Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “TOM complex”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 703 records · Page 39Linked to original sources
PubMed2006

Revised direct radiocarbon dating of the Vindija G1 Upper Paleolithic Neandertals.

The 1998/1999 direct dating of two Neandertal specimens from level G(1) of Vindija Cave in Croatia to approximately 28,000 and approximately 29,000 radiocarbon ((14)C) years ago has led to interpretations concerning the late survival of Neandertals in south-central Europe, patterns of interaction between Neandertals and in-dispersing early modern humans in Europe, and complex biocultural scenarios for the earlier phases of the Upper Paleolithic. Given improvements, particularly in sample pretreatment techniques for bone radiocarbon samples, especially ultrafiltration of collagen samples, these Vindija G(1) Neandertal fossils are redated to approximately 32,000-33,000 (14)C years ago and possibly earlier. These results and the recent redating of a number of purportedly old modern human skeletal remains in Europe to younger time periods highlight the importance of fine chronological control when studying this biocultural time period and the tenuous nature of monolithic scenarios for the establishment of modern humans and earlier phases of the Upper Paleolithic in Europe.

Anthropology↗
PubMed2003

Breeding performance of great tits (Parus major) along a gradient of heavy metal pollution.

The possible effects of heavy metal pollution on various breeding parameters of the great tit (Parus major) were studied at four study sites in a pollution gradient near a large nonferrous smelter in Belgium during three consecutive breeding seasons. Significantly more females interrupted their laying period near the pollution source than did females farther away. At the two most polluted sites, hatching success was significantly reduced compared to two lesser-polluted study sites. Overall breeding success was also significantly lower toward the factory complex. This lowered breeding success was caused not only by the decreased hatching success toward the pollution source but also by the significant difference in fledging success among sites. Although a clear relationship was observed between the exposure to heavy metal pollution and an impaired reproduction, not all reproductive parameters were affected. We found no significant differences in the onset of laying, clutch size, length of the incubation period, and the proportion of nests with low-quality eggs among sites. Although nest box occupancy was every year slightly lower toward the smelter compared to farther away, differences among study sites were never significant.

Animals↗
PubMed2006

Ribbon synapses of the retina.

Vision is a highly complex task that involves several steps of parallel information processing in various areas of the central nervous system. Complex processing of visual signals occurs as early as at the retina, the first stage in the visual system. Various aspects of visual information are transmitted in parallel from the photoreceptors (the input neurons of the retina) through their interconnecting bipolar cells to the ganglion cells (the output neurons). Photoreceptors and bipolar cells transfer information via the release of the neurotransmitter glutamate at a specialized synapse, the ribbon synapse. Although known from early days of electron microscopy, the precise functioning of ribbon synapses has yet to be explained. In this review, we highlight recent advances towards understanding the molecular composition and function of this enigmatic synapse.

Animals↗
PubMed2003

Ykt6p is a multifunctional yeast R-SNARE that is required for multiple membrane transport pathways to the vacuole.

Intracellular membrane fusion requires that membrane-bound soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins on both vesicle and target membranes form a highly specific complex necessary to bring the membranes close in space. Ykt6p is a yeast R-SNARE protein that has been implicated in retrograde transport to the cis-Golgi compartment. Ykt6p has been also been found to fractionate with vacuole membranes and participate in a vacuolar SNARE complex in homotypic vacuole fusion. To investigate the role of Ykt6p in membrane traffic to the vacuole we generated temperature-sensitive mutations in YKT6. One mutation produces an early Golgi block to secretion, and overexpression of the SNARE protein Sft1p suppresses the growth and secretion defects of this mutation. These results are consistent with Ykt6p and Sft1p participating in a SNARE complex associated with retrograde transport to the cis-Golgi. A second set of mutations in YKT6 specifically affects post-Golgi membrane traffic to the vacuole, and the effects of these mutations are not suppressed by Sft1p overexpression. Defects are seen in carboxypeptidase Y sorting, alkaline phosphatase transport, and aminopeptidase I delivery, and in one mutant, overexpression of the SNARE protein Nyv1p suppresses the alkaline phosphatase transport defect. By mutationally separating early and late requirements for Ykt6p, our findings have revealed that Ykt6p is a R-SNARE protein that functions directly in the three biosynthetic pathways to the vacuole.

Alkaline Phosphatase↗
PubMed2005

In vitro galactosylation of human IgG at 1 kg scale using recombinant galactosyltransferase.

The Fc effector functions of immunoglobulin G (IgG) antibodies are in part determined by structural features of carbohydrates linked to each of the paired gamma heavy chains in the antibody constant domain (C(H)2). One glycoform that has been shown to be advantageous is G2, where both arms of complex bi-antennary N-glycans terminate in galactose. In vitro treatment with glycosyltransferases can remodel heterogeneous IgG glycoforms, enabling preparation of IgG molecules with homogeneous glycan chains. Here we describe optimization of conditions for use of a soluble recombinant galactosyltransferase in vitro to remodel glycans of human serum IgG, and we demonstrate a scaled-up reaction in which >98% of neutral glycans attached to 1 kg IgG are converted to the G2 glycoform. Removal of glycosylation reagents from the product is achieved in one step by affinity chromatography on immobilized Protein A.

Animals↗
PubMed2003

Functional map and domain structure of MET, the product of the c-met protooncogene and receptor for hepatocyte growth factor/scatter factor.

Little is known about the large ectodomain of MET, the product of the c-met protooncogene and receptor for hepatocyte growth factor/scatter factor (HGF/SF). Here, we establish by deletion mutagenesis that the HGF/SF and heparin-binding sites of MET are contained within a large N-terminal domain spanning the alpha-chain (amino acids 25-307) and the first 212 amino acids of the beta-chain (amino acids 308-519). Neither the cystine-rich domain (amino acids 520-561) nor the C-terminal half of MET (amino acids 562-932) bind HGF/SF or heparin directly. The MET ectodomain, which behaves as a rod-shaped monomer with a large Stokes radius in solution, binds HGF/SF in the absence or presence of heparin, and forms a stable HGF/SF-heparin-MET complex with 1:1:1 stoichiometry. We also show that the ligand-binding domain adopts a beta-propeller fold, which is similar to the N-terminal domain of alphaV integrin, and that the C-terminal half contains four Ig domains (amino acids 563-654, 657-738, 742-836, and 839-924) of the unusual structural E set, which could be modeled on bacterial enzymes. Our studies provide 3D models and a functional map of the MET ectodomain. They have broad implications for structure-function of the MET receptor and the related semaphorin and plexin proteins.

Amino Acid Sequence↗
PubMed2004

Epigenetic changes activate widespread signals in response to double-strand breaks.

Double-strand breaks are one the most severe types of DNA damage with respect to cell survival and the preservation of genomic integrity. Therefore, cells have evolved complex mechanisms including cell cycle regulation, activation of repair pathways and in certain cases induction of apoptosis in response to these lesions. The molecular details of many of the cellular responses to double-strand breaks have been well characterized. Our understanding of these responses in the context of chromatin has also progressed recently. In this review, we focus our discussion on the significance of DNA damage-induced chromatin modifications in double-strand break signaling and repair pathways. In particular, findings from recent studies suggest mechanisms by which highly localized double-strand breaks may activate widespread signals throughout the cell by inducing alterations in chromatin structure.

Animals↗
PubMed2003

The epidemiology of malaria in Papua New Guinea.

Papua New Guinea (PNG) is a patchwork of different ecological zones, inhabited by human populations of exceptional cultural and linguistic diversity. This results in complex variations in vector ecology and malaria epidemiology. Malaria is the main cause of morbidity in many health facilities in lowland areas, but it is absent in much of the highlands. All four human malaria species occur, but endemicity varies widely, with Plasmodium falciparum locally reaching holo-endemic levels that are rarely found outside sub-Saharan Africa. The high frequency of Plasmodium vivax is an important difference to most African situations. PNG is therefore a prime location for studies of interactions between different parasite species, and of the biology of local human genetic adaptation and its implications for malaria morbidity and mortality.

Animals↗
PubMed1998

Tom40 forms the hydrophilic channel of the mitochondrial import pore for preproteins [see comment].

The mitochondrial outer membrane contains machinery for the import of preproteins encoded by nuclear genes. Eight different Tom (translocase of outer membrane) proteins have been identified that function as receptors and/or are related to a hypothetical general import pore. Many mitochondrial membrane channel activities have been described, including one related to Tim23 of the inner-membrane protein-import system; however, the pore-forming subunit(s) of the Tom machinery have not been identified until now. Here we describe the expression and functional reconstitution of Tom40, an integral membrane protein with mainly beta-sheet structure. Tom40 forms a cation-selective high-conductance channel that specifically binds to and transports mitochondrial-targeting sequences added to the cis side of the membrane. We conclude that Tom40 is the pore-forming subunit of the mitochondrial general import pore and that it constitutes a hydrophilic, approximately 22 A wide channel for the import of preproteins.

Amino Acid Sequence↗
PubMed2006

Evolutionary complexity of MADS complexes.

Developmental programs rely on the timely and spatially correct expression of sets of interacting factors, many of which appear to be transcription factors. Examples of these can be found in the MADS-box gene family. This gene family has greatly expanded, particularly in plants, by a range of duplications that have enabled the genes to diversify in structure and function. MADS-box genes appear to have been instrumental in shaping one of the great evolutionary innovations, the true flower, which originated around 120-150 million years ago and led to the enormous radiation of the angiosperms. We propose a shift from analyzing individual gene functions towards studying MADS-box gene function at the subfamily level. This will enable us to distinguish subfunctionalization events from the evolutionary changes that defined floral morphology.

Biological Evolution↗
PubMed2006

Modulation of protein delivery from modular polymer scaffolds.

Growth factors are increasingly employed to promote tissue regeneration with various biomaterial scaffolds. In vitro release kinetics of protein growth factors from tissue engineering scaffolds are often investigated in aqueous environment, which is significantly different from in vivo environment. This study investigates the release of model proteins with net-positive (histone) and net-negative charge (bovine serum albumin, BSA) from various scaffolding surfaces and from encapsulated microspheres in the presence of ions, proteins, and cells. The release kinetics of proteins in media with varying concentrations of ions (NaCl) suggests stronger electrostatic interaction between the positively charged histone with the negatively charged substrates. While both proteins released slowly from hydrophobic PCL surfaces, plasma etching resulted in rapid release of BSA, but not histone. Interestingly, although negatively charged BSA released readily from negatively charged collagen (col), BSA released slowly from col-coated PCL scaffolds. Such electrostatic interaction effects were abolished in the presence of serum proteins and cells as evidenced by the rapid release of proteins from col-coated scaffolds. To achieve sustained release in the complex environment of serum proteins and cells, the model proteins were encapsulated into poly(D,L-lactic-co-glycolic acid) (PLGA) microspheres, which were embedded within col-coated PCL scaffolds. Protein release from microspheres was modulated by changing the lactide-to-glycolide ratio of PLGA polymer. BSA adsorbed to col released faster than histone encapsulated in microspheres in the presence of serum and cells. Collectively, the data suggest that growth factor release is highly influenced by scaffold surface and the presence of ions, proteins, and cells in the media. Strategies to deliver multiple growth factors and studies which investigate their release should consider these important variables.

Animals↗
PubMed2004

Application and optimization of microarray technologies for human postmortem brain studies.

A number of microarray investigations using human postmortem brain tissue have been published recently, exploring a multitude of human brain disorders with the aim of unraveling the underlying pathologies. Although the technology is still developing and lacks sufficient sensitivity with regard to detecting splice variants and low abundance transcripts, microarrays are becoming the prominent method for candidate gene screening in complex neuropsychiatric disorders. The use of postmortem tissue harbors a variety of potential pitfalls, however, which could result in unreliable or, at worst, meaningless results. During the course of our large-scale gene expression study on 150 human postmortem brain samples, using more than 200 Affymetrix GeneChips, we have identified several aspects within microarray experimental procedure that allows for the early identification of potentially unreliable samples. The general application of the guidelines and technical tips described here increase the efficiency, reliability, and amount of data generated by this powerful screening technology while reducing superfluous consumption of time and resources.

Brain Chemistry↗
PubMed2002

Biodegradation of VOCs from printing press air by an on-site pilot plant bioscrubber and laboratory scale continuous yeast cultures.

The volatile organic compound composition (VOCs) of printing press air was found to contain mostly ethanol, but also ethyl acetate, 1-propanol, 2-propanol, 1-methoxy-2-propanol and 3-ethoxy-1-propanol. A pilot plant bioscrubber inoculated with a mixed microbial population was constructed on-site. The bioscrubber was able to treat the polluted gas efficiently. It, however, suffered from strong wall growth and blockages in the column. The efficiencies of the pilot plant and a bioreactor is compared. The yeasts Candida guilliermondii and Saccharomyces cerevisiae known to tolerate ethanol were selected instead of mixed population to avoid the wall growth a nd blockages inthe bioreactor. The removal of the VOCs both individually and as a complex mixture was tested in a microcultivation system and in continuous chemostat cultures with and without cell recycling. The Candida yeast could use all the compounds as a carbon source while growth of S. cerevisiae was markedly slower on the methoxylated and ethoxylated propanols. Best total removal of the VOCs was 99% and achieved by C. guilliermondii. The only compound that was not totally removable in the chemostat experiment with C. guilliermondii was 1-methoxy-2-propanol. In laboratory scale the total and volumetric removal of VOCs by C. guilliermondii was more efficient compared to the pilot plant encouraging to scale up and applying the yeast bioreactor to real field conditions.

Air Pollutants, Occupational↗
PubMed2003

DNA sequence specificity of triplex-binding ligands.

We have examined the ability of naphthylquinoline, a 2,7-disubstituted anthraquinone and BePI, a benzo[e]pyridoindole derivative, to stabilize parallel DNA triplexes of different base composition. Fluorescence melting studies, with both inter- and intramolecular triplexes, show that all three ligands stabilize triplexes that contain blocks of TAT triplets. Naphthylquinoline has no effect on triplexes formed with third strands composed of (TC)n or (CCT)n, but stabilizes triplexes that contain (TTC)n. In contrast, BePI slightly destabilizes the triplexes that are formed at (TC)n (CCT)n and (TTC)n. 2,7-Anthraquinone stabilizes (TC)n (CCT)n and (TTC)n, although it has the greatest effect on the latter. DNase I footprinting studies confirm that triplexes formed with (CCT)n are stabilized by the 2,7-disubstituted amidoanthraquinone but not by naphthylquinoline. Both ligands stabilize the triplex formed with (CCTT)n and neither affects the complex with (CT)n. We suggest that BePI and naphthylquinoline can only bind between adjacent TAT triplets, while the anthraquinone has a broader sequence of selectivity. These differences may be attributed to the presence (naphthylquinoline and BePI) or absence (anthraquinone) of a positive charge on the aromatic portion of the ligand, which prevents intercalation adjacent to C+GC triplets. The most stable structures are formed when the stacked rings (bases or ligand) alternate between charged and uncharged species. Triplexes containing alternating C+GC and TAT triplets are not stabilized by ligands as they would interrupt the alternating pattern of charged and uncharged residues.

Anthraquinones↗
PubMed2004

Involvement of SirABC in iron-siderophore import in Staphylococcus aureus.

Staphylococcus aureus SirA was previously identified as a lipoprotein, and SirB and SirC are thought to encode the transmembrane domains of an ABC transporter. Sir proteins show similarity to iron-siderophore transporters in several bacteria. Here, we show that the iron-regulated sirABC operon is divergently transcribed from the sbn operon that encodes enzymes involved in the synthesis of staphylobactin, a recently described siderophore produced by S. aureus. Mutation of either sirA or sirB increased the resistance of iron-starved S. aureus to streptonigrin and resulted in compromised growth in iron-restricted, but not iron-rich, media. We also demonstrated that sirA and sirB mutants are compromised in the ability to transport iron complexed to staphylobactin but are not compromised for uptake of other iron complexes, such as ferric hydroxamates, ferric enterobactin, or ferric citrate. SirA- and SirB-deficient S. aureus, however, retain the ability to produce staphylobactin. Moreover, we found that transcription from the sbn operon was increased, relative to the wild type, in both sirA and sirB knockout strains, likely in response to an increased level of iron starvation in these cells. These results provide evidence of a role for these proteins in iron import in S. aureus and for full fitness of the bacterium in iron-restricted environments and demonstrate a function for S. aureus genes encoding proteins involved in the transport of an endogenously produced siderophore.

ATP-Binding Cassette Transporters↗
PubMed2002

Anti-inflammatory effects of a p38 mitogen-activated protein kinase inhibitor during human endotoxemia.

The p38 mitogen-activated protein kinase (MAPK) participates in intracellular signaling cascades resulting in inflammatory responses. Therefore, inhibition of the p38 MAPK pathway may form the basis of a new strategy for treatment of inflammatory diseases. However, p38 MAPK activation during systemic inflammation in humans has not yet been shown, and its functional significance in vivo remains unclear. Hence, we exposed 24 healthy male subjects to an i.v. dose of LPS (4 ng/kg), preceded 3 h earlier by orally administered 600 or 50 mg BIRB 796 BS (an in vitro p38 MAPK inhibitor) or placebo. Both doses of BIRB 796 BS significantly inhibited LPS-induced p38 MAPK activation in the leukocyte fraction of the volunteers. Cytokine production (TNF-alpha, IL-6, IL-10, and IL-1R antagonist) was strongly inhibited by both low and high dose p38 MAPK inhibitor. In addition, p38 MAPK inhibition diminished leukocyte responses, including neutrophilia, release of elastase-alpha(1)-antitrypsin complexes, and up-regulation of CD11b with down-regulation of L-selectin. Finally, blocking p38 MAPK decreased C-reactive protein release. These data identify p38 MAPK as a principal mediator of the inflammatory response to LPS in humans. Furthermore, the anti-inflammatory potential of an oral p38 MAPK inhibitor in humans in vivo suggests that p38 MAPK inhibitors may provide a new therapeutic option in the treatment of inflammatory diseases.

Administration, Oral↗
PubMed1999

Subordinate-level object classification reexamined.

The classification of a table as round rather than square, a car as a Mazda rather than a Ford, a drill bit as 3/8-inch rather than 1/4-inch, and a face as Tom have all been regarded as a single process termed "subordinate classification." Despite the common label, the considerable heterogeneity of the perceptual processing required to achieve such classifications requires, minimally, a more detailed taxonomy. Perceptual information relevant to subordinate-level shape classifications can be presumed to vary on continua of (a) the type of distinctive information that is present, nonaccidental or metric, (b) the size of the relevant contours or surfaces, and (c) the similarity of the to-be-discriminated features, such as whether a straight contour has to be distinguished from a contour of low curvature versus high curvature. We consider three, relatively pure cases. Case 1 subordinates may be distinguished by a representation, a geon structural description (GSD), specifying a nonaccidental characterization of an object's large parts and the relations among these parts, such as a round table versus a square table. Case 2 subordinates are also distinguished by GSDs, except that the distinctive GSDs are present at a small scale in a complex object so the location and mapping of the GSDs are contingent on an initial basic-level classification, such as when we use a logo to distinguish various makes of cars. Expertise for Cases 1 and 2 can be easily achieved through specification, often verbal, of the GSDs. Case 3 subordinates, which have furnished much of the grist for theorizing with "view-based" template models, require fine metric discriminations. Cases 1 and 2 account for the overwhelming majority of shape-based basic- and subordinate-level object classifications that people can and do make in their everyday lives. These classifications are typically made quickly, accurately, and with only modest costs of viewpoint changes. Whereas the activation of an array of multiscale, multiorientation filters, presumed to be at the initial stage of all shape processing, may suffice for determining the similarity of the representations mediating recognition among Case 3 subordinate stimuli (and faces), Cases 1 and 2 require that the output of these filters be mapped to classifiers that make explicit the nonaccidental properties, parts, and relations specified by the GSDs.

Classification↗
PubMed2002

Diastereoselective silacyclopropanations of functionalized chiral alkenes.

Lithium reduction of di-tert-butyldichlorosilane and thermal silylene transfer (105-125 degrees C) are complementary methods for the highly diastereoselective silacyclopropanations of a range of functionalized chiral olefins to afford complex silacycles. We have shown that functionalized cyclohexenes, cyclopentenes, norbornenes, and 1,1-disubstituted alkenes undergo silacyclopropanation with excellent diastereoselectivity (92:8 to >99:1). Our results demonstrate that steric interactions, rather than oxygen-directing effects, control the approach of the silylene or silylenoid intermediate to the olefin. We believe that the sterically demanding nature of the di-tert-butylsilylene species prevents coordination to the oxygen functionality. Thermal silylene transfer conditions exhibit broad functional group tolerance; the elevated temperatures for silylene transfer, however, cannot be employed for the silacyclopropanation of substituted cyclohexenes and 1,1-disubstituted alkenes. Elaboration of the resulting functionalized silacyclopropanes provides an efficient route to polyoxygenated products.

Alkenes↗