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PubMed1995

Silencing and heritable domains of gene expression.

Silencing is a process that assembles particular regions of eukaryotic chromosomes into transcriptionally inactive chromatin structures. Silencing involves specialized regulatory sites known as silencers and a combination of general DNA-binding proteins and proteins dedicated to silencing. In the yeast Saccharomyces cerevisiae, these proteins include transcription factors and the origin recognition complex (ORC). Silencing has three recognizably separate phases: establishment, maintenance, and inheritance. At least some silencers are origins of replication, and the establishment of the silenced state requires an S phase-specific event. Once established, the silenced state is heritable, even in the absence of proteins required for its establishment. The silencing of mating-type genes bears many similarities to telomere position effects, and the two processes require many of the same proteins.

Alleles↗
PubMed2001

Glomerular laminin isoform transitions: errors in metanephric culture are corrected by grafting.

Glomerular basement membrane (GBM) assembly and maturation are marked by the replacement of laminin-1 (containing alpha 1-, beta 1-, and gamma 1-chains) with laminin-11 (consisting of alpha 5-, beta 2-, and gamma 1-chains). Similarly, the alpha 1- and alpha 2-chains of type IV collagen are replaced by collagen alpha 3-, alpha 4-, and alpha 5(IV)-chains. The cellular origins of these molecules and mechanisms for isoform removal and substitution are unknown. To explore glomerular laminin isoform transitions in vitro, we assessed metanephric organ cultures. Standard culture conditions do not support endothelial cell differentiation, and glomerular structures that form in vitro are avascular. Nevertheless, extensive podocyte development occurs in these cultures, including the formation of foot processes and assembly of a GBM-like matrix. Here, we show that the podocyte-specific markers, glomerular epithelial protein 1 and nephrin, which are normally expressed in capillary loop stage glomeruli in vivo, are also expressed by glomerular figures that form in organ culture. However, the GBM-like segments that form in vitro do not undergo normal laminin isoform switching. Instead, both laminin alpha 1- and alpha 5-chains are present, as is the beta 1-chain, but not beta 2. When avascular organ-cultured kidneys are grafted into anterior eye chambers, however, kidney-derived angioblasts establish extensive vasculature by 6 days, and glomeruli are lined by endothelial cells. We evaluated embryonic day 12 (E12) vascular endothelial growth factor receptor (Flk1)-lacZ kidneys that had first been grown in organ culture for 6--7 days and then grafted into wild-type mice. Correct laminin isoform substitution occurred and correlated with the appearance of endothelial cells expressing Flk1. Our findings indicate that endothelial cells, and/or factors present in the circulation, mediate normal GBM laminin isoform transitions in vivo.

Amino Acid Sequence↗
PubMed2005

Nucleolus: from structure to dynamics.

The nucleolus, a large nuclear domain, is the ribosome factory of the cells. Ribosomal RNAs are synthesized, processed and assembled with ribosomal proteins in the nucleolus, and the ribosome subunits are then transported to the cytoplasm. In this review, the structural organization of the nucleolus and the dynamics of the nucleolar proteins are discussed in an attempt to link both information. By electron microscopy, three main nucleolar components corresponding to different steps of ribosome biogenesis are identified and the nucleolar organization reflects its activity. Time-lapse videomicroscopy and fluorescent recovery after photobleaching (FRAP) demonstrate that mobility of GFP-tagged nucleolar proteins is slower in the nucleolus than in the nucleoplasm. Fluorescent recovery rates change with inhibition of transcription, decreased temperature and depletion of ATP, indicating that recovery is correlated with cell activity. At the exit of mitosis, the nucleolar processing machinery is first concentrated in prenucleolar bodies (PNBs). The dynamics of the PNBs suggests a steady state favoring residence of processing factors that are then released in a control- and time-dependent manner. Time-lapse analysis of fluorescence resonance energy transfer demonstrates that processing complexes are formed in PNBs. Finally, the nucleolus appears at the center of several trafficking pathways in the nucleus.

Animals↗
PubMed1993

Salmonella typhimurium fliG and fliN mutations causing defects in assembly, rotation, and switching of the flagellar motor.

FliG, FliM, and FliN are three proteins of Salmonella typhimurium that affect the rotation and switching of direction of the flagellar motor. An analysis of mutant alleles of FliM has been described recently (H. Sockett, S. Yamaguchi, M. Kihara, V. M. Irikura, and R. M. Macnab, J. Bacteriol. 174:793-806, 1992). We have now analyzed a large number of mutations in the fliG and fliN genes that are responsible for four different types of defects: failure to assembly flagella (nonflagellate phenotype), failure to rotate flagella (paralyzed phenotype), and failure to display normal chemotaxis as a result of an abnormally high bias to clockwise (CW) or counterclockwise (CCW) rotation (CW-bias and CCW-bias phenotypes, respectively). The null phenotype for fliG, caused by nonsense or frameshift mutations, was nonflagellate. However, a considerable part of the FliG amino acid sequence was not needed for flagellation, with several substantial in-frame deletions preventing motor rotation but not flagellar assembly. Missense mutations in fliG causing paralysis or abnormal switching occurred at a number of positions, almost all within the middle one-third of the gene. CW-bias and CCW-bias mutations tended to segregate into separate subclusters. The null phenotype of fliN is uncertain, since frameshift and nonsense mutations gave in some cases the nonflagellate phenotype and in other cases the paralyzed phenotype; in none of these cases was the phenotype a consequence of polar effects on downstream flagellar genes. Few positions in FliN were found to affect switching: only one gave rise to the CW mutant bias and only four gave rise to the CCW mutant bias. The different properties of the FliM, FliG, and FliN proteins with respect to the processes of assembly, rotation, and switching are discussed.

Alleles↗
PubMed2002

Folding in vitro of light-harvesting chlorophyll a/b protein is coupled with pigment binding.

The major light-harvesting chlorophyll a/b protein (LHCIIb) of the plant photosynthetic apparatus is able to self-organise in vitro. When the recombinant apoprotein, Lhcb1, is solubilised in the denaturing detergent sodium (or lithium) dodecylsulfate (SDS or LDS) and then mixed with chlorophylls and carotenoids under renaturing conditions, structurally authentic LHCIIb forms. Assembly of functional LHCIIb, as indicated by the establishment of energy transfer between complex-bound chlorophyll molecules, occurs in two apparent kinetic steps with time constants of 10 to 30 seconds and 50 to 300 seconds, depending on the reaction conditions. Here, we use circular dichroism (CD) in the far-UV range to monitor the folding of the LHCIIb apoprotein as it is complexed with pigments. The alpha-helix content in the protein's secondary structure increases in two apparent kinetic steps with time constants similar to those observed for the establishment of chlorophyll energy transfer. When the carotenoid concentration in the reaction mixture is reduced, the time constants of alpha-helix formation increase, as do those for the appearance of chlorophyll energy transfer. This indicates that both processes, pigment assembly and secondary structure formation, are tightly coupled. A substantial amount of alpha-helix is present in dodecylsulfate-solubilised LHCIIb apoprotein and appears to be distributed among various protein domains.

Circular Dichroism↗
PubMed2006

The role of thickness transitions in convective assembly.

Here we examine the microscopic details of convective assembly, a process in which thin colloidal crystals are deposited on a substrate from suspensions of nearly monodisperse spheres. Previously, such crystals have been shown to exhibit a strong tendency toward the face-centered cubic structure, which is difficult to explain on thermodynamic grounds. Using real-time microscopic visualization, electron microscopy, and scanning confocal microscopy, we obtain clues about the crystallization mechanism. Our results indicate that the regions at which a growing crystal transitions from n to n + 1 layers can play an important and previously unrecognized role in the crystallization. For thin crystals, we show both from experiment and through simple modeling that these transition regions can generate specific crystal structures. In thicker crystals, the crystallization is more complicated, but the transition regions must still be considered before a complete understanding of convective assembly can be obtained.

Colloids↗
PubMed1985

Inhibition of testicular cytochrome P-450-dependent steroid biosynthesis by cis-platinum. Reversal by human chorionic gonadotropin.

The treatment of rats with cis-platinum for 7 days caused a profound, and seemingly selective, decrease (70-80%) in the microsomal cytochrome P-450 levels in the testis. This decrease was accompanied by marked reductions (70-80%) in steroid 17 alpha-hydroxylase activity and in plasma testosterone concentration. The treatment of rats with human chorionic gonadotropin partially restored the cytochrome P-450 concentration and 17 alpha-hydroxylase activity and permitted the plasma testosterone level to approach control values. The effect of cis-platinum on the testicular cytochrome P-450 appeared unrelated to deficiencies in heme metabolic processes, in so far that neither was the activity of delta-aminolevulinate synthetase decreased, nor was that of heme oxygenase increased. These enzymes are rate-limiting in heme biosynthesis and degradation pathways, respectively. Also, the activities of uroporphyrinogen I synthetase, delta-aminolevulinate dehydratase, and ferrochelatase and the concentration of total porphyrins in the testis remained unchanged. The sodium dodecyl sulfate-gel electrophoresis of the microsomal preparation did not reveal a diminished level of apocytochrome; however, in this preparation, heme could not be detected in molecular weight regions corresponding to cytochrome P-450. The microsomal cytochrome b5 and the mitochondrial heme concentrations were not decreased in cis-platinum-treated rats. It is suggested that the mechanism of depletive action of cis-platinum on microsomal cytochrome P-450 involves an impairment of the effective assembly of heme and apoprotein moieties. It is further suggested that the anterior pituitary hormones control the factor(s) involved in this assembly, a process which is interrupted by cis-platinum.

Animals↗
PubMed2003

The Saccharomyces cerevisiae spindle pole body is a dynamic structure.

During spindle pole body (SPB) duplication, the new SPB is assembled at a distinct site adjacent to the old SPB. Using quantitative fluorescence methods, we studied the assembly and dynamics of the core structural SPB component Spc110p. The SPB core exhibits both exchange and growth in a cell cycle-dependent manner. During G1/S phase, the old SPB exchanges approximately 50% of old Spc110p for new Spc110p. In G2 little Spc110p is exchangeable. Thus, Spc110p is dynamic during G1/S and becomes stable during G2. The SPB incorporates additional Spc110p in late G2 and M phases; this growth is followed by reduction in the next G1. Spc110p addition to the SPBs (growth) also occurs in response to G2 and mitotic arrests but not during a G1 arrest. Our results reveal several dynamic features of the SPB core: cell cycle-dependent growth and reduction, growth in response to cell cycle arrests, and exchange of Spc110p during SPB duplication. Moreover, rather than being considered a conservative or dispersive process, the assembly of Spc110p into the SPB is more readily considered in terms of growth and exchange.

Calmodulin-Binding Proteins↗
PubMed2000

Analysis of a human immunodeficiency virus type 1 gag mutant with an engineered 110-amino-acid insertion in the matrix protein domain.

A human immunodeficiency virus (HIV) matrix (MA) protein mutant was constructed by duplication of 107 codons of the HIV-1 MA domain. This MA protein duplication mutant (MAII) still could assemble and process particles, had a wild-type (wt) HIV particle density, and possessed reverse transcriptase activity of about 80% of the wild type virus level. The incorporation of HIV Env and viral RNA genome was not greatly affected. The MAII was noninfectious or poorly infectious, however, when pseudotyped with an amphotropic murine leukemia virus envelope protein or with the HIV envelope protein. Although the MAII mutant displayed an immunofluorescence staining pattern similar to that of the wild type virus, subcellular fractionation studies indicated that the membrane association of MAII Gag precursors was unstable under high-salt conditions. Electron microscopic studies showed that the mutant had a decreased density of particle cores compared with that of the wild type virus, suggesting an altered arrangement of the packed proteins. As this insertion in the MA gene caused no major effects on virus assembly implies that the HIV-1 gag has the potential to adapt large insertions of extra coding sequences without loss of the ability to direct particle assembly and release.

Blotting, Western↗
PubMed1998

Related alphaN- and epsilonN-methyltransferases methylate the large and small subunits of Rubisco.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is methylated at the ax amino position of the N-terminal methionyl residue of the processed and assembled form of the small subunit (SS), and is also methylated in some species at the epsilon-amino group of lysine-14 in the large subunit (LS). The gene (rbcMT-S) and cDNAs for the SS alphaN-methyltransferase (SSMT) from spinach (Spinach oleracea) have been cloned, sequenced, and expressed. The gene is closely related to a previously characterized LS methyltransferase (Rubisco LSMT) cDNA from pea (Rubisco LSMT) and a Rubisco LSMT gene from tobacco. Sequence analysis of the cDNA and transcript mapping experiments demonstrate that the rbcMT-S pre-mRNAs experience alternative 3' splice site selection, such that mRNAs for a long form with a four amino acid insertion and a short form are expressed at approximately equal abundance. The coding sequence of spinach SSMT includes a putative targeting presequence with sequence identity at a plastid processing site. A N-terminal truncated form of spinach SSMT was expressed and purified from E. coli cells. Both long and short forms of the cDNAs were shown to catalyze methylation of the a amine of the N-terminal methionine of the SS of Rubisco.

Alternative Splicing↗
PubMed1991

Rapid 'on-line' image processing as a tool in the evaluation of kinetic and morphological aspects of receptor-induced cell activation.

Transmembrane signalling involves rapid and spatially well defined changes in cytosolic free Ca2+, [Ca2+]i. Specific technologies involving image processing permit the analysis of kinetic and morphological aspects of [Ca2+]i at the subcellular level with the fluorescent Ca2+ probe fura-2. Fluorescence excitation wavelengths (340 nm or 380 nm) are alternated in synchrony with the acquisition at video rate of images captured with an intensified CCD camera. Images are digitized, recursively filtered, divided, and displayed after calibration of the 'ratio' image into a numerical [Ca2+]i scale. The image processor IMAGINE (Synoptics Ltd., UK) permits these operations at video rate. This produces 'on-line' [Ca2+]i images in real time which are stored on video tapes for subsequent analysis. The present communication summarizes the rationale for the selection of our current technologies. A comparison with alternative solutions should highlight the particular advantages and drawbacks of our approach. The present text thus should serve as a help for investigators who try to assemble image processing tools for work in the receptor and cellular signalling field.

Calcium↗
PubMed2002

Operational intensification by direct product sequestration from cell disruptates: application of a pellicular adsorbent in a mechanically integrated disruption-fluidised bed adsorption process.

A novel prototype adsorbent, designed for intensified fluidised bed adsorption processes, was assembled by the emulsification coating of 4% (w/v) porous agarose upon a zirconia-silica solid core. The adsorbent, designated ZSA (particle density 1.75 g/ml, maximum pellicle depth 40 microm), was subjected to physical and biochemical comparison with the performance of two commercial adsorbents (Streamline and Macrosorb K4AX). Bed expansion qualities and hydrodynamic characteristics (N, D(axl) and B(o)) of ZSA demonstrated a marked robustness in the face of elevated velocities (up to 550 cm/h) and biomass loading (up to 30% (ww/v)) disrupted yeast cells. Cibracron Blue derivatives of the pellicular prototype (ZSA-CB), evaluated in the batch and fluidised bed recovery of glyceraldehyde 3-phosphate dehydrogenase (G3PDH) from unclarified yeast disruptates, exhibited superior capacities and adsorption/desorption performance to the commercial derivatives. These advanced physical and biochemical properties facilitated a demonstration of the direct, mechanical coupling of bead-milling and fluidised bed adsorption in a fully integrated process for the accelerated recovery of G3PDH from yeast. The generic application of such pellicular adsorbents and integrated processes to the recovery of labile, intracellular products is discussed.

Adsorption↗
PubMed1992

Chondrodysplasia in transgenic mice harboring a 15-amino acid deletion in the triple helical domain of pro alpha 1(II) collagen chain.

We have generated transgenic mice by microinjection of a 39-kb mouse pro alpha 1(II) collagen gene construct containing a deletion of exon 7 and intron 7. This mutation was expected to disturb the assembly and processing of the homotrimeric type II collagen molecule in cartilage. Expression of transgene mRNA at levels equivalent or higher than the endogenous mRNA in the offspring of two founder animals resulted in a severe chondrodysplastic phenotype with short limbs, hypoplastic thorax, abnormal craniofacial development, and other skeletal deformities. The affected pups died at birth due to respiratory distress. Light microscopy of epiphyseal growth plates of transgenic pups demonstrated a marked reduction in cartilaginous extracellular matrix and disruption of the normal organization of the growth plate. The zone of proliferating chondrocytes was greatly reduced whereas the zone of hypertrophic chondrocytes was markedly increased extending deep into the diaphysis suggestive of a defect in endochondral ossification. Electron microscopic examination revealed chondrocytes with extended RER, a very severe reduction in the amount of cartilage collagen fibrils, and abnormalities in their structure. We postulate that the deletion in the alpha 1(II) collagen acts as a dominant negative mutation disrupting the assembly and secretion of type II collagen molecules. The consequences of the mutation include interference with normal endochondral ossification. These mice constitute a valuable model to study the mechanisms underlying human chondrodysplasias and normal bone formation.

Animals↗
PubMedDate not supplied

A combination of ion exchange and electrochemical reduction for nitrate removal from drinking water. Part II: electrochemical treatment of a spent regenerant solution.

The process of electrochemical treatment of a solution after strong basic anion exchanger regeneration was studied. The goal of the study was to reduce the nitrate content in the solution to allow its use in a closed loop. Diaphragmless, flow-through cells in a recirculation mode with and without a fluidizing bed of inert particles in the interelectrode space equipped with copper (Cu) cathodes and activated titanium anodes were used. The temperature was maintained at 20 degrees C. To assess the influence of recirculation of the regenerant solution on the quality of the treated water, the effect of the addition of copper ions to the solution, postelectrolysis cathode treatment, and enhanced mass transfer on the electrolysis results with respect to current efficiency and residual nitrate and nitrite concentration were investigated using an artificial solution. On the basis of the experimental results, a laboratory-scale unit for selective nitrate removal was designed and constructed that integrated ion exchange and electrochemical cell to one assembly. The process of recirculation of regenerant solution was tested using groundwater.

Ammonia↗
PubMed1996

Hebb's concept of cell assemblies and the psychophysiology of word processing.

Hebb's brain-theoretical approach suggests that tightly connected networks of neurons, Hebbian cell assemblies, are the building blocks of cognitive functions. These assemblies are not necessarily restricted to a small cortical locus but may be dispersed over distant cortical areas. Assemblies with different topographies can be postulated for different kinds of words, such as meaningful content versus grammatical function words or words eliciting motor versus visual associations. Evidence from evoked potentials and gamma-band electrocortical responses elicited by lexical material supports a cell assembly model of language and other higher cognitive functions.

Brain↗
PubMed1989

Monkey primary motor and premotor cortex: single-cell activity related to prior information about direction and extent of an intended movement.

1. This study was devoted to the neuronal processes underlying the construction of the motor program. Two monkeys were trained in a choice reaction time task to perform precise wrist flexion and extension movements of small and large extent. During a trial, the first visual signal, the preparatory signal (PS), informed the animal completely, partially, or not at all about direction and/or extent of the forthcoming movement. After a constant waiting period, a second visual signal, the response signal (RS), was illuminated calling for execution of the requested movement. 2. Reaction time (RT) and movement time (MT) measurements during the training as well as the recording sessions revealed that providing prior information about movement parameters strongly affected RT, but only slightly affected MT. Reaction time decreased in relation to the amount (number of movement parameters precued) and the type of prior information. Providing information about movement direction shortened RT much more than providing information about movement extent. Behavioral data support a parametric conception of motor programming, i.e., that the programming of the different movement parameters results from assembling separate processes of different duration. These results are compatible with the model in which programming processes are serially and hierachically ordered, movement direction being processed before movement extent. 3. Single-cell recording techniques were used to study neuronal activity of the primary motor (MI) and the premotor (PM) cortex, contralateral to the active arm. The activity of 155 neurons of MI and 158 neurons of PM was recorded during performance of the task. Of these 313 neurons, only 14 neurons did not change their activity during execution of the task. Two hundred and seven neurons whose activity changes were related to movement direction and/or movement extent have been selected for the further study. They were classified into three main groups: 1) execution-related neurons (49 in MI, 27 in PM), 2) preparation- and execution-related neurons (48 in MI, 54 in PM), and 3) preparation-related neurons (8 in MI, 21 in PM). 4. Directionally selective, execution-related neurons were found to be more frequently located within MI (81/105, 77.1%) than within PM (55/102, 53.9%), whereas directionally selective, preparation-related neurons appeared to be more frequently located within PM (47/102, 46.1%) than within MI (24/105, 22.9%).(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1984

Kinetics and mechanism in the reaction of gene regulatory proteins with DNA.

We have measured the kinetic properties of the Escherichia coli cAMP receptor protein (CAP) and lac repressor interacting with lac promoter restriction fragments. Under our reaction conditions (10 mM-Tris X HCl (pH 8.0 at 21 degrees C), 1 mM-EDTA, 10 microM-cAMP, 50 micrograms bovine serum albumin/ml, 5% glycerol), the association of CAP is at least a two-step process, with an initial, unstable complex formed with rate constant kappa a = 5(+/- 2.5) X 10(7) M-1 s-1. Subsequent formation of a stable complex occurs with an apparent bimolecular rate constant kappa a = 6.7 X 10(6) M-1 s-1. At low total DNA concentration, the dissociation rate constant for the specific CAP-DNA complex is 1.2 X 10(-4) s-1. The ratio of formation and dissociation rate constants yields an estimate of the equilibrium constant, Keq = 5 X 10(10) M-1, in good agreement with static results. We observed that the dissociation rate constant of both CAP-DNA and repressor-DNA complexes is increased by adding non-specific "catalytic" DNA to the reaction mixture. CAP dissociation by the concentration-dependent pathway is second-order in added non-specific DNA, consistent with either the simultaneous or the sequential participation of two DNA molecules in the reaction mechanism. The results imply a role for distal DNA in assembly-disassembly of specific CAP-DNA complexes, and are consistent with a model in which the subunits in the CAP dimer separate in the assembly-disassembly process. The dissociation of lac repressor-operator complexes was found to be DNA concentration-dependent as well, although in contrast to CAP, the reaction is first-order in catalytic DNA. Added excess operator-rich DNA gave more rapid dissociation than equivalent concentrations of non-specific DNA, indicating that the sequence content of the competing DNA influences the rate of repressor dissociation. The simplest interpretation of these observations is that lac repressor can be transferred directly from one DNA molecule to another. A comparison of the translocation rates calculated for direct transfer with those predicted by the one-dimensional sliding model indicates that direct transfer may play a role in the binding site search of lac repressor.

Bacterial Proteins↗
PubMed1997

Functional RT and IN incorporated into HIV-1 particles independently of the Gag/Pol precursor protein.

The expression and incorporation of retroviral enzymes into virions in the form of Gag/Pol precursor polyproteins is believed to be important for the assembly of infectious viral particles. HIV-1 encodes a 160 kDa Gag/Pol precursor that includes Gag, protease (PR), reverse transcriptase (RT) and integrase (IN). We have developed the use of HIV accessory proteins (Vpr and Vpx) as vehicles to incorporate protein of both viral and non-viral origin into virions by expression in trans as heterologous fusion proteins (Wu et al., 1995, 1996a). To analyze the role of Gag/Pol in the formation of infectious virions, we incorporated RT and IN into HIV-1 particles in trans, as fusion partners of viral protein R (Vpr). Virions derived from an RT and IN minus proviral clone were infectious and replicated through a complete cycle of infection when RT and IN proteins were provided in trans. These results demonstrate that functional RT and IN proteins can be provided in trans, and that their expression and incorporation into virions as components of Gag/Pol are not required for the formation of infectious virions. Thus, for the first time, we have demonstrated for a human pathogenic retrovirus that processes of assembly and the function of critical viral enzymes can be unlinked. This finding will provide unique opportunities to explore retroviral RT/IN function and the role of Gag/Pol in the formation of infectious virions in the context of a replicating virus (in vivo).

Blotting, Western↗