Crystal Structure of the Streptomyces coelicolor Sortase E1 Transpeptidase Provides Insight into the Binding Mode of the Novel Class E Sorting Signal
Abstract not provided
Kattke, Michele D.↗
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Ankyrin repeats as a dimerization module
Highlights: • We determined crystal structure of Legionella effector AnkC. • The structure displays seven ankyrin repeats with unique structural features. • AnkC dimerizes using outer surface of loops between ankyrin repeats. • This is the first example of ankyrin repeats-mediated dimerization. Legionella pneumophila is a pathogen, causing severe pneumonia in humans called Legionnaires' disease. AnkC (LegA12) is a poorly characterized 495-residue effector protein conserved in multiple Legionella species. Here, we report the crystal structure of a C-terminally truncated AnkC (2–384) at 3.2 Å resolution. The structure shows seven ankyrin repeats (ARs) with unique structural features. AnkC forms a dimer along the outer surface of loops between ARs. The dimer exists both in the crystal form and in solution, as shown by analytical ultracentrifugation. This is the first example of ARs as a dimerization module as opposed to solely a protein interaction domain. In addition, a novel α-helix insert between AR3-AR4 is positioned across the surface opposite the ankyrin groove. Sequence conservation suggests that the ankyrin groove of AnkC is a functional site that interacts with binding targets. This ankyrin domain structure is an important step towards a functional characterization of AnkC.
60 APPLIED LIFE SCIENCES↗
Fast jet tagging with MLP-Mixers on FPGAs
We explore the innovative use of MLP-Mixer models for real-time jet tagging and establish their feasibility on resource-constrained hardware like FPGAs. MLP-Mixers excel in processing sequences of jet constituents, achieving state-of-the-art performance on datasets mimicking Large Hadron Collider conditions. By using advanced optimization techniques such as High-Granularity Quantization and Distributed Arithmetic, we achieve unprecedented efficiency. These models match or surpass the accuracy of previous architectures, reduce hardware resource usage by up to 97%, double the throughput, and half the latency. Additionally, non-permutation-invariant architectures enable smart feature prioritization and efficient FPGA deployment, setting a new benchmark for machine learning in real-time data processing at particle colliders.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles.
Cells of most bacterial species are around 2 micrometers in length, with some of the largest specimens reaching 750 micrometers. Using fluorescence, x-ray, and electron microscopy in conjunction with genome sequencing, we characterized Candidatus ( Ca. ) Thiomargarita magnifica, a bacterium that has an average cell length greater than 9000 micrometers and is visible to the naked eye. These cells grow orders of magnitude over theoretical limits for bacterial cell size, display unprecedented polyploidy of more than half a million copies of a very large genome, and undergo a dimorphic life cycle with asymmetric segregation of chromosomes into daughter cells. These features, along with compartmentalization of genomic material and ribosomes in translationally active organelles bound by bioenergetic membranes, indicate gain of complexity in the Thiomargarita lineage and challenge traditional concepts of bacterial cells.
Volland, Jean-Marie↗
The Tp0684 (MglB-2) Lipoprotein of Treponema pallidum : A Glucose-Binding Protein with Divergent Topology
Treponema pallidum , the bacterium that causes syphilis, is an obligate human parasite. As such, it must acquire energy, in the form of carbon sources, from the host. There is ample evidence that the principal source of energy for this spirochete is D-glucose acquired from its environment, likely via an ABC transporter. Further, there is genetic evidence of a D-glucose chemotaxis system in T. pallidum . Both of these processes may be dependent on a single lipidated chemoreceptor: Tp0684, also called TpMglB-2 for its sequence homology to MglB of Escherichia coli . To broaden our understanding of this potentially vital protein, we determined a 2.05-Å X-ray crystal structure of a soluble form of the recombinant protein. Like its namesake, TpMglB-2 adopts a bilobed fold that is similar to that of the ligand-binding proteins (LBPs) of other ABC transporters. However, the protein has an unusual, circularly permuted topology. This feature prompted a series of biophysical studies that examined whether the protein’s topological distinctiveness affected its putative chemoreceptor functions. Differential scanning fluorimetry and isothermal titration calorimetry were used to confirm that the protein bound D-glucose in a cleft between its two lobes. Additionally, analytical ultracentrifugation was employed to reveal that D-glucose binding is accompanied by a significant conformational change. TpMglB-2 thus appears to be fully functional in vitro, and given the probable central importance of the protein to T. pallidum’s physiology, our results have implications for the viability and pathogenicity of this obligate human pathogen.
Science & Technology - Other Topics↗
Whither the genus Caldicellulosiruptor and the order Thermoanaerobacterales: phylogeny, taxonomy, ecology, and phenotype
The order Thermoanaerobacterales currently consists of fermentative anaerobic bacteria, including the genus Caldicellulosiruptor. Caldicellulosiruptor are represented by thirteen species; all, but one, have closed genome sequences. Interest in these extreme thermophiles has been motivated not only by their high optimal growth temperatures (≥70°C), but also by their ability to hydrolyze polysaccharides including, for some species, both xylan and microcrystalline cellulose. Caldicellulosiruptor species have been isolated from geographically diverse thermal terrestrial environments located in New Zealand, China, Russia, Iceland and North America. Evidence of their presence in other terrestrial locations is apparent from metagenomic signatures, including volcanic ash in permafrost. Here, phylogeny and taxonomy of the genus Caldicellulosiruptor was re-examined in light of new genome sequences. Based on genome analysis of 15 strains, a new order, Caldicellulosiruptorales, is proposed containing the family Caldicellulosiruptoraceae, consisting of two genera, Caldicellulosiruptor and Anaerocellum. Furthermore, the order Thermoanaerobacterales also was re-assessed, using 91 genome-sequenced strains, and should now include the family Thermoanaerobacteraceae containing the genera Thermoanaerobacter, Thermoanaerobacterium, Caldanaerobacter, the family Caldanaerobiaceae containing the genus Caldanaerobius, and the family Calorimonaceae containing the genus Calorimonas. A main outcome of ANI/AAI analysis indicates the need to reclassify several previously designated species in the Thermoanaerobacterales and Caldicellulosiruptorales by condensing them into strains of single species. Comparative genomics of carbohydrate-active enzyme inventories suggested differentiating phenotypic features, even among strains of the same species, reflecting available nutrients and ecological roles in their native biotopes.
59 BASIC BIOLOGICAL SCIENCES↗
Suppression of Stacking Order with Doping in 1T-TaS 2–x Se x
In 1T-TaS 2–x Se x , the charge density wave (CDW) state features a star of David lattice that expands across layers as the system becomes commensurate upon cooling. The layers can also order along the c-axis, and different stacking orders have been proposed. For this work, using neutron scattering on powder samples, we compared the stacking order previously observed in 1T-TaS 2 when the system is doped with Se. While at low temperature, a 13c layer sequence stacking was observed in TaS 2 ; this type of ordering was not evident with doping. Doping with Se results in a metallic state in which the Mott transition is suppressed, which may be linked to the absence of layer stacking.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Information contained in protein shapes
The sequence of local conformations at C-alpha atoms of a protein has been considered as an informational message string. The total self-information contents and self-information per letter have been evaluated for 83 globular proteins whose structures are known from X-ray crystallography. The derived information contents provide a method of quantitating structural specificity of proteins. This method of analysis enables repeating, intricate structural features to be recognized. Among the globular proteins whose structures have been solved, high potential iron protein stands out with the largest three-letter dependence.
Sundaram, K.↗
Observing rotation and deformation of sea ice with synthetic aperture radar
The ESA's ERS-1 satellite will carry SARs over the polar regions; an important component in the use of these data is an automated scheme for the extraction of sea ice velocity fields from a sequence of SAR images of the same geographical region. The image pyramid area-correlation hierarchical method is noted to be vulnerable to uncertainties for sea ice rotations greater than 10-15 deg between SAR observations. Rotation-invariant methods can successfully track isolated floes in the marginal ice zone. Hu's (1962) invariant moments are also worth considering as a possible basis for rotation-invariant tracking methods. Feature tracking is inherently robust for tracking rotating sea ice, but is limited when features are floe-lead boundaries. A variety of techniques appears neccessary.
Vesecky, J. F.↗
Adams-Based Rover Terramechanics and Mobility Simulator - ARTEMIS
The Mars Exploration Rovers (MERs), Spirit and Opportunity, far exceeded their original drive distance expectations and have traveled, at the time of this reporting, a combined 29 kilometers across the surface of Mars. The Rover Sequencing and Visualization Program (RSVP), the current program used to plan drives for MERs, is only a kinematic simulator of rover movement. Therefore, rover response to various terrains and soil types cannot be modeled. Although sandbox experiments attempt to model rover-terrain interaction, these experiments are time-intensive and costly, and they cannot be used within the tactical timeline of rover driving. Imaging techniques and hazard avoidance features on MER help to prevent the rover from traveling over dangerous terrains, but mobility issues have shown that these methods are not always sufficient. ARTEMIS, a dynamic modeling tool for MER, allows planned drives to be simulated before commands are sent to the rover. The deformable soils component of this model allows rover-terrain interactions to be simulated to determine if a particular drive path would take the rover over terrain that would induce hazardous levels of slip or sink. When used in the rover drive planning process, dynamic modeling reduces the likelihood of future mobility issues because high-risk areas could be identified before drive commands are sent to the rover, and drives planned over these areas could be rerouted. The ARTEMIS software consists of several components. These include a preprocessor, Digital Elevation Models (DEMs), Adams rover model, wheel and soil parameter files, MSC Adams GUI (commercial), MSC Adams dynamics solver (commercial), terramechanics subroutines (FORTRAN), a contact detection engine, a soil modification engine, and output DEMs of deformed soil. The preprocessor is used to define the terrain (from a DEM) and define the soil parameters for the terrain file. The Adams rover model is placed in this terrain. Wheel and soil parameter files can be altered in the respective text files. The rover model and terrain are viewed in Adams View, the GUI for ARTEMIS. The Adams dynamics solver calls terramechanics subroutines in FORTRAN containing the Bekker-Wong equations.
Trease, Brian P.↗
Asc-Seurat: analytical single-cell Seurat-based web application
Abstract Background Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data and uncover relevant biological information. A diversity of tools has been developed to address the multiple aspects of scRNA-seq data analysis. However, an easy-to-use web application capable of conducting all critical steps of scRNA-seq data analysis is still lacking. Summary We present Asc-Seurat, a feature-rich workbench, providing an user-friendly and easy-to-install web application encapsulating tools for an all-encompassing and fluid scRNA-seq data analysis. Asc-Seurat implements functions from the Seurat package for quality control, clustering, and genes differential expression. In addition, Asc-Seurat provides a pseudotime module containing dozens of models for the trajectory inference and a functional annotation module that allows recovering gene annotation and detecting gene ontology enriched terms. We showcase Asc-Seurat’s capabilities by analyzing a peripheral blood mononuclear cell dataset. Conclusions Asc-Seurat is a comprehensive workbench providing an accessible graphical interface for scRNA-seq analysis by biologists. Asc-Seurat significantly reduces the time and effort required to analyze and interpret the information in scRNA-seq datasets.
60 APPLIED LIFE SCIENCES↗
Accelerating strain phenotyping with desorption electrospray ionization-imaging mass spectrometry and untargeted analysis of intact microbial colonies
Significance Synthetic biology has entered an era in which reading and writing DNA sequences are no longer rate-limiting steps in microbial strain engineering. Indeed, analytical methods measuring the resulting metabolic outcomes of specific gene edits have lagged behind the ability to generate new recombinant strains. Herein, we report a mass spectrometry strategy to accelerate these analytical workflows by directly analyzing metabolites and molecules produced from engineered microorganisms in a multiplexed process. Using untargeted acquisitions and unsupervised analytics, we assess the molecular features that change across discrete strains including primary target species, secondary products, and species outside the engineered fatty acid biosynthesis pathway.
09 BIOMASS FUELS↗
Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism
Abstract Background Crassulacean acid metabolism (CAM), a specialized mode of photosynthesis, enables plant adaptation to water-limited environments and improves photosynthetic efficiency via an inorganic carbon-concentrating mechanism. Kalanchoë fedtschenkoi is an obligate CAM model featuring a relatively small genome and easy stable transformation. However, the molecular responses to light quality and intensity in CAM plants remain understudied. Results Here we present a genome-wide expression atlas of K. fedtschenkoi plants grown under 12 h/12 h photoperiod with different light quality (blue, red, far-red, white light) and intensity (0, 150, 440, and 1,000 μmol m–2 s–1) based on RNA sequencing performed for mature leaf samples collected at dawn (2 h before the light period) and dusk (2 h before the dark period). An eFP web browser was created for easy access of the gene expression data. Based on the expression atlas, we constructed a light-responsive co-expression network to reveal the potential regulatory relationships in K. fedtschenkoi. Measurements of leaf titratable acidity, soluble sugar, and starch turnover provided metabolic indicators of the magnitude of CAM under the different light treatments and were used to provide biological context for the expression dataset. Furthermore, CAM-related subnetworks were highlighted to showcase genes relevant to CAM pathway, circadian clock, and stomatal movement. In comparison with white light, monochrome blue/red/far-red light treatments repressed the expression of several CAM-related genes at dusk, along with a major reduction in acid accumulation. Increasing light intensity from an intermediate level (440 μmol m-2 s-1) of white light to a high light treatment (1,000 μmol m–2 s–1) increased expression of several genes involved in dark CO2 fixation and malate transport at dawn, along with an increase in organic acid accumulation. Conclusions This study provides a useful genomics resource for investigating the molecular mechanism underlying the light regulation of physiology and metabolism in CAM plants. Our results support the hypothesis that both light intensity and light quality can modulate the CAM pathway through regulation of CAM-related genes in K. fedtschenkoi.
59 BASIC BIOLOGICAL SCIENCES↗
Predicting variable gene content in Escherichia coli using conserved genes
Having the ability to predict the protein-encoding gene content of an incomplete genome or metagenome-assembled genome is important for a variety of bioinformatic tasks. In this study, as a proof of concept, we built machine learning classifiers for predicting variable gene content in Escherichia coli genomes using only the nucleotide k-mers from a set of 100 conserved genes as features. Protein families were used to define orthologs, and a single classifier was built for predicting the presence or absence of each protein family occurring in 10%–90% of all E. coli genomes. The resulting set of 3,259 extreme gradient boosting classifiers had a per-genome average macro F1 score of 0.944 [0.943–0.945, 95% CI]. We show that the F1 scores are stable across multi-locus sequence types and that the trend can be recapitulated by sampling a smaller number of core genes or diverse input genomes. Surprisingly, the presence or absence of poorly annotated proteins, including “hypothetical proteins” was accurately predicted (F1 = 0.902 [0.898–0.906, 95% CI]). Models for proteins with horizontal gene transfer-related functions had slightly lower F1 scores but were still accurate (F1s = 0.895, 0.872, 0.824, and 0.841 for transposon, phage, plasmid, and antimicrobial resistance-related functions, respectively). Finally, using a holdout set of 419 diverse E. coli genomes that were isolated from freshwater environmental sources, we observed an average per-genome F1 score of 0.880 [0.876–0.883, 95% CI], demonstrating the extensibility of the models. Overall, this study provides a framework for predicting variable gene content using a limited amount of input sequence data.
59 BASIC BIOLOGICAL SCIENCES↗
Considering the Lives of Microbes in Microbial Communities
ABSTRACT Over the last decades, sequencing technologies have transformed our ability to investigate the composition and functional capacity of microbial communities. Yet, critical questions remain about these complex systems that cannot be addressed by the bulk, community-averaged data typically provided by sequencing methods. In this Perspective, I propose that future advances in microbiome research will emerge from considering “the lives of microbes”: we need to create methods to explicitly interrogate how microbes exist and interact in native-setting-like microenvironments. This approach includes developing approaches that expose the phenotypic heterogeneity of microbes; exploring the effects of coculture cues on cellular differentiation and metabolite production; and designing visualization systems that capture features of native microbial environments while permitting the nondestructive observation of microbial interactions over space and time with single-cell resolution.
59 BASIC BIOLOGICAL SCIENCES↗
Influenza A Virus Multicycle Replication Yields Comparable Viral Population Emergence in Human Respiratory and Ocular Cell Types
While primarily considered a respiratory pathogen, influenza A virus (IAV) is nonetheless capable of spreading to, and replicating in, numerous extrapulmonary tissues in humans. However, within-host assessments of genetic diversity during multicycle replication have been largely limited to respiratory tract tissues and specimens. As selective pressures can vary greatly between anatomical sites, there is a need to examine how measures of viral diversity may vary between influenza viruses exhibiting different tropisms in humans, as well as following influenza virus infection of cells derived from different organ systems. Here, we employed human primary tissue constructs emulative of the human airway or corneal surface, and we infected both with a panel of human- and avian-origin IAV, inclusive of H1 and H3 subtype human viruses and highly pathogenic H5 and H7 subtype viruses, which are associated with both respiratory disease and conjunctivitis following human infection. While both cell types supported productive replication of all viruses, airway-derived tissue constructs elicited greater induction of genes associated with antiviral responses than did corneal-derived constructs. We used next-generation sequencing to examine viral mutations and population diversity, utilizing several metrics. With few exceptions, generally comparable measures of viral diversity and mutational frequency were detected following homologous virus infection of both respiratory-origin and ocular-origin tissue constructs. Expansion of within-host assessments of genetic diversity to include IAV with atypical clinical presentations in humans or in extrapulmonary cell types can provide greater insight into understanding those features most prone to modulation in the context of viral tropism.
59 BASIC BIOLOGICAL SCIENCES↗
IMG Annotation Pipeline (IMGAP) v5.1.13
The IMG Annotation Pipeline is a collection of Bash and Python scripts to control a workflow for structural and functional annotation of prokaryotic genomes, metagenomes, and metatranscriptomes. The bash scripts in general control the overall workflow and are wrappers around 3rd party executables (not included in repo) that predict features or functions. Whereas the Python scripts do post-processing of raw output in terms of filtering or format transformation and in some cases contain some logic for picking the correct predictions or resolving overlaps. The pipeline is tailored to produce results required by IMG (https://img.jgi.doe.gov/) and is executed on every dataset submitted to IMG via https://img.jgi.doe.gov/submit. These consist of internal genomes, metagenomes and metatranscriptomes sequenced and assembled at the JGI, as well as datasets submitted by external users (non-lab/JGI affiliates).
Huntemann, Marcel↗
Vibration of thermally buckled composite plates with initial deflections using triangular elements
A consistent finite element formulation is presented for the analysis of thermal postbuckling and free vibration of thermally buckled thin, laminated composite plates subjected to large temperature change. The influence of moderately large initial imperfections in deflection on the thermal postbuckling deflection and the vibration characteristics of the buckled plate is also investigated. The finite element equations of motion are derived from the principle of virtual work. These equations can be mathematically separated into two sets and solved in sequence. The first set of equations yields the particular solution of static thermal postbuckling deflection, and the second set of equations gives the homogeneous solution of vibration characteristics on the buckled plate. The first set of static equations is solved by using Newton-Raphson iteration method. The tangent stiffness matrix in the final iteration is equal to the total stiffness matrix of the second set of dynamic equations. This feature saves tremendous computation time in comparing with using the conventional approach. The influence of lamination angle, temperature distribution, plate planform of arbitrary shape, and boundary support conditions on postbuckling and vibration behavior are investigated.
Zhou, R. C.↗