Transcriptome of iPSC-derived neuronal cells reveals a module of co-expressed genes consistently associated with autism spectrum disorder.

Evaluation of expression profile in autism spectrum disorder (ASD) patients is an important approach to understand possible similar functional consequences that may underlie disease pathophysiology regardless of its genetic heterogeneity. Induced pluripotent stem cell (iPSC)-derived neuronal models have been useful to explore this question, but larger cohorts and different ASD endophenotypes still need to be investigated. Moreover, whether changes seen in this in vitro model reflect previous findings in ASD postmortem brains and how consistent they are across the studies remain underexplored questions. We examined the transcriptome of iPSC-derived neuronal cells from a normocephalic ASD cohort composed mostly of high-functioning individuals and from non-ASD individuals. ASD patients presented expression dysregulation of a module of co-expressed genes involved in protein synthesis in neuronal progenitor cells (NPC), and a module of genes related to synapse/neurotransmission and a module related to translation in neurons. Proteomic analysis in NPC revealed potential molecular links between the modules dysregulated in NPC and in neurons. Remarkably, the comparison of our results to a series of transcriptome studies revealed that the module related to synapse has been consistently found as upregulated in iPSC-derived neurons-which has an expression profile more closely related to fetal brain-while downregulated in postmortem brain tissue, indicating a reliable association of this network to the disease and suggesting that its dysregulation might occur in different directions across development in ASD individuals. Therefore, the expression pattern of this network might be used as biomarker for ASD and should be experimentally explored as a therapeutic target.

Where do we aspire to publish? A position paper on scientific communication in biochemistry and molecular biology.

The scientific publication landscape is changing quickly, with an enormous increase in options and models. Articles can be published in a complex variety of journals that differ in their presentation format (online-only or in-print), editorial organizations that maintain them (commercial and/or society-based), editorial handling (academic or professional editors), editorial board composition (academic or professional), payment options to cover editorial costs (open access or pay-to-read), indexation, visibility, branding, and other aspects. Additionally, online submissions of non-revised versions of manuscripts prior to seeking publication in a peer-reviewed journal (a practice known as pre-printing) are a growing trend in biological sciences. In this changing landscape, researchers in biochemistry and molecular biology must re-think their priorities in terms of scientific output dissemination. The evaluation processes and institutional funding for scientific publications should also be revised accordingly. This article presents the results of discussions within the Department of Biochemistry, University of São Paulo, on this subject.

Where do we aspire to publish? A position paper on scientific communication in biochemistry and molecular biology

The scientific publication landscape is changing quickly, with an enormous increase in options and models. Articles can be published in a complex variety of journals that differ in their presentation format (online-only or in-print), editorial organizations that maintain them (commercial and/or society-based), editorial handling (academic or professional editors), editorial board composition (academic or professional), payment options to cover editorial costs (open access or pay-to-read), indexation, visibility, branding, and other aspects. Additionally, online submissions of non-revised versions of manuscripts prior to seeking publication in a peer-reviewed journal (a practice known as pre-printing) are a growing trend in biological sciences. In this changing landscape, researchers in biochemistry and molecular biology must re-think their priorities in terms of scientific output dissemination. The evaluation processes and institutional funding for scientific publications should also be revised accordingly. This article presents the results of discussions within the Department of Biochemistry, University of São Paulo, on this subject.

Sorovares e perfil de suscetibilidade a antimicrobianos em Salmonella spp. isoladas de produtos de origem suína / Serovars and antimicrobial susceptibility of Salmonella spp. product isolated from swine

Foi analisado um total de 1824 cepas de Salmonella, isoladas de alimentos de origem suína, no período de janeiro/2005 a junho/2010. As cepas, provenientes de diferentes regiões do país, foram recebidas pelo Labent/IOC/FIocruz para caracterização antigênica conclusiva. Foram identificados 41 sorovares, destacando-se: Typhimurium, Derby, Enteritidis, Panama, Infantis e Anatum. Aspectos bacteriológicos e epidemiológicos relacionados a esses sorovares foram discutidos. O teste de suscetibilidade aos antimicrobianos foi realizado em 357 amostras, 257 (72%) foram resistentes a uma ou mais drogas, e destas, 31,9% mostraram-se multirresistentes. A variedade de sorovares observada neste estudo confirma o papel dos suínos na cadeia alimentar como importantes reservatórios de Salmonella, agravado ainda pelo elevado percentual de cepas resistentes a um ou mais antimicrobianos, alertando para uma condição de risco à saúde pública.

We analyzed a total of 1824 strains of Salmonella isolated from swine-origin foods from January/2005 to June/2010. The strains from different regions of the country were received by Labent/IOC/FIOCRUZ for conclusive antigenic characterization. We identified 41 serovars, of which these stood out: Typhimurium, Derby, Enteritidis, Panama, Infantis and Anatum. Bacteriological and epidemiological aspects related to these serovars were discussed. The antimicrobial susceptibility test was performed on 357 samples, 257 (72%) were resistant to one or more of these drugs and 31,9% were multiresistant. A variety of serovars were identified reinforcing the swine as an important reservoir of Salmonella in the food chain. The high rates of antimicrobial resistance obtained in this evaluation may represent a risk condition to human health.

Mycobacterium leprae DNA in peripheral blood may indicate a bacilli migration route and high-risk for leprosy onset.

Leprosy epidemiological studies have been restricted to Mycobacterium leprae DNA detection in nasal and oral mucosa samples with scarce literature on peripheral blood. We present the largest study applying quantitative real-time PCR (qPCR) for the detection of M. leprae DNA in peripheral blood samples of 200 untreated leprosy patients and 826 household contacts, with results associated with clinical and laboratory parameters. To detect M. leprae DNA a TaqMan qPCR assay targeting the M. leprae ML0024 genomic region was performed. The ML0024 qPCR in blood samples detected the presence of bacillus DNA in 22.0% (44/200) of the leprosy patients: 23.2% (16/69) in paucibacillary (PB), and 21.4% (28/131) in multibacillary (MB) patients. Overall positivity among contacts was 1.2% (10/826), with similar percentages regardless of whether the index case was PB or MB. After a follow-up period of 7 years, 26 contacts have developed leprosy. Comparing the results of healthy contacts with those that become ill, ML0024 qPCR positivity at the time of diagnosis of their index case represented an impressive 14.78-fold greater risk for leprosy onset (95% CI 3.6-60.8; p <0.0001). In brief, contacts with positive PCR in blood at diagnosis of index cases are at higher risk of later leprosy onset and this marker might be combined with other prognostic markers for management of contacts, which requires further studies.

Chicken feet bacteriological quality at 4 steps of technological processing.

The production of chicken feet is primarily intended for foreign markets, and there is still no specific legislation in Brazil that determines the quality standard of these products. The bacteriological quality of chicken feet was evaluated as a product for human consumption at different steps of the technological processes. Eighty broiler feet from 20 lots at 4 steps of processing were collected for quantitative analysis, total count of aerobic mesophilic bacteria, and determining the most probable number of coliforms and fecal coliforms. Thirty-eight pools of 15 broiler feet each from 19 lots were used for qualitative analysis and the isolation of Salmonella enterica spp. and Escherichia coli O157:H7. Escherichia coli O157:H7 was not found in any of the samples. Salmonella spp. were isolated in 68% (13/19) of the lots. The Salmonella Schwarzengrund serotype was found in 12 of the 13 lots of positive samples and the Salmonella Anatum and Salmonella Corvallis serotypes were identified in the remaining lot. Processing is effective in reducing contamination by mesophilic bacteria, coliforms, and Salmonella spp. in these products. This work constitutes the first study in Brazil on microbiological quality of chicken feet.

Incidence and antimicrobial resistance of enteropathogens isolated from an integrated aquaculture system.

AIMS: To evaluate an integrated aquaculture system, microbiological analyses of water used in this system were carried out and the incidence and antimicrobial resistance of enteropathogens were determined in the related ecosystem. METHODS AND RESULTS: Microbiological analysis was undertaken for Salmonella sp., Shigella sp., Vibrio sp. and Aeromonas sp. The disc-diffusion method was performed according to the Clinical and Laboratory Standards Institute. Water samples tested had 32.9% of faecal coliform rates (≤1600 per 100 ml) in accordance with WHO for pisciculture in wastewater. Salmonella spp. were detected in 14.5% of the samples. From a total of 33 strains, 15.1% were resistant to one or two antimicrobial drugs tested and multidrug resistance was not observed. Aeromonas spp. were identified in 91.6% of the samples. From a total of 416 strains, resistance to one antimicrobial class was observed in 66.3% and multidrug resistance in 37.7%. CONCLUSIONS: This system reflects the community profile, drawing attention to the circulation of pathogens, because the genes coding for resistance to classical antibiotics and broad spectrum are a public health problem. SIGNIFICANCE AND IMPACT OF THE STUDY: The reuse of water resources requires continuous monitoring as the system is subject to treatment failure, which can result in the spread of bacterial pathogens.

Antimicrobial resistance and subtyping of Salmonella enterica subspecies enterica serovar Enteritidis isolated from human outbreaks and poultry in southern Brazil.

To investigate antimicrobial resistance, 96 Salmonella enterica subspecies enterica serovar Enteritidis strains isolated from salmonellosis outbreaks and poultry-related products obtained in southern Brazil were analyzed. Macrorestriction patterns, obtained by pulsed-field gel electrophoresis and phage types, were assessed. Although 43.75% of samples were sensitive to all drugs tested, resistance to sulfonamide (34.37%), trimethoprim-sulfamethoxazole (25.00%), nalidixic acid (14.58%), streptomycin (2.08%), gentamicin, and tetracycline (1.04%) was identified. Furthermore, 89.60% of strains belonged to phage type 4, and a predominant pulsed-field gel electrophoresis genotype represented by 82.29% of the strains was identified, suggesting that a clonal group was distributed in poultry, food, and human isolates. Although it was not possible to associate strains from different sources, the occurrence of antimicrobial-resistant Salmonella Enteritidis strains supports the need to establish monitoring programs to identify the emergence of potential resistance patterns and to direct policies for use of these drugs in food-producing animals.

Transcriptome analysis of nicotine-exposed cells from the brainstem of neonate spontaneously hypertensive and Wistar Kyoto rats.

In this study, the effects of nicotine on global gene expression of cultured cells from the brainstem of spontaneously hypertensive rat (SHR) and normotensive Wistar Kyoto (WKY) rats were evaluated using whole-genome oligoarrays. We found that nicotine may act differentially on the gene expression profiles of SHR and WKY. The influence of strain was present in 321 genes that were differentially expressed in SHR as compared with WKY brainstem cells independently of the nicotine treatment. A total of 146 genes had their expression altered in both strains after nicotine exposure. Interaction between nicotine treatment and the strain was observed to affect the expression of 229 genes that participate in cellular pathways related to neurotransmitter secretion, intracellular trafficking and cell communication, and are possibly involved in the phenotypic differentiation between SHR and WKY rats, including hypertension. Further characterization of their function in hypertension development is warranted.

Clonality and antimicrobial resistance gene profiles of multidrug- resistant Salmonella enterica serovar infantis isolates from four public hospitals in Rio de Janeiro, Brazil.

In Brazil, Salmonella enterica serovar Infantis resistant to various antimicrobials, including cephalosporins, has been identified as an etiological agent of severe gastroenteritis in hospitalized children since 1994. In this study, 35 serovar Infantis strains, isolated from children admitted to four different Rio de Janeiro, Brazil, hospitals between 1996 and 2001, were characterized by pulsed-field gel electrophoresis (PFGE) and antimicrobial susceptibility testing in order to determine their genetic relatedness and antimicrobial resistance profiles. Thirty-four serovar Infantis strains were resistant to at least two antibiotic classes, and all 35 strains were susceptible to fluoroquinolones, cephamycin, and carbapenem. Extended-spectrum beta-lactamase (ESBL) screening by double-disk diffusion indicated that 32 serovar Infantis strains (91.4%) produced beta-lactamases that were inhibited by clavulanic acid. Antimicrobial resistance gene profiles were determined by PCR for a subset of 11 multidrug-resistant serovar Infantis strains, and putative ESBLs were detected by isoelectric focusing. Ten serovar Infantis strains carried bla(TEM), catI, ant(3")Ia and/or ant(3")Ib, sulI and/or sulII, and tet(D) genes as well as an integron-associated aac(6')-Iq cassette. Eight strains possessed at least four different beta-lactamases with pI profiles that confirmed the presence of both ESBLs and non-ESBLs. Our PFGE profiles indicated that 33 serovar Infantis strains isolated from Rio de Janeiro hospitals came from the same genetic lineage.

Auto-antibodies in prostate cancer: humoral immune response to antigenic determinants coded by the differentially expressed transcripts FLJ23438 and VAMP3.

BACKGROUND: Here we evaluate auto-antibody response against two potential antigenic determinants of genes highly expressed in low Gleason Score prostate cancer (PC) tumor samples, namely FLJ23438 and VAMP3. METHODS: RT-PCR assays were used to analyze mRNA expression profiles of FLJ23438 and VAMP3 transcripts. The auto-antibody response against FLJ23438 and VAMP3 recombinant proteins was tested by immunoblot assays using PC, benign prostate hyperplasia (BPH), healthy donors (HD), and other human cancers plasma samples. RESULTS: Our data showed that 37% (10/27) and 7.4% (2/27) of PC plasma samples presented auto-antibodies against FLJ23438 and VAMP3, respectively. Only 8.3% (1/12) of BPH plasma samples were reactive for both auto-antibodies, while none (0/12) of HD plasma samples tested were reactive. CONCLUSIONS: The prevalence of 37% of positive PC plasma samples for anti-FLJ23438 antibodies suggests that humoral immune response against this antigenic determinant could be a potential serum marker for this cancer.

Characterization of a Salmonella enterica serovar Agona strain harbouring a class 1 integron containing novel OXA-type beta-lactamase (blaOXA-53) and 6'-N-aminoglycoside acetyltransferase genes [aac(6')-I30].

OBJECTIVE: To characterize by molecular methods a multidrug-resistant Salmonella enterica serovar Agona (S. enterica Agona) isolated from a hospitalized patient in Rio de Janeiro, Brazil. METHODS: The S. enterica Agona strain was screened by PCR and DNA sequencing for TEM, SHV and CTX-M-type beta-lactamase genes, tet(A), (B), (C) and (D) tetracycline resistance genes, chloramphenicol resistance genes and class 1 integrons. Plasmid characterization was carried out by PCR and Southern hybridization analysis. PCR and PFGE were used to characterize nine other S. enterica Agona strains collected from hospitals in Rio de Janeiro. RESULTS: The study strain was found to harbour a 105 kb plasmid, which contained catA1, bla(TEM-1), a class 1 integron with two novel genes labelled bla(OXA-53) and aac(6')-I30, respectively, and an additional unidentified aminoglycoside resistance gene. A second 53 kb plasmid from the same strain contained tet(D) and bla(SHV-5). OXA-53 was shown to provide reduced susceptibility to ceftazidime, and its activity was inhibited in the presence of clavulanic acid. PFGE analysis of the nine other S. enterica Agona strains revealed two clusters of related strains (78% similarity), and PCR analysis showed that all strains contained the novel integron. CONCLUSION: An S. enterica Agona strain was found to harbour three plasmid-encoded beta-lactamases, one (OXA-53) on a novel class 1 integron that also contains a new aminoglycoside resistance gene, aac(6')-I30. The multidrug resistance plasmids appear to have disseminated to other city hospitals via other S. enterica Agona strains.

Vibrio cholerae resistant to 2,4-diamino-6,7-diisopropylpteridine (O/129) isolated from patients with enteritis in Ceará, Brazil.

This paper reports the characterization of clinical Vibrio cholerae resistant to vibriostatic agent O/129, using classical and plasmid analysis. In a study conducted during December 1991-September 1993, two of 7,058 V. cholerae strains, obtained from patients suspected to have cholera in the State of Ceará, northeast Brazil, were resistant to 150 micrograms of the vibriostatic agent O/129 (2,4-diamino-6,7-diisopropylpteridine). One strain was identified as V. cholerae O1 El Tor Inaba and the other one as serogroup O22. Only one O1 strain harboured a plasmid of 147 kb transferable to Escherichia coli K12, and five strains of V. cholerae O1 and non-O1 were sensitive to O/129 and plasmid-negative at a frequency between 8 x 10(-2) and 3.6 x 10(-5). Additionally, O/129-resistant strains of V. cholerae O1 and O22 were resistant to trimethoprim/sulphamethoxazole.

Biological treatment of wastewater from the cassava meal industry.

Biological treatments of cassava meal processing wastewaters were investigated by aerobic and combined anaerobic/aerobic reactors. As a pretreatment, flocculation and sedimentation with aluminum salts and natural polyelectrolytes were employed, in order to change the effluent concentration of organics from 14,000 to 2000 mg/L in the bench scale reactor, with a hydraulic retention time of 37 min and an influent rate of 0.56 L/cm. Biological degradation by an activated sludge process was carried out using a reactor volume of 20 L. The observed organic matter removal rates were 89 to 93%, the cyanide removal was 95 to 99%, and the food to microorganisms ratio was found to be in the range of 0.166 to 0.242/day, with a hydraulic residence time of 1.4 to 4.2 days. As a posttreatment, flocculation and coagulation were employed, resulting in an effluent of good quality, as shown by turbidity measurements and negative tests for fecal and total coliforms.

N-terminal chimeric constructs improve the expression of sarcoplasmic reticulum Ca(2+)-ATPase in yeast.

Wild-type and chimeric constructs comprising rabbit sarcoplasmic reticulum (SR) Ca(2+)-ATPase and the N-terminal cytoplasmic portion of yeast plasma membrane H(+)-ATPase were expressed in yeast under control of a heat-shock regulated promoter. The wild-type ATPase was found predominantly in endoplasmic reticulum (ER) membranes. Addition of the first 88 residues of H(+)-ATPase to the Ca(2+)-ATPase N-terminal end promoted a marked shift in the localization of chimeric H(+)/Ca(2+)-ATPase which accumulated in a light membrane fraction associated with yeast smooth ER. Furthermore, there was a three-fold increase in the overall level of expression of chimeric H(+)/Ca(2+)-ATPase. Similar results were obtained for a chimeric Ca(2+)-ATPase containing a hexahistidine sequence added to its N-terminal end. Both H(+)/Ca(2+)-ATPase and 6xHis-Ca(2+)-ATPase were functional as demonstrated by their ability to form a phosphorylated intermediate and undergo fast turnover. Conversely, a replacement chimera in which the N-terminal end of SR Ca(2+)-ATPase was replaced by the corresponding segment of H(+)-ATPase was not stably expressed in yeast membranes. These results indicate that the N-terminal segment of Ca(2+)-ATPase plays an important role in enzyme assembly and contains structural determinants necessary for ER retention of the ATPase.

[The emergence of multiple antimicrobial resistance in Vibrio cholerae isolated from gastroenteritis patients in Ceará, Brazil]. / Emergência da múltipla resistência a antimicrobianos em Vibrio cholerae isolados de pacientes com gastroenterite no Ceará, Brasil.

Of 7058 Vibrio cholerae strains recovered from patients suspected of cholera in the State of Ceará between December 1991 and September 1993, two were resistant to antimicrobials (Ampicillin, erythromycin, trimethoprim-sulfamethoxazole, tetracycline) and to vibriostatic agent O/129 (2,4-diamino-6,7-diisopropylpteridine). From the bacteriological standpoint, one strain was identified as V. cholerae serogroup O:1, biotype El Tor, serovar Inaba, and another as V. cholerae serogroup O:22, biochemically classified as Heiberg type II. It was shown that only in the serogroup O:1 strain, multiple resistance was encoded by a plasmid transferrable by conjugation to Escherichia coli K12 and a sensitive strains of V. cholerae O1 and non-O1, with at a frequency between 8 x 10(-2) and 5 x 10(-6). The plasmid, with a molecular weight of 147 Kb, encoded both multiple resistance to antimicrobials and the vibriostatic compound (O/129), compatible with descriptions reported in other parts of world.

Structural and phylogenetic relationships among plant and animal cystatins.

The plant cystatins or phytocystatins (PhyCys) are cysteine proteinase inhibitors containing the QxVxG motif and have been placed in the cystatin superfamily of proteins. The primary sequences of PhyCys have a high degree of homology with the members of the cystatin family, but they resemble stefins by the absence of disulfide bonds and cysteine residues. A multialignment and a phylogenetic analysis of 63 cystatins, 32 of which are PhyCys, demonstrate that all PhyCys cluster in a major evolutionary tree branch and support the classification of PhyCys as a new cystatin family. The PhyCys also possess a specific consensus sequence [LVI]-[AGT]-[RKE]-[FY]-[AS]-[VI]-x-[EDQV]-[HYFQ] -N placed on the region corresponding to a predictable amino-terminal alpha-helix. This sequence can be used to specifically identify PhyCys on protein data banks and to differentiate them from the other members of the superfamily.

Colimetry of marine waters off Fortaleza (Ceará State, Brazil) and detection of enteropathogenic Escherichia coli strains.

Bacteriological analyses of seawater from three main beaches in Fortaleza, Brazil were performed during 1997. Thirty-six samples per beach were collected for a total of 108 samples. For Meireles Beach, 44% of the samples had MPN total coliforms values of at least 1100 or over 2400/100 ml, followed by Formosa and Diários beaches showing lower counts. For fecal coliforms the highest numbers were demonstrated for Formosa, followed by Meireles and Diários beaches in this descending order: 13.0%, 11.1% and 8.3%, respectively. Escherichia coli strains were identified in 76.8% of the 108 samples. Among 295 strains of E. coli, 21 belonged to serogroups O25, O26, O91, O112, O119, O158 and O164. Strains from serogroup O26 were tested using PCR, ELISA and Vero cells to detect Verotoxins VT1 and VT2 and all strains were negative. No LT and ST, as determined by ELISA and suckling mice assays, were detected among the 295 strains. All strains of E. coli were sensitive to ampicillin, cephalothin, gentamicin, tetracycline, sulfametox-trimethoprim, chloramphenicol and ciprofloxacin. Although the E. coli strains were not toxigenic, their presence in high numbers could be of public health significance.

Heterologous expression of sarcoplasmic reticulum Ca(2+)-ATPase.

In recent years, expression of rabbit sarcoplasmic reticulum (SR) Ca(2+)-ATPase in heterologous systems has been a widely used strategy to study altered enzymes generated by site-directed mutagenesis. Various eukaryotic expression systems have been tested, all of them yielding comparable amounts of recombinant protein. However, the relatively low yield of recombinant protein obtained so far suggests that novel purification techniques will be required to allow further characterization of this enzyme based on direct ligand-binding measurements.

Lysotypes and plasmidial profile of Salmonella serovar typhimurium isolated from children with enteric processes in the cities of Rio de Janeiro, RJ, and Salvador, BA - Brazil.

The lysotypes, plasmidial profiles, and profiles of resistance to antimicrobial agents were determined in 111 Salmonella Typhimurium strains isolated from feces and blood of children treated in Rio de Janeiro and in Salvador. Six distinct lysotypes (19, 41, 97, 105, 120 and 193) were recognized, with a predominance of lysotype 193 (59.7%) in Rio de Janeiro and of phage type 105 (38.4) in Salvador. Approximately 86.7% of the lysotype 193 strains presented multiple resistance to more than six antimicrobial agents, whereas 93% of lysotype 105 strains were fully susceptible. More than 90% of the strains presented plasmids distributed into 36 different profiles in Rio de Janeiro and into 10 profiles in Salvador. A 40 MDa plasmid was the most frequent (47%) in the strains from Rio de Janeiro, whereas a 61 MDa plasmid predominated (14.5%) in Salvador. Combined analysis of plasmid profile and classification into lysotypes (especially those belonging to types 105 and 103, proved to be more discriminatory than the other methods applied).