Elucidating the Role of Microprocessor Protein DGCR8 in Bending RNA Structures

Although conformational dynamics of RNA molecules are potentially important in microRNA (miRNA) processing, the role of the protein binding partners in facilitating the requisite structural changes is not well understood. In previous work, we and others have demonstrated that nonduplex structural elements and the conformational flexibility they support are necessary for efficient RNA binding and cleavage by the proteins associated with the two major stages of miRNA processing. However, recent studies showed that the protein DGCR8 binds primary miRNA and duplex RNA with similar affinities. Here, we study RNA binding by a small recombinant construct of the DGCR8 protein and the RNA conformation changes that result. This construct, the DGCR8 core, contains two double-stranded RNA-binding domains (dsRBDs) and a C-terminal tail. To assess conformational changes resulting from binding, we applied small-angle x-ray scattering with contrast variation to detect conformational changes of primary-miR-16-1 in complex with the DGCR8 core. This method reports only on the RNA conformation within the complex and suggests that the protein bends the RNA upon binding. Supporting work using smFRET to study the conformation of RNA duplexes bound to the core also shows bending. Together, these studies elucidate the role of DGCR8 in interacting with RNA during the early stages of miRNA processing.     

Mitochondrial and Peroxisomal β-Oxidation of Stearic and Lignoceric Acids by Rat Brain

Crude subcellular fractions were prepared from adult rat brains by differential centrifugation of brain homogenates. Greater than 98% of the cellular mitochondrial marker enzyme activity sedimented in the heavy and light mitochondrial pellets, and less than 1% of the activity sedimented in microsomal pellets. Lysosomal marker enzyme activities mainly (71-78% of cellular activity) sedimented in the heavy and light mitochondrial pellets. Significant amounts of the lysosomal marker enzyme activity also sedimented in the crude microsomal pellets (9-13% of total) and high-speed supernatants (14-16% of total). The specific activities of microsomal and peroxisomal marker enzyme activities were highest in the crude microsomal pellets. Fractionation of the crude microsomal pellets on Nycodenz gradients resulted in the separation of the bulk of the remaining mitochondrial, lysosomal, and microsomal enzyme activities from peroxisomes. Fatty acyl-CoA synthetase activities separated on Nycodenz gradients as two distinct peaks, and the minor peak of the activities was in the peroxisomal enriched fraction. Fatty acid beta-oxidation activities also separated as two distinct peaks, and the activities were highest in the peroxisomal enriched fractions. Mitochondria were purified from the heavy mitochondrial pellets by Percoll density gradients. Fatty acyl-CoA synthetase and fatty acid beta-oxidation activities were present in both the purified mitochondrial and peroxisomal enriched fractions. Stearoyl-CoA synthetase activities were severalfold greater compared to lignoceroyl-CoA synthetase, and stearic acid beta-oxidation was severalfold greater compared to lignoceric acid beta-oxidation in purified mitochondrial and peroxisomal enriched fractions.(ABSTRACT TRUNCATED AT 250 WORDS)     

Abnormal in vivo metabolism of apoB-containing lipoproteins in human apoE deficiency

The present study was undertaken to elucidate the metabolic basis for the increased remnants and lipoprotein(a) [Lp(a)] and decreased LDL apolipoprotein B (apoB) levels in human apoE deficiency. A primed constant infusion of (13)C(6)-phenylalanine was administered to a homozygous apoE-deficient subject. apoB-100 and apoB-48 were isolated, and tracer enrichments were determined by gas chromatography-mass spectrometry, then kinetic parameters were calculated by multicompartmental modeling. In the apoE-deficient subject, fractional catabolic rates (FCRs) of apoB-100 in VLDL and intermediate density lipoprotein and apoB-48 in VLDL were 3x, 12x, and 12x slower than those of controls. On the other hand, the LDL apoB-100 FCR was increased by 2.6x. The production rate of VLDL apoB-100 was decreased by 45%. In the Lp(a) kinetic study, two types of Lp(a) were isolated from plasma with apoE deficiency: buoyant and normal Lp(a). (125)I-buoyant Lp(a) was catabolized at a slower rate in the patient. However, (125)I-buoyant Lp(a) was catabolized at twice as fast as (131)I-normal Lp(a) in the control subjects. In summary, apoE deficiency results in: 1) a markedly impaired catabolism of VLDL/chylomicron and their remnants due to lack of direct removal and impaired lipolysis; 2) an increased rate of catabolism of LDL apoB-100, likely due to upregulation of LDL receptor activity; 3) reduced VLDL apoB production; and 4) a delayed catabolism of a portion of Lp(a).     

Age estimates of two common mutations causing factor XI deficiency: recent genetic drift is not necessary for elevated disease incidence among Ashkenazi Jews

The type II and type III mutations at the FXI locus, which cause coagulation factor XI deficiency, have high frequencies in Jewish populations. The type III mutation is largely restricted to Ashkenazi Jews, but the type II mutation is observed at high frequency in both Ashkenazi and Iraqi Jews, suggesting the possibility that the mutation appeared before the separation of these communities. Here we report estimates of the ages of the type II and type III mutations, based on the observed distribution of allelic variants at a flanking microsatellite marker (D4S171). The results are consistent with a recent origin for the type III mutation but suggest that the type II mutation appeared >120 generations ago. This finding demonstrates that the high frequency of the type II mutation among Jews is independent of the demographic upheavals among Ashkenazi Jews in the 16th and 17th centuries.     

Characterization of anti-TIMP-1 monoclonal antibodies for immunohistochemical localization in formalin-fixed, paraffin-embedded tissue.

The aim of this study was to evaluate seven anti-TIMP-1 (tissue inhibitor of metalloproteinase-1) monoclonal antibodies by immunohistochemical (IHC) staining of formalin-fixed, paraffin-embedded (FFPE) tissue. Detection of the TIMP-1 protein was studied by IHC in FFPE human archival normal and neoplastic samples. Indirect IHC technique was used, and the seven antibodies (clones VT1, VT2, VT4, VT5, VT6, VT7, and VT8) were tested in various concentrations using different pretreatment protocols. All seven VT antibodies specifically immunostained the cytoplasm of islets of Langerhans cells in normal pancreas, epithelial cells of hyperplastic prostate, tumor cells of medullary thyroid carcinoma, and fibroblast-like cells of malignant melanoma. Specificity of the anti-TIMP-1 antibodies was confirmed by several controls, e.g., Western blotting on proteins extracted from FFPE tissue showed that the VT7 antibody reacted specifically with a protein band of approximately 28 kDa, corresponding to the molecular mass of TIMP-1. However, sensitivity varied with the different antibodies. Use of heat-induced epitope retrieval (HIER) and the VT7 clone applied at low concentrations demonstrated more intense immunoreactivity with the TIMP-1-positive cell types compared to the other six clones. Furthermore, when tested on a range of normal and neoplastic endocrine tissues, the VT7 clone demonstrated immunoreactivity with all neuroendocrine cell types. In conclusion, all seven antibodies detected TIMP-1 protein in various normal and neoplastic FFPE tissues, but one clone, VT7, was superior for IHC staining of TIMP-1 in FFPE tissue sections when using HIER.     

In search of genohype: A content analysis of biotechnology company documents

A symbology of power is assigned to DNA and genetics both in the media and in scientific publications. The term 'genohype' was offered by Holtzman (Are genetic tests adequately regulated? Science , 286 (4539), pp. 409-410, 1999) to characterize the discourse of exaggerated claims and hyperbole attached to DNA and the effort to map the human genome. In this paper, I examine the relationship between language and ideology in a systematic search for 'genohype' in biotechnology industry investor handbooks and annual reports. Three forms for 'genohype' are identified and one of these - 'possessing nature' - is isolated as involving the making of medicine. Using the NVivo software, a search of finance-related and health-related keywords showed that 'genohype' is basically not present in this investor material. The results are interpreted as reflecting the separate domains of financial capital and intellectual capital that are the ideological theatres for the production of medical commodities.     

INFLUENCE OF VARIOUS EXPOSURE PERIODS ON THE BIOMASS AND CHLOROPHYLL A OF CLADOPHORA GLOMERATA (CHLOROPHYTA)1

The biomass of Cladophora glomerata (L.) Kütz. was estimated at selected sites in the Colorado River between Glen Canyon Dam, Arizona, and River Kilometer 354. C. glomerata biomass was significantly higher at sites above Lees Ferry (25 km downstream from the Dam) than sites below the Ferry. Biomass and chlorophyll a were significantly reduced when C. glomerata was subjected to one-time exposures to the atmosphere for 12 daylight h in more. Repeated 12/12 h and 24/24 h (exposure/submergence) cycles over a two-week period also showed a significant reduction in biomass. The adaptations of C. glomerata to “stranding” during regulated flows are discussed.     

Recombination between Homoeologous Chromosomes of Lager Yeasts Leads to Loss of Function of the Hybrid GPH1 Gene

Yeasts used in the production of lagers contain complex allopolyploid genomes, resulting from the fusion of two different yeast species closely related to Saccharomyces cerevisiae and Saccharomyces bayanus. Recombination between the homoeologous chromosomes has generated a number of hybrid chromosomes. These recombination events provide potential for adaptive evolution through the loss or gain of gene function. We have examined the genotypic and phenotypic effects of one of the conserved recombination events that occurred on chromosome XVI in the region of YPR159W and YPR160W. Our analysis shows that the recombination event occurred within the YPR160W gene, which encodes the enzyme glycogen phosphorylase and generates a hybrid gene that does not produce mature mRNA and is nonfunctional due to frameshifts in the coding region. The loss of function of the hybrid gene leads to glycogen levels similar to those found in haploid yeast strains. The implications for the control of glycogen levels in fermentative yeasts are discussed.Yeasts used in the production of lagers, originally referred to as Saccharomyces carlsbergensis, are now classified as Saccharomyces pastorianus (18). Lager yeasts contain complex polyploid genomes with general tetraploid DNA content and are believed to have arisen from a natural fusion of two different haploid species followed by a genome duplication event or alternatively from the fusion of two diploid yeast species (2, 4, 14, 18). Subsequent genome changes, such as chromosome loss and/or duplication and translocations, have resulted in unequal numbers of chromosomes in the present-day strains, a state referred to as aneuploidy.A sequence analysis of individual genes indicated that the parental strains contributing to the hybrid strain closely resemble Saccharomyces cerevisiae and Saccharomyces bayanus (6, 15, 16). A whole-genome sequence analysis of the lager yeast strain Weihenstephan (15) identified the presence of three types of chromosomes, referred to as (i) S. cerevisiae-like chromosomes, (ii) S. bayanus-like chromosomes, and (iii) hybrids resulting from recombination events between the homoeologous parental chromosomes.Competitive genomic hybridization (CGH) analysis of two S. pastorianus strains, named CMBS-33 and 6701, identified as many as 28 specific locations where recombination between homoeologous pairs of chromosomes or chromosomal translocations may have occurred (3). Of the 28 sites identified, 13 occur at unique sites on eight different chromosomes, while the rest are in subtelomeric X elements or within 25 kbp of the telomere. Many of the genes adjacent to the recombination sites encode proteins that play essential roles in fermentation, including ADH2, ADH4, AAD6 and TDH2 (ethanol metabolism), FLO10, and PHD1 (3).We have recently shown that recombination at these “hot spots” can be induced by the exposure of lager yeasts to environmental stresses such as high temperature and high osmotic stress (13). Furthermore, fermentation under stress conditions leads to the amplification and loss of telomeric regions on a selected set of chromosomes and gene amplification radiating from the rRNA locus on chromosome XII and the DUP locus on chromosome I (13). Since a number of genes, including the MAL (maltose utilization) and the FLO (flocculation) genes, encoding proteins required for the fermentation process reside at the telomeres, such genome dynamics can have important consequences for the immediate quality and outcome of fermentation in addition to severe consequences on strain stability and purity.One of the recombination events identified by CGH analysis is located on chromosome XVI in the region of YPR159W and YPR160W. DNA to the left of the region hybridizes to S. cerevisiae microarrays, while genes between YPR160W and YPR190C and encompassing approximately 58 kb of DNA displayed a lack of hybridization to these microarrays, suggestive of a hybrid chromosome (3). Whole-genome sequence analysis of the Weihenstephan strain confirmed the existence of hybrid chromosome XVI and indicated the presence a second type of chromosome XVI containing S. bayanus-like sequences to the left of YPR159W (15, 16).To examine the genotypic and phenotypic outcomes of this recombination event, the right arm of chromosome XVI has been cloned from the yeast strain CMBS-33. Our analysis reveals that the recombination event occurred within the open reading frame (ORF) of YPR160W (GPH1) encoding the enzyme glycogen phosphorylase, which is required for the mobilization of stored glycogen through its conversion into glucose-1-P. The recombination event generates a hybrid gene that does not produce a mature mRNA and is nonfunctional due to frameshifts in the coding region.