Heterosis in yeast hybrids

We are particularly interested in the performance of the first hybrid generation (F1 hybrids), especially when hybrids are viable and able to outperform one or both parents under different environmental conditions, a phenomenon known as heterosis. The aim of our work was to understand mechanisms underlying heterosis, thus we used Saccharomyces yeasts as a model system due to their laboratory practicality, ability to form viable hybrids and reliable fitness measurements. First, we competed a range of different F1 hybrids with wild or domesticated background; we identified prevalent heterosis for crosses between domesticated and wild populations of different yeast species but not for crosses between wild populations of the same yeast species. By using monosporic clones as parental strains in heterosis studies we might be inflating heterosis measurements due to parental disadvantage and not the F1 hybrid advantage. Thus we set out to compared asexual fitness of heterozygous yeast isolates with homozygous monosporic clones for both domesticated and wild yeast populations; we found that domesticated monosporic clones have a significant decrease in fitness, which can potentially account for the difference in heterosis of D1 hybrids with a domesticated or a wild background. Finally we analysed the transcription of a representative heterotic F1 hybrid in comparison to its parents. Hybrid transcription was dynamic, resembling the fitter parent for the environments tested. For the first time to our knowledge, specific transcription at a multigenic level was identified has a source of heterosis, which render the F1 hybrid better adapted than its parents to variable environmental conditions. Heterosis studies in Saccharomyces yeasts, due to their simplicity, can evidence characteristics with an impact on heterosis while also tracing the evolutionary history of divergent populations

Genetic adaptive mechanisms mediating response and tolerance to acetic acid stress in the human pathogen Candida glabrata: role of the CgHaa1-dependent signaling pathway

The increased resilience of Candida glabrata to azoles and the continuous emergence of strains resistant to other antifungals demands the development of new therapeutic approaches focused on non-conventional biological targets. Genes contributing to increase C. glabrata competitiveness in the different infection sites are an interesting and unexplored cohort of therapeutic targets. To thrive in the vaginal tract and avoid exclusion C. glabrata cells have evolved dedicated responses rendering them capable of tolerating multiple environmental challenges, including the presence of acetic and lactic acids produced by the commensal microbiota. In this work a cohort of vaginal clinical isolates were phenotyped for their tolerance to acetic acid stress at a low pH as well as for several traits that are known to influence sensitivity to this organic acid, including the structure of the cell envelope and the ability to consume the acid in the presence of glucose. The role played by the ORF CAGL0L09339g, an homologue of the ScHaa1, a critical regulator of acetic acid resistance in S. cerevisiae[1], in C. glabrata response and tolerance to acetic acid stress at pH 4 was also scrutinized using a transcriptomic analysis. The role of CgHaa1 as well as of several of its target genes in mediating virulence of C. glabrata against epithelial vaginal cells was also studied.Funding received by the Institute for Bioengineering and Biosciences from the Portuguese Foundation for Science and Technology (FCT) (UID/BIO/04565/2013) and from Programa Operacional Regional de Lisboa 2020 (project no. 007317) is acknowledged. FCT is also acknowledged for funding the Centre of Biological Engineering through contracts FCOMP-01-0124-FEDER- 020243 and PTDC/EBB-EBI/120495/2010info:eu-repo/semantics/publishedVersio

Antimicrobial activity of propolis nanoparticles against some common meat contamination bacteria

Raw meat is a highly perishable product that requires a great amount of care, from its handling to the conservation conditions at low temperatures. The reduction of microbial proliferation in meat is necessary to achieve an increase of shelf life, food safety, while maintaining product features. For this reason, a technology based on natural antimicrobial agent may offer a potential alternative to protect and control the proliferation of microorganisms on food products. Propolis is a natural resinous substance collected from the leaf buds of different tree species by honeybees and known for its biological properties (antibacterial, antifungal, antioxidant) (Koo et. al, 2000). The aim of this work was to evaluate the antimicrobial activity of propolis nanoparticles in comparison with ethanol-propolis extract against some common meat contamination bacteria. The ethanol-propolis extract was obtained from green propolis resin, in absolute ethanol under agitation during 15 days. To obtain the propolis nanoparticles, ethanol-propolis extract at 13.75% (w/v) was mixed with polyvinyl-alcohol solution at 0.1% (w/v). Antimicrobial activity of propolis nanoparticles and ethanol-propolis extract was tested against 8 microorganisms typically present in meat. Minimum inhibitory concentrations (MIC) of both solutions were evaluated by agar-well diffusion method; all strains were susceptible and MIC values ranged from 0.57 to 2.29% (w/v) for propolis nanoparticles and from 0.68 to 6.88% (w/v) for ethanol-propolis extract. The MIC of propolis nanoparticles for Escherichia coli, Staphylococcus aureus, Salmonella thompson, Listeria monocytogenes, Enterococcus faecalis, Enterobacter helveticus, Lactobacillus bucheneri and Leuconostoc mesenteroideswas 1.15%, 0.57%, 2.29%, 1.72%, 1.72%, 2.29%, 2.29%, 1.72%, respectively, and the MIC for ethanol-propolis extract to the same species was 3.44%, 0.68%, 3.44%, 3.44%, 3.44%, 6.88%, 6.88%, 3.44%, respectively. The shown antimicrobial activity of propolis nanoparticles is of potential interest for food applications (e.g. in edible coatings formulation). Therefore, results obtained in this study, set the bases for future studies, using films as support for propolis nanoparticles, for application in meat products. References Koo, H.; Gomes, B.P.F.A.; Rosalen, P. L.; Ambrosano, G.M.B.; Park, Y. K.; Cury, J. A. (2000) In vitro antimicrobial activity of propolis and Arnica montana against oral pathogens. Archives of Oral Biology 45: 141-14

Swarm Learning for decentralized and confidential clinical machine learning

Fast and reliable detection of patients with severe and heterogeneous illnesses is a major goal of precision medicine1,2. Patients with leukaemia can be identified using machine learning on the basis of their blood transcriptomes3. However, there is an increasing divide between what is technically possible and what is allowed, because of privacy legislation4,5. Here, to facilitate the integration of any medical data from any data owner worldwide without violating privacy laws, we introduce Swarm Learning—a decentralized machine-learning approach that unites edge computing, blockchain-based peer-to-peer networking and coordination while maintaining confidentiality without the need for a central coordinator, thereby going beyond federated learning. To illustrate the feasibility of using Swarm Learning to develop disease classifiers using distributed data, we chose four use cases of heterogeneous diseases (COVID-19, tuberculosis, leukaemia and lung pathologies). With more than 16,400 blood transcriptomes derived from 127 clinical studies with non-uniform distributions of cases and controls and substantial study biases, as well as more than 95,000 chest X-ray images, we show that Swarm Learning classifiers outperform those developed at individual sites. In addition, Swarm Learning completely fulfils local confidentiality regulations by design. We believe that this approach will notably accelerate the introduction of precision medicine

Swarm Learning for decentralized and confidential clinical machine learning

Fast and reliable detection of patients with severe and heterogeneous illnesses is a major goal of precision medicine. Patients with leukaemia can be identified using machine learning on the basis of their blood transcriptomes. However, there is an increasing divide between what is technically possible and what is allowed, because of privacy legislation. Here, to facilitate the integration of any medical data from any data owner worldwide without violating privacy laws, we introduce Swarm Learning—a decentralized machine-learning approach that unites edge computing, blockchain-based peer-to-peer networking and coordination while maintaining confidentiality without the need for a central coordinator, thereby going beyond federated learning. To illustrate the feasibility of using Swarm Learning to develop disease classifiers using distributed data, we chose four use cases of heterogeneous diseases (COVID-19, tuberculosis, leukaemia and lung pathologies). With more than 16,400 blood transcriptomes derived from 127 clinical studies with non-uniform distributions of cases and controls and substantial study biases, as well as more than 95,000 chest X-ray images, we show that Swarm Learning classifiers outperform those developed at individual sites. In addition, Swarm Learning completely fulfils local confidentiality regulations by design. We believe that this approach will notably accelerate the introduction of precision medicine

How can we improve the success of cardiac resynchronization therapy implantation?

© The Author(s) 2019.Introduction: The left ventricular (LV) lead implantation in cardiac resynchronization therapy (CRT) is one of the most important and complex steps, leading to implantation failure in 10–15% of cases. New LV lead implantation techniques are needed to allow better resynchronization and decrease mortality and hospitalizations. Objectives: To evaluate the efficacy and safety of the snare technique in the LV lead implantation in cases of standard technique failure.info:eu-repo/semantics/publishedVersio

Activating Transcription Factor 6 Mediates Inflammatory Signals in Intestinal Epithelial Cells Upon Endoplasmic Reticulum Stress.

BACKGROUND & AIMS: Excess and unresolved endoplasmic reticulum (ER) stress in intestinal epithelial cells (IECs) promotes intestinal inflammation. Activating transcription factor 6 (ATF6) is one of the signaling mediators of ER stress. We studied the pathways that regulate ATF6 and its role for inflammation in IECs. METHODS: We performed an RNA interference screen, using 23,349 unique small interfering RNAs targeting 7783 genes and a luciferase reporter controlled by an ATF6-dependent ERSE (ER stress-response element) promoter, to identify proteins that activate or inhibit the ATF6 signaling pathway in HEK293 cells. To validate the screening results, intestinal epithelial cell lines (Caco-2 cells) were transfected with small interfering RNAs or with a plasmid overexpressing a constitutively active form of ATF6. Caco-2 cells with a CRISPR-mediated disruption of autophagy related 16 like 1 gene (ATG16L1) were used to study the effect of ATF6 on ER stress in autophagy-deficient cells. We also studied intestinal organoids derived from mice that overexpress constitutively active ATF6, from mice with deletion of the autophagy related 16 like 1 or X-Box binding protein 1 gene in IECs (Atg16l1ΔIEC or Xbp1ΔIEC, which both develop spontaneous ileitis), from patients with Crohn's disease (CD) and healthy individuals (controls). Cells and organoids were incubated with tunicamycin to induce ER stress and/or chemical inhibitors of newly identified activator proteins of ATF6 signaling, and analyzed by real-time polymerase chain reaction and immunoblots. Atg16l1ΔIEC and control (Atg16l1fl/fl) mice were given intraperitoneal injections of tunicamycin and were treated with chemical inhibitors of ATF6 activating proteins. RESULTS: We identified and validated 15 suppressors and 7 activators of the ATF6 signaling pathway; activators included the regulatory subunit of casein kinase 2 (CSNK2B) and acyl-CoA synthetase long chain family member 1 (ACSL1). Knockdown or chemical inhibition of CSNK2B and ACSL1 in Caco-2 cells reduced activity of the ATF6-dependent ERSE reporter gene, diminished transcription of the ATF6 target genes HSP90B1 and HSPA5 and reduced NF-κB reporter gene activation on tunicamycin stimulation. Atg16l1ΔIEC and or Xbp1ΔIEC organoids showed increased expression of ATF6 and its target genes. Inhibitors of ACSL1 or CSNK2B prevented activation of ATF6 and reduced CXCL1 and tumor necrosis factor (TNF) expression in these organoids on induction of ER stress with tunicamycin. Injection of mice with inhibitors of ACSL1 or CSNK2B significantly reduced tunicamycin-mediated intestinal inflammation and IEC death and expression of CXCL1 and TNF in Atg16l1ΔIEC mice. Purified ileal IECs from patients with CD had higher levels of ATF6, CSNK2B, and HSPA5 messenger RNAs than controls; early-passage organoids from patients with active CD show increased levels of activated ATF6 protein, incubation of these organoids with inhibitors of ACSL1 or CSNK2B reduced transcription of ATF6 target genes, including TNF. CONCLUSIONS: Ileal IECs from patients with CD have higher levels of activated ATF6, which is regulated by CSNK2B and HSPA5. ATF6 increases expression of TNF and other inflammatory cytokines in response to ER stress in these cells and in organoids from Atg16l1ΔIEC and Xbp1ΔIEC mice. Strategies to inhibit the ATF6 signaling pathway might be developed for treatment of inflammatory bowel diseases

Targeted deletion of von-Hippel-Lindau in the proximal tubule conditions the kidney against early diabetic kidney disease.

peer reviewedDiabetic kidney disease (DKD) is the leading cause of end-stage renal disease. Glomerular hyperfiltration and albuminuria subject the proximal tubule (PT) to a subsequent elevation of workload, growth, and hypoxia. Hypoxia plays an ambiguous role in the development and progression of DKD and shall be clarified in our study. PT-von-Hippel-Lindau (Vhl)-deleted mouse model in combination with streptozotocin (STZ)-induced type I diabetes mellitus (DM) was phenotyped. In contrary to PT-Vhl-deleted STZ-induced type 1 DM mice, proteinuria and glomerular hyperfiltration occurred in diabetic control mice the latter due to higher nitric oxide synthase 1 and sodium and glucose transporter expression. PT Vhl deletion and DKD share common alterations in gene expression profiles, including glomerular and tubular morphology, and tubular transport and metabolism. Compared to diabetic control mice, the most significantly altered in PT Vhl-deleted STZ-induced type 1 DM mice were Ldc-1, regulating cellular oxygen consumption rate, and Zbtb16, inhibiting autophagy. Alignment of altered genes in heat maps uncovered that Vhl deletion prior to STZ-induced DM preconditioned the kidney against DKD. HIF-1α stabilization leading to histone modification and chromatin remodeling resets most genes altered upon DKD towards the control level. These data demonstrate that PT HIF-1α stabilization is a hallmark of early DKD and that targeting hypoxia prior to the onset of type 1 DM normalizes renal cell homeostasis and prevents DKD development

iBox-CRT : better response, less complicated, equally fast

Copyright © 2019 Oxford University PressIntroduction: The optimization of the left ventricle (LV) pacing site guided by the electrical delay increases CRT response rate (RR), however it’s necessary to develop technology that allows its universal use. Purpose: The aim is automatically, and operator-independent, access the conduction delay between the right ventricular (RV) stimulus and the LV available veins in order to select the LV pacing site. It is further intended to compare the total procedure and radiation times in relation to an historical control group.info:eu-repo/semantics/publishedVersio