Publications

frodos found: behold the cenp-a "ring" bearers.	cenp-a is a histone h3-like protein specific to centromeres that is essential for kinetochore formation and accurate chromosome segregation in eukaryotes. recent studies (dunleavy et al., 2009; foltz et al., 2009; perpelescu et al., 2009; pidoux et al., 2009; williams et al., 2009) analyze cenp-a binding proteins required for the recruitment of cenp-a to centromeres in humans and in fission yeast, bringing us closer to understanding how centromere identity is faithfully propagated.	2009	19410539
the secret message of heterochromatin: new insights into the mechanisms and function of centromeric and pericentric repeat sequence transcription.	in the fission yeast, s. pombe, small dsrna generated by rnai-dependent mechanisms are involved in the establishment and maintenance of heterochromatic regions. the existence of conserved features within the general organization of centromeric and pericentromeric repeats in yeast, mouse and human argues in favor of a conserved role for centromeric and pericentromeric-derived transcripts across these species. in support of this, evidence is accumulating that centromeric and pericentromeric sequen ...	2009	19412885
nutrient control of torc1, a cell-cycle regulator.	it is well established that the target of rapamycin (tor) protein kinase has pivotal roles in controlling cell functions (including protein synthesis, cell growth and cell proliferation) and is implicated in numerous human diseases. mammalian tor complex 1 (mtorc1) signalling is activated by hormones and growth factors, and is also stimulated by intracellular amino acids. recent research has provided important new insight into the poorly understood mechanism by which amino acids activate mtorc1 ...	2009	19419870
the dyslexia-associated protein kiaa0319 interacts with adaptor protein 2 and follows the classical clathrin-mediated endocytosis pathway.	recently, genetic studies have implicated kiaa0319 in developmental dyslexia, the most common of the childhood learning disorders. the first functional data indicated that the kiaa0319 protein is expressed on the plasma membrane and may be involved in neuronal migration. further analysis of the subcellular distribution of the overexpressed protein in mammalian cells indicates that kiaa0319 can colocalize with the early endosomal marker early endosome antigen 1 (eea1) in large intracellular vesic ...	2009	19419997
the yeast pif1 helicase prevents genomic instability caused by g-quadruplex-forming ceb1 sequences in vivo.	in budding yeast, the pif1 dna helicase is involved in the maintenance of both nuclear and mitochondrial genomes, but its role in these processes is still poorly understood. here, we provide evidence for a new pif1 function by demonstrating that its absence promotes genetic instability of alleles of the g-rich human minisatellite ceb1 inserted in the saccharomyces cerevisiae genome, but not of other tandem repeats. inactivation of other dna helicases, including sgs1, had no effect on ceb1 stabil ...	2009	19424434
expression of candida glabrata adhesins after exposure to chemical preservatives.	adherence of candida glabrata, an opportunistic yeast pathogen, to host cells is mediated in part by the epa family of adhesins, which are encoded largely at subtelomeric loci, where they are subject to transcriptional silencing. in analyzing the regulation of the subtelomeric epa6 gene, we found that its transcription is highly induced after exposure to methylparaben, propylparaben, or sorbate. these weak acid-related chemicals are widely used as antifungal preservatives in many consumer goods, ...	2009	19426114
assessing reliability of protein-protein interactions by integrative analysis of data in model organisms.	protein-protein interactions play vital roles in nearly all cellular processes and are involved in the construction of biological pathways such as metabolic and signal transduction pathways. although large-scale experiments have enabled the discovery of thousands of previously unknown linkages among proteins in many organisms, the high-throughput interaction data is often associated with high error rates. since protein interaction networks have been utilized in numerous biological inferences, th ...	2009	19426453
hset1: a novel approach for colon cancer therapy.	histone-methyl transferases (hmts) are key enzymes that post-translationally modify histones, and serve key role in gene expression, epigenetic regulation, and as determinants of survival in malignant cells. recent studies have shed light on the role of hset1 which is a key element of highly conserved multi-protein hmt complex that catalyze methylation of histone h3 lysine 4 (h3k4) regulating expression of specific proteins important for the malignant phenotype. to understand the importance of d ...	2009	19426701
n-acetyl cysteine protects against ionizing radiation-induced dna damage but not against cell killing in yeast and mammals.	ionizing radiation (ir) induces dna strand breaks leading to cell death or deleterious genome rearrangements. in the present study, we examined the role of n-acetyl-l-cysteine (nac), a clinically proven safe agent, for it's ability to protect against gamma-ray-induced dna strand breaks and/or dna deletions in yeast and mammals. in the yeast saccharomyces cerevisiae, dna deletions were scored by reversion to histidine prototrophy. human lymphoblastoid cells were examined for the frequency of gamm ...	2009	19427509
a novel recombinant human lactoferrin augments the bcg vaccine and protects alveolar integrity upon infection with mycobacterium tuberculosis in mice.	lactoferrin, an iron binding glycoprotein, possesses multiple immune modulatory activities, including the ability to promote antigen specific cell-mediated immunity. previous studies showed that adding bovine lactoferrin to the bcg vaccine (an attenuated strain of mycobacterium bovis bacillus calmette guerin) resulted in increased host protective responses upon subsequent challenge with virulent erdman mycobacterium tuberculosis (mtb) in mice. the studies outlined here investigate utility of a n ...	2009	19428915
a novel member of solute carrier family 25 (slc25a42) is a transporter of coenzyme a and adenosine 3',5'-diphosphate in human mitochondria.	mitochondrial carriers are a family of proteins that transport metabolites, nucleotides, and cofactors across the inner mitochondrial membrane thereby connecting cytosolic and matrix functions. the essential cofactor coenzyme a (coa) is synthesized outside the mitochondrial matrix and therefore must be transported into mitochondria where it is required for a number of fundamental processes. in this work we have functionally identified and characterized slc25a42, a novel human member of the mitoc ...	2009	19429682
decapping is preceded by 3' uridylation in a novel pathway of bulk mrna turnover.	both end structures of eukaryotic mrnas, namely the 5' cap and 3' poly(a) tail, are necessary for transcript stability, and loss of either is sufficient to stimulate decay. mrna turnover is classically thought to be initiated by deadenylation, as has been particularly well described in saccharomyces cerevisiae. here we describe two additional, parallel decay pathways in the fission yeast schizosaccharomyces pombe. first, in fission yeast mrna decapping is frequently independent of deadenylation. ...	2009	19430462
expression of hepatitis b surface antigen s domain in recombinant saccharomyces cerevisiae using gal1 promoter.	hepatitis b virus, a member of the hepadnavirus family, causes the acute and chronic diseases of the human liver. the s domain of hepatitis b virus surface antigen (shbsag) was expressed under the control of the galactose-inducible gal1 promoter in recombinant saccharomyces cerevisiae. batch fermentation of s. cerevisiae 2805/pdeltamfalpha-shbsag resulted in 4.92gl(-1) dry cell mass and 2.21mgl(-1) shbsag concentration. to improve the expression level of shbsag, the pdi1 gene encoding protein di ...	2009	19433220
[hev capsid protein interacts with cyp 2a6 and decreases its coumarin 7-hydroxylation activity].	e2 is a recombinant hepatitis e virus capsid protein including its main antigenic determinants but lacking of the particle assembling domain. p239 was the c-terminal extending protein of e2 and could self-assemble to form virus like particles, which might serve as mimicry of virions both structurally and antigenically. we previously used yeast two-hybrid system to screen proteins interacting with e2 based on a human hepatocyte cdna library. one candidate was identified as the segment (aa388-437) ...	2009	19437879
prl-3 promotes epithelial mesenchymal transition by regulating cadherin directly.	prl-3 is a key gene associated with progression and metastasis of colorectal cancer. recently prl-3 was suggested to promote epithelial mesenchymal transition (emt) by downregulating e-cadherin expression. but the mechanisms of emt induced by prl-3 remain largely unknown. here we found that prl-3 could also promote emt in a colorectal cancer cell model sw480 with deficient e-cadherin expression in vivo and in vitro. prl-3 stable overexpression or knockdown sw480 cells were injected subcutaneousl ...	2009	19440036
hares and tortoises: the high- versus low-throughput proteomic race.	the analysis of the proteome can be undertaken with parallel, high-throughput techniques or those that analyze proteins in a serial, one-at-a-time manner. the former include 2-d gels and shotgun ms/ms; the latter includes libraries containing fusion proteins (gst, green fluorescent protein, tap-tag and others) that are engineered onto each protein in a proteome and then studied one by one. in this review, we explore the progress that these scientifically contrasting paradigms have made in measur ...	2009	19441020
the search for a human holliday junction resolvase.	four-way dna intermediates, known as holliday junctions, are formed during mitotic and meiotic recombination, and their efficient resolution is essential for proper chromosome segregation. bacteria, bacteriophages and archaea promote holliday junction resolution by the introduction of symmetrically related nicks across the junction, in reactions mediated by holliday junction resolvases. in 2008, after a search that lasted almost 20 years, a holliday junction resolvase was identified in humans. t ...	2009	19442245
plasmodial aspartyl-trna synthetases and peculiarities in plasmodium falciparum.	distinctive features of aspartyl-transfer rna (trna) synthetases (asprs) from the protozoan plasmodium genus are described. these apicomplexan asprss contain 29-31 amino acid insertions in their anticodon binding domains, a remarkably long n-terminal appendix that varies in size from 110 to 165 amino acids and two potential initiation codons. this article focuses on the atypical functional and structural properties of plasmodium falciparum cytosolic asprs, the causative parasite of human malaria ...	2009	19443655
what was the set of ubiquitin and ubiquitin-like conjugating enzymes in the eukaryote common ancestor?	ubiquitin (ub)-conjugating enzymes (e2) are key enzymes in ubiquitination or ub-like modifications of proteins. we searched for all proteins belonging to the e2 enzyme super-family in seven species (homo sapiens, mus musculus, drosophila melanogaster, caenorhabditis elegans, schizosaccharomyces pombe, saccharomyces cerevisiae, and arabidopsis thaliana) to identify families and to reconstruct each family's phylogeny. our phylogenetic analysis of 207 genes led us to define 17 e2 families, with 37 ...	2009	19452197
artificial beta-defensin based on a minimal defensin template.	we have designed and chemically synthesized an artificial beta-defensin based on a minimal template derived from the comparative analysis of over 80 naturally occurring sequences. this molecule has the disulfide-bridged beta-sheet core structure of natural beta-defensins and shows a robust salt-sensitive antimicrobial activity against bacteria and yeast, as well as a chemotactic activity against immature dendritic cells. an sar (structure-activity relationship) study using two truncated fragment ...	2009	19453294
inhibitor of nuclear factor-kappab alpha derepresses hypoxia-inducible factor-1 during moderate hypoxia by sequestering factor inhibiting hypoxia-inducible factor from hypoxia-inducible factor 1alpha.	hypoxia and inflammation often develop concurrently in numerous diseases, and both hypoxia-inducible factor (hif)-1alpha and nuclear factor-kappab (nf-kappab) are key transcription factors of stress response genes. an nf-kappab inhibitor, inhibitor of nf-kappab alpha (ikappab alpha), was found to interact with factor inhibiting hif (fih) and to be hydroxylated by fih. however, fih did not functionally regulate ikappab alpha, and the consequence of the fih-ikappab alpha interaction thus remains u ...	2009	19456861
schizosacharomyces pombe rna polymerase ii at 3.6-a resolution.	the second structure of a eukaryotic rna polymerase ii so far determined, that of the enzyme from the fission yeast schizosaccharomyces pombe, is reported here. comparison with the previous structure of the enzyme from the budding yeast saccharomyces cerevisiae reveals differences in regions implicated in start site selection and transcription factor interaction. these aspects of the transcription mechanism differ between s. pombe and s. cerevisiae, but are conserved between s. pombe and humans. ...	2009	19458260
regenerative medicine bioprocessing: concentration and behavior of adherent cell suspensions and pastes.	regenerative medicines based on human cells demand their harvesting, culture, and processing. manufacturing processes are likely to include cell concentration and subsequent controlled dosing of concentrates, for example, to the patient or tissue construct. the integrity and functionality of the cells must be maintained during these processing stages. in this study the performance of two different cell concentration protocols (involving centrifugation and resuspension) are compared and considera ...	2009	19459141
[overexpression, purification and helicase activity analysis of recombinant human pif1 protein].	pif1 subfamily helicase is conserved from yeast to humans with a lot of cellular functions. in order to elucidate the function of human pif1 helicase from biochemical level, we cloned human pif1 gene by pcr from hela cell cdna library. we co-transformed a pmstrna1 plasmid encoding rare trna codons and a plasmid encoding molecular chaperon to greatly enhance the overexpression of human pif1 protein. finally we purified full-length pif1 helicase by column chromatograph carried out at 4 degrees c u ...	2009	19459334
evidence that ct694 is a novel chlamydia trachomatis t3s substrate capable of functioning during invasion or early cycle development.	chlamydia trachomatis is an obligate intracellular parasite, occupies a membrane-bound vacuole throughout development and is capable of manipulating the eukaryotic host by translocating effector molecules via a type iii secretion system (t3ss). the infectious chlamydial elementary body (eb) is metabolically inactive yet possesses a functional t3s apparatus capable of translocating effector proteins into the host cell to facilitate invasion and other early cycle events. we present evidence here t ...	2009	19460098
candida albicans cas5, a regulator of cell wall integrity, is required for virulence in murine and toll mutant fly models.	candida albicans is the most common human fungal pathogen, yet the pathogenesis of c. albicans infection remains incompletely understood. we hypothesized that c. albicans has developed evolutionarily conserved mechanisms to invade disparate hosts and tested whether toll mutant flies could serve as a model host for high-throughput screening of c. albicans virulence genes. we screened 34 c. albicans mutants defective in putative transcription factor genes (see http://www.tigr.org/tigr-scripts/e2k1 ...	2009	19463063
thromboxane a2-induced signal transduction is negatively regulated by kiaa1005 that directly interacts with thromboxane a2 receptor.	thromboxane a(2) (txa(2)), a potent inducer of platelet aggregation and smooth muscle contraction, exerts its action through txa(2) receptor (tp). there are two alternative splicing variants of tp, tp alpha and tp beta. to clarify the signal transduction of tp pathway, we searched for putative tp binding proteins using a yeast two-hybrid system with the c-terminal region of tp alpha or tp beta as bait. we found kiaa1005 as a novel interacting protein of the tp alpha and tp beta c-terminal region ...	2009	19464661
genome sequence of the recombinant protein production host pichia pastoris.	the methylotrophic yeast pichia pastoris is widely used for the production of proteins and as a model organism for studying peroxisomal biogenesis and methanol assimilation. p. pastoris strains capable of human-type n-glycosylation are now available, which increases the utility of this organism for biopharmaceutical production. despite its biotechnological importance, relatively few genetic tools or engineered strains have been generated for p. pastoris. to facilitate progress in these areas, we ...	2009	19465926
solution structure of s. cerevisiae pdcd5-like protein and its promoting role in h(2)o(2)-induced apoptosis in yeast.	human pdcd5 protein is a novel programmed cell death-promoting molecule. however, the function of ymr074cp, a s. cerevisiae homologue of hpdcd5, is still unknown. heteronuclear nmr methods were used to determine the solution structure of the n-terminal 116-residue fragment (n116) of ymr074cp protein. n116 is shown to be a heterogeneous ensemble of flexibly folded conformations, adopting an extended triple-helix bundle fold that is connected to a mobile but structured alpha-helix in the n-terminu ...	2009	19469552
biotechnological synthesis of the designer drug metabolite 4'-hydroxymethyl-alpha-pyrrolidinohexanophenone in fission yeast heterologously expressing human cytochrome p450 2d6--a versatile alternative to multistep chemical synthesis.	1-(4-methylphenyl)-2-pyrrolidin-1-ylhexan-1-one (4'-methyl-alpha-pyrrolidinohexanophenone, mphp) is a new designer drug that appeared on the illicit drug market. it is mainly metabolized to 4'-hydroxymethyl-alpha-pyrrolidinohexanophenone (ho-mphp) followed by oxidation to the respective carboxylic acid. for studies on the quantitative involvement of human cytochrome p450 (cyp) isoenzymes in the initial hydroxylation, a reference standard of ho-mphp was needed. therefore, the aim of this study wa ...	2009	19470220
mouse models of altered protein kinase a signaling.	protein kinase a (pka) is an evolutionarily conserved protein which has been studied in model organisms from yeast to man. although the camp-pka signaling system was the first mammalian second messenger system to be characterized, many aspects of this pathway are still not well understood. owing to findings over the past decade implicating pka signaling in endocrine (and other) tumorigenesis, there has been renewed interest in understanding the role of this pathway in physiology, particularly as ...	2009	19470615
tax1 enhances cancer cell proliferation via ras-raf-mek-erk signaling pathway.	erbin is an erbb2 binding protein, which belongs to the lap (leucine-rich repeat (lrr) and pdz domain) protein family. we previously reported that tax1, a protein of the human t-cell leukemia virus type i (htlv-i), associated with erbin by using erbin pdz domain as a bait to screen a human t lymphocyte cdna library by a yeast two hybrid strategy. in the present study, we demonstrated that tax1 enhances cancer cell proliferation via ras-raf-mek-erk signaling pathway by using molecular section str ...	2009	19472191
small rnas derived from snornas.	small nucleolar rnas (snornas) guide rna modification and are localized in nucleoli and cajal bodies in eukaryotic cells. components of the rna silencing pathway associate with these structures, and two recent reports have revealed that a human and a protozoan snorna can be processed into mirna-like rnas. here we show that small rnas with evolutionary conservation of size and position are derived from the vast majority of snorna loci in animals (human, mouse, chicken, fruit fly), arabidopsis, an ...	2009	19474147
an additional role for sumo in ubiquitin-mediated proteolysis.	although the post-translational modification of proteins with small ubiquitin-like modifier (sumo) has a role in many biological processes, it was thought that sumo, unlike ubiquitin, does not target proteins for degradation. however, these views need to be revised, as recent findings in yeast and human cells indicate that sumo can act as a signal for the recruitment of e3 ubiquitin ligases, which leads to the ubiquitylation and degradation of the modified protein.	2009	19474794
mitofusins and opa1 mediate sequential steps in mitochondrial membrane fusion.	mitochondrial fusion requires the coordinated fusion of the outer and inner membranes. three large gtpases--opa1 and the mitofusins mfn1 and mfn2--are essential for the fusion of mammalian mitochondria. opa1 is mutated in dominant optic atrophy, a neurodegenerative disease of the optic nerve. in yeast, the opa1 ortholog mgm1 is required for inner membrane fusion in vitro; nevertheless, yeast lacking mgm1 show neither outer nor inner membrane fusion in vivo, because of the tight coupling between ...	2009	19477917
family classification without domain chaining.	motivation: classification of gene and protein sequences into homologous families, i.e. sets of sequences that share common ancestry, is an essential step in comparative genomic analyses. this is typically achieved by construction of a sequence homology network, followed by clustering to identify dense subgraphs corresponding to families. accurate classification of single domain families is now within reach due to major algorithmic advances in remote homology detection and graph clustering. howe ...	2009	19478015
region of elongation factor 1a1 involved in substrate recognition by legionella pneumophila glucosyltransferase lgt1: identification of lgt1 as a retaining glucosyltransferase.	lgt1 is one of the glucosyltransferases produced by the gram-negative bacterium legionella pneumophila. this enzyme modifies eukaryotic elongation factor 1a (eef1a) at serine 53, which leads to inhibition of protein synthesis and death of target cells. here we studied the region of eef1a, which is essential for substrate recognition by lgt1. we report that the decapeptide (50)gkgsfkyawv(59) of eef1a is efficiently modified by lgt1. this peptide covers the loop of the helix-loop-helix region form ...	2009	19478083
a novel human nata nalpha-terminal acetyltransferase complex: hnaa16p-hnaa10p (hnat2-hard1).	protein acetylation is among the most common protein modifications. the two major types are post-translational nepsilon-lysine acetylation catalyzed by kats (lysine acetyltransferases, previously named hats (histone acetyltransferases) and co-translational nalpha-terminal acetylation catalyzed by nats (n-terminal acetyltransferases). the major nat complex in yeast, nata, is composed of the catalytic subunit naa10p (n alpha acetyltransferase 10 protein) (ard1p) and the auxiliary subunit naa15p (n ...	2009	19480662
[anti-glycan antibodies establish an unexpected link between c. albicans and crohn disease].	almost 80 % of the dry weight of the yeast cell wall is composed of glycans including mannans, glucans and chitin. within this variable and complex edifice, glycans play a major role in their relation with the environment. experimental antibodies allowed to define the localization, the variability of expression and the biological role of numerous natural oligosaccharidic sequences. these glycans and their synthetic analogues were used to study the human humoral response during invasive candidias ...	2009	19480828
dynamics of the spindle pole body of the pathogenic yeast cryptococcus neoformans examined by freeze-substitution electron microscopy.	cryptococcus neoformans is an opportunistic human pathogen belonging to basidiomycetous fungi and has unique properties in cell cycle progression. in the present study, dynamics of the spindle pole body (spb) during the cell cycle was examined using freeze-substitution and serial thin-sectioning electron microscopy. the spb was located on the outer nuclear envelope and appeared either dumbbell- or bar-shaped in g1 through g2 phases. at the beginning of prophase, globular elements of the spb enla ...	2009	19486162
laminin-511 and fibronectin degradation with candida yeast.	the invasion mechanism of candida yeast is still partly unknown. in this study, we tested the ability of different commensal candida yeast to degrade two basement membrane and extracellular matrix proteins: laminin-511 (lm-511) and plasma fibronectin.	2009	19486268
multivesicular endosome biogenesis in the absence of escrts.	the endosomal sorting complex required for transport (escrt) protein machinery comprises four complexes, escrt-0, escrt-i, escrt-ii and escrt-iii, that facilitate receptor sorting into the lumen of multivesicular endosomes (mves) in order to terminate signalling receptors for final degradation within the lysosomes. even though escrt proteins appear to be essential for the biogenesis of mves in saccharomyces cerevisae, it is not clear whether escrt-independent pathways for mve biogenesis exist in ...	2009	19490536
suppression of rft1 expression does not impair the transbilayer movement of man5glcnac2-p-p-dolichol in sealed microsomes from yeast.	to further evaluate the role of rft1 in the transbilayer movement of man(5)glcnac(2)-p-p-dolichol (m5-dlo), a series of experiments was conducted with intact cells and sealed microsomal vesicles. first, an unexpectedly large accumulation (37-fold) of m5-dlo was observed in rft1-depleted cells (yg1137) relative to glc(3)man(9)glcnac(2)-p-p-dol in wild type (ss328) cells when glycolipid levels were compared by fluorophore-assisted carbohydrate electrophoresis analysis. when sealed microsomes from ...	2009	19494107
identification and characterisation of a novel anti-viral peptide against avian influenza virus h9n2.	avian influenza viruses (aiv) cause high morbidity and mortality among the poultry worldwide. their highly mutative nature often results in the emergence of drug resistant strains, which have the potential of causing a pandemic. the virus has two immunologically important glycoproteins, hemagglutinin (ha), neuraminidase (na), and one ion channel protein m2 which are the most important targets for drug discovery, on its surface. in order to identify a peptide-based virus inhibitor against any of ...	2009	19497129
new atpase regulators--p97 goes to the pub.	the conserved eukaryotic aaa-type atpase complex, known as p97 or vcp in mammals and cdc48 in yeast, is involved in a number of cellular pathways, including fusion of homotypic membranes, protein degradation, and activation of membrane-bound transcription factors. most likely, p97 is directed to this broad spectrum of cellular functions through its binding to specific cofactors. more than 20 different p97 cofactors have been described to date and our understanding of their cellular functions is ...	2009	19497384
identification of autophagy genes in ciona intestinalis: a new experimental model to study autophagy mechanism.	programmed cell death (pcd) is a mechanism implicated in many physiological and pathological processes. until recently, apoptosis (self-killing) was the most largely studied mechanism of pcd but a growing number of laboratories are now interested in autophagy (self-eating). in the past few years data showing a tight link between both pathways has accumulated. until now our laboratory used ciona intestinalis, a chordate model in which in vivo experiments are possible, to study apoptosis. recently ...	2009	19502774
the c-terminal domain of cenp-c displays multiple and critical functions for mammalian centromere formation.	cenp-c is a fundamental component of functional centromeres. the elucidation of its structure-function relationship with centromeric dna and other kinetochore proteins is critical to the understanding of centromere assembly. cenp-c carries two regions, the central and the c-terminal domains, both of which are important for the ability of cenp-c to associate with the centromeric dna. however, while the central region is largely divergent in cenp-c homologues, the c-terminal moiety contains two re ...	2009	19503796
systematic study of protein sumoylation: development of a site-specific predictor of sumosp 2.0.	protein sumoylation is an important reversible post-translational modification on proteins, and orchestrates a variety of cellular processes. recently, computational prediction of sumoylation sites has attracted much attention for its cost-efficiency and power in genomic data mining. in this work, we developed sumosp 2.0, an accurate computing program with an improved group-based phosphorylation scoring algorithm. our analysis demonstrated that sumosp 2.0 has greater prediction accuracy than sum ...	2009	19504496
combined therapy with amphotericin b and caspofungin in an experimental model of disseminated histoplasmosis.	to assess the effect of amphotericin b and caspofungin, as well as their combinations in the therapy of experimental disseminated histoplasmosis.	2009	19507469
yip1a regulates the copi-independent retrograde transport from the golgi complex to the er.	yip1a, a mammalian homologue of yeast yip1p, is a multi-spanning membrane protein that is considered to be involved in transport between the endoplasmic reticulum (er) and the golgi. however, the precise role of yip1a in mammalian cells remains unclear. we show here that endogenous yip1a is localized to the er-golgi intermediate compartment (ergic). knockdown of yip1a by rnai did not induce morphological changes in the golgi, er, or ergic. by analyzing a number of intracellular transport pathway ...	2009	19509059
functional role for senataxin, defective in ataxia oculomotor apraxia type 2, in transcriptional regulation.	ataxia oculomotor apraxia type 2 (aoa2) is an autosomal recessive neurodegenerative disorder characterized by cerebellar ataxia and oculomotor apraxia. the gene mutated in aoa2, setx, encodes senataxin, a putative dna/rna helicase which shares high homology to the yeast sen1p protein and has been shown to play a role in the response to oxidative stress. to investigate further the function of senataxin, we identified novel senataxin-interacting proteins, the majority of which are involved in tran ...	2009	19515850
structural and functional divergence within the dim1/ksga family of rrna methyltransferases.	the enzymes of the ksga/dim1 family are universally distributed throughout all phylogeny; however, structural and functional differences are known to exist. the well-characterized function of these enzymes is to dimethylate two adjacent adenosines of the small ribosomal subunit in the normal course of ribosome maturation, and the structures of ksga from escherichia coli and dim1 from homo sapiens and plasmodium falciparum have been determined. to this point, no examples of archaeal structures ha ...	2009	19520088
role of picln in methylation of sm proteins by prmt5.	picln is an essential, highly conserved 26-kda protein whose functions include binding to sm proteins in the cytoplasm of human cells and mediating the ordered and regulated assembly of the cell's rna-splicing machinery by the survival motor neurons complex. picln also interacts with prmt5, the enzyme responsible for generating symmetric dimethylarginine modifications on the carboxyl-terminal regions of three of the canonical sm proteins. to better understand the role of picln in these cellular ...	2009	19520849
a genome-wide screen for regulators of torc1 in response to amino acid starvation reveals a conserved npr2/3 complex.	torc1 is a central regulator of cell growth in response to amino acid availability, yet little is known about how it is regulated. here, we performed a reverse genetic screen in yeast for genes necessary to inactivate torc1. the screen consisted of monitoring the expression of a torc1 sensitive gfp-based transcriptional reporter in all yeast deletion strains using flow cytometry. we find that in response to amino acid starvation, but not to carbon starvation or rapamycin treatment, cells lacking ...	2009	19521502
influenza a virus matrix protein 1 interacts with htfiiic102-s, a short isoform of the polypeptide 3 subunit of human general transcription factor iiic.	influenza a virus matrix protein 1 (m1) is a multifunctional protein that plays important roles during replication, assembly and budding of the virus. to search for intracellular protein components that interact with m1 protein and explore the potential roles of these interactions in the pathogenesis of influenza virus infection, 11 independent proteins, including htfiiic102-s protein, encoding a short isoform of the tfiiic102 subunit of the human tfiiic transcription factor, were screened from ...	2009	19521658
the epigenetic basis for centromere identity.	the centromere serves as the control locus for chromosome segregation at mitosis and meiosis. in most eukaryotes, including mammals, the location of the centromere is epigenetically defined. the contribution of both genetic and epigenetic determinants to centromere function is the subject of current investigation in diverse eukaryotes. here we highlight key findings from several organisms that have shaped the current view of centromeres, with special attention to experiments that have elucidated ...	2009	19521810
over expression and analysis of o-glycosylated recombinant human granulocyte colony stimulating factor in pichia pastoris using agilent 2100 bioanalyzer.	recombinant human granulocyte colony stimulating factor (rhgcsf) was expressed in methylotrophic yeast pichia pastoris under the control of aox1 promoter after integration of the gcsf gene into p. pastoris genome. methanol induction of the pichia integrants yielded only 2mgl(-1) of rhgcsf whereas inclusion of surfactants during induction enhanced the yields to the level of 200-250mgl(-1) in shake flask studies after 72h of induction. preliminary studies in a bioreactor showed rhgcsf expression l ...	2009	19527756
a robust correlation estimator and nonlinear recurrent model to infer genetic interactions in saccharomyces cerevisiae and pathways of pulmonary disease in homo sapiens.	in order to identify genes involved in complex diseases, it is crucial to study the genetic interactions at the systems biology level. by utilizing modern high throughput microarray technology, it has become feasible to obtain gene expressions data and turn it into knowledge that explains the regulatory behavior of genes. in this study, an unsupervised nonlinear model was proposed to infer gene regulatory networks on a genome-wide scale. the proposed model consists of two components, a robust co ...	2009	19527770
rep1p negatively regulating mdr1 efflux pump involved in drug resistance in candida albicans.	overexpression of mdr1 efflux pump is a major mechanism contributing to drug resistance in candida albicans, the most common human fungal pathogen. to elucidate the regulatory pathway of drug resistance, we have identified a negative regulator of mdr1 and named it regulator of efflux pump 1 (rep1). overexpression of rep1 in saccharomyces cerevisiae increased susceptibility to fluconazole. furthermore, null mutations on rep1 decreased the susceptibility to antifungal drugs in c. albicans resultin ...	2009	19527793
conservation and dispersion of sequence and function in fungal trk potassium transporters: focus on candida albicans.	trk proteins - essential potassium (k(+)) transporters in fungi and bacteria, as well as in plants - are generally absent from animal cells, which makes them potential targets for selective drug action. indeed, in the human pathogen candida albicans, the single trk isoform (catrk1p) has recently been demonstrated to be required for activity of histidine-rich salivary antimicrobial peptides (histatins). background for a detailed molecular investigation of trk-protein design and function is provid ...	2009	19175416
protein phosphatase 5 regulates the function of 53bp1 after neocarzinostatin-induced dna damage.	53bp1 (p53-binding protein 1) is a conserved nuclear protein that is phosphorylated in response to dna damage and rapidly recruited to the site of dna double strand breaks, demonstrating its role in the early events to dna damage and repair of damaged dna. in this study, we used the yeast two-hybrid system to identify proteins that interact with 53bp1. identification and characterization of 53bp1 protein interactions may help to further elucidate the function and regulation of 53bp1. we identifi ...	2009	19176521
isolation of mammalian 26s proteasomes and p97/vcp complexes using the ubiquitin-like domain from hhr23b reveals novel proteasome-associated proteins.	recent studies, mainly in yeast, have identified various cofactors that associate with the 26s proteasome and appear to influence its function. to identify these proteins in different cells and physiological states, we developed a method to gently and rapidly isolate 26s proteasomes and associated proteins without the need for genetic modifications of the proteasome. this method is based on the affinity of this complex for the ubiquitin-like (ubl) domain of hhr23b and elution with a competing po ...	2009	19182904
modulation of the beta-catenin signaling pathway by the dishevelled-associated protein hipk1.	wnts are evolutionarily conserved ligands that signal through beta-catenin-dependent and beta-catenin-independent pathways to regulate cell fate, proliferation, polarity, and movements during vertebrate development. dishevelled (dsh/dvl) is a multi-domain scaffold protein required for virtually all known wnt signaling activities, raising interest in the identification and functions of dsh-associated proteins.	2009	19183803
mcrs2 represses the transactivation activities of nrf1.	nrf1 [p45 nuclear factor-erythroid 2 (p45 nf-e2)-related factor 1], a member of the cnc-bzip (cnc basic region leucine zipper) family, is known to be a transcriptional activator by dimerization with distinct partners, such as maf, fosb, c-jun, jund, etc. the transcriptional roles of cnc-bzip family are demonstrated to be involved in globin gene expression as well as the antioxidant response. for example, cnc-bzip factors can regulate the expression of detoxification proteins through ares, such a ...	2009	19187526
telomere capping and cellular checkpoints: clues from fruit flies.	in most organisms, telomeres consist of repetitive g-rich sequences that are elongated by a specific reverse transcriptase, telomerase. a large number of proteins are recruited by these terminal repeats, forming specialized structures that regulate telomerase activity and protect telomeres from degradation and recombination. drosophila lacks telomerase and telomere length is maintained by transposition of three specialized retrotransposons. in addition, unlike yeast and mammals, drosophila telom ...	2009	19188707
strong inducible knockdown of apc/ccdc20 does not cause mitotic arrest in human somatic cells.	the anaphase-promoting complex/cyclosome (apc/c) is a conserved ubiquitin ligase controlling mitosis and g1 phase of the cell cycle. the apc/c is activated by two regulatory subunits cdc20 (apc/c(cdc20)) and cdh1 (apc/c(cdh1)) to target securin, mitotic cyclins and other cell cycle regulatory proteins. cdc20 is essential for sister chromatid separation at the meta- to anaphase transition in yeast, drosophila and perhaps mouse embryos. however, whether cdc20 is essential for mitotic control of hu ...	2009	19197151
trf2 promotes, remodels and protects telomeric holliday junctions.	the ability of the telomeric dna-binding protein, trf2, to stimulate t-loop formation while preventing t-loop deletion is believed to be crucial to maintain telomere integrity in mammals. however, little is known on the molecular mechanisms behind these properties of trf2. in this report, we show that trf2 greatly increases the rate of holliday junction (hj) formation and blocks the cleavage by various types of hj resolving activities, including the newly identified human gen1 protein. by using ...	2009	19197240
procedure for identification and characterization of drugs efficient against mammalian prion: from a yeast-based antiprion drug screening assay to in vivo mouse models.	prion diseases are fatal and incurable infectious neurodegenerative disorders affecting humans and other mammals. prions are composed essentially if not solely of prp(sc), a misfolded form of the host-encoded prp protein. prp(sc) catalyzes the transconformation of the normal endogenous prp (prp(c)) into more prp(sc). prion replication thus corresponds to the propagation of an altered folding state of prp. several prion proteins have also been identified in the simple model organism saccharomyces ...	2009	19200013
human ctip mediates cell cycle control of dna end resection and double strand break repair.	in g(0) and g(1), dna double strand breaks are repaired by nonhomologous end joining, whereas in s and g(2), they are also repaired by homologous recombination. the human ctip protein controls double strand break (dsb) resection, an event that occurs effectively only in s/g(2) and that promotes homologous recombination but not non-homologous end joining. here, we mutate a highly conserved cyclin-dependent kinase (cdk) target motif in ctip and reveal that mutating thr-847 to ala impairs resection ...	2009	19202191
human gene expression sensitivity according to large scale meta-analysis.	genes show different sensitivities in expression corresponding to various biological conditions. systematical study of this concept is required because of its important implications in microarray analysis etc. j.h. ohn et al. first studied this gene property with yeast transcriptional profiling data.	2009	19208159
mitominer, an integrated database for the storage and analysis of mitochondrial proteomics data.	mitochondria are a vital component of eukaryotic cells with functions that extend beyond energy production to include metabolism, signaling, cell growth, and apoptosis. their dysfunction is implicated in a large number of metabolic, degenerative, and age-related human diseases. therefore, it is important to characterize and understand the mitochondrion. many experiments have attempted to define the mitochondrial proteome, resulting in large and complex data sets that are difficult to analyze. to ...	2009	19208617
efficient and robust prediction algorithms for protein complexes using gomory-hu trees.	two-hybrid (y2h) protein-protein interaction (ppi) data suffer from high false positive and false negative rates, thus making searching for protein complexes in ppi networks a challenge. to overcome these limitations, we propose an efficient approach which measures connectivity between proteins not by edges, but by edge-disjoint paths. we model the number of edge-disjoint paths as a network flow and efficiently represent it in a gomory-hu tree. by manipulating the tree, we are able to isolate gr ...	2009	19209703
nutrient-dependent mtorc1 association with the ulk1-atg13-fip200 complex required for autophagy.	autophagy is an intracellular degradation system, by which cytoplasmic contents are degraded in lysosomes. autophagy is dynamically induced by nutrient depletion to provide necessary amino acids within cells, thus helping them adapt to starvation. although it has been suggested that mtor is a major negative regulator of autophagy, how it controls autophagy has not yet been determined. here, we report a novel mammalian autophagy factor, atg13, which forms a stable approximately 3-mda protein comp ...	2009	19211835
population genomics of domestic and wild yeasts.	since the completion of the genome sequence of saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions, population structure and sexual versus asexual reproduction. less well understood at the whole ...	2009	19212322
adenovirus-mediated cytosine deaminase/5-fluorocytosine suicide gene therapy of human hepatoblastoma in vitro.	multidrug resistance is a key factor for the sobering outcome of relapsed and metastatic human hepatoblastoma (hb). gene directed treatment approaches were recently identified as possible treatment options against advanced hb, in which standard chemotherapy regimens are partially insufficient. the aim of this study was to systematically analyze the effects of suicide gene therapy in three hb cell lines using a yeast-derived cytosine deaminase (ycd)-combined yeast uracil phosphoribosyltransferase ...	2009	19213079
human papillomaviruses and genital co-infections in gynaecological outpatients.	high grade hpv infections and persistence are the strongest risk factors for cervical cancer. nevertheless other genital microorganisms may be involved in the progression of hpv associated lesions.	2009	19216747
cytomegaloviral proteins that associate with the nuclear lamina: components of a postulated nuclear egress complex.	the nuclear egress of cytomegaloviral capsids traversing the nuclear envelope is dependent on a locally restricted destabilization of the rigid nuclear lamina. it has been suggested that the multi-component nuclear egress complex (nec) that is formed is comprised of both viral and cellular proteins which act to recruit lamin-phosphorylating protein kinases. recently, we reported that the lamina-associated human cytomegalovirus-encoded proteins pul50 and pul53, conserved among herpesviruses, inte ...	2009	19218202
intranuclear degradation of polyglutamine aggregates by the ubiquitin-proteasome system.	huntington disease and its related autosomal-dominant polyglutamine (pq) neurodegenerative diseases are characterized by intraneuronal accumulation of protein aggregates. studies on protein aggregates have revealed the importance of the ubiquitin-proteasome system as the front line of protein quality control (pqc) machinery against aberrant proteins. recently, we have shown that the autophagy-lysosomal system is also involved in cytoplasmic aggregate degradation, but the nucleus lacked this acti ...	2009	19218238
characterization of a mimivirus rna cap guanine-n2 methyltransferase.	a 2,2,7-trimethylguanosine (tmg) cap is a signature feature of eukaryal snrnas, telomerase rnas, and trans-spliced nematode mrnas. tmg and 2,7-dimethylguanosine (dmg) caps are also present on mrnas of two species of alphaviruses (positive strand rna viruses of the togaviridae family). it is presently not known how viral mrnas might acquire a hypermethylated cap. mimivirus, a giant dna virus that infects amoeba, encodes many putative enzymes and proteins implicated in rna transactions, including ...	2009	19218551
origins, distribution and expression of the duarte-2 (d2) allele of galactose-1-phosphate uridylyltransferase.	duarte galactosemia is a mild to asymptomatic condition that results from partial impairment of galactose-1-phosphate uridylyltransferase (galt). patients with duarte galactosemia demonstrate reduced galt activity and carry one profoundly impaired galt allele (g) along with a second, partially impaired galt allele (duarte-2, d2). molecular studies reveal at least five sequence changes on d2 alleles: a p.n314d missense substitution, three intronic base changes and a 4 bp deletion in the 5' proxim ...	2009	19224951
excretion-secretion products and proteases from live sporothrix schenckii yeast phase: immunological detection and cleavage of human igg.	antigenic preparations from sporothrix schenckii usually involve materials from mixed cultures of yeast and mycelia presenting cross-reactions with other deep mycoses. we have standardized pure yeast phase with high viability of the cells suitable to obtain specific excretion-secretion products without somatic contaminations. these excretion-secretion products were highly immunogenic and did not produce noticeable cross-reactions in either double immunodiffusion or western blot. the antigenic pr ...	2009	19229383
oncogenic nucleoporin can/nup214 interacts with vitamin d receptor and modulates its function.	vitamin d receptor (vdr) is a ligand-dependent transcription factor and should be located in nucleus to transactivate target genes. to explore the molecules that interact with vdr and facilitate its nuclear localization, we screened a human kidney cdna library using the yeast two-hybrid approach, and found that vdr binds to the carboxy-terminal region of an oncogenic nucleoporin, can/nup214. can/nup214 was originally identified through its involvement in a certain type of acute myeloid leukemia, ...	2009	19229862
trim36 interacts with the kinetochore protein cenp-h and delays cell cycle progression.	the tripartite motif-containing protein (trim) family is defined by the presence of a common domain structure composed of a ring finger, a b-box, and a coiled-coil motif. trim family proteins are involved in a broad range of biological processes and, consistently, their alterations result in diverse pathological conditions such as genetic diseases, viral infection, and cancer development. in this study, we found by using yeast two-hybrid screening that trim36 has a ubiquitin ligase activity and ...	2009	19232519
protein kinase ck2 interacts with adiponectin receptor 1 and participates in adiponectin signaling.	adiponectin is an adipokine with anti-atherogenic, anti-diabetic and insulin sensitizing properties. its effects on energy homeostasis, glucose and lipid metabolism are mediated by two ubiquitously expressed seven-transmembrane receptors, adipor1 and -r2. with the exception of appl1 and rack1, no intracellular binding partners of adiponectin receptors are reported and thus signaling pathways downstream of these receptors remain largely unknown. to incorporate adiponectins protective potential in ...	2009	19233263
the use of probiotics in the prevention and treatment of antibiotic-associated diarrhea with special interest in clostridium difficile-associated diarrhea.	antimicrobials are effective agents used to combat virulent bacterial, yeast, and fungal infections that may otherwise cause rampant disease leading to skyrocketing social/economic costs and possible epidemic morbidity and mortality rates. antibiotics are designed to attack specific bacterial pathogens but, in the process, indiscreetly reduce the number of beneficial human microbiota that is part of the gut-associated lymphatic tissue. broad-spectrum antibiotics can upset this uniquely balanced ...	2009	19244146
histone h3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells.	lysine 56 acetylation in the helical core of histone h3 opens yeast chromatin and enables histone gene transcription, dna replication, and dna repair and prevents epigenetic silencing. while k56ac is globally abundant in yeast and flies, its presence has been uncertain in mammals. we show here using mass spectrometry and genome-wide analyses that k56ac is present in human embryonic stem cells (hescs), overlapping strongly at active and inactive promoters with the binding of the key regulators of ...	2009	19250903
measuring strand discontinuity-directed mismatch repair in yeast saccharomyces cerevisiae by cell-free nuclear extracts.	mismatch repair corrects biosynthetic errors generated during dna replication, whose deficiency causes a mutator phenotype and directly underlies hereditary non-polyposis colorectal cancer and sporadic cancers. because of remarkably high conservation of the mismatch repair machinery between the budding yeast (saccharomyces cerevisiae) and humans, the study of mismatch repair in yeast has provided tremendous insights into the mechanisms of this repair pathway in humans. in addition, yeast cells p ...	2009	19250969
the major human pregnane x receptor (pxr) splice variant, pxr.2, exhibits significantly diminished ligand-activated transcriptional regulation.	the pregnane x receptor (pxr; pxr.1) can be activated by structurally diverse lipophilic ligands. pxr.2, an alternatively spliced form of pxr, lacks 111 nucleotides encoding 37 amino acids in the ligand binding domain. pxr.2 bound a classic cyp3a4 pxr response element (pxre) in electrophoretic mobility shift assays, but transfected pxr.2 failed to transactivate a cyp3a4-promoter-luciferase reporter plasmid in hepg2 cells treated with various pxr ligands. cotransfection experiments showed that px ...	2009	19251824
mammalian cell display for antibody engineering.	antibody engineering has generally been carried out by displaying mouse or human antibodies or antibody fragments on the surface of microorganisms (phage, bacteria, and yeast). we have shown that mammalian cells can be used to display single-chain antibody fragments (scfvs) for affinity maturation. using mammalian cell display one can isolate and engineer scfvs, fabs, or whole iggs for increased affinity and other specific biological functions. here, we describe a mammalian cell display strategy ...	2009	19252852
phenotypic associations of crohn's disease with antibodies to flagellins a4-fla2 and fla-x, asca, p-anca, pab, and nod2 mutations in a swiss cohort.	distinct crohn's disease (cd) phenotypes correlate with antibody reactivity to microbial antigens. we examined the association between antibody response to 2 new flagellins called a4-fla2 and fla-x, anti-saccharomyces cerevisiae antibodies (asca), anti-neutrophil cytoplasmic antibodies (p-anca), anti-pancreas antibodies (pab), nod2 mutations (r702w, g908r, and l1007fsinsc), and clinical cd phenotypes (according to vienna criteria).	2009	19253375
p4 atpases - lipid flippases and their role in disease.	p4 atpases (type 4 p-type atpases) are multispan transmembrane proteins that have been implicated in phospholipid translocation from the exoplasmic to the cytoplasmic leaflet of biological membranes. studies in saccharomyces cerevisiae have indicated that p4 atpases are important in vesicle biogenesis and are required for vesicular trafficking along several intracellular vesicular transport routes. although little is known about mammalian p4 atpases, some members of this subfamily appear to be a ...	2009	19254779
the cationic region of rhes mediates its interactions with specific gbeta subunits.	ras homologue enriched in striatum (rhes) is a small monomeric g protein which functions in a variety of cellular processes, including attenuation of g protein-coupled receptor (gpcr) signalling. there have been many studies into the effects of rhes, but there is no molecular information about how rhes might bring about these effects. rhes shares striking sequence homology to ags1 (activator of g protein signalling 1) and we considered whether the two proteins function in similar ways. ags1 bind ...	2009	19255495
reproductive health of bass in the potomac, u.s.a., drainage: part 2. seasonal occurrence of persistent and emerging organic contaminants.	the seasonal occurrence of organic contaminants, many of which are potential endocrine disruptors, entering the potomac river, usa, watershed was investigated using a two-pronged approach during the fall of 2005 and spring of 2006. passive samplers (semipermeable membrane device and polar organic chemical integrative sampler [pocis]) were deployed in tandem at sites above and below wastewater treatment plant discharges within the watershed. analysis of the samplers resulted in detection of 84 of ...	2009	19108592
tax1bp1 interacts with papillomavirus e2 and regulates e2-dependent transcription and stability.	the papillomavirus e2 proteins regulate viral replication, gene transcription, and genome maintenance by interacting with other viral and host proteins. from a yeast two-hybrid screen, we identified the cellular protein tax1bp1 as a novel binding partner of human papillomavirus type 18 (hpv18) e2. tax1bp1 also interacts with the hpv16 and bovine papillomavirus type 1 (bpv1) e2 proteins, with the c-terminal region of tax1bp1 interacting with the n-terminal transactivation domain of bpv1 e2. tax1b ...	2009	19109394
spe-39 family proteins interact with the hops complex and function in lysosomal delivery.	yeast and animal homotypic fusion and vacuole protein sorting (hops) complexes contain conserved subunits, but hops-mediated traffic in animals might require additional proteins. here, we demonstrate that spe-39 homologues, which are found only in animals, are present in rab5-, rab7-, and rab11-positive endosomes where they play a conserved role in lysosomal delivery and probably function via their interaction with the core hops complex. although caenorhabditis elegans spe-39 mutants were initia ...	2009	19109425
interaction of dengue virus envelope protein with endoplasmic reticulum-resident chaperones facilitates dengue virus production.	dengue virus infection is an important mosquito-borne disease and a public health problem worldwide. a better understanding of interactions between human cellular host and dengue virus proteins will provide insight into dengue virus replication and cellular pathogenesis. the glycosylated envelope protein of dengue virus, denv e, is processed in the endoplasmic reticulum of host cells and therefore reliant on host processing functions. the complement of host er functions involved and nature of th ...	2009	19105951
atp-dependent unwinding of u4/u6 snrnas by the brr2 helicase requires the c terminus of prp8.	the spliceosome is a highly dynamic machine requiring multiple rna-dependent atpases of the dexd/h-box family. a fundamental unanswered question is how their activities are regulated. brr2 function is necessary for unwinding the u4/u6 duplex, a step essential for catalytic activation of the spliceosome. here we show that brr2-dependent dissociation of u4/u6 snrnas in vitro is activated by a fragment from the c terminus of the u5 snrnp protein prp8. in contrast to its helicase-stimulating activit ...	2009	19098916
papa-1 is a nuclear binding partner of igfbp-2 and modulates its growth-promoting actions.	igf-binding proteins (igfbps) have multiple cellular effects, which occur by both igf-dependent and -independent mechanisms. igfbp-2 is involved in the regulation of both normal and carcinogenic cell growth. to further understand the actions of igfbp-2, we carried out a yeast two-hybrid screen to search for intracellular partner proteins using a human prostate cdna library. we isolated pim-1-associated protein-1 (pap-1)-associated protein-1 (papa-1) as an igfbp-2-binding protein, whose expressio ...	2009	19095771
polar mapper: a computational tool for integrated visualization of protein interaction networks and mrna expression data.	polar mapper is a computational application for exposing the architecture of protein interaction networks. it facilitates the system-level analysis of mrna expression data in the context of the underlying protein interaction network. preliminary analysis of a human protein interaction network and comparison of the yeast oxidative stress and heat shock gene expression responses are addressed as case studies.	2009	19091689
functional rescue of mutant human cystathionine beta-synthase by manipulation of hsp26 and hsp70 levels in saccharomyces cerevisiae.	many human diseases are caused by missense substitutions that result in misfolded proteins that lack biological function. here we express a mutant form of the human cystathionine beta-synthase protein, i278t, in saccharomyces cerevisiae and show that it is possible to dramatically restore protein stability and enzymatic function by manipulation of the cellular chaperone environment. we demonstrate that hsp70 and hsp26 bind specifically to i278t but that these chaperones have opposite biological ...	2009	19074437