Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer.

We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival. mRNA expression clustering refined prior clustering analyses and identified a poor-survival "neuronal" subtype in which the majority of tumors lacked small cell or neuroendocrine histology. Clustering by mRNA, long non-coding RNA (lncRNA), and miRNA expression converged to identify subsets with differential epithelial-mesenchymal transition status, carcinoma in situ scores, histologic features, and survival. Our analyses identified 5 expression subtypes that may stratify response to different treatments.

Bridge: A New Algorithm for Rooting Orthologous Genes in Large-Scale Evolutionary Analyses.

Orthology information has been used for searching patterns in high-dimensional data, allowing transferring functional information between species. The key concept behind this strategy is that orthologous genes share ancestry to some extent. While reconstructing the history of a single gene is feasible with the existing computational resources, the reconstruction of entire biological systems remains challenging. In this study, we present Bridge, a new algorithm designed to infer the evolutionary root of orthologous genes in large-scale evolutionary analyses. The Bridge algorithm infers the evolutionary root of a given gene based on the distribution of its orthologs in a species tree. The Bridge algorithm is implemented in R and can be used either to assess genetic changes across the evolutionary history of orthologous groups or to infer the onset of specific traits in a biological system.

spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.

MOTIVATION: Cancer is one of the leading causes of death worldwide. Despite significant improvements in prevention and treatment, mortality remains high for many cancer types. Hence, innovative methods that use molecular data to stratify patients and identify biomarkers are needed. Promising biomarkers can also be inferred from competing endogenous RNA (ceRNA) networks that capture the gene-miRNA gene regulatory landscape. Thus far, the role of these biomarkers could only be studied globally but not in a sample-specific manner. To mitigate this, we introduce spongEffects, a novel method that infers subnetworks (or modules) from ceRNA networks and calculates patient- or sample-specific scores related to their regulatory activity. RESULTS: We show how spongEffects can be used for downstream interpretation and machine learning tasks such as tumor classification and for identifying subtype-specific regulatory interactions. In a concrete example of breast cancer subtype classification, we prioritize modules impacting the biology of the different subtypes. In summary, spongEffects prioritizes ceRNA modules as biomarkers and offers insights into the miRNA regulatory landscape. Notably, these module scores can be inferred from gene expression data alone and can thus be applied to cohorts where miRNA expression information is lacking. AVAILABILITY AND IMPLEMENTATION: https://bioconductor.org/packages/devel/bioc/html/SPONGE.html.

Towards a unified vision on animal navigation.

The study of animal navigation is a complex and fertile field of research: Several questions regarding how animals relate to external stimuli, integrating them to perform their everyday movement routine, have been or are being addressed in different organisms and taxa, both from the behavioural and the neuronal activity point of view. Several invertebrate model organisms are the object of studies aimed at unravelling how they navigate and their ability to precisely return to a starting point and also how navigational information is communicated to conspecifics when precise social structures are present. Also, vertebrates are studied because of the interest in their orientation abilities while migrating, homing over impressive distances and studying exploration, orientation and space recognition. Last, research on the navigation capabilities of humans pursues a better understanding of the neural architecture involved in these processes in the remarkable effort to find answers and possible solutions to impairments, lesions and diseases. However, an 'all-inclusive' vision of navigation still appears to be in its embryonic state: A better perspective could (and should) shift from a paradigm where single research teams are centred on studying navigation in a single genus or species towards a more comprehensive evolutionary-centred view, searching systematically for behavioural analogies, and possibly for homologies in neural architecture between different taxa. In this review, we introduce examples of relevant topics in animal navigation from distinct animal groups, highlighting the similar approaches of those studies, and why, in our opinion, this research field could profit from a 'new' perspective.

TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves.

MOTIVATION: Dendrogram is a classical diagram for visualizing binary trees. Although efficient to represent hierarchical relations, it provides limited space for displaying information on the leaf elements, especially for large trees. RESULTS: Here, we present TreeAndLeaf, an R/Bioconductor package that implements a hybrid layout strategy to represent tree diagrams with focus on the leaves. The TreeAndLeaf package combines force-directed graph and tree layout algorithms using a single visualization system, allowing projection of multiple layers of information onto a graph-tree diagram. The Supplementary Information provides two case studies that use breast cancer data from epidemiological and experimental studies. AVAILABILITY AND IMPLEMENTATION: TreeAndLeaf is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/TreeAndLeaf/ (version≥1.4.2). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Hsp65-producing Lactococcus lactis inhibits experimental autoimmune encephalomyelitis by preventing cell migration into spinal cord.

Multiple sclerosis is an autoimmune disease that affects the central nervous system. Because of its complexity and the difficulty to treat, searching for immunoregulatory responses that reduce the clinical signs of disease by non-aggressive mechanisms and without adverse effects is a scientific challenge. Herein we propose a protocol of oral tolerance induction that prevented and controlled MOG-induced experimental autoimmune encephalomyelitis (EAE) in C57BL/6 mice. The genetically modified strain HSP65-producing Lactococcus lactis was orally administered for 5 consecutive days either before or during disease development in mice. Both protocols of feeding HSP65 resulted in significant reduction in the clinical score of EAE. Frequencies of LAP+CD4+Foxp3- regulatory T cells were higher in spleens and inguinal lymph nodes of fed mice. In addition, intravital microscopy showed that adherence of leukocytes to venules in the spinal cord was reduced in orally treated mice. Oral treatment with HSP65-producing L.lactis prevented leukocytes to leave the secondary lymphoid organs, therefore they could not reach the central nervous system. Despite the inhibition of pathological immune response that drive EAE development, activated T cells were at normal frequencies suggesting that oral tolerance did not induce general immunosuppression, but it led to specific control of pathogenic T cells. Our results indicate a novel therapeutic strategy to prevent and control autoimmune diseases such as multiple sclerosis.

Anorectic effect of COR659 in a rat model of overeating.

COR659 is a new compound, the action of which is exerted via a dual mechanism: positive allosteric modulation of the GABAB receptor; antagonism or inverse agonism at the cannabinoid CB1 receptor. Recent lines of experimental evidence have indicated that COR659 potently and effectively reduced operant self-administration of and reinstatement of seeking behaviour for a chocolate-flavoured beverage. The present study was designed to assess whether the ability of COR659 to diminish these addictive-like, food-motivated behaviours extended to a rat model of overeating palatable food. To this end, rats were habituated to feed on a standard rat chow for 3 h/day; every 4 days, the 3-hour chow-feeding session was followed by a 1-hour feeding session with highly palatable, calorie-rich Danish butter cookies. Even though satiated, rats overconsumed cookies. COR659 (0, 2.5, 5, and 10 mg/kg, i.p.) was administered before the start of the cookie-feeding session. Treatment with all 3 doses of COR659 produced a substantial decrease in intake of cookies and calories from cookies. These results extend the anorectic profile of COR659 to overconsumption of a highly palatable food and intake of large amounts of unnecessary calories.

Alternative metabolic pathways and strategies to high-titre terpenoid production in Escherichia coli.

Covering: up to 2021Terpenoids are a diverse group of chemicals used in a wide range of industries. Microbial terpenoid production has the potential to displace traditional manufacturing of these compounds with renewable processes, but further titre improvements are needed to reach cost competitiveness. This review discusses strategies to increase terpenoid titres in Escherichia coli with a focus on alternative metabolic pathways. Alternative pathways can lead to improved titres by providing higher orthogonality to native metabolism that redirects carbon flux, by avoiding toxic intermediates, by bypassing highly-regulated or bottleneck steps, or by being shorter and thus more efficient and easier to manipulate. The canonical 2-C-methyl-D-erythritol 4-phosphate (MEP) and mevalonate (MVA) pathways are engineered to increase titres, sometimes using homologs from different species to address bottlenecks. Further, alternative terpenoid pathways, including additional entry points into the MEP and MVA pathways, archaeal MVA pathways, and new artificial pathways provide new tools to increase titres. Prenyl diphosphate synthases elongate terpenoid chains, and alternative homologs create orthogonal pathways and increase product diversity. Alternative sources of terpenoid synthases and modifying enzymes can also be better suited for E. coli expression. Mining the growing number of bacterial genomes for new bacterial terpenoid synthases and modifying enzymes identifies enzymes that outperform eukaryotic ones and expand microbial terpenoid production diversity. Terpenoid removal from cells is also crucial in production, and so terpenoid recovery and approaches to handle end-product toxicity increase titres. Combined, these strategies are contributing to current efforts to increase microbial terpenoid production towards commercial feasibility.

Structural Chirality of Polar Skyrmions Probed by Resonant Elastic X-Ray Scattering.

An escalating challenge in condensed-matter research is the characterization of emergent order-parameter nanostructures such as ferroelectric and ferromagnetic skyrmions. Their small length scales coupled with complex, three-dimensional polarization or spin structures makes them demanding to trace out fully. Resonant elastic x-ray scattering (REXS) has emerged as a technique to study chirality in spin textures such as skyrmions and domain walls. It has, however, been used to a considerably lesser extent to study analogous features in ferroelectrics. Here, we present a framework for modeling REXS from an arbitrary arrangement of charge quadrupole moments, which can be applied to nanostructures in materials such as ferroelectrics. With this, we demonstrate how extended reciprocal space scans using REXS with circularly polarized x rays can probe the three-dimensional structure and chirality of polar skyrmions. Measurements, bolstered by quantitative scattering calculations, show that polar skyrmions of mixed chirality coexist, and that REXS allows valuation of relative fractions of right- and left-handed skyrmions. Our quantitative analysis of the structure and chirality of polar skyrmions highlights the capability of REXS for establishing complex topological structures toward future application exploits.

Blockade of the GABAB receptor suppressed alcohol self-administration in rats: an effect similar to that produced by GABAB receptor activation.

Literature data suggest that activation and blockade of the GABAB receptor may produce similar effects on several reward-related behaviours. Accordingly, the present study was designed to investigate whether treatment with the GABAB receptor antagonist, SCH 50911, reproduced the suppressing effect of the GABAB receptor agonist, baclofen, and several positive allosteric modulators of the GABAB receptor on operant oral alcohol self-administration in rats. To this end, Sardinian alcohol-preferring (sP) rats were trained to lever-respond for alcohol (15% v/v) under the fixed ratio (FR) 4 (FR4) schedule of reinforcement. Once lever-responding had stabilized, rats were exposed to test sessions preceded by treatment with SCH 50911 (0, 25, 50, and 100 mg/kg; i.p.). Two independent experiments were conducted, differing solely in the set of rats used. Selectivity of SCH 50911 effect on alcohol self-administration was assessed by evaluating the effect of SCH 50911 (0, 25, 50, and 100 mg/kg; i.p.) on self-administration of a sucrose solution (0.7% w/v) in sP rats exposed to the FR4 schedule. In both 'alcohol' experiments, treatment with SCH 50911 reduced lever-responding for alcohol and amount of self-administered alcohol. SCH 50911 effect was characterized by large interindividual variability, with several instances of dose-unrelated reductions, and frequent occurrence of complete suppression of lever-responding for alcohol. Similar data were collected in the 'sucrose' experiment. These results extend to alcohol self-administration with the notion that activation and blockade of GABAB receptor may produce unidirectional effects on reward-related behaviours; these similarities are discussed in terms of differential contribution of pre- and postsynaptic GABAB receptors.

The Effects of Physical Fitness on Postactivation Potentiation in Professional Soccer Athletes.

ABSTRACT: Guerra, MA Jr, Caldas, LA, Souza, HL, Tallis, J, Duncan, MJ, and Guimarães-Ferreira, L. The effects of physical fitness on postactivation potentiation in professional soccer athletes. J Strength Cond Res 36(6): 1643-1647, 2022-To investigate the relationship of the response to postactivation potentiation (PAP) with scores of physical fitness. Twenty-four professional male soccer players undertook tests of agility, muscular power, aerobic capacity, and body composition. Conditioning activities (CAs) were performed consisting of plyometrics exercises and sprints with sled towing. In the first and second sessions, body composition, agility, power, and aerobic capacity were assessed. At the third session, countermovement jumps (CMJ) were performed with 1, 3, and 5 minutes after the execution of the CA. Significant differences were found for CMJ height 1, 3, and 5 minutes after the CA compared with baseline values (3.58, 5.10, 5.48%, respectively). There was a significant positive correlation between the level of general physical fitness and PAP (CMJ height increase) 5 minutes after (r = 0.73). When the athletes were divided into groups with higher and lower physical fitness, the CA caused a significant increase in CMJ height in both groups, but a significant difference (p < 0.05) was observed at all times after PAP induction, with better performance in higher versus lower fitness level. The results suggest that plyometrics exercises associated with sled towing sprints as a CA result in an increase in CMJ performance in athletes and that physical fitness directly influences the PAP occurrence, with higher fit players demonstrating an enhanced PAP response.

Essential oil of Aloysia citriodora Paláu and citral: sedative and anesthetic efficacy and safety in Rhamdia quelen and Ctenopharyngodon idella.

OBJECTIVE: To verify the efficacy of citral in inducing sedation and anesthesia in silver catfish (Rhamdia quelen) and grass carp (Ctenopharyngodon idella) and to assess the safety of essential oil (EO) of Aloysia citriodora and citral in inducing and maintaining anesthesia in silver catfish. STUDY DESIGN: Clinical study, randomized, parallel, multi-arm with control group in target species. ANIMALS: A total of 96 juvenile and 72 adult silver catfish and 80 juvenile grass carp were used. METHODS: Silver catfish and grass carp were exposed to different concentrations of citral, 15-675 and 15-600 µL L-1, respectively, during the maximum period of 30 minutes to verify sedation and anesthesia induction and recovery times. In addition, for anesthetic induction, silver catfish were exposed to the EO of A. citriodora and citral at 225 µL L-1 for 3.5 minutes. Then, fish were transferred to an anesthesia maintenance solution at 50 µL L-1 for 10 minutes to assess hematologic and biochemical variables at 60 minutes, 2 and 6 days after treatment. RESULTS: Citral only induced sedation from 15, 25 and 40 µLL-1 in both species. Anesthesia without mortality was induced in silver catfish at 50-600 µL L-1 and grass carp at 75-450 µL L-1. At 675 and 600 µL L-1, mortality was recorded in silver catfish and grass carp, respectively. The EO of A. citriodora and citral were safe in inducing and maintaining anesthesia in silver catfish, with mean corpuscular hemoglobin concentration being the only variable that varied in relation to time and treatments. CONCLUSIONS AND CLINICAL RELEVANCE: Citral was effective in inducing sedation and anesthesia in both species. In addition, A. citriodora EO and citral were safe in inducing and maintaining anesthesia in silver catfish. Both agents are promising substances for the development of new drugs for fish.

Novel lncRNAs Co-Expression Networks Identifies LINC00504 with Oncogenic Role in Luminal A Breast Cancer Cells.

Long non-coding RNAs (lncRNAs) are functional transcripts with more than 200 nucleotides. These molecules exhibit great regulatory capacity and may act at different levels of gene expression regulation. Despite this regulatory versatility, the biology of these molecules is still poorly understood. Computational approaches are being increasingly used to elucidate biological mechanisms in which these lncRNAs may be involved. Co-expression networks can serve as great allies in elucidating the possible regulatory contexts in which these molecules are involved. Herein, we propose the use of the pipeline deposited in the RTN package to build lncRNAs co-expression networks using TCGA breast cancer (BC) cohort data. Worldwide, BC is the most common cancer in women and has great molecular heterogeneity. We identified an enriched co-expression network for the validation of relevant cell processes in the context of BC, including LINC00504. This lncRNA has increased expression in luminal subtype A samples, and is associated with prognosis in basal-like subtype. Silencing this lncRNA in luminal A cell lines resulted in decreased cell viability and colony formation. These results highlight the relevance of the proposed method for the identification of lncRNAs in specific biological contexts.

Is BMI a Factor in Compliance to Adjuvant Chemotherapy for Locally Advanced Rectal Cancer?

Background: Compliance to adjuvant chemotherapy (AC) for patients undergoing rectal surgery ranges from 43% to 73.6%. Reasons reported for not initiating or completing AC include onset of postoperative complications, drug toxicity, disease progression and/or patient preferences. Little is known regarding the impact of obesity on the compliance to AC in this setting. Methods: This multicenter, retrospective study analyzed compliance to AC and treatment-related morbidity in 511 patients having undergone surgery with curative intent for rectal cancer in six Italian colorectal centers between January 2013 and December 2017. Results: 70 patients were obese (BMI 30 kg/m2). The proportion of open procedures (22.9% vs. 13.4%) and conversions (14.3% vs. 4.8%) was greater in obese compared to non-obese patients (p 0.001). Median hospital stay was one day longer for obese patients (9 days vs. 10 days, p=0.038) while there was no statistically significant difference in the complication rate, whether overall (58.6% in obese vs. 52.3% in non-obese) or with a Clavien-Dindo score 3 (17.1% vs 10.9%). AC was offered to 49/70 (70%) patients in the obese group and 306/441 (69.4%) in the non-obese group (p=0.43). There was no statistically significant difference in AC compliance: 18.4% and 22.9% did not start AC, while 36.7% and 34.6%, started AC but did not complete the scheduled treatment (p=0.79) in the obese and non-obese group, respectively. Overall, 55% of patients who started AC successfully completed their adjuvant treatment. Conclusions: Obesity did not impact compliance to AC for locally advanced rectal cancer: compliance was poor in obese and non-obese patients with no statistically significant difference between the two groups. Major complication rate was not statistically significantly affected by increased BMI.

Trauma Prehospital Hypothermia Prevention and Treatment: An Observational Study.

BACKGROUND: Hypothermia in trauma patients causes increased morbidity and mortality. Swift recognition and treatment are important to prevent any further heat loss. In addition, patient discomfort from cold decreases satisfaction with care. The administration of active and passive rewarming measures is important in the prevention and treatment of hypothermia, but their use in prehospital trauma patients in Portugal has not been previously reported. OBJECTIVE: To assess the prevalence of hypothermia, the impact of rewarming measures, and the management of the discomfort caused by cold. METHODS: This is a prospective cohort study conducted in Immediate Life Support Ambulances in Portugal between March 1, 2019, and April 30, 2020. RESULTS: This study included records of 586 trauma patients; of whom, 66.2% were men. Cranioencephalic trauma was the most common trauma observed, followed by lower limb and thoracic traumas. Mean body temperature increased 0.12 °C between the first and last assessments (p < .05). Most patients experiencing a level of discomfort of 5 or more on a 0-10 scale reported improvement (from 17.2% to 2.4% after nurses' intervention). Warmed intravenous fluids proved to be effective (p < .05) in increasing body temperature, and passive rewarming measures were effective in preventing hypothermia. CONCLUSIONS: Hypothermia management has to consider the initial temperature, the season, the available rewarming measures, and the objectives to be achieved. The optimization of resources for the monitoring and treatment of hypothermia should be a priority in prehospital assistance. The implementation of rewarming measures improves patients' outcomes and decreases the discomfort caused by cold in prehospital care.

Rotaxanating Metallo-supramolecular Nano-cylinder Helicates to Switch DNA Junction Binding.

A class of rotaxane is created, not by encapsulating a conventional linear thread, but rather by wrapping a large cucurbit[10]uril macrocycle about a three-dimensional, cylindrical, nanosized, self-assembled supramolecular helicate as the axle. The resulting pseudo-rotaxane is readily converted into a proper interlocked rotaxane by adding branch points to the helicate strands that form the surface of the cylinder (like branches and roots on a tree trunk). The supramolecular cylinder that forms the axle is itself a member of a unique and remarkable class of helicate metallo-drugs that bind Y-shaped DNA junction structures and induce cell death. While pseudo-rotaxanation does not modify the DNA-binding properties, proper, mechanically-interlocked rotaxanation transforms the DNA-binding and biological activity of the cylinder. The ability of the cylinder to de-thread from the rotaxane (and thus to bind DNA junction structures) is controlled by the extent of branching: fully-branched cylinders are locked inside the cucurbit[10]uril macrocycle, while cylinders with incomplete branch points can de-thread from the rotaxane in response to competitor guests. The number of branch points can thus afford kinetic control over the drug de-threading and release.

RTNsurvival: an R/Bioconductor package for regulatory network survival analysis.

MOTIVATION: Transcriptional networks are models that allow the biological state of cells or tumours to be described. Such networks consist of connected regulatory units known as regulons, each comprised of a regulator and its targets. Inferring a transcriptional network can be a helpful initial step in characterizing the different phenotypes within a cohort. While the network itself provides no information on molecular differences between samples, the per-sample state of each regulon, i.e. the regulon activity, can be used for describing subtypes in a cohort. Integrating regulon activities with clinical data and outcomes would extend this characterization of differences between subtypes. RESULTS: We describe RTNsurvival, an R/Bioconductor package that calculates regulon activity profiles using transcriptional networks reconstructed by the RTN package, gene expression data, and a two-tailed Gene Set Enrichment Analysis. Given regulon activity profiles across a cohort, RTNsurvival can perform Kaplan-Meier analyses and Cox Proportional Hazards regressions, while also considering confounding variables. The Supplementary Information provides two case studies that use data from breast and liver cancer cohorts and features uni- and multivariate regulon survival analysis. AVAILABILITY AND IMPLEMENTATION: RTNsurvival is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/RTNsurvival/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons.

MOTIVATION: Transcription factors (TFs) are key regulators of gene expression, and can activate or repress multiple target genes, forming regulatory units, or regulons. Understanding downstream effects of these regulators includes evaluating how TFs cooperate or compete within regulatory networks. Here we present RTNduals, an R/Bioconductor package that implements a general method for analyzing pairs of regulons. RESULTS: RTNduals identifies a dual regulon when the number of targets shared between a pair of regulators is statistically significant. The package extends the RTN (Reconstruction of Transcriptional Networks) package, and uses RTN transcriptional networks to identify significant co-regulatory associations between regulons. The Supplementary Information reports two case studies for TFs using the METABRIC and TCGA breast cancer cohorts. AVAILABILITY AND IMPLEMENTATION: RTNduals is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/RTNduals/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Purinergic signaling and gene expression of purinoceptors in the head kidney of the silver catfish Rhamdia quelen experimentally infected by Flavobacterium columnare.

The head kidney is a lymphoid immune organ that plays a key role in the immune and inflammatory responses of teleost fish. It is associated with immunoglobulin G production and differentiation of B cells. The presence of a multi-enzymatic complex found anchored in the plasma membrane makes the head kidney an important purinergic-dependent tissue. Purinergic signaling has been associated with these responses under pathological conditions via regulation of extracellular adenosine triphosphate (ATP), the main damage molecular associated pattern agent released during bacterial infections. The aim of this study was to determine whether purinergic signaling is a pathway associated with impairment of immune responses in silver catfish (Rhamdia quelen) experimentally infected by Flavobacterium columnare, as well as to evaluate the role of P2 purine receptors in this response. Triphosphate diphosphohydrolase (NTPDase) activity in the head kidney was significantly lower in silver catfish experimentally-infected F. columnare 72 h post-infection (hpi) than in the control group, while no significant difference was observed with respect NTPDase activity on adenosine diphosphate, as well as on 5'-nucleotidase and adenosine deaminase activities. Extracellular ATP levels were significantly higher in the head kidney of experimentally-infected fish than in the control group at 72 hpi. Finally, p2ry11 and p2rx3 purine receptor levels were significantly higher in experimentally-infected fish than in the control group at 72 hpi. We conclude that purinergic signaling in the head kidney of silver catfish infected by F. columnare creates a pro-inflammatory profile that may contribute to impairment of immune and inflammatory responses via reduction of ATP hydrolysis and its accumulation in the extracellular milieu, accompanied by upregulation of p2ry11 and p2rx3 purine receptors, leading to pro-inflammatory status.