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At least 271 records · Page 15

Ancient co-option of LTR retrotransposons as yeast centromeres

Centromeres ensure accurate chromosome segregation, yet their DNA evolves rapidly across eukaryotes leaving the origins of new centromere architectures unclear. The brewer’s yeast Saccharomyces cerevisiae exemplifies this long-standing puzzle. Its centromeres shifted ancestrally from large, repeat-rich, epigenetically specified forms to the compact, genetically defined ‘point’ centromeres. How this transition occurred has remained unresolved6. Here we identify evolutionarily related ‘proto-point’ centromeres that provide a resolution to the evolutionary origins of point centromeres. Proto-point centromeres contain a single centromeric nucleosome positioned over an AT-rich core, accompanied by relaxed organization and sequence variability of flanking cis-elements. In two species, these proto-point centromeres lie within retrotransposon-derived repeat clusters, linking ancestral repeat-rich centromeres to genetically encoded ones. Comparative and phylogenetic analyses indicate that proto-point and point centromeres evolved in an ancestor with retrotransposon-rich centromeres. These results identify long-terminal-repeat retrotransposons, specifically Ty5 sequences, as the genetic substrate for point-centromere evolution and provide a mechanistic route by which an epigenetic centromere can become genetically specified. More broadly, they show how selfish elements can be co-opted to perform essential chromosomal functions.

Haase, Max A. B. [Max Planck Institute of Molecula↗

A computational model for dynamic vision

This paper describes a novel computational model for dynamic vision which promises to be both powerful and robust. Furthermore the paradigm is ideal for an active vision system where camera vergence changes dynamically. Its basis is the retinotopically indexed object-centered encoding of the early visual information. Specifically, the relative distances of objects to a set of referents is encoded in image registered maps. To illustrate the efficacy of the method, it is applied to the problem of dynamic stereo vision. Integration of depth information over multiple frames obtained by a moving robot generally requires precise information about the relative camera position from frame to frame. Usually, this information can only be approximated. The method facilitates the integration of depth information without direct use or knowledge of camera motion.

Moezzi, Saied↗

Flexible Data and Frame Synchronization Structure for the LunaNet PNT Signal

A LunaNet Lunar Augmented Navigation Service (LANS) is being developed to enable a position, navigation, and timing service for future Lunar operations. The signal includes two components. An in-phase data channel signal is spread by a 1.023 MCPS ranging code that provides a high-rate data message at 250 bps and is encoded by a strong Low Density Parity Check (LDPC) code. A pilot channel with a 5.115 MCPS spreading code is also provided. The pilot code is configured with a secondary (overlay) code that does not currently provide absolute time or frame Synchronization as is the case for L1C. This work shows the advantage of implementing an overlay structure that provides absolute time for the LunaNet LANS signal structure known as the Augmented Forward Signal (AFS). The LunaNet AFS structure was developed to service two classes of user receivers. The first class is a low-complexity user receiver that only receives the 1.023 MCPS signal and does not use the 5.115 MCPS pilot channel. For this class of user, a data frame Sync word is needed. The second class of receiver is a high-end receiver that can processes both data and pilot channels to take advantage of the higher chip rate pilot channel for enhanced robustness and improved accuracy. In the current draft LunaNet LANS AFS design, these users must employ the frame Sync word in the data channel and obtain absolute time after decoding the AFS navigation message. The signal structure would greatly benefit from the addition of a pilot overlay structure that provides absolute time and robust frame Sync for high-end users as done for L1C. To provide a more robust and interoperable AFS structure, this work summarizes a study and recommends alternatives for a new overlay code on the pilot channel that provides absolute time and a Sync word approach on the data channel. The overlay code and Sync word are designed to allow for flexible and robust data synchronization for both low- complexity and high-end user receivers. The new overlay code structure permits frame synchronization performance that is as good as or better than the L1 C signal, while enabling a determination of absolute time upon frame Sync to aid high-end assisted LANS AFS user receivers at low signal to noise levels. We also present the design of rate-matched 5G new radio (5GNR) LDPC codes that fit within the current 6000-symbol frame size along with a time of interval (TOI) word, frame ID (FID) word, and the remaining LunaNet AFS data message blocks. The paper describes and demonstrates robust frame Synchronization performance of the overlay code and Synch word approaches. The results are described in terms of probability of missed detection and probability of false alarm for a correct frame Synchronization at low Eb/No levels expected for decoding the TOI word and LDPC encoded data. Advantages of the proposed data Synchronization structure will be described along with use cases for low-end and high-end receivers. Practical implementation considerations will also be described.

LunaNet↗

Plant invasion impacts on fungal community structure and function depend on soil warming and nitrogen enrichment

The impacts of invasive species on biodiversity may be mitigated or exacerbated by abiotic environmental changes. Invasive plants can restructure soil fungal communities with important implications for native biodiversity and nutrient cycling, yet fungal responses to invasion may depend on numerous anthropogenic stressors. In this study, we experimentally invaded a long-term soil warming and simulated nitrogen deposition experiment with the widespread invasive plant Alliaria petiolata (garlic mustard) and tested the responses of soil fungal communities to invasion, abiotic factors, and their interaction. We focused on the phytotoxic garlic mustard because it suppresses native mycorrhizae across forests of North America. We found that invasion in combination with warming, but not under ambient conditions or elevated nitrogen, significantly reduced soil fungal biomass and ectomycorrhizal relative abundances and increased relative abundances of general soil saprotrophs and fungal genes encoding for hydrolytic enzymes. These results suggest that warming potentially exacerbates fungal responses to plant invasion. Soils collected from uninvaded and invaded plots across eight forests spanning a 4 °C temperature gradient further demonstrated that the magnitude of fungal responses to invasion was positively correlated with mean annual temperature. Our study is one of the first empirical tests to show that the impacts of invasion on fungal communities depends on additional anthropogenic pressures and were greater in concert with warming than under elevated nitrogen or ambient conditions.

59 BASIC BIOLOGICAL SCIENCES↗

Flexible Data and Frame Synchronization Structure for the LunaNet PNT Signal

A LunaNet Lunar Augmented Navigation Service (LANS) is being developed to enable a position, navigation, and timing service for future Lunar operations [1]. The signal includes two components. An in-phase data channel signal is spread by a 1.023 MCPS ranging code that provides a high-rate data message at 250 bps and is encoded by a strong Low Density Parity Check (LDPC) code. A pilot channel with a 5.115 MCPS spreading code is also provided. The pilot code is configured with a secondary (overlay) code that does not currently provide absolute time or frame Synchronization as is the case for L1C [2] [3]. This work shows the advantage of implementing an overlay structure that provides absolute time for the LunaNet LANS signal structure known as the Augmented Forward Signal (AFS). The LunaNet AFS structure was developed to service two classes of user receivers. The first class is a low-complexity user receiver that only receives the 1.023 MCPS signal and does not use the 5.115 MCPS pilot channel. For this class of user, a data frame Sync word is needed. The second class of receiver is a high-end receiver that can processes both data and pilot channels to take advantage of the higher chip rate pilot channel for enhanced robustness and improved accuracy. In the current draft LunaNet LANS AFS design, these users must employ the frame Sync word in the data channel and obtain absolute time after decoding the AFS navigation message [2]. The signal structure would greatly benefit from the addition of a pilot overlay structure that provides absolute time and robust frame Sync for high-end users as done for L1C [3]. To provide a more robust and interoperable AFS structure, this work summarizes a study and recommends alternatives for a new overlay code on the pilot channel that provides absolute time and a Sync word approach on the data channel. The overlay code and Sync word are designed to allow for flexible and robust data synchronization for both low- complexity and high-end user receivers. The new overlay code structure permits frame synchronization performance that is as good as or better than the L1 C signal, while enabling a determination of absolute time upon frame Sync to aid high-end assisted LANS AFS user receivers at low signal to noise levels. We also present the design of rate-matched 5G new radio (5GNR) LDPC codes that fit within the current 6000-symbol frame size along with a time of interval (TOI) word, frame ID (FID) word, and the remaining LunaNet AFS data message blocks. The paper describes and demonstrates robust frame Synchronization performance of the overlay code and Synch word approaches. The results are described in terms of probability of missed detection and probability of false alarm for a correct frame Synchronization at low Eb/No levels expected for decoding the TOI word and LDPC encoded data. Advantages of the proposed data Synchronization structure will be described along with use cases for low-end and high-end receivers. Practical implementation considerations will also be described.

Philip Dafesh↗

Vestibulospinal control of reflex and voluntary head movement

Secondary canal-related vestibulospinal neurons respond to an externally applied movement of the head in the form of a firing rate modulation that encodes the angular velocity of the movement, and reflects in large part the input "head velocity in space" signal carried by the semicircular canal afferents. In addition to the head velocity signal, the vestibulospinal neurons can carry a more processed signal that includes eye position or eye velocity, or both (see Boyle on ref. list). To understand the control signals used by the central vestibular pathways in the generation of reflex head stabilization, such as the vestibulocollic reflex (VCR), and the maintenance of head posture, it is essential to record directly from identified vestibulospinal neurons projecting to the cervical spinal segments in the alert animal. The present report discusses two key features of the primate vestibulospinal system. First, the termination morphology of vestibulospinal axons in the cervical segments of the spinal cord is described to lay the structural basis of vestibulospinal control of head/neck posture and movement. And second, the head movement signal content carried by the same class of secondary vestibulospinal neurons during the actual execution of the VCR and during self-generated, or active, rapid head movements is presented.

Review, Tutorial↗

System and method for x-ray compatible 2D streak camera for a snapshot multiframe imager

The present disclosure is directed to a snapshot multiframe imager having an aperture element having at least one aperture, an adjacently positioned random mask, an imaging element and a computer. The random mask has a plurality of micron scale apertures and receives light passing through the aperture element, which represents the spatial information from the scene being imaged, and generates a plurality of image frames encoded in a spatial domain. The imaging element may operate in a drift-scan mode receives the encoded image frames and generates a streaked pattern of electrons representing a plurality of images of the scene at a plurality of different times. The computer analyzes the streaked pattern of electrons and mathematically reconstructs the plurality of images.

Dayton, Matthew S.↗

An Ensemble Approach to Building Mercer Kernels with Prior Information

This paper presents a new methodology for automatic knowledge driven data mining based on the theory of Mercer Kernels, which are highly nonlinear symmetric positive definite mappings from the original image space to a very high, possibly dimensional feature space. we describe a new method called Mixture Density Mercer Kernels to learn kernel function directly from data, rather than using pre-defined kernels. These data adaptive kernels can encode prior knowledge in the kernel using a Bayesian formulation, thus allowing for physical information to be encoded in the model. Specifically, we demonstrate the use of the algorithm in situations with extremely small samples of data. We compare the results with existing algorithms on data from the Sloan Digital Sky Survey (SDSS) and demonstrate the method's superior performance against standard methods. The code for these experiments has been generated with the AUTOBAYES tool, which automatically generates efficient and documented C/C++ code from abstract statistical model specifications. The core of the system is a schema library which contains templates for learning and knowledge discovery algorithms like different versions of EM, or numeric optimization methods like conjugate gradient methods. The template instantiation is supported by symbolic-algebraic computations, which allows AUTOBAYES to find closed-form solutions and, where possible, to integrate them into the code.

Srivastava, Ashok N.↗

Extended-Range Passive RFID and Sensor Tags

Extended-range passive radio-frequency identification (RFID) tags and related sensor tags are undergoing development. A tag of this type incorporates a retroreflective antenna array, so that it reflects significantly more signal power back toward an interrogating radio transceiver than does a comparable passive RFID tag of prior design, which does not incorporate a retroreflective antenna array. Therefore, for a given amount of power radiated by the transmitter in the interrogating transceiver, a tag of this type can be interrogated at a distance greater than that of the comparable passive RFID or sensor tag of prior design. The retroreflective antenna array is, more specifically, a Van Atta array, named after its inventor and first published in a patent issued in 1959. In its simplest form, a Van Atta array comprises two antenna elements connected by a transmission line so that the signal received by each antenna element is reradiated by the other antenna element (see Figure 1). The phase relationships among the received and reradiated signals are such as to produce constructive interference of the reradiated signals; that is, to concentrate the reradiated signal power in a direction back toward the source. Hence, an RFID tag equipped with a Van Atta antenna array automatically tracks the interrogating transceiver. The effective gain of a Van Atta array is the same as that of a traditional phased antenna array having the same number of antenna elements. Additional pairs of antenna elements connected by equal-length transmission lines can be incorporated into a Van Atta array to increase its directionality. Like some RFID tags here-to-fore commercially available, an RFID or sensor tag of the present developmental type includes one-port surface-acoustic-wave (SAW) devices. In simplified terms, the mode of operation of a basic one-port SAW device as used heretofore in an RFID device is the following: An interrogating radio signal is converted, at an input end, from an electrical signal to an acoustic wave that propagates along a surface and encounters multiple reflectors suitably positioned along the surface. Upon returning to the input end, the reflected acoustic wave is re-converted to an electrical signal, which, in turn, is reradiated from an antenna. The distances between the reflectors in the SAW device and the corresponding times between reflections encode the identifying or sensory information onto the reradiated signal. The fundamental problem in the present development is how to combine a Van Atta antenna array (which is inherently a multiple-port device) and one or more one-port SAW device(s) into a single, compact, passive unit that can function as a retroreflective RFID tag. The solution is to use one or more hybrid, half-power 90 couplers. A basic unit of this type, shown in Figure 2, includes a half-power 90 hybrid coupler; two identical SAW devices (SAW1 and SAW2) connected to ports 3 and 4 of the coupler, respectively; and antenna elements connected to ports 1 and 2 of the coupler. Necessarily omitting details for the sake of brevity, it must suffice to report that the phase relationships among the coupler inputs and outputs are such as to couple the incident signal from the antenna elements to the SAW devices and couple the reflected signals from the SAW devices back to the antenna elements in the phase relationships required for a Van Atta array. Hence, the reradiated signal is automatically directed back toward the interrogating transceiver and contains identifying and/or sensory information encoded in time intervals between reflections.

Fink, Patrick W.↗

A strong loss-of-function mutation in RAN1 results in constitutive activation of the ethylene response pathway as well as a rosette-lethal phenotype

A recessive mutation was identified that constitutively activated the ethylene response pathway in Arabidopsis and resulted in a rosette-lethal phenotype. Positional cloning of the gene corresponding to this mutation revealed that it was allelic to responsive to antagonist1 (ran1), a mutation that causes seedlings to respond in a positive manner to what is normally a competitive inhibitor of ethylene binding. In contrast to the previously identified ran1-1 and ran1-2 alleles that are morphologically indistinguishable from wild-type plants, this ran1-3 allele results in a rosette-lethal phenotype. The predicted protein encoded by the RAN1 gene is similar to the Wilson and Menkes disease proteins and yeast Ccc2 protein, which are integral membrane cation-transporting P-type ATPases involved in copper trafficking. Genetic epistasis analysis indicated that RAN1 acts upstream of mutations in the ethylene receptor gene family. However, the rosette-lethal phenotype of ran1-3 was not suppressed by ethylene-insensitive mutants, suggesting that this mutation also affects a non-ethylene-dependent pathway regulating cell expansion. The phenotype of ran1-3 mutants is similar to loss-of-function ethylene receptor mutants, suggesting that RAN1 may be required to form functional ethylene receptors. Furthermore, these results suggest that copper is required not only for ethylene binding but also for the signaling function of the ethylene receptors.

NASA Discipline Plant Biology↗

LIDAR Metrology for Prescription Characterization and Alignment of Large Mirrors

We describe the use of LIDAR, or "laser radar," (LR) as a fast, accurate, and non-contact tool for the measurement of the radius of curvature (RoC) of large mirrors. We report the results of a demonstration of this concept using a commercial laser radar system. We measured the RoC of a 1.4m x 1m spherical mirror with a nominal RoC of 4.6 m with a manufacturing tolerance of 4600mm +/- 6mm. The prescription of the mirror is related to its role as ground support equipment used in the test of part of the James Webb Space Telescope (JWST). The RoC of such a large mirror is not easily measured without contacting the surface. From a position near the center of curvature of the mirror, the LIDAR scanned the mirror surface, sampling it with 1 point per 3.5 sq cm. The measurement consisted of 3983 points and lasted only a few minutes. The laser radar uses the LIDAR signal to provide range, and encoder information from angular azimuth and elevation rotation stages provide the spherical coordinates of a given point. A best-fit to a sphere of the measured points was performed. The resulting RoC was within 20 ppm of the nominal RoC, also showing good agreement with the results of a laser tracker-based, contact metrology. This paper also discusses parameters such as test alignment, scan density, and optical surface type, as well as future possible application for full prescription characterization of aspherical mirrors, including radius, conic, off-axis distance, and aperture.

Eegholm, B.↗

The Exoproteome and Surfaceome of Toxigenic Corynebacterium diphtheriae 1737 and Its Response to Iron Restriction and Growth on Human Hemoglobin

Toxin-producing Corynebacterium diphtheriae strains are the etiological agents of the severe upper respiratory disease, diphtheria. A global phylogenetic analysis revealed that biotype gravis is particularly lethal as it produces diphtheria toxin and a range of other virulence factors, particularly when it encounters low levels of iron at sites of infection. Here, to gain insight into how it colonizes its host, we have identified iron-dependent changes in the exoproteome and surfaceome of C. diphtheriae strain 1737 using a combination of whole-cell fractionation, intact cell surface proteolysis, and quantitative proteomics. In total, we identified 1414 of the predicted 2265 proteins (62%) encoded by its reference genome. For each protein, we quantified its degree of secretion and surface exposure, revealing that exoproteases and hydrolases predominate in the exoproteome, while the surfaceome is enriched with adhesins, particularly DIP2093. Our analysis provides insight into how components in the heme-acquisition system are positioned, showing pronounced surface exposure of the strain-specific ChtA/ChtC paralogues and high secretion of the species-conserved heme-binding HtaA protein, suggesting it functions as a hemophore. Profiling the response of the exoproteome and surfaceome after microbial exposure to human hemoglobin and iron limitation reveals potential virulence factors that may be expressed at sites of infection. Data are available via ProteomeXchange with identifier PXD051674.

cell envelope↗

Conformational ensembles reveal the origins of serine protease catalysis

Enzymes exist in ensembles of states that encode the energetics underlying their catalysis. Conformational ensembles built from 1231 structures of 17 serine proteases revealed atomic-level changes across their reaction states. By comparing the enzymatic and solution reaction, we identified molecular features that provide catalysis and quantified their energetic contributions to catalysis. Serine proteases precisely position their reactants in destabilized conformers, creating a downhill energetic gradient that selectively favors the motions required for reaction while limiting off-pathway conformational states. The same catalytic features have repeatedly evolved in proteases and additional enzymes across multiple distinct structural folds. In conclusion, our ensemble-function analyses revealed previously unknown catalytic features, provided quantitative models based on simple physical and chemical principles, and identified motifs recurrent in nature that may inspire enzyme design.

Du, Siyuan [Stanford Univ., CA (United States)] (O↗

Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library

Protein-protein interaction specificity is often encoded at the primary sequence level. However, the contributions of individual residues to specificity are usually poorly understood and often obscured by mutational robustness, sequence degeneracy, and epistasis. Using bacterial toxin-antitoxin systems as a model, we screened a combinatorially complete library of antitoxin variants at three key positions against two toxins. This library enabled us to measure the effect of individual substitutions on specificity in hundreds of genetic backgrounds. These distributions allow inferences about the general nature of interface residues in promoting specificity. We find that positive and negative contributions to specificity are neither inherently coupled nor mutually exclusive. Further, a wild-type antitoxin appears optimized for specificity as no substitutions improve discrimination between cognate and non-cognate partners. By comparing crystal structures of paralogous complexes, we provide a rationale for our observations. Collectively, this work provides a generalizable approach to understanding the logic of molecular recognition.

59 BASIC BIOLOGICAL SCIENCES↗

University of Maryland walking robot: A design project for undergraduate students

The design and construction required that the walking robot machine be capable of completing a number of tasks including walking in a straight line, turning to change direction, and maneuvering over an obstable such as a set of stairs. The machine consists of two sets of four telescoping legs that alternately support the entire structure. A gear-box and crank-arm assembly is connected to the leg sets to provide the power required for the translational motion of the machine. By retracting all eight legs, the robot comes to rest on a central Bigfoot support. Turning is accomplished by rotating the machine about this support. The machine can be controlled by using either a user operated remote tether or the on-board computer for the execution of control commands. Absolute encoders are attached to all motors (leg, main drive, and Bigfoot) to provide the control computer with information regarding the status of the motors (up-down motion, forward or reverse rotation). Long and short range infrared sensors provide the computer with feedback information regarding the machine's relative position to a series of stripes and reflectors. These infrared sensors simulate how the robot might sense and gain information about the environment of Mars.

Olsen, Bob↗

Bayesian Learning of Adatom Interactions from Atomically Resolved Imaging Data

Atomic structures and adatom geometries of surfaces encode information about the thermodynamics and kinetics of the processes that lead to their formation, and which can be captured by a generative physical model. In this work, we develop a workflow based on a machine-learning-based analysis of scanning tunneling microscopy images to reconstruct the atomic and adatom positions, and a Bayesian optimization procedure to minimize statistical distance between the chosen physical models and experimental observations. We optimize the parameters of a 2- and 3-parameter Ising model describing surface ordering and use the derived generative model to make predictions across the parameter space. For concentration dependence, we compare the predicted morphologies at different adatom concentrations with the dissimilar regions on the sample surfaces that serendipitously had different adatom concentrations. The proposed workflow can be used to reconstruct the thermodynamic models and associated uncertainties from the experimental observations of materials microstructures. The code used in the manuscript is available at https://github.com/saimani5/Adatom_interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

AFM Microcantilever With a Collocated AlN Sensor-Actuator Pair: Enabling Efficient Q-Control for Dynamic Imaging

This manuscript presents a novel microcantilever with an embedded piezoelectric sensor-actuator pair for dynamic atomic force microscopy (AFM). The transducer pair is constructed from a two-layered AlN stack. Stacking the piezoelectric transducers in this manner leads to a minimal feedthrough from actuation to sense electrode, granting a high dynamic range frequency response for dynamic mode AFM. The cantilever's design allows for dual mode operation at 1 st and 2 nd resonance modes. High resolution tapping mode imaging results are reported, while the cantilever is operated at these modes. A feedback control loop is used to modify quality factor of the 1 st mode of the cantilever, using a positive position feedback (PPF) controller. Here, a faster response time is achieved by reducing the Q-factor, enabling the cantilever to track the topography at a higher scan rate. Results of bimodal AFM imaging are reported, using amplitude changes of the 1 st mode for surface topography, while material properties are encoded in phase changes of the 2 nd mode.

47 OTHER INSTRUMENTATION↗

Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties

KRAS, the most frequently mutated oncogene in human cancer, produces two isoforms, KRAS4a and KRAS4b, through alternative splicing. These isoforms differ in exon 4, which encodes the final 15 residues of the G-domain and hypervariable regions (HVRs), vital for trafficking and membrane localization. While KRAS4b has been extensively studied, KRAS4a has been largely overlooked. Our multidisciplinary study compared the structural and functional characteristics of KRAS4a and KRAS4b, revealing distinct structural properties and thermal stability. Position 151 influences KRAS4a’s thermal stability, while position 153 affects binding to RAF1 CRD protein. Nuclear magnetic resonance analysis identified localized structural differences near sequence variations and provided a solution-state conformational ensemble. Notably,KRAS4aexhibits substantial transcript abundance in bile ducts, liver, and stomach, with transcript levels approachingKRAS4bin the colon and rectum. Functional disparities were observed in full-length KRAS variants, highlighting the impact of HVR variations on interaction with trafficking proteins and downstream effectors like RAF and PI3K within cells.

Science & Technology - Other Topics↗