Technology In Biomedical Research Research Articles

Efficient Sample Tracking With OpenLabFramework

The advance of new technologies in biomedical research has led to a dramatic growth in experimental throughput. Projects therefore steadily grow in size and involve a larger number of researchers. Spreadsheets traditionally used are thus no longer suitable for keeping track of the vast amounts of samples created and need to be replaced with state-of-the-art laboratory information management systems. Such systems have been developed in large numbers, but they are often limited to specific research domains and types of data. One domain so far neglected is the management of libraries of vector clones and genetically engineered cell lines. OpenLabFramework is a newly developed web-application for sample tracking, particularly laid out to fill this gap, but with an open architecture allowing it to be extended for other biological materials and functional data. Its sample tracking mechanism is fully customizable and aids productivity further through support for mobile devices and barcoded labels.

Biocompatible surface-enhanced Raman scattering nanotags for in vivo cancer detection.

The advancement of surface-enhanced Raman scattering (SERS) is significantly increasing as an ultra-sensitive sensing technology in biomedical research. In this review, we focus on the most recent developments of biocompatible nanoprobes for cancer research. First, we discuss coating approaches to enhance the biocompatibility of SERS substrate and Raman reporters. Furthermore, interesting ligands such as antibodies, aptamers and polypeptides are attached to the surface of nanotags for targeting the cancerous cells in vitro. The unique multiplexing capabilities of the SERS technique have been applied for simultaneous multiple target recognition. Finally, these noninvasive, ultrasensitive tools are mostly highlighted for in vivo tumor detection. Potential application of SERS nanotags in therapeutic study and the possibility of SERS nanotags in biomedical applications are outlined briefly in this review.

Generation of targeted mouse mutants by embryo microinjection of TALENs

Gene engineering for generating targeted mouse mutants is a key technology for biomedical research. Using TALENs as nucleases to induce targeted double-strand breaks, the mouse genome can be directly modified in zygotes in a single step, without the need for embryonic stem cells. Thereby, knockout and knockin alleles can be generated fast and efficiently by embryo microinjection of TALEN mRNAs and targeting vectors. In this article we present an introduction into the TALEN technology and provide protocols for the application of TALENs in mouse zygotes.

Identification of short terminal motifs enriched by antibodies using peptide mass fingerprinting

Mass spectrometry-based protein profiling has become a key technology in biomedical research and biomarker discovery. Sample preparation strategies that reduce the complexity of tryptic digests by immunoaffinity substantially increase throughput and sensitivity in proteomic mass spectrometry. The scarce availability of peptide-specific capture antibodies limits these approaches. Recently antibodies directed against short terminal motifs were found to enrich subsets of peptides with identical terminal sequences. This approach holds the promise of a significant gain in efficiency. TXP (Triple X Proteomics) and context-independent motif specific/global proteome survey binders are variants of this concept. Principally the binding motifs of such antibodies have to be elucidated after generating these antibodies. This entails a substantial effort in the lab, as it requires synthetic peptide libraries and numerous mass spectrometry experiments. We present an algorithm for predicting the antibody-binding motif in a mass spectrum obtained from a tryptic digest of a common cell line after immunoprecipitation. The epitope prediction, based on peptide mass fingerprinting, reveals the most enriched terminal epitopes. The tool provides a P-value for each potential epitope, estimated by sampling random spectra from a peptide database. The second algorithm combines the predicted sequences to more complex binding motifs. A comparison with library screenings shows that the predictions made by the novel methods are reliable and reproducible indicators of the binding properties of an antibody.

Hands-on Workshops as An Effective Means of Learning Advanced Technologies Including Genomics, Proteomics and Bioinformatics

Genomics and proteomics have emerged as key technologies in biomedical research, resulting in a surge of interest in training by investigators keen to incorporate these technologies into their research. At least two types of training can be envisioned in order to produce meaningful results, quality publications and successful grant applications: (1) immediate short-term training workshops and (2) long-term graduate education or visiting scientist programs. We aimed to fill the former need by providing a comprehensive hands-on training course in genomics, proteomics and informatics in a coherent, experimentally-based framework. This was accomplished through a National Heart, Lung, and Blood Institute (NHLBI)-sponsored 10-day Genomics and Proteomics Hands-on Workshop held at National Jewish Health (NJH) and the University of Colorado School of Medicine (UCD). The course content included comprehensive lectures and laboratories in mass spectrometry and genomics technologies, extensive hands-on experience with instrumentation and software, video demonstrations, optional workshops, online sessions, invited keynote speakers, and local and national guest faculty. Here we describe the detailed curriculum and present the results of short- and long-term evaluations from course attendees. Our educational program consistently received positive reviews from participants and had a substantial impact on grant writing and review, manuscript submissions and publications.

INMEX—a web-based tool for integrative meta-analysis of expression data

The widespread applications of various ‘omics’ technologies in biomedical research together with the emergence of public data repositories have resulted in a plethora of data sets for almost any given physiological state or disease condition. Properly combining or integrating these data sets with similar basic hypotheses can help reduce study bias, increase statistical power and improve overall biological understanding. However, the difficulties in data management and the complexities of analytical approaches have significantly limited data integration to enable meta-analysis. Here, we introduce integrative meta-analysis of expression data (INMEX), a user-friendly web-based tool designed to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner. INMEX is freely available at http://www.inmex.ca.

The Case for Phasing Out Experiments on Primates

AbstractWhether they realize it or not, most stakeholders in the debate about using animals for research agree on the common goal of seeking an end to research that causes animals harm. The central issues in the controversy are about how much effort should be devoted to that goal and when we might reasonably expect to achieve it. Some progress has already been made: The number of animals used for research is about half what it was in the 1970s, and biomedical research has reached the point where we can reasonably begin to envision a time when it could advance without causing harm to animals. With some effort and aggressive development of new biomedical research technologies, full replacement of animals in harmful research is within our grasp. The goal will not be reached all at once, however, and phasing out invasive research on all nonhuman primates should be the priority.

Using Galaxy to perform large-scale interactive data analyses.

Innovations in biomedical research technologies continue to provide experimental biologists with novel and increasingly large genomic and high-throughput data resources to be analyzed. As creating and obtaining data has become easier, the key decision faced by many researchers is a practical one: where and how should an analysis be performed? Datasets are large and analysis tool set-up and use is riddled with complexities outside of the scope of core research activities. The authors believe that Galaxy provides a powerful solution that simplifies data acquisition and analysis in an intuitive Web application, granting all researchers access to key informatics tools previously only available to computational specialists working in Unix-based environments. We will demonstrate through a series of biomedically relevant protocols how Galaxy specifically brings together (1) data retrieval from public and private sources, for example, UCSC's Eukaryote and Microbial Genome Browsers, (2) custom tools (wrapped Unix functions, format standardization/conversions, interval operations), and 3rd-party analysis tools.

Design and Statistical Analysis of Pooled Next Generation Sequencing for Rare Variants

Next generation sequencing (NGS) is a revolutionary technology for biomedical research. One highly cost-efficient application of NGS is to detect disease association based on pooled DNA samples. However, several key issues need to be addressed for pooled NGS. One of them is the high sequencing error rate and its high variability across genomic positions and experiment runs, which, if not well considered in the experimental design and analysis, could lead to either inflated false positive rates or loss in statistical power. Another important issue is how to test association of a group of rare variants. To address the first issue, we proposed a new blocked pooling design in which multiple pools of DNA samples from cases and controls are sequenced together on same NGS functional units. To address the second issue, we proposed a testing procedure that does not require individual genotypes but by taking advantage of multiple DNA pools. Through a simulation study, we demonstrated that our approach provides a good control of the type I error rate, and yields satisfactory power compared to the test-based on individual genotypes. Our results also provide guidelines for designing an efficient pooled.

Snapshot liver transcriptome in hepatocellular carcinoma

Lately, advances in high throughput technologies in biomedical research have led to a dramatic increase in the accessibility of molecular insights at different levels of cancer biology such as genome, epigenome, transcriptome, proteome, and others. Among the diverse biological layers, the transcriptome has been most extensively studied especially due to the successful and broad introduction of the microarray technology. The future prospect of broad disposability of deep sequencing technology will furthermore lead to a more sensitive detection of lowly expressed transcripts and to an increase in the number of newly identified transcripts, but also to increase the discovery and characterization of alternative splicing. A common goal of large scale transcriptome profiling methods is the stratification of patients, eventually leading to personalized prognostic predictions and therapeutic strategies. Also, the observation that diverse etiologies of the mostly underlying liver cirrhosis (alcohol, HBV, HCV a.o.) are represented by different transcriptome profiles may be valuable for the identification of essential tumor targets [3] .I n

Population-Based Cohort Studies: Still Relevant?

This commentary discusses the question whether observational epidemiology studies using a population-based cohort design continue to make an impact on the prevention and treatment of cardiovascular disease. Although these studies are large and comprehensive, have they advanced from the early recognition of traditional risk factors to become relevant in the current complex research environment? Five themes are discussed: 1) their role in scientific discovery, including in the context of clinical trials' role in interventional research; 2) their value in encompassing diverse ethnic and age groups to remain relevant to the changing diversity of the United States; 3) the research potential of combining these datasets into large consortia; 4) the ability to use advances in biomedical research technologies; and 5) the recognition that these are national resources that allow outside research community to analyze the collected data and to originate novel ancillary studies. The National Heart, Lung, and Blood Institute longitudinal cohort studies offer opportunities that hold great promise in improving evaluation of personal risk, identifying mechanisms of disease, and directing potential targets for behavior and medical interventions.

Optimal selection of epitopes for TXP-immunoaffinity mass spectrometry

BackgroundMass spectrometry (MS) based protein profiling has become one of the key technologies in biomedical research and biomarker discovery. One bottleneck in MS-based protein analysis is sample preparation and an efficient fractionation step to reduce the complexity of the biological samples, which are too complex to be analyzed directly with MS. Sample preparation strategies that reduce the complexity of tryptic digests by using immunoaffinity based methods have shown to lead to a substantial increase in throughput and sensitivity in the proteomic mass spectrometry approach. The limitation of using such immunoaffinity-based approaches is the availability of the appropriate peptide specific capture antibodies. Recent developments in these approaches, where subsets of peptides with short identical terminal sequences can be enriched using antibodies directed against short terminal epitopes, promise a significant gain in efficiency.ResultsWe show that the minimal set of terminal epitopes for the coverage of a target protein list can be found by the formulation as a set cover problem, preceded by a filtering pipeline for the exclusion of peptides and target epitopes with undesirable properties.ConclusionsFor small datasets (a few hundred proteins) it is possible to solve the problem to optimality with moderate computational effort using commercial or free solvers. Larger datasets, like full proteomes require the use of heuristics.

The next-generation sequencing technology and application

As one of the key technologies in biomedical research, DNA sequencing has not only improved its productivity with an exponential growth rate but also been applied to new areas of application over the past few years. This is largely due to the advent of newer generations of sequencing platforms, offering ever-faster and cheaper ways to analyze sequences. In our previous review, we looked into technical characteristics of the next-generation sequencers and provided prospective insights into their future development. In this article, we present a brief overview of the advantages and shortcomings of key commercially available platforms with a focus on their suitability for a broad range of applications.

Asymmetric RNA duplexes mediate RNA interference in mammalian cells

RNA interference (RNAi) has become an indispensable technology for biomedical research and has demonstrated the potential to become a new class of therapeutic. Current RNAi technology in mammalian cells relies on short interfering RNA (siRNA) consisting of symmetrical duplexes of 19-21 base pairs (bp) with 3' overhangs. Here we report that asymmetric RNA duplexes with 3' and 5' antisense overhangs silence mammalian genes effectively. An asymmetric interfering RNA (aiRNA) of 15 bp was incorporated into the RNA-induced silencing complex (RISC) and mediated sequence-specific cleavage of the target mRNA between base 10 and 11 relative to the 5' end of the antisense strand. The gene silencing mediated by aiRNA was efficacious, durable and correlated with reduced off-target silencing by the sense strand. These results establish aiRNA as a scaffold structure for designing RNA duplexes to induce RNAi in mammalian cells.

DNA-binding Specificity Is a Major Determinant of the Activity and Toxicity of Zinc-finger Nucleases

The engineering of proteins to manipulate cellular genomes has developed into a promising technology for biomedical research, including gene therapy. In particular, zinc-finger nucleases (ZFNs), which consist of a nonspecific endonuclease domain tethered to a tailored zinc-finger (ZF) DNA-binding domain, have proven invaluable for stimulating homology-directed gene repair in a variety of cell types. However, previous studies demonstrated that ZFNs could be associated with significant cytotoxicity due to cleavage at off-target sites. Here, we compared the in vitro affinities and specificities of nine ZF DNA-binding domains with their performance as ZFNs in human cells. The results of our cell-based assays reveal that the DNA-binding specificity-in addition to the affinity-is a major determinant of ZFN activity and is inversely correlated with ZFN-associated toxicity. In addition, our data provide the first evidence that engineering strategies, which account for context-dependent DNA-binding effects, yield ZFs that function as highly efficient ZFNs in human cells.

A Shared Vision

One of today's most powerful technologies in biomedical research--the creation of mutant mice by gene targeting in embryonic stem (ES) cells--was finally celebrated in this year's Nobel Prize in Medicine. The history of how ES cells were first discovered and genetically manipulated highlights the importance of collaboration among scientists from different backgrounds with a shared vision.

CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling

With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.

A microfluidic platform for sequential ligand labeling and cell binding analysis

Developing biochemical and cell biological assay for screening biomolecules, evaluating their characteristics in biological processes, and determining their pharmacological effects represents a key technology in biomedical research. A PDMS-based integrated microfluidic platform was fabricated and tested for facilitating the labeling of ligand on the nanogram scale and sequential cell binding analysis in a manner that saves both time and reagents. Within this microfluidic platform, ligand labeling, cell immobolization, and optical analysis are performed in a miniaturized, continuous and semi-automated manner. This microfluidic device for ligand labeling and cell analysis is composed of two functional modules: (i) a circular reaction loop for fluorophore-labeling of the ligand and (ii) four parallel-oriented incubation chambers for immobilization of cells, binding of ligand to different cell populations, and optical evaluation of interactions between the labeled ligand and its cell targets. Epidermal growth factor (EGF) as the ligand and different cell lines with various levels of EGF receptor expression have been utilized to test the feasiblity of this microfluidic platform. When compared to studies with traditional Petri dish handling of cells and tissues, or even microwell analyses, experiments with the microfluidic platform described here are much less time consuming, conserve reagents, and are programmable, which makes these platforms a very promising new tool for biological studies.

Joint International Conference on EPR Spectroscopy and Wound Healing

The International Conference on Electron Paramagnetic Resonance Spectroscopy and Imaging of Biological Systems (EPR 2005) was held September 4 through 9, 2005, at Columbus, Ohio, U.S.A. Nearly 200 participants from 16 countries presented recent advances on the use of EPR technology to study biologic processes, with an emphasis on human health. For the first time, the EPR conference allied with the Wound Healing Conference, and the alliance opened an avenue for successful amalgamation of the basic biomedical and clinical aspects of wound healing with EPR technology and vice versa. This should lead to emerging applications of EPR technology in biomedical research and clinical practice.

172. Spatially-Controlled Delivery of Cyclodextrin-Based Polyplexes from Solid Surfaces

Localized, nucleic acid delivery from solid surfaces is an important technology for biomedical research, with applications ranging from gene therapy to tissue engineering to functional genomics. The spatially-controlled delivery of growth factor is required for creating a well-organized, complex cellular architecture by tissue engineering. Non-viral gene delivery vehicles have been immobilized to solid surfaces by physical adsorption, biotin-streptavidin interaction, and chemical conjugation1. Here, we present a new approach for surface-mediated gene delivery based on inclusion complex formation between the solid surface and delivery vehicles. Through this method, the delivery of transgenes can be spatially controlled by gene delivery through specific interactions between the delivery vehicles and the surface. Cyclodextrins (CD), cyclic oligomers of glucose, form inclusion complexes with small, hydrophobic compounds such as adamantane. In this work, nanoparticle composites of cyclodextrin polycations and nucleic acids were specifically immobilized on adamantane-coated surfaces. The interaction was characterized by surface plasmon resonance (SPR) spectroscopy and by atomic force microscopy (AFM).