Preliminary Survey and Diet Analysis of Anurans in The Riparian Zone of Calayagon Watershed, Agusan Del Norte, Philippines

Watersheds are critical habitats for a diverse array of organisms. Among all the fauna, anurans are excellent biological indicators of environmental health. The community structure is often associated with a relationship between species diversity and diet. An anuran survey was conducted along riparian zones of three selected barangays of Calayagon Watershed (Guinabsan, Rizal, and Malpoc), Philippines. Extensive opportunistic methods for a total of 480 man-hours were spent traversing the area. A total of 195 individuals, consisting of seven species from four families, were recorded. Seventy-two percent of the individual species were regarded as Least concern, and 14 % were Near-threatened. Of the species recorded, 57 % are Philippine endemic, and 29 % are Invasive alien species. Fejervarya vittigera (44.66 %) gained the highest number of individuals across sampling stations. Overall diversity index is high H’= 1.43. The most abundant species in each sampling site were subjected to diet analysis (R. marina, F. vittigera, and F. moodiei). The most dominant prey item were plant matters followed by insect orders. In terms of the number of prey items, the order Hymenoptera was the most abundant. The study was the first to record the diet of the Philippine endemic F. vittigera, and F. moodiei. Noted anthropogenic threats include agricultural expansion and urbanization. Strict implementation of ordinances and policies towards the conservation and protection of a healthy bio-system for anurans and all organisms in the area is highly recommended

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation

Motivation: Gene expression profiling using RNA-seq is a powerful technique for screening RNA species’ landscapes and their dynamics in an unbiased way. While several advanced methods exist for differential expression analysis of RNA-seq data, proper tools to anal.yze RNA-seq time-course have not been proposed. Results: In this study, we use RNA-seq to measure gene expression during the early human T helper 17 (Th17) cell differentiation and T-cell activation (Th0). To quantify Th17-specific gene expression dynamics, we present a novel statistical methodology, DyNB, for analyzing time-course RNA-seq data. We use non-parametric Gaussian processes to model temporal correlation in gene expression and combine that with negative binomial likelihood for the count data. To account for experiment-specific biases in gene expression dynamics, such as differences in cell differentiation efficiencies, we propose a method to rescale the dynamics between replicated measurements. We develop an MCMC sampling method to make inference of differential expression dynamics between conditions. DyNB identifies several known and novel genes involved in Th17 differentiation. Analysis of differentiation efficiencies revealed consistent patterns in gene expression dynamics between different cultures. We use qRT-PCR to validate differential expression and differentiation efficiencies for selected genes. Comparison of the results with those obtained via traditional timepoint-wise analysis shows that time-course analysis together with time rescaling between cultures identifies differentially expressed genes which would not otherwise be detected. Availability: An implementation of the proposed computational methods will be available at http://research.ics.aalto.fi/csb/software/Academy of Finland (Centre of Excellence in Moleculary Systems Immunology and Physiology Research (2012-2017) Grant 135320)Seventh Framework Programme (European Commission) (Grant EC-FP7-SYBILLA-201106)EU ERASysBio ERA-NETSigrid Juslius FoundationFICS Graduate Schoo

Genome-wide Analysis of STAT3-Mediated Transcription during Early Human Th17 Cell Differentiation

The development of therapeutic strategies to combat immune-associated diseases requires the molecular mechanisms of human Th17 cell differentiation to be fully identified and understood. To investigate transcriptional control of Th17 cell differentiation, we used primary human CD4+ T cells in small interfering RNA (siRNA)-mediated gene silencing and chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) to identify both the early direct and indirect targets of STAT3. The integrated dataset presented in this study confirms that STAT3 is critical for transcriptional regulation of early human Th17 cell differentiation. Additionally, we found that a number of SNPs from loci associated with immune-mediated disorders were located at sites where STAT3 binds to induce Th17 cell specification. Importantly, introduction of such SNPs alters STAT3 binding in DNA affinity precipitation assays. Overall, our study provides important insights for modulating Th17-mediated pathogenic immune responses in humans.</p

Comparative analysis of human and mouse transcriptomes of Th17 cell priming

Uncontrolled Th17 cell activity is associated with cancer and autoimmune and inflammatory diseases. To validate the potential relevance of mouse models of targeting the Th17 pathway in human diseases we used RNA sequencing to compare the expression of coding and non-coding transcripts during the priming of Th17 cell differentiation in both human and mouse. In addition to already known targets, several transcripts not previously linked to Th17 cell polarization were found in both species. Moreover, a considerable number of human-specific long non-coding RNAs were identified that responded to cytokines stimulating Th17 cell differentiation. We integrated our transcriptomics data with known disease-associated polymorphisms and show that conserved regulation pinpoints genes that are relevant to Th17 cell-mediated human diseases and that can be modelled in mouse. Substantial differences observed in non-coding transcriptomes between the two species as well as increased overlap between Th17 cell-specific gene expression and disease-associated polymorphisms underline the need of parallel analysis of human and mouse models. Comprehensive analysis of genes regulated during Th17 cell priming and their classification to conserved and non-conserved between human and mouse facilitates translational research, pointing out which candidate targets identified in human are worth studying by using in vivo mouse models

Vainoamislain oikeuskäytäntö vuosina 2015-2016 ja asianomistajien psyykkinen hyvinvointi

Tavoitteet. Vainoaminen voi aiheuttaa sen uhrille useita psyykkisiä oireita ja sosiaalista haittaa. Ulkomailla vainoamistuomiot vaihtelevat sakoista ehdottomaan vankeuteen. Tuomitsemiseen voivat lain lisäksi vaikuttaa myös erilaiset havaintovääristymät. Vainoaminen kriminalisoitiin Suomessa vuoden 2014 alussa, mutta lain oikeuskäytäntöä ja tuomitsemiseen ja korvauksiin vaikuttavia tekijöitä ei ole juurikaan vielä tutkittu. Tämän tutkimuksen tarkoituksena oli selvittää vainoamisen psyykkisiin seurauksiin ja korvauksiin vaikuttavia tekijöitä, tutkia rangaistusten ja tuomitsemisen eroja suhteessa syytetyn demografisiin piirteisiin, sekä ennustaa vainoamistuomion saamista. Menetelmät. Tutkimuksen aineisto koostui kaikista Suomen käräjäoikeuksissa ratkaistuista vainoamispäätöksistä vuosina 2015-2016 (n = 246). Päätöksistä arvioitiin vastaajan ja asianomistajan demografisia piirteitä, heidän välistään suhdetta, vainoamistapoja, vainon kestoa, psyykkisiä seurauksia ja varotoimia sekä rangaistus- ja korvausseuraamuksia. Vertailut korvaussummissa, rangaistusseuraamuksissa ja tuomittujen ja tuomitsematta jätettyjen välillä suoritettiin t-testeillä ja x2-testeillä. Psyykkisiä seurauksia ja vainoamisesta tuomitsemista ennustavia tekijöitä tutkittiin logistisella regressioanalyysillä. Tulokset ja johtopäätökset. Suomessa vainoamisesta tuomitseminen perustuu vainoamisen piirteisiin, eivätkä lain ulkopuoliset tekijät vaikuttaneet tuomitsemiseen tai rangaistusseuraamuksiin merkitsevästi. Vainon seurauksena aiheutuneet psyykkiset oireet vaikuttivat määrättyihin korvauksiin, mutta varotoimet eivät. Tulevaisuudessa vainoamisen havaintovääristymiä tulisi tutkia poliiseilla ja syyttäjillä, sillä vääristymät voivat vaikuttaa tapauksien oikeuteen etenemiseen. Lisäksi lisäämällä psykologien ja viranomaisten tietoutta vainoamisesta ja sen seurauksista voitaisiin varmistaa vainoamisen uhrin sensitiivinen kohtaaminen ja oikeanlainen neuvominen vainoamisen lopettamisessa ja taltioinnissa rikostutkintaa ja oikeusistuinta varten.Object. Stalking can cause many psychological symptoms and social disadvantage. Abroad the criminal justice response to stalking varies from fine to a prison sentence. Besides the law, also perceptions of stalking can affect sentencing. Stalking was criminalized in Finland in the beginning of 2014, but there have only been a few studies regarding the case law of stalking and the factors affecting compensation. The aims of this study were to clarify the factors affecting the psychological consequences and the compensations of stalking, to examine the differences in convictions and sentencing in relation to demographic features of the defendant and to predict stalking convictions. Methods. Altogether we collected 246 verdicts of stalking cases from district courts in Finland. We analyzed demographic features of and the relationship between the defendant and the complainant, the psychological consequences of stalking and taken countermeasures, the longitude and ways of stalking and the convictions and compensations. The comparisons in compensations, convictions and sentencing were analyzed using t-test and chi square test. Logistic regression was used to examine the factors affecting psychological consequences and the sentencing of stalking. Results and conclusions. In Finland, the sentencing of stalking is based on the features of stalking, and the extra-legal factors did not affect the sentencing nor the convictions. The psychological symptoms caused by stalking affected the compensations, but the countermeasures did not. In the future it would be important to study the perceptions of stalking in policemen and prosecutors because the perceptional biases may affect whether the cases proceed to court. Also, by increasing the knowledge about stalking and its’ consequences one could ensure the sensitive encountering of the victim and the advising of the right kind to stop the stalking and documenting it for criminal investigation and for court

Genome-wide Analysis of STAT3-Mediated Transcription during Early Human Th17 Cell Differentiation

The development of therapeutic strategies to combat immune-associated diseases requires the molecular mechanisms of human Th17 cell differentiation to be fully identified and understood. To investigate transcriptional control of Th17 cell differentiation, we used primary human CD4+ T cells in small interfering RNA (siRNA)-mediated gene silencing and chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) to identify both the early direct and indirect targets of STAT3. The integrated dataset presented in this study confirms that STAT3 is critical for transcriptional regulation of early human Th17 cell differentiation. Additionally, we found that a number of SNPs from loci associated with immune-mediated disorders were located at sites where STAT3 binds to induce Th17 cell specification. Importantly, introduction of such SNPs alters STAT3 binding in DNA affinity precipitation assays. Overall, our study provides important insights for modulating Th17-mediated pathogenic immune responses in humans.Peer reviewe

Quantitative Proteomics Reveals the Dynamic Protein Landscape during Initiation of Human Th17 Cell Polarization

Summary: Th17 cells contribute to the pathogenesis of inflammatory and autoimmune diseases and cancer. To reveal the Th17 cell-specific proteomic signature regulating Th17 cell differentiation and function in humans, we used a label-free mass spectrometry-based approach. Furthermore, a comprehensive analysis of the proteome and transcriptome of cells during human Th17 differentiation revealed a high degree of overlap between the datasets. However, when compared with corresponding published mouse data, we found very limited overlap between the proteins differentially regulated in response to Th17 differentiation. Validations were made for a panel of selected proteins with known and unknown functions. Finally, using RNA interference, we showed that SATB1 negatively regulates human Th17 cell differentiation. Overall, the current study illustrates a comprehensive picture of the global protein landscape during early human Th17 cell differentiation. Poor overlap with mouse data underlines the importance of human studies for translational research. : Immunology; Components of the Immune System; Omics; Proteomics Subject Areas: Immunology, Components of the Immune System, Omics, Proteomic

Comparative analysis of human and mouse transcriptomes of Th17 cell priming

Uncontrolled Th17 cell activity is associated with cancer and autoimmune and inflammatory diseases. To validate the potential relevance of mouse models of targeting the Th17 pathway in human diseases we used RNA sequencing to compare the expression of coding and non-coding transcripts during the priming of Th17 cell differentiation in both human and mouse. In addition to already known targets, several transcripts not previously linked to Th17 cell polarization were found in both species. Moreover, a considerable number of human-specific long non-coding RNAs were identified that responded to cytokines stimulating Th17 cell differentiation. We integrated our transcriptomics data with known disease-associated polymorphisms and show that conserved regulation pinpoints genes that are relevant to Th17 cell-mediated human diseases and that can be modelled in mouse. Substantial differences observed in non-coding transcriptomes between the two species as well as increased overlap between Th17 cell-specific gene expression and disease-associated polymorphisms underline the need of parallel analysis of human and mouse models. Comprehensive analysis of genes regulated during Th17 cell priming and their classification to conserved and non-conserved between human and mouse facilitates translational research, pointing out which candidate targets identified in human are worth studying by using in vivo mouse models.Peer reviewe