The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. An improved alignment strategy uses the ...Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new analysis features include a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.
Calcineurin is a highly conserved Ca2+/calmodulin-dependent serine/threonine-specific protein phosphatase that orchestrates cellular Ca2+ signaling responses. In Cryptococcus neoformans, calcineurin ...is activated by multiple stresses including high temperature, and is essential for stress adaptation and virulence. The transcription factor Crz1 is a major calcineurin effector in Saccharomyces cerevisiae and other fungi. Calcineurin dephosphorylates Crz1, thereby enabling Crz1 nuclear translocation and transcription of target genes. Here we show that loss of Crz1 confers phenotypes intermediate between wild-type and calcineurin mutants, and demonstrate that deletion of the calcineurin docking domain results in the inability of Crz1 to translocate into the nucleus under thermal stress. RNA-sequencing revealed 102 genes that are regulated in a calcineurin-Crz1-dependent manner at 37°C. The majority of genes were down-regulated in cna1Δ and crz1Δ mutants, indicating these genes are normally activated by the calcineurin-Crz1 pathway at high temperature. About 58% of calcineurin-Crz1 target genes have unknown functions, while genes with known or predicted functions are involved in cell wall remodeling, calcium transport, and pheromone production. We identified three calcineurin-dependent response element motifs within the promoter regions of calcineurin-Crz1 target genes, and show that Crz1 binding to target gene promoters is increased upon thermal stress in a calcineurin-dependent fashion. Additionally, we found a large set of genes independently regulated by calcineurin, and Crz1 regulates 59 genes independently of calcineurin. Given the intermediate crz1Δ mutant phenotype, and our recent evidence for a calcineurin regulatory network impacting mRNA in P-bodies and stress granules independently of Crz1, calcineurin likely acts on factors beyond Crz1 that govern mRNA expression/stability to operate a branched transcriptional/post-transcriptional stress response network necessary for fungal virulence. Taken together, our findings reveal the core calcineurin-Crz1 stress response cascade is maintained from ascomycetes to a pathogenic basidiomycete fungus, but its output in C. neoformans appears to be adapted to promote fungal virulence.
•Acoustic imaging is used to perform the diagnosis of a rotating machine.•Beamforming method allows obtaining the acoustic signals radiated by the machine.•The identified signals feed a spectral ...kurtosis (SK) algorithm.•Mapping the SK allows localizing impulsive sources in spatial and frequency domains.•The impulsive sources can eventually be related to faulted parts of the mechanism.
Rotating machines diagnosis is conventionally related to vibration analysis. Sensors are usually placed on the machine to gather information about its components. The recorded signals are then processed through a fault detection algorithm allowing the identification of the failing part. This paper proposes an acoustic-based diagnosis method. A microphone array is used to record the acoustic field radiated by the machine. The main advantage over vibration-based diagnosis is that the contact between the sensors and the machine is no longer required. Moreover, the application of acoustic imaging makes possible the identification of the sources of acoustic radiation on the machine surface. The display of information is then spatially continuous while the accelerometers only give it discrete. Beamforming provides the time-varying signals radiated by the machine as a function of space. Any fault detection tool can be applied to the beamforming output. Spectral kurtosis, which highlights the impulsiveness of a signal as function of frequency, is used in this study. The combination of spectral kurtosis with acoustic imaging makes possible the mapping of the impulsiveness as a function of space and frequency. The efficiency of this approach lays on the source separation in the spatial and frequency domains. These mappings make possible the localization of such impulsive sources. The faulty components of the machine have an impulsive behavior and thus will be highlighted on the mappings. The study presents experimental validations of the method on rotating machines.
Eukaryotic cell growth is coordinated in response to nutrient availability, growth factors, and environmental stimuli, enabling cell-cell interactions that promote survival. The rapamycin-sensitive ...Tor1 protein kinase, which is conserved from yeasts to humans, participates in a signaling pathway central to cellular nutrient responses. To gain insight into Tor-mediated processes in human fungal pathogens, we have characterized Tor signaling in Candida albicans. Global transcriptional profiling revealed evolutionarily conserved roles for Tor1 in regulating the expression of genes involved in nitrogen starvation responses and ribosome biogenesis. Interestingly, we found that in C. albicans Tor1 plays a novel role in regulating the expression of several cell wall and hyphal specific genes, including adhesins and their transcriptional repressors Nrg1 and Tup1. In accord with this transcriptional profile, rapamycin induced extensive cellular aggregation in an adhesin-dependent fashion. Moreover, adhesin gene induction and cellular aggregation of rapamycin-treated cells were strongly dependent on the transactivators Bcr1 and Efg1. These findings support models in which Tor1 negatively controls cellular adhesion by governing the activities of Bcr1 and Efg1. Taken together, these results provide evidence that Tor1-mediated cellular adhesion might be broadly conserved among eukaryotic organisms.
Central Americans are the third largest and fastest growing Latino population in the United States. And yet, despite their demographic presence, there has been little scholarship focused on this ...group.Constituting Central American-Americansis an exploration of the historical and disciplinary conditions that have structured U.S. Central American identity and of the ways in which this identity challenges how we frame current discussions of Latina/o, American ethnic, and diasporic identities. By focusing on the formation of Central American identity in the U.S., Maritza E. Cárdenas challenges us to think about Central America and its diaspora in relation to other U.S. ethno-racial identities.
•Clinical target volume definition in radiotherapy is challenging.•The contribution of computational methods is discussed.•Goals are automation, consistency, and ultimately improvements.•Image ...segmentation algorithms can automate the process in parts.•Mathematical models may quantitatively describe tumor progression patterns.
Treatment planning in radiotherapy distinguishes three target volume concepts: the gross tumor volume (GTV), the clinical target volume (CTV), and the planning target volume (PTV). Over time, GTV definition and PTV margins have improved through the development of novel imaging techniques and better image guidance, respectively. CTV definition is sometimes considered the weakest element in the planning process. CTV definition is particularly complex since the extension of microscopic disease cannot be seen using currently available in-vivo imaging techniques. Instead, CTV definition has to incorporate knowledge of the patterns of tumor progression. While CTV delineation has largely been considered the domain of radiation oncologists, this paper, arising from a 2019 ESTRO Physics research workshop, discusses the contributions that medical physics and computer science can make by developing computational methods to support CTV definition. First, we overview the role of image segmentation algorithms, which may in part automate CTV delineation through segmentation of lymph node stations or normal tissues representing anatomical boundaries of microscopic tumor progression. The recent success of deep convolutional neural networks has also enabled learning entire CTV delineations from examples. Second, we discuss the use of mathematical models of tumor progression for CTV definition, using as example the application of glioma growth models to facilitate GTV-to-CTV expansion for glioblastoma that is consistent with neuroanatomy. We further consider statistical machine learning models to quantify lymphatic metastatic progression of tumors, which may eventually improve elective CTV definition. Lastly, we discuss approaches to incorporate uncertainty in CTV definition into treatment plan optimization as well as general limitations of the CTV concept in the case of infiltrating tumors without natural boundaries.
Phospholipids can interact strongly with ions at physiological concentrations, and these interactions can alter membrane properties. Here, we describe the effects of calcium ions on the dynamics in ...phospholipid membranes. We used a combination of time-resolved ultrafast two-dimensional infrared spectroscopy and molecular dynamics simulations. We found that millimolar Ca2+ concentrations lead to slower fluctuations in the local environment at the lipid-water interface of membranes with phosphatidylserine. The effect was only observed in bilayers containing anionic phosphatidylserine; membranes composed of only zwitterionic phosphatidylcholine did not experience a slowdown. Local water dynamics were measured using the ester groups as label-free probes and were found to be up to 50% slower with 2.5 mM Ca2+. Molecular dynamics simulations show that Ca2+ primarily binds to the carboxylate group of phosphatidylserines. These findings have implications for apoptotic and diseased cells in which phosphatidylserine is exposed to extracellular calcium and for the biophysical effects of divalent cations on lipid bilayers.
The conserved target of rapamycin complex 1 (TORC1) integrates nutrient signals to orchestrate cell growth and proliferation. Leucine availability is conveyed to control TORC1 activity via the ...leu-tRNA synthetase/EGOC-GTPase module in yeast and mammals, but the mechanisms sensing leucine remain only partially understood. We show here that both leucine and its α-ketoacid metabolite, α-ketoisocaproate, effectively activate the yeast TORC1 kinase via both EGOC GTPase-dependent and -independent mechanisms. Leucine and α-ketoisocaproate are interconverted by ubiquitous branched-chain aminotransferases (BCAT), which in yeast are represented by the mitochondrial and cytosolic enzymes Bat1 and Bat2, respectively. BCAT yeast mutants exhibit severely compromised TORC1 activity, which is partially restored by expression of Bat1 active site mutants, implicating both catalytic and structural roles of BCATs in TORC1 control. We find that Bat1 interacts with branched-chain amino acid metabolic enzymes and, in a leucine-dependent fashion, with the tricarboxylic acid (TCA)-cycle enzyme aconitase. BCAT mutation perturbed TCA-cycle intermediate levels, consistent with a TCA-cycle block, and resulted in low ATP levels, activation of AMPK, and TORC1 inhibition. We propose the biosynthetic capacity of BCAT and its role in forming multicomplex metabolons connecting branched-chain amino acids and TCA-cycle metabolism governs TCA-cycle flux to activate TORC1 signaling. Because mammalian mitochondrial BCAT is known to form a supramolecular branched-chain α-keto acid dehydrogenase enzyme complex that links leucine metabolism to the TCA-cycle, these findings establish a precedent for understanding TORC1 signaling in mammals.
The Ca
/calmodulin-dependent protein phosphatase calcineurin orchestrates sexual reproduction, stress responses, and virulence via branched downstream pathways in the opportunistic human fungal ...pathogen
The calcineurin-binding protein Cbp1, the calcineurin temperature suppressor Cts1, the calcineurin-responsive zinc finger transcription factor Crz1, and the calcineurin targets Pbp1, Tif3, and Puf4, all function downstream of calcineurin to orchestrate distinct cellular processes. To elucidate how the calcineurin pathway regulatory network governs unisexual reproduction, stress responses, and virulence, we have analyzed the self-filamentous
strain, XL280α, and generated double mutants of these calcineurin downstream genes. We demonstrated that calcineurin governs unisexual reproduction at different sexual developmental stages, in which the initiation of the yeast-hyphal morphological transition is independent of Crz1, whereas the sporulation process is dependent on Crz1. Calcineurin-dependent unisexual reproduction is independent of the pheromone response pathway. Crz1 synergistically interacts with different calcineurin downstream targets in responding to ER, high-calcium, and cell wall stresses. We observed a widespread synergy suggesting that these proteins function in complex branched pathways downstream of calcineurin with some functional redundancy, which may allow efficient signaling network rewiring within the pathway for prompt adaptation to changing environments. Finally, we showed that deletion of
or
in the
∆ mutant background conferred a modest level of growth tolerance at 37°, but that the
∆
∆ and
∆
∆ double mutants were both avirulent, suggesting that calcineurin may control virulence via mechanisms beyond thermotolerance.
•It is possible to prepare chars from rabbit manure for environmental applications.•Pyrochar thermostability is higher than hydrochar thermostability.•Pyrochar produced at 600 °C shows lower ...phytotoxicity than hydrochars.•Pyrolysis and HTC can be considered as carbon fixation technologies.
Large amounts of manure waste are produced worldwide. Land application of manure waste is the most common approach to valorization. This practice has several environmental concerns, including pathogen spreading, emissions of odorous chemicals (ammonia or methane) and the pollution of waterbodies with nitrogen and phosphorous compounds. The pyrolysis of manure for biochar production has been tested as a useful treatment to avoid these concerns but the high moisture of some wastes hinders its thermo-chemical valorisation in the absence of a pre-drying step. Recently, hydrothermal carbonization (HTC) of wet biomass has been identified as a cost-effective valorisation method of biomass without the need for energy-intensive drying processes. The objective of this study is to compare the properties of pyrochars and hydrochars prepared from thermal treatment of rabbit manure (MW). Pyrochars were prepared at 450 °C (BMW450) and 600 °C (BMW600) and hydrochars were obtained using a rabbit manure solution (solid:water ratio 30:70) that was heated at 190 °C (HMW190) and 240 °C (HMW240). The final temperature was maintained during 1 h for pyrochars and 6 h for hydrochars. Results showed that HTC generated more micro-, meso- and macro-porosity than pyrolysis. Pyrochar produced at 600 °C possessed a high thermal, chemical and biological stability, probably due to its highly aromatic structure. Hydrochars (HMW190 and HMW240) were predominantly aliphatic, and this was associated to a lower chemical and thermal stability than pyrochars. The germination index values indicated that the pyrochar BMW450 and the two hydrochars were highly phytotoxic while pyrochar MWB600 presented a moderate phytotoxicity, which was lower than the manure waste. Finally, CO2 emissions of different materials after 60 days followed the order: MW > HMW190 > HMW240 > BMW450 > BMW600. Specifically, pyrolysis evolved CO2 was reduced between 97.8−88.7% with respect to raw material after pyrolysis. The HTC treatment diminished evolved CO2 between 68.8−59.0%, with respect to the manure. These results indicate that both processes can be considered as carbon fixation technologies.
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