An Introductory Guide to Aligning Networks Using SANA, the Simulated Annealing Network Aligner.

Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological networks holds similar promise. Biological networks generally model interactions between biomolecules such as proteins, genes, metabolites, or mRNAs. There is strong evidence that the network topology-the "structure" of the network-is correlated with the functions performed, so that network topology can be used to help predict or understand function. However, unlike sequence comparison and alignment-which is an essentially solved problem-network comparison and alignment is an NP-complete problem for which heuristic algorithms must be used.Here we introduce SANA, the Simulated Annealing Network Aligner. SANA is one of many algorithms proposed for the arena of biological network alignment. In the context of global network alignment, SANA stands out for its speed, memory efficiency, ease-of-use, and flexibility in the arena of producing alignments between two or more networks. SANA produces better alignments in minutes on a laptop than most other algorithms can produce in hours or days of CPU time on large server-class machines. We walk the user through how to use SANA for several types of biomolecular networks

Expression of TGFβ Family in the Developing Internal Ear of Rat Embryos

In order to investigate the expression patterns of the transforming growth factor (TGF)β isoforms in the internal ear, an immunohistochemical study of rat embryos was performed. Rat embryos were taken on the 13th, 15th, 17th, and 19th day after conception and their internal ears were immunohistochemically stained against TGFβ1, β2, and β3. As a result, the 13-day-old embryo showed a very weak positivity to TGFβ1. After the 15th day of pregnancy, no reactivity to TGFβ1 was defected. Immunoreactivity to TGFβ2 was observed from the 15th day of pregnancy throughout the rest of the period. The ampulla of the semicircular canal and the cochlear duct showed a notably strong immunohistochemical reaction. A strong reaction to TGFβ3 was observed on the 15th day of pregnancy. However, no positive reactions were observed thereafter. A strong immunoreactivity was observed especially on the apical cytoplasms, the surfaces of the epithelial cells, and basement membranes of the cochlear duct, as well as the semicircular canals of the developing internal ear of rat embryo

Cyclebase.org—a comprehensive multi-organism online database of cell-cycle experiments

The past decade has seen the publication of a large number of cell-cycle microarray studies and many more are in the pipeline. However, data from these experiments are not easy to access, combine and evaluate. We have developed a centralized database with an easy-to-use interface, Cyclebase.org, for viewing and downloading these data. The user interface facilitates searches for genes of interest as well as downloads of genome-wide results. Individual genes are displayed with graphs of expression profiles throughout the cell cycle from all available experiments. These expression profiles are normalized to a common timescale to enable inspection of the combined experimental evidence. Furthermore, state-of-the-art computational analyses provide key information on both individual experiments and combined datasets such as whether or not a gene is periodically expressed and, if so, the time of peak expression. Cyclebase is available at http://www.cyclebase.org

Changes in body mass index by age, gender, and socio-economic status among a cohort of Norwegian men and women (1990–2001)

<p>Abstract</p> <p>Background</p> <p>Consistent with global trends, the prevalence of obesity is increasing among Norwegian adults. This study aimed to investigate individual trends in BMI (kg/m²) by age, gender, and socio-economic status over an 11-year period.</p> <p>Methods</p> <p>A cohort of 1169 adults (n = 581 men; n = 588 women) self-reported BMI during a general health interview twice administered in two regions in Norway.</p> <p>Results</p> <p>Average BMI increased significantly from 23.7 (SD = 3.4) to 25.4 (SD = 3.8), with equivalent increases for both genders. Proportion of obesity (BMI ≥ 30) increased from 4% to 11% for women and 5% to 13% for men. Of those already classified as overweight or obese in 1990, 68% had gained additional weight 10 years later, by an average increase of 2.6 BMI units. The greatest amount of weight gain occurred for the youngest adults (aged 20–29 years). Age-adjusted general linear models revealed that in 1990, women with a lower level of education had a significantly greater BMI than more educated women. In both 1990 and 2001, rural men with the highest level of household income had a greater BMI than rural men earning less income. Weight gain occurred across all education and income brackets, with no differential associations between SES strata and changes in BMI for either gender or region.</p> <p>Conclusion</p> <p>Results demonstrated significant yet gender-equivalent increases in BMI over an 11-year period within this cohort of Norwegian adults. Whereas socio-economic status exerted minimal influence on changes in BMI over time, young adulthood appeared to be a critical time period at which accelerated weight gain occurred.</p

Functional claudication distance: a reliable and valid measurement to assess functional limitation in patients with intermittent claudication

BACKGROUND: Disease severity and functional impairment in patients with intermittent claudication is usually quantified by the measurement of pain-free walking distance (intermittent claudication distance, ICD) and maximal walking distance (absolute claudication distance, ACD). However, the distance at which a patient would prefer to stop because of claudication pain seems a definition that is more correspondent with the actual daily life walking distance. We conducted a study in which the distance a patient prefers to stop was defined as the functional claudication distance (FCD), and estimated the reliability and validity of this measurement. METHODS: In this clinical validity study we included patients with intermittent claudication, following a supervised exercise therapy program. The first study part consisted of two standardised treadmill tests. During each test ICD, FCD and ACD were determined. Primary endpoint was the reliability as represented by the calculated intra-class correlation coefficients. In the second study part patients performed a standardised treadmill test and filled out the Rand-36 questionnaire. Spearman's rho was calculated to assess validity. RESULTS: The intra-class correlation coefficients of ICD, FCD and ACD were 0.940, 0.959, and 0.975 respectively. FCD correlated significantly with five out of nine domains, namely physical function (rho = 0.571), physical role (rho = 0.532), vitality (rho = 0.416), pain (rho = 0.416) and health change (rho = 0.414). CONCLUSION: FCD is a reliable and valid measurement for determining functional capacity in trained patients with intermittent claudication. Furthermore it seems that FCD better reflects the actual functional impairment. In future studies, FCD could be used alongside ICD and ACD

What factors in rural and remote extended clinical placements may contribute to preparedness for practice, from the perspective of students and clinicians?

What factors in rural and remote extended clinical placements may contribute to preparedness for practice, from the perspective of students and clinicians? Michele Daly, David Perkins, Koshila Kumar, Chris Roberts and Malcolm Moore Background: Community based rural education opportunities have expanded in Australia, attracting more medical students to placements in rural and remote settings. Aim: To identify the factors in an integrated, community engaged rural placement that may contribute to preparedness for practice (P4P), from the perspective of students and clinicians Methods: Forty two semi-structured interviews with medical students, supervisors and clinicians analysed thematically. Results: Opportunities for clinical learning, personal and professional development and cultural awareness were reported by students and clinicians as key factors that contribute to preparedness for practice. Potential barriers in rural and remote settings included geographical and academic isolation, perceived educational risk and differing degrees of program engagement. Conclusions: A longitudinal clinical placement in a rural setting may enable development of enhanced competencies leading to P4P. A rural setting can help provide a unique experience through hands-on learning, enhanced personal and professional development opportunities and observation of the cultural and contextual impact on health

Parvovirus B19 DNA CpG Dinucleotide Methylation and Epigenetic Regulation of Viral Expression

CpG DNA methylation is one of the main epigenetic modifications playing a role in the control of gene expression. For DNA viruses whose genome has the ability to integrate in the host genome or to maintain as a latent episome, a correlation has been found between the extent of DNA methylation and viral quiescence. No information is available for Parvovirus B19, a human pathogenic virus, which is capable of both lytic and persistent infections. Within Parvovirus B19 genome, the inverted terminal regions display all the characteristic signatures of a genomic CpG island; therefore we hypothesised a role of CpG dinucleotide methylation in the regulation of viral genome expression

Molecular Time-Course and the Metabolic Basis of Entry into Dauer in Caenorhabditis elegans

When Caenorhabditis elegans senses dauer pheromone (daumone), signaling inadequate growth conditions, it enters the dauer state, which is capable of long-term survival. However, the molecular pathway of dauer entry in C. elegans has remained elusive. To systematically monitor changes in gene expression in dauer paths, we used a DNA microarray containing 22,625 gene probes corresponding to 22,150 unique genes from C. elegans. We employed two different paths: direct exposure to daumone (Path 1) and normal growth media plus liquid culture (Path 2). Our data reveal that entry into dauer is accomplished through the multi-step process, which appears to be compartmentalized in time and according to metabolic flux. That is, a time-course of dauer entry in Path 1 shows that dauer larvae formation begins at post-embryonic stage S4 (48 h) and is complete at S6 (72 h). Our results also suggest the presence of a unique adaptive metabolic control mechanism that requires both stage-specific expression of specific genes and tight regulation of different modes of fuel metabolite utilization to sustain the energy balance in the context of prolonged survival under adverse growth conditions. It is apparent that worms entering dauer stage may rely heavily on carbohydrate-based energy reserves, whereas dauer larvae utilize fat or glyoxylate cycle-based energy sources. We created a comprehensive web-based dauer metabolic database for C. elegans (www.DauerDB.org) that makes it possible to search any gene and compare its relative expression at a specific stage, or evaluate overall patterns of gene expression in both paths. This database can be accessed by the research community and could be widely applicable to other related nematodes as a molecular atlas