PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-8 (8)
 

Clipboard (0)
None
Journals
Authors
more »
Year of Publication
Document Types
1.  Integration of bioinformatics to biodegradation 
Bioinformatics and biodegradation are two primary scientific fields in applied microbiology and biotechnology. The present review describes development of various bioinformatics tools that may be applied in the field of biodegradation. Several databases, including the University of Minnesota Biocatalysis/Biodegradation database (UM-BBD), a database of biodegradative oxygenases (OxDBase), Biodegradation Network-Molecular Biology Database (Bionemo) MetaCyc, and BioCyc have been developed to enable access to information related to biochemistry and genetics of microbial degradation. In addition, several bioinformatics tools for predicting toxicity and biodegradation of chemicals have been developed. Furthermore, the whole genomes of several potential degrading bacteria have been sequenced and annotated using bioinformatics tools.
doi:10.1186/1480-9222-16-8
PMCID: PMC4012781  PMID: 24808763
2.  Next generation sequencing in cancer research and clinical application 
The wide application of next-generation sequencing (NGS), mainly through whole genome, exome and transcriptome sequencing, provides a high-resolution and global view of the cancer genome. Coupled with powerful bioinformatics tools, NGS promises to revolutionize cancer research, diagnosis and therapy. In this paper, we review the recent advances in NGS-based cancer genomic research as well as clinical application, summarize the current integrative oncogenomic projects, resources and computational algorithms, and discuss the challenge and future directions in the research and clinical application of cancer genomic sequencing.
doi:10.1186/1480-9222-15-4
PMCID: PMC3599179  PMID: 23406336
Next generation sequencing; Cancer research; Clinical application
3.  Ocular Proteomics with Emphasis on Two-Dimensional Gel Electrophoresis and Mass Spectrometry 
The intention of this review is to provide an overview of current methodologies employed in the rapidly developing field of ocular proteomics with emphasis on sample preparation, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Appropriate sample preparation for the diverse range of cells and tissues of the eye is essential to ensure reliable results. Current methods of protein staining for 2D-PAGE, protein labelling for two-dimensional difference gel electrophoresis, gel-based expression analysis and protein identification by MS are summarised. The uses of gel-free MS-based strategies (MuDPIT, iTRAQ, ICAT and SILAC) are also discussed. Proteomic technologies promise to shed new light onto ocular disease processes that could lead to the discovery of strong novel biomarkers and therapeutic targets useful in many ophthalmic conditions.
doi:10.1007/s12575-009-9019-7
PMCID: PMC3055252  PMID: 21406065
ocular proteomics; sample preparation; 2D-PAGE; 2D-DIGE; mass spectrometry
4.  A Practical Guide to Rodent Islet Isolation and Assessment 
Pancreatic islets of Langerhans secrete hormones that are vital to the regulation of blood glucose and are, therefore, a key focus of diabetes research. Purifying viable and functional islets from the pancreas for study is an intricate process. This review highlights the key elements involved with mouse and rat islet isolation, including choices of collagenase, the collagenase digestion process, purification of islets using a density gradient, and islet culture conditions. In addition, this paper reviews commonly used techniques for assessing islet viability and function, including visual assessment, fluorescent markers of cell death, glucose-stimulated insulin secretion, and intracellular calcium measurements. A detailed protocol is also included that describes a common method for rodent islet isolation that our laboratory uses to obtain viable and functional mouse islets for in vitro study of islet function, beta-cell physiology, and in vivo rodent islet transplantation. The purpose of this review is to serve as a resource and foundation for successfully procuring and purifying high-quality islets for research purposes.
doi:10.1007/s12575-009-9021-0
PMCID: PMC3056052  PMID: 19957062
islets of Langerhans; pancreatic islets; beta-cell; beta cells; cytokines; transplantation; calcium; insulin; apoptosis; necrosis; isolation; islet isolation; collagenase; rodent; mouse; rat; islet
5.  Size and Shape of Protein Molecules at the Nanometer Level Determined by Sedimentation, Gel Filtration, and Electron Microscopy 
An important part of characterizing any protein molecule is to determine its size and shape. Sedimentation and gel filtration are hydrodynamic techniques that can be used for this medium resolution structural analysis. This review collects a number of simple calculations that are useful for thinking about protein structure at the nanometer level. Readers are reminded that the Perrin equation is generally not a valid approach to determine the shape of proteins. Instead, a simple guideline is presented, based on the measured sedimentation coefficient and a calculated maximum S, to estimate if a protein is globular or elongated. It is recalled that a gel filtration column fractionates proteins on the basis of their Stokes radius, not molecular weight. The molecular weight can be determined by combining gradient sedimentation and gel filtration, techniques available in most biochemistry laboratories, as originally proposed by Siegel and Monte. Finally, rotary shadowing and negative stain electron microscopy are powerful techniques for resolving the size and shape of single protein molecules and complexes at the nanometer level. A combination of hydrodynamics and electron microscopy is especially powerful.
doi:10.1007/s12575-009-9008-x
PMCID: PMC3055910  PMID: 19495910
Protein shape; hydrodynamics; gel filtration; sedimentation; electron microscopy
6.  Computational Biology Methods and Their Application to the Comparative Genomics of Endocellular Symbiotic Bacteria of Insects 
Comparative genomics has become a real tantalizing challenge in the postgenomic era. This fact has been mostly magnified by the plethora of new genomes becoming available in a daily bases. The overwhelming list of new genomes to compare has pushed the field of bioinformatics and computational biology forward toward the design and development of methods capable of identifying patterns in a sea of swamping data noise. Despite many advances made in such endeavor, the ever-lasting annoying exceptions to the general patterns remain to pose difficulties in generalizing methods for comparative genomics. In this review, we discuss the different tools devised to undertake the challenge of comparative genomics and some of the exceptions that compromise the generality of such methods. We focus on endosymbiotic bacteria of insects because of their genomic dynamics peculiarities when compared to free-living organisms.
doi:10.1007/s12575-009-9004-1
PMCID: PMC3055744  PMID: 19495914
Comparative Genomics; Orthologs search; BLAST; Functional Categories; Genomics Dynamics
7.  Yeast Two-Hybrid: State of the Art 
Genome projects are approaching completion and are saturating sequence databases. This paper discusses the role of the two-hybrid system as a generator of hypotheses. Apart from this rather exhaustive, financially and labour intensive procedure, more refined functional studies can be undertaken. Indeed, by making hybrids of two-hybrid systems, customised approaches can be developed in order to attack specific function-related problems. For example, one could set-up a "differential" screen by combining a forward and a reverse approach in a three-hybrid set-up. Another very interesting project is the use of peptide libraries in two-hybrid approaches. This could enable the identification of peptides with very high specificity comparable to "real" antibodies. With the technology available, the only limitation is imagination.
doi:10.1251/bpo16
PMCID: PMC140126  PMID: 12734586
yeasts; hybrid cells
8.  Science through the Internet: Researching, Evaluating and Citing Websites 
Biological Procedures Online  1999;1:S100-S106.
This article attempts to convey the joys and frustrations of skimming the Internet trying to find relevant information concerning an academic's work as a scientist, a student or an instructor. A brief overview of the Internet and the "do's and don'ts" for the neophyte as well for the more seasoned "navigator" are given. Some guidelines of "what works and what does not" and "what is out there" are provided for the scientist with specific emphasis for biologists, as well as for all others having an interest in science but with little interest in spending countless hours "surfing the net". An extensive but not exhaustive list of related websites is provided.
doi:10.1251/bpo15
PMCID: PMC140117  PMID: 12734595
internet; research

Results 1-8 (8)