Publications

a comprehensive platform for highly multiplexed mammalian functional genetic screens.	abstract: background: genome-wide screening in human and mouse cells using rna interference and open reading frame over-expression libraries is rapidly becoming a viable experimental approach for many research labs. there are a variety of gene expression modulation libraries commercially available, however, detailed and validated protocols as well as the reagents necessary for deconvolving genome-scale gene screens using these libraries are lacking. as a solution, we designed a comprehensive pla ...	2011	21548937
a missense mutation in prpf6 causes impairment of pre-mrna splicing and autosomal-dominant retinitis pigmentosa.	retinitis pigmentosa (rp) is an inherited form of retinal degeneration that leads to progressive visual-field constriction and blindness. although the disease manifests only in the retina, mutations in ubiquitously expressed genes associated with the tri-snrnp complex of the spliceosome have been identified in patients with dominantly inherited rp. we screened for mutations in prpf6 (nm_012469.3), a gene on chromosome 20q13.33 encoding an essential protein for tri-snrnp assembly and stability, i ...	2011	21549338
substitution patterns are gc-biased in divergent sequences across the metazoans.	the fastest-evolving regions in the human and chimpanzee genomes show a remarkable excess of weak (a,t) to strong (g,c) nucleotide substitutions since divergence from their common ancestor. we investigated the phylogenetic extent and possible causes of this weak to strong (w ôåæ s) bias in divergent sequences (bds) using recently sequenced genomes and recombination maps from eight trios of eukaryotic species. to quantify evidence for bds, we inferred substitution histories using an efficient max ...	2011	21670083
a hybrid model to study pathological mutations of the human adp/atp carriers.	the adenine nucleotide carrier (ancp) plays an essential role in the metabolism of cellular energy by catalyzing the transport of adp and atp across the inner mitochondrial membrane. previous reports have indicated that mutations in the hanc1 gene, encoding the muscle isoform of human ancp (hanc1p), are directly involved in several diseases, including autosomal dominant progressive external ophthalmoplegia and cardiomyopathies. in this work, we studied three pathogenic hanc1 mutations at the bio ...	2011	21549803
identification of mek2-mapk kinase as a novel partner of the scaffolding protein human homolog of disc-large (hdlg).	human disc-large homolog (hdlg), also known as synapse-associated protein 97 (sap97), is a scaffold protein, member of the membrane-associated guanylate kinase (maguk) family, implicated in neuronal synapses and epithelial-epithelial cell junctions whose expression and function remains poorly characterized in most tissues, particularly in the vasculature. our data show that, in human vascular tissues, hdlg is highly expressed in smooth muscle cells (vsmcs). using the yeast two-hybrid system to s ...	2011	21615688
interaction of the receptor fgfrl1 with the negative regulator spred1.	fgfrl1 is a member of the fibroblast growth factor receptor family. it plays an essential role during branching morphogenesis of the metanephric kidneys, as mice with a targeted deletion of the fgfrl1 gene show severe kidney dysplasia. here we used the yeast two-hybrid system to demonstrate that fgfrl1 binds with its c-terminal, histidine-rich domain to spred1 and to other proteins of the sprouty/spred family. members of this family are known to act as negative regulators of the ras/raf/erk sign ...	2011	21616146
interaction with polyglutamine expanded huntingtin alters cellular distribution and rna processing of huntingtin yeast two-hybrid protein a (hypa).	huntington's disease (hd) is an autosomal inherited disorder that causes the deterioration of brain cells. the polyglutamine (polyq) expansion of huntingtin (htt) is implicated in the pathogenesis of hd via interaction with an rna splicing factor, htt yeast two-hybrid protein a/formin binding protein 11 (hypa/fbp11). besides the pathogenic polyq expansion, htt also contains a proline-rich region (prr) located exactly in the c-terminus to the polyq tract. however, how the polyq expansion influenc ...	2011	21566141
structure-function studies of an engineered scaffold protein derived from stefin a. ii: development and applications of the sqt variant.	constrained binding peptides (peptide aptamers) may serve as tools to explore protein conformations and disrupt protein-protein interactions. the quality of the protein scaffold, by which the binding peptide is constrained and presented, is of crucial importance. sqt (stefin a quadruple mutant-tracy) is our most recent development in the stefin a-derived scaffold series. stefin a naturally uses three surfaces to interact with its targets. sqt tolerates peptide insertions at all three positions. ...	2011	21616931
the role of hsl7 in morphology and pathogenicity and its interaction with other signaling components in the plant pathogen, ustilago maydis.	the phytopathogenic fungus ustilago maydis undergoes a dimorphic transition in response to mating pheromone, host, and environmental cues. on solid media deficient in ammonium (slad), u. maydis produces a filamentous colony morphology, while in liquid slad the cells do not form filaments. the p21-activated protein kinases (paks) play a substantial role in regulating the dimorphic transition in fungi. the pak-like ste20 homologue, smu1, is required for a normal response to pheromone via up-regula ...	2011	21622903
downstream of human ndr kinases: impacting on c-myc and p21 protein stability to control cell cycle progression.	the mammalian genome encodes four members of the ndr/lats kinase family: ndr1 (stk38), ndr2 (stk38l), lats1 and lats2, which are highly conserved from yeast to man. members of the ndr/lats kinase family have been implicated in a variety of biological processes ranging from cell division and morphology to apoptosis and tumor suppression. in mammals lats1/2 function as central parts of the hippo tumor suppressor pathway by restricting the activity of the yap/taz proto-oncogenes. recent evidence su ...	2011	21593588
ddx60, a dexd/h box helicase, is a novel antiviral factor promoting rig-i-like receptor-mediated signaling.	the cytoplasmic viral rna sensors rig-i and mda5 are important for the production of type i interferon and other inflammatory cytokines. ddx60 is an uncharacterized dexd/h box rna helicase similar to s. cerevisiae ski2, a cofactor of rna exosome, a protein complex required for the integrity of cytoplasmic rna. the expression of ddx60 increases after viral infection, and the protein localizes at cytoplasmic region. after viral infection, the ddx60 protein binds to endogenous rig-i protein. the pr ...	2011	21791617
the involvement of smile/tmtc3 in endoplasmic reticulum stress response.	thestate of operational tolerance has been detected sporadically in some renal transplanted patients that stopped immunosuppressive drugs, demonstrating that allograft tolerance might exist in humans. several years ago, a study by brouard et al. identified a molecular signature of several genes that were significantly differentially expressed in the blood of such patients compared with patients with other clinical situations. the aim of the present study is to analyze the role of one of these mo ...	2011	21603654
gisao.db: a database for ageing research.	abstract: background: age-related gene expression patterns of homo sapiens as well as of model organisms such as mus musculus, saccharomyces cerevisiae, caenorhabditis elegans and drosophila melanogaster are a basis for understanding the genetic mechanisms of ageing. for an effective analysis and interpretation of expression profiles it is necessary to store and manage huge amounts of data in an organized way, so that these data can be accessed and processed easily. description gisao.db (genes i ...	2011	21609420
turnover of atp synthase subunits in f(1)-depleted hela and yeast cells.	mitochondrial translation of the saccharomyces cerevisiae atp6p subunit of f(1)-f(0) atp synthase is regulated by the f(1) atpase. here we show normal expression of atp6p in hela cells depleted of the f(1) ß subunit. instead of being translationally down-regulated, hela cells lacking f(1) degrade atp6p, thereby preventing proton leakage across the inner membrane. mammalian mitochondria also differ in the way they minimize the harmful effect of unassembled f(1) a subunit. while yeast mutants lack ...	2011	21784071
[activity of macrolides and fluoroquinolones against intracellular legionella pneumophila].	to evaluate the activity of macrolides and fluoroquinolones against legionella pneumophila by intracellular susceptibility testing.	2011	21781510
identification of an evolutionary conserved family of inorganic polyphosphate endopolyphosphatases.	inorganic polyphosphate (poly-p) consists of just a chain of phosphate groups linked by high-energy bonds. it is found in every organism and is implicated in a wide variety of cellular processes, e.g. phosphate storage, blood coagulation, pathogenicity. its metabolism has been studied mainly in bacteria, while remaining largely uncharacterized in eukaryotes. it has recently been suggested that poly-p metabolism is connected to that of highly phosphorylated inositol species (inositol pyrophosphat ...	2011	21775424
[the effects of tata-box in cyc1 promoter on the reporter gene regulated by ere in the recombinant yeast cell].	the complementary oligonucleotides, each with two consensus estrogen response element (ere)-sequences and 5'-hind iii and 3'-sph i sticky ends were artificially synthesized. a solution with both the complementary dna sequences was heated to 95'c and cooled down to room temperature to form double strand dna (dsdna). the set was cloned into the corresponding sites of cyc1 promoter of the pere-cyc-yegfp to yield pere-cycalpha-yegfp vector. the two different reporter vectors, pere-cyc-yegfp and pere ...	2011	21774222
effect of phyllanthus emblica linn. on candida adhesion to oral epithelium and denture acrylic.	to investigate the effect of phyllanthus emblica (p. emblica) linn. ethanolic extract on the adhesion of candida albicans (c. albicans) to human buccal epithelial cells (becs) and denture acrylic surfaces.	2011	21771413
plant ornithine decarboxylase is not post-transcriptionally feedback regulated by polyamines but can interact with a cytosolic ribosomal protein s15 polypeptide.	the formation of putrescine by ornithine decarboxylase (odc) is a key regulatory step in polyamine biosynthesis in metazoa and fungi. excess polyamines post-transcriptionally induce the synthesis of a unique non-competitive protein inhibitor of odc, termed antizyme. binding of antizyme to an odc monomer subunit results in enzymatic inhibition, rapid ubiquitin-independent degradation of odc by the 26s proteasome and recycling of antizyme. plants possess an additional route for synthesizing putres ...	2011	21814791
detection of antibodies against paracoccidioides brasiliensis melanin: in vitro and in vivo studies during infection.	several cell-wall constituents, including melanins or melanin-like compounds, have been implicated in the pathogenesis of a wide variety of microbial diseases caused by diverse species of pathogenic bacteria, fungi and helminthes. among these microorganisms, the dimorphic fungal pathogen paracoccidioides brasiliensis produces melanin in its conidial and yeast forms. in the present study, melanin particles from p. brasiliensis were injected into balb/c mice in order to produce monoclonal antibodi ...	2011	21813659
human cabin1 is a functional member of the human hira/ubn1/asf1a histone h3.3 chaperone complex.	the mammalian hira/ubn1/asf1a complex is a histone chaperone complex that is conserved from yeast to humans. this complex preferentially deposits the histone variant h3.3 into chromatin in a dna replication-independent manner, and is implicated in diverse chromatin regulatory events from gene activation to heterochromatinization. in yeast, the orthologous complex consists of three hir proteins (hir1p, hir2p and hir3p), hpc2p and asf1p. yeast hir3p has weak homology to, cabin1, a fourth member of ...	2011	21807893
phospholipid scramblase 1 mediates hepatitis c virus entry into host cells.	hepatitis c virus (hcv) infects human hepatocytes through several host factors. however, other prerequisite factors for viral entry remain to be identified. using a yeast two-hybrid screen, we found that human phospholipid scramblase 1 interacts with hcv envelope proteins e1 and e2. these physical interactions were confirmed by co-immunoprecipitation and gst pull-down assays. knocking down the expression of plscr1 inhibited the entry of hcv pseudoparticles. moreover, plscr1 was required for the ...	2011	21806988
cell surface display of functional human mhc class ii proteins: yeast display versus insect cell display.	reliable and robust systems for engineering functional major histocompatibility complex class ii (mhcii) proteins have proved elusive. availability of such systems would enable the engineering of peptide-mhcii (pmhcii) complexes for therapeutic and diagnostic applications. in this paper, we have developed a system based on insect cell surface display that allows functional expression of heterodimeric dr2 molecules with or without a covalently bound human myelin basic protein (mbp) peptide, which ...	2011	21752831
the incorporation of 5-fluorouracil into rna affects the ribonucleolytic activity of the exosome subunit rrp6.	5-fluorouracil (5fu) is a fluoropyrimidine used for the treatment of solid tumors. 5fu is a precursor of dttp and utp during biogenesis, and it interferes with both dna and rna metabolism. the rna exosome, a multisubunit complex with ribonucleolytic activity, has been identified as one of the targets of 5fu in yeast. studies in human cells have shown that the catalytic subunit of the nuclear exosome, rrp6, is specifically targeted. here, we have investigated the direct effect of 5fu on the activ ...	2011	21289297
resilience of protein-protein interaction networks as determined by their large-scale topological features.	the relationship between the structure and function of biological networks constitutes a fundamental issue in systems biology. particularly, the structure of protein-protein interaction networks is related to important biological functions. in this work, we investigated how such a resilience is determined by the large scale features of the respective networks. four species are taken into account, namely yeast saccharomyces cerevisiae, worm caenorhabditis elegans, fly drosophila melanogaster and ...	2011	21298132
simulating and validating proteomics data and search results.	the computational simulation of complete proteomic data sets and their utility to validate detection and interpretation algorithms, to aid in the design of experiments and to assess protein and peptide false discovery rates is presented. the simulation software has been developed for emulating data originating from data-dependent and data-independent lc-ms workflows. data from all types of commonly used hybrid mass spectrometers can be simulated. the algorithms are based on empirically derived p ...	2011	21298790
psm3 acetylation on conserved lysine residues is dispensable for viability in fission yeast but contributes to eso1-mediated sister chromatid cohesion by antagonizing wpl1.	in budding yeast and humans, cohesion establishment during s phase requires the acetyltransferase eco1/esco1-2, which acetylates the cohesin subunit smc3 on two conserved lysine residues. whether smc3 is the sole eco1/esco1-2 effector and how smc3 acetylation promotes cohesion are unknown. in fission yeast (schizosaccharomyces pombe), as in humans, cohesin binding to g(1) chromosomes is dynamic and the unloading reaction is stimulated by wpl1 (human ortholog, wapl). during s phase, a subpopulati ...	2011	21300781
subunit organization of the human ino80 chromatin remodeling complex: an evolutionarily conserved core complex catalyzes atp-dependent nucleosome remodeling.	we previously identified and purified a human atp-dependent chromatin remodeling complex with similarity to the saccharomyces cerevisiae ino80 complex (jin, j., cai, y., yao, t., gottschalk, a. j., florens, l., swanson, s. k., gutierrez, j. l., coleman, m. k., workman, j. l., mushegian, a., washburn, m. p., conaway, r. c., and conaway, j. w. (2005) j. biol. chem. 280, 41207-41212) and demonstrated that it is composed of (i) a snf2 family atpase (hino80) related in sequence to the s. cerevisiae i ...	2011	21303910
accurate quantification of functional analogy among close homologs.	correctly evaluating functional similarities among homologous proteins is necessary for accurate transfer of experimental knowledge from one organism to another, and is of particular importance for the development of animal models of human disease. while the fact that sequence similarity implies functional similarity is a fundamental paradigm of molecular biology, sequence comparison does not directly assess the extent to which two proteins participate in the same biological processes, and has l ...	2011	21304936
redox regulation of the tumor suppressor pten by glutaredoxin 5 and ycp4.	human pten (phosphatase and tensin homolog deleted on chromosome 10; a phosphatidylinositol 3-phosphatase) expressed in saccharomyces cerevisiae was oxidized in a time- and h(2)o(2)-concentration-dependent manner. oxidized hpten was reduced by cellular reductants as in human cells. the reduction rate of oxidized hpten was monitored in s. cerevisiae mutants in which the genes involved in redox homeostasis had been disrupted. reduction of hpten was delayed in each of s. cerevisiae grx5? and ycp4? ...	2011	21371429
requirement for acetyl-coa carboxylase in trypanosoma brucei is dependent upon the growth environment.	trypanosoma brucei, the causative agent of human african trypanosomiasis, possesses two fatty acid synthesis pathways: a major de novo synthesis pathway in the er and a mitochondrial pathway. the 2-carbon donor for both pathways is malonyl-coa, which is synthesized from acetyl-coa by acetyl-coa carboxylase (acc). here, we show that t. brucei acc shares the same enzyme architecture and moderate ~ 30% identity with yeast and human accs. acc is cytoplasmic and appears to be distributed throughout t ...	2011	21306439
saccharomyces cerevisiae as a model organism: a comparative study.	model organisms are used for research because they provide a framework on which to develop and optimize methods that facilitate and standardize analysis. such organisms should be representative of the living beings for which they are to serve as proxy. however, in practice, a model organism is often selected ad hoc, and without considering its representativeness, because a systematic and rational method to include this consideration in the selection process is still lacking.	2011	21311596
rho gtpase cdc42 is a direct interacting partner of adenomatous polyposis coli protein and can alter its cellular localization.	adenomatous polyposis coli (apc) is a tumor suppressor gene product involved in colon cancer. apc is a large multidomain molecule of 2843 amino acid residues and connects cell-cell adhesion, the f-actin/microtubule cytoskeleton and the nucleus. here we show that cdc42 interacts directly with the first three armadillo repeats of apc by yeast two-hybrid screens. we confirm the cdc42-apc interaction using pulldown assays in vitro and fret assays in vivo. interestingly, cdc42 interacts with apc at l ...	2011	21311754
synthesis and biological activity of splitomicin analogs targeted at human nad(+)-dependent histone deacetylases (sirtuins).	small molecules interfering with posttranslational modification of histones are of interest as tools to study epigenetic regulation of gene transcription. specifically, drugs that interfere with histone deacetylation could be useful to induce differentiation, growth arrest as well as apoptotic cell death in tumor cells. one class of histone deacetylases is known as sirtuins some of which (saccharomyces cerevisiae sir2) are for example inhibited by the lactone splitomicin leading to telomeric sil ...	2011	21315612
proteasome activator 200: the heat is on...	proteasomes play a key regulatory role in all eukaryotic cells by removing proteins in a timely manner. there are two predominant forms: the 20s core particle (cp) can hydrolyze peptides and certain unstructured proteins, and the 26s holoenzyme is able to proteolyse most proteins conjugated to ubiquitin. the 26s complex consists of a cp barrel with a 19s regulatory particle (rp; a.k.a pa700) attached to its outer surface. several studies purified another proteasome activator with a mw of 200 kda ...	2011	21389348
detecting protein-protein interactions in vesicular stomatitis virus using a cytoplasmic yeast two hybrid system.	protein-protein interactions play an important role in many virus-encoded functions and in virus-host interactions. while a "classical" yeast two-hybrid system (y2h) is one of the most common techniques to detect such interactions, it has a number of limitations, including a requirement for the proteins of interest to be relocated to the nucleus. modified y2h, such as the sos recruitment system (srs), which detect interactions occurring in the cytoplasm rather than the nucleus, allow proteins fr ...	2011	21320532
a generic system for the expression and purification of soluble and stable influenza neuraminidase.	the influenza surface glycoprotein neuraminidase (na) is essential for the efficient spread of the virus. antiviral drugs such as tamiflu (oseltamivir) and relenza (zanamivir) that inhibit na enzyme activity have been shown to be effective in the treatment of influenza infections. the recent 'swine flu' pandemic and world-wide emergence of tamiflu-resistant seasonal human influenza a(h1n1) h(274)y have highlighted the need for the ongoing development of new anti-virals, efficient production of v ...	2011	21326879
[os-9 and xtp3-b: lectins that regulate endoplasmic reticulum-associated degradation (erad)].		2011	21404621
cellular functions of ufd2 and ufd3 in proteasomal protein degradation depend on cdc48 binding.	the chaperone-related aaa atpase cdc48 (p97/vcp in higher eukaryotes) segregates ubiquitylated proteins for subsequent degradation by the 26s proteasome or for nonproteolytic fates. the specific outcome of cdc48 activity is controlled by the evolutionary conserved cofactors ufd2 and ufd3, which antagonistically regulate the substrates' ubiquitylation states. in contrast to the interaction of ufd3 and cdc48, the interaction between the ubiquitin chain elongating enzyme ufd2 and cdc48 has not been ...	2011	21282470
a role for oxysterol-binding protein-related protein 5 in endosomal cholesterol trafficking.	oxysterol-binding protein (osbp) and its related proteins (orps) constitute a large and evolutionarily conserved family of lipid-binding proteins that target organelle membranes to mediate sterol signaling and/or transport. here we characterize orp5, a tail-anchored orp protein that localizes to the endoplasmic reticulum. knocking down orp5 causes cholesterol accumulation in late endosomes and lysosomes, which is reminiscent of the cholesterol trafficking defect in niemann pick c (npc) fibroblas ...	2011	21220512
metabolic pathways of ochratoxin a.	ochratoxin a (ota) as a carcinogenic of group 2b to humans is produced by various fungi strains as aspergillus and penicillium. it is one of the most common contaminant in foodstuff. ota is nephrotoxic, hepatotoxic, teratogenic, and immunotoxic and is assumed to cause balkan endemic nephropathy (ben), a chronic kidney disease in humans when it is digested in combination with mycotoxin citrinin. the metabolism affects greatly the fates and the toxicity of a mycotoxins in humans, animals, and plan ...	2011	21222585
peptides and aptamers targeting hsp70: a novel approach for anticancer chemotherapy.	the inhibition of heat shock protein 70 (hsp70) is an emerging strategy in cancer therapy. unfortunately, no specific inhibitors are clinically available. by yeast two-hybrid screening, we have identified multiple peptide aptamers that bind hsp70. when expressed in human tumor cells, two among these peptide aptamers-a8 and a17-which bind to the peptide-binding and the atp-binding domains of hsp70, respectively, specifically inhibited the chaperone activity, thereby increasing the cells' sensitiv ...	2011	21224349
a comprehensive study of tp53 mutations in chronic lymphocytic leukemia: analysis of 1287 diagnostic and 1148 follow-up cll samples.	tp53 plays a pivotal role in the process of dna repair and apoptosis. in 10-20% of patients with chronic lymphocytic leukemia (cll), the tp53 pathway is affected. in this study, we analyzed the tp53 mutation status in 2435 consecutive cll samples, including 1287 diagnostic samples and 1148 samples during follow-up, using fasay (functional analysis of separated alleles in yeast) and direct sequencing. in a cohort of 1287 diagnostic cll samples, we identified 237 cases with tp53 variants, includin ...	2011	21232794
human cdc14a becomes a cell cycle gene in controlling cdk1 activity at the g₂/m transition.	cdc14 belongs to a dual-specificity phosphatase family highly conserved through evolution that preferentially reverses cdk (cyclin dependent kinases) -dependent phosphorylation events. in the yeast saccharomyces cerevisiae, cdc14 is an essential regulator of late mitotic events and exit from mitosis by counteracting cdk activity at the end of mitosis. however, many studies have shown that cdc14 is dispensable for exiting mitosis in all other model systems analyzed. in fission yeast, the cdc14 ho ...	2011	21233601
structural basis for the removal of ubiquitin and interferon-stimulated gene 15 by a viral ovarian tumor domain-containing protease.	the attachment of ubiquitin (ub) and the ub-like (ubl) molecule interferon-stimulated gene 15 (isg15) to cellular proteins mediates important innate antiviral responses. ovarian tumor (otu) domain proteases from nairoviruses and arteriviruses were recently found to remove these molecules from host proteins, which inhibits ub and isg15-dependent antiviral pathways. this contrasts with the ub-specific activity of known eukaryotic otu-domain proteases. here we describe crystal structures of a viral ...	2011	21245344
the chaperone network connected to human ribosome-associated complex.	mammalian ribosome-associated complex (mrac), consisting of the j-domain protein mpp11 and the atypical hsp70 homolog (70-homolog) hsp70l1, can partly complement the function of rac, which is the homologous complex from saccharomyces cerevisiae. rac is the j-domain partner exclusively of the 70-homolog ssb, which directly and independently of rac binds to the ribosome. we here show that growth defects due to mrac depletion in hela cells resemble those of yeast strains lacking rac. functional con ...	2011	21245388
zinc-finger protein 90 negatively regulates neuron-restrictive silencer factor-mediated transcriptional repression of fetal cardiac genes.	neuron-restrictive silencer factor (nrsf) is a zinc-finger transcription factor that binds to specific dna sequences (nrse) to repress transcription. by down-regulating the transcription of its target genes, nrsf contributes to the regulation of various biological processes, including neuronal differentiation, carcinogenesis and cardiovascular homeostasis. we previously reported that nrsf regulates expression of the cardiac fetal gene program, and that attenuation of nrsf-mediated repression con ...	2011	21284946
the essential role of fkbp38 in regulating phosphatase of regenerating liver 3 (prl-3) protein stability.	the phosphatase of regenerating liver-3 (prl-3) is a member of protein tyrosine phosphatases and whose deregulation is implicated in tumorigenesis and metastasis of many cancers. however, the underlying mechanism by which prl-3 is regulated is not known. in this study, we identified the peptidyl prolyl cis/trans isomerase fk506-binding protein 38 (fkbp38) as an interacting protein of prl-3 using a yeast two-hybrid system. fkbp38 specifically binds to prl-3 in vivo, and that the n-terminal region ...	2011	21320469
ubiquitin-proteasome genes as targets for modulation of cisplatin sensitivity in fission yeast.	the ubiquitin(ub)-proteasome pathway is implicated in the regulation of a variety of cellular functions and plays a major role in stress response in eukaryotic cells, by targeting misfolded and damaged proteins for degradation. in addition, in the presence of dna damage, the ub-proteasome system regulates proteins involved in sensing, repairing, and/or tolerating the damage. antitumor agents such as cisplatin can activate the pathway, but the role of specific pathway components in cell sensitivi ...	2011	21247416
xenopus hjurp and condensin ii are required for cenp-a assembly.	centromeric protein a (cenp-a) is the epigenetic mark of centromeres. cenp-a replenishment is necessary in each cell cycle to compensate for the dilution associated to dna replication, but how this is achieved mechanistically is largely unknown. we have developed an assay using xenopus egg extracts that can recapitulate the spatial and temporal specificity of cenp-a deposition observed in human cells, providing us with a robust in vitro system amenable to molecular dissection. here we show that ...	2011	21321101
tbc proteins: gaps for mammalian small gtpase rab?	the tbc (tre-2/bub2/cdc16) domain was originally identified as a conserved domain among the tre-2 oncogene product and the yeast cell cycle regulators bub2 and cdc16, and it is now widely recognized as a conserved protein motif that consists of approx. 200 amino acids in all eukaryotes. since the tbc domain of yeast gyps [gap (gtpase-activating protein) for ypt proteins] has been shown to function as a gap domain for small gtpase ypt/rab, tbc domain-containing proteins (tbc proteins) in other sp ...	2011	21250943
expression of water-soluble, ligand-binding concatameric extracellular domains of the human neuronal nicotinic receptor alpha4 and beta2 subunits in the yeast pichia pastoris: glycosylation is not required for ligand binding.	nicotinic acetylcholine receptors (nachrs) are ligand-gated cation channels that are responsible for cell communication via the neurotransmitter acetylcholine. the predominant nachr subtype in the mammalian brain with a high affinity for nicotine is composed of a4 and ß2 subunits. this nachr subtype is responsible for addiction to nicotine and is thought to be implicated in alzheimer and parkinson diseases and therefore presents an important target for drug design. in an effort to obtain water-s ...	2011	21252231
a mutation in the gene encoding mitochondrial mg²+ channel mrs2 results in demyelination in the rat.	the rat demyelination (dmy) mutation serves as a unique model system to investigate the maintenance of myelin, because it provokes severe myelin breakdown in the central nervous system (cns) after normal postnatal completion of myelination. here, we report the molecular characterization of this mutation and discuss the possible pathomechanisms underlying demyelination. by positional cloning, we found that a g-to-a transition, 177 bp downstream of exon 3 of the mrs2 (mrs2 magnesium homeostasis fa ...	2011	21253565
distinct regulation of p53-mediated apoptosis by protein kinase ca, d, e and ?: evidence in yeast for transcription-dependent and -independent p53 apoptotic mechanisms.	the role of individual protein kinase c (pkc) isoforms in the regulation of p53-mediated apoptosis is still uncertain. using yeast cells co-expressing the human wild-type p53 and a single mammalian pkca, d, e or ?, we showed a differential regulation of p53-mediated apoptosis by these pkc isoforms. whereas pkca and ? had no effect on p53 activity, pkcd and e stimulated a p53-mediated mitochondria-dependent apoptosis. moreover, using pifithrin-a and -µ, selective inhibitors of p53 transcriptional ...	2011	21338602
glycosylation status of the c. albicans cell wall affects the efficiency of neutrophil phagocytosis and killing but not cytokine signaling.	the cell wall of the opportunistic human fungal pathogen, candida albicans is a complex, layered network of rigid structural polysaccharides composed of β-glucans and chitin that is covered with a fibrillar matrix of highly glycosylated mannoproteins. polymorphonuclear cells (pmns, neutrophils) are the most prevalent circulating phagocytic leukocyte in peripheral blood and they are pivotal in the clearance of invading fungal cells from tissues. the importance of cell-wall mannans for the recogni ...	2011	21254968
(1→3)-β-d-glucan inhibits a dual mechanism of peroxynitrite stroke.	the antioxidative and antinitrative activities of (1→3)-β-d-glucan (1-4μg/ml) from the yeast cell walls of saccharomyces cerevisiae in human plasma treated with strong oxidants - peroxynitrite (onoo(-)) (0.1mm) and hydrogen peroxide (h(2)o(2)) (2mm) were studied in vitro. the main purpose of this study was to assess if (1→3)-β-d-glucan, a well known strong immunostimulatory agent, possesses a protective function against dual mechanism of onoo(-) stroke associated with nitrative and oxidative dam ...	2011	21255603
microrna expression patterns of the kidney in hyperuricemia mice treated with xiezhuo chubi decoction.	to investigate the effects of xiezhuo chubi decoction (xzcbd) on the microrna expression patterns of kidney in mice with hyperuricemia.	2011	21258895
shox interacts with the chondrogenic transcription factors sox5 and sox6 to activate the aggrecan enhancer.	shox (short stature homeobox-containing gene) encodes a transcription factor implicated in skeletal development. shox haploinsufficiency has been demonstrated in leri-weill dyschondrosteosis (lwd), a skeletal dysplasia associated with disproportionate short stature, as well as in a variable proportion of cases with idiopathic short stature (iss). in order to gain insight into the shox signalling pathways, we performed a yeast two-hybrid screen to identify shox-interacting proteins. two transcrip ...	2011	21262861
pharmacokinetic-pharmacodynamic modeling of the inhibitory effects of naproxen on the time-courses of inflammatory pain, fever, and the ex vivo synthesis of txb2 and pge2 in rats.	to quantify and compare the time-course and potency of the analgesic and antipyretic effects of naproxen in conjunction with the inhibition of pge(2) and txb(2).	2011	21347567
rna polymerase i-specific subunits promote polymerase clustering to enhance the rrna gene transcription cycle.	rna polymerase i (pol i) produces large ribosomal rnas (rrnas). in this study, we show that the rpa49 and rpa34 pol i subunits, which do not have counterparts in pol ii and pol iii complexes, are functionally conserved using heterospecific complementation of the human and schizosaccharomyces pombe orthologues in saccharomyces cerevisiae. deletion of rpa49 leads to the disappearance of nucleolar structure, but nucleolar assembly can be restored by decreasing ribosomal gene copy number from 190 to ...	2011	21263028
allele-specific effects of thoracic aortic aneurysm and dissection alpha-smooth muscle actin mutations on actin function.	twenty-two missense mutations in acta2, which encodes a-smooth muscle actin, have been identified to cause thoracic aortic aneurysm and dissection. limited access to diseased tissue, the presence of multiple unresolvable actin isoforms in the cell, and lack of an animal model have prevented analysis of the biochemical mechanisms underlying this pathology. we have utilized actin from the yeast saccharomyces cerevisiae, 86% identical to human a-smooth muscle actin, as a model. two of the known hum ...	2011	21288906
role of the interface between the fmn and fad domains in the control of redox potential and electronic transfer of nadph-cytochrome p450 reductase.	cpr (nadph-cytochrome p450 reductase) is a multidomain protein containing two flavin-containing domains joined by a connecting domain thought to control the necessary movements of the catalytic domains during electronic cycles. we present a detailed biochemical analysis of two chimaeric cprs composed of the association of human or yeast fmn with the alternative connecting/fad domains. despite the assembly of domains having a relatively large evolutionary distance between them, our data support t ...	2011	21265736
haploinsufficiency and the sex chromosomes from yeasts to humans.	haploinsufficient (hi) genes are those for which a reduction in copy number in a diploid from two to one results in significantly reduced fitness. haploinsufficiency is increasingly implicated in human disease, and so predicting this phenotype could provide insights into the genetic mechanisms behind many human diseases, including some cancers.	2011	21356089
nutrient stress does not cause retrograde transport of cytoplasmic trna to the nucleus in evolutionarily diverse organisms.	intracellular trafficking of trna was long thought to be a one-way trip from the site of biogenesis in the nucleus to the translation machinery in the cytoplasm. this view has recently been challenged, however, by the discovery that trna can move retrograde from the cytoplasm back to the nucleus in saccharomyces cerevisiae and rat hepatoma h4iie cells during nutrient stress and in s. cerevisiae after intron-containing pre-trnas are spliced in the cytoplasm. contrary to studies reported, we prese ...	2011	21289100
dissection of the relative contribution of the schizosaccharomyces pombe ctr4 and ctr5 proteins to the copper transport and cell surface delivery functions.	the ctr1 family of proteins mediates high-affinity copper (cu) acquisition in eukaryotic organisms. in the fission yeast schizosaccharomyces pombe, cu uptake is carried out by a heteromeric complex formed by the ctr4 and ctr5 proteins. unlike human and saccharomyces cerevisiae ctr1 proteins, ctr4 and ctr5 are unable to function independently in cu acquisition. instead, both proteins physically interact with each other to form a ctr4-ctr5 heteromeric complex, and are interdependent for secretion ...	2011	21273250
tyrosine 656 in topoisomerase iiß is important for the catalytic activity of the enzyme: identification based on artifactual +80-da modification at this site.	topoisomerase (topo) ii catalyzes topological changes in dna. although both human isozymes, topo iia and ß are phosphorylated, site-specific phosphorylation of topo iiß is poorly characterized. using lc-ms/ms analysis of topo iiß, cleaved with trypsin, arg c or cyanogen bromide (cnbr) plus trypsin, we detected four +80-da modified sites: tyr656, ser1395, thr1426 and ser1545. phosphorylation at ser1395, thr1426 and ser1545 was established based on neutral loss of h(3) po(4) (-98?da) in the cid sp ...	2011	21280220
elongator protein 3b negatively regulates ribosomal dna transcription in african trypanosomes.	eukaryotic cells limit ribosomal dna (rdna) transcription by rna polymerase i (rnap-i) to maintain genome integrity. african trypanosomes present an excellent model for studies on rnap-i regulation because they possess a bifunctional rnap-i and because rnap-ii transcription appears unregulated. since elp3, the catalytic component of elongator, controls rnap-ii transcription in yeast and human cells, we predicted a role for a trypanosome elp3-related protein, elp3a or elp3b, in rnap-i regulation. ...	2011	21357738
a simple model for the influence of meiotic conversion tracts on gc content.	a strong correlation between gc content and recombination rate is observed in many eukaryotes, which is thought to be due to conversion events linked to the repair of meiotic double-strand breaks. in several organisms, the length of conversion tracts has been shown to decrease exponentially with increasing distance from the sites of meiotic double-strand breaks. i show here that this behavior leads to a simple analytical model for the evolution and the equilibrium state of the gc content of sequ ...	2011	21249197
comparative genomics of proteins involved in rna nucleocytoplasmic export.	the establishment of the nuclear membrane resulted in the physical separation of transcription and translation, and presented early eukaryotes with a formidable challenge: how to shuttle rna from the nucleus to the locus of protein synthesis. in prokaryotes, mrna is translated as it is being synthesized, whereas in eukaryotes mrna is synthesized and processed in the nucleus, and it is then exported to the cytoplasm. in metazoa and fungi, the different rna species are exported from the nucleus by ...	2011	21223572
infection acquisition following intensive care unit room privatization.	patients in intensive care units (icus) often acquire infections, which impose a heavy human and financial burden. the use of private rooms may reduce the acquisition of certain pathogens, but the limited evidence on this topic is inconsistent.	2011	21220658
selected reaction monitoring by linear ion-trap mass spectrometry can effectively be applicable to simultaneous quantification of multiple peptides.	selected reaction monitoring (srm) mass spectrometry (ms) is becoming a popular approach for targeted quantitative proteomics. triple-quadrupole mass spectrometers have been historically considered as the instrument of choice for this type of quantitative analysis. recently, however, it has been reported that the srm ms with a linear ion-trap (lit) mass spectrometer is rather more appropriate for quantitative analysis of large peptides than the triple-quadrupole ones. in this study, we demonstra ...	2011	21212531
candida albicans sfl2, a temperature-induced transcriptional regulator, is required for virulence in a murine gastrointestinal infection model.	many transcriptional regulators play roles in morphogenesis of the human pathogen candida albicans. recently, sfl2, a sequence homolog of c. albicans sfl1, has been shown to be required for hyphal development. in this report, we show that, like sfl1, sfl2 could complement the phenotypes of the saccharomyces cerevisiae sfl1 mutant, and green fluorescent protein-tagged sfl2 localized in the nuclei of both yeast and hyphal cells in c. albicans, reflecting its role as a transcriptional regulator. in ...	2011	21205158
mutation to bax beyond the bh3 domain disrupts interactions with pro-survival proteins and promotes apoptosis.	pro-survival members of the bcl-2 family of proteins restrain the pro-apoptotic activity of bax, either directly through interactions with bax or indirectly by sequestration of activator bh3-only proteins, or both. mutations in bax that promote apoptosis can provide insight into how bax is regulated. here, we describe crystal structures of the pro-survival proteins mcl-1 and bcl-x(l) in complex with a 34-mer peptide from bax that encompasses its bh3 domain. these structures reveal canonical inte ...	2011	21199865
single-cell tracking with a reversing flow cytometer.	we have developed an instrument based on a flow cytometer platform that is capable of tracking individual, suspended cells over extended time periods. the instrument repeatedly moves in a capillary the same volume segment of fluid containing tens to hundreds of suspended cells through the focal point of a laser. individual cells are then tracked based on the timing of when they cross the laser, and cell properties are measured as in a conventional flow cytometer. because cells are repeatedly mea ...	2011	21182184
biclustering of gene expression data by correlation-based scatter search.		2011	21261986
defining potentially conserved rna regulons of homologous zinc-finger rna-binding proteins.	abstract: background: glucose inhibition of gluconeogenic growth suppressor 2 protein (gis2p) and zinc-finger protein 9 (znf9) are conserved yeast and human zinc-finger proteins. the function of yeast gis2p is unknown, but human znf9 has been reported to bind nucleic acids, and mutations in the znf9 gene cause the neuromuscular disease myotonic dystrophy type 2. to explore the impact of these proteins on rna regulation, we undertook a systematic analysis of the rna targets and of the global impl ...	2011	21232131
isobase: a database of functionally related proteins across ppi networks.	we describe isobase, a database identifying functionally related proteins, across five major eukaryotic model organisms: saccharomyces cerevisiae, drosophila melanogaster, caenorhabditis elegans, mus musculus and homo sapiens. nearly all existing algorithms for orthology detection are based on sequence comparison. although these have been successful in orthology prediction to some extent, we seek to go beyond these methods by the integration of sequence data and protein-protein interaction (ppi) ...	2011	21177658
a novel neuron-enriched protein sdim1 is down regulated in alzheimer's brains and attenuates cell death induced by dnajb4 over-expression in neuro-progenitor cells.		2011	21255413
cell biology. why starving cells eat themselves.		2011	21273476
ubiquitin-dependent proteasomal degradation of human liver cytochrome p450 2e1: identification of sites targeted for phosphorylation and ubiquitination.	human liver cyp2e1 is a monotopic, endoplasmic reticulum-anchored cytochrome p450 responsible for the biotransformation of clinically relevant drugs, low molecular weight xenobiotics, carcinogens, and endogenous ketones. cyp2e1 substrate complexation converts it into a stable slow-turnover species degraded largely via autophagic lysosomal degradation. substrate decomplexation/withdrawal results in a fast turnover cyp2e1 species, putatively generated through its futile oxidative cycling, that inc ...	2011	21209460
surface display of human lactoferrin using a glycosylphosphatidylinositol-anchored protein of saccharomyces cerevisiae in pichia pastoris.	a cell surface display system was developed in pichia pastoris using the gene tip1, encoding the glycosylphosphatidylinositol (gpi)-anchored protein of saccharomyces cerevisiae (sctip). human lactoferrin cdna (hlf) was fused to a full-length tip1 dna (sctip ( 630 )) or a short-tip1 fragment (sctip ( 120 )) encoding the 40 c-terminal amino acids of sctip. both hlf-sctip fusion genes were expressed in p. pastoris smd 1168. the fused protein was detected by western blotting after extraction of the ...	2011	21267758
miip, a cytoskeleton regulator that blocks cell migration and invasion, delays mitosis, and suppresses tumorogenesis.	the migration and invasion inhibitory protein (miip) was initially discovered in a yeast two-hybrid screen for proteins that interact and inhibit the migration and invasion-promoting protein insulin-like growth factor binding protein 2 (igfbp2). recent studies have shown that miip not only modulates igfbp2 but also regulates microtubule by binding to and inhibiting hdac6, a class 2 histone deacetylase that deacetylates α-tubulin, heat-shock protein 90 (hsp90), and cortactin. in addition, miip al ...	2011	21190522
role of the ubiquitin-like protein urm1 as a noncanonical lysine-directed protein modifier.	the ubiquitin (ub)-related modifier urm1 functions as a sulfur carrier in trna thiolation by means of a mechanism that requires the formation of a thiocarboxylate at the c-terminal glycine residue of urm1. however, whether urm1 plays an additional role as a ub-like protein modifier remains unclear. here, we show that urm1 is conjugated to lysine residues of target proteins and that oxidative stress enhances protein urmylation in both saccharomyces cerevisiae and mammalian cells. similar to ubiqu ...	2011	21209336
telomere protein complexes and interactions with telomerase in telomere maintenance.	telomeres are the termini of linear chromosomes. they are composed of dna and dna-binding proteins critical for maintaining chromosome integrity and cellular function. telomere binding proteins regulate the structure and function of telomeres through the formation of different complexes with telomeric dna. double- and single-stranded telomeric dna binding protein complexes have shared and unique functions that regulate telomere homeostasis. recent studies have shown that telomerase interacts wit ...	2011	21196166
drosophila glia use a conserved cotransporter mechanism to regulate extracellular volume.	the nervous system is protected by blood barriers that use multiple systems to control extracellular solute composition, osmotic pressure, and fluid volume. in the human nervous system, misregulation of the extracellular volume poses serious health threats. here, we show that the glial cells that form the drosophila blood-nerve barrier have a conserved molecular mechanism that regulates extracellular volume: the serine/threonine kinase fray, which we previously showed is an ortholog of mammalian ...	2011	21125654
miniaturization of a panel of high-throughput yeast-cell-based nuclear receptor assays in 384- and 1536-well microplates.	a panel of luminescent saccharomyces cerevisiae cell-based nuclear receptor assays, consisting of human estrogen receptors α and β, androgen receptor, and aryl hydrocarbon receptor, was miniaturized from the standard 96-well microplate format to high-throughput 384- and 1536-well microplate formats. in these assays, firefly luciferase lacking the peroxisome targeting sequence was used as a reporter and d-luciferin substrate was pre-mixed with the yeast cells before the incubation step, eliminati ...	2011	20958257
phosphoproteome resource for systems biology research.	phospopep version 2.0 is a project to support systems biology signaling research by providing interactive interrogation of ms-derived phosphorylation data from four different organisms. currently the database hosts phosphorylation data from the fly (drosophila melanogaster), human (homo sapiens), worm (caenorhabditis elegans), and yeast (saccharomyces cerevisiae). the following will give an overview of the content and usage of the phosphopep database.	2011	21082442
fission yeast homologs of human xpc and csb, rhp41 and rhp26, are involved in transcription-coupled repair of methyl methanesulfonate-induced dna damage.	methyl methanesulfonate (mms) methylates nitrogen atoms in purines, and predominantly produces 7-methylguanine and 3-methyladenine (3-mea). previously, we showed that base excision repair (ber) and nucleotide excision repair (ner) synergistically function to repair mms-induced dna damage in the fission yeast schizosaccharomyces pombe. here, we studied the roles of ner components in repair of 3-mea and ber intermediates such as the ap site and single strand breaks. mutants of rhp41 (xpc homolog) ...	2011	21670547
a yeast-based assay identifies drugs active against human mitochondrial disorders.	due to the lack of relevant animal models, development of effective treatments for human mitochondrial diseases has been limited. here we establish a rapid, yeast-based assay to screen for drugs active against human inherited mitochondrial diseases affecting atp synthase, in particular narp (neuropathy, ataxia, and retinitis pigmentosa) syndrome. this method is based on the conservation of mitochondrial function from yeast to human, on the unique ability of yeast to survive without production of ...	2011	21715656
p53 transactivation and the impact of mutations, cofactors and small molecules using a simplified yeast-based screening system.	the p53 tumor suppressor, which is altered in most cancers, is a sequence-specific transcription factor that is able to modulate the expression of many target genes and influence a variety of cellular pathways. inactivation of the p53 pathway in cancer frequently occurs through the expression of mutant p53 protein. in tumors that retain wild type p53, the pathway can be altered by upstream modulators, particularly the p53 negative regulators mdm2 and mdm4.	2011	21674059
papd5, a noncanonical poly(a) polymerase with an unusual rna-binding motif.	papd5 is one of the seven members of the family of noncanonical poly(a) polymerases in human cells. papd5 was shown to polyadenylate aberrant pre-ribosomal rnas in vivo, similar to degradation-mediating polyadenylation by the noncanonical poly(a) polymerase trf4p in yeast. papd5 has been reported to be also involved in the uridylation-dependent degradation of histone mrnas. to test whether papd5 indeed catalyzes adenylation as well as uridylation of rna substrates, we analyzed the in vitro prope ...	2011	21788334
ca(v)2.3 ca2+ channel interacts with the g1-subunit of v-atpase.	calcium channels are essential in coupling action potential to signal transduction in cells. there are several types of calcium channels, which can be pharmacologically classified as l-, n-, p/q-, r- and t-type. but molecular basis of r-type channels is less clearly understood compared the other channel types. therefore the current study aims at understanding the molecular functions of r-type calcium channels by identifying interaction partners of the channel.	2011	21691059
aggresome formation and segregation of inclusions influence toxicity of α-synuclein and synphilin-1 in yeast.	pd (parkinson's disease) is a neurodegenerative disorder, caused by a selective loss of dopaminergic neurons in the substantia nigra, which affects an increasing number of the elderly population worldwide. one of the major hallmarks of pd is the occurrence of intracellular protein deposits in the dying neurons, termed lewy bodies, which contain different proteins, including aggregated α-synuclein and its interacting protein synphilin-1. during the last decade, a number of groups developed yeast ...	2011	21936837
endoplasmic reticulum-associated degradation (erad) and free oligosaccharide generation in saccharomyces cerevisiae.	in saccharomyces cerevisiae, proteins with misfolded lumenal, membrane, and cytoplasmic domains are cleared from the endoplasmic reticulum (er) by er-associated degradation (erad)-l, -m, and -c, respectively. erad-l is n-glycan-dependent and is characterized by er mannosidase (mns1p) and er mannosidase-like protein (mnl1p), which generate man(7)glcnac(2) (d1) n-glycans with non-reducing α1,6-mannosyl residues. glycoproteins bearing this motif bind yos9p and are dislocated into the cytoplasm and ...	2011	21979948
oxidative protein folding: selective pressure for prolamin evolution in rice.	during seed development, endosperm cells of highly productive cereals, including rice, synthesize disulfide-rich proteins in large amounts and deposit them into storage organelles. disulfide bond formation involves electron transfer and generates h 2o 2 as a by-product. to ensure proper development and maturation of seeds, the endosperm cells must supply large amounts of oxidizing equivalents to dithiols in nascent proteins in a controlled manner. this review compares multiple oxidative protein ...	2011	22112460
myst protein acetyltransferase activity requires active site lysine autoacetylation.	the myst protein lysine acetyltransferases are evolutionarily conserved throughout eukaryotes and acetylate proteins to regulate diverse biological processes including gene regulation, dna repair, cell-cycle regulation, stem cell homeostasis and development. here, we demonstrate that myst protein acetyltransferase activity requires active site lysine autoacetylation. the x-ray crystal structures of yeast esa1 (yesa1/kat5) bound to a bisubstrate h4k16coa inhibitor and human mof (hmof/kat8/myst1) ...	2011	22020126
interaction profiling identifies the human nuclear exosome targeting complex.	the rna exosome is a conserved degradation machinery, which obtains full activity only when associated with cofactors. the most prominent activator of the yeast nuclear exosome is the rna helicase mtr4p, acting in the context of the trf4p/air2p/mtr4p polyadenylation (tramp) complex. the existence of a similar activator(s) in humans remains elusive. by establishing an interaction network of the human nuclear exosome, we identify the trimeric nuclear exosome targeting (next) complex, containing hm ...	2011	21855801
structural and binding studies of the c-terminal domains of yeast tfiif subunits tfg1 and tfg2.	the general transcription factor tfiif plays essential roles at several steps during eukaryotic transcription. while several studies have offered insights into the structure/function relationship in human tfiif, much less is known about the yeast system. here, we describe the first nmr structural and binding studies of the c-terminal domains (ctds) of tfg1 and tfg2 subunits of saccharomyces cerevisiae tfiif. we used the program cs-rosetta to determine the three-dimensional folds of these domains ...	2011	22095626
An integrated genomic approach identifies ARID1A as a candidate tumor-suppressor gene in breast cancer.	Tumor-suppressor genes (TSGs) have been classically defined as genes whose loss of function in tumor cells contributes to the formation and/or maintenance of the tumor phenotype. TSGs containing nonsense mutations may not be expressed because of nonsense-mediated RNA decay (NMD). We combined inhibition of the NMD process, which clears transcripts that contain nonsense mutations, with the application of high-density single-nucleotide polymorphism arrays analysis to discriminate allelic content in ...	2011	21892209
a non-motor microtubule binding site is essential for the high processivity and mitotic function of kinesin-8 kif18a.	members of the kinesin-8 subfamily are plus end-directed molecular motors that accumulate at the plus-ends of kinetochore-microtubules (kt-mts) where they regulate mt dynamics. loss of vertebrate kinesin-8 function induces hyperstable mts and elongated mitotic spindles accompanied by severe chromosome congression defects. it has been reported that the motility of human kinesin-8, kif18a, is required for its accumulation at the plus tips of kt-mts.	2011	22102900