LINNAEUS: A species name identification system for biomedical literature

Background  

The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition, species-specific document retrieval, and semantic enrichment of biomedical articles.     

A compatible support system for cell culture in biomedical research

The lack of a suitable system to culture epithelial cells for a long period under a luminal-antiluminal medium gradient, was the reason to develop a new system. It consists of an interchangeable sheet of permeable support material, which is set in place by two tight fitting holding rings. For special demands the supports can be coated with extracellular matrix proteins improving cellular attachment and terminal differentiation. The handling of the sheets by forceps proceeds easily and quickly, thus fastening the transfer of cultured cells without additional manipulations. The sheets can be transferred to a newly developed microperfusion chamber on which an apical and a basal perfusion over a long culture period parallel to a transepithelial electrophysiological registration becomes possible. The chamber has an extremely low amount of fluid dead space. The separate perfusion of cultured cells under isotonic, hypotonic or hypertonic conditions opens new possibilities. Thus, culture can be performed under most natural conditions e.g., that found within the kidney.     

Tightly regulated, beta-estradiol dose-dependent expression system for yeast

We have refined the regulated expression of UASGAL1, 10-driven genes in yeast by modifying a vector encoding the beta-estradiol inducible activator, GAL4.ER.VP16 (GEV). The expression of GEV was placed under the regulation of the low-level, constitutive MRP7 promoter, and beta-estradiol-regulated expression was monitored by the expression of an integrated UASGAL10-lacZ reporter and by immunoblot analysis of a UASGAL1-regulated gene product. Target gene expression regulated by low levels of GEV has several advantages over the standard galactose-inducible expression systems. (i) Most importantly, the target gene expression is undetectable in the absence of hormone; (ii) target gene expression is beta-estradiol dose-dependent, and variable levels of target gene expression from low to several hundred-fold induction can be achieved; and (iii) induction or depletion studies can be conducted independent of carbon source in gal4 delta strains. In addition, any UASGAL1,10 expression construct can be used without modification of the target gene or many gal4 delta host strains, and GEV vectors are compatible with other inducible yeast expression systems. This method may be useful to researchers investigating the functions of essential genes, dominant negative mutants, mitochondrial genes, and viral, plant, and mammalian genes in yeast assay systems.     

A cell-free system for regulated exocytosis in PC12 cells

We have developed a cell-free system for regulated exocytosis in the PC12 neuroendocrine cell line. Secretory vesicles were preloaded with acridine orange in intact cells, and the cells were sonicated to produce flat, carrier-supported plasma membrane patches with attached vesicles. Exocytosis resulted in the release of acridine orange which was visible as a disappearance of labeled vesicles and, under optimal conditions, produced light flashes by fluorescence dequenching. Exocytosis in vitro requires cytosol and Ca(2+) at concentrations in the micromolar range, and is sensitive to Tetanus toxin. Imaging of membrane patches at diffraction- limited resolution revealed that 42% of docked granules were released in a Ca(2+)-dependent manner during 1 min of stimulation. Electron microscopy of membrane patches confirmed the presence of dense-core vesicles. Imaging of membrane patches by atomic force microscopy revealed the presence of numerous particles attached to the membrane patches which decreased in number upon stimulation. Thus, exocytotic membrane fusion of single vesicles can be monitored with high temporal and spatial resolution, while providing access to the site of exocytosis for biochemical and molecular tools.     

A genome sequencing system for universal newborn screening,diagnosis, and precision medicine for severe genetic diseases

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An optimized, chemically regulated gene expression system for Chlamydomonas

Background

Chlamydomonas reinhardtii is a model system for algal and cell biology and is used for biotechnological applications, such as molecular farming or biological hydrogen production. The Chlamydomonas metal-responsive CYC6 promoter is repressed by copper and induced by nickel ions. However, induction by nickel is weak in some strains, poorly reversible by chelating agents like EDTA, and causes, at high concentrations, toxicity side effects on Chlamydomonas growth. Removal of these bottlenecks will encourage the wide use of this promoter as a chemically regulated gene expression system.

Methodology

Using a codon-optimized Renilla luciferase as a reporter gene, we explored several strategies to improve the strength and reversibility of CYC6 promoter induction. Use of the first intron of the RBCS2 gene or of a modified TAP medium increases the strength of CYC6 induction up to 20-fold. In the modified medium, induction is also obtained after addition of specific copper chelators, like TETA. At low concentrations (up to 10 µM) TETA is a more efficient inducer than Ni, which becomes a very efficient inducer at higher concentrations (50 µM). Neither TETA nor Ni show toxicity effects at the concentrations used. Unlike induction by Ni, induction by TETA is completely reversible by micromolar copper concentrations, thus resulting in a transient “wave” in luciferase activity, which can be repeated in subsequent growth cycles.

Conclusions

We have worked out a chemically regulated gene expression system that can be finely tuned to produce temporally controlled “waves” in gene expression. The use of cassettes containing the CYC6 promoter, and of modified growth media, is a reliable and economically sustainable system for the temporally controlled expression of foreign genes in Chlamydomonas.     

Zebrafish as a model system for biomedical studies

Zebrafish (Danio rerio) is now firmly recognized as a powerful research model for many areas of biology and medicine. Here, we review some achievements of zebrafish-based assays for modeling human diseases and for drug discovery and development. For drug discovery, zebrafish is especially valuable during the earlier stages of research as its represents a model organism to demonstrate a new treatment’s efficacy and toxicity before more costly mammalian models are used. This review considers some examples of known compounds which exhibit both physiological activity and toxicity in humans and zebrafish. The major advantages of zebrafish embryos consist in their permeability to small molecules added to their incubation medium and chorion transparency that enables the easy observation of the development. Assay of acute toxicity (LC₅₀ estimation) in embryos can also include the screening for developmental disorders as an indicator of teratogenic effects. We have used the zebrafish model for toxicity testing of new drugs based on phospholipid nanoparticles (e.g. doxorubicin). Genome organization and the pathways involved into control of signal transduction appear to be highly conserved between zebrafish and humans and therefore zebrafish may be used for modeling of human diseases. The review provides some examples of zebrafish application in this field.     

A sterile sea water circulating system for the jar culture of developing fish eggs

A sterile sea water circulating system for the jar culture of developing fish eggs is described. An ultra–violet filter unit is used to sterilise the water and the system is one of a double-circulation the advantages of which are discussed. This is an effective method for maintaining the developing embryos of Blennius pholis L. under controlled conditions, and would be applicable to studies on other demersal fish species or marine organisms.     

A new solution for biomedical experiments

This article discusses mutual interactions phenomena especially in the case of Transverse ElectroMagnetic (TEM) cell applications as an exposure system in technical and biomedical studies. Problem of mutual interactions between tested objects placed in the electromagnetic field (EMF) is described. A new device for exposure system is presented. Its role is elimination of mentioned harmful phenomenon that leads to falsifications of results.     

Design of a fault-tolerant decision-making system for biomedical applications

This paper describes the design of a fault-tolerant classification system for medical applications. The design process follows the systems engineering methodology: in the agreement phase, we make the case for fault tolerance in diagnosis systems for biomedical applications. The argument extends the idea that machine diagnosis systems mimic the functionality of human decision-making, but in many cases they do not achieve the fault tolerance of the human brain. After making the case for fault tolerance, both requirements and specification for the fault-tolerant system are introduced before the implementation is discussed. The system is tested with fault and use cases to build up trust in the implemented system. This structured approach aided in the realisation of the fault-tolerant classification system. During the specification phase, we produced a formal model that enabled us to discuss what fault tolerance, reliability and safety mean for this particular classification system. Furthermore, such a formal basis for discussion is extremely useful during the initial stages of the design, because it helps to avoid big mistakes caused by a lack of overview later on in the project. During the implementation, we practiced component reuse by incorporating a reliable classification block, which was developed during a previous project, into the current design. Using a well-structured approach and practicing component reuse we follow best practice for both research and industry projects, which enabled us to realise the fault-tolerant classification system on time and within budget. This system can serve in a wide range of future health care systems.     

A web service for biomedical term look-up

Recent years have seen a huge increase in the amount of biomedical information that is available in electronic format. Consequently, for biomedical researchers wishing to relate their experimental results to relevant data lurking somewhere within this expanding universe of on-line information, the ability to access and navigate biomedical information sources in an efficient manner has become increasingly important. Natural language and text processing techniques can facilitate this task by making the information contained in textual resources such as MEDLINE more readily accessible and amenable to computational processing. Names of biological entities such as genes and proteins provide critical links between different biomedical information sources and researchers' experimental data. Therefore, automatic identification and classification of these terms in text is an essential capability of any natural language processing system aimed at managing the wealth of biomedical information that is available electronically. To support term recognition in the biomedical domain, we have developed Termino, a large-scale terminological resource for text processing applications, which has two main components: first, a database into which very large numbers of terms can be loaded from resources such as UMLS, and stored together with various kinds of relevant information; second, a finite state recognizer, for fast and efficient identification and mark-up of terms within text. Since many biomedical applications require this functionality, we have made Termino available to the community as a web service, which allows for its integration into larger applications as a remotely located component, accessed through a standardized interface over the web.     

MBA: a literature mining system for extracting biomedical abbreviations

Background  

The exploding growth of the biomedical literature presents many challenges for biological researchers. One such challenge is from the use of a great deal of abbreviations. Extracting abbreviations and their definitions accurately is very helpful to biologists and also facilitates biomedical text analysis. Existing approaches fall into four broad categories: rule based, machine learning based, text alignment based and statistically based. State of the art methods either focus exclusively on acronym-type abbreviations, or could not recognize rare abbreviations. We propose a systematic method to extract abbreviations effectively. At first a scoring method is used to classify the abbreviations into acronym-type and non-acronym-type abbreviations, and then their corresponding definitions are identified by two different methods: text alignment algorithm for the former, statistical method for the latter.     

GIS: a biomedical text-mining system for gene information discovery

We present a biomedical text-mining system focused on four types of gene-related information: biological functions, associated diseases, related genes and gene-gene relations. The aim of this system is to provide researchers an easy-to-use bio-information service that will rapidly survey the rapidly burgeoning biomedical literature. AVAILABILITY: http://iir.csie.ncku.edu.tw/~yuhc/gis/