Analysis of polymorphism at site -174 G/C of interleukin-6 promoter region in multiple myeloma

It is well established that interleukin-6 (IL-6) is an essential growth factor for multiple myeloma (MM) and patients with increased IL-6 levels have a poor prognosis. In healthy subjects, the presence of the C allele at a polymorphic site (-174 G/C) of the IL-6 gene is related to low IL-6 levels. In view of the potential association of this particular polymorphism with IL-6 concentration, and the relevance of IL-6 in MM pathogenesis, the objective of the present study was to investigate the prevalence of IL-6 (-174 G/C) promoter polymorphism and its association with development of MM in Brazilian individuals. We investigated the prevalence of these alleles in 52 patients and 60 healthy subjects (matched by age, sex, and race) of a Brazilian population. Thirty patients were male (42.4%), 24 (46.2%) were white and the median age at diagnosis was 58.5 years (range: 28 to 84 years). To determine the IL-6 (-174 G/C) polymorphism, molecular analysis was performed by polymerase chain reaction followed by endonuclease restriction digestion. The genotype distributions observed in the group of patients were 4% CC, 42% GC and 54% GG. The C allele frequency was 0.25. These results were similar to the control group, suggesting no impact of this polymorphism on the susceptibility to MM.

Identification of fungemia agents using the polymerase chain reaction and restriction fragment length polymorphism analysis

Prompt and specific identification of fungemia agents is important in order to define clinical treatment. However, in most cases conventional culture identification can be considered to be time-consuming and not without errors. The aim of the present study was to identify the following fungemia agents: Candida albicans, Candida parapsilosis, Candida tropicalis, Candida glabrata, Cryptococcus neoformans, Cryptococcus gattii, and Histoplasma capsulatum using the polymerase chain reaction and restriction fragment length polymorphism analysis (PCR/RFLP). More specifically: a) to evaluate 3 different amplification regions, b) to investigate 3 different restriction enzymes, and c) to use the best PCR/RFLP procedure to indentify 60 fungemia agents from a culture collection. All 3 pairs of primers (ITS1/ITS4, NL4/ITS5 and Primer1/Primer2) were able to amplify DNA from the reference strains. However, the size of these PCR products did not permit the identification of all the species studied. Three restriction enzymes were used to digest the PCR products: HaeIII, Ddel and Bfal. Among the combinations of pairs of primers and restriction enzymes, only one (primer pair NL4/ITS5 and restriction enzyme Ddel) produced a specific RFLP pattern for each microorganism studied. Sixty cultures of fungemia agents (selected from the culture collection of Fundação de Medicina Tropical do Amazonas - FMTAM) were correctly identified by PCR/RFLP using the prime pair NL4/ITS5 and Ddel. We conclude that the method proved to be both simple and reproducible, and may offer potential advantages over phenotyping methods.

Comparative proteomics analysis of chronic atrophic gastritis: changes of protein expression in chronic atrophic gastritis without Helicobacter pylori infection

Chronic atrophic gastritis (CAG) is a very common gastritis and one of the major precursor lesions of gastric cancer, one of the most common cancers worldwide. The molecular mechanism underlying CAG is unclear, but its elucidation is essential for the prevention and early detection of gastric cancer and appropriate intervention. A combination of two-dimensional gel electrophoresis and mass spectrometry was used in the present study to analyze the differentially expressed proteins. Samples from 21 patients (9 females and 12 males; mean age: 61.8 years) were used. We identified 18 differentially expressed proteins in CAG compared with matched normal mucosa. Eight proteins were up-regulated and 10 down-regulated in CAG when compared with the same amounts of proteins in individually matched normal gastric mucosa. Two novel proteins, proteasome activator subunit 1 (PSME1), which was down-regulated in CAG, and ribosomal protein S12 (RPS12), which was up-regulated in CAG, were further investigated. Their expression was validated by Western blot and RT-PCR in 15 CAG samples matched with normal mucosa. The expression level of RPS12 was significantly higher in CAG than in matched normal gastric mucosa (P < 0.05). In contrast, the expression level of PSME1 in CAG was significantly lower than in matched normal gastric mucosa (P < 0.05). This study clearly demonstrated that there are some changes in protein expression between CAG and normal mucosa. In these changes, down-regulation of PSME1 and up-regulation of RPS12 could be involved in the development of CAG. Thus, the differentially expressed proteins might play important roles in CAG as functional molecules.

Early detection of metabolic and energy disorders by thermal time series stochastic complexity analysis

Maintenance of thermal homeostasis in rats fed a high-fat diet (HFD) is associated with changes in their thermal balance. The thermodynamic relationship between heat dissipation and energy storage is altered by the ingestion of high-energy diet content. Observation of thermal registers of core temperature behavior, in humans and rodents, permits identification of some characteristics of time series, such as autoreference and stationarity that fit adequately to a stochastic analysis. To identify this change, we used, for the first time, a stochastic autoregressive model, the concepts of which match those associated with physiological systems involved and applied in male HFD rats compared with their appropriate standard food intake age-matched male controls (n=7 per group). By analyzing a recorded temperature time series, we were able to identify when thermal homeostasis would be affected by a new diet. The autoregressive time series model (AR model) was used to predict the occurrence of thermal homeostasis, and this model proved to be very effective in distinguishing such a physiological disorder. Thus, we infer from the results of our study that maximum entropy distribution as a means for stochastic characterization of temperature time series registers may be established as an important and early tool to aid in the diagnosis and prevention of metabolic diseases due to their ability to detect small variations in thermal profile.

Analysis of Automotive Cybersecurity - Attack surfaces and users’ privacy concerns

Modern automobiles are no longer just mechanical tools. The electronics and computing services they are shipping with are making them not less than a computer. They are massive kinetic devices with sophisticated computing power. Most of the modern vehicles are made with the added connectivity in mind which may be vulnerable to outside attack. Researchers have shown that it is possible to infiltrate into a vehicle’s internal system remotely and control the physical entities such as steering and brakes. It is quite possible to experience such attacks on a moving vehicle and unable to use the controls. These massive connected computers can be life threatening as they are related to everyday lifestyle. First part of this research studied the attack surfaces in the automotive cybersecurity domain. It also illustrated the attack methods and capabilities of the damages. Online survey has been deployed as data collection tool to learn about the consumers’ usage of such vulnerable automotive services. The second part of the research portrayed the consumers’ privacy in automotive world. It has been found that almost hundred percent of modern vehicles has the capabilities to send vehicle diagnostic data as well as user generated data to their manufacturers, and almost thirty five percent automotive companies are collecting them already. Internet privacy has been studies before in many related domain but no privacy scale were matched for automotive consumers. It created the research gap and motivation for this thesis. A study has been performed to use well established consumers privacy scale – IUIPC to match with the automotive consumers’ privacy situation. Hypotheses were developed based on the IUIPC model for internet consumers’ privacy and they were studied by the finding from the data collection methods. Based on the key findings of the research, all the hypotheses were accepted and hence it is found that automotive consumers’ privacy did follow the IUIPC model under certain conditions. It is also found that a majority of automotive consumers use the services and devices that are vulnerable and prone to cyber-attacks. It is also established that there is a market for automotive cybersecurity services and consumers are willing to pay certain fees to avail that.

Effects of isometric elbow flexion on electromyographic spike analysis

The main objective of this research was to examine the relationship between surface electromyographic (SEMG) spike activity and force. The secondary objective was to determine to what extent subcutaneous tissue impacts the high frequency component of the signal, as well as, examining the relationship between measures of SEMG spike shape and their traditional time and frequency analogues. A total of96 participants (46 males and 50 females) ranging in age (18-35 years), generated three 5-second isometric step contractions at each force level of 40, 60, 80, and 100 percent of maximal voluntary contraction (MVC). The presentation of the contractions was balanced across subjects. The right arm of the subject was positioned in the sagittal plane, with the shoulder and elbow flexed to 90 degrees. The elbow rested on a support in a neutral position (mid pronation/mid supination) and placed within a wrist cuff, fastened below the styloid process. The wrist cuff was attached to a load cell (JR3 Inc., Woodland, CA) recording the force produced. Biceps brachii activity was monitored with a pair of Ag/AgCI recording electrodes (Grass F-E9, Astro-Med Inc., West Warwick, RI) placed in a bipolar configuration, with an interelectrode distance (lED) of 2cm distal to the motor point. Data analysis was performed on a I second window of data in the middle of the 5-second contraction. The results indicated that all spike shape measures exhibited significant (p < 0.01) differences as force increase~ from 40 to 100% MVC. The spike shape measures suggest that increased motor unit (MU) recruitment was responsible for increasing force up to 80% MVC. The results suggested that further increases in force relied on MU III synchronization. The results also revealed that the subcutaneous tissue (skin fold thickness) had no relationship (r = 0.02; P > 0.05) with the mean number of peaks per spike (MNPPS), which was the high frequency component of the signal. Mean spike amplitude (MSA) and mean spike frequency (MSF) were highly correlated with their traditional measures root mean square (RMS) and mean power frequency (MPF), respectively (r = 0.99; r = 0.97; P < 0.01).

Molecular cloning and restriction endonuclease analysis of bovine adenovirus type 3

Bovine adenovirus type 3 (BAV3) is a medium size DNA virus that causes respiratory and gastrointestinal disorders in cattle. The viral genome consists of a 35,000 base pair, linear, double-stranded DNA molecule with inverted terminal repeats and a 55 kilodalton protein covalently linked to each of the 5' ends. In this study, the viral genome was cloned in the form of subgenomic restriction fragments. Five EcoRI internal fragments spanning 3.4 to 89.0 % and two Xb a I internal fragments spanning 35.7 to 82.9 % of the viral genome were cloned into the EcoRI and Xbal sites of the bacterial vector pUC19. To generate overlap between cloned fragments, ten Hi n dIll internal fragments spanning 3.9 to 84.9 and 85.5 to 96% and two BAV3 BamHI internal fragments spanning 59.8 to 84.9% of the viral genome were cloned into the HindllI and BamHI sites of pUC19. The HindlII cloning strategy also resulted in six recombinant plasmids carrying two or more Hi ndII I fragments. These fragments provided valuable information on the linear orientation of the cloned fragments within the viral genome. Cloning of the terminal fragments required the removal of the residual peptides that remain attached to the 5' ends of the genome. This was accomplished by alkaline hydrolysis of the DNA-peptide bond. BamH I restriction fragments of the peptide-free DNA were cloned into pUC19 and resulted in two plasmids carrying the BAV3 Bam HI terminal fragments spanning 0 to 53.9% and 84.9 to 100% of the viral genome.

Development of the Physical Activity Interactive Recall (PAIR) for Aboriginal children

Affiliation: Margaret Cargo : Département de médecine sociale et préventive, Faculté de médecine, Université de Montréal

Metabolomics analysis in rats with thiamine deficiency identifies key metabolites in vulnerable brain regions and suggests neural stem progenitor cells play a role in ameliorating metabolic dysfunction

La documentation scientifique fait état de la présence, chez l’adulte, de cellules souches et progénitrices neurales (CSPN) endogènes dans les zones sous-ventriculaire et sous-granulaire du cerveau ainsi que dans le gyrus denté de l’hippocampe. De plus, un postulat selon lequel il serait également possible de retrouver ce type de cellules dans la moelle épinière et le néocortex des mammifères adultes a été énoncé. L’encéphalopathie de Wernicke, un trouble neurologique grave toutefois réversible qui entraîne un dysfonctionnement, voire une défaillance du cerveau, est causée principalement par une carence importante en thiamine (CT). Des observations récentes laissent envisager que les facteurs en cause dans la prolifération et la différenciation des CSPN pourraient également jouer un rôle important lors d’un épisode de CT. L’hypothèse, selon laquelle l’identification de nouveaux métabolites entrant dans le mécanisme ou la séquence de réactions se soldant en une CT pourraient en faciliter la compréhension, a été émise au moyen d'une démarche en cours permettant d’établir le profil des modifications métaboliques qui surviennent en de telles situations. Cette approche a été utilisée pour constater les changements métaboliques survenus au niveau du foyer cérébral dans un modèle de rats déficients en thiamine (rats DT), particulièrement au niveau du thalamus et du colliculus inférieur (CI). La greffe de CSPN a quant à elle été envisagée afin d’apporter de nouvelles informations sur la participation des CSPN lors d’un épisode de CT et de déterminer les bénéfices thérapeutiques potentiels offerts par cette intervention. Les sujets de l’étude étaient répartis en quatre groupes expérimentaux : un premier groupe constitué de rats dont la CT était induite par la pyrithiamine (rats DTiP), un deuxième groupe constitué de rats-contrôles nourris ensemble (« pair-fed control rats » ou rats PFC) ainsi que deux groupes de rats ayant subi une greffe de CSPN, soit un groupe de rats DTiP greffés et un dernier groupe constitué de rats-contrôles (rats PFC) greffés. Les échantillons de foyers cérébraux (thalamus et CI) des quatre groupes de rats ont été prélevés et soumis à des analyses métabolomiques non ciblées ainsi qu’à une analyse visuelle par microscopie à balayage électronique (SEM). Une variété de métabolites-clés a été observée chez les groupes de rats déficients en thiamine (rats DTiP) en plus de plusieurs métabolites dont la documentation ne faisait pas mention. On a notamment constaté la présence d’acides biliaires, d’acide cynurénique et d’acide 1,9— diméthylurique dans le thalamus, alors que la présence de taurine et de carnosine a été observée dans le colliculus inférieur. L’étude a de plus démontré une possible implication des CSPN endogènes dans les foyers cérébraux du thalamus et du colliculus inférieur en identifiant les métabolites-clés ciblant les CSPN. Enfin, les analyses par SEM ont montré une amélioration notable des tissus à la suite de la greffe de CSPN. Ces constatations suggèrent que l’utilisation de CSPN pourrait s’avérer une avenue thérapeutique intéressante pour soulager la dégénérescence symptomatique liée à une grave carence en thiamine chez l’humain.

Development, implementation and application of electronic structural descriptors to the analysis of the chemical bonding, aromaticity and chemical reactivity

En la literatura sobre mecànica quàntica és freqüent trobar descriptors basats en la densitat de parells o la densitat electrònica, amb un èxit divers segons les aplicacions que atenyin. Per tal de que tingui sentit químic un descriptor ha de donar la definició d'un àtom en una molècula, o ésser capaç d'identificar regions de l'espai molecular associades amb algun concepte químic (com pot ser un parell solitari o zona d'enllaç, entre d'altres). En aquesta línia, s'han proposat diversos esquemes de partició: la teoria d'àtoms en molècules (AIM), la funció de localització electrònica (ELF), les cel·les de Voroni, els àtoms de Hirshfeld, els àtoms difusos, etc. L'objectiu d'aquesta tesi és explorar descriptors de la densitat basats en particions de l'espai molecular del tipus AIM, ELF o àtoms difusos, analitzar els descriptors existents amb diferents nivells de teoria, proposar nous descriptors d'aromaticitat, així com estudiar l'habilitat de totes aquestes eines per discernir entre diferents mecanismes de reacció.

The effectiveness of assessment learning objects produced using pair programming

Pair Programming is a technique from the software development method eXtreme Programming (XP) whereby two programmers work closely together to develop a piece of software. A similar approach has been used to develop a set of Assessment Learning Objects (ALO). Three members of academic staff have developed a set of ALOs for a total of three different modules (two with overlapping content). In each case a pair programming approach was taken to the development of the ALO. In addition to demonstrating the efficiency of this approach in terms of staff time spent developing the ALOs, a statistical analysis of the outcomes for students who made use of the ALOs is used to demonstrate the effectiveness of the ALOs produced via this method.

A multispacecraft analysis of a small-scale transient entrained by solar wind streams

The images taken by the Heliospheric Imagers (HIs), part of the SECCHI imaging package onboard the pair of STEREO spacecraft, provide information on the radial and latitudinal evolution of the plasma compressed inside corotating interaction regions (CIRs). A plasma density wave imaged by the HI instrument onboard STEREO-B was found to propagate towards STEREO-A, enabling a comparison between simultaneous remotesensing and in situ observations of its structure to be performed. In situ measurements made by STEREO-A show that the plasma density wave is associated with the passage of a CIR. The magnetic field compressed after the CIR stream interface (SI) is found to have a planar distribution. Minimum variance analysis of the magnetic field vectors shows that the SI is inclined at 54° to the orbital plane of the STEREO-A spacecraft. This inclination of the CIR SI is comparable to the inclination of the associated plasma density wave observed by HI. A small-scale magnetic cloud with a flux rope topology and radial extent of 0.08 AU is also embedded prior to the SI. The pitch-angle distribution of suprathermal electrons measured by the STEREO-A SWEA instrument shows that an open magnetic field topology in the cloud replaced the heliospheric current sheet locally. These observations confirm that HI observes CIRs in difference images when a small-scale transient is caught up in the compression region.

Stray light analysis of SALEX instrument

Discrepancies between recent global earth albedo anomaly data obtained from the climate models, space and ground observations call for a new and better earth reflectance measurement technique. The SALEX (Space Ashen Light Explorer) instrument is a space-based visible and IR instrument for precise estimation of the global earth albedo by measuring the ashen light reflected off the shadowy side of the Moon from the low earth orbit. The instrument consists of a conventional 2-mirror telescope, a pair of a 3-mirror visible imager and an IR bolometer. The performance of this unique multi-channel optical system is sensitive to the stray light contamination due to the complex optical train incorporating several reflecting and refracting elements, associated mounts and the payload mechanical enclosure. This could be further aggravated by the very bright and extended observation target (i.e. the Moon). In this paper, we report the details of extensive stray light analysis including ghosts and cross-talks, leading to the optimum set of stray light precautions for the highest signal-to-noise ratio attainable.

Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription

BACKGROUND: Serial Analysis of Gene Expression (SAGE) is a powerful tool for genome-wide transcription studies. Unlike microarrays, it has the ability to detect novel forms of RNA such as alternatively spliced and antisense transcripts, without the need for prior knowledge of their existence. One limitation of using SAGE on an organism with a complex genome and lacking detailed sequence information, such as the hexaploid bread wheat Triticum aestivum, is accurate annotation of the tags generated. Without accurate annotation it is impossible to fully understand the dynamic processes involved in such complex polyploid organisms. Hence we have developed and utilised novel procedures to characterise, in detail, SAGE tags generated from the whole grain transcriptome of hexaploid wheat. RESULTS: Examination of 71,930 Long SAGE tags generated from six libraries derived from two wheat genotypes grown under two different conditions suggested that SAGE is a reliable and reproducible technique for use in studying the hexaploid wheat transcriptome. However, our results also showed that in poorly annotated and/or poorly sequenced genomes, such as hexaploid wheat, considerably more information can be extracted from SAGE data by carrying out a systematic analysis of both perfect and "fuzzy" (partially matched) tags. This detailed analysis of the SAGE data shows first that while there is evidence of alternative polyadenylation this appears to occur exclusively within the 3' untranslated regions. Secondly, we found no strong evidence for widespread alternative splicing in the developing wheat grain transcriptome. However, analysis of our SAGE data shows that antisense transcripts are probably widespread within the transcriptome and appear to be derived from numerous locations within the genome. Examination of antisense transcripts showing sequence similarity to the Puroindoline a and Puroindoline b genes suggests that such antisense transcripts might have a role in the regulation of gene expression. CONCLUSION: Our results indicate that the detailed analysis of transcriptome data, such as SAGE tags, is essential to understand fully the factors that regulate gene expression and that such analysis of the wheat grain transcriptome reveals that antisense transcripts maybe widespread and hence probably play a significant role in the regulation of gene expression during grain development.

Global transcript analysis of rice leaf and seed using SAGE technology.

We have compiled two comprehensive gene expression profiles from mature leaf and immature seed tissue of rice (Oryza sativa ssp. japonica cultivar Nipponbare) using Serial Analysis of Gene Expression (SAGE) technology. Analysis revealed a total of 50 519 SAGE tags, corresponding to 15 131 unique transcripts. Of these, the large majority (approximately 70%) occur only once in both libraries. Unexpectedly, the most abundant transcript (approximately 3% of the total) in the leaf library was derived from a type 3 metallothionein gene. The overall frequency profiles of the abundant tag species from both tissues differ greatly and reveal seed tissue as exhibiting a non-typical pattern of gene expression characterized by an over abundance of a small number of transcripts coding for storage proteins. A high proportion ( approximately 80%) of the abundant tags (> or = 9) matched entries in our reference rice EST database, with many fewer matches for low abundant tags. Singleton transcripts that are common to both tissues were collated to generate a summary of low abundant transcripts that are expressed constitutively in rice tissues. Finally and most surprisingly, a significant number of tags were found to code for antisense transcripts, a finding that suggests a novel mechanism of gene regulation, and may have implications for the use of antisense constructs in transgenic technology.