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Proteomic assessment of serum biomarkers of longevity in older men
The biological bases of longevity are not well understood, and there are limited biomarkers for the prediction of long life. We used a high-throughput, discovery-based proteomics approach to identify serum peptides and proteins that were associated with the attainment of longevity in a longitudinal study of community-dwelling men age ≥65 years. Baseline serum in 1196 men were analyzed using liquid chromatography–ion mobility–mass spectrometry, and lifespan was determined during ~12 years of follow-up. Men who achieved longevity (≥90% expected survival) were compared to those who died earlier. Rigorous statistical methods that controlled for false positivity were utilized to identify 25 proteins that were associated with longevity. All these proteins were in lower abundance in long-lived men and included a variety involved in inflammation or complement activation. Lower levels of longevity-associated proteins were also associated with better health status, but as time to death shortened, levels of these proteins increased. Pathway analyses implicated a number of compounds as important upstream regulators of the proteins and implicated shared networks that underlie the observed associations with longevity. Overall, these results suggest that complex pathways, prominently including inflammation, are linked to the likelihood of attaining longevity. This work may serve to identify novel biomarkers for longevity and to understand the biology underlying lifespan.
PHALANX: Expendable Projectile Sensor Networks for Planetary Exploration
Technologies enabling long-term, wide-ranging measurement in hard-to-reach areas are a critical need for planetary science inquiry. Phenomena of interest include flows or variations in volatiles, gas composition or concentration, particulate density, or even simply temperature. Improved measurement of these processes enables understanding of exotic geologies and distributions or correlating indicators of trapped water or biological activity. However, such data is often needed in unsafe areas such as caves, lava tubes, or steep ravines not easily reached by current spacecraft and planetary robots. To address this capability gap, we have developed miniaturized, expendable sensors which can be ballistically lobbed from a robotic rover or static lander - or even dropped during a flyover. These projectiles can perform sensing during flight and after anchoring to terrain features. By augmenting exploration systems with these sensors, we can extend situational awareness, perform long-duration monitoring, and reduce utilization of primary mobility resources, all of which are crucial in surface missions. We call the integrated payload that includes a cold gas launcher, smart projectiles, planning software, network discovery, and science sensing: PHALANX. In this paper, we introduce the mission architecture for PHALANX and describe an exploration concept that pairs projectile sensors with a rover “mothership.” Science use cases explored include reconnaissance using ballistic cameras, volatiles detection, and building timelapse maps of temperature and illumination conditions. Strategies to autonomously coordinate constellations of deployed sensors to self-discover and localize with peer ranging (i.e. a “local GPS”) are summarized, thus providing communications infrastructure beyond-line-of-sight (BLOS) of the rover. Capabilities were demonstrated through both simulation and physical testing with a terrestrial prototype. The approach to developing a terrestrial prototype is discussed, including design of the launching mechanism, projectile optimization, micro-electronics fabrication, and sensor selection. Results from early testing and characterization of commercial-off-the-shelf (COTS) components are reported. Nodes were subjected to successful burn-in tests over 48 hours at full logging duty cycle. Integrated field tests were conducted in the Roverscape, a half-acre planetary analog environment at NASA Ames, where we tested up to 10 sensor nodes simultaneously coordinating with an exploration rover. Ranging accuracy has been demonstrated to be within +/-10cm over 20m using commodity radios when compared to high-resolution laser scanner ground truthing. Evolution of the design, including progressive miniaturization of the electronics and iterated modifications of the enclosure housing for streamlining and optimized radio performance are described. Finally, lessons learned to date, gaps toward eventual flight mission implementation, and continuing future development plans are discussed.
Plant Defense Proteins: Recent Discoveries and Applications
Proteins play pivotal roles in safeguarding plants against numerous biotic and abiotic stresses. Understanding their biological functions and mechanisms of action is essential for advancing plant biology, agriculture, and biotechnology. This review considers the diversity and potential applications of plant defense proteins including pathogenesis-related (PR) proteins, chitinases, glucanases, protease inhibitors, lectins, and antimicrobial peptides. Recent advances, such as the omics technologies, have enabled the discovery of new plant defense proteins and regulatory networks that govern plant defense responses and unveiled numerous roles of plant defense proteins in stress perception, signal transduction, and immune priming. The molecular affinities and enzymatic activities of plant defense proteins are essential for their defense functions. Applications of plant defense proteins span agriculture, biotechnology, and medicine, including the development of resistant crop varieties, bio-based products, biopharmaceuticals, and functional foods. Future research directions include elucidating the structural bases of defense protein functions, exploring protein interactions with ligands and other proteins, and engineering defense proteins for enhanced efficacy. Overall, this review illuminates the significance of plant defense proteins against biotic stresses in plant biology and biotechnology, emphasizing their potential for sustainable agriculture and environmental management.
Uncovering Sequence and Structural Characteristics of Fungal Expansin‐Related Proteins With Potential to Drive Substrate Targeting
Expansins loosen plant cell wall networks through disrupting non-covalent bonds between cellulose microfibrils and matrix polysaccharides. Whereas expansins were first discovered in plants, expansin-related proteins have since been identified in bacteria and fungi. The biological function of microbial expansins remains unclear; however, several studies have shown distinct binding preferences toward different structural polysaccharides. Earlier studies of bacterial expansin-related proteins uncovered sequence and structural features that correlate to substrate binding. Herein, 20 fungal expansin-related sequences were recombinantly produced in Komagataella phaffii, and the purified proteins were compared in terms of substrate binding to cellulosic and chitinous substrates. The impact of pH on the zeta potential of prioritized substrates was also measured, and Principal Component Analysis was performed to uncover correlations between protein characteristics (e.g., pI, hydrophobicity, surface charge distribution) and measured substrate binding preferences. Whereas acidic proteins with a predicted pI less than 5.0 preferentially bound to chitin, basic proteins with pI greater than 8.0 preferentially bound to xylan and xylan-containing fiber. Similar to many cellulases, binding to cellulose was correlated to relatively high aromatic amino acid content in the protein sequence and presence of a carbohydrate binding module (CBM), which in the case of expansins is a C-terminal CBM63. Whereas overall sequence characteristics could be correlated to substrate binding preference, the identity of amino acids occupying conserved positions that impact protein activity was better correlated with loosenin versus expansin classifications.
Eliater: a Python package for estimating outcomes of perturbations in biomolecular networks
We introduce Eliater, a Python package for estimating the effect of perturbation of an upstream molecule on a downstream molecule in a biomolecular network. The estimation takes as input a biomolecular network, observational biomolecular data, and a perturbation of interest, and outputs an estimated quantitative effect of the perturbation. We showcase the functionalities of Eliater in a case study of Escherichia coli transcriptional regulatory network.
A General Framework to Learn Tertiary Structure for Protein Sequence Characterization
During the past five years, deep-learning algorithms have enabled ground-breaking progress towards the prediction of tertiary structure from a protein sequence. Very recently, we developed SAdLSA, a new computational algorithm for protein sequence comparison via deep-learning of protein structural alignments. SAdLSA shows significant improvement over established sequence alignment methods. In this contribution, we show that SAdLSA provides a general machine-learning framework for structurally characterizing protein sequences. By aligning a protein sequence against itself, SAdLSA generates a fold distogram for the input sequence, including challenging cases whose structural folds were not present in the training set. About 70% of the predicted distograms are statistically significant. Although at present the accuracy of the intra-sequence distogram predicted by SAdLSA self-alignment is not as good as deep-learning algorithms specifically trained for distogram prediction, it is remarkable that the prediction of single protein structures is encoded by an algorithm that learns ensembles of pairwise structural comparisons, without being explicitly trained to recognize individual structural folds. As such, SAdLSA can not only predict protein folds for individual sequences, but also detects subtle, yet significant, structural relationships between multiple protein sequences using the same deep-learning neural network. The former reduces to a special case in this general framework for protein sequence annotation.
Effect of MODIS Terra Radiometric Calibration Improvements on Collection 6 Deep Blue Aerosol Products: Validation and Terra/Aqua Consistency
The Deep Blue (DB) algorithm's primary data product is midvisible aerosol optical depth (AOD). DB applied to Moderate Resolution Imaging Spectroradiometer (MODIS) measurements provides a data record since early 2000 for MODIS Terra and mid-2002 for MODIS Aqua. In the previous data version (Collection 5, C5), DB production from Terra was halted in 2007 due to sensor degradation; the new Collection 6 (C6) has both improved science algorithms and sensor radiometric calibration. This includes additional calibration corrections developed by the Ocean Biology Processing Group to address MODIS Terra's gain, polarization sensitivity, and detector response versus scan angle, meaning DB can now be applied to the whole Terra record. Through validation with Aerosol Robotic Network (AERONET) data, it is shown that the C6 DB Terra AOD quality is stable throughout the mission to date. Compared to the C5 calibration, in recent years the RMS error compared to AERONET is smaller by approximately 0.04 over bright (e.g., desert) and approximately 0.01-0.02 over darker (e.g., vegetated) land surfaces, and the fraction of points in agreement with AERONET within expected retrieval uncertainty higher by approximately 10% and approximately 5%, respectively. Comparisons to the Aqua C6 time series reveal a high level of correspondence between the two MODIS DB data records, with a small positive (Terra-Aqua) average AOD offset <0.01. The analysis demonstrates both the efficacy of the new radiometric calibration efforts and that the C6 MODIS Terra DB AOD data remain stable (to better than 0.01 AOD) throughout the mission to date, suitable for quantitative scientific analyses.
Navigation Performance of the BioSentinel Deep Space CubeSat Mission
The BioSentinel mission was recently launched aboard the SLS launch vehicle (LV) as part of the Artemis- 1 campaign. The BioSentinel navigation team successfully tracked and guided the spacecraft through a lunar gravity assist to its destination Earth-trailing heliocentric orbit. This 6U CubeSat carries live yeast cells to analyze the effects of radiation at large distances from Earth, becoming the first biological payload in Deep Space. Prelaunch activities included mission design updates, orbit determination rehearsals and the development of a tracking schedule in coordination with the Artemis-1 payload office and the Deep Space Network (DSN). An important influence on the trajectories of Artemis I secondaries was the uncertainty associated with deployment from the Interim Cryogenic Propulsion System (ICPS), the upper stage of the SLS LV. The ICPS was rotating at a rate of 1 rpm; there was also an uncertainty in the spin axis attitude, which translated into an unknown clock angle of deployment. The variability in this angle and magnitude of deployment implied the existence of a non-negligible risk of a lunar impact, which was evaluated for various potential launch dates. We present the results of Monte Carlo analyses and compute the pertinent maneuvers to avoid it. In addition, we present a comparison with the actual deployment once the mission launched by reconstructing our trajectory with tracking data. On November 16th 2022 BioSentinel successfully deployed from ICPS and the navigation team started to receive 2-way Doppler and Sequential Ranging data from the DSN. We processed early data to try to obtain a first ephemeris using Initial Orbit Determination (IOD) methods such as the least squares. Soon after deployment, the spacecraft was tumbling and entered safe mode, creating a period where the tracking data were sparse. The mission team recovered the spacecraft and after four tracking passes, we solved for a first ephemeris that was sent to the DSN for better tracking of the spacecraft. After propagating this first ephemeris solution, we determined that we avoided impact with a margin of a few hundred km from the lunar surface. More tracking data over the next few days (from DSN as well as ESA antennas) allowed for a more refined orbit solution predicting a periselene altitude of 406 km and a lunar eclipse lasting 36.5 minutes. Therefore, BioSentinel operators aborted any correction maneuvers. This periselene altitude also gave us the necessary energy to achieve a heliocentric orbit. The next challenge was due to the necessary adjustments in our orbit determination method due to the large energy boost resulting from the lunar flyby. After a series of tracking passes we were able to get a nominal solution that resulted into a stable trajectory. This paper discusses in detail the navigation performance using the X-band IRIS transponder, as well as the challenges and lessons learned prior to and during this deep space, CubeSat mission.
BioSentinel Deep Space CubeSat Mission
The BioSentinel mission was recently launched aboard the SLS launch vehicle (LV) as part of the Artemis-1 campaign. This 6U CubeSat carries yeast cells to analyze the effects of radiation at large distances from Earth, becoming the first biological payload in Deep Space. Prelaunch activities included mission design updates, orbit determination rehearsals and the development of a tracking schedule in coordination with the Artemis-1 payload office and the Deep Space Network (DSN). An important influence on the trajectories of Artemis I secondaries was the uncertainty associated with deployment from the Interim Cryogenic Propulsion System (ICPS), the upper stage of the SLS LV. The ICPS was rotating at a rate of 1 rpm; there was also uncertainty in the spin axis attitude, which translated into an unknown clock angle of deployment. The variability in this angle and magnitude of deployment implied the existence of a non-negligible risk of a lunar impact, which was evaluated for various potential launch dates. On November 16 th 2022 BioSentinel successfully deployed from ICPS and the navigation team started to receive tracking data from the DSN and ESA antennas. Soon after deployment, the spacecraft was tumbling and entered safe mode. The mission team recovered the spacecraft and after four tracking passes, we solved for a first ephemeris that was sent to the DSN for better tracking of the spacecraft. After propagating this first ephemeris solution, we determined that we avoided impact with a margin of a few hundred km from the lunar surface. More tracking data over the next few days allowed for a more refined orbit solution predicting a periselene altitude of 406 km and a lunar eclipse lasting 36.5 minutes. Therefore, BioSentinel operators avoided any correction maneuvers on the trajectory and successfully tracked and guide the spacecraft. The spacecraft performed a nominal lunar flyby which provided the pertinent energy to achieve a final Earth-trailing heliocentric orbit. Over the course of two weeks, the mission operators corroborated that the subsystems were functioning as expected after the lunar eclipse and the large ΔV incurred. Science operations started once the mission achieved the nominal orbit in Deep Space. This paper discusses in detail the BioSentinel flight performance, as well as the challenges and lessons learned prior to and during this CubeSat mission.
Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function
One of the reasons for the high efficiency and selectivity of biological catalysts arise from their ability to control the pathways of substrates and products using protein channels, and by modulating the transport in the channels using the interaction with the protein residues and the water/hydrogen-bonding network. Here, this process is clearly demonstrated in Photosystem II (PS II), where its light-driven water oxidation reaction catalyzed by the Mn 4 CaO 5 cluster occurs deep inside the protein complex and thus requires the transport of two water molecules to and four protons from the metal center to the bulk water. Based on the recent advances in structural studies of PS II from X-ray crystallography and cryo-electron microscopy, in this review we compare the channels that have been proposed to facilitate this mass transport in cyanobacteria, red and green algae, diatoms, and higher plants. The three major channels (O1, O4, and Cl1 channels) are present in all species investigated; however, some differences exist in the reported structures that arise from the different composition and arrangement of membrane extrinsic subunits between the species. Among the three channels, the Cl1 channel, including the proton gate, is the most conserved among all photosynthetic species. We also found at least one branch for the O1 channel in all organisms, extending all the way from Ca/O1 via the ‘water wheel’ to the lumen. However, the extending path after the water wheel varies between most species. The O4 channel is, like the Cl1 channel, highly conserved among all species while having different orientations at the end of the path near the bulk. The comparison suggests that the previously proposed functionality of the channels in T. vestitus (Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Hussein et al., Nat Commun 12:6531, 2021) is conserved through the species, i.e. the O1-like channel is used for substrate water intake, and the tighter Cl1 and O4 channels for proton release. The comparison does not eliminate the potential role of O4 channel as a water intake channel. However, the highly ordered hydrogen-bonded water wire connected to the Mn 4 CaO 5 cluster via the O4 may strongly suggest that it functions in proton release, especially during the S 0 → S 1 transition (Saito et al., Nat Commun 6:8488, 2015; Kern et al., Nature 563:421–425, 2018; Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Sakashita et al., Phys Chem Chem Phys 22:15831–15841, 2020; Hussein et al., Nat Commun 12:6531, 2021).
FSM: Fast and scalable network motif discovery for exploring higher-order network organizations
Not provided.
Effects of artificial defoliation of pines on the structure and physiology of the soil fungal community of a mixed pine-spruce forest
Loss of photosynthetic area can affect soil microbial communities by altering the availability of fixed carbon. We used denaturing gradient gel electrophoresis (DGGE) and Biolog filamentous-fungus plates to determine the effects of artificial defoliation of pines in a mixed pine-spruce forest on the composition of the fungal community in a forest soil. As measured by DGGE, two fungal species were affected significantly by the defoliation of pines (P < 0.001); the frequency of members of the ectomycorrhizal fungus genus Cenococcum decreased significantly, while the frequency of organisms of an unidentified soil fungus increased. The decrease in the amount of Cenococcum organisms may have occurred because of the formation of extensive hyphal networks by species of this genus, which require more of the carbon fixed by their host, or because this fungus is dependent upon quantitative differences in spruce root exudates. The defoliation of pines did not affect the overall composition of the soil fungal community or fungal-species richness (number of species per core). Biolog filamentous-fungus plate assays indicated a significant increase (P < 0.001) in the number of carbon substrates utilized by the soil fungi and the rate at which these substrates were used, which could indicate an increase in fungal-species richness. Thus, either small changes in the soil fungal community give rise to significant increases in physiological capabilities or PCR bias limits the reliability of the DGGE results. These data indicate that combined genetic and physiological assessments of the soil fungal community are needed to accurately assess the effect of disturbance on indigenous microbial systems.
A goldilocks computational protocol for inhibitor discovery targeting DNA damage responses including replication-repair functions
While many researchers can design knockdown and knockout methodologies to remove a gene product, this is mainly untrue for new chemical inhibitor designs that empower multifunctional DNA Damage Response (DDR) networks. Here, we present a robust Goldilocks (GL) computational discovery protocol to efficiently innovate inhibitor tools and preclinical drug candidates for cellular and structural biologists without requiring extensive virtual screen (VS) and chemical synthesis expertise. By computationally targeting DDR replication and repair proteins, we exemplify the identification of DDR target sites and compounds to probe cancer biology. Our GL pipeline integrates experimental and predicted structures to efficiently discover leads, allowing early-structure and early-testing (ESET) experiments by many laboratories. By employing an efficient VS protocol to examine protein-protein interfaces (PPIs) and allosteric interactions, we identify ligand binding sites beyond active sites, leveraging in silico advances for molecular docking and modeling to screen PPIs and multiple targets. A diverse 3,174 compound ESET library combines Diamond Light Source DSI-poised, Protein Data Bank fragments, and FDA-approved drugs to span relevant chemotypes and facilitate downstream hit evaluation efficiency for academic laboratories. Two VS per library and multiple ranked ligand binding poses enable target testing for several DDR targets. This GL library and protocol can thus strategically probe multiple DDR network targets and identify readily available compounds for early structural and activity testing to overcome bottlenecks that can limit timely breakthrough drug discoveries. By testing accessible compounds to dissect multi-functional DDRs and suggesting inhibitor mechanisms from initial docking, the GL approach may enable more groups to help accelerate discovery, suggest new sites and compounds for challenging targets including emerging biothreats and advance cancer biology for future precision medicine clinical trials.
Improving the reliability of machine learned potentials for modeling inhomogeneous liquids
The atomic-scale response of inhomogeneous fluids at interfaces and surrounding solute particles plays a critical role in governing chemical, electrochemical, and biological processes. Classical molecular dynamics simulations have been applied extensively to simulate the response of fluids to inhomogeneities directly, but are limited by the accuracy of the underlying interatomic potentials. Here, we use neural network potentials (NNPs) trained to ab initio simulations to accurately predict the inhomogeneous responses of two distinct fluids: liquid water and molten NaCl. Although NNPs can be readily trained to model complex bulk systems across a range of state points, we show that to appropriately model a fluid's response at an interface, relevant inhomogeneous configurations must be included in the training data. In order to sufficiently sample appropriate configurations of such inhomogeneous fluids, we develop protocols based on molecular dynamics simulations in the presence of external potentials. We demonstrate that NNPs trained on inhomogeneous fluid configurations can more accurately predict several key properties of fluids—including the density response, surface tension and size-dependent cavitation free energies—for liquid water and molten NaCl, compared to both empirical interatomic potentials and NNPs that are not trained on such inhomogeneous configurations. This work therefore provides a first demonstration and framework to extract the response of inhomogeneous fluids from first principles for classical density-functional treatment of fluids free from empirical potentials.
Multitask Machine Learning of Collective Variables for Enhanced Sampling of Rare Events
Computing accurate reaction rates is a central challenge in computational chemistry and biology because of the high cost of free energy estimation with unbiased molecular dynamics. In this work, a data-driven machine learning algorithm is devised to learn collective variables with a multitask neural network, where a common upstream part reduces the high dimensionality of atomic configurations to a low dimensional latent space and separate downstream parts map the latent space to predictions of basin class labels and potential energies. Here, the resulting latent space is shown to be an effective low-dimensional representation, capturing the reaction progress and guiding effective umbrella sampling to obtain accurate free energy landscapes. This approach is successfully applied to model systems including a 5D Müller Brown model, a 5D three-well model, the alanine dipeptide in vacuum, and an Au(110) surface reconstruction unit reaction. It enables automated dimensionality reduction for energy controlled reactions in complex systems, offers a unified and data-efficient framework that can be trained with limited data, and outperforms single-task learning approaches, including autoencoders.
Anisotropic Dynamics and Mechanics of Macromolecular Crystals Containing Lattice-Patterned Polymer Networks
The mechanical and functional properties of many crystalline materials depend on cooperative changes in lattice arrangements in response to external perturbations. However, the flexibility and adaptiveness of crystalline materials are limited. Additionally, the bottom-up, molecular-level design of crystals with desired dynamic and mechanical properties at the macroscopic level remains a considerable challenge. To address these challenges, we had previously integrated mesoporous, cubic ferritin crystals with hydrogel networks, resulting in hybrid materials (polymer integrated crystals or PIX) which could undergo dramatic structural changes while maintaining crystalline periodicity and display efficient self-healing. Here, the dynamics and mechanics of these ferritin-PIX were devoid of directionality, which is an important attribute of many molecular and macroscopic materials/devices. In this study, we report that such directionality can be achieved through the use of ferritin crystals with anisotropic symmetries (rhombohedral or trigonal), which enable the templated formation of patterned hydrogel networks in crystallo. The resulting PIX expand and contract anisotropically without losing crystallinity, undergo prompt bending motions in response to stimuli, and self-heal efficiently, capturing some of the essential features of sophisticated biological devices like skeletal muscles.
Climate, soil mineralogy and mycorrhizal fungi influence soil organic matter fractions in eastern US temperate forests
Identifying the primary controls of particulate (POM) and mineral-associated organic matter (MAOM) content in soils is critical for determining future stocks of soil carbon (C) and nitrogen (N) across the globe. However, drivers of these soil organic matter fractions are likely to vary among ecosystems in response to climate, soil type and the composition of local biological communities. We tested how soil factors, climate and plant–fungal associations influenced the distribution and concentrations of C and N in MAOM and POM in seven temperate forests in the National Ecological Observatory Network (NEON) across the eastern United States. Samples of upper mineral horizon soil within each forest were collected in plots representing a gradient of dominant tree–mycorrhizal association, allowing us to test how plant and microbial communities influenced POM and MAOM across sites differing in climate and soil conditions. We found that concentrations of C and N in soil organic matter were primarily driven by soil mineralogy, but the relative abundance of MAOM versus POM C was strongly linked to plot-level mycorrhizal dominance. Furthermore, the effect of dominant tree mycorrhizal type on the distribution of N among POM and MAOM fractions was sensitive to local climate: in cooler sites, an increasing proportion of ectomycorrhizal-associated trees was associated with lower proportions of N in MAOM, but in warmer sites, we found the reverse. As an indicator of soil carbon age, we measured radiocarbon in the MAOM fraction but found that within and across sites, Δ 14 C was unrelated to mycorrhizal dominance, climate, or soil factors, suggesting that additional site-specific factors may be primary determinants of long-term SOM persistence. Our results indicate that while soil mineralogy primarily controls SOM C and N concentrations, the distribution of SOM among density fractions depends on the composition of vegetation and microbial communities, with these effects varying across sites with distinct climates. Here we also suggest that within biomes, the age of mineral-associated soil carbon is not clearly linked to the factors that control concentrations of MAOM C and N.