Analytical strategies for the comprehensive profiling of histone post translational modifications by mass spectrometry and implications for functional analyses

Le long bio-polymère d'ADN est condensé à l’intérieur du noyau des cellules eukaryotes à l'aide de petites protéines appelées histones. En plus de leurs fonctions condensatrices,ces histones sont également la cible de nombreuses modifications post-traductionnelles(MPT), particulièrement au niveau de leur section N-terminale. Ces modifications réversibles font partie d’un code d’histones épi-génétique transmissible qui orchestre et module dynamiquement certains événements impliquant la chromatine, tels l’activation et la désactivation de gènes ainsi que la duplication et la réparation d’ADN. Ces modifications sont impliquées subséquemment dans la signalisation et la progression de cancers, tels que la leucémie. En conséquence, l'élucidation des modifications d’histones est importante pour comprendre leurs fonctions biologiques. Une méthodologie analytique a été mise au point en laboratoire pour isoler, détecter, et quantifier les MPT d’histones en utilisant une approche rapide à deux volets à l’aide d’outils bioinformatiques spécialisés. La méthodologie développée en laboratoire a été validée en utilisant des histones de souche sauvage ainsi que deux types d’histones mutants déficients en enzymes acétyltransferase. Des trois sources d’histones utilisées, la seule MPT qui a démontré un changement significatif est l’acétylation de l’histone H3 à lysine 56 (H3K56ac). L’expression et la stoechiométrie de cette MPT, issue de cellules de souche sauvage et de cellules mutantes, ont été déterminées avec précision et comparées. Les fonctions de balayage polyvalentes d'un instrument à trappe ionique quadrupôle linéaire hybride ont été utilisées pour améliorer la détection de protéines intactes. Le mode de balayage « enhanced multiply charged » (EMC) a été modifié pour contenir et détecter les ions de protéines intactes situées dans la trappe ionique linéaire. Ce mode de balayage nommé « targeted EMC » (tEMC) a permis de quadrupler le niveau de sensibilité (signal/interférence), et quintupler la résolution du mode de balayage conventionnel. De plus, la capacité de séparation des charges du tEMC a réduit de façon significative les effets de « space charge » dans la trappe ionique linéaire. La résolution supérieure du mode tEMC a permis de différencier plusieurs isoformes modifiées, particulièrement pour l’histone H3. L’analyse des peptides d’histones trypsiques à l’aide du mode de balayage « MRM » a permis le séquençage et la quantification de MPT avec un haut degré de précision. La seule MPT qui était sous-exprimée entre l’histone de souche sauvage et le mutant DOT1L fut la méthylation de l’histone H3 lysine 79(H3K79me1). Les effets de deux inhibiteurs d’enzymes HDAC (HDACi) sur l’expression de MPT d’histone ont été évalués en utilisant la méthodologie analytique mentionnée. Les histones extraites de cellules normales et cancéreuses ont été exposées à du Vorinostat(SAHA) ou du Entinostat (MS-275) pour une période de 24 à 72 heures. Deux histones furent principalement affectées, soit H3 et H4. Étonnamment, les mêmes effets n'ont pas été détectés lorsque les cellules normales ont été traitées avec le HDACi pour une période de 48 à 72 heures. Une méthode absolue de quantification avec une courbe d’étalonnage a été développée pour le peptide H3K56ac. Contrairement à certaines publications, nos résultats démontrent que cette MPT est présente dans les cellules mammifères avec une stoechiométrie très basse (< 0,1%) et n'est pas surexprimée de façon significative après le traitement au HDACi.

Prediction and functional analysis of native disorder in proteins from the Three Kingdoms of Life

An automatic method for recognizing natively disordered regions from amino acid sequence is described and benchmarked against predictors that were assessed at the latest critical assessment of techniques for protein structure prediction (CASP) experiment. The method attains a Wilcoxon score of 90.0, which represents a statistically significant improvement on the methods evaluated on the same targets at CASP. The classifier, DISOPRED2, was used to estimate the frequency of native disorder in several representative genomes from the three kingdoms of life. Putative, long (>30 residue) disordered segments are found to occur in 2.0% of archaean, 4.2% of eubacterial and 33.0% of eukaryotic proteins. The function of proteins with long predicted regions of disorder was investigated using the gene ontology annotations supplied with the Saccharomyces genome database. The analysis of the yeast proteome suggests that proteins containing disorder are often located in the cell nucleus and are involved in the regulation of transcription and cell signalling. The results also indicate that native disorder is associated with the molecular functions of kinase activity and nucleic acid binding.

Cwc24p, a novel Saccharomyces cerevisiae nuclear ring finger protein, affects pre-snoRNA U3 splicing

U3 snoRNA is transcribed from two intron-containing genes in yeast, snR17A and snR17B. Although the assembly of the U3 snoRNP has not been precisely determined, at least some of the core box C/D proteins are known to bind pre-U3 co-transcriptionally, thereby affecting splicing and 3 `-end processing of this snoRNA. We identified the interaction between the box C/D assembly factor Nop17p and Cwc24p, a novel yeast RING finger protein that had been previously isolated in a complex with the splicing factor Cef1p. Here we show that, consistent with the protein interaction data, Cwc24p localizes to the cell nucleus, and its depletion leads to the accumulation of both U3 pre-snoRNAs. U3 snoRNA is involved in the early cleavages of 35 S pre-rRNA, and the defective splicing of pre-U3 detected in cells depleted of Cwc24p causes the accumulation of the 35 S precursor rRNA. These results led us to the conclusion that Cwc 24p is involved in pre-U3 snoRNA splicing, indirectly affecting pre-rRNA processing.

Encapsulation of single hMSCs in polyelectrolyte shells

The main objective of this Thesis was to encapsulate single viable cells within polyelectrolyte films using the Layer-by-Layer (LbL) technique. Most of the experiments used human mesenchymal stem cells (MSCs) whose characteristics (capacity of selfrenewal and potential to differentiate into several types of cells) make them particularly interesting to be used in biomedical applications. Also, most of the experiments used alginate (ALG) as the anionic polyelectrolyte and chitosan (CHI) or poly(allylamine hydrochloride) (PAH) as the cationic polyelectrolyte. Hyaluronic acid (HA) was also tested as an anionic polyelectrolyte. At the beginning of the work, the experimental conditions necessary to obtain the encapsulation of individual cells were studied and established. Through fluorescence microscopy visualization by staining the cell nucleus and using polyelectrolytes conjugated to fluorescent dyes, it was possible to prove the obtainment of capsules containing one single cell inside. Capsules aggregation was an observed problem which, despite the efforts to design an experimental process to avoid this situation (namely, by playing with cell concentration and different means of re-suspending and stirring the cells), was not completely overcome. In a second part of the project, single cells were encapsulated within polyelectrolyte layers made of CHI/ALG, PAH/ALG and PAH/HA and their viability was evaluated through the resazurin reduction assay and the Live/Dead assay. In these experiments, during the LbL process, polyelectrolyte solutions were used at a concentration of 1mg/mL based on literature. In general, the viability of the encapsulated cells was shown to be very low/absent. Then, as a consequence of the lack of viability of cells encapsulated within polyelectrolyte layers, the LbL technique was applied in cells growing adherent to the surface of cell culture plates. The cells were cultured like in a sandwich, between the surface of the cell culture dish and the polyelectrolyte layers. Also here, the polyelectrolyte solutions were used at a concentration of 1mg/mL during the LbL process. Surprisingly, cell viability was also absent in these systems. A systematic study (dose-effect study) was performed to evaluate the effect of the concentration of the individual polyelectrolytes (ALG, CHI and PAH were studied) in cell viability. Experiments were performed using cells growing adherent to the surface of cell culture plates. The results pointed out that a very high (cytotoxic) concentration of polyelectrolytes had been in use. Also, in general, PAH was much more cytotoxic than CHI, whereas ALG was the less cytotoxic polyelectrolyte. Finally, using alginate and chitosan solutions with adequate concentrations (low concentrations: 50ng/mL and 1μg/mL), the encapsulation of single viable cells was again attempted. Once again, the encapsulated cells were not shown to be viable. In conclusion, the viability of the encapsulated cells is not only dependent on the cytotoxic characteristics (or combined cytotoxic characteristics) of the polyelectrolytes but it seems that, when detached from the culture plates, the cells become too fragile and lose their viability very easily.

Effects of Statin and Aerobic Physical Exercise Association in the Cardiomyocytes of the Rat. Morphometric Study

Physical exercise and statins, recommended interventions to dyslipidaemia treatment, are independently related to cardiomyocytes alterations, characterized by miocardic hypertrophy and apoptosis, respectively. Thus, the objective of the present study was to analyze the effects of statin and aerobic physical exercise association in the morphometric parameters of cardiac cell nucleus. 40 male rats adults were divided into four groups: exercised (DE); sedentary (DS), exercised and statin use (DES); sedentary and statin use (DSS). The animals received during the whole experimental period a hiperlipidic diet added 20% of coconut oil and 1.25% of cholesterol; after 30 days of its ingestion, a blood collection was made to verify the dyslipidaemia. Simvastatin (20 mg) was taken five days a week, during eight weeks. During this period, the animals exercised 60 minutes daily in the treadmill. After the last day of the protocol, the cardiac muscle was collected and maintained in liquid nitrogen (-180 degrees C); the cuts were stained by Hematoxilin-Eosin method, and the cardiac fibers were submitted to the nuclear morphometric analyses. The data were analyzed using descriptive analyses, paired T test, Kruskal-Wallis test and Dunn post hoc test; for all analyses, it was adopted p<0.05. It was verified that the group receiving statin presented values statistically significant in comparison to the other groups, in the tridimensional and linear variables. The exercised and statin group, the values obtained in the morphometric analyses were similar to the control group. It is suggested that statins alone can cause alterations in the nucleus of cardiac cells that can be related to apoptosis occurrence and, when exercise is practiced associated to statin administration, the effects of statin can be reduced, what can be related to beneficial adaptations of cardiac mitochondrial in response to physical exercise, turning them more resistant to apoptotic stimuli.

Action of the chemical agent fipronil (active ingredient of acaricide Frontline (R)) on the liver of mice: An ultrastructural analysis

Fipronil, active ingredient of the acaricide Frontiline (R), is a phenyl-pyrazolic derivative, and its efficacy in the elimination of several plagues, even in low concentrations, has already been demonstrated; however, its effect on nontarget organisms has not been thoroughly explained. In this sense, the objective of this study was to evaluate the effects of different dosages of fipronil on the liver of mice in artificial conditions. Results showed that the animals exposed to fipronil present significant ultrastrucutural changes in hepatic cells with evident cellular and cytoplasm disorganization in hepatocytes characterized by an increase in the number of organelles, mainly mitochondria and rough endoplasmic reticulum, organelles that, in the case of the exposed animals, were probably responsible for the enzymes' synthesis that have the function of inactivating the toxic metabolites. A fat accumulation in the hepatocytes' cytoplasm (steatosis) was observed, in addition to extended vacuolated areas, mainly in regions next to the cell nucleus. Alterations observed in the nuclei of the hepatocytes pointed out cell death processes. Moreover, Kupffer cells increased in number (hyperplasia) suggesting an increase in the phagocytic activity of the liver in the exposed animals. Microsc. Res. Tech., 2011. (c) 2011 Wiley Periodicals, Inc.

Caracterização da região 3'-terminal do genoma de um isolado brasileiro do Southern bean mosaic virus

O presente trabalho caracteriza a região 3'-terminal do genoma de um isolado do Southern bean mosaic virus encontrado no Estado de São Paulo (SBMV-SP). O RNA foi extraído de partículas virais purificadas e submetido a RT-PCR usando oligonucleotídeos desenhados para amplificar 972 nt da região 3'-terminal do RNA viral. Foi obtido fragmento de tamanho esperado que inclui o gene da proteína capsidial e a região 3'-terminal não codificadora. O gene da proteína capsidial (ORF4) contém 801 nucleotídeos, incluindo-se o códon de terminação UGA, com seqüência deduzida de 266 aminoácidos e massa molecular estimada de 28.800 Da. Sessenta e um aminoácidos terminais da ORF2 estão sobrepostos na ORF4. O sinal de localização nuclear, encontrado dentro do Domínio R na região 5'-terminal da ORF4 de alguns sobemovírus, não foi identificado no SBMV-SP. Esse dado pode explicar a ausência de partículas virais do SBMV-SP no núcleo celular. A seqüência do SBMV-SP apresentou identidade de nucleotídeos e aminoácidos de, respectivamente, 91% e 93% com o isolado Arkansas (SBMV-ARK) descrito nos EUA. Os resultados obtidos indicam que o SBMV-SP e o SBMV-ARK são isolados muito proximamente relacionados.

Urinary bladder washings in autopsies. A cytopathologic study of 63 cases

The sediment from urinary bladder washings from 63 consecutive autopsies was cytologically studied in order to achieve a better understanding of the changes in urothelial cells collected from hospital populations. The observed alterations were correlated with alterations in the urinary system and with therapy preceding death. The specimens obtained were of good quality. In 39.7% of the cases, the sediment contained giant superficial multinucleated cells. Three of nine cases previously subjected to radiation or chemotherapy showed atypical urothelial cells. In three cases with immunosuppression, there was cytologic evidence of subclinical infection by polyomavirus, and virus particles were identified by electron microscopy of the vesical mucosa. The study of the smear background offered additional information: the sediment contained hyaline or hematic or hyaline-cellular casts in 17.4% of the cases, in all of which there were renal tubulopathies when the kidney sections were studied. The method is useful for a good evaluation of the autopsy as well as for training in urinary cytopathology.

The fine structure of the swine sweat gland. II. The coiled ducts

The duct of the swine sweat gland crosses the dermis and epidermis in sequence. The cells of the dermic segment seem to be related with cellular secretion and absorption. In the epidermic segment of the duct the whole morphology of the cells resembles the cellular morphology of the epidermic cells.

Características ultra-estruturais das células de Sertoli do morecego hematófago (Desmodus rotundus rotundus, Geoffrey, 1810).

This paper deals with the ultrastructural study of mature vampire bat Sertoli cells and their relationships with the different stages of testicular germ cells. In vampire bat seminiferous epithelium there are different types of junctional specializations among Sertoli cells and among Sertoli cells and different germ cells, with special emphasis to tight junctions and to junctions like as desmosomes. Ectoplasmic junctions through the Sertoli cells, including the smooth ER, are observed. These cellular interactions and their cytophysiological roles are discussed. Also are related some ultrastructural peculiarities of the Sertoli cell nucleus, nucleolus, cytoplasmic organelles and lipidic inclusions.

Ultrastructural study of the coagulating gland of Wistar rats submitted to experimental chronic alcohol ingestion

Morphological changes of coagulating gland of Wistar rats submitted to the experimental chronic alcoholism were noted. Ultrastructurally, it was observed reduction of the granular endoplasmic reticulum cisternae and nuclei with basal position and irregular shape. The epithelial cells presented pycnotic nuclei and the mitochondrial cristae disappeared, characteristic of cellular degeneration.

Peripheral ameloblastoma.

A case of peripheral ameloblastoma in a 57-years-old woman is presented, along with a discussion of the clinical and histological characteristics of the lesion. After clinical and radiographic examinations, and with a differential diagnosis of pyogenic granuloma, an excisional biopsy was performed and the material collected was sent for histological examination. On the basis of the histopathological diagnosis, a second operation was performed with a wide safety margin, including bone tissue, which did not show any involvement with the odontogenic neoplasm.

Nuclear DNA content of thirty species of neotropical fishes

The present paper reports nuclear DNA content in 30 Neotropical freshwater fish species and summarizes the data on other Neotropical species presented in the literature. Among Neotropical fishes, the nuclear DNA content ranges from 1.04 ± 0.09 pg/nucleus in Corydoras cf. simulatus (2n = 62) to 248.0 pg/nucleus in Lepidosiren paradoxa (2n = 38). A general analysis of the data obtained in the present study for each species showed that DNA measurements were practically constant at the individual level, while significant differences were observed among individuals of the same population. This observation was valid for all species analyzed and was more evident in those species that presented other karyotypic particularities such as sex chromosomes or supernumerary chromosomes. The importance of changes in nuclear DNA content in the evolutionary process of Neotropical fishes is discussed.

Preparation of N2, N2,7-trimethylguanosine affinity columns

2,2,7-trimethylguanosine (TMG) binding proteins from human cells were purified through TMG-affinity columns. TMG synthesis was improved and the TMG obtained was shown to be similar to the TMG in the 5' cap of the UsnRNAs. The eluates obtained with TMG-affinity chromatographies were very different from those isolated with m7G-affinity columns, thus suggesting that specific TMG- binding proteins were obtained. The fraction may be enriched with factors associated with import and/or hypermethylation of UsnRNPs.

Arginine methylation and binding of Hrp1p to the efficiency element for mRNA 3'-end formation

Hrp1p is a heterogeneous ribonucleoprotein (hnRNP) from the yeast Saccharomyces cerevisiae that is involved in the cleavage and polyadenylation of the 3'-end of mRNAs and mRNA export. In addition, Hrp1p is one of several RNA-binding proteins that are posttranslationally modified by methylation at arginine residues. By using-functional recombinant Hrp1p, we have identified RNA sequences with specific high affinity binding sites. These sites correspond to the efficiency element for mRNA 3'-end formation, UAUAUA. To examine the effect of methylation on specific RNA binding, purified recombinant arginine methyltransferase (Hmt1p) was used to methylate Hrp1p. Methylated Hrp1p binds with the same affinity to UAUAUA-containing RNAs as unmethylated Hrp1p indicating that methylation does not affect specific RNA binding. However, RNA itself inhibits the methylation of Hrp1p and this inhibition is enhanced by RNAs that specifically bind Hrp1p. Taken together, these data support a model in which protein methylation occurs prior to protein-RNA binding in the nucleus.