Differential Flo8p-dependent regulation of FLO1 and FLO11 for cell–cell and cell–substrate adherence of S. cerevisiae S288c

Cell–cell and cell–surface adherence represents initial steps in forming multicellular aggregates or in establishing cell–surface interactions. The commonly used Saccharomyces cerevisiae laboratory strain S288c carries a flo8 mutation, and is only able to express the flocculin-encoding genes FLO1 and FLO11, when FLO8 is restored. We show here that the two flocculin genes exhibit differences in regulation to execute distinct functions under various environmental conditions. In contrast to the laboratory strain Σ1278b, haploids of the S288c genetic background require FLO1 for cell–cell and cell–substrate adhesion, whereas FLO11 is required for pseudohyphae formation of diploids. In contrast to FLO11, FLO1 repression requires the Sin4p mediator tail component, but is independent of the repressor Sfl1p. FLO1 regulation also differs from FLO11, because it requires neither the KSS1 MAP kinase cascade nor the pathways which lead to the transcription factors Gcn4p or Msn1p. The protein kinase A pathway and the transcription factors Flo8p and Mss11p are the major regulators for FLO1 expression. Therefore, S. cerevisiae is prepared to simultaneously express two genes of its otherwise silenced FLO reservoir resulting in an appropriate cellular surface for different environments

A Remote Patient-Monitoring System for Intensive Care Medicine: Mixed Methods Human-Centered Design and Usability Evaluation

Background: Continuous monitoring of vital signs is critical for ensuring patient safety in intensive care units (ICUs) and is becoming increasingly relevant in general wards. The effectiveness of health information technologies such as patient-monitoring systems is highly determined by usability, the lack of which can ultimately compromise patient safety. Usability problems can be identified and prevented by involving users (ie, clinicians). Objective: In this study, we aim to apply a human-centered design approach to evaluate the usability of a remote patient-monitoring system user interface (UI) in the ICU context and conceptualize and evaluate design changes. Methods: Following institutional review board approval (EA1/031/18), a formative evaluation of the monitoring UI was performed. Simulated use tests with think-aloud protocols were conducted with ICU staff (n=5), and the resulting qualitative data were analyzed using a deductive analytic approach. On the basis of the identified usability problems, we conceptualized informed design changes and applied them to develop an improved prototype of the monitoring UI. Comparing the UIs, we evaluated perceived usability using the System Usability Scale, performance efficiency with the normative path deviation, and effectiveness by measuring the task completion rate (n=5). Measures were tested for statistical significance using a 2-sample t test, Poisson regression with a generalized linear mixed-effects model, and the N-1 chi-square test. P<.05 were considered significant. Results: We found 37 individual usability problems specific to monitoring UI, which could be assigned to six subcodes: usefulness of the system, response time, responsiveness, meaning of labels, function of UI elements, and navigation. Among user ideas and requirements for the UI were high usability, customizability, and the provision of audible alarm notifications. Changes in graphics and design were proposed to allow for better navigation, information retrieval, and spatial orientation. The UI was revised by creating a prototype with a more responsive design and changes regarding labeling and UI elements. Statistical analysis showed that perceived usability improved significantly (System Usability Scale design A: mean 68.5, SD 11.26, n=5; design B: mean 89, SD 4.87, n=5; P=.003), as did performance efficiency (normative path deviation design A: mean 8.8, SD 5.26, n=5; design B: mean 3.2, SD 3.03, n=5; P=.001), and effectiveness (design A: 18 trials, failed 7, 39% times, passed 11, 61% times; design B: 20 trials, failed 0 times, passed 20 times; P=.002). Conclusions: Usability testing with think-aloud protocols led to a patient-monitoring UI with significantly improved usability, performance, and effectiveness. In the ICU work environment, difficult-to-use technology may result in detrimental outcomes for staff and patients. Technical devices should be designed to support efficient and effective work processes. Our results suggest that this can be achieved by applying basic human-centered design methods and principles. Trial Registration: ClinicalTrials.gov NCT03514173; https://clinicaltrials.gov/ct2/show/NCT0351417

Carbon redistribution by erosion processes in an intensively disturbed catchment

29 Pags.- 6 Tabls.- 6 Figs. This article belongs to a special issue of Catena titled "Geoecology in Mediterranean mountain areas. Tribute to Professor José María García Ruiz". The definitive version is available at: http://www.sciencedirect.com/science/journal/03418162Understanding how organic carbon (OC) moves with sediments along the fluvial system is crucial to determining catchment scale carbon budgets and helps the proper management of fragile ecosystems. Especially challenging is the analysis of OC dynamics during fluvial transport in heterogeneous, fragile, and disturbed environments with ephemeral and intense hydrological pulses, typical of Mediterranean conditions. This paper explores the catchment scale OC redistribution by lateral flows in extreme Mediterranean environmental conditions, from a geomorphological perspective. The study area is a catchment (Cárcavo) in SE Spain with a semiarid climate, erodible lithologies, and shallow soils, which is highly disturbed by agricultural terraces, land levelling, reforestation, and construction of check-dams. To increase our understanding of catchment scale OC redistribution induced by erosion, we studied in detail the subcatchments of eight check-dams distributed along the catchments main channel. We determined 137Cs, physicochemical characteristics, and the OC pools of the catchment soils and sediments deposited behind each check-dam, performed spatial analysis of catchment properties and buffer areas around the check-dams, and carried out geomorphological analysis of the slope-channel connections. The soils showed very low total organic carbon (TOC) values, oscillating between 15.2 and 4.4 g kg− 1 for forest and agricultural soils, respectively. Sediments mobilized by erosion were poor in TOC (6.6 ± 0.7 g kg– 1) compared to the eroded (forest) soils, and the redistribution of OC through the catchment, especially of the mineral associated organic carbon (MAC) pool, showed the same pattern as clay particles and 137Cs. The TOC erosion rates estimated for the Cárcavo watershed are relatively low (0.031 ± 0.03 Mg ha− 1 y− 1) but similar to those reported for subhumid Mediterranean catchments that are less fragile and more conducive to plant growth. The TOC erosion/total erosion ratio was lower (0.06%) than other estimates, although the average OC concentration of the sediments was higher than that of the agricultural soils of the catchment, underlining the problem of maintaining sustainable soil OC contents. The OC in deposited sediments came not only from surface erosion processes, but also from deeper soil or sediment layers mobilized by concentrated erosion processes. Sediment richer in OC came from the surface soil of vegetated (reforested) areas close and well connected to the channels. Subcatchments dominated by laminar erosion processes showed a TOC erosion/total erosion ratio that was two times higher than that of subcatchments dominated by concentrated flow erosion processes. The lithology, soils, and geomorphology exert a more important control on OC redistribution than land use and vegetation cover in this geomorphologically very active catchment.This work was financially supported by the projects ADAPT (CGL2013-42009-R) and DISECO (CGL2014-55-405-R) from the Spanish Government, National Plan of Science; the project CAMBIO (18933/JLI/13) of the Seneca Foundation, Regional Government of Murcia (Spain); and the project SOGLO (P7/24 IAP BELSPO) from the Belgian Government. Joris de Vente was supported by a ‘Ramón y Cajal’ grant (RYC-2012-10375).Peer reviewe

MicroRNA-Related Polymorphism and Their Association with Fibromyalgia.

MicroRNAs are tissue-specific expressed short RNAs that serve post-transcriptional gene regulation. A specific microRNA can bind to mRNAs of different genes and thereby suppress their protein production. In the context of the complex phenotype of fibromyalgia, we used the Axiom miRNA Target Site Genotyping Array to search genome-wide for DNA variations in microRNA genes, their regulatory regions, and in the 3'UTR of protein-coding genes. To identify disease-relevant DNA polymorphisms, a cohort of 176 female fibromyalgia patients was studied in comparison to a cohort of 162 healthy women. The association between 48,329 markers and fibromyalgia was investigated using logistic regression adjusted for population stratification. Results show that 29 markers had p-values < 1 × 10(-3), and the strongest association was observed for rs758459 (p-value of 0.0001), located in the Neurogenin 1 gene which is targeted by hsa-miR-130a-3p. Furthermore, variant rs2295963 is predicted to affect binding of hsa-miR-1-3p. Both microRNAs were previously reported to be differentially expressed in fibromyalgia patients. Despite its limited statistical power, this study reports two microRNA-related polymorphisms which may play a functional role in the pathogenesis of fibromyalgia. For a better understanding of the disease pattern, further functional analyses on the biological significance of microRNAs and microRNA-related polymorphisms are required

Intraoperative vs. postoperative side-effects-thresholds during pallidal and thalamic DBS

Background: It is currently unknown whether results from intraoperative test stimulation of two types of Deep Brain Stimulation (DBS), either during awake pallidal (GPi) or thalamic (Vim), are comparable to the results generated by chronic stimulation through the definitive lead.Objective: To determine whether side-effects-thresholds from intraoperative test stimulation are indicative of postoperative stimulation findings.Methods: Records of consecutive patients who received GPi or Vim were analyzed. Thresholds for the induction of either capsular or non-capsular side-effects were compared at matched depths and at group-level.Results: Records of fifty-two patients were analyzed (20 GPis, 75 Vims). The induction of side-effects was not significantly different between intraoperative and postoperative assessments at matched depths, although a large variability was observed (capsular: GPi DBS: p = 0.79; Vim DBS: p = 0.68); non-capsular: GPi DBS: p = 0.20; and Vim DBS: p = 0.35). Linear mixed-effect models revealed no differences between intraoperative and postoperative assessments, although the Vim had significantly lower thresholds (capsular side-effects p = 0.01, non-capsular side-effects p < 0.01). Unpaired survival analyses demonstrated lower intraoperative than postoperative thresholds for capsular side-effects in patients under GPi DBS (p = 0.01), while higher intraoperative thresholds for non-capsular side-effects in patients under Vim DBS (p = 0.01).Conclusion: There were no significant differences between intraoperative and postoperative assessments of GPi and Vim DBS, although thresholds cannot be directly extrapolated at an individual level due to high variability.Scientific Assessment and Innovation in Neurosurgical Treatment Strategie

Medical and surgical treatment for medication-induced tremor: case report and systematic review

Objective To present a case of refractory medication-induced tremor successfully treated with deep brain stimulation (DBS) of the thalamic ventral intermediate nucleus (Vim) and to propose a medical and surgical treatment algorithm based on a systematical review of the literature. Methods Patient data were retrospectively collected. A systematic search was performed in PubMed, Embase, and Cochrane Library. Subjective and objective data were pooled for analysis by classifying them into 5 predefined categories(no, minimal, moderate, good, and excellent effects). Results The patient presented with lithium-induced bilateral progressive hand tremor lasting 25 years. After DBS, he reported excellent tremor suppression until the last follow-up (36 months after Vim-DBS). For the review, 34 of 140 studies were included and evaluated (178 unique subjects, 31 different treatments). A good-to-excellent tremor suppression (50%-100%) in at least 50% of subjects was achieved using propranolol (12 studies, 50% of 56 subjects), tetrabenazine (5 studies, 51% of 13 subjects), and metoprolol (4 studies, 75% of 8 subjects). The effect of benztropine and diphenhydramine was none or only minimal to moderate (up to 50% improvement; both: 3 studies, 50% of 4 patients). One article reported minimal-to-moderate effectiveness after DBS of the ventral oral posterior nucleus of the thalamus. Methods were highly heterogeneous. All studies scored grade III or IV quality of evidence, which was insufficient for recommendations (level U). Conclusion Treatment decision making should be performed on a case-by-case basis considering the low level of evidence, and we propose a practically oriented treatment algorithm. Propranolol, tetrabenazine, and metoprolol might be effective. For selected and refractory cases, DBS might be considered.Neurological Motor Disorder

StreptomeDB:a resource for natural compounds isolated from <i>Streptomyces</i> species

Bacteria from the genus Streptomyces are very important for the production of natural bioactive compounds such as antibiotic, antitumour or immunosuppressant drugs. Around two-thirds of all known natural antibiotics are produced by these bacteria. An enormous quantity of crucial data related to this genus has been generated and published, but so far no freely available and comprehensive database exists. Here, we present StreptomeDB (http://www.pharmaceutical-bioinformatics.de/streptomedb/). To the best of our knowledge, this is the largest database of natural products isolated from Streptomyces. It contains >2400 unique and diverse compounds from >1900 different Streptomyces strains and substrains. In addition to names and molecular structures of the compounds, information about source organisms, references, biological role, activities and synthesis routes (e.g. polyketide synthase derived and non-ribosomal peptides derived) is included. Data can be accessed through queries on compound names, chemical structures or organisms. Extraction from the literature was performed through automatic text mining of thousands of articles from PubMed, followed by manual curation. All annotated compound structures can be downloaded from the website and applied for in silico screenings for identifying new active molecules with undiscovered properties

Low-Dosage Inhibition of DII4 Signaling Promotes Wound Healing by Inducing Functional Neo-Angiogenesis

Recent findings regarding Dll4 function in physiological and pathological conditions indicate that this Notch ligand may constitute an important therapeutic target. Dll4 appears to be a major anti-angiogenic agent, occupying a central role in various angiogenic pathways. The first trials of anti-Dll4 therapy in mice demonstrated a paradoxical effect, as it reduced tumor perfusion and growth despite leading to an increase in vascular density. This is seen as the result of insufficient maturation of the newly formed vasculature causing a circulatory defect and increased tumor hypoxia. As Dll4 function is known to be closely dependent on expression levels, we envisioned that the therapeutic anti-Dll4 dosage could be modulated to result in the increase of adequately functional blood vessels. This would be useful in conditions where vascular function is a limiting factor for recovery, like wound healing and tissue hypoxia, especially in diabetic patients. Our experimental results in mice confirmed this possibility, revealing that low dosage inhibition of Dll4/Notch signaling causes improved vascular function and accelerated wound healing

Multiple Signals Converge on a Differentiation MAPK Pathway

An important emerging question in the area of signal transduction is how information from different pathways becomes integrated into a highly coordinated response. In budding yeast, multiple pathways regulate filamentous growth, a complex differentiation response that occurs under specific environmental conditions. To identify new aspects of filamentous growth regulation, we used a novel screening approach (called secretion profiling) that measures release of the extracellular domain of Msb2p, the signaling mucin which functions at the head of the filamentous growth (FG) MAPK pathway. Secretion profiling of complementary genomic collections showed that many of the pathways that regulate filamentous growth (RAS, RIM101, OPI1, and RTG) were also required for FG pathway activation. This regulation sensitized the FG pathway to multiple stimuli and synchronized it to the global signaling network. Several of the regulators were required for MSB2 expression, which identifies the MSB2 promoter as a target “hub” where multiple signals converge. Accessibility to the MSB2 promoter was further regulated by the histone deacetylase (HDAC) Rpd3p(L), which positively regulated FG pathway activity and filamentous growth. Our findings provide the first glimpse of a global regulatory hierarchy among the pathways that control filamentous growth. Systems-level integration of signaling circuitry is likely to coordinate other regulatory networks that control complex behaviors

Biological nitrate transport in sediments on the Peruvian margin mitigates benthic sulfide emissions and drives pelagic N loss during stagnation events

Highlights • Very high rates of dissimilatory nitrate reduction to ammonium by Thioploca. • Non-steady state model predicts Thioploca survival on intracellular nitrate reservoir. • Ammonium release by Thioploca may be coupled to pelagic N loss by anammox. • Thioploca may contribute to anammox long after bottom water nitrate disappearance. • Model indicates that benthic foraminifera account for 90% of benthic N2 production. Abstract Benthic N cycling in the Peruvian oxygen minimum zone (OMZ) was investigated at ten stations along 12oS from the middle shelf (74 m) to the upper slope (1024 m) using in situ flux measurements, sediment biogeochemistry and modelling. Middle shelf sediments were covered by mats of the filamentous bacteria Thioploca spp. and contained a large ‘hidden’ pool of nitrate that was not detectable in the porewater. This was attributed to a biological nitrate reservoir stored within the bacteria to oxidize sulfide to sulfate during ‘dissimilatory nitrate reduction to ammonium’ (DNRA). The extremely high rates of DNRA on the shelf (15.6 mmol m-2 d-1 of N), determined using an empirical steady-state model, could easily supply all the ammonium requirements for anammox in the water column. The model further showed that denitrification by foraminifera may account for 90% of N2 production at the lower edge of the OMZ. At the time of sampling, dissolved oxygen was below detection limit down to 400 m and the water body overlying the shelf had stagnated, resulting in complete depletion of nitrate and nitrite. A decrease in the biological nitrate pool was observed on the shelf during fieldwork concomitant with a rise in porewater sulfide levels in surface sediments to 2 mM. Using a non-steady state model to simulate this natural anoxia experiment, these observations were shown to be consistent with Thioploca surviving on a dwindling intracellular nitrate reservoir to survive the stagnation period. The model shows that sediments hosting Thioploca are able to maintain high ammonium fluxes for many weeks following stagnation, potentially sustaining pelagic N loss by anammox. In contrast, sulfide emissions remain low, reducing the economic risk to the Peruvian fishery by toxic sulfide plume development