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At least 829 records · Page 46Linked to original sources
PubMed1997

Hepatitis E virus in Nepal: similarities with the Burmese and Indian variants.

Hepatitis E has been the predominant type of acute hepatitis in Nepal both in adults and children, in sporadic and epidemic forms. We examined six hepatitis E virus (HEV) isolates obtained during an 8-year period, from 1987 to 1995, in the Kathmandu valley of Nepal. Analysis of portions of the putative helicase, polymerase and capsid genes demonstrated close genetic relatedness among themselves (> 96.4% identity) and with the Burmese (> 95.5%) and Indian (> 95.3%) isolates, and less so with the African (> 94.4%) and the Chinese (> 91%) isolates within the Asian genotype. Phylogenetic analysis placed the Nepali isolates in the Burma-India evolutionary branch and showed that the oldest isolate, TK78/87 was more similar to the Burmese isolates whereas the most recent isolates were closer to the Indian ones. Assuming no frameshifts, the Nepali isolates showed high amino acid conservation, but also unique changes when compared to other HEV isolates. Amino acid residue 614 of the capsid protein was identified as a possible marker to distinguish the Burma-Nepal-India from the China-Central Asian Republics subgenotype, and the Mexico genotype.

Adolescent↗
PubMed2001

Genomic tools for gene and protein discovery in malaria: toward new vaccines.

Advances in malaria vaccine and drug development have been hindered in part by the complex multistage life cycle of the parasite, much of which is inaccessible to study, and by a large genome encoding over 5000 genes. Two human models of immunity to malaria, however, suggest that the development of an effective vaccine is within reach. We have outlined a strategy to identify the expression of hundreds to thousands of potential vaccine targets employing recently developed technologies for gene and protein expression. Combined with the exciting developments of malaria DNA vaccine technologies, these approaches form the basis for malaria subunit vaccines that may mimic the protective efficacy of our human model systems and provide the foundation for novel approaches to vaccine development for a range of pathogens.

Animals↗
PubMed1998

Multiple sequence alignment with the Divide-and-Conquer method.

An improved algorithm for the simultaneous alignment of multiple protein and nucleic acid sequences, the Divide-and-Conquer Alignment procedure (DCA), is presented. The basic method described in Tönges,et al. (1996) (Tönges, U., Perrey, S.W., Stoye, J., Dress, A.W.M., 1996. A general method for fast multiple sequence alignment. Gene, 172, GC33-GC41) is generalized to align any number of sequences to work arbitrary (e.g. affine linear) gap penalty functions. Also, the practical efficiency of the method is improved so that families of more than 10 sequences can now be aligned simultaneously within a few seconds or minutes. After a brief description of the general method, we assess the time and memory requirements of our implementation of DCA. We present several examples showing that the program is able to deal with real-world alignment problems.

Algorithms↗
PubMed2003

Molecular genetics in the pediatric intensive care unit.

Molecular genetics and genomics have become highly relevant tools in the field of pediatric critical care medicine. The most immediate examples involve the use of molecular genetics as routine diagnostic tests (eg, detection of herpes simplex virus by PCR). Perhaps the most exciting and promising examples involve the research efforts based in these fields, which hold the potential to gain novel insight regarding the complex mechanisms involved in critical illness. Ultimately, the generation of more comprehensive and fundamental knowledge can lead to the design of more effective and specific therapeutic strategies.

Critical Care↗
PubMed2002

Novel insights into the molecular mechanisms of the antiatherosclerotic properties of antioxidants: the alternatives to radical scavenging.

Since the oxidation hypothesis of atherogenesis was first proposed, mechanisms of low density lipoprotein (LDL) oxidation and the biological properties of oxidized LDL have been investigated in depth. The major mechanism for the antiatherogenic effects of antioxidants, especially radical scavenging antioxidants, has been thought to be direct inhibition of LDL oxidation. The recently developed genomic technology has allowed this hypothesis to be addressed more rigorously than relying on the simple chemical properties of these therapeutic agents. Oxidized LDL, which is known to be proatherogenic, induces many categories of genes that have a potential involvement in the development of atherosclerotic lesions. The genes involved in cell growth, survival, adhesion, and inflammatory responses were upregulated through some nuclear receptor-depending pathways in cells exposed to stimulants such as shear stress, TNF-alpha, and oxidized LDL. On the other hand, these transcriptome analyses have shown a novel mechanism underlying phenolic antioxidants contribute to antiatherogenicity by regulating the expression of genes involved in protein degradation and transcriptional pathways. These studies reveal the often-suspected complexity of the atherogenic process and have the potential for novel therapeutic intervention.

Animals↗
PubMed2002

Lumican is a major proteoglycan component of the bone matrix.

MC3T3-E1 mouse calvaria cells are a clonal population of committed osteoprogenitors that in the presence of appropriate supplements form a mineralized bone matrix. The development of the MC3T3-E1 cells can be divided into three major stages, namely, proliferation, differentiation, and mineralization. Recently, using the cDNA microarray technology we found lumican to be abundantly expressed during the mineralization and differentiation stages of the MC3T3-E1 development and not during the proliferation stage. Lumican has been shown to play essential roles in regulating collagen fibril formation in different extracellular matrices but its expression in the developing bone matrix remains elusive. By examining the expression profile of this gene during the different stages of MC3T3-E1 development, utilizing the 'real-time' PCR technology, we observed that the expression of lumican increases as the osteoblast culture differentiates and matures, suggesting that lumican may be involved in regulating collagen fibrillogenesis in bone matrices. Using immunostaining, we observed that during the early embryonic development of mouse (E11 to E13), lumican is mainly expressed in the cartilaginous matrices. However, in the older embryos (E14 to E16), the expression of lumican is more prominent in the developing bone matrices. Our data suggest that lumican is a significant proteoglycan component of bone matrix, which is secreted by differentiating and mature osteoblasts only and therefore it can be used as a marker to distinguish proliferating pre-osteoblasts from the differentiating osteoblasts.

Animals↗
PubMed2001

MAPK specificity in the yeast pheromone response independent of transcriptional activation.

The mechanisms whereby different external cues stimulate the same mitogen-activated protein kinase (MAPK) cascade, yet trigger an appropriately distinct biological response, epitomize the conundrum of specificity in cell signaling. In yeast, shared upstream components of the mating pheromone and filamentous growth pathways activate two related MAPKs, Fus3 and Kss1, which in turn regulate programs of gene expression via the transcription factor Ste12. As fus3, but not kss1, strains are impaired for mating, Fus3 exhibits specificity for the pheromone response. To account for this specificity, it has been suggested that Fus3 physically occludes Kss1 from pheromone-activated signaling complexes, which are formed on the scaffold protein Ste5. However, we find that genome-wide expression profiles of pheromone-treated wild-type, fus3, and kss1 deletion strains are highly correlated for all induced genes and, further, that two catalytically inactive versions of Fus3 fail to abrogate the pheromone-induced transcriptional response. Consistently, Fus3 and Kss1 kinase activity is induced to an equivalent extent in pheromone-treated cells. In contrast, both in vivo and in an in vitro-reconstituted MAPK system, Fus3, but not Kss1, exhibits strong substrate selectivity toward Far1, a bifunctional protein required for polarization and G(1) arrest. This effect accounts for the failure to repress G(1)-S specific transcription in fus3 strains and, in part, explains the mating defect of such strains. MAPK specificity in the pheromone response evidently occurs primarily at the substrate level, as opposed to specific kinase activation by dedicated signaling complexes.

Cell Cycle Proteins↗
PubMed2002

Cell-biological applications of transfected-cell microarrays.

Cell microarrays are a recent addition to the set of tools available for functional genomic studies. Each cell microarray is a slide with thousands of cell clusters that are each transfected with a defined DNA, which directs either the overproduction or the inhibition of a particular gene product. By using a range of detection assays, the phenotypic consequences of perturbing each gene in mammalian cells can be probed in a systematic, high-throughput fashion. Combining well-established methods for cellular investigation with the miniaturization and multiplexing capabilities of microarrays, cell arrays are a versatile tool that can be useful in many cell-biological applications.

Cell Biology↗
PubMed2002

The use of inducible engrailed fusion proteins to study the cellular functions of eukaryotic transcription factors.

Transcription factors determine cell lineages, control cell fate, and regulate cellular responses to stimuli. Many methods are currently used to study the function of transcription factors in a cellular context and several of these involve overexpressing a constitutively active form of the protein and studying its effects. Here we outline an alternative approach involving the inducible expression of dominant-negative transcription factors in human cell lines. Dominant-negative transcription factors can be used to investigate the effect of signaling pathways on complex cellular processes that are regulated by a particular transcription factor. Potent dominant-negative transcription factors can be created by using fusions to the engrailed repressor domain. These fusion proteins can be coupled to inducible expression systems such as the ecdysone-inducible system. The ability to control protein expression has several benefits including the ability to create stable cell lines that express potentially cytotoxic proteins. Therefore when used in tandem, these two methods constitute a new and improved approach for dissecting the cellular role and transcriptional targets of many transcription factors. Here we illustrate this integrated approach by using a conditional dominant-negative Elk-1 protein to identify candidate Elk-1-regulated target genes.

Animals↗
PubMed1999

Discrimination of DNA duplexes with matched and mismatched tandem repeats by T4 endonuclease VII.

A simple in situ method for scoring short tandem DNA repeat length has been developed using T4 endonuclease VII. This method measures tandem repeated simple sequences embedded in unique sequences. Single-stranded loops are formed on duplexes containing mismatched (different) numbers of tandem repeats. No single stranded loops are formed on structures containing matched (identical) numbers of tandem repeats. The matched and mismatched loop structures were distinguished and differentially labeled by enzymatic treatment with T4 endonuclease VII.

Bacteriophage T4↗
PubMed2000

Monitoring gene expression using DNA microarrays.

The concurrent development of high-density array technologies and the complete sequencing of a number of microbial genomes is providing the opportunity to comprehensively and efficiently survey the transcription profile of microorganisms under different conditions and well-defined genotypes. Microarray-based studies are uncovering broad patterns of genetic activity, providing new understanding of gene functions and, in some cases, generating unexpected insight into transcriptional processes and biological mechanisms. One topic that has come to the forefront is how best to effectively manage and interpret the large data sets being generated. Although progress has been made, this remains a challenging opportunity for functional genomics research.

Gene Expression Regulation, Bacterial↗
PubMed2006

Functional characterization of gibberellin-regulated genes in rice using microarray system.

Gibberellin (GA) is collectively referred to a group of diterpenoid acids, some of which act as plant hormones and are essential for normal plant growth and development. DNA microarray technology has become the standard tool for the parallel quantification of large numbers of messenger RNA transcripts. The power of this approach has been demonstrated in dissecting plant physiology and development, and in unraveling the underlying cellular signaling pathways. To understand the molecular mechanism by which GA regulates the growth and development of plants, with reference to the monocot model plant-rice, it is essential to identify and analyze more genes and their products at the transcription and translation levels that are regulated by GA. With the availability of draft sequences of two major rice types, indica and japonica rice, it has become possible to analyze global expression profiles of genes on a genome scale. In this review, the progress made in finding new genes in rice leaf sheath using microarray system and their characterization is discussed. It is believed that the findings made in this regard have important implications for understanding the mechanism by which GA regulates the growth and development of rice.

Gene Expression Regulation, Plant↗