Computational analysis of the LRRK2 interactome

LRRK2 was identified in 2004 as the causative protein product of the Parkinson’s disease locus designated PARK8. In the decade since then, genetic studies have revealed at least 6 dominant mutations in LRRK2 linked to Parkinson’s disease, alongside one associated with cancer. It is now well established that coding changes in LRRK2 are one of the most common causes of Parkinson’s. Genome-wide association studies (GWAs) have, more recently, reported single nucleotide polymorphisms (SNPs) around the LRRK2 locus to be associated with risk of developing sporadic Parkinson’s disease and inflammatory bowel disorder. The functional research that has followed these genetic breakthroughs has generated an extensive literature regarding LRRK2 pathophysiology; however, there is still no consensus as to the biological function of LRRK2. To provide insight into the aspects of cell biology that are consistently related to LRRK2 activity, we analysed the plethora of candidate LRRK2 interactors available through the BioGRID and IntAct data repositories. We then performed GO terms enrichment for the LRRK2 interactome. We found that, in two different enrichment portals, the LRRK2 interactome was associated with terms referring to transport, cellular organization, vesicles and the cytoskeleton. We also verified that 21 of the LRRK2 interactors are genetically linked to risk for Parkin- son’s disease or inflammatory bowel disorder. The implications of these findings are discussed, with particular regard to potential novel areas of investigation.

Cancer patients taking herbal medicines: a review of clinical purposes, associated factors, and perceptions of benefit or harm

Ethnopharmacological relevance: Cancer patients in all cultures are high consumers of herbal medicines (HMs) usually as part of a regime consisting of several complementary and alternative medicine (CAM) modalities, but the type of patient, the reasons for choosing such HM-CAM regimes, and the benefits they perceive from taking them are poorly understood. There are also concerns that local information may be ignored due to language issues. This study investigates aspects of HM-CAM use in cancer patients using two different abstracting sources: Medline, which contains only peer-reviewed studies from SCI journals, and in order to explore whether further data may be available regionally, the Thai national databases of HM and CAM were searched as an example. Materials and methods: the international and Thai language databases were searched separately to identify relevant studies, using key words chosen to include HM use in all traditions. Analysis of these was undertaken to identify socio-demographic and clinical factors, as well as sources of information, which may inform the decision to use HMs. Results: Medline yielded 5,638 records, with 49 papers fitting the criteria for review. The Thai databases yielded 155, with none relevant for review. Factors associated with HM-CAM usage were: a younger age, higher education or economic status, multiple chemotherapy treatment, late stage of disease. The most common purposes for using HM-CAM cited by patients were to improve physical symptoms, support emotional health, stimulate the immune system, improve quality of life, and relieve side-effects of conventional treatment. Conclusions: Several indicators were identified for cancer patients who are most likely to take HM-CAM. However, interpreting the clinical reasons why patients decide to use HM-CAM is hampered by a lack of standard terminology and thematic coding, because patients' own descriptions are too variable and overlapping for meaningful comparison. Nevertheless, fears that the results of local studies published regionally are being missed, at least in the case of Thailand, appeared to be unfounded.

Immunomodulatory effects of Pteridium aquilinum on natural killer cell activity and select aspects of the cellular immune response of mice

Pteridium aquilinum (bracken fern) is one of the most common plants. Epidemiological studies have revealed a higher risk of certain types of cancers (i.e., esophageal, gastric) in people who consume bracken fern directly ( as crosiers or rhizomes) or indirectly through the consumption of milk from livestock that fed on the plant. In animals, evidence exists regarding the associations between chronic bracken fern intoxication, papilloma virus infection, and the development of carcinomas. While it is possible that some carcinogens in bracken fern could be responsible for these cancers in both humans and animals, it is equally plausible that the observed increases in cancers could be related to induction of an overall immunosuppression by the plant/its various constituents. Under the latter scenario, normal tumor surveillance responses against nascent (non-bracken-induced) cancers or responses against viral infections ( specifically those linked to induction of cancers) might be adversely impacted by continuous dietary exposure to this plant. Therefore, the overall objective of this study was to evaluate the immunomodulatory effects of bracken fern following daily ingestion of its extract by a murine host over a period of 14 ( or up to 30) days. In C57BL/6 mice administered ( by gavage) the extract, histological analyses revealed a significant reduction in splenic white pulp area. Among a variety of immune response parameters/functions assessed in these hosts and isolated cells, both delayed-type hypersensitivity (DTH) analysis and evaluation of IFN gamma. production by NK cells during T(H)1 priming were also reduced. Lastly, the innate response in these hosts-assessed by analysis of NK cell cytotoxic functionality-was also diminished. The results here clearly showed the immunosuppressive effects of P. aquilinum and that many of the functions that were modulated could contribute to the increased risk of cancer formation in exposed hosts.

Alternative splicing and genetic diversity: silencers are more frequently modified by SNVs associated with alternative exon/intron borders

With the availability of a large amount of genomic data it is expected that the influence of single nucleotide variations (SNVs) in many biological phenomena will be elucidated. Here, we approached the problem of how SNVs affect alternative splicing. First, we observed that SNVs and exonic splicing regulators (ESRs) independently show a biased distribution in alternative exons. More importantly, SNVs map more frequently in ESRs located in alternative exons than in ESRs located in constitutive exons. By looking at SNVs associated with alternative exon/intron borders (by their common presence in the same cDNA molecule), we observed that a specific type of ESR, the exonic splicing silencers (ESSs), are more frequently modified by SNVs. Our results establish a clear association between genetic diversity and alternative splicing involving ESSs.

Biogeography of Glandulocaudinae (Teleostei : Characiformes : Characidae) revisited: phylogenetic patterns, historical geology and genetic connectivity

The biogeography of the Glandulocaudinae ( former Glandulocaudini) is reviewed. The major pattern of diversification presented by this group of freshwater fishes can be clearly associated to the main aspects of the tectonic evolution of the southern portion of the Cis-Andean South American Platform. The phylogenetic relationships within the group suggest that the clade represented by Lophiobrycon is the sister-group of the more derived clade represented by the genus Glandulocauda and Mimagoniates. Lophiobrycon and Glandulocauda occur in areas of the ancient crystalline shield of southeastern Brazil and their present allopatric distribution is probably due to relict survival and tectonic vicariant events. Populations of Glandulocauda melanogenys are found in contiguous drainages in presently isolated upper parts of the Tiete, Guaratuba, Itatinga, and Ribeira de Iguape basins and this pattern of distribution is probably the result of river capture caused by tectonic processes that affected a large area in eastern and southeastern Brazil. The species of Mimagoniates are predominantly distributed along the eastern and southeastern coastal areas, but M. microlepis is additionally found in the rio Iguacu and Tibagi basins. Mimagoniates barberi occurs in both SW margin of the upper rio Parana basin and the lower Paraguay and Mimagoniates sp. occurs in the upper Paraguay river basin. Tectonic activations of the Continental Rift of Southeastern Brazil along the eastern margin of the Upper Parana basin promoted population fragmentation responsible of the present day distribution presented by Glandulocauda melanogenys. We hypothesize that occurrence of Mimagoniates along the lowland area around the Parana basin was due to a single or a multiple fragmentation of populations along the W-SW border of the upper Parana Basin, probably due to the major tectonic origin of the Chaco-Pantanal wetland foreland basins since the Miocene as well as Cenozoic tectonic activity along the borders of the upper Parana basin, such as in the eastern Paraguay, in the Asuncion Rift. Distributional pattern of Mimagoniates suggests that its initial diversification may be related to the tectonic evolution of the Chaco-Pantanal foreland basin system and a minimum age of 2.5 M.Y are proposed for this monophyletic group. Previous hypotheses on sea level fluctuations of the late Quaternary as being the main causal mechanism promoting cladogenesis and speciation of the group are critically reviewed. Phylogeographic studies based on molecular data indicate significant differences among the isolated populations of M. microlepis. These findings suggest that a much longer period of time and a paleogeographic landscape configuration of the Brazilian southeastern coastal region explain the present observed phylogenetic and biogeographic patterns.

Effects of let-7 microRNA on Cell Growth and Differentiation of Papillary Thyroid Cancer

Papillary thyroid carcinoma (PTC) is the most common endocrine malignancy and RET/PTC rearrangements represent key genetic events frequently associated to this cancer, enhancing proliferation and dedifferentiation by activation of the RET/PTC-RAS-BRAF-mitogen-activated protein kinase (MAPK) pathway. Recently, let-7 microRNA was found to reduce RAS levels in lung cancer, acting as a tumor suppressor gene. Here, we report that RET/PTC3 oncogenic activation in PCCL3 rat thyroid cells markedly reduces let-7f expression. Moreover, stable transfection of let-7 microRNA in TPC-1 cells, which harbor RET/PTC1 rearrangement, inhibits MAPK activation. As a result, let-7f was capable of reducing TPC-1 cell growth, and this might be explained, at least in part, by decreased messenger RNA (mRNA) expression of cell cycle stimulators such as MYC and CCND1 (cyclin D1) and increased P21 cell cycle inhibitor mRNA. In addition, let-7 enhanced transcriptional expression of molecular markers of thyroid differentiation such as TITF1 and TG. Thus, reduced expression of let-7f might be an essential molecular event in RET/PTC malignant transformation. Moreover, let-7f effects on thyroid growth and differentiation might attenuate neoplastic process of RET/PTC papillary thyroid oncogenesis through impairment of MAPK signaling pathway activation. This is the first functional demonstration of an association of let-7 with thyroid cancer cell growth and differentiation.

Multi-objective clustering ensemble for gene expression data analysis

In this paper, we present an algorithm for cluster analysis that integrates aspects from cluster ensemble and multi-objective clustering. The algorithm is based on a Pareto-based multi-objective genetic algorithm, with a special crossover operator, which uses clustering validation measures as objective functions. The algorithm proposed can deal with data sets presenting different types of clusters, without the need of expertise in cluster analysis. its result is a concise set of partitions representing alternative trade-offs among the objective functions. We compare the results obtained with our algorithm, in the context of gene expression data sets, to those achieved with multi-objective Clustering with automatic K-determination (MOCK). the algorithm most closely related to ours. (C) 2009 Elsevier B.V. All rights reserved.

Human papillomavirus type 16 variants in cervical cancer from an admixtured population in Brazil

Several studies indicate that molecular variants of HPV-16 have different geographic distribution and risk associated with persistent infection and development of high-grade cervical lesions. In the present study, the frequency of HPV-16 variants was determined in 81 biopsies from women with cervical intraepithelial neoplasia grade III or invasive cervical cancer from the city of Belem, Northern Brazil. Host DNAs were also genotyped in order to analyze the ethnicity-related distribution of these variants. Ninie different HPV-16 LCR variants belonging to four phylogenetic branches were identified. Among these, two new isolates were characterized. The most prevalent HPV-16 variant detected was the Asian-American B-2,followed by the European B-12 and the European prototype. Infections by multiple variants were observed in both invasive cervical cancer and cervical intraepithelial neoplasia grade III cases. The analysis of a specific polymorphism within the E6 viral gene was performed in a subset of 76 isolates. The E6-350G polymorphism was significantly more frequent in Asian-American variants. The HPV-16 variability detected followed the same pattern of the genetic ancestry observed in Northern Brazil, with European, Amerindian and African roots. Although African ancestry was higher among women infected by the prototype, no correlation between ethnical origin and HPV-16 variants was found. These results corroborate previous data showing a high frequency of Asian-American variants in cervical neoplasia among women with multiethnic origin.

Push or pull? : The relationship between quality of care and use of complementary and alternative medicine among patients with lung cancer in Sweden

Little is known about relationships between quality of care (QoC) and use of complementary and alternative medicine (CAM) among patients with lung cancer (LC). Purpose: This study examines CAM-use among patients with LC in Sweden, associations between QoC and CAM-use among these patients, and reported aspects of LC-care perceived as particularly positive and negative by patients, as well as suggestions for improving QoC. Methods: Survey data from 94 patient members of the Swedish LC patient organization about CAM-use and QoC as measured by the instrument “Quality from the patient’s perspective” were analyzed. Results: Fifty (53%) LC-patients used CAM, with 40 of the CAM-users reporting that CAM helped them. The most common CAMs used were dietary supplements and natural remedies, followed by prayer. Significantly more patients reported using prayer and meditation for cure than was the case for other types of CAM used. Less than half the CAM-users reported having spoken with staff from the biomedical health care system about their CAM-use. Patients provided numerous suggestions for improving LC-care in a variety of areas, aiming at a more effective and cohesive care trajectory. No differences in QoC were found between CAM-users and non-CAM-users, but differences in CAM-use i.e. type of CAM, reasons for using CAM, and CAM-provider consulted could be associated with different experiences of care. Conclusions: It is important to recognize that CAM-users are not a homogeneous group but might seek different types of CAMs and CAM-providers in different situations depending on experiences of care.

Agronomical and phytochemical aspects of fafia

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Avaliação do potencial mutagênico da água do açude de Lucrécia (RN- Brasil): um enfoque na relação saúde e ambiente

The water quality of many reservoirs in the world has been reduced due to percolation of contaminants to water, which can have natural or anthropogenic origin, increasing the level of genotoxic compounds in aquatic ecosystems. This fact has contributed to the reduction of environmental quality, and commitment the health of living beings that inhabit these ecosystems, including the human population. In this backdrop of reduced water quality, is the Lucrecia dam, which is a major surface water reservoirs by volume of semi-arid region of Rio Grande do Norte, and that has shown contamination by heavy metals, cyanobacteria toxic and the natural presence of Radon. The population that use this source has been showing high rates of cancer, popularly associated with the consumption of this water, with a prevalence about three times higher compared to the whole state of Rio Grande do Norte. Based on this, the present study aimed to evaluate the mutagenic potencial of surface water from the Lucrecia dam, using the Micronucleus Test in Tradescantia pallida (Trad-MN) and in human peripheral blood lymphocytes (CBMN) assay, as well as identify the concentrations of some heavy metals in this water. Water samples were collected on a dry season and a rainy season, in two distinct points. Moreover, in order to bring a completely view about the relationship of man-health-environment in this local, through the knowledge of knowing / acting environmental from residents of Lucrecia, and the use and perceptions they have about the dam of your city, a study of Environmental Perception was carried out with local residents. The results obtained for the both micronucleus test, showed significant results for the three points analyzed. The strongest mutagenic effect was observed in the dry season for both assays. Chemical analyses detected an increase of heavy metal levels in different points and season above the maximum allowed by legislation. Regarding the study of Environmental Perception with local residents, it was observed the knowledge of the environment that the residents have, as well as the strong ties and perceptions with the dam of the city. Thus, the combination of these two aspects (the genetic toxicity tests conducted in the dam together with analysis of environmental perception with the residents of Lucrecia) allowed to draw a more complete diagnosis on the local situation

Assessment of genetic damage induced by dental bleaching agents on mouse lymphoma cells by single cell gel (comet) assay

Dental bleaching is a simple and conservative procedure for aesthetic restoration of vital discoloured teeth. However, dental bleaching agents may represent a hazard to human health, especially by causing DNA strand breaks. Genotoxicity tests form an important part of cancer research and risk assessment of potential carcinogens. In the current study, the genotoxic potential associated with exposure to dental bleaching agents was assessed by the single cell gel (comet) assay in vitro. Six commercial dental bleaching agents (Clarigel Gold - Dentsply; Whitespeed - Discus Dental; Nite White - Discus Dental; Magic Bleaching - Vigodent; Whiteness HP - FGM and Lase Peroxide - DMC) were exposed to mouse lymphoma cells in vitro. The results pointed out that all dental bleaching agents tested contributed to the DNA damage as depicted by the mean tail moment. Clear concentration-related effects were obtained for DNA damaging, being the strongest effect observed at the highest dose of the hydrogen peroxide (Whiteness HP and Lase Peroxide, at 35% concentration). on the contrary, Whitespeed (Discus Dental) induced the lowest level of DNA breakage. Taken together, these results suggest that dental bleaching agents may be a factor that increases the level of DNA damage as detected by the single cell gel (comet) assay.

Genomic instability in blood cells is able to predict the oral cancer risk: an experimental study in rats

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

Classic and molecular cytogenetic analyses reveal chromosomal gains and losses correlated with survival in head and neck cancer patients

Purpose: Genetic biomarkers of head and neck tumors could be useful for distinguishing among patients with similar clinical and histopathologic characteristics but having differential probabilities of survival. The purpose of this study was to investigate chromosomal alterations in head and neck carcinomas and to correlate the results with clinical and epidentiologic variables.Experimental Design: Cytogenetic analysis of short-term cultures from 64 primary untreated head and neck squamous cell carcinomas was used to determine the overall pattern of chromosome aberrations. A representative subset of tumors was analyzed in detail by spectral karyotyping and/or confirmatory fluorescence in situ hybridization analysis.Results: Recurrent losses of chromosomes Y (26 cases) and 19 (14 cases), and gains of chromosomes 22 (23 cases), 8 and 20 (11 cases each) were observed. The most frequent structural aberration was del(22)(q13.1) followed by rearrangements involving 6q and 12p. The presence of specific cytogenetic aberrations was found to correlate significantly with an unfavorable outcome. There was a significant association between survival and gains in chromosomes 10 (P = 0.008) and 20 (P = 0.002) and losses of chromosomes 15 (P = 0.005) and 22 (P = 0.021). Univariate analysis indicated that acquisition of monosomy 17 was a significant (P = 0.0012) factor for patients with a previous family history of cancer.Conclusions: the significant associations found in this study emphasize that alterations of distinct regions of the genome may be genetic biomarkers for a poor prognosis. Losses of chromosomes 17 and 22 can be associated with a family history of cancer.

Epidemiological aspects in leptospirosis. Research of anti-Leptospira spp antibodies, isolation and biomolecular research in bovines, rodents and workers in rural properties from Botucatu, SP, Brazil.

Leptospirosis is a worldwide infection, transmitted between man and animals that causes a decrease in the production of bovine flocks, and offer risks for public health, as an important zoonosis. The rodents are the main reservoirs of leptospires. It was studied 27 dairy farm properties located in or near from Botucatu-SP, Brazil. In these farms were collected blood and kidney samples from rodents, blood and urine samples from bovines and blood samples from the workers. The serology was performed with microscopic agglutination test (MAT). Samples of bovine urine and rodent kidneys were cultivated searching for leptospires isolation. The polymerase chain reaction (PCR) of the kidneys of the rodents was performed. In MAT, 46/ 140 (32.85%) bovine and 8/34 (23.53%) human sera samples were positive, respectively. In human samples, the serovar Brastilava (37.51%) presented the highest occurrence, while in bovines, the serovars Hardjo and Castellonis were most frequent, with 26.08% each one. All of the rodents were negatives in serology. No leptospire was isolated, and kidney samples were negative in PCR. In bovines, the dam water and the bad hygiene quality of milking process were considered important risks of infection in the affected properties (p<0.05), where other reproductive problems, except abortion, can be related. In other side, to human beings the drainage system was the most important risk factor in the studied properties. Thus, it was verified the necessity of an improvement in zoosanitary handling of the properties, mainly of water supply.