Dendrimer-like DNA-based fluorescence nanobarcodes

A major challenge in clinical diagnostics and environmental analysis is the difficulty in rapid and sensitive detection of multiple target molecules simultaneously (i.e., multiplexed detections). Our group has designed and synthesized a dendrimer-like DNA (DL-DNA) that is multivalent and anisotropic; using this unique DNA structure, we have developed a fluorescence-tagged nanobarcode system for multiplex detection. This nanobarcode system allows the rapid and sensitive detection of multiple pathogens simultaneously using the ratios of two different fluorescent dyes, green and red, with which different DL-DNAs are labeled. The key step of our nanobarcode model lies in the monodisperse preparation of DL-DNA. Two methods, solution phase and solid phase, are presented here. With slight modifications, this platform technology can also be extended to the multiplexed detection of RNA and proteins. This protocol can be completed in 2-5 d.     

Screening and industrial application of unique microbial reactions involved in nucleic acid and lipid metabolisms

Bioprocesses, which involve biocatalysts for the production of useful compounds, are expected to become a leading player in green chemistry. The first step in bioprocess development is screening for useful biological reactions in the immense number of microorganisms with infinite diversity and versatility. This review introduces some examples of bioprocess development that started from process design stemming from the discovery of unique metabolic processes, reactions, and enzymes in microbial nucleic acid and lipid metabolisms.     

Create and assess protein networks through molecular characteristics of individual proteins

MOTIVATION: The study of biological systems, pathways and processes relies increasingly on analyses of networks. Most often, such analyses focus on network topology, thereby treating all proteins or genes as identical, featureless nodes. Integrating molecular data and insights about the qualities of individual proteins into the analysis may enhance our ability to decipher biological pathways and processes. RESULTS: Here, we introduce a novel platform for data integration that generates networks on the macro system-level, analyzes the molecular characteristics of each protein on the micro level, and then combines the two levels by using the molecular characteristics to assess networks. It also annotates the function and subcellular localization of each protein and displays the process on an image of a cell, rendering each protein in its respective cellular compartment. By thus visualizing the network in a cellular context we are able to analyze pathways and processes in a novel way. As an example, we use the system to analyze proteins implicated with Alzheimers disease and show how the integrated view corroborates previous observations and how it helps in the formulation of new hypotheses regarding the molecular underpinnings of the disease. AVAILABILITY: http://www.rostlab.org/services/pinat.     

Acute depletion of heme by succinylacetone alters vascular responses but does not induce hypertension

Heme plays a critical role in blood pressure regulation because it is required by a number of enzymes that synthesize vascular modulators, including nitric oxide (NO), carbon monoxide (CO), guanosine 3',5'-cyclic monophosphate (cGMP), endothelium-derived hyperpolarizing factor (EDHF), and prostacyclin. The goal of this study was to examine the vascular effects of a short-term depletion of heme achieved through administration of the heme-synthesis inhibitor succinylacetone (SA), an irreversible inhibitor of aminolevulinic acid dehydratase (ALAD). Rats were depleted of heme by using a 4-day treatment with SA. This treatment impacted hemoenzyme function, decreasing renal nitric oxide synthase (NOS) activity (as indicated by decreased in vitro NOS activity), and increasing kidney microsomal heme oxygenase (HO) activity by 27%. SA treatment also resulted in enhanced reduction in blood pressure after infusions of exogenous NO donor MAHMA NONOate (at high dose) and acetylcholine (at low doses). Nevertheless, this SA treatment was insufficient to produce an overt elevation of basal arterial pressure. This latter lack of effect may be the result of multiple compensatory mechanisms for the regulation of blood pressure.     

Chimeric Human Immunodeficiency Virus Type 1 Containing Murine Leukemia Virus Matrix Assembles in Murine Cells

Murine cells do not support efficient assembly and release of human immunodeficiency virus type 1 (HIV-1) virions. HIV-1-infected mouse cells that express transfected human cyclin T1 synthesize abundant Gag precursor polyprotein, but inefficiently assemble and release virions. This assembly defect may result from a failure of the Gag polyprotein precursor to target to the cell membrane. Plasma membrane targeting of the precursor is mediated by the amino-terminal region of polyprotein. To compensate for the assembly block, we substituted the murine leukemia virus matrix coding sequences into an infectious HIV-1 clone. Transfection of murine fibroblasts expressing cyclin T1 with the chimeric proviruses resulted in viruses that were efficiently assembled and released. Chimeric viruses, in which the cytoplasmic tail of the transmembrane subunit, gp41, was truncated to prevent potential interference between the envelope glycoprotein and the heterologous matrix, could infect human and murine cells. They failed to further replicate in the murine cells, but replicated with delayed kinetics in human MT-4 cells. These findings may be useful for establishing a murine model for HIV-1 replication.     

Enzymatic production of pyruvate from fumarate — an application of microbial cyclic-imide-transforming pathway

For the purpose of producing pyruvate from fumarate through microbial cyclic-imide-transforming pathway, various cyclic-imide-utilizing microorganisms were isolated from soil. Among them, strain g31 was the best producer and was identified as Pseudomonas sp. With the resting cells of the strain, the conditions were optimized for pyruvate production from fumarate. The cells cultivated in the medium containing 2% (w/v) of fumarate showed the highest production with sufficient yield. The optimized wet-cell concentration, pH and temperature of the reaction were 1% (w/v), pH 6 to 7, and 30°C, respectively. Aeration was found to be an effective factor, and vigorous shaking during the reaction mixture resulted in higher production. Under the optimized reaction conditions, 100 mM of fumarate was almost stoichiometrically converted into pyruvate (94 mM) in 24 h.