In silico phylogenetic and virulence gene profile analyses of avian pathogenic Escherichia coli genome sequences

Avian pathogenic Escherichia coli (APEC) infections are responsible for significant losses in the poultry industry worldwide. A zoonotic risk has been attributed to APEC strains because they present similarities to extraintestinal pathogenic E. coli (ExPEC) associated with illness in humans, mainly urinary tract infections and neonatal meningitis. Here, we present in silico analyses with pathogenic E. coli genome sequences, including recently available APEC genomes. The phylogenetic tree, based on multi-locus sequence typing (MLST) of seven housekeeping genes, revealed high diversity in the allelic composition. Nevertheless, despite this diversity, the phylogenetic tree was able to cluster the different pathotypes together. An in silico virulence gene profile was also determined for each of these strains, through the presence or absence of 83 well-known virulence genes/traits described in pathogenic E. coli strains. The MLST phylogeny and the virulence gene profiles demonstrated a certain genetic similarity between Brazilian APEC strains, APEC isolated in the United States, UPEC (uropathogenic E. coli) and diarrheagenic strains isolated from humans. This correlation corroborates and reinforces the zoonotic potential hypothesis proposed to APEC.

Using Moodle to provide added value in the teaching of a software development course

The rate of adoption and use of learning management systems to support teaching and learning processes in academic institutions is growing rapidly. Universities are acquiring systems with functionalities that can match with their specific needs and requirements. Moodle is one of the most popular and widely deployed learning management systems in academic institutions today. However, apart from the system, universities tend to maintain other applications for the purpose of supplementing their teaching and learning processes. This situation is similar to Lappeenranta University of Technology (LUT), which is our case study in this project. Apart from Moodle, the university also maintains other systems such as Oodi, Noppa and Uni portal for the purpose of supporting its educational activities. This thesis has two main goals. The first goal is to understand the specific role of Moodle at LUT. This information is fundamental in assessing whether Moodle is needed in the university’s current teaching and learning environment. The second aim is to provide insights to teachers and other departmental stakeholders on how Moodle can provide added value in the teaching of a software development course. In response to this, a Moodle module for a software development course is created and the underlying features are tested. Results of the constructive work proposed some improvements through (i) the use of Moodle for in-class surveys, (ii) transfer of grades from Moodle to Oodi, (iii) use of Moodle in self-study courses and MOOCs, (iv) online examinations, and (v) Moodle integrations with third party applications. The proposed items were then evaluated for their utility through interviews of five expert interviews. The final results of this work are considered useful to LUT administration and management specifically on ways that Moodle can bring changes to the university at managerial, economical and technical level. It also poses some challenges on platform innovations and research.

Building the ‘Digital’ Library: Routes to Managing our Institutional Digital Learning, Teaching and Research Assets Together

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Phylogenetic analyses of Cladophora vagabunda (L.) C. Hoek (Cladophorales, Chlorophyta) from Brazil based on SSU rDNA sequences

The complete SSU rDNA was sequenced for 10 individuals of Cladophora vagabunda collected along the coast of Brazil. For C. rupestris (L.) Kütz. a partial SSU rDNA sequence (1634 bp) was obtained. Phylogenetic trees indicate that Cladophora is paraphyletic, but the section Glomeratae sensu lato including C. vagabunda from Brazil, Japan and France, C. albida (Nees) Kütz., C. sericea (Hudson) Kütz., and C. glomerata (L.) Kütz. is monophyletic. Within this group C. vagabunda is paraphyletic. The sequence identity for the SSU rDNA varied from 98.9% to 100% for the Brazilian C. vagabunda, and from 98.3% to 99.7% comparing the Brazilian individuals to the ones from France and Japan. Sequence identity of the Brazilian C. vagabunda to C. albida and C. sericea vary from 98.0% to 98.6%. The SSU rDNA phylogeny support partially the morphological characteristics presented by Brazilian populations of C. vagabunda. On the other hand, C. rupestris from Brazil does not group with C. rupestris from France, both sequences presenting only 96.9% of identity. The inclusion of sequences of individuals from Brazil reinforces the need of taxonomical revision for the genus Cladophora and for the complex C. vagabunda.

A 37-kb restriction map of the human immunoglobulin lambda variable locus, VB cluster, harboring four functional genes and two non-coding Vl sequences

The human immunoglobulin lambda variable locus (IGLV) is mapped at chromosome 22 band q11.1-q11.2. The 30 functional germline v-lambda genes sequenced untill now have been subgrouped into 10 families (Vl1 to Vl10). The number of Vl genes has been estimated at approximately 70. This locus is formed by three gene clusters (VA, VB and VC) that encompass the variable coding genes (V) responsible for the synthesis of lambda-type Ig light chains, and the Jl-Cl cluster with the joining segments and the constant genes. Recently the entire variable lambda gene locus was mapped by contig methodology and its one- megabase DNA totally sequenced. All the known functional V-lambda genes and pseudogenes were located. We screened a human genomic DNA cosmid library and isolated a clone with an insert of 37 kb (cosmid 8.3) encompassing four functional genes (IGLV7S1, IGLV1S1, IGLV1S2 and IGLV5a), a pseudogene (VlA) and a vestigial sequence (vg1) to study in detail the positions of the restriction sites surrounding the Vl genes. We generated a high resolution restriction map, locating 31 restriction sites in 37 kb of the VB cluster, a region rich in functional Vl genes. This mapping information opens the perspective for further RFLP studies and sequencing

Control of the rat angiotensin I converting enzyme gene by CRE-like sequences

We characterized the role of potential cAMP-responsive elements (CRE) in basal and in induced angiotensin converting enzyme (ACE) gene promoter activity in order to shed light on the regulation of somatic ACE expression. We identified stimulators and repressors of basal expression between 122 and 288 bp and between 415 and 1303 bp upstream from the transcription start site, respectively, using a rabbit endothelial cell (REC) line. These regions also contained elements associated with the response to 8BrcAMP. When screening for CRE motifs we found pCRE, a proximal sequence between 209 and 222 bp. dCRE, a distal tandem of two CRE-like sequences conserved between rats, mice and humans, was detected between 834 and 846 bp. Gel retardation analysis of nuclear extracts of REC indicated that pCRE and dCRE bind to the same protein complexes as bound by a canonical CRE. Mutation of pCRE and dCRE in REC established the former as a positive element and the latter as a negative element. In 293 cells, a renal cell line, pCRE and dCRE are negative regulators. Co-transfection of ATF-2 or ATF-2 plus c-Jun repressed ACE promoter activity, suggesting that the ACE gene is controlled by cellular stress. Although mapping of cAMP responsiveness was consistent with roles for pCRE and dCRE, mutation analysis indicated that they were not required for cAMP responsiveness. We conclude that the basal activity of the somatic ACE promoter is controlled by proximal and distal CREs that can act as enhancers or repressors depending on the cell context.

Automatic recognition of fish from video sequences

The problem of automatic recognition of the fish from the video sequences is discussed in this Master’s Thesis. This is a very urgent issue for many organizations engaged in fish farming in Finland and Russia because the process of automation control and counting of individual species is turning point in the industry. The difficulties and the specific features of the problem have been identified in order to find a solution and propose some recommendations for the components of the automated fish recognition system. Methods such as background subtraction, Kalman filtering and Viola-Jones method were implemented during this work for detection, tracking and estimation of fish parameters. Both the results of the experiments and the choice of the appropriate methods strongly depend on the quality and the type of a video which is used as an input data. Practical experiments have demonstrated that not all methods can produce good results for real data, whereas on synthetic data they operate satisfactorily.

Pediatric pain: prevalence, assessment, and management in a teaching hospital

The goal of this study was to examine the prevalence, assessment and management of pediatric pain in a public teaching hospital. The study sample consisted of 121 inpatients (70 infants, 36 children, and 15 adolescents), their families, 40 physicians, and 43 nurses. All participants were interviewed except infants and children who could not communicate due to their clinical status. The interview included open-ended questions concerning the inpatients’ pain symptoms during the 24 h preceding data collection, as well as pain assessment and pharmacological/non-pharmacological management of pain. The data were obtained from 100% of the eligible inpatients. Thirty-four children/adolescents (28%) answered the questionnaire and for the other 72% (unable to communicate), the family/health professional caregivers reported pain. Among these 34 persons, 20 children/adolescents reported pain, 68% of whom reported that they received pharmacological intervention for pain relief. Eighty-two family caregivers were available on the day of data collection. Of these, 40 family caregivers (49%) had observed their child’s pain response. In addition, 74% reported that the inpatients received pharmacological management. Physicians reported that only 38% of the inpatients exhibited pain signs, which were predominantly acute pain detected during clinical procedures. They reported that 66% of patients received pharmacological intervention. The nurses reported pain signs in 50% of the inpatients, which were detected during clinical procedures. The nurses reported that pain was managed in 78% of inpatients by using pharmacological and/or non-pharmacological interventions. The findings provide evidence of the high prevalence of pain in pediatric inpatients and the under-recognition of pain by health professionals.

Metal-Ion-Binding Oligonucleotides: High-Affinity Probes for Nucleic Acid Sequences

Small non-coding RNAs have numerous biological functions in cell and are divided into different classes such as: microRNA, snoRNA, snRNA and siRNA. MicroRNA (miRNA) is the most studied non-coding RNA to date and is found in plants, animals and some viruses. miRNA with short sequences is involved in suppressing translation of target genes by binding to their mRNA post-transcriptionally and silencing it. Their function besides silencing of the viral gene, can be oncogenic and therefore the cause of cancer. Hence, their roles are highlighted in human diseases, which increases the interest in using them as biomarkers and drug targets. One of the major problems to overcome is recognition of miRNA. Owing to a stable hairpin structure, chain invasion by conventional Watson-Crick base-pairing is difficult. One way to enhance the hybridization is exploitation of metal-ion mediated base-pairing, i. e. oligonucleotide probes that tightly bind a metal ions and are able to form a coordinative bonds between modified and natural nucleobases. This kind of metallo basepairs containing short modified oligonucleotides can also be useful for recognition of other RNA sequences containing hairpin-like structural motives, such as the TAR sequence of HIV. In addition, metal-ion-binding oligonucleotides will undoubtedly find applications in DNA-based nanotechnology. In this study, the 3,5-dimethylpyrazol-1-yl substituted purine derivatives were successfully incorporated within oligonucleotides, into either a terminal or non-terminal position. Among all of the modified oligonucleotides studied, a 2-(3,5-dimethylpyrazol-1-yl)-6-oxopurine base containing oligonucleotide was observed to bind most efficiently to their unmodified complementary sequences in the presence of both Cu2+ or Zn2+. The oligonucleotide incorporating 2,6-bis(3,5-dimethylpyrazol-1-yl)purine base also markedly increased the stability of duplexes in the presence of Cu2+ without losing the selectivity.

Exploring Relationship between Pakistani Teachers’ Pedagogical Beliefs and ICT Use for Teaching and Learning

Background: The aim of present study is to investigate relationship between Pakistani teachers’ pedagogical beliefs and ICT use for teaching and learning. Previous studies found close relationship between pedagogical beliefs and teaching practices including use of ICT. However, variation in results is also reported and attributed to cultural and contextual differences. Methodology: Quantitative approach was used to study a sample of 231 Pakistani basic education teachers from middle and upper-middle range private schools, mostly from large urban centres. Results: This study confirmed previously study results that constructivist-compatible pedagogical beliefs are significantly related to both traditional and constructivist use of ICT. However, it is also found that traditional-transmission pedagogical beliefs are significantly related to traditional use of ICT – a finding not reported in previous studies. Some amounts of ICT training for pedagogical purpose exhibit significant impact on ICT use, in particular constructivist use of ICT. Similarly age also play a role as younger teachers are more likely to use ICT, however, no significant difference of pedagogical beliefs and ICT use was found between male and female teachers. Recommendation for practice and further investigation are made in chapter 5.

Perceptions of some teachers about the similarities and/or differences in teaching online versus in a classroom environment /

The introduction of computer and communications technology, and particularly the internet, into education has opened up some new possibilities for teaching and learning. Courses designed and delivered in an online environment offer the possibility of highly interactive and individually focussed teaching and learning experiences. However, online courses also present new challenges for both teachers and students. A qualitative study was conducted to explore teachers' perceptions about the similarities and differences in teaching in the online and face-to-face (F2F) environments. Focus group discussions were held with 5 teachers; 2 teachers were interviewed in depth. The participants, 3 female and 2 male, were full-time teachers from a large College of Applied Arts & Technology in southern Ontario. Each of them had over 10 years of F2F teaching experience and each had been involved in the development and teaching of at least one online course. i - -; The study focussed on how teaching in the online environment compares with teaching in the F2F environment, what roles teachers and students adopt in each setting, what learning communities mean online and F2F and how they are developed, and how institutional policies, procedures, and infrastructure affect teaching and learning F2F and online. This study was emic in nature, that is the teachers' words determine the themes identified throughout the study. The factors identified as affecting teaching in an online environment included teacher issues such as course design, motivation to teach online, teaching style, role, characteristics or skills, and strategies. Student issues as perceived by the teachers included learning styles, role, and characteristics or skills. As well, technology issues such as a reliable infrastructure, clear role and responsibilities for maintaining the infrastructure, support, and multimedia capability affected teaching online. Finally, administrative policies and procedures, including teacher selection and training, registration and scheduling procedures, intellectual property and workload policies, and the development and communication of a comprehensive strategic plan were found to impact on teaching online. The teachers shared some of the benefits they perceived about teaching online as well as some of the challenges they had faced and challenges they perceived students had faced online. Overall, the teachers feh that there were more similarities than differences in teaching between the two environments, with the main differences being the change from F2F verbal interactions involving body language to online written interactions without body language cues, and the fundamental reliance on technology in the online environment. These findings support previous research in online teaching and learning, and add teachers' perspectives on the factors that stay the same and the factors that change when moving from a F2F environment to an online environment.