Interviewing. Each course is based on behavioral objectives, includes pretest and posttest, and is followed up after a 3-month interval by a supervisor's assessment of changes in trainees' job performance. Results show good transfer of skills and knowledge to the work situation. Posttest results in the Basic Family Planning course showed an overall gain of 35 percentage points, reflecting a high level of competency.

Ambulatory Care Facilities↗

PubMed1989

Spectrometric and chromatographic methods for the analysis of polymeric explant materials.

Several analytical pyrolysis methods, namely pyrolysis mass spectrometry (Py-MS), time-resolved pyrolysis mass spectrometry (TRPy-MS), and pyrolysis short column gas chromatography mass spectrometry (Py-GC/MS) were used to analyze polymers of clinical interest both before and after implantation. A sample of Biomer, a poly(ether urethane urea) used in the Utah artificial heart, was analyzed using these methods. Two poly(ether urethanes) (Tecoflex and Pellethane) and a poly(dimethylsilicone) (Silastic) sample were analyzed using Py-GC/MS. The direct Py-MS of Biomer identified the components used in the manufacture of Biomer. Py-GC/MS of Biomer, Tecoflex, Pellethane, and Silastic also identified the components used in their manufacture. The analysis of explanted Biomer detected the presence of adsorbed cholestadiene, the reaction of chloride ions with a stabilizer, and the presence of a siloxane contaminant. The cholestadiene was detected on the outside housing of an artificial heart which had been implanted for 297 days. The cholestadiene was detected at low levels and was identified by library search on the MS data system. The siloxane contaminant was also identified by the MS data system. All of the methods demonstrated required only short instrumental analysis times (10 min or less). Data analysis required much more time, but much of the data analysis can be automated.

Biocompatible Materials↗

PubMed2001

In silico mining of EST databases for novel pre-implantation embryo-specific zinc finger protein genes.

Progress in the understanding of early mammalian embryo development has been severely hampered by scarcity of study materials. To circumvent such a constraint, we have developed a strategy that involves a combination of in silico mining of new genes from expressed sequence tags (EST) databases and rapid determination of expression profiles of the dbEST-derived genes using a PCR-based assay and a panel of cDNA libraries derived from different developmental stages and somatic tissues. We demonstrate that in a random sample of 49 independent dbEST-derived zinc finger protein genes mined from a mouse embryonic 2-cell cDNA library, more than three-quarters of these genes are novel. Examination of characteristics of the human orthologues derived from these mouse genes reveals that many of them are associated with human malignancies. Expression studies have further led to the identification of three novel genes that are exclusively expressed in mouse embryos before or up to the 8-cell stage. Two of the genes, designated 2czf45 and 2czf48 (2czf for 2-cell zinc finger), are zinc finger protein genes coding for a RBCC protein with a RFP domain and a protein with three C2H2 fingers, respectively. The third gene, designated 2cpoz56, codes for a protein with a POZ domain that is often associated with zinc finger proteins. These three genes are candidate genes for regulatory or other functions in early embryogenesis. The strategy described in this report should generally be applicable to rapid and large-scale mining of other classes of rare genes involved in other biological and pathological processes. Mol. Reprod. Dev. 59:249-255, 2001.

Animals↗

PubMed2005

The effectiveness of computer-aided learning in teaching orthodontics: a review of the literature.

INTRODUCTION: The purposes of this review were to evaluate the effectiveness of computer-aided learning (CAL) in orthodontic education, to make evidence-based recommendations for the use of CAL in orthodontics, and to develop guidelines for conducting comparative trials to evaluate CAL as a mode of learning in orthodontic education. METHODS: Medline, the Cochrane Library Database, ERIC, CINAHL, LISA, Psycinfo, and IPA were searched for randomized controlled trials evaluating the effectiveness of CAL in orthodontics. Outcome measures included objectively measured posttest scores on multiple choice, written, or oral tests; performance on a clinical procedure or clinical interview; time spent on CAL programs to learn the material presented; and responses to questionnaires conveying participants' attitudes toward various modes of learning. RESULTS: Four randomized controlled trials comparing CAL with conventional teaching fulfilled the inclusion criteria and met the cutoff quality assessment checklist (QAC) score of > or = 8. Each study was assessed for quality by 2 independent reviewers. The validity and strength of the selected studies were assessed by using a QAC for an educational intervention. CONCLUSIONS: The controlled trials of CAL in orthodontics that met our QAC cutoff score of 8 were split, with 2 showing that CAL enjoyed a significant advantage over conventional teaching, 1 showing no difference, and 1 showing that the conventional tutorial method was better. More high-quality trials evaluating the effectiveness of CAL in orthodontics are needed. CAL programs in orthodontics elicit mostly positive responses and attitudes from students toward learning.

Attitude of Health Personnel↗

PubMed2006

Degradable gene carriers based on oligomerized polyamines.

The focus of this work was to develop potentially biodegradable, polycationic gene carriers possessing high efficiency for gene delivery and being essentially non-toxic. A library of 37 soluble polycations was synthesized by oligomerization of low molecular weight oligoamines with three different crosslinkers, dithiobis-succinimidyl proprionate, dimethyl dithiobis-propionamidate, and hexanediol diacrylate. The types of oligoamine and crosslinker influenced biophysical properties such as DNA binding, hemolytic and endosomolytic membrane activity, transfection efficiency and cytotoxicity of the gene carrier. Degradability of polymers based on reductive cleavage of disulfide bonds or ester hydrolysis was demonstrated. Within the library, oligoethylenimine (800 Da)-based polymers showed the highest gene transfer efficiencies and exceeded the golden standard linear polyethylenimine (22 kDa) in terms of activity/toxicity profile.

Animals↗

PubMed2004

Genetic variation of Cordyceps sinensis, a fruit-body-producing entomopathogenic species from different geographical regions in China.

Cordyceps sinensis is one of the most valuable medicinal fungi in the Orient. It is naturally distributed in the eastern extension area of the Qinghai-Tibet plateau, at an altitude over 4000 m high. In order to investigate genetic variation and evolutionary relationships of C. sinensis from different geographical regions, 17 isolates of C. sinensis were collected from different provinces and the complete sequences of rDNA ITS were determined. On the basis of 5.8S rDNA and ITS region analysis, it was clearly shown that the ITS sequences within C. sinensis are highly homologous regardless of geographical origin. The distance values between the sequences in this study were lower than 0.03. This implied that C. sinensis from different geographic regions are the same species; they are not different species or a species complex. The results also showed that distance values between C. sinensis and Hirsutella sinensis are of the same order as those within C. sinensis from different geographic regions. This confirmed our previous results that C. sinensis should only have H. sinensis as its asexual stage whatever the geographic region from which the samples were collected. An rDNA ITS clone library was established to obtain further evidence for the interpretation of the fungal community structure from C. sinensis and to confirm the accuracy of the taxonomic identities produced by directly sequencing the rDNA ITS region. The discrimination between intraspecies of C. sinensis might provide additional data for the authentication of medicinal material at the species or intraspecies level.

Animals↗

PubMed1986

Isolation of a cDNA encoding a portion of the cyclic nucleotide phosphodiesterase of Dictyostelium discoideum.

The cyclic nucleotide phosphodiesterase (phosphodiesterase) of Dictyostelium discoideum is one of a group of developmentally regulated proteins which enable cells to aggregate by chemotaxis during the early stages of development. We report the identification and DNA sequence of a cDNA clone encoding the amino-terminal region of the phosphodiesterase. The clone, pPD-3, was selected from a cDNA library created by priming first strand synthesis using a set of oligonucleotides with sequences predicted from the amino-terminal amino acid sequence of purified phosphodiesterase. The DNA sequence of pPD-3 encodes perfectly the available phosphodiesterase amino acid sequence, and pPD-3 selects an mRNA which can be translated into material recognized by phosphodiesterase antisera. The nucleotide sequence of pPD-3 indicates there are 49 amino acids, which contain a segment possessing the characteristics of a signal peptide, that separate the amino-terminal residue identified in the purified protein from the methionine codon at which translation originates. DNA blot analysis demonstrates that the phosphodiesterase gene exists as a single copy in the nuclear genome. Analysis of RNA indicates that the phosphodiesterase transcript is 2.1 kb long, which is approximately 0.8 kb more than the minimum required to encode this protein.

3',5'-Cyclic-AMP Phosphodiesterases↗

PubMed2001

The Patient Informatics Consult Service (PICS): an approach for a patient-centered service.

The Patient Informatics Consult Service (PICS) at the Eskind Biomedical Library at Vanderbilt University Medical Center (VUMC) provides patients with consumer-friendly information by using an information prescription mechanism. Clinicians refer patients to the PICS by completing the prescription and noting the patient's condition and any relevant factors. In response, PICS librarians critically appraise and summarize consumer-friendly materials into a targeted information report. Copies of the report are given to both patient and clinician, thus facilitating doctor-patient communication and closing the clinician-librarian feedback loop. Moreover, the prescription form also circumvents many of the usual barriers for patients in locating information, namely, patients' unfamiliarity with medical terminology and lack of knowledge of authoritative sources. PICS librarians capture the time and expertise put into these reports by creating Web-based pathfinders on prescription topics. Pathfinders contain librarian-created disease overviews and links to authoritative resources and seek to minimize the consumer's exposure to unreliable information. Pathfinders also adhere to strict guidelines that act as a model for locating, appraising, and summarizing information for consumers. These mechanisms--the information prescription, research reports, and pathfinders--serve as steps toward the long-term goal of full integration of consumer health information into patient care at VUMC.

Drug Information Services↗

PubMed1987

Telefacsimile from a user perspective.

A study conducted at Montana State University compared telefacsimile service with mail delivery. Recipients of telefax materials who answered questions about the purpose, timeliness, and quality of the materials were generally well pleased. Telefacsimile was found to be a cost-effective and efficient method of document delivery over long distances.

Interlibrary Loans↗

PubMed2002

Historical background and anticipated developments.

Expression profiling using DNA arrays is often believed to have appeared during the second half of the 1990s, and to be based exclusively on nonisotopic methods. In fact, the first article describing the application of cDNA arrays to expression analysis was published in 1992, relied on radioactive labeling, and was a new development of "high-density" membranes used until then essentially for efficient screening of libraries. Several papers described the use of this technology for simultaneous expression measurement of thousands of genes at the time when the first glass microarrays were published. Simultaneously, oligonucleotide chips, originally developed for resequencing and mutation detection applications, were shown to be capable of expression measurement as well. The three approaches have developed over the years and still coexist, as each of them has specific advantages (and drawbacks); the major issues have become those of data quality, data analysis and storage (ideally in a common public database). Meanwhile, the technology continues to evolve. The most obvious trend is a shift towards using arrays of relatively long oligonucleotides that combine most of the advantages of very long (cDNA) and very short (25-mer) DNA segments. The search for better detection methods, ideally without labeling of the sample, is continuing, although it seems difficult to reach the required sensitivity. New materials for microarray manufacture and new implementations of existing methods have appeared. In addition, the field is progressively becoming segmented into high gene number, low volume (research) applications on the one hand, and low gene number, high throughput (diagnostic) uses on the other.

Computational Biology↗