CO-dependent H2 evolution by Rhodospirillum rubrum: Role of CODH:CooF complex

AbstractUpon exposure to CO during anaerobic growth, the purple phototrophic bacterium Rhodospirillum rubrum expresses a CO-oxidizing H2 evolving enzymatic system. The CO-oxidizing enzyme, carbon monoxide dehydrogenase (CODH), has been purified and extensively characterized. However the electron transfer pathway from CODH to the CO-induced hydrogenase that evolves H2 is not well understood. CooF is an Fe–S protein that is the proposed mediator of electron transfer between CODH and the CO-induced hydrogenase. Here we present the spectroscopic and biochemical properties of the CODH:CooF complex. The characteristic EPR signals observed for CODH are largely insensitive to CooF complexation. Metal analysis and EPR spectroscopy show that CooF contains 2 Fe4S4 clusters. The observation of 2 Fe4S4 clusters for CooF contradicts the prediction of 4 Fe4S4 clusters based on analysis of the amino acid sequence of CooF and structural studies of CooF homologs. Comparison of in vivo and in vitro CO-dependent H2 evolution indicates that ∼90% of the activity is lost upon cell lysis. We propose that the loss of two labile Fe–S clusters from CooF during cell lysis may be responsible for the low in vitro CO-dependent H2 evolution activity. During the course of these studies, a new assay for CODH:CooF was developed using membranes from an R. rubrum mutant that did not express CODH:CooF, but expressed high levels of the CO-induced hydrogenase. The assay revealed that the CO-induced hydrogenase requires the presence of CODH:CooF for optimal H2 evolution activity

Picturing Marty Gardner / Remembering Professor Martin Gardner / Remembering Marty Gardner / In Memoriam Professor Marty Gardner / In Memoriam to Professor Martin (Marty) Gardner

Tributes to Martin (“Marty”) R. Gardner, professor for forty-three years at the University of Nebraska College of Law

Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization

The hydrocarbonoclastic bacterium Acinetobacter venetianus RAG-1 has attracted substantial attention due to its powerful oil-degrading capabilities and its potential to play an important ecological role in the cleanup of alkanes. In this study, we compare the transcriptome of the strain RAG-1 grown in dodecane, the corresponding alkanol (dodecanol), and sodium acetate for the characterization of genes involved in dodecane uptake and utilization. Comparison of the transcriptional responses of RAG-1 grown on dodecane led to the identification of 1074 genes that were differentially expressed relative to sodium acetate. Of these, 622 genes were upregulated when grown in dodecane. The highly upregulated genes were involved in alkane catabolism, along with stress response. Our data suggest AlkMb to be primarily involved in dodecane oxidation. Transcriptional response of RAG-1 grown on dodecane relative to dodecanol also led to the identification of permease, outer membrane protein and thin fimbriae coding genes potentially involved in dodecane uptake. This study provides the first model for key genes involved in alkane uptake and metabolism in A. venetianus RAG-1

Microbial Community Structure and Functional Potential Along a Hypersaline Gradient

Salinity is one of the strongest environmental drivers of microbial evolution and community composition. Here we aimed to determine the impact of salt concentrations (2.5, 7.5, and 33.2%) on the microbial community structure of reclaimed saltern ponds near San Francisco, California, and to discover prospective enzymes with potential biotechnological applications. Community compositions were determined by 16S rRNA amplicon sequencing revealing both higher richness and evenness in the pond sediments compared to the water columns. Co-occurrence network analysis additionally uncovered the presence of microbial seed bank communities, potentially primed to respond to rapid changes in salinity. In addition, functional annotation of shotgun metagenomic DNA showed different capabilities if the microbial communities at different salinities for methanogenesis, amino acid metabolism, and carbohydrate-active enzymes. There was an overall shift with increasing salinity in the functional potential for starch degradation, and a decrease in degradation of cellulose and other oligosaccharides. Further, many carbohydrate-active enzymes identified have acidic isoelectric points that have potential biotechnological applications, including deconstruction of biofuel feedstocks under high ionic conditions. Metagenome-assembled genomes (MAGs) of individual halotolerant and halophilic microbes were binned revealing a variety of carbohydrate-degrading potential of individual pond inhabitants

Doing it alone : unisexual reproduction in filamentous ascomycete fungi

Unisexuality in fungi is the result of sexual reproduction in a single isolate that harbors genes associated with only a single mating type. To date, unisexual reproduction has been described in only three genera of filamentous fungi. Consequently, our understanding of this unusual pathway is limited. In this critical review, we compare genetic, genomic and transcriptomic data from a variety of unisexual species to similar data from their primary homothallic and heterothallic relatives. These analyses show that unisexual reproduction is likely derived from heterothallism via the mutation of genes involved in the initiation of sexual reproduction. We show that significant changes in mating-type genes, pheromone precursor genes and pheromone receptor genes are common in unisexual species, but that similar changes are not evident in their primary homothallic or heterothallic relatives. These findings are particularly notable because the unisexual species are accommodated in unrelated genera, illustrating that a similar transition to unisexuality has likely occurred independently in their lineages.The University of Pretoria, the Department of Science and Innovation (DSI)/National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology and the Genomics Research Institute (University of Pretoria Institutional Research Theme).http://www.elsevier.com/locate/fbr2022-01-13hj2021BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Demographic profile of families and children in the Study to Explore Early Development (SEED): Case-control study of autism spectrum disorder

The Study to Explore Early Development (SEED) is designed to enhance knowledge of autism spectrum disorder characteristics and etiologies

Model Evaluation Guidelines for Geomagnetic Index Predictions

Geomagnetic indices are convenient quantities that distill the complicated physics of some region or aspect of near‐Earth space into a single parameter. Most of the best‐known indices are calculated from ground‐based magnetometer data sets, such as Dst, SYM‐H, Kp, AE, AL, and PC. Many models have been created that predict the values of these indices, often using solar wind measurements upstream from Earth as the input variables to the calculation. This document reviews the current state of models that predict geomagnetic indices and the methods used to assess their ability to reproduce the target index time series. These existing methods are synthesized into a baseline collection of metrics for benchmarking a new or updated geomagnetic index prediction model. These methods fall into two categories: (1) fit performance metrics such as root‐mean‐square error and mean absolute error that are applied to a time series comparison of model output and observations and (2) event detection performance metrics such as Heidke Skill Score and probability of detection that are derived from a contingency table that compares model and observation values exceeding (or not) a threshold value. A few examples of codes being used with this set of metrics are presented, and other aspects of metrics assessment best practices, limitations, and uncertainties are discussed, including several caveats to consider when using geomagnetic indices.Plain Language SummaryOne aspect of space weather is a magnetic signature across the surface of the Earth. The creation of this signal involves nonlinear interactions of electromagnetic forces on charged particles and can therefore be difficult to predict. The perturbations that space storms and other activity causes in some observation sets, however, are fairly regular in their pattern. Some of these measurements have been compiled together into a single value, a geomagnetic index. Several such indices exist, providing a global estimate of the activity in different parts of geospace. Models have been developed to predict the time series of these indices, and various statistical methods are used to assess their performance at reproducing the original index. Existing studies of geomagnetic indices, however, use different approaches to quantify the performance of the model. This document defines a standardized set of statistical analyses as a baseline set of comparison tools that are recommended to assess geomagnetic index prediction models. It also discusses best practices, limitations, uncertainties, and caveats to consider when conducting a model assessment.Key PointsWe review existing practices for assessing geomagnetic index prediction models and recommend a “standard set” of metricsAlong with fit performance metrics that use all data‐model pairs in their formulas, event detection performance metrics are recommendedOther aspects of metrics assessment best practices, limitations, uncertainties, and geomagnetic index caveats are also discussedPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147764/1/swe20790_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147764/2/swe20790.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147764/3/swe20790-sup-0001-2018SW002067-SI.pd

Angiographic Findings and Outcome in Diabetec Patients Treated With Thrombolytic Therapy for Acute Myocardial Infarction: The GUSTO-I Experience

OBJECTIVES: This study sought to determine whether diabetes mellitus, in the setting of thrombolysis for acute myocardial infarction, affects 1) early infarct-related artery patency and reocclusion rates; and 2) global and regional ventricular function indexes. We also sought to assess whether angiographic or baseline clinical variables, or both, can account for the known excess mortality after myocardial infarction in the diabetic population. BACKGROUND: Mortality after acute myocardial infarction in patients with diabetes is approximately twice that of nondiabetic patients. It is uncertain whether this difference in mortality is due to a lower rate of successful thrombolysis, increased reocclusion after successful thrombolysis, greater ventricular injury or a more adverse angiographic or clinical profile in diabetic patients. METHODS: Patency rates and global and regional left ventricular function were determined in patients enrolled in the GUSTO-I Angiographic Trial. Thirty-day mortality differences between those with and without diabetes were compared. RESULTS: The diabetic cohort had a significantly higher proportion of female and elderly patients, and th

Adaptation-Dependent Synchronous Activity Contributes to Receptive Field Size Change of Bullfrog Retinal Ganglion Cell

Nearby retinal ganglion cells of similar functional subtype have a tendency to discharge spikes in synchrony. The synchronized activity is involved in encoding some aspects of visual input. On the other hand, neurons always continuously adjust their activities in adaptation to some features of visual stimulation, including mean ambient light, contrast level, etc. Previous studies on adaptation were primarily focused on single neuronal activity, however, it is also intriguing to investigate the adaptation process in population neuronal activities. In the present study, by using multi-electrode recording system, we simultaneously recorded spike discharges from a group of dimming detectors (OFF-sustained type ganglion cells) in bullfrog retina. The changes in receptive field properties and synchronization strength during contrast adaptation were analyzed. It was found that, when perfused using normal Ringer's solution, single neuronal receptive field size was reduced during contrast adaptation, which was accompanied by weakening in synchronization strength between adjacent neurons' activities. When dopamine (1 µM) was applied, the adaptation-related receptive field area shrinkage and synchronization weakening were both eliminated. The activation of D1 receptor was involved in the adaptation-related modulation of synchronization and receptive field. Our results thus suggest that the size of single neuron's receptive field is positively related to the strength of its synchronized activity with its neighboring neurons, and the dopaminergic pathway is responsible for the modulation of receptive field property and synchronous activity of the ganglion cells during the adaptation process

Digital Signal Processing Research Program

Contains table of contents for Part III, table of contents for Section 1, an introduction and reports on seventeen research projects.U.S. Navy - Office of Naval Research Contract N00014-90-J-1544Charles S. Draper Laboratory Contract DL-H-404158Rockwell Corporation Doctoral FellowshipU.S. Navy - Office of Naval Research Grant N00014-89-J-1489U.S. Navy - Office of Naval Research Grant N00014-90-J-1109The Federative Republic of Brazil ScholarshipLockheed Sanders, Inc.National Science Foundation Grant MIP 87-14969AT&T Bell Laboratories Doctoral ProgramBell Northern Research Ltd.Defense Advanced Research Projects Agency Contract N00014-87-K-0825IBM CorporationSloan FoundationU.S. Air Force - Office of Scientific Research FellowshipU.S. Air Force - Office of Scientific Research Grant AFOSR-91-0034National Science Foundation Graduate FellowshipCanada, Natural Science and Engineering Research Council ScholarshipU.S. Air Force - Office of Scientific Research Grant AFOSR-91-0034Texas Instruments, Inc