Hypochlorous acid inhibition by acetoacetate: Implications on neutrophil functions

Type-1 diabetic patients experience hyperketonemia caused by an increase in fatty acid metabolism. Thus, the aim of this study was to measure the effect of ketone bodies as suppressors of oxidizing species produced by stimulated neutrophils. Both acetoacetate and 3-hydroxybutyrate have suppressive effect on the respiratory burst measured by luminol-enhanced chemiluminescence. Through measurements of hypochlorous acid production, using neutrophils or the myeloperoxidase/H2O2/Cl- system, it was found that acetoacetate but not 3-hydroxybutyrate is able to inhibit the generation of this antimicrobial oxidant. The superoxide anion scavenging properties were confirmed by ferricytochrome C reduction and lucigenin-enhanced chemiluminescence assays. However, ketone bodies did not alter the rate of oxygen uptake by stimulated neutrophils, measured with an oxygen electrode. A strong inhibition of the expression of the cytokine IL-8 by cultured neutrophils was also observed; this is discussed with reference to the antioxidant-like property of acetoacetate. © 2004 Pharmaceutical Society of Japan.

Caracterização genotípica microrganismos isolados de infecções da corrente sanguína relacionadas a cateteres em recém-nascidos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Caracterização funcional de eIF5A: análise genética e molecular utilizando o modelo de Saccharomyces cerevisiae

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Atividade hipolidêmica e protetora da bixina no fígado de ratos tratados com dieta hipercalórica

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudos funcionais da rgs-CaM, uma calmodulina envolvida na supressão de silenciamento por RNA

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

RNA Interference and cyclooxygenase-2 (COX-2) regulation in colon cancer cells

Despite new methods and combined strategies, conventional cancer chemotherapy still lacks specificity and induces drug resistance. Gene therapy can offer the potential to obtain the success in the clinical treatment of cancer and this can be achieved by replacing mutated tumour suppressor genes, inhibiting gene transcription, introducing new genes encoding for therapeutic products, or specifically silencing any given target gene. Concerning gene silencing, attention has recently shifted onto the RNA interference (RNAi) phenomenon. Gene silencing mediated by RNAi machinery is based on short RNA molecules, small interfering RNAs (siRNAs) and microRNAs (miRNAs), that are fully o partially homologous to the mRNA of the genes being silenced, respectively. On one hand, synthetic siRNAs appear as an important research tool to understand the function of a gene and the prospect of using siRNAs as potent and specific inhibitors of any target gene provides a new therapeutical approach for many untreatable diseases, particularly cancer. On the other hand, the discovery of the gene regulatory pathways mediated by miRNAs, offered to the research community new important perspectives for the comprehension of the physiological and, above all, the pathological mechanisms underlying the gene regulation. Indeed, changes in miRNAs expression have been identified in several types of neoplasia and it has also been proposed that the overexpression of genes in cancer cells may be due to the disruption of a control network in which relevant miRNA are implicated. For these reasons, I focused my research on a possible link between RNAi and the enzyme cyclooxygenase-2 (COX-2) in the field of colorectal cancer (CRC), since it has been established that the transition adenoma-adenocarcinoma and the progression of CRC depend on aberrant constitutive expression of COX-2 gene. In fact, overexpressed COX-2 is involved in the block of apoptosis, the stimulation of tumor-angiogenesis and promotes cell invasion, tumour growth and metastatization. On the basis of data reported in the literature, the first aim of my research was to develop an innovative and effective tool, based on the RNAi mechanism, able to silence strongly and specifically COX-2 expression in human colorectal cancer cell lines. In this study, I firstly show that an siRNA sequence directed against COX-2 mRNA (siCOX-2), potently downregulated COX-2 gene expression in human umbilical vein endothelial cells (HUVEC) and inhibited PMA-induced angiogenesis in vitro in a specific, non-toxic manner. Moreover, I found that the insertion of a specific cassette carrying anti-COX-2 shRNA sequence (shCOX-2, the precursor of siCOX-2 previously tested) into a viral vector (pSUPER.retro) greatly increased silencing potency in a colon cancer cell line (HT-29) without activating any interferon response. Phenotypically, COX-2 deficient HT-29 cells showed a significant impairment of their in vitro malignant behaviour. Thus, results reported here indicate an easy-to-use, powerful and high selective virus-based method to knockdown COX-2 gene in a stable and long-lasting manner, in colon cancer cells. Furthermore, they open up the possibility of an in vivo application of this anti-COX-2 retroviral vector, as therapeutic agent for human cancers overexpressing COX-2. In order to improve the tumour selectivity, pSUPER.retro vector was modified for the shCOX-2 expression cassette. The aim was to obtain a strong, specific transcription of shCOX-2 followed by COX-2 silencing mediated by siCOX-2 only in cancer cells. For this reason, H1 promoter in basic pSUPER.retro vector [pS(H1)] was substituted with the human Cox-2 promoter [pS(COX2)] and with a promoter containing repeated copies of the TCF binding element (TBE) [pS(TBE)]. These promoters were choosen because they are partculary activated in colon cancer cells. COX-2 was effectively silenced in HT-29 and HCA-7 colon cancer cells by using enhanced pS(COX2) and pS(TBE) vectors. In particular, an higher siCOX-2 production followed by a stronger inhibition of Cox-2 gene were achieved by using pS(TBE) vector, that represents not only the most effective, but also the most specific system to downregulate COX-2 in colon cancer cells. Because of the many limits that a retroviral therapy could have in a possible in vivo treatment of CRC, the next goal was to render the enhanced RNAi-mediate COX-2 silencing more suitable for this kind of application. Xiang and et al. (2006) demonstrated that it is possible to induce RNAi in mammalian cells after infection with engineered E. Coli strains expressing Inv and HlyA genes, which encode for two bacterial factors needed for successful transfer of shRNA in mammalian cells. This system, called “trans-kingdom” RNAi (tkRNAi) could represent an optimal approach for the treatment of colorectal cancer, since E. Coli in normally resident in human intestinal flora and could easily vehicled to the tumor tissue. For this reason, I tested the improved COX-2 silencing mediated by pS(COX2) and pS(TBE) vectors by using tkRNAi system. Results obtained in HT-29 and HCA-7 cell lines were in high agreement with data previously collected after the transfection of pS(COX2) and pS(TBE) vectors in the same cell lines. These findings suggest that tkRNAi system for COX-2 silencing, in particular mediated by pS(TBE) vector, could represent a promising tool for the treatment of colorectal cancer. Flanking the studies addressed to the setting-up of a RNAi-mediated therapeutical strategy, I proposed to get ahead with the comprehension of new molecular basis of human colorectal cancer. In particular, it is known that components of the miRNA/RNAi pathway may be altered during the progressive development of colorectal cancer (CRC), and it has been already demonstrated that some miRNAs work as tumor suppressors or oncomiRs in colon cancer. Thus, my hypothesis was that overexpressed COX-2 protein in colon cancer could be the result of decreased levels of one or more tumor suppressor miRNAs. In this thesis, I clearly show an inverse correlation between COX-2 expression and the human miR- 101(1) levels in colon cancer cell lines, tissues and metastases. I also demonstrate that the in vitro modulating of miR-101(1) expression in colon cancer cell lines leads to significant variations in COX-2 expression, and this phenomenon is based on a direct interaction between miR-101(1) and COX-2 mRNA. Moreover, I started to investigate miR-101(1) regulation in the hypoxic environment since adaptation to hypoxia is critical for tumor cell growth and survival and it is known that COX-2 can be induced directly by hypoxia-inducible factor 1 (HIF-1). Surprisingly, I observed that COX-2 overexpression induced by hypoxia is always coupled to a significant decrease of miR-101(1) levels in colon cancer cell lines, suggesting that miR-101(1) regulation could be involved in the adaption of cancer cells to the hypoxic environment that strongly characterize CRC tissues.

Ricerca di marcatori molecolari nella prevenzione dei tumori di testa e collo

Oral cavity cancers (OSCC) are among the most malignances worldwide. OSCC tipically affects men in their IV or V dedade of life, and the most relevant risk factors are tobacco and alcohol consumption. OSCCs generally exhibit poor prognosis, and late stage identification correlates with higher mortality rates. Basic prognostic factors, are tumor size and presence of lymph node and/or distance metastases (T classification, N, M). However, tumors with the same TNM grade and similar morphology may have completely different evolution, because of their intrinsic biological characteristics. For these reasons, the identification of new molecular markers with a predictive value, could represent useful tools in OSCC prevention, prognosis and treatment. In the first part of my PhD project I evaluated the loss of heterozygosity as a possible cause of deregulation of well-known tumor suppressors genes. Obtained data put on light the importance of this rearrangement and genes PDCD4, CTNB1, CASP4 and HSP23, in the onset and progression of OSCC. Subsequently, the analysis of the expression profile of miRNAs, led to the identification of some miRNAs that seems to be involved in cancer development and metastatic progression. In both cases, we need further investigations to understand whether these molecules may be used ideal markers in OSCC diagnosis and treatment.

Mechanismen zur Suppression der experimentellen akuten Graft-versus-Host-Disease

Die Transplantation von allogenen hämatopoetischen Stammzellen stellt für viele Patienten mit hämatologischen Erkrankungen, wie beispielsweise akuter Leukämie, oftmals die einzige kurative Therapieoption dar. Die Erkennung von Empfängerantigenen durch immunkompetente Zellen des Spenders bietet dabei die Basis für erwünschte Graft-versus-Tumor-Effekte, verursacht jedoch häufig außerdem die unerwünschte Graft-versus-Host Disease (GvHD), eine mitunter schwerwiegende Komplikation. In der vorliegenden Arbeit wurden potentielle Mechanismen zur Hemmung alloreaktiver CD4+ und CD8+ T-Zellen (TZ) und folglich zur Hemmung der akuten GvHD in einem experimentellen GvHD-Modell untersucht, welches auf dem Transfer von allogenen Zellen zwischen MHC-inkompatiblen Mausstämmen basiert. Die vorliegende Arbeit weist zum Einen darauf hin, dass das Fehlen MyD88- und TRIF-vermittelter Toll-like-Rezeptor-Signale zumindest im Rahmen des hier verwendeten Transplantationsmodells nicht zwingend zu einer Hemmung der akuten GvHD führt. Zum Anderen konnte belegt werden, dass CD4+ CD25+ regulatorische T-Zellen (Tregs) kompetente Suppressoren der durch alloreaktive CD4+ und CD8+ TZ ausgelösten akuten GvHD darstellen. In weiterführenden Experimenten ist gezeigt worden, dass die Tregs sich verschiedener Mechanismen bedienen, um ihre Zielzellen zu inhibieren. Das suppressive Zytokin Interleukin-10 kann als löslicher Mediator zumindest in vitro offenbar eine Rolle bei der Treg-vermittelten Suppression alloreaktiver TZ spielen. Da jedoch auch Tregs aus Interleukin-10-defizienten Spendern die GvHD-Entstehung in den Empfängern abschwächen konnten, müssen noch weitere Mechanismen involviert sein. Es konnte in einer gemischten Leukozyten Reaktion in vitro eine zellkontaktabhängige Kommunikation mittels gap junctions hauptsächlich zwischen den Tregs und den allogenen Dendritischen Zellen (DCs) nachgewiesen werden, welche prinzipiell den Transfer von cAMP möglich macht. Die Kommunikation zwischen Tregs und DCs resultierte in einem supprimierten Phänotyp der DCs, gekennzeichnet durch eine verminderte Expression kostimulatorischer Moleküle auf ihrer Oberfläche. Solche supprimierten DCs können als Folge die alloreaktiven Spender-TZ vermutlich nicht aktivieren. Das cAMP-erhöhende Rolipram konnte in einer gemischten Leukozyten Reaktion in vitro die Proliferation alloreaktiver CD4+ und CD8+ TZ hemmen. Daneben konnte die Treg-vermittelte Suppression alloreaktiver TZ und der GvHD in vivo durch die zusätzliche Verabreichung von Rolipram noch gesteigert werden. Im letzten Kapitel dieser Arbeit wurde beschrieben, dass die alleinige Aktivierung alloreaktiver CD8+ TZ ausreichend ist, um eine akute GvHD auszulösen. In diesem Zusammenhang konnte nachgewiesen werden, dass CD4+ CD25+ Tregs die akute GvHD auch in einer scheinbar MHC-II-unabhängigen Weise hemmen können. Zusammenfassend belegt die vorliegende Arbeit, dass Tregs in einem MHC-inkompatiblen Transplantationsmodell alloreaktive CD4+ und CD8+ TZ und folglich die Entstehung einer GvHD effizient hemmen können. Bei der Hemmung der GvHD kommen wahrscheinlich verschiedene Mechanismen zum Tragen. Zumindest in vivo scheint von Tregs produziertes Interleukin-10 eine untergeordnete Rolle bei der Suppression alloreaktiver TZ und der GvHD zu spielen, hierbei steht vermutlich vielmehr der cAMP-abhängige Suppressionsmechanismus im Vordergrund.

Immunregulatorische Mechanismen bei einer experimentellen akuten Graft-versus-Host-Disease

Die allogene hämatopoetische Stammzelltransplantation ist bereits seit mehreren Jahrzehnten zur Therapie von Leukämien und anderen malignen Erkrankungen etabliert, aber ihre Effektivität wird durch Graft-versus-Host Reaktionen weiterhin deutlich eingeschränkt. Um die zu Grunde liegenden Mechanismen besser zu verstehen und Möglichkeiten zur Modulation zu untersuchen, wurden in dieser Arbeit verschiedene Ansätze verfolgt.rnRegulatorische T-Zellen sind in der Lage allogene T-Zell-Antworten, wie sie auch bei einer GvH-Erkrankung auftreten zu supprimieren. Es konnte gezeigt werden, dass dies unabhängig von Interleukin-10 geschieht, dafür jedoch ein kontaktabhängiger Mechanismus eine wichtige Rolle spielt. Dabei wird cAMP von Treg über Gap-Junctions in allogene Dendritische Zellen übertragen und deren Aktivierung dadurch verhindert. Versuche zur Modulation dieses Mechanismus mithilfe von Phosphodiesterase-Inhibitoren haben gezeigt, dass diese nicht nur die suppressiven Fähigkeiten von Treg verbessern, sondern ebenfalls direkt auf die T-Zellen einwirken, die schließlich die GvH-Erkrankung auslösen. Diese Ergebnisse konnten in vivo bestätigt werden und zeigen somit einen möglichen Ansatz hin zu einer kombinierten zellulären und pharmakologischen Therapie von GvH-Erkrankungen. Ein großer Vorteil dabei wäre, dass bereits eine Palette an PDE-Inhibitoren in der Klinik zur Verfügung steht.rnInterleukin-10 ist ein immunsuppressives und anti-inflammatorisches Zytokin, dem bei der Regulation des Immunsystems eine wichtige Rolle zukommt. Wie in dieser und anderen Arbeiten gezeigt, ist diese Funktion von IL-10 auch bei GvH-Erkrankungen essentiell. Ein Ziel war es daher, die Zellpopulationen, die für die Produktion des Zytokins verantwortlich sind, zu identifizieren. Mittels einer IL-10 Reporter-Maus konnten B-Zellen vom Spender, wie auch vom Empfänger als IL-10 Produzenten ausgemacht werden. Darüberhinaus zeigen die so gefundenen Zellen auch einen typischen Phänotyp für sog. immunregulatorische B-Zellen. Transplantationsexperimente mit Mäusen, die einen B-Zell-spezifischen Knock-out für IL-10 tragen, konnten die Relevanz der B Zellen als IL-10 Produzenten in vivo belegen.rnDendritische Zellen sind sehr potente Antigenpräsentierende Zellen und somit in der Lage GvH-Reaktionen zu induzieren. Überraschenderweise ist das Überleben von Versuchsmäusen, denen alle DC oder auch nur die BATF3-abhängige Subpopulation der CD8α+ DC fehlt, nicht besser als das des WT, sondern sogar deutlich schlechter. Dies geht einher mit entsprechenden Veränderungen im Zytokinmilieu der peripheren lymphatischen Organe. Bei Abwesenheit der CD8α+ DC sind die Zellen der mesenterialen Lymphknoten nach dem Konditionierungsprotokoll stärkere Stimulatoren für allogene T-Zell-Proliferation, was eine Erklärung für die stärkere GvH-Erkrankung ist. Eine Erklärung für diese Befunde liefert die verringerte Anzahl an Treg, die nach einer Transplantation in Abwesenheit der CD8α+ DC zu beobachten ist.rnDie aufgezeigten immunsupressiven Mechanismen stellen gute Ansatzpunkte dar, um GvH-Erkrankungen besser zu verstehen und damit die Effektivität der allogenen hämatopoetischen Stammzelltransplantation zu verbessern.rn

Mining tissue microarray data to uncover combinations of biomarker expression patterns that improve intermediate staging and grading of clear cell renal cell cancer

PURPOSE: Tumor stage and nuclear grade are the most important prognostic parameters of clear cell renal cell carcinoma (ccRCC). The progression risk of ccRCC remains difficult to predict particularly for tumors with organ-confined stage and intermediate differentiation grade. Elucidating molecular pathways deregulated in ccRCC may point to novel prognostic parameters that facilitate planning of therapeutic approaches. EXPERIMENTAL DESIGN: Using tissue microarrays, expression patterns of 15 different proteins were evaluated in over 800 ccRCC patients to analyze pathways reported to be physiologically controlled by the tumor suppressors von Hippel-Lindau protein and phosphatase and tensin homologue (PTEN). Tumor staging and grading were improved by performing variable selection using Cox regression and a recursive bootstrap elimination scheme. RESULTS: Patients with pT2 and pT3 tumors that were p27 and CAIX positive had a better outcome than those with all remaining marker combinations. A prolonged survival among patients with intermediate grade (grade 2) correlated with both nuclear p27 and cytoplasmic PTEN expression, as well as with inactive, nonphosphorylated ribosomal protein S6. By applying graphical log-linear modeling for over 700 ccRCC for which the molecular parameters were available, only a weak conditional dependence existed between the expression of p27, PTEN, CAIX, and p-S6, suggesting that the dysregulation of several independent pathways are crucial for tumor progression. CONCLUSIONS: The use of recursive bootstrap elimination, as well as graphical log-linear modeling for comprehensive tissue microarray (TMA) data analysis allows the unraveling of complex molecular contexts and may improve predictive evaluations for patients with advanced renal cancer.

Hit proteins, mitochondria and cancer

The histidine triad (HIT) superfamily comprises proteins that share the histidine triad motif, His-ϕ-His-ϕ-His-ϕ-ϕ, where ϕ is a hydrophobic amino acid. HIT proteins are ubiquitous in prokaryotes and eukaryotes. HIT proteins bind nucleotides and exert dinucleotidyl hydrolase, nucleotidylyl transferase or phosphoramidate hydrolase enzymatic activity. In humans, 5 families of HIT proteins are recognized. The accumulated epidemiological and experimental evidence indicates that two branches of the superfamily, the HINT (Histidine Triad Nucleotide Binding) members and FHIT (Fragile Histidine Triad), have tumor suppressor properties but a conclusive physiological role can still not be assigned to these proteins. Aprataxin forms another discrete branch of the HIT superfamily, is implicated in DNA repair mechanisms and unlike the HINT and FHIT members, a defective protein can be conclusively linked to a disease, ataxia with oculomotor apraxia type 1. The scavenger mRNA decapping enzyme, DcpS, forms a fourth branch of the HIT superfamily. Finally, the GalT enzymes, which exert specific nucleoside monophosphate transferase activity, form a fifth branch that is not implicated in tumorigenesis. The molecular mechanisms by which the HINT and FHIT proteins participate in bioenergetics of cancer are just beginning to be unraveled. Their purported actions as tumor suppressors are highlighted in this review.

Classification of suppressor additives based on synergistic and antagonistic ensemble effects

Three fundamental types of suppressor additives for copper electroplating could be identified by means of potential Transient measurements. These suppressor additives differ in their synergistic and antagonistic interplay with anions that are chemisorbed on the metallic copper surface during electrodeposition. In addition these suppressor chemistries reveal different barrier properties with respect to cupric ions and plating additives (Cl, SPS). While the type-I suppressor selectively forms efficient barriers for copper inter-diffusion on chloride-terminated electrode surfaces we identified a type-II suppressor that interacts non-selectively with any kind of anions chemisorbed on copper (chloride, sulfate, sulfonate). Type-I suppressors are vital for the superconformal copper growth mode in Damascene processing and show an antagonistic interaction with SPS (Bis-Sodium-Sulfopropyl-Disulfide) which involves the deactivation of this suppressor chemistry. This suppressor deactivation is rationalized in terms of compositional changes in the layer of the chemisorbed anions due to the competition of chloride and MPS (Mercaptopropane Sulfonic Acid) for adsorption sites on the metallic copper surface. MPS is the product of the dissociative SPS adsorption within the preexisting chloride matrix on the copper surface. The non-selectivity in the adsorption behavior of the type-II suppressor is rationalized in terms of anion/cation pairing effects of the poly-cationic suppressor and the anion-modified copper substrate. Atomic-scale insights into the competitive Cl/MPS adsorption are gained from in situ STM (Scanning Tunneling Microscopy) using single crystalline copper surfaces as model substrates. Type-III suppressors are a third class of suppressors. In case of type-land type-II suppressor chemistries the resulting steady-state deposition conditions are completely independent on the particular succession of additive adsorption. In contrast to that a strong dependence of the suppressing capabilities on the sequence of additive adsorption ("first comes, first serves" principle) is observed for the type-IIIsuppressor. This behavior:is explained by a suppressor barrier that impedes not only the copper inter-diffusion but also the transport of other additives (e.g. SPS) to the copper surface. (C) 2011 Elsevier Ltd. All rights reserved.

Acinetobacter baumannii isolates from pets and horses in Switzerland: molecular characterization and clinical data

OBJECTIVES: We investigated whether Acinetobacter baumannii isolates of veterinary origin shared common molecular characteristics with those described in humans. METHODS: Nineteen A. baumannii isolates collected in pets and horses were analysed. Clonality was studied using repetitive extragenic palindromic PCR (rep-PCR) and multilocus sequence typing (MLST). PCR and DNA sequencing for various beta-lactamase, aminoglycoside-modifying enzyme, gyrA and parC, ISAba1 and IS1133, adeR and adeS of the AdeABC efflux pump, carO porin and class 1/2/3 integron genes were performed. RESULTS: Two main clones [A (n = 8) and B (n = 9)] were observed by rep-PCR. MLST indicated that clone A contained isolates of sequence type (ST) ST12 (international clone II) and clone B contained isolates of ST15 (international clone I). Two isolates of ST10 and ST20 were also noted. Seventeen isolates were resistant to gentamicin, 12 to ciprofloxacin and 3 to carbapenems. Isolates of ST12 carried bla(OXA-66), bla(ADC-25), bla(TEM-1), aacC2 and IS1133. Strains of ST15 possessed bla(OXA-69), bla(ADC-11), bla(TEM-1) and a class 1 integron carrying aacC1 and aadA1. ISAba1 was found upstream of bla(ADC) (one ST10 and one ST12) and/or bla(OXA-66) (seven ST12). Twelve isolates of different STs contained the substitutions Ser83Leu in GyrA and Ser80Leu or Glu84Lys in ParC. Significant disruptions of CarO porin and overexpressed efflux pumps were not observed. The majority of infections were hospital acquired and in animals with predisposing conditions for infection. CONCLUSIONS: STs and the molecular background of resistance observed in our collection have been frequently described in A. baumannii detected in human patients. Animals should be considered as a potential reservoir of multidrug-resistant A. baumannii.

Bayesian Hidden Markov Modeling of Array CGH Data

Genomic alterations have been linked to the development and progression of cancer. The technique of Comparative Genomic Hybridization (CGH) yields data consisting of fluorescence intensity ratios of test and reference DNA samples. The intensity ratios provide information about the number of copies in DNA. Practical issues such as the contamination of tumor cells in tissue specimens and normalization errors necessitate the use of statistics for learning about the genomic alterations from array-CGH data. As increasing amounts of array CGH data become available, there is a growing need for automated algorithms for characterizing genomic profiles. Specifically, there is a need for algorithms that can identify gains and losses in the number of copies based on statistical considerations, rather than merely detect trends in the data. We adopt a Bayesian approach, relying on the hidden Markov model to account for the inherent dependence in the intensity ratios. Posterior inferences are made about gains and losses in copy number. Localized amplifications (associated with oncogene mutations) and deletions (associated with mutations of tumor suppressors) are identified using posterior probabilities. Global trends such as extended regions of altered copy number are detected. Since the posterior distribution is analytically intractable, we implement a Metropolis-within-Gibbs algorithm for efficient simulation-based inference. Publicly available data on pancreatic adenocarcinoma, glioblastoma multiforme and breast cancer are analyzed, and comparisons are made with some widely-used algorithms to illustrate the reliability and success of the technique.

Point mutations in the stem region and the fourth AAA domain of cytoplasmic dynein heavy chain partially suppress the phenotype of NUDF/LIS1 loss in Aspergillus nidulans

Cytoplasmic dynein performs multiple cellular tasks but its regulation remains unclear. The dynein heavy chain has a N-terminal stem that binds to other subunits and a C-terminal motor unit that contains six AAA (ATPase associated with cellular activities) domains and a microtubule-binding site located between AAA4 and AAA5. In Aspergillus nidulans, NUDF (a LIS1 homolog) functions in the dynein pathway, and two nudF6 partial suppressors were mapped to the nudA dynein heavy chain locus. Here we identified these two mutations. The nudAL1098F mutation resides in the stem region, and nudAR3086C is in the end of AAA4. These mutations partially suppress the phenotype of nudF deletion but do not suppress the phenotype exhibited by mutants of dynein intermediate chain and Arp1. Surprisingly, the stronger DeltanudF suppressor, nudAR3086C, causes an obvious decrease in the basal level of dynein's ATPase activity and an increase in dynein's distribution along microtubules. Thus, suppression of the DeltanudF phenotype may result from mechanisms other than simply the enhancement of dynein's ATPase activity. The fact that a mutation in the end of AAA4 negatively regulates dynein's ATPase activity but partially compensates for NUDF loss indicates the importance of the AAA4 domain in dynein regulation in vivo.