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At least 235 records · Page 13

Daily evapotranspiration changes during heatwaves at 32 NEON sites, 2019-2021

This dataset provides partitioned evapotranspiration (ET, the combined loss of water from soil and plant surfaces) anomalies during heatwave events—soil evaporation (E) and transpiration (T)—for 268 heatwave events across 32 National Ecological Observatory Network (NEON) flux sites in the contiguous United States from 2019–2021. Using an ensemble of four high-frequency turbulence methods (Flux-variance Similarity, Conditional Eddy Covariance [CEC], CEC with Water-Use Efficiency, and Conditional Eddy Accumulation; see Zahn and Bou-Zeid 2024), half-hourly transpiration-to-evapotranspiration (T/ET) ratios were derived from 20 hertz (Hz, cycles per second) eddy covariance measurements of carbon dioxide (CO₂) and water vapor (H₂O) concentrations. The dataset spans six vegetation types including evergreen and deciduous forests, grasslands, cultivated crops, shrublands, and emergent herbaceous wetlands. Data Package Contents: The dataset includes a single CSV (comma-separated values) file containing daily anomalies (deviations from baseline conditions) for transpiration (Delta_T), evaporation (Delta_E), total evapotranspiration (Delta_ET), and T/ET ratio (Delta_T_ET) during each day of identified heatwave events. The file also includes site codes, dates, heatwave event identifiers, and day-of-heatwave indicators. The CSV file can be opened with spreadsheet software (Microsoft Excel, Google Sheets) or programming environments (Python, R, MATLAB). This resource enables researchers to investigate ecosystem-specific responses to thermal extremes, validate land surface model partitioning of ET fluxes, and examine feedbacks between water cycling and surface energy balance during heatwaves. The dataset is particularly valuable for studies linking vegetation hydraulic strategies to climate resilience, as it captures the divergent responses of shallow-rooted versus deep-rooted ecosystems. Potential applications include improving drought early warning systems, informing irrigation management strategies, and advancing our mechanistic understanding of land-atmosphere interactions under extreme heat conditions.

Day of Heatwave↗

Protocol for Communication Networking for Formation Flying

An application-layer protocol and a network architecture have been proposed for data communications among multiple autonomous spacecraft that are required to fly in a precise formation in order to perform scientific observations. The protocol could also be applied to other autonomous vehicles operating in formation, including robotic aircraft, robotic land vehicles, and robotic underwater vehicles. A group of spacecraft or other vehicles to which the protocol applies could be characterized as a precision-formation- flying (PFF) network, and each vehicle could be characterized as a node in the PFF network. In order to support precise formation flying, it would be necessary to establish a corresponding communication network, through which the vehicles could exchange position and orientation data and formation-control commands. The communication network must enable communication during early phases of a mission, when little positional knowledge is available. Particularly during early mission phases, the distances among vehicles may be so large that communication could be achieved only by relaying across multiple links. The large distances and need for omnidirectional coverage would limit communication links to operation at low bandwidth during these mission phases. Once the vehicles were in formation and distances were shorter, the communication network would be required to provide high-bandwidth, low-jitter service to support tight formation-control loops. The proposed protocol and architecture, intended to satisfy the aforementioned and other requirements, are based on a standard layered-reference-model concept. The proposed application protocol would be used in conjunction with conventional network, data-link, and physical-layer protocols. The proposed protocol includes the ubiquitous Institute of Electrical and Electronics Engineers (IEEE) 802.11 medium access control (MAC) protocol to be used in the datalink layer. In addition to its widespread and proven use in diverse local-area networks, this protocol offers both (1) a random- access mode needed for the early PFF deployment phase and (2) a time-bounded-services mode needed during PFF-maintenance operations. Switching between these two modes could be controlled by upper-layer entities using standard link-management mechanisms. Because the early deployment phase of a PFF mission can be expected to involve multihop relaying to achieve network connectivity (see figure), the proposed protocol includes the open shortest path first (OSPF) network protocol that is commonly used in the Internet. Each spacecraft in a PFF network would be in one of seven distinct states as the mission evolved from initial deployment, through coarse formation, and into precise formation. Reconfiguration of the formation to perform different scientific observations would also cause state changes among the network nodes. The application protocol provides for recognition and tracking of the seven states for each node and for protocol changes under specified conditions to adapt the network and satisfy communication requirements associated with the current PFF mission phase. Except during early deployment, when peer-to-peer random access discovery methods would be used, the application protocol provides for operation in a centralized manner.

Jennings, Esther↗

Mechanosensitive channels of Escherichia coli: the MscL gene, protein, and activities

Although mechanosensory responses are ubiquitous and diverse, the molecular bases of mechanosensation in most cases remain mysterious MscL, a mechanosensitive channel of large conductance of Escherichia coli and its bacterial homologues are the first and currently only channel molecules shown to directly sense mechanical stretch of the membrane. In response to the tension conveyed via the lipid bilayer, MscL increases its open probability by several orders of magnitude. In the present review we describe the identification, cloning, and first sets of biophysical and structural data on this simplest mechanosensory molecule. We discovered a 2.5-ns mechanosensitive conductance in giant E. coli spheroplasts. Using chromatographies to enrich the target and patch clamp to assay the channel activity in liposome-reconstituted fractions, we identified the MscL protein and cloned the mscL gene. MscL comprises 136 amino acid residues (15 kDa), with two highly hydrophobic regions, and resides in the inner membrane of the bacterium. PhoA-fusion experiments indicate that the protein spans the membrane twice with both termini in the cytoplasm. Spectroscopic techniques show that it is highly helical. Expression of MscL tandems and covalent cross-linking suggest that the active channel complex is a homo-hexamer. We have identified several residues, which when deleted or substituted, affect channel kinetics or mechanosensitivity. Although unique when discovered, highly conserved MscL homologues in both gram-negative and gram-positive bacteria have been found, suggesting their ubiquitous importance among bacteria.

Non-NASA Center↗

Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three-dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe, PDBe.org) as an open-source, web-based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. Across RCSB.org, the RCSB PDB research-focused web portal, Mol* has been implemented to support single-mouse-click atomic-level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small-molecule ligands, ions, water molecules, or other macromolecules. RCSB.org Mol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within various RCSB.org tools—allowing users to view polymer sequence and structure-based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available at RCSB.org, Standalone Mol* is freely available for visualizing any atomic-level or multi-scale biostructure at rcsb.org/3d-view.

3D biostructure↗

Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding

Abstract Motivation The vast expansion of sequence data generated from single organisms and microbiomes has precipitated the need for faster and more sensitive methods to assess evolutionary and functional relationships between proteins. Representing proteins as sets of short peptide sequences (kmers) has been used for rapid, accurate classification of proteins into functional categories; however, this approach employs an exact-match methodology and thus may be limited in terms of sensitivity and coverage. We have previously used similarity groupings, based on the chemical properties of amino acids, to form reduced character sets and recode proteins. This amino acid recoding (AAR) approach simplifies the construction of protein representations in the form of kmer vectors, which can link sequences with distant sequence similarity and provide accurate classification of problematic protein families. Results Here, we describe Snekmer, a software tool for recoding proteins into AAR kmer vectors and performing either (i) construction of supervised classification models trained on input protein families or (ii) clustering for de novo determination of protein families. We provide examples of the operation of the tool against a set of nitrogen cycling families originally collected using both standard hidden Markov models and a larger set of proteins from Uniprot and demonstrate that our method accurately differentiates these sequences in both operation modes. Availability and implementation Snekmer is written in Python using Snakemake. Code and data used in this article, along with tutorial notebooks, are available at http://github.com/PNNL-CompBio/Snekmer under an open-source BSD-3 license. Supplementary information Supplementary data are available at Bioinformatics Advances online.

59 BASIC BIOLOGICAL SCIENCES↗

Using Data Science Tools to Reveal and Understand Subtle Relationships of Inhibitor Structure in Frontal Ring-Opening Metathesis Polymerization

The rate of frontal ring-opening metathesis polymerization (FROMP) using the Grubbs generation II catalyst is impacted by both the concentration and choice of monomers and inhibitors, usually organophosphorus derivatives. Herein we report a data-science-driven workflow to evaluate how these factors impact both the rate of FROMP and how long the formulation of the mixture is stable (pot life). Using this workflow, we built a classification model using a single-node decision tree to determine how a simple phosphine structural descriptor (V bur-near ) can bin long versus short pot life. Additionally, we applied a nonlinear kernel ridge regression model to predict how the inhibitor and selection/concentration of comonomers impact the FROMP rate. Furthermore, the analysis provides selection criteria for material network structures that span from highly cross-linked thermosets to non-cross-linked thermoplastics as well as degradable and nondegradable materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Controlling the helicity of light by electrical magnetization switching

Controlling the intensity of emitted light and charge current is the basis of transferring and processing information. By contrast, robust information storage and magnetic random-access memories are implemented using the spin of the carrier and the associated magnetization in ferromagnets. In this study, the missing link between the respective disciplines of photonics, electronics and spintronics is to modulate the circular polarization of the emitted light, rather than its intensity, by electrically controlled magnetization. Here we demonstrate that this missing link is established at room temperature and zero applied magnetic field in light-emitting diodes through the transfer of angular momentum between photons, electrons and ferromagnets. With spin-orbit torque a charge current generates also a spin current to electrically switch the magnetization. This switching determines the spin orientation of injected carriers into semiconductors, in which the transfer of angular momentum from the electron spin to photon controls the circular polarization of the emitted light. The spin-photon conversion with the nonvolatile control of magnetization opens paths to seamlessly integrate information transfer, processing and storage. Our results provide substantial advances towards electrically controlled ultrafast modulation of circular polarization and spin injection with magnetization dynamics for the next-generation information and communication technology, including space-light data transfer. The same operating principle in scaled-down structures or using two-dimensional materials will enable transformative opportunities for quantum information processing with spin-controlled single-photon sources, as well as for implementing spin-dependent time-resolved spectroscopies.

74 ATOMIC AND MOLECULAR PHYSICS↗

Remote Asynchronous Message Service Gateway

The Remote Asynchronous Message Service (RAMS) gateway is a special-purpose AMS application node that enables exchange of AMS messages between nodes residing in different AMS "continua," notionally in different geographical locations. JPL s implementation of RAMS gateway functionality is integrated with the ION (Interplanetary Overlay Network) implementation of the DTN (Delay-Tolerant Networking) bundle protocol, and with JPL s implementation of AMS itself. RAMS protocol data units are encapsulated in ION bundles and are forwarded to the neighboring RAMS gateways identified in the source gateway s AMS management information base. Each RAMS gateway has interfaces in two communication environments: the AMS message space it serves, and the RAMS network - the grid or tree of mutually aware RAMS gateways - that enables AMS messages produced in one message space to be forwarded to other message spaces of the same venture. Each gateway opens persistent, private RAMS network communication channels to the RAMS gateways of other message spaces for the same venture, in other continua. The interconnected RAMS gateways use these communication channels to forward message petition assertions and cancellations among themselves. Each RAMS gateway subscribes locally to all subjects that are of interest in any of the linked message spaces. On receiving its copy of a message on any of these subjects, the RAMS gateway node uses the RAMS network to forward the message to every other RAMS gateway whose message space contains at least one node that has subscribed to messages on that subject. On receiving a message via the RAMS network from some other RAMS gateway, the RAMS gateway node forwards the message to all subscribers in its own message space.

Wang, Shin-Ywan↗

Onset of long-lived silicic and alkaline magmatism in eastern North America preceded CAMP emplacement

The White Mountain Magma Series (WMMS) is the largest Mesozoic felsic igneous province on the Eastern North American Margin (ENAM). Existing geochronology has suggested that magmatism occurred over 50 Myr with published ages for the oldest units apparently coeval with the ca. 201 Ma Central Atlantic Magmatic Province (CAMP), the flood basalt province associated with the end-Triassic mass extinction and the opening of the Atlantic Ocean. We use zircon U-Pb geochronology to show that emplacement of WMMS plutons was already underway at 207.5 Ma. The largest volcanic-plutonic complex, the White Mountain Batholith, was emplaced episodically from ca. 198.5 Ma to ca. 180 Ma, ca. 25 Myr older than published ages suggest, and all samples we dated from the Moat Volcanics are between ca. 185 to 180 Ma. This result shows that the Moat Volcanics and the White Mountain Batholith are broadly comagmatic, and it also constrains the age of a key Jurassic paleomagnetic pole. Our data suggest that a regional mantle thermal anomaly in eastern North America developed at least ca. 5 Myr prior to the main stage of CAMP flood basalt volcanism and suggests a geodynamic link between the WMMS and the CAMP.

Sean T. Kinney↗

Emission, absorption and group delay of microwaves in the atmosphere in relation to water vapour content over the Indian subcontinent

The advent of satellite communication for global coverage has apparently indicated a renewed interest in the studies of radio wave propagation through the atmosphere, in the VHF, UHF and microwave bands. The extensive measurements of atmosphere constituents, dynamics and radio meterological parameters during the Middle Atmosphere Program (MAP) have opened up further the possibilities of studying tropospheric radio wave propagation parameters, relevant to Earth/space link design. The three basic parameters of significance to radio propagation are thermal emission, absorption and group delay of the atmosphere, all of which are controlled largely by the water vapor content in the atmosphere, particular at microwave bands. As good emitters are also good absorbers, the atmospheric emission as well as the absorption attains a maximum at the frequency of 22.235 GHz, which is the peak of the water vapor line. The group delay is practically independent of frequency in the VHF, UHF and microwave bands. However, all three parameters exhibit a similar seasonal dependence originating presumably from the seasonal dependence of the water vapor content. Some of the interesting results obtained from analyses of radiosonde data over the Indian subcontinent collected by the India Meteorological Department is presented.

Sen, A. K.↗

Europa Clipper Payload Verification and Validation: Avionics-Instrument Interface Test Campaign

NASA's Europa Clipper mission will investigate Jupiter's icy moon Europa using a payload suite consisting of nine instruments to address a range of scientific objectives concerning Europa's habitability. As the project proceeds past its Critical Design Review, confidence is being built in the system's ability to achieve mission objectives through the implementation of a rigorous payload verification and validation (V&V) program. As part of this payload V&V program, instrument box-level testing was performed by the payload team to verify select instrument-avionics interface requirements. This testing was performed at JPL using the avionics testbed's Bulk Data Storage Emulator (BDSEM) with visiting instrument Test Models. This paper summarizes the Data Link test campaign involving roughly four days of functional testing per instrument, including planning, testing methods, types of issues found, and the requirement closure process. Detail is also provided on the development, deployment, and validation of a standardized analysis tool used in data reviews. This testing verified requirements related to commanding rates, loss of link, packet format, clock counters, loopback test capability, and SpaceWire jitter and skew margins. Additional risk reduction testing of basic commanding, counter behavior, science data collection and transfer, and interface swapping was also performed. Because the BDSEM venue was not originally designed to be a run for record venue, the process of characterizing venue fidelity and establishing suitability for requirement closure using data collected in this venue will also be addressed.In order to close requirements, an extensible tool was developed to post-process instrument command and telemetry data from their original binary to a human-readable format and give visibility to errors detected within the data, such as packets with Cyclic Redundancy Check errors. This tool, called payload-packet-parser, is a Python 3.9 command line tool built using a variety of open-source Python libraries. Payload-packet-parser was designed to support parsing command and telemetry packets for all Europa Clipper instruments and additional analysis tools were developed for verification of specific information interface requirements. This test campaign, including post-processing using a single parsing and verification toolset, allowed for early interface testing, alleviating testing burdens on instrument teams and buying down risk on the instrument-avionics interface by finding hardware and software issues and idiosyncrasies prior to integration with system test venues. Over twenty issues were discovered across the payload, resulting in software updates and instrument rework well in advance of any system impacts. This paper concludes with an assessment of benefits and costs of this type of testing and lessons learned.

Montanez, Leticia↗

Search for Pulsations from a Nearby Millisecond Pulsar and Wasilewski 49: Mirror for a Hidden Seyfert 1 Nucleus

Five studies are reported in this final report. The recently discovered 5.3 ms pulsar J1012+5307 at a distance of 520 pc is in an area of the sky which is particularly deficient in absorbing gas. The column density along the line of sight is less than 7.5 x 10(exp 19) CM(exp -2) which facilitates soft X-ray observations. Halpern reported a possible ROSAT Position Sensitive Proportional Counter (PSPC) detection of the pulsar in a serendipitous, off-axis observation. We have now confirmed the X-ray emission of PSR J1012+,5307 in a 23 ksec observation with the ROSAT High Resolution Imager (HRI). A point source is detected within 3" of the radio position. Its count rate of 1.6 +/- 0.3 x 10(exp -3) s(exp -1) corresponds to an unabsorbed 0. 1-2.4 keV flux of 6.4 x 10(exp -14) ergs cm(exp -2) s(exp -1), similar to that reported previously. This counts-to-flux conversion is valid for N(sub H) = 5 x 10(exp 19) cm(exp -2), and either a power-law spectrum of photon index 2.5 or a blackbody of kT = 0.1 keV. The implied X-ray luminosity of 2.0 x 10(exp 30) ergs s(exp -1) is 5 X 10(exp -4) of the pulsar's spin-down power dot-E, and similar to that of the nearest millisecond pulsar J0437-4715, which is nearly a twin of J1012+5307 in P dot-E. We subjected the 37 photons (and 13 background counts) within the source region to a pulsar search, but no evidence for pulsation was found. The pulsar apparently emits over a large fraction of its rotation cycle, and the absence of sharp modulation can be taken as evidence for surface thermal emission, as is favored for PSR J0437-4715, rather than magnetospheric X-ray emission which is apparent in the sharp pulses of the much more energetic millisecond pulsar B1821-24. A further test of this interpretation will be made with a longer ROSAT observation, which will increase the number of photons collected by a factor of 5, and permit a more sensitive examination of the light curve for modulation due to emission from heated polar caps. If found, such modulation will be further evidence that surface reheating by the impact of particles accelerated along open fiel;d lines operates in these approximately 10(exp -9) year old pulsars. In a second study, a new AM Her star serendipitously in a 25 day observation was detected with the EUVE satellite. A coherent period of 85.82 min is present in the EUVE Deep Survey imager light curve of this source. A spectroscopic optical identification is made with a 19th magnitude blue star that has H and He emission lines, and broad cyclotron humps typical of a magnetic cataclysmic variable. A lower limit to the polar magnetic field of 50 MG is estimated from the spacing of the cyclotron harmonics. EUVE J0425.6-5714 is also detected in archival ROSAT HRI observations spanning two months, and its stable and highly structured light curve permits us to fit a coherent ephemeris linking the ROSAT and EUVE data over a 1.3 yr gap. The derived period is 85.82107 +/- 0.00020 min, and the ephemeris should be accurate to 0.1 cycles until the year 2005. A narrow but partial X-ray eclipse suggests that this object belongs to the group of AM Her stars whose viewing geometry is such that the accretion stream periodically occults the soft X-ray emitting accretion spot on the surface of the white dwarf. A non-detection of hard X-rays from ASCA observations that are contemporaneous with the ROSAT HRI shows that the soft X-rays must dominate by at least an order of magnitude, which is consistent with a known trend among AM Her stars with large magnetic field. This object should not be confused with the Seyfert galaxy IH 0419-577 (= LB 1727), another X-ray/EUV source which lies only 3'95 away, and was the principal target of these monitoring observations. In a third report; the identity of the persistent high-energy (> 100 MeV) gamma-ray sources in the Galaxy, still largely a mystery is investigated. The second installment of the EGRET (2EG) lists a total of 128 sources, of which 51 are likely or possibly identified with AGNs, five with rotation-powered pulsars, and one is the LMC. There are 71 unidentified sources, of which 33, or almost half, lie in the narrow band of absolute value of b < 10 degrees along the Galactic plane. This excess of low-latitude sources must, therefore, constitute a Galactic population that is either similar to the already identified gamma-ray pulsars, or an entirely new class of gamma-ray emitters associated with the disk population. We are continuing our program, begun in A06, that is aimed at intermediate-latitude sources, arguing that X-ray detection of them is the most plausible method of identifying the Galactic population. The sources at high latitude must statistically be mostly AGNS, and are more straightforwardly identified through radio and optical means. For the fourth report, identification of the EGRET Source the identity of the persistent, high-energy gamma-ray sources in the Galactic plane is a mystery. The most likely scenario is a population of middle-aged pulsars, many of which could be radio quiet like Geminga. We have an ongoing program of ROSAT, VLA, and optical observations of selected EGRET error circles at intermediate Galactic latitude. For one of these fields, at (l, b) = (106 degrees, +3), our complete census of X-ray and radio sources, reveals a remarkable association between a radio shell with unique properties, and a complete census of X-ray and radio sources reveals a remarkable association between a radio shell with unique properties, and a compact X-ray source. Further observations are needed to determine whether or not this source has a hard X-ray spectrum like that of other gamma ray pulsars and, ideally, to find its pulsations. A fifth report reviews, Wasilewski 49, an interacting pair of Seyfert galaxies at z = 0.063, one of which contains a hidden Seyfert I nucleus as evidenced by broad wings on its Balmer lines.

Halpern, Jules P.↗

Reduction of Helicopter BVI Noise, Vibration, and Power Consumption Through Individual Blade Control

A wind tunnel test was conducted with a full-scale BO 105 helicopter rotor to evaluate the potential of open-loop individual blade control (IBC) to improve rotor performance, to reduce blade vortex interaction (BVI) noise, and to alleviate helicopter vibrations. The wind tunnel test was an international collaborative effort between NASA/U.S. Army AFDD, ZF Luftfahrttechnik, Eurocopter Deutschland, and the German Aerospace Laboratory (DLR) and was conducted under the auspices of the U.S./German MOU on Rotorcraft Aeromechanics. In this test the normal blade pitch links of the rotor were replaced by servo-actuators so that the pitch of each blade could be controlled independently of the other blades. The specially designed servoactuators and IBC control system were designed and manufactured by ZF Luftfahrttechnik, GmbH. The wind tunnel test was conducted in the 40- by 80-Foot Wind Tunnel at the NASA Ames Research Center. An extensive amount of measurement information was acquired for each IBC data point. These data include rotor performance, static and dynamic hub forces and moments, rotor loads, control loads, inboard and outboard blade pitch motion, and BVI noise data. The data indicated very significant (80 percent) simultaneous reductions in both BVI noise and hub vibrations could be obtained using multi-harmonic input at the critical descent (terminal approach) condition. The data also showed that performance improvements of up to 7 percent could be obtained using 2P input at high-speed forward flight conditions.

Jacklin, Stephen A.↗

A Case Study on Pathogen Transport, Deposition, Evaporation and Transmission: Linking High-Fidelity Computational Fluid Dynamics Simulations to Probability of Infection

A high-fidelity, low-Mach computational fluid dynamics simulation tool that includes evaporating droplets and variable-density turbulent flow coupling is well-suited to ascertain transmission probability and supports risk mitigation methods development for airborne infectious diseases such as COVID-19. A multi-physics large-eddy simulation-based paradigm is used to explore droplet and aerosol pathogen transport from a synthetic cough emanating from a kneeling humanoid. For an outdoor configuration that mimics the recent open-space social distance strategy of San Francisco, maximum primary droplet deposition distances are shown to approach 8.1 m in a moderate wind configuration with the aerosol plume transported in excess of 15 m. In quiescent conditions, the aerosol plume extends to approximately 4 m before the emanating pulsed jet becomes neutrally buoyant. A dose–response model, which is based on previous SARS coronavirus (SARS-CoV) data, is exercised on the high-fidelity aerosol transport database to establish relative risk at eighteen virtual receptor probe locations.

59 BASIC BIOLOGICAL SCIENCES↗

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

Background: Metagenomics and metatranscriptomics studies provide valuable insight into the composition and function of microbial populations from diverse environments, however the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. Results: Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome and metatranscriptome data. Genome-centric resolution and abundance estimates are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. Conclusions: ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome and metatranscriptome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.

59 BASIC BIOLOGICAL SCIENCES↗

An Investigation of Synchrony in Transport Networks

The cumulative degree distributions of transport networks, such as air transportation networks and respiratory neuronal networks, follow power laws. The significance of power laws with respect to other network performance measures, such as throughput and synchronization, remains an open question. Evolving methods for the analysis and design of air transportation networks must address network performance in the face of increasing demands and the need to contain and control local network disturbances, such as congestion. Toward this end, we investigate functional relationships that govern the performance of transport networks; for example, the links between the first nontrivial eigenvalue of a network's Laplacian matrix - a quantitative measure of network synchronizability - and other global network parameters. In particular, among networks with a fixed degree distribution and fixed network assortativity (a measure of a network's preference to attach nodes based on a similarity or difference), those with the small eigenvalue are shown to be poor synchronizers, to have much longer shortest paths and to have greater clustering in comparison to those with large. A simulation of a respiratory network adds data to our investigation. This study is a beginning step in developing metrics and design variables for the analysis and active design of air transport networks.

Kincaid, Rex K.↗

Structural models of the MscL gating mechanism

Three-dimensional structural models of the mechanosensitive channel of large conductance, MscL, from the bacteria Mycobacterium tuberculosis and Escherichia coli were developed for closed, intermediate, and open conformations. The modeling began with the crystal structure of M. tuberculosis MscL, a homopentamer with two transmembrane alpha-helices, M1 and M2, per subunit. The first 12 N-terminal residues, not resolved in the crystal structure, were modeled as an amphipathic alpha-helix, called S1. A bundle of five parallel S1 helices are postulated to form a cytoplasmic gate. As membrane tension induces expansion, the tilts of M1 and M2 are postulated to increase as they move away from the axis of the pore. Substantial expansion is postulated to occur before the increased stress in the S1 to M1 linkers pulls the S1 bundle apart. During the opening transition, the S1 helices and C-terminus amphipathic alpha-helices, S3, are postulated to dock parallel to the membrane surface on the perimeter of the complex. The proposed gating mechanism reveals critical spatial relationships between the expandable transmembrane barrel formed by M1 and M2, the gate formed by S1 helices, and "strings" that link S1s to M1s. These models are consistent with numerous experimental results and modeling criteria.

NASA Discipline Cell Biology↗

Plant Bioengineering Atlas: A Knowledge Graph of Genes, DNA Constructs, and Plant Traits.

Plant bioengineering has generated tens of thousands of genotype-to-phenotype relationships, but this knowledge remains fragmented across narrative literature and difficult to use computationally. Inconsistent descriptions of DNA constructs, host species, and traits, including variable species names, omitted regulatory elements, and inconsistent gene symbols, impede data reuse, comparative analysis, and design-build-test-learn cycles. Here, we present the Plant Bioengineering Atlas, a literature-mined, ontology-grounded knowledge base assembled using an artificial intelligence (AI)-aided extraction pipeline. A large language model parsed open-access primary research articles to generate structured, provenance-anchored records of engineered genes, modification types, promoter-gene-terminator constructs, host species, target traits, and reported phenotypes, with every record traceable to its source. The current release contains 14,358 curated records encompassing 6,998 distinct genes across 436 plant species from 6,452 papers published between 2000 and 2026. Corpus analysis reveals that experiments are concentrated in a small group of model and crop species, disease and pathogen resistance is the most frequently engineered trait class, and constitutive regulatory parts (particularly the CaMV 35S promoter and NOS terminator) remain pervasive. Two in five records omit one or both flanking regulatory elements (i.e., promoter and terminator), while only 23.4% describe cassettes in which both elements resolve to named part classes, exposing a systematic reproducibility gap. We organize these data into a knowledge graph linking genes, constructs, species, and traits; provide access through an interactive web portal; and propose an AI-compatible documentation standard for AI-ready reporting. The Plant Bioengineering Atlas provides a foundation for data-driven hypothesis generation and AI-aided plant biodesign.

, Genes, DNA Constructs↗