Transcriptomic and computational analysis identified LPA metabolism, KLHL14 and KCNE3 as novel regulators of Epithelial-Mesenchymal Transition.

Epithelial-mesenchymal transition (EMT) is a complex biological program between physiology and pathology. Here, amniotic epithelial cells (AEC) were used as in vitro model of transiently inducible EMT in order to evaluate the transcriptional insights underlying this process. Therefore, RNA-seq was used to identify the differentially expressed genes and enrichment analyses were carried out to assess the intracellular pathways involved. As a result, molecules exclusively expressed in AEC that experienced EMT (GSTA1-1 and GSTM3) or when this process is inhibited (KLHL14 and KCNE3) were identified. Lastly, the network theory was used to obtain a computational model able to recognize putative controller genes involved in the induction and in the prevention of EMT. The results suggested an opposite role of lysophosphatidic acid (LPA) synthesis and degradation enzymes in the regulation of EMT process. In conclusion, these molecules may represent novel EMT regulators and also targets for developing new therapeutic strategies.

Draft Genome Sequences of Mycoplasma mycoides subsp. mycoides Strains APF9 and AP108, Isolated in Nigeria in 2014 to 2016.

Mycoplasma mycoides subsp. mycoides is the etiological agent of contagious bovine pleuropneumonia (CBPP). While several findings on CBPP prevalence in Nigeria were documented, no data were reported about the genomic characterization of Nigerian M. mycoides subsp. mycoides strains. Here, we present the draft genome sequences of two novel M. mycoides subsp. mycoides strains isolated in Nigeria.

Impaired decision-making and time perception in individuals with stroke: Behavioral and neural correlates.

Several studies have demonstrated that stroke subjects present impairment of functions related to decision-making and timing, involving the information processing in the neural circuits of the cerebellum in association with the prefrontal cortex. This review is aimed to identify the gaps, and demonstrate a better understanding of decision-making and timing functions in the patients with stroke. Electronic literature database was searched and the findings of relevant studies were used to explore the mechanisms of decision-making and timing in patients with stroke, as well as the circuit connections in timing mediated by prefrontal cortex and cerebellum. A literature review was conducted with 65 studies that synthesized findings on decision-making and time perception in individuals with stroke. Types of neurobiological modalities in this study included: Relationships among decision-making, time perception, related cognitive aspects (such as discrimination tasks, verbal estimation, bisection tasks, time production and motor reproduction), and motor control. We demonstrate that the timing processes are important for the performance in cognitive tasks and that the cerebellum and prefrontal cortex are involved in decision-making and time perception. In the context, the decision-making is impaired in stroke patients has a great impact on executive functions, and this seems to be important in determining neurobiological aspects relevant to the time interval interpretation.

Neurophysiological changes after cognitive-motor tasks in Parkinson's disease patients with deep brain stimulation.

Chronic deep brain stimulation (CDBS) is a surgical treatment that reduces the cardinal signs of Parkinson's disease (PD). Although CDBS has been in use for a long time, very little has been reported on its supposed effects on cognition, particularly in relation to implants in the subthalamic nucleus. The results of the rare studies that do exist are controversial, and in many cases the studies have several design flaws. The present study compared cortical activation during three tasks (action execution, action observation and motor imagery) in PD patients with and without subthalamic implants. The study sample consisted of 36 volunteers, divided into three groups: healthy controls, PD patients with CDBS of the subthalamic nucleus, and PD patients without CDBS. Through a quantitative electroencephalogram assessment, absolute beta power was examined to observe the interaction between group and cognitive motor tasks. The electrodes at sites Fp1, Fp2, F7, F8, F3, Fz and F4, located in the prefrontal and frontal regions, were analyzed and a Group x Task interaction (p < 0.05) was observed for all of them. These findings suggest that CDBS of the subthalamic nucleus is efficient in reducing some of the effects of PD in these study tasks. At the same time, the dysfunctions found in several cortical areas, characteristic of PD, limited the effects of the CDBS. The results of this study suggest that CDBS of the subthalamic nucleus can modulate cognitive-motor aspects of PD.

A novel Bluetongue virus serotype 3 strain in Tunisia, November 2016.

Since 1998, southern Europe has experienced multiple incursions of different serotypes and topotypes of Bluetongue virus, a vector-borne transmitted virus, the causative agent of Bluetongue (BT), a major disease of ruminants. Some of these incursions originated from northern Africa, likely because of wind-blown dissemination of infected midges. In this report, we describe the detection and whole genome characterization of a novel BTV-3 strain identified in a symptomatic sheep in Tunisia. Sequences were immediately deposited with the GenBank Database under Accession Nos KY432369-KY432378. Alert and preparedness are requested to face the next vector seasons in northern Africa and the potential incursion of this novel strain in southern Europe.

Usutu virus infections in humans: a retrospective analysis in the municipality of Modena, Italy.

OBJECTIVE: To monitor the spread and to evaluate the role for public health of Usutu virus (USUV) in an endemic area of Italy. METHODS: The survey was retrospectively conducted by detecting USUV RNA and USUV antibodies in cerebrospinal fluid and serum samples collected between 2008 and 2011 from 915 patients with or without neurologic impairments in the area of the municipality of Modena, Italy. Organs of birds and pools of mosquitoes were also tested for USUV RNA. Positive samples were partially sequenced and used for phylogenetic analysis. RESULTS: The presence of USUV RNA (1.1%; 95% confidence interval (CI) 0.6-2.0) was significantly (p <0.05) higher than that of West Nile virus (0%; 95% CI 0-0.33). USUV antibody level was 6.57% (95% CI 4.87-8.82), and it was significantly higher (p <0.05) compared to that of West Nile virus (p 2.96, 95% CI 1.89-4.62). Partial genome sequencing of USUV strains detected in humans, birds and mosquitoes revealed high nucleotide sequence identity within them and with the USUV strains isolated in Central Europe. CONCLUSIONS: USUV infection in humans is not a sporadic event in the studied area, and USUV neuroinvasiveness has been confirmed.

Fluorescence based cell counting in collagen monolayer cultures of primary hepatocytes.

Accurate determination of cell number is essential for the quantitative description of biological processes. The changes should be related to a measurable reference e.g. in the case of cell culture, the viable cell number is a very valuable reference parameter. Indirect methods of cell number/viability measurements may have up to 10 % standard deviation. This can lead to undesirable large deviations in the analysis of "-omics" data as well as time course studies. Such data should be preferably normalized to the exact viable cell number at a given time to allow meaningful interpretation and understanding of the biological processes. Manual counting of cell number is very laborious and not possible in certain experimental setups. We therefore, developed a simple and reliable fluorescence based method with an accuracy of 95-98 % for the determination of the viable cell number in situ. We optimized the seeding cell densities for primary rat hepatocytes for optimal cell adhesion. This will help in efficient use of primary cells which are usually limited in availability. The method will be very useful in the application of "-omics" techniques, especially metabolome analysis where the specific rates of uptake/production of metabolites can be reliably calculated.

Whole-Genome Sequencing of Mycoplasma mycoides subsp. mycoides Italian Strain 57/13, the Causative Agent of Contagious Bovine Pleuropneumonia.

Mycoplasma mycoides subsp. mycoides is generally considered one of most pathogenic Mycoplasma species, and it is the etiological agent of contagious bovine pleuropneumonia (CBPP). Here, we present the annotated genome sequence of M. mycoides subsp. mycoides Italian strain 57/13, isolated in 1992 during CBPP outbreaks in Italy.

Vitamin D is associated with degree of disability in patients with fully ambulatory relapsing-remitting multiple sclerosis.

BACKGROUND AND PURPOSE: Vitamin D deficiency is a recognized risk factor for multiple sclerosis (MS) and is associated with increased disease activity. It has also been proposed that the lower the vitamin D levels are, the higher is the handicap. METHODS: To refine the links between vitamin D insufficiency and disability in MS patients, a retrospective cohort analysis was performed including 181 patients prospectively followed without previous vitamin D supplementation, and age, gender, age at MS onset, MS type, MS activity, Expanded Disability Status Scale (EDSS) were analysed in correlation with plasma vitamin D levels. RESULTS: Vitamin D levels were significantly higher in relapsing-remitting MS than in progressive forms of MS in multivariate analyses adjusted for age, ethnicity, gender, disease duration and season (P = 0.0487). Overall, there was a negative correlation between vitamin D level and EDSS score (P = 0.0001, r = -0.33). In relapsing-remitting MS, vitamin D levels were only correlated with disability scores for EDSS < 4 (P = 0.0012). Patients with >20 ng/ml of vitamin D were 2.78 times more likely to have an EDSS < 4 (P = 0.0011, 95% confidence interval 1.49-5.00). CONCLUSION: Data support previous work suggesting that vitamin D deficiency is associated with higher risk of disability in MS. Vitamin D levels also correlated with the degree of disability in fully ambulatory patients with relapsing-remitting MS. These additional results support the pertinence of randomized controlled trials analysing the interest of an early vitamin D supplementation in MS patients to influence evolution of disability.

Cancer markers: integratively annotated classification.

Translational cancer genomics research aims to ensure that experimental knowledge is subject to computational analysis, and integrated with a variety of records from omics and clinical sources. The data retrieval from such sources is not trivial, due to their redundancy and heterogeneity, and the presence of false evidence. In silico marker identification, therefore, remains a complex task that is mainly motivated by the impact that target identification from the elucidation of gene co-expression dynamics and regulation mechanisms, combined with the discovery of genotype-phenotype associations, may have for clinical validation. Based on the reuse of publicly available gene expression data, our aim is to propose cancer marker classification by integrating the prediction power of multiple annotation sources. In particular, with reference to the functional annotation for colorectal markers, we indicate a classification of markers into diagnostic and prognostic classes combined with susceptibility and risk factors.

Warehousing re-annotated cancer genes for biomarker meta-analysis.

Translational research in cancer genomics assigns a fundamental role to bioinformatics in support of candidate gene prioritization with regard to both biomarker discovery and target identification for drug development. Efforts in both such directions rely on the existence and constant update of large repositories of gene expression data and omics records obtained from a variety of experiments. Users who interactively interrogate such repositories may have problems in retrieving sample fields that present limited associated information, due for instance to incomplete entries or sometimes unusable files. Cancer-specific data sources present similar problems. Given that source integration usually improves data quality, one of the objectives is keeping the computational complexity sufficiently low to allow an optimal assimilation and mining of all the information. In particular, the scope of integrating intraomics data can be to improve the exploration of gene co-expression landscapes, while the scope of integrating interomics sources can be that of establishing genotype-phenotype associations. Both integrations are relevant to cancer biomarker meta-analysis, as the proposed study demonstrates. Our approach is based on re-annotating cancer-specific data available at the EBI's ArrayExpress repository and building a data warehouse aimed to biomarker discovery and validation studies. Cancer genes are organized by tissue with biomedical and clinical evidences combined to increase reproducibility and consistency of results. For better comparative evaluation, multiple queries have been designed to efficiently address all types of experiments and platforms, and allow for retrieval of sample-related information, such as cell line, disease state and clinical aspects.

High prevalence of micropenis in 2710 male newborns from an intensive-use pesticide area of Northeastern Brazil.

Exposure to endocrine-disrupting chemicals (EDCs) has been suggested to contribute to the increasing trends of external genital malformation in male newborns. In Northeastern Brazil, the poor sanitary conditions found in the favelas encourage the widespread use of pesticides. This 2-year study of a total birth cohort of full-term male newborns in the regional hospitals of Campina Grande (Paraíba, Brazil) sought to (1) accurately establish for the first time the incidences of neonatal male genital malformations, (2) investigate the endocrine and genetic aetiologies of these malformations, and (3) evaluate their associations with possible prenatal exposure to EDCs. A total of 2710 male newborns were explored for cryptorchidism, hypospadias and micropenis. Cases were referred to the Pediatric Endocrine Clinic for endocrine and genetic investigations, and all parents were interviewed about their environmental/occupational exposure to EDCs before/during pregnancy by paediatric endocrinologists using a detailed questionnaire. We observed 56 cases of genital malformation (2.07%), including 23 cryptorchidism (0.85%), 15 hypospadias (0.55%), and 18 micropenis (0.66%). All cases exhibited normal/subnormal testosterone production and none presented androgen receptor or 5α-reductase gene mutation. More than 92% of these newborns presented foetal contamination by EDCs, as their mothers reported daily domestic use of pesticides (i.e., DDT) and other EDCs. Most of these undervirilized male newborns presented additional EDC contamination, as 80.36% of the mothers and 58.63% of the fathers reported paid or unpaid work that entailed the use of pesticides and other EDCs before/during pregnancy for the mothers and around the time of fertilization for the fathers. The high rate of micropenis in our population associated with an elevated percentage of parental environmental/occupational exposure to EDCs before/during pregnancy indicates that foetal contamination may be a risk factor for the development of male external genital malformation.

Improved high-performance liquid chromatography-diode array detection method for the determination of phenolic compounds in leaves and peels from different apple varieties.

Hydroxycinnamic acids derivatives, monomeric and oligomeric flavan-3-ols, flavonols, and dihydrocalcones are four of the major polyphenolic groups found in apples leaves and peels. A simple extraction with minimal pre-treatment and a high-performance liquid chromatography-diode array detection determination are optimized and validated, in order to identify and quantitate the polyphenolic profile of leaves and peels of four apples varieties (Gala, Topaz, Golden Delicious, and Florina). The improved chromatographic method has led to better separation of some known polyphenols in a single course, and diode-array detection has been used for the previsional identification of some polyphenolic compounds not available as standards. Because the mobile phase and the chromatographic column are compatible with a mass spectrometer, this method could investigate the unknown flavanols, flavonols, hydrocinnamic acid derivatives, and chalcone-related compounds found in apple leaves and peel extracts analyzed.

The mepsMAP server. Mapping epitopes on protein surface: mining annotated proteins.

For a growing number of biologists DNA or protein data are typically retrieved and managed on the Web, and not in the laboratory. A large number of bioinformatics datasets from primary and (thousands of) secondary databases are scattered on the Web in various formats. A biologist end-user might need to access and use tens of databases and tools every day. For this reason, the bioinformatics community is developing more and more service-oriented architectures (SOAs): software architecture of loosely coupled software services that can be accessed without knowledge of, or control over, their internal architecture. Data-processing and analysis tasks can be automated by having free access to bioinformatics Web services (WSs) that are the building blocks of the SOAs. In this paper we introduce a new bioinformatics Web server, mepsMAP (mapping epitopes on protein surface: Mining Annotated Proteins), developed to identify the recognition sites between antibodies and their cognate antigens. In some cases, the recognition site is represented by a continuous segment of the antigen sequence, but much more often the epitope is "conformational," i.e., the antibody recognizes the location and type of exposed antigen side chains that are not necessarily contiguous in the antigen's sequence, but brought together by its three-dimensional structure. A facility on the server allows the user to search putative conformational epitopes on protein surface, querying the system for proteins with a given annotation. The mepsMAP server has been implemented as a SOA composed by a database and a set of four WSs. We present here the software architecture of the system with a detailed description of the WS dataflow that has been optimized to provide the best computing performance while maintaining the easiest end-user access to the system via a Web interface.

Electrochemically promoted C-N bond formation from amines and CO2 in ionic liquid BMIm-BF4: Synthesis of carbamates.

A new electrochemical procedure for the synthesis of organic carbamates from amines and carbon dioxide has been developed using selective cathodic reduction of carbon dioxide in CO2-saturated room-temperature ionic liquid BMIm-BF4 solutions containing amines 1a-j, followed by addition of EtI as an alkylating agent. The synthesis was carried out under mild (PCO2 = 1.0 atm, t = 55 degrees C) and safe conditions, and the use of volatile and toxic solvents and catalysts (according to the growing demand for ecofriendly synthetic methodologies), as well as of any supporting electrolyte (for a very easy workup of the reaction mixture), was avoided. Carbamates 2a-j were isolated in good to high yields.

Methods to evaluate profile preferences for the anteroposterior position of the mandible.

INTRODUCTION: Facial profile disharmonies in the anteroposterior (AP) position of the mandible are among the most frequent reasons that patients seek orthodontic treatment. Various methods are available for assessing profile preferences, and differences between them could affect treatment decisions. The purposes of this study were to compare and contrast 3 methods of evaluating profile preferences for the AP position of the mandible. METHODS: Facial profile preferences of white orthodontists (n = 28) and white (n = 56) and Japanese-American (n = 55) laypeople were evaluated. The esthetic significance of variations in the AP position of the mandible was investigated by using 3 methods: a traditional semantic differential scale, the Perceptometrics method (Health Programs Intl, Wellesley, Mass), and the implicit association test (IAT). RESULTS: Findings from the semantic differential scale show that, overall, there is a general preference among orthodontists and laypeople for an orthognathic profile (P <.001). Findings from the Perceptometrics method indicate that orthodontists consider the most pleasing profile to be more forward than do lay subjects (P <.001). The IAT results show a positive bias among all 3 groups toward orthognathic profiles and a negative bias toward profiles with mandibular retrognathism or prognathism. The IAT suggested that laypeople were more tolerant of mandibular prognathism in men than in women (P <.01), and more tolerant of mandibular retrognathia in white women than in men (P = .03). CONCLUSIONS: These results support the benefits of using both implicit and explicit methods to assess facial profile preferences.