Genomic Analysis of Stress Response Against Arsenic in \u3cem\u3eCaenorhabditis elegans\u3c/em\u3e

Arsenic, a known human carcinogen, is widely distributed around the world and found in particularly high concentrations in certain regions including Southwestern US, Eastern Europe, India, China, Taiwan and Mexico. Chronic arsenic poisoning affects millions of people worldwide and is associated with increased risk of many diseases including arthrosclerosis, diabetes and cancer. In this study, we explored genome level global responses to high and low levels of arsenic exposure in Caenorhabditis elegans using Affymetrix expression microarrays. This experimental design allows us to do microarray analysis of dose-response relationships of global gene expression patterns. High dose (0.03%) exposure caused stronger global gene expression changes in comparison with low dose (0.003%) exposure, suggesting a positive dose-response correlation. Biological processes such as oxidative stress, and iron metabolism, which were previously reported to be involved in arsenic toxicity studies using cultured cells, experimental animals, and humans, were found to be affected in C. elegans. We performed genome-wide gene expression comparisons between our microarray data and publicly available C. elegans microarray datasets of cadmium, and sediment exposure samples of German rivers Rhine and Elbe. Bioinformatics analysis of arsenic-responsive regulatory networks were done using FastMEDUSA program. FastMEDUSA analysis identified cancer-related genes, particularly genes associated with leukemia, such as dnj-11, which encodes a protein orthologous to the mammalian ZRF1/MIDA1/MPP11/DNAJC2 family of ribosome-associated molecular chaperones. We analyzed the protective functions of several of the identified genes using RNAi. Our study indicates that C. elegans could be a substitute model to study the mechanism of metal toxicity using high-throughput expression data and bioinformatics tools such as FastMEDUSA

Genomic Analysis of Immune Response against Vibrio Cholerae Hemolysin in Caenorhabditis elegans

Vibrio cholerae cytolysin (VCC) is among the accessory V. cholerae virulence factors that may contribute to disease pathogenesis in humans. VCC, encoded by hlyA gene, belongs to the most common class of bacterial toxins, known as poreforming toxins (PFTs). V. cholerae infects and kills Caenorhabditis elegans via cholerae toxin independent manner. VCC is required for the lethality, growth retardation and intestinal cell vacuolation during the infection. However, little is known about the host gene expression responses against VCC. To address this question we performed a microarray study in C. elegans exposed to V. cholerae strains with intact and deleted hlyA genes. Many of the VCC regulated genes identified, including C-type lectins, Prion-like (glutamine [Q]/asparagine [N]-rich)-domain containing genes, genes regulated by insulin/ IGF-1-mediated signaling (IIS) pathway, were previously reported as mediators of innate immune response against other bacteria in C. elegans. Protective function of the subset of the genes up-regulated by VCC was confirmed using RNAi. By means of a machine learning algorithm called FastMEDUSA, we identified several putative VCC induced immune regulatory transcriptional factors and transcription factor binding motifs. Our results suggest that VCC is a major virulence factor, which induces a wide variety of immune response- related genes during V. cholerae infection in C. elegans

Recurrence Plot Based Measures of Complexity and its Application to Heart Rate Variability Data

The knowledge of transitions between regular, laminar or chaotic behavior is essential to understand the underlying mechanisms behind complex systems. While several linear approaches are often insufficient to describe such processes, there are several nonlinear methods which however require rather long time observations. To overcome these difficulties, we propose measures of complexity based on vertical structures in recurrence plots and apply them to the logistic map as well as to heart rate variability data. For the logistic map these measures enable us not only to detect transitions between chaotic and periodic states, but also to identify laminar states, i.e. chaos-chaos transitions. The traditional recurrence quantification analysis fails to detect the latter transitions. Applying our new measures to the heart rate variability data, we are able to detect and quantify the laminar phases before a life-threatening cardiac arrhythmia occurs thereby facilitating a prediction of such an event. Our findings could be of importance for the therapy of malignant cardiac arrhythmias

The very low-dose dexamethasone suppression test in the general population: A cross-sectional study

Determinants of the hypothalamic-pituitary-adrenal (HPA) axis functioning are increasingly explored in population-based studies. However, functional tests measuring the negative feedback of the HPA axis cannot easily be implemented into large observational studies. Furthermore, high doses of dexamethasone often completely suppress the HPA axis in healthy persons. This study aimed to detect the effects of the health, lifestyle and sociodemographic factors, psychiatric problems and cognitive functions on the negative feedback of the HPA axis using a very low-dose (0.25 mg) dexamethasone suppression test (DST). We evaluated the associations of several determinants with the saliva cortisol concentrations after dexamethasone intake in a confounder-adjusted model also corrected for baseline saliva cortisol concentrations in the Rotterdam Study, a large population-based study (N = 1822). We found that female sex, low income, lack of exercise, instrumental disability and smoking were all independently associated with stronger suppression of the HPA axis. Even though there were no linear associations between psychiatric measures and cortisol suppression, we found that depressive symptoms and anxiety disorders were more common in persons with non-suppression of cortisol. Conversely, psychotropic medication use was related to enhanced suppression of cortisol after DST. In this large study, we found that female gender, low socioeconomic status and poor health were all related to suppression of the HPA axis. Non-linear associations were detected between the suppression of the HPA axis and common psychiatric disorders in community-dwelling persons

The complete mitochondrial genome of the foodborne parasitic pathogen Cyclospora cayetanensis

Cyclospora cayetanensis is a human-specific coccidian parasite responsible for several food and water-related outbreaks around the world, including the most recent ones involving over 900 persons in 2013 and 2014 outbreaks in the USA. Multicopy organellar DNA such as mitochondrion genomes have been particularly informative for detection and genetic traceback analysis in other parasites. We sequenced the C. cayetanensis genomic DNA obtained from stool samples from patients infected with Cyclospora in Nepal using the Illumina MiSeq platform. By bioinformatically filtering out the metagenomic reads of non-coccidian origin sequences and concentrating the reads by targeted alignment, we were able to obtain contigs containing Eimeria-like mitochondrial, apicoplastic and some chromosomal genomic fragments. A mitochondrial genomic sequence was assembled and confirmed by cloning and sequencing targeted PCR products amplified from Cyclospora DNA using primers based on our draft assembly sequence. The results show that the C. cayetanensis mitochondrion genome is 6274 bp in length, with 33% GC content, and likely exists in concatemeric arrays as in Eimeria mitochondrial genomes. Phylogenetic analysis of the C. cayetanensis mitochondrial genome places this organism in a tight cluster with Eimeria species. The mitochondrial genome of C. cayetanensis contains three protein coding genes, cytochrome (cytb), cytochrome C oxidase subunit 1 (cox1), and cytochrome C oxidase subunit 3 (cox3), in addition to 14 large subunit (LSU) and nine small subunit (SSU) fragmented rRNA genes

Preliminary analysis of an instructional alternative to exclusionary discipline

37 pagesDecades of research have shown that exclusionary discipline practices are not only ineffective for changing student behavior, they lead to worse social, behavioral, and academic outcomes for students. This article explores the findings from a pilot study of the Inclusive Skill-Building Learning Approach (ISLA), an instructional alternative to exclusionary discipline practices. The purposes of ISLA are to improve student social and behavioral problem-solving, teacher and administrator practices, and student-teacher relationships while also reducing lost instructional time for student excluded from their learning environment. Results from the pilot indicated that implementation of ISLA was associated with reductions in exclusionary discipline practices (Cohen’s h effect sizes ranged from .06 to .18 across schools and outcomes), and a substantial decrease in instructional minutes lost (~ 92%). Educational staff also reported favorable impressions of the intervention. Practical and conceptual implications, limitations of this study, and directions for future research are further discussed.The research reported here was supported by the Fairway Fund, a College of Education Faculty Research Award at the University of Oregon and by the Institute of Education Sciences, U.S. Department of Education, through Grant R305A180006 to the University of Oregon

Biological Determinants of Depression: An epidemiological approach

Understanding the biology behind depression has a long history in research. To date, no unique marker or specific etiological factor was detected. However, we know more about the possible mechanisms that predispose depression or affect clinical presentation and prognosis of depression. In this thesis, we studied various hypotheses to extend our knowledge about biological determinants of depression using an epidemiological approach. The main aims of this thesis were 1) to scrutinize the determinants and the genetic control of different functions of the HPA axis, a well-known neurohormonal correlate of depression, 2) to revisit the vascular depression hypothesis and explored the associations of non-clinical cerebrovascular alterations with depression, and 3) to explore genetic etiology of depression using the genome-wide association approach

Metodi e prospettive della ricerca linguistica

Il volume presenta e discute criticamente alcuni approcci all'analisi linguistica, con particolare riguardo per le modalità di raccolta dati e il loro trattamento. Il volume vuole fornire una integrazione e un approfondimento per gli studenti dei corsi triennali (ed eventualmente magistrali) di vari indirizzi, che abbiano incrociato il loro cammino con la linguistica generale e desiderino saperne di più

Barley grain (1,3;1,4)-β-glucan content:effects of transcript and sequence variation in genes encoding the corresponding synthase and endohydrolase enzymes

The composition of plant cell walls is important in determining cereal end uses. Unlike other widely consumed cereal grains barley is comparatively rich in (1,3;1,4)-β-glucan, a source of dietary fibre. Previous work showed Cellulose synthase-like genes synthesise (1,3;1,4)-β-glucan in several tissues. HvCslF6 encodes a grain (1,3;1,4)-β-glucan synthase, whereas the function of HvCslF9 is unknown. Here, the relationship between mRNA levels of HvCslF6, HvCslF9, HvGlbI (1,3;1,4)-β-glucan endohydrolase, and (1,3;1,4)-β-glucan content was studied in developing grains of four barley cultivars. HvCslF6 was differentially expressed during mid (8-15 DPA) and late (38 DPA) grain development stages while HvCslF9 transcript was only clearly detected at 8-10 DPA. A peak of HvGlbI expression was detected at 15 DPA. Differences in transcript abundance across the three genes could partially explain variation in grain (1,3;1,4)-β-glucan content in these genotypes. Remarkably narrow sequence variation was found within the HvCslF6 promoter and coding sequence and does not explain variation in (1,3;1,4)-β-glucan content. Our data emphasise the genotype-dependent accumulation of (1,3;1,4)-β-glucan during barley grain development and a role for the balance between hydrolysis and synthesis in determining (1,3;1,4)-β-glucan content, and suggests that other regulatory sequences or proteins are likely to be involved in this trait in developing grain.Guillermo Garcia-Gimenez, Joanne Russell, Matthew K. Aubert, Geoffrey B. Fincher, Rachel A. Burton, Robbie Waugh, Matthew R. Tucker, Kelly Housto