A Taxonomy of Causality-Based Biological Properties

We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a theoretical point of view, biochemical reactions are abstractly represented as causal implications and the produced metabolites as causal consequences of the implication representing the corresponding reaction. The fact that a reactant is produced is represented by means of the chain of reactions that have made it exist. Such representation abstracts away from quantities, stoichiometric and thermodynamic parameters and constitutes the basis for the characterization of our properties. Moreover, we propose an effective method for verifying our properties based on an abstract model of system dynamics. This consists of a new abstract semantics for the system seen as a concurrent network and expressed using the Chemical Ground Form calculus. We illustrate an application of this framework to a portion of a real metabolic pathway

PrognoScan: a new database for meta-analysis of the prognostic value of genes

<p>Abstract</p> <p>Background</p> <p>In cancer research, the association between a gene and clinical outcome suggests the underlying etiology of the disease and consequently can motivate further studies. The recent availability of published cancer microarray datasets with clinical annotation provides the opportunity for linking gene expression to prognosis. However, the data are not easy to access and analyze without an effective analysis platform.</p> <p>Description</p> <p>To take advantage of public resources in full, a database named "PrognoScan" has been developed. This is 1) a large collection of publicly available cancer microarray datasets with clinical annotation, as well as 2) a tool for assessing the biological relationship between gene expression and prognosis. PrognoScan employs the minimum <it>P</it>-value approach for grouping patients for survival analysis that finds the optimal cutpoint in continuous gene expression measurement without prior biological knowledge or assumption and, as a result, enables systematic meta-analysis of multiple datasets.</p> <p>Conclusion</p> <p>PrognoScan provides a powerful platform for evaluating potential tumor markers and therapeutic targets and would accelerate cancer research. The database is publicly accessible at <url>http://gibk21.bse.kyutech.ac.jp/PrognoScan/index.html</url>.</p

Ostomy closure rate during COVID-19 pandemic. An Italian multicentre observational study

During the corona virus disease 2019 (COVID-19) pandemic, most of the surgical procedures were performed for emergencies or oncologic reasons to the detriment of the remaining elective procedures for benign conditions. Ileostomy or colostomy creation are sequelae of oncologic or emergency colorectal surgery, but their closure does not fall within the definition of oncologic or emergency surgery. The aim of this retrospective multicentre observational study is to report the impact of COVID-19 pandemic on the ostomy closure rate in Italy. Data regarding ileostomy and colostomy creation and closure from 24 Italian centres, during the study period (March 2020–February 2021) and during the control period (March 2019–February 2020) were collected. Three hospitals (12.5%) were COVID free. The number of colostomies and ileostomies created and closed in the same period was lower (-18.8% and-30%, respectively) in the study period in comparison to the control period (p = 0.1915 and p = 0.0001, respectively), such as the ostomies closed in the analysed periods but created before (colostomy-36.2% and ileostomy-7.4%, p = 0.2211 and p = 0.1319, respectively). Overall, a 19.5% reduction in ostomies closed occurred in the study period. Based on the present study, a reduction in ostomy closure rate occurred in Italy between March 2020 and February 2021. During the pandemic, the need to change the clinical practice probably prolonged deterioration of quality of life in patients with ostomies, increasing number of stomas that will never be closed, and related management costs, even if these issues have not been investigated in this study

Low-complexity regions within protein sequences have position-dependent roles

<p>Abstract</p> <p>Background</p> <p>Regions of protein sequences with biased amino acid composition (so-called Low-Complexity Regions (LCRs)) are abundant in the protein universe. A number of studies have revealed that i) these regions show significant divergence across protein families; ii) the genetic mechanisms from which they arise lends them remarkable degrees of compositional plasticity. They have therefore proved difficult to compare using conventional sequence analysis techniques, and functions remain to be elucidated for most of them. Here we undertake a systematic investigation of LCRs in order to explore their possible functional significance, placed in the particular context of Protein-Protein Interaction (PPI) networks and Gene Ontology (GO)-term analysis.</p> <p>Results</p> <p>In keeping with previous results, we found that LCR-containing proteins tend to have more binding partners across different PPI networks than proteins that have no LCRs. More specifically, our study suggests i) that LCRs are preferentially positioned towards the protein sequence extremities and, in contrast with centrally-located LCRs, such terminal LCRs show a correlation between their lengths and degrees of connectivity, and ii) that centrally-located LCRs are enriched with transcription-related GO terms, while terminal LCRs are enriched with translation and stress response-related terms.</p> <p>Conclusions</p> <p>Our results suggest not only that LCRs may be involved in flexible binding associated with specific functions, but also that their positions within a sequence may be important in determining both their binding properties and their biological roles.</p

Epithelial-Mesenchymal Transition in Cancer: Parallels Between Normal Development and Tumor Progression

From the earliest stages of embryonic development, cells of epithelial and mesenchymal origin contribute to the structure and function of developing organs. However, these phenotypes are not always permanent, and instead, under the appropriate conditions, epithelial and mesenchymal cells convert between these two phenotypes. These processes, termed Epithelial-Mesenchymal Transition (EMT), or the reverse Mesenchymal-Epithelial Transition (MET), are required for complex body patterning and morphogenesis. In addition, epithelial plasticity and the acquisition of invasive properties without the full commitment to a mesenchymal phenotype are critical in development, particularly during branching morphogenesis in the mammary gland. Recent work in cancer has identified an analogous plasticity of cellular phenotypes whereby epithelial cancer cells acquire mesenchymal features that permit escape from the primary tumor. Because local invasion is thought to be a necessary first step in metastatic dissemination, EMT and epithelial plasticity are hypothesized to contribute to tumor progression. Similarities between developmental and oncogenic EMT have led to the identification of common contributing pathways, suggesting that the reactivation of developmental pathways in breast and other cancers contributes to tumor progression. For example, developmental EMT regulators including Snail/Slug, Twist, Six1, and Cripto, along with developmental signaling pathways including TGF-β and Wnt/β-catenin, are misexpressed in breast cancer and correlate with poor clinical outcomes. This review focuses on the parallels between epithelial plasticity/EMT in the mammary gland and other organs during development, and on a selection of developmental EMT regulators that are misexpressed specifically during breast cancer

H2S biosynthesis and catabolism: new insights from molecular studies

Hydrogen sulfide (H2S) has profound biological effects within living organisms and is now increasingly being considered alongside other gaseous signalling molecules, such as nitric oxide (NO) and carbon monoxide (CO). Conventional use of pharmacological and molecular approaches has spawned a rapidly growing research field that has identified H2S as playing a functional role in cell-signalling and post-translational modifications. Recently, a number of laboratories have reported the use of siRNA methodologies and genetic mouse models to mimic the loss of function of genes involved in the biosynthesis and degradation of H2S within tissues. Studies utilising these systems are revealing new insights into the biology of H2S within the cardiovascular system, inflammatory disease, and in cell signalling. In light of this work, the current review will describe recent advances in H2S research made possible by the use of molecular approaches and genetic mouse models with perturbed capacities to generate or detoxify physiological levels of H2S gas within tissue

The effects of shoulder load and pinch force on electromyographic activity and blood flow in the forearm during a pinch task

The object of the current study was to determine whether static contraction of proximal musculature has an effect on the blood flow more distally in the upper extremity. Static contractions of muscles in the neck shoulder region at three levels (relaxed, shoulders elevated and shoulders elevated loaded with 4.95 kg each) were combined with intermittent pinch forces at 0, 10 and 25% of the maximum voluntary contraction (MVC). Blood flow to the forearm was measured with Doppler ultrasound. Myoelectric activity of the forearm and neck-shoulder muscles was recorded to check for the workload levels. Across all levels of shoulder load, blood flow increased significantly with increasing pinch force (21% at 10% MVC and by 44% at 25% MVC). Blood flow was significantly affected by shoulder load, with the lowest blood flow at the highest shoulder load. Interactions of pinch force and shoulder load were not significant. The myoelectric activity of forearm muscles increased with increasing pinch force. The activation of the trapezius muscle decreased with increasing pinch force and increased with increasing shoulder load. The precise mechanisms accounting for the influence of shoulder load remains unclear. The results of this study indicate that shoulder load might influence blood flow to the forearm