Abstract
Bacteria and archaea employ dedicated signal transduction systems that modulate gene expression, second-messenger turnover, quorum sensing, biofilm formation, motility, host-pathogen and ...beneficial interactions. The updated MiST database provides a comprehensive classification of microbial signal transduction systems. This update is a result of a substantial scaling to accommodate constantly growing microbial genomic data. More than 125 000 genomes, 516 million genes and almost 100 million unique protein sequences are currently stored in the database. For each bacterial and archaeal genome, MiST 3.0 provides a complete signal transduction profile, thus facilitating theoretical and experimental studies on signal transduction and gene regulation. New software infrastructure and distributed pipeline implemented in MiST 3.0 enable regular genome updates based on the NCBI RefSeq database. A novel MiST feature is the integration of unique profile HMMs to link complex chemosensory systems with corresponding chemoreceptors in bacterial and archaeal genomes. The data can be explored online or via RESTful API (freely available at https://mistdb.com).
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•Successional stages of biocrusts control the structure of soil bacterial communities.•Biocrust cover influences the total abundance of soil bacteria.•Some bacterial taxa are ...specifically associated to each biocrust type.•Parallel changes occur in soil chemistry and soil bacteria with biocrust succession.•Alpha-diversity is higher in soils colonized by late-successional biocrusts.
Biocrusts are an important drylands landscape component, which enriches the upper millimeters of the soil with organic matter and initiates biogeochemical cycles. However, little is known about the influence of biocrusts on soil bacterial community structure and diversity. Different biocrust types representing a successional gradient were studied. This gradient, from the earliest to the latest successional stages, consisted of an incipient cyanobacterial biocrust < mature cyanobacterial biocrusts < biocrust dominated by the Squamarina lentigera and Diploschistes diacapsis lichens < Biocrust characterized by the Lepraria isidiata lichen. Moreover, in each biocrust type, four different percentages of biocrust cover were also selected. Soil diversity gradually increased with biocrust successional stage and percentage of biocrust cover. The biocrust cover had an important role in the total abundance of bacteria, generally increasing in soils colonized by the highest percentages of cover. Biocrust successional stage was the most important factor, significantly influencing 108 soil bacteria genera, whereas biocrust cover showed significant differences in only 10 genera. Principal Component Analysis showed contrasting microbial composition across the biocrust successional gradient. Some bacterial taxa were dominant in the soil colonized by different biocrust types. Thus, Leptolyngbya, Rubrobacter, Solirubrobacter, Geodermatophilus, etc., were more abundant in incipient cyanobacteria; Nostocales, Chroococcidiopsaceae, Coleofasciculaceae etc., under mature cyanobacterial biocrusts; Truepera, Sphingobacteriaceae, Actinophytocola, Kribella, etc., below the S. lentigera and D. diacapsis community, and Bryobacter, Ohtaekwangia, Opitutus, Pedosphaeraceae, etc., in soils colonized by L. isidiata. Several soil bacteria taxa showed significant correlations (p < 0.05) with chemical soil properties (pH, total nitrogen, total organic carbon, available phosphorous and electrical conductivity). We discuss the role of biocrusts influencing these chemical soil parameters, including the presence of certain metabolites secreted by biocrusts, and also their effects on soil moisture and several physical soil features, as well as their association with different microclimates, all of which could favor a more selective environment for certain bacteria.
The Century of mRNA Vaccines: COVID-19 Vaccines and Allergy Ortega Rodríguez, N R; Audícana Berasategui, M T; de la Hoz Caballer, B ...
Journal of investigational allergology & clinical immunology,
01/2021, Letnik:
31, Številka:
1
Journal Article
Three-dimensional electron microscopy techniques like electron tomography provide valuable insights into cellular structures, and present significant challenges for data storage and dissemination. ...Here we explored a novel method to publicly release more than 11,000 such datasets, more than 30 TB in total, collected by our group. Our method, based on a peer-to-peer file sharing network built around a blockchain ledger, offers a distributed solution to data storage. In addition, we offer a user-friendly browser-based interface, https://etdb.caltech.edu, for anyone interested to explore and download our data. We discuss the relative advantages and disadvantages of this system and provide tools for other groups to mine our data and/or use the same approach to share their own imaging datasets.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Analyse the importance of components of Mediterranean diet in functional feeding.
We have based the study in a bibliographic review.
Many of the characteristic components of the traditional ...Mediterranean diet (MD) are known to have positive effects on health, capacity and well-being, and can be used to design functional foods. Vegetables, fruits and nuts are all rich in phenols, flavonoids, isoflavonoids, phytosterols and phytic acid--essential bioactive compounds providing health benefits. The polyunsaturated fatty acids found in fish effectively regulate haemostatic factors, protect against cardiac arrhythmias, cancer and hypertension, and play a vital role in the maintenance of neural functions and the prevention of certain psychiatric disorders. Accumulating evidence suggests that olive oil, an integral component of the MD, may have health benefits, including the reduction of the risk of coronary heart disease, the prevention of several types of cancer and the modification of the immune and inflammatory responses. Olive oil is known for its high levels of monounsaturated fatty acids and is a good source of phytochemicals, such as polyphenolic compounds, squalene and alpha-tocopherol. In the context of the MD, the benefits associated with the consumption of several functional components may be intensified by certain forms of food preparation. In addition, the practice of more physical activity (once common among Mediterranean populations) and the following of other healthy lifestyle habits may have additive effects.
The identification of the active constituents of the MD is crucial in the formulation of appropriate dietary guidelines. Research into the pharmacological properties of the minor components of this diet (vitamins, sterols, polyphenols, etc.) is very active and could lead to the formulation of functional foods and nutraceuticals.
Drylands affected by serious disturbances such as mining activities lose their vegetation cover and organic soil horizons, becoming CO2 emissions sources. Applications of organic amendments could be ...a good restoration solution that favours vegetation establishment and soil carbon sequestration; however, they are also associated with CO₂ emissions. Experimental plots with different organic amendments (sewage sludge, garden and greenhouse vegetable composts, and mixtures of both) and unamended soils were installed in a quarry in southeast Spain. The aim of this study was: i) to evaluate the magnitude and changes of in situ CO₂ emission from each experimental plot during a year and a half, and ii) to assess the effects of several physical–chemical (total organic carbon, total nitrogen, water retention, pH and electrical conductivity) and environmental parameters (moisture and temperature) in CO2 emissions. The results showed an initial CO2 emission (priming effect), produced from all restored plots just after the application of the organic amendment, which was significantly higher (P < 0.05) in soils with sewage sludge and their mixtures in comparison to vegetable compost. Garden compost had low emission rates, similar to soils without amendment and showed lower CO2 emission rates than the rest of the restoration treatments. Nevertheless, CO2 emissions decreased in each field campaign over time, showing that all restored soils had lower emissions than natural soils at the end of the sampled period. The different composition of organic amendments had a different effect on soil CO2 emissions. DistLM analysis showed that soil properties such as total organic carbon, total nitrogen, pH and soil moisture, associated with rainfall periods, strongly influenced CO₂ emissions, whereas temperature did not affect the CO2 flow. In conclusion, the compost from plant remains could serve better as treatment to restore degraded soils in drylands than sewage sludge because of its lower CO2 emissions and concomitant effect on climate warming and carbon balance.
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•CO₂ emissions from soils with gardens waste compost were lower than natural soils.•Sewage sludge produced much higher CO₂ emissions than compost from vegetal waste.•CO₂ emission decreased over time in restored soils with all the different amendments.•Organic waste amendments modified physico-chemical properties in restored soils.•Moisture and organic carbon strongly influence CO₂ emissions in restored mining soils.
A nonlinear observer for surface-mount permanent-magnet synchronous motors (SPMSMs) was recently proposed by Ortega et al. (LSS, Gif-sur-Yvette Cedex, France, LSS Internal Rep., Jan. 2009). The ...nonlinear observer generates the position estimate ¿¿ via the estimates of sin ¿ and cos ¿. In contrast to Luenberger-type observers, it does not require speed information, thus eliminating the complexity associated with speed estimation errors. Further, it is simple to implement. In this study, the nonlinear observer performance is verified experimentally. To obtain speed estimates from the position information, a proportional-integral (PI) tracking controller speed estimator was utilized. The results are good with and without loads, above 10 r/min.
A new method to design asymptotically stabilizing and adaptive control laws for nonlinear systems is presented. The method relies upon the notions of system immersion and manifold invariance and, in ...principle, does not require the knowledge of a (control) Lyapunov function. The construction of the stabilizing control laws resembles the procedure used in nonlinear regulator theory to derive the (invariant) output zeroing manifold and its friend. The method is well suited in situations where we know a stabilizing controller of a nominal reduced order model, which we would like to robustify with respect to higher order dynamics. This is achieved by designing a control law that asymptotically immerses the full system dynamics into the reduced order one. We also show that in adaptive control problems the method yields stabilizing schemes that counter the effect of the uncertain parameters adopting a robustness perspective. Our construction does not invoke certainty equivalence, nor requires a linear parameterization, furthermore, viewed from a Lyapunov perspective, it provides a procedure to add cross terms between the parameter estimates and the plant states. Finally, it is shown that the proposed approach is directly applicable to systems in feedback and feedforward form, yielding new stabilizing control laws. We illustrate the method with several academic and practical examples, including a mechanical system with flexibility modes, an electromechanical system with parasitic actuator dynamics and an adaptive nonlinearly parameterized visual servoing application.
Mineral elements, often at the trace level, play a considerable role in physiology and pathology of biological systems. Metallogenomics, metalloproteomics, and metallomics are among the emerging ...disciplines which are critically dependent on spatially resolved concentration maps of trace elements in a cell or tissue, on information on chemical speciation, and on that on metal-binding coordination sites. The mini-review discusses recent progress in analytical techniques for element profiling on the genome scale, biological trace element imaging, and probing, identification and quantification of chemical species in the biological environment. Imaging of the element distribution in cells and tissue sections is becoming possible with sub-micrometer spatial resolution and picogram-level sensitivity owing to advances in laser ablation MS, ion beam and synchrotron radiation X-ray fluorescence microprobes. Progress in nanoflow chromatography and capillary electrophoresis coupled with element specific ICP MS and molecule-specific electrospray MS/MS and MALDI enables speciation of elements in microsamples in a complex biological environment. Laser ablation ICP MS, micro-SXRF, and micro-PIXE allow mapping of trace element distribution in 1D and 2D proteomics gels. The increasing sensitivity of EXAFS and XANES owing to the use of more intense synchrotron beams and efficient focusing optics provide information about oxidation state, fingerprint speciation of metal sites and metal-site structures.
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