Transcriptome analysis of osteosarcoma identifies suppression of wnt pathway and up-regulation of adiponectin as potential biomarker

Osteosarcoma (OS) is primary malignant bone tumour with complicated early diagnosis. There are no specific markers currently available for predicting the prognosis and chemosensitivity of OS. In present study we performed transcriptome profiling of single patient tumour tissue with RNA-seq technology. We analysed surgically removed sarcoma sample from single 16 years old male patient. Transciptome analysis was done with RNA-seq technology, bioinformatics with Lifescope and R Bioconductor. Validation experiments were done with quantitative real-time PCR (QRTPCR). After quality and coverage filtering, RNA-seq experiment resulted 29,311,899 mapped reads for sarcoma and 22,099,159 mapped reads for normal bone tissue. 65 genes were differentially expressed with FDR corrected statistical significance below 0.05. Seven genes were down-regulated and 58 genes were up-regulated in sarcoma. The most highly up-regulated gene in sarcoma was adiponectin, ADIPOQ (with adjusted p-value 5.5E-07, log2 fold change was 7.9). Many of the genes we found are related to the adipose tissue metabolism (ADIPOQ, PLIN1, FABP4) and to the Wnt signalling suppression (WIF1, SOST). We also found novel fusion transcript between the genes LMTK2 and ZSWIM5. LMTK2 is lemur tyrosine kinase 2, and it has been shown to be involved in NGF-TrkA signalling. Interestingly, studies support the involvement of LMTK2 in development of prostate cancer. ZSWIM5 is zinc finger SWIM domain protein 5 and its function is not known. Immunohistochemical analysis confirmed positive staining for adiponectin in osteosarcoma. This paper is a good illustration how transcriptome analysis can find new biomarkers and targets for complex diseases

Parental Involvement and Academic Performance of High School Students: A Correlational Study

The main purpose of this study was to examine the correlation between parental involvement (PI) and academic performance (AP) among junior high school (JHS) students in selected schools in Cebu. This study employed a quantitative correlational design. There were thirty (30) JHS students who participated in this research who were identified using a simple random sampling method. Descriptive statistical tools, particularly mean and standard deviation were used to describe the level of PI and AP of the students. Consequently, the Pearson product-moment coefficient of correlation test was run to assess the correlation between PI and AP among JHS students. Based on the findings, it showed that there is a very low negative correlation between the two variables. Thus, there is no significant correlation between PI and AP among JHS students, r (30) = - .06, p = .74. With these results, the null hypothesis was not rejected since the p-value is greater than the significance level, p > .05. Therefore, PI does not affect the AP of the students. Findings suggest that educational staff and administrators be able to identify other factors that influence the AP of the students. Because the scope of this study is restricted within the perception of students towards PI, it would be better for the future studies to let the parents of the students be involved, and their side will be taken into consideration; new variables in the inquiry – motivation and self-competence among students; and to conduct a qualitative or a mixed-method study for future studies about the topic

A new, fast algorithm for detecting protein coevolution using maximum compatible cliques

<p>Abstract</p> <p>Background</p> <p>The MatrixMatchMaker algorithm was recently introduced to detect the similarity between phylogenetic trees and thus the coevolution between proteins. MMM finds the largest common submatrices between pairs of phylogenetic distance matrices, and has numerous advantages over existing methods of coevolution detection. However, these advantages came at the cost of a very long execution time.</p> <p>Results</p> <p>In this paper, we show that the problem of finding the maximum submatrix reduces to a multiple maximum clique subproblem on a graph of protein pairs. This allowed us to develop a new algorithm and program implementation, MMMvII, which achieved more than 600× speedup with comparable accuracy to the original MMM.</p> <p>Conclusions</p> <p>MMMvII will thus allow for more more extensive and intricate analyses of coevolution.</p> <p>Availability</p> <p>An implementation of the MMMvII algorithm is available at: <url>http://www.uhnresearch.ca/labs/tillier/MMMWEBvII/MMMWEBvII.php</url></p

Extraordinarily high biomass benthic community on Southern Ocean seamounts

We describe a previously unknown assemblage of seamount-associated megabenthos that has by far the highest peak biomass reported in the deep-sea outside of vent communities. The assemblage was found at depths of 2–2.5 km on rocky geomorphic features off the southeast coast of Australia, in an area near the Sub-Antarctic Zone characterised by high rates of surface productivity and carbon export to the deep-ocean. These conditions, and the taxa in the assemblage, are widely distributed around the Southern mid-latitudes, suggesting the high-biomass assemblage is also likely to be widespread. The role of this assemblage in regional ecosystem and carbon dynamics and its sensitivities to anthropogenic impacts are unknown. The discovery highlights the lack of information on deep-sea biota worldwide and the potential for unanticipated impacts of deep-sea exploitation

Physicochemical Characteristics and Lipid Oxidation of Chicken Inner Fillets Subjected to Different Thermal Processing Types

ABSTRACT The objective of this study was to evaluate the effects of different types of thermal processing on the physiochemical characteristics and lipid oxidation of chicken inner fillets. The study was divided into three assays. In the first assay, 50 chicken inner fillets were divided into five treatments, totaling 10 samples per treatment. Treatments consisted in cooking in water bath, electric oven, microwave oven, deep frying, or grilling. The analyzed variables were: cooking weight loss (CWL) and lipid oxidation determined by thiobarbituric acid reactive substances (TBARS). In the second assay, 50 chicken inner fillets were divided into five treatments, totaling 10 samples per treatment. Each treatment consisted of the same cooking methods applied in the first assay, and storage for 48 hours under refrigeration and reheating in a microwave oven. The variable analyzed in the second assay was lipid oxidation (TBARS). In the third assay, 30 samples of chicken inner fillets were subjected to one, four and eight freeze-thaw cycles, after which meat pH, myofibrillar fragmentation index (MFI), water retention capacity (WRC), and lipid oxidation (TBARS) were determined. Chicken inner fillets submitted to deep frying and cooked in a microwave oven presented greater lipid oxidation than the other cooking methods, and deep frying resulted in the highest cooking weight loss. Reheating chicken inner fillets in a microwave oven caused the highest meat lipid oxidation. Increasing the number of freeze-thaw cycles increases the pH, MFI, WRC and TBARS values of chicken inner fillets

Acceptability of HIV self-sampling kits (TINY vial) among people of black African ethnicity in the UK: a qualitative study

Background: Increasing routine HIV testing among key populations is a public health imperative, so improving access to acceptable testing options for those in need is a priority. Despite increasing targeted distribution and uptake of HIV self-sampling kits (SSKs) among men who have sex with men in the UK, little is known about why targeted SSK interventions for black African users are not as wide-spread or well-used. This paper addresses this key gap, offering insight into why some groups may be less likely than others to adopt certain types of SSK interventions in particular contexts. These data were collected during the development phase of a larger study to explore the feasibility and acceptability of targeted distribution of SSKs to black African people. Methods: We undertook 6 focus groups with members of the public who self-identified as black African (n = 48), 6 groups with specialists providing HIV and social services to black African people (n = 53), and interviews with HIV specialist consultants and policy-makers (n = 9). Framework analysis was undertaken, using inductive and deductive analysis to develop and check themes. Results: We found three valuable components of targeted SSK interventions for this population: the use of settings and technologies that increase choice and autonomy; targeted offers of HIV testing that preserve privacy and do not exacerbate HIV stigma; and ensuring that the specific kit being used (in this case, the TINY vial) is perceived as simple and reliable. Conclusions: This unique and rigorous research offers insights into participants’ views on SSK interventions, offering key considerations when targeting this population.. Given the plethora of HIV testing options, our work demonstrates that those commissioning and delivering SSK interventions will need to clarify (for users and providers) how each kit type and intervention design adds value. Most significantly, these findings demonstrate that without a strong locus of control over their own circumstances and personal information, black African people are less likely to feel that they can pursue an HIV test that is safe and secure. Thus, where profound social inequalities persist, so will inequalities in HIV testing uptake – by any means

Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms

Copyright: © 2015 Solà et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article

Diversity of Zoanthids (Anthozoa: Hexacorallia) on Hawaiian Seamounts: Description of the Hawaiian Gold Coral and Additional Zoanthids

The Hawaiian gold coral has a history of exploitation from the deep slopes and seamounts of the Hawaiian Islands as one of the precious corals commercialised in the jewellery industry. Due to its peculiar characteristic of building a scleroproteic skeleton, this zoanthid has been referred as Gerardia sp. (a junior synonym of Savalia Nardo, 1844) but never formally described or examined by taxonomists despite its commercial interest. While collection of Hawaiian gold coral is now regulated, globally seamounts habitats are increasingly threatened by a variety of anthropogenic impacts. However, impact assessment studies and conservation measures cannot be taken without consistent knowledge of the biodiversity of such environments. Recently, multiple samples of octocoral-associated zoanthids were collected from the deep slopes of the islands and seamounts of the Hawaiian Archipelago. The molecular and morphological examination of these zoanthids revealed the presence of at least five different species including the gold coral. Among these only the gold coral appeared to create its own skeleton, two other species are simply using the octocoral as substrate, and the situation is not clear for the final two species. Phylogenetically, all these species appear related to zoanthids of the genus Savalia as well as to the octocoral-associated zoanthid Corallizoanthus tsukaharai, suggesting a common ancestor to all octocoral-associated zoanthids. The diversity of zoanthids described or observed during this study is comparable to levels of diversity found in shallow water tropical coral reefs. Such unexpected species diversity is symptomatic of the lack of biological exploration and taxonomic studies of the diversity of seamount hexacorals

Serum Amyloid Alpha Is Downregulated in Peripheral Tissues of Parkinson’s Disease Patients

We report the changed levels of serum amyloid alpha, an immunologically active protein, in Parkinson’s disease (PD) patients’ peripheral tissues. We have previously shown that Saa-1 and -2 (serum amyloid alpha-1,-2, genes) were among the top downregulated genes in PD patients’ skin, using whole-genome RNA sequencing. In the current study, we characterized the gene and protein expression profiles of skin and blood samples from patients with confirmed PD diagnosis and age/sex matched controls. qRT-PCR analysis of PD skin demonstrated downregulation of Saa-1 and -2 genes in PD patients. However, the lowered amount of protein could not be visualized using immunohistochemistry, due to low quantity of SAA (Serum Amyloid Alpha, protein) in skin. Saa-1 and -2 expression levels in whole blood were below detection threshold based on RNA sequencing, however significantly lowered protein levels of SAA1/2 in PD patients’ serum were shown with ELISA, implying that SAA is secreted into the blood. These results show that SAA is differentially expressed in the peripheral tissues of PD patients