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PubMed2000

ACAPELLA-1K, a capillary-based submicroliter automated fluid handling system for genome analysis.

The Genomation Laboratory in the Electrical Engineering Department at the University of Washington has been developing an automated, high-throughput, submicroliter-scale fluid-handling system for use in molecular biology, especially as part of the Human Genome Project and other high-throughput DNA sequencing endeavors. Small glass capillaries enable the preparation, handling, and monitoring of 1-microliter reaction volumes. The Genomation Laboratory, with corporate partners Orca Photonic Systems, Inc. and Engineering Arts, has developed modules for aspiration, dispensing, mixing, transport, and rapid thermal processing of biological samples contained in glass capillaries. The ACAPELLA-1K is the first integration of these modules, designed to process 1000 samples in an eight-hour day. It has served as a test bed for the technologies as well as for performing biological experiments in conjunction with the University of Washington Genome Center. This system and related results are presented in this paper. A video of the system in operation is provided at. The Genomation Laboratory is presently developing the next-stage ACAPELLA-5K system based on the results of the ACAPELLA-1K system.

Automation↗
PubMed2004

Transcription and replication of nonsegmented negative-strand RNA viruses.

The nonsegmented negative-strand (NNS) RNA viruses of the order Mononegavirales include a wide variety of human, animal, and plant pathogens. The NNS RNA genomes of these viruses are templates for two distinct RNA synthetic processes: transcription to generate mRNAs and replication of the genome via production of a positive-sense antigenome that acts as template to generate progeny negative-strand genomes. The four virus families within the Mononegavirales all express the information encoded in their genomes by transcription of discrete subgenomic mRNAs. The key feature of transcriptional control in the NNS RNA viruses is entry of the virus-encoded RNA-dependent RNA polymerase at a single 3' proximal site followed by obligatory sequential transcription of the linear array of genes. Levels of gene expression are primarily regulated by position of each gene relative to the single promoter and also by cis-acting sequences located at the beginning and end of each gene and at the intergenic junctions. Obligatory sequential transcription dictates that termination of each upstream gene is required for initiation of downstream genes. Therefore, termination is a means to regulate expression of individual genes within the framework of a single transcriptional promoter. By engineering either whole virus genomes or subgenomic replicon derivatives, elements important for signaling transcript initiation, 5' end modification, 3' end polyadenylation, and transcription termination have been identified. Although the diverse families of NNS RNA virus use different sequences to control these processes, transcriptional termination is a common theme in controlling gene expression and overall transcriptional regulation is key in controlling the outcome of viral infection. The latest models for control of replication and transcription are discussed.

Gene Expression Regulation, Viral↗
PubMed2004

Fractal genomics modeling: a new approach to genomic analysis and biomarker discovery.

Reverse engineering of genetics networks generally requires establishing correlative behavior within and between a very large number of genes. This becomes a difficult analytical problem for even a few hundred genes and the difficulty tends to grow exponentially as more genes are examined. Using a hybrid data analysis method known as Fractal Genomics Modeling (FGM), this problem is reduced to examining correlative behavior within small gene groups that can then be compared and integrated to produce a picture of larger networks using a type pf shotgun approach. We have applied FGM toward examining genetic networks involved in HIV infection in the brain. These networks have relevance both to processes related to HIV infection and neurodegenerative disorders. Our preliminary findings have produced conjectures of related pathways and networks as well new candidates for genetic markers in HIV brain infection. Evidence has also been produced which appears to show the presence of a hierarchical network structure within the genes studied. We will discuss the background and methodology of FGM as well as our recent findings.

AIDS Dementia Complex↗
PubMed2006

Contribution of rpoB2 RNA polymerase beta subunit gene to rifampin resistance in Nocardia species.

Nocardia species are gram-positive environmental saprophytes, but some cause the infectious disease nocardiosis. The complete genomic sequence of Nocardia farcinica IFM 10152 has been determined, and analyses indicated the presence of two different RNA polymerase beta subunit genes, rpoB and rpoB2, in the genome (J. Ishikawa, A. Yamashita, Y. Mikami, Y. Hoshino, H. Kurita, K. Hotta, T. Shiba, and M. Hattori, Proc. Natl. Acad. Sci. USA 101:14925-14930, 2004). These genes share 88.8% identity at the nucleotide level. Moreover, comparison of their amino acid sequences with those of other bacterial RpoB proteins suggested that the nocardial RpoB protein is likely to be rifampin (RIF) sensitive, whereas RpoB2 protein contains substitutions at the RIF-binding region that are likely to confer RIF resistance. Southern analysis indicated that rpoB duplication is widespread in Nocardia species and is correlated with the RIF-resistant phenotype. The introduction of rpoB2 by using a newly developed Nocardia-Escherichia coli shuttle plasmid vector and transformation system conferred RIF resistance to Nocardia asteroides IFM 0319T, which has neither RIF resistance nor rpoB duplication. Furthermore, unmarked rpoB2 deletion mutants of N. farcinica IFM 10152 showed no significant resistance to RIF. These results indicated the contribution of rpoB2 to RIF resistance in Nocardia species. Since this is the first example of genetic engineering of the Nocardia genome, we believe that this study, as well as our determination of the N. farcinica genome sequence, will be a landmark in Nocardia genetics.

Amino Acid Sequence↗
PubMedDate not supplied

Autoregulated multicistronic expression vectors provide one-step cloning of regulated product gene expression in mammalian cells.

Regulated expression of a cloned gene often provides much higher final expression of the gene product. Also, regulated expression of an activity can enable optional metabolic engineering and simplify functional genomic research. We constructed di-, tri-, and quattrocistronic mammalian expression vectors which allow the simultaneous, coordinated, and adjustable expression of up to two product genes. A single, tetracycline-regulatable promoter, PhCMV*-1, drives high-level expression of a multicistronic expression unit, containing the product gene(s), the gene for tetracycline-responsive transactivator (tTA), and, in the case of pQuattro-tTA, also the neomycin resistance gene. This autoregulatory genetic configuration retains a very low basal transcription activity in the presence of tetracycline, thereby reducing or eliminating possible toxic effects of tTA expression. However, upon withdrawal of tetracycline, a positive feedback regulation loop is activated which leads to higher levels of tTA expression and consequently also to higher expression levels of all other cistrons encoded on the multicistronic expression unit. Since such multicistronic expression vectors combine all genetic elements necessary for high-level expression as well as regulation in a single multicistronic expression unit, they alleviate limitations of previously reported tetracycline-regulatable vector systems and allow straightforward, one-step genetic engineering of eucaryotic cells to give an adjustable phenotype under strict control of the external stimulus, here tetracycline. Because the expression vectors described here were used for the expression for several heterologous product genes such as the green fluorescent protein and the tumor suppressor gene p21 in several cell lines (CHO-K1, BHK-21, and HeLa), we expect these multicistronic, positive feedback regulation vectors to function in a wide variety of eucaryotic cells and to be useful for basic as well as for applied research applications. Other vectors based upon the same autoregulation and multicistronic expression concepts can be constructed using other regulator gene-regulated promoter elements.

Animals↗
PubMed2003

Recombinant AAV serotype 1 transduction efficiency and tropism in the murine brain.

Recombinant adeno-associated virus serotype 2 (rAAV2) vectors have shown promise as therapeutic agents for neurologic disorders. However, intracerebral administration of this vector leads to preferential transduction of neurons and a restricted region of transgene expression. The recently developed rAAV vectors based upon nonserotype 2 viruses have the potential to overcome these limitations. Therefore, we directly compared a rAAV type 1 to a type 2 vector in the murine brain. The vectors were engineered to carry identical genomes (AAV2 terminal repeat elements flanking an enhanced green fluorescent protein expression cassette) and were administered by stereotaxic-guided intracerebral injection. We found that the rAAV1 vector (rAAV1-GFP) had a 13- to 35-fold greater transduction efficiency than that of the rAAV2 vector (rAAV2-GFP). Also, rAAV1-transduced cells were observed at a greater distance from the injection site than rAAV2-transduced cells. Neurons were the predominant cell type transduced by both vector types. However, in contrast to rAAV2-GFP, rAAV1-GFP was capable of transducing glial and ependymal cells. Thus, rAAV1-based vectors have biologic properties within the brain distinct from that of rAAV2. These differences might be capitalized upon to develop novel gene transfer strategies for neurologic disorders.

Animals↗
PubMed2006

MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa.

BACKGROUND: Mitochondria are sub-cellular organelles that have a central role in energy production and in other metabolic pathways of all eukaryotic respiring cells. In the last few years, with more and more genomes being sequenced, a huge amount of data has been generated providing an unprecedented opportunity to use the comparative analysis approach in studies of evolution and functional genomics with the aim of shedding light on molecular mechanisms regulating mitochondrial biogenesis and metabolism. In this context, the problem of the optimal extraction of representative datasets of genomic and proteomic data assumes a crucial importance. Specialised resources for nuclear-encoded mitochondria-related proteins already exist; however, no mitochondrial database is currently available with the same features of MitoRes, which is an update of the MitoNuc database extensively modified in its structure, data sources and graphical interface. It contains data on nuclear-encoded mitochondria-related products for any metazoan species for which this type of data is available and also provides comprehensive sequence datasets (gene, transcript and protein) as well as useful tools for their extraction and export. DESCRIPTION: MitoRes http://www2.ba.itb.cnr.it/MitoRes/ consolidates information from publicly external sources and automatically annotates them into a relational database. Additionally, it also clusters proteins on the basis of their sequence similarity and interconnects them with genomic data. The search engine and sequence management tools allow the query/retrieval of the database content and the extraction and export of sequences (gene, transcript, protein) and related sub-sequences (intron, exon, UTR, CDS, signal peptide and gene flanking regions) ready to be used for in silico analysis. CONCLUSION: The tool we describe here has been developed to support lab scientists and bioinformaticians alike in the characterization of molecular features and evolution of mitochondrial targeting sequences. The way it provides for the retrieval and extraction of sequences allows the user to overcome the obstacles encountered in the integrative use of different bioinformatic resources and the completeness of the sequence collection allows intra- and interspecies comparison at different biological levels (gene, transcript and protein).

Animals↗
PubMed2001

Engineered antibodies take center stage.

The start of the post-genomic era provides a useful juncture for reflection on the state of antibody engineering, which will be a critical technology for relating function and pathology to genomic sequence in biology and medicine. The phenomenal progress in deciphering the human genome has given significant impetus to the application of engineered antibodies in proteomics. Thus, advances in phage display antibody libraries can now help to define novel gene function and the measurement of abnormal protein expression in pathological states. Furthermore, intrabody and antibody engineering provide vehicles for the development of molecular medicines of the future. In addition to these new directions, antibody engineering has begun to show concrete success in its long-term efforts to develop targeted immunotherapies for cancer and other diseases. The cornerstones of clinical development are the detailed academic clinical trials that continue to push the boundaries of engineered antibodies into the real world. The field displays a healthy impatience for practical results, as research accelerates with concerted efforts to transfer preclinical insights into clinical trials. Growing private and governmental expenditures will lead to the rapid expansion of life-saving immunotherapeutic agents. The present review developed from our effort to report on the 11th Annual International Conference on Antibody Engineering (3-6 December 2000). This annual meeting is a forum for discussions on the latest advances in antibody engineering groups from around the world, and now includes the broader agenda of engineering in molecular immunology. In bringing scientists together to exchange ideas at this open forum, new collaborations and the threads of new discoveries are woven. For example, Professors Gerhard Wagner (Harvard Medical School), Dennis Burton (Scripps Research Institute), and Peter Hudson (CSIRO, Melbourne, Australia) gave exciting insights on structural immunobiology that had implications across many disciplines. The growth in antibody engineering was highlighted by the attendance of some 600 participants at the meeting, doubling that of the 1999 meeting. Dramatic clinical acceptance of monoclonal antibodies during the past two years has fostered this growth, with sales in 2000 of 1.8 billion dollars and projections for 2001 of 3 billion dollars. However, economic measures cannot begin to convey the medical revolution that is being effected by these first humanized and chimerized monoclonal antibodies. At this juncture, the 10 monoclonal antibody therapeutics in clinical use are of murine origin, of which 3 are entirely murine (OKT3, Mylotarg, 90Y-labeled Bexxar), 4 have been chimerized (human constant domains replacing murine) (ReoPro, Rituxan and its 131I-labeled analogue (Zevalin), Simulect, Remicade) and 3 were chimerized and humanized (human residues being substituted for at least some mouse-specific framework residues in VH and VL) (Zenapax, Herceptin, Synagis). Fully humanized anti-CD52 (CAMPATH-1H) has also been approved by the FDA for the treatment of B-cell chronic lymphocytic leukemia and should become available in late 2001. Humanization was initially developed by Dr. Greg Winter at the MRC Laboratory of Molecular Biology (Cambridge, UK), who presented the meeting's keynote address, "Antibodies as a Paradigm for Molecular Evolution". His pioneering work in antibody phage display libraries has been reformulated into a daring approach to develop truly novel proteins with genetically paired structural elements. He described studies in combinatorial protein engineering with enormous implications for both industrial and therapeutic applications of macromolecules.

Animals↗
PubMed2000

Amorpha-4,11-diene synthase of Artemisia annua: cDNA isolation and bacterial expression of a terpene synthase involved in artemisinin biosynthesis.

Artemisia annua, an indigenous plant to Korea, contains an antimalarial sesquiterpene, artemisinin. The first committed step of artemisinin biosynthesis is the cyclization of farnesyl diphosphate by a sesquiterpene synthase to produce an amorphane-type ring system. The aims of this research were to molecularly clone and express amorpha-4,11-diene synthase for metabolic engineering. PCR amplification of genomic DNA with a pair of primers, designed from the conserved regions of sesquiterpene synthases of several plants, produced a 184-bp DNA fragment. This fragment was used in Northern blot analysis as a probe, showing approximately 2.2 kb of a single band. Its sequence information was used to produce 2106 bp of a full-length cDNA sequence including 1641 bp of open reading frame for 546 amino acids (kcs12) through a rapid amplification of cDNA ends (RACE). The deduced amino acid sequence displayed 36% identity with 5-epi-aristolochene synthase of Nicotiana tabacum. A soluble fraction of Escherichia coli harboring kcs12 catalyzed the cyclization of farnesyl diphosphate to produce a sesquiterpene, which was identified through GC-MS analysis as amorpha-4,11-diene.

Alkyl and Aryl Transferases↗
PubMed1999

On the concept of eugenics: preliminaries to a critical appraisal.

This paper's main issue is linked to what can be foreseen as the increasing capability of medical genetics to modify the genetic composition of the human species through direct interventions in the human genome for medical and non-medical purposes, i.e., the "risk" of a resurgence of eugenics. In current discussions on the topic (briefly presented in the first section), the "phantom of eugenics" is raised several times, but there is a great deal of confusion on what counts as eugenics, partly because of broad conceptual disagreement over the notion itself. Furthermore, according to some scholars there is no hope of overcoming this unsatisfactory conceptual uncertainty. Partly challenging this opinion, the second and third sections of this paper attempt to identify some basic features which could be seen as intrinsically linked to the notion of eugenics, with the aim of reducing the range of conceptual disagreement as a preliminary step in bringing into focus what exactly is wrong with practicing eugenics. The subsequent sections deal with the substantive issue of whether or not to practice eugenics from the point of view of the interest of future generations in the human species' genetic composition. The main moral arguments for and against eugenics are examined from the point of view of our obligations towards future generations, and the conclusion is in favor of a cautious "open-door" position.

Bioethics↗
PubMed2001

Biotechnology--updates and new developments.

Areas of priority for intensive discovery would be the agbiotechnology and biomedical sectors using gene technology as a platform. The use of genetic manipulation in farming and the use of plants as 'pharma' factories to manufacture therapeutics would be on the rise. The human genome will continue to have a powerful impact on research and development of human diseases and healthcare. Discovery of genetics and pharmacogenomics will have great impact on drug development and will allow the prediction of the patient' s response to various drugs as well as the onset of individualised or 'designer drugs'. Human stem cells could have their cellular clocks reset by the cloning process, enhancing opportunities to grow young cells, tissues and organs for an aging population. The cellular clock could also be reset by therapeutic cloning. Bioinformatics would be a technology which would be synonymous with biotechnology. The analyses of biotechnology research would be conducted in silico and would involve the exchange of information among sophisticated computer databases. Applications of biotechnology would be even more evident in environmental technology, food development and food processing. In electronics, the use of the specificity of proteins in biochips is underway. In tandem with the explosions in research, regulatory issues, legislation and intellectual property rights will evolve to enhance the climate of discovery and innovation. Public education will have to be continually enhanced as awareness could negate any fear resulting from novel and innovative improvements from biotechnology.

Agriculture↗
PubMed1995

Exploring molecular biology. An older surgeon looks at a new universe.

The rapidity and the magnitude of progress in molecular biology slipped by many of us practicing surgeons. Although articles about molecular medicine appear regularly in our surgical literature, for many of us, their content is rather mysterious. The articles often end with a glossary, because most readers do not understand the language. In November 1993, the entire issue of the Archives of Surgery was devoted to molecular medicine. In an editorial, Claude Organ, Jr, MD, a member of this association, encouraged the surgeon to "cohabit" with the molecular scientist. Many university departments of surgery have professors who are both surgeons and molecular biologists. Ed Passaro, MD, also a member of this association, observed in 1992 that most surgeons had overlooked this new field and needed to learn about it to play a role in applying it to clinical medicine. That means knowing what new tests and treatments are available and how to apply them. It means being able to counsel patients. Also, it is important for knowledgeable surgeons to serve on the regular hospital committees that will oversee these new tests and treatments, and to offer their unique judgment in assessing risk, reward, and ethical implications.

DNA↗
PubMed1996

Targeting of retroviral integrase by fusion to a heterologous DNA binding domain: in vitro activities and incorporation of a fusion protein into viral particles.

Retroviral DNA integration is catalyzed by a viral protein, the integrase (IN). IN recognizes sequences at the viral DNA ends, specifically nicks these ends (the processing reaction), and inserts them into host DNA (the joining reaction). The mechanism by which host DNA integration sites are selected is unknown, although it is clear that many regions are accessible to the retroviral integration machinery. To investigate integration site selection, and to possibly influence this process, we have used a model system in which the avian sarcoma virus (ASV) IN, and segments thereof, have been fused to the Escherichia coli LexA repressor protein DNA binding domain (DBD). We provide evidence that a variety of such IN-LexA DBD fusion proteins can be directed to cognate lexA operators in vitro. Binding of precise N- and C-terminal fusion proteins to the operators is associated with a significant increase in the joining of viral DNA to sites immediately adjacent to the lexA operator region. We also carried out domain exchange and deletion experiments which revealed that the highly conserved "zinc-finger" domain of ASV IN is not essential for processing of viral DNA ends or joining of viral DNA ends to DNA target sequences. Last, the C-terminal fusion was engineered into the viral genome and we show that this protein can be incorporated into viral particles. Our results suggest that it might be possible to augment IN function in vivo through a heterologous domain. These observations have implications for retroviral-mediated gene therapy.

Amino Acid Sequence↗
PubMed2006

The current status of natural products from marine fungi and their potential as anti-infective agents.

A growing number of marine fungi are the sources of novel and potentially life-saving bioactive secondary metabolites. Here, we have discussed some of these novel antibacterial, antiviral, antiprotozoal compounds isolated from marine-derived fungi and their possible roles in disease eradication. We have also discussed the future commercial exploitation of these compounds for possible drug development using metabolic engineering and post-genomics approaches.

Anti-Infective Agents↗
PubMed2004

Identification of compounds that enhance the anti-lymphoma activity of rituximab using flow cytometric high-content screening.

In this report, we describe a new flow cytometry technique termed flow cytometric high-content screening (FC-HCS) which involves semi-automated processing and analysis of multiparameter flow cytometry samples. As a first test of the FC-HCS technique, we used it to screen a 2000-compound library, called the National Cancer Institute (NCI) Diversity Set, to identify agents that would enhance the anti-lymphoma activity of the therapeutic monoclonal antibody rituximab. FC-HCS identified 15 compounds from the Diversity Set that significantly enhanced the ability of rituximab to inhibit cell cycle progression and induce apoptosis in lymphoma cells. The validity of the screening results was confirmed for several compounds using additional assays of cell proliferation, apoptosis and cell growth. The FC-HCS technique was relatively simple and reliable and could process up to 1000 samples/day on a single flow cytometer. The FC-HCS technique may be useful for a variety of applications including drug discovery, immunologic monitoring of patients, functional genomics studies and tissue engineering efforts.

Antibodies, Monoclonal↗
PubMed2006

Gene regulatory network models for plant development.

Accumulated genetic data are stimulating the use of mathematical and computational tools for studying the concerted action of genes during cell differentiation and morphogenetic processes. At the same time, network theory has flourished, enabling analyses of complex systems that have multiple elements and interactions. Reverse engineering methods that use genomic data or detailed experiments on gene interactions have been used to propose gene network architectures. Experiments on gene interactions incorporate enough detail for relatively small developmental modules and thus allow dynamical analyses that have direct functional interpretations. Generalities are beginning to emerge. For example, biological genetic networks are robust to environmental and genetic perturbations. Such dynamical studies also enable novel predictions that can lead to further experimental tests, which might then feedback to the theoretical analyses. This interplay is proving productive for understanding plant development. Finally, both experiments on gene interactions and theoretical analyses allow the identification of frequent or fixed evolutionary solutions to developmental problems, and thus are contributing to an understanding of the genetic basis of the evolution of development and body plan.

Biological Evolution↗
PubMed2003

Lignins and lignocellulosics: a better control of synthesis for new and improved uses.

The composition and structure of lignified walls has a dramatic impact on the technological value of raw materials. The chemical flexibility of the secondary cell wall has been demonstrated and it is now possible to develop strategies to optimize its composition through genetic engineering. Thanks to functional genomics, new target genes of both plant and microbial origin are rapidly becoming available for this purpose and their use will open new avenues for producing tailor-made plant products with improved properties. Moreover, the major proportion of terrestrial plant biomass comprises lignified cell walls and this reservoir of carbon should be increasingly exploited for the production of chemicals and energy within the context of sustainable development. For example, the design of plants suitable for downstream conversion processes, such as the production of bioethanol, and the exploitation of microorganisms and microbial enzymes for biomass pretreatments or for the production of novel chemicals.

Biomass↗