Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by "embedded bioinformaticians," i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the "Sequence a genome" class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s) and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2233 putative proteins. Estrella also possesses a 9136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.

Nanomotors: new strategies of (bio)sensing based on motion

Nanomotors are nanoscale devices capable of converting energy into movement and forces. Among them, self-propelled nanomotors offer considerable promise for developing new and novel bioanalytical and biosensing strategies based on the direct isolation of target biomolecules or changes in their movement in the presence of target analytes. The mainachievements of this project consists on the development of receptor-functionalized nanomotors that offer direct and rapid target detection, isolation and transport from raw biological samples without preparatory and washing steps. For example, microtube engines functionalized with aptamer, antibody, lectin and enzymes receptors were used for the direct isolation of analytes of biomedical interest, including proteins and whole cells, among others. A target protein was also isolated from a complex sample by using an antigen-functionalized microengine navigating into the reservoirs of a lab-on-a-chip device. The new nanomotorbased target biomarkers detection strategy not only offers highly sensitive, rapid, simple and low cost alternative for the isolation and transport of target molecules, but also represents a new dimension of analytical information based on motion. The recognition events can be easily visualized by optical microscope (without any sophisticated analytical instrument) to reveal the target presence and concentration. The use of artificial nanomachines has shown not only to be useful for (bio)recognition and (bio)transport but also for detection of environmental contamination and remediation. In this context, micromotors modified with superhydrophobic layer demonstrated that effectively interacted, captured, transported and removed oil droplets from oil contaminated samples. Finally, a unique micromotor-based strategy for water-quality testing, that mimics live-fish water-quality testing, based on changes in the propulsion behavior of artificial biocatalytic microswimmers in the presence of aquatic pollutants was also developed. The attractive features of the new micromachine-based target isolation and signal transduction protocols developed in this project offer numerous potential applications in biomedical diagnostics, environmental monitoring, and forensic analysis.

Fatores terapêuticos em grupo de diabéticos

O objetivo da presente pesquisa foi analisar os fatores terapêuticos presentes nos relatos dos participantes de um grupo de diabéticos. Pesquisa exploratória, de avaliação, cujos dados foram obtidos por meio de entrevista semiestruturada, cuja análise permitiu a identificação dos seguintes fatores terapêuticos: oferecimento de informações (100%); coesão (100%); universalidade (86%); aprendizagem interpessoal (57%); desenvolvimento de técnicas de socialização (57%); altruísmo (28,5%); comportamento imitativo (28,5%) e instilação de esperança (28,5%). Intervenções grupais, realizadas na promoção do autocuidado às pessoas portadoras de diabetes, podem promover interação benéfica entre os membros, permitindo troca de experiências, compreensão de uma dimensão maior do problema e outras vivências positivas evidenciadas pela presença dos fatores terapêuticos.

Identification and modelling of human breast cancer subtypes

Résumé Le cancer du sein est le cancer le plus commun chez les femmes et est responsable de presque 30% de tous les nouveaux cas de cancer en Europe. On estime le nombre de décès liés au cancer du sein en Europe est à plus de 130.000 par an. Ces chiffres expliquent l'impact social considérable de cette maladie. Les objectifs de cette thèse étaient: (1) d'identifier les prédispositions et les mécanismes biologiques responsables de l'établissement des sous-types spécifiques de cancer du sein; (2) les valider dans un modèle ín vivo "humain-dans-souris"; et (3) de développer des traitements spécifiques à chaque sous-type de cancer du sein identifiés. Le premier objectif a été atteint par l'intermédiaire de l'analyse des données d'expression de gènes des tumeurs, produite dans notre laboratoire. Les données obtenues par puces à ADN ont été produites à partir de 49 biopsies des tumeurs du sein provenant des patientes participant dans l'essai clinique EORTC 10994/BIG00-01. Les données étaient très riches en information et m'ont permis de valider des données précédentes des autres études d'expression des gènes dans des tumeurs du sein. De plus, cette analyse m'a permis d'identifier un nouveau sous-type biologique de cancer du sein. Dans la première partie de la thèse, je décris I identification des tumeurs apocrines du sein par l'analyse des puces à ADN et les implications potentielles de cette découverte pour les applications cliniques. Le deuxième objectif a été atteint par l'établissement d'un modèle de cancer du sein humain, basé sur des cellules épithéliales mammaires humaines primaires (HMECs) dérivées de réductions mammaires. J'ai choisi d'adapter un système de culture des cellules en suspension basé sur des mammosphères précédemment décrit et pat décidé d'exprimer des gènes en utilisant des lentivirus. Dans la deuxième partie de ma thèse je décris l'établissement d'un système de culture cellulaire qui permet la transformation quantitative des HMECs. Par la suite, j'ai établi un modèle de xénogreffe dans les souris immunodéficientes NOD/SCID, qui permet de modéliser la maladie humaine chez la souris. Dans la troisième partie de ma thèse je décris et je discute les résultats que j'ai obtenus en établissant un modèle estrogène-dépendant de cancer du sein par transformation quantitative des HMECs avec des gènes définis, identifiés par analyse de données d'expression des gènes dans le cancer du sein. Les cellules transformées dans notre modèle étaient estrogène-dépendantes pour la croissance, diploïdes et génétiquement normales même après la culture cellulaire in vitro prolongée. Les cellules formaient des tumeurs dans notre modèle de xénogreffe et constituaient des métastases péritonéales disséminées et du foie. Afin d'atteindre le troisième objectif de ma thèse, j'ai défini et examiné des stratégies de traitement qui permettent réduire les tumeurs et les métastases. J'ai produit un modèle de cancer du sein génétiquement défini et positif pour le récepteur de l'estrogène qui permet de modéliser le cancer du sein estrogène-dépendant humain chez la souris. Ce modèle permet l'étude des mécanismes impliqués dans la formation des tumeurs et des métastases. Abstract Breast cancer is the most common cancer in women and accounts for nearly 30% of all new cancer cases in Europe. The number of deaths from breast cancer in Europe is estimated to be over 130,000 each year, implying the social impact of the disease. The goals of this thesis were first, to identify biological features and mechanisms --responsible for the establishment of specific breast cancer subtypes, second to validate them in a human-in-mouse in vivo model and third to develop specific treatments for identified breast cancer subtypes. The first objective was achieved via the analysis of tumour gene expression data produced in our lab. The microarray data were generated from 49 breast tumour biopsies that were collected from patients enrolled in the clinical trial EORTC 10994/BIG00-01. The data set was very rich in information and allowed me to validate data of previous breast cancer gene expression studies and to identify biological features of a novel breast cancer subtype. In the first part of the thesis I focus on the identification of molecular apacrine breast tumours by microarray analysis and the potential imptìcation of this finding for the clinics. The second objective was attained by the production of a human breast cancer model system based on primary human mammary epithelial cells {HMECs) derived from reduction mammoplasties. I have chosen to adopt a previously described suspension culture system based on mammospheres and expressed selected target genes using lentiviral expression constructs. In the second part of my thesis I mainly focus on the establishment of a cell culture system allowing for quantitative transformation of HMECs. I then established a xenograft model in immunodeficient NOD/SCID mice, allowing to model human disease in a mouse. In the third part of my thesis I describe and discuss the results that I obtained while establishing an oestrogen-dependent model of breast cancer by quantitative transformation of HMECs with defined genes identified after breast cancer gene expression data analysis. The transformed cells in our model are oestrogen-dependent for growth; remain diploid and genetically normal even after prolonged cell culture in vitro. The cells farm tumours and form disseminated peritoneal and liver metastases in our xenograft model. Along the lines of the third objective of my thesis I defined and tested treatment schemes allowing reducing tumours and metastases. I have generated a genetically defined model of oestrogen receptor alpha positive human breast cancer that allows to model human oestrogen-dependent breast cancer in a mouse and enables the study of mechanisms involved in tumorigenesis and metastasis.

Health effects of occupational exposure in a dairy food industry, with a specific assessment of exposure to airborne lactic acid bacteria

OBJECTIVE:: Lactic acid bacteria (LAB) are used in food industries as probiotic agents. The aim of this study is to assess the potential health effects of airborne exposure to a mix of preblend (LAB and carbohydrate) and milk powder in workers. METHODS:: A medical questionnaire, lung function tests, and immunologic tests were carried out on 50 workers. Occupational exposure to inhalable dust and airborne LAB was measured. RESULTS:: Workers not using respiratory masks reported more symptoms of irritation than workers using protection. Workers from areas with higher levels of airborne LAB reported the most health symptoms and the immune responses of workers to LAB was higher than the immune responses of a control population. CONCLUSIONS:: Measures to reduce exposure to airborne LAB and milk powder in food industries are recommended.

In silico meets in vivo

A report of the 6th Georgia Tech-Oak Ridge National Lab International Conference on Bioinformatics 'In silico Biology: Gene Discovery and Systems Genomics', Atlanta, USA, 15-17 November, 2007.

Gene finding in the chicken genome

Background: Despite the continuous production of genome sequence for a number of organisms,reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularlytrue for genomes for which there is not a large collection of known gene sequences, such as therecently published chicken genome. We used the chicken sequence to test comparative andhomology-based gene-finding methods followed by experimental validation as an effective genomeannotation method.Results: We performed experimental evaluation by RT-PCR of three different computational genefinders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram wascomputed and each component of it was evaluated. The results showed that de novo comparativemethods can identify up to about 700 chicken genes with no previous evidence of expression, andcan correctly extend about 40% of homology-based predictions at the 5' end.Conclusions: De novo comparative gene prediction followed by experimental verification iseffective at enhancing the annotation of the newly sequenced genomes provided by standardhomology-based methods.

Investgiation into Improved Pavement Curing Materials and Techniques: Part 1 - Phases I and II, April 2002

Concrete curing is closely related to cement hydration, microstructure development, and concrete performance. Application of a liquid membrane-forming curing compound is among the most widely used curing methods for concrete pavements and bridge decks. Curing compounds are economical, easy to apply, and maintenance free. However, limited research has been done to investigate the effectiveness of different curing compounds and their application technologies. No reliable standard testing method is available to evaluate the effectiveness of curing, especially of the field concrete curing. The present research investigates the effects of curing compound materials and application technologies on concrete properties, especially on the properties of surface concrete. This report presents a literature review of curing technology, with an emphasis on curing compounds, and the experimental results from the first part of this research—lab investigation. In the lab investigation, three curing compounds were selected and applied to mortar specimens at three different times after casting. Two application methods, single- and double-layer applications, were employed. Moisture content, conductivity, sorptivity, and degree of hydration were measured at different depths of the specimens. Flexural and compressive strength of the specimens were also tested. Statistical analysis was conducted to examine the relationships between these material properties. The research results indicate that application of a curing compound significantly increased moisture content and degree of cement hydration and reduced sorptivity of the near-surface-area concrete. For given concrete materials and mix proportions, optimal application time of curing compounds depended primarily upon the weather condition. If a sufficient amount of a high-efficiency-index curing compound was uniformly applied, no double-layer application was necessary. Among all test methods applied, the sorptivity test is the most sensitive one to provide good indication for the subtle changes in microstructure of the near-surface-area concrete caused by different curing materials and application methods. Sorptivity measurement has a close relation with moisture content and degree of hydration. The research results have established a baseline for and provided insight into the further development of testing procedures for evaluation of curing compounds in field. Recommendations are provided for further field study.

Iowa Gender Wage Study, 1999

In 1993, Iowa Workforce Development (then the Department of Employment Services) conducted a survey to determine if there was a gender gap in wages paid. The results of that survey indicated that women were paid 68 cents per dollar paid to males. We felt a need to determine if this relationship of wages paid to each gender has changed since the 1993 study. In 1999, the Commission on the Status of Women requested that Iowa Workforce Development conduct research to update the 1993 information. A survey, cosponsored by the Commission on the Status of Women and Iowa Workforce Development, was conducted in 1999. The results of the survey showed that women earned 73 percent of what men earned when both jobs were considered. (The survey asked respondents to provide information on a primary job and a secondary job.) The ratio for the primary job was 72 percent, while the ratio for the secondary job was 85 percent. Additional survey results detail the types of jobs respondents had, the types of companies for which they worked and the education and experience levels. All of these characteristics can contribute to these ratios. While the large influx of women into the labor force may be over, it is still important to look at such information to determine if future action is needed. We present these results with that goal in mind. We are indebted to those Iowans, female and male, who voluntarily completed the survey. This study was completed under the general direction of Judy Erickson. The report was written by Shazada Khan, Teresa Wageman, Ann Wagner, and Yvonne Younes with administrative and technical assistance from Michael Blank, Margaret Lee and Gary Wilson. The Iowa State University Statistical Lab provided sampling advice, data entry and coding and data analysis.

Low density lipoprotein signaling and pancreatic beta cells protection

SummaryLow-density lipoproteins (LDLs) have an important physiological role in organism transporting cholesterol and other fatty substances to target tissues. However, elevated LDL levels in the blood are associated with the formation of arterial plaques and consequently atherosclerosis. It is therefore important to characterize the intracellular pathways induced upon LDL stimulation as they might be involved in the pathological properties of these lipoproteins. It has been previously found that LDL stimulation of mouse embryonic fibroblasts activates p38 mitogen activated protein kinases (MAPKs). This leads to cell spreading and increase in the wound healing capabilities of the cells. These two responses might occur within atherosclerotic plaques.The aim of this project is to reveal the missing links between LDL particle and activation of p38 MAPK kinase. As previously shown in our lab activation of p38 MAPK kinase by the LDL particles occur independently of classical LDL receptor (LDLR). In this study we have shown that scavenger receptor type Β class I (SR-BI) is responsible for the signal transduction from the LDLs to the p38 MAPK. We have also shown that Mitogen activated kinase kinases (MKKs) that can directly activate ρ 38 MAPK in these conditions are MKK3 and MKK6 but not MKK4. We have also tested some of the intermediate components of the pathway like Ras and PI3 kinase but found that they do not play a role.The data obtained in this study showed a part of molecular mechanism responsible for p38 MAPK activation and subsequent wound healing and can contribute to our knowledge on function of the fibroblasts in the development of the atherosclerotic plaques.Diabetes Mellitus is a condition caused by disordered metabolism of blood glucose level. It is one of the most commonly spread disease in the western world, with the incidence reaching 8% of population in United States. Two most common types of diabetes are type 1 and 2 that differs slightly in the mechanism of the development. However in the basis of both types lies the cell death of pancreatic beta cells. The aim of this work is to improve beta cells survival in different pathophysiological settings. This could be extrapolated to the conditions in which Diabetes develops in humans. We decided to use RasGAP- derived fragment Ν with its strong antiapoptotic effect in beta cells. In our lab we have demonstrated that in the mild stress conditions RasGAP can be cleaved by caspases at the position 455 producing two fragments, fragment Ν and fragment C. Fragment Ν exerts

Materials and Mix Optimization Procedures for PCC Pavements, March 2006

Severe environmental conditions, coupled with the routine use of deicing chemicals and increasing traffic volume, tend to place extreme demands on portland cement concrete (PCC) pavements. In most instances, engineers have been able to specify and build PCC pavements that met these challenges. However, there have also been reports of premature deterioration that could not be specifically attributed to a single cause. Modern concrete mixtures have evolved to become very complex chemical systems. The complexity can be attributed to both the number of ingredients used in any given mixture and the various types and sources of the ingredients supplied to any given project. Local environmental conditions can also influence the outcome of paving projects. This research project investigated important variables that impact the homogeneity and rheology of concrete mixtures. The project consisted of a field study and a laboratory study. The field study collected information from six different projects in Iowa. The information that was collected during the field study documented cementitious material properties, plastic concrete properties, and hardened concrete properties. The laboratory study was used to develop baseline mixture variability information for the field study. It also investigated plastic concrete properties using various new devices to evaluate rheology and mixing efficiency. In addition, the lab study evaluated a strategy for the optimization of mortar and concrete mixtures containing supplementary cementitious materials. The results of the field studies indicated that the quality management concrete (QMC) mixtures being placed in the state generally exhibited good uniformity and good to excellent workability. Hardened concrete properties (compressive strength and hardened air content) were also satisfactory. The uniformity of the raw cementitious materials that were used on the projects could not be monitored as closely as was desired by the investigators; however, the information that was gathered indicated that the bulk chemical composition of most materials streams was reasonably uniform. Specific minerals phases in the cementitious materials were less uniform than the bulk chemical composition. The results of the laboratory study indicated that ternary mixtures show significant promise for improving the performance of concrete mixtures. The lab study also verified the results from prior projects that have indicated that bassanite is typically the major sulfate phase that is present in Iowa cements. This causes the cements to exhibit premature stiffening problems (false set) in laboratory testing. Fly ash helps to reduce the impact of premature stiffening because it behaves like a low-range water reducer in most instances. The premature stiffening problem can also be alleviated by increasing the water–cement ratio of the mixture and providing a remix cycle for the mixture.

Body Size, Activity, Employment and Wages in Europe: A First Approach

In this article we present the first empirical analysis on the associations between body size, activity, employment and wages for several European countries. The main advantage of the present work with respect to the previous literature is offered by the comparability of the data and its large geographical coverage. According to our results, for Spanish women, being obese is associated with both a 9% lower wage and probability of being employed, while for Swedish and Danish, obesity is associated with a 12% lower probability of being employed, and a 10% lower wage respectively. In Belgium, obesity is associated with a 19% lower probability of being employed for men. These robust estimates are strongly informative and may be used as a simple statistical rule of thumb to decide the countries in which lab and field experiments should be run.