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DOE OSTI2025

Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community

ABSTRACT Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein‐coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer‐term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non‐coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency‐inverse document frequency (TF‐IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high‐quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within‐domain and involve non‐coding DNA. A relatively high proportion of the predicted protein‐coding HGTs appear to encode transposase activity, restriction‐modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF‐IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.

Microbiology↗

NASA NTRS2012

Optical Phase Recovery and Locking in a PPM Laser Communication Link

Free-space optical communication holds great promise for future space missions requiring high data rates. For data communication in deep space, the current architecture employs pulse position modulation (PPM). In this scheme, the light is transmitted and detected as pulses within an array of time slots. While the PPM method is efficient for data transmission, the phase of the laser light is not utilized. The phase coherence of a PPM optical signal has been investigated with the goal of developing a new laser communication and ranging scheme that utilizes optical coherence within the established PPM architecture and photon-counting detection (PCD). Experimental measurements of a PPM modulated optical signal were conducted, and modeling code was developed to generate random PPM signals and simulate spectra via FFT (Fast Fourier Transform) analysis. The experimental results show very good agreement with the simulations and confirm that coherence is preserved despite modulation with high extinction ratios and very low duty cycles. A real-time technique has been developed to recover the phase information through the mixing of a PPM signal with a frequency-shifted local oscillator (LO). This mixed signal is amplified, filtered, and integrated to generate a voltage proportional to the phase of the modulated signal. By choosing an appropriate time constant for integration, one can maintain a phase lock despite long dark times between consecutive pulses with low duty cycle. A proof-of-principle demonstration was first achieved with an RF-based PPM signal and test setup. With the same principle method, an optical carrier within a PPM modulated laser beam could also be tracked and recovered. A reference laser was phase-locked to an independent pulsed laser signal with low-duty-cycle pseudo-random PPM codes. In this way, the drifting carrier frequency in the primary laser source is tracked via its phase change in the mixed beat note, while the corresponding voltage feedback maintains the phase lock between the two laser sources. The novelty and key significance of this work is that the carrier phase information can be harnessed within an optical communication link based on PPM-PCD architecture. This technology development could lead to quantum-limited efficient performance within the communication link itself, as well as enable high-resolution optical tracking capabilities for planetary science and spacecraft navigation.

Aveline, David C.↗

DOE OSTI2021

Inter-well connectivity detection in CO 2 WAG projects using statistical recurrent unit models

Routine well-wise injection and production measurements contain significant information on subsurface structure and properties. Data-driven technology that interprets surface data into subsurface structure or properties can assist operators in making informed decisions by providing a better understanding of field assets. Our machine-learning framework is built on the statistical recurrent unit (SRU) model and interprets well-based injection/production data into inter-well connectivity without relying on a geologic model. We test it on synthetic and field-scale CO 2 EOR projects utilizing the water-alternating-gas (WAG) process. SRU is a special type of recurrent neural network (RNN) that allows for better characterization of temporal trends, by learning various statistics of the input at different time scales. In our application, the complete states (injection rate, pressure and cumulative injection) at injectors and pressure states at producers are fed to SRU as the input and the phase rates at producers are treated as the output. Once the SRU is trained and validated, it is then used to assess the connectivity of each injector to any producer using permutation variable importance method, wherein inputs corresponding to an injector are shuffled and the increase in prediction error at a given producer is recorded as the importance (connectivity metric) of the injector to the producer. This method is tested in both synthetic and field-scale cases. The validation of the proposed data-driven inter-well connectivity assessment is performed using synthetic data from simulation models where inter-well connectivity can be easily measured using the streamline-based flux allocation. The SRU model is shown to offer excellent prediction performance on the synthetic case. Despite significant measurement noise and frequent well shut-ins imposed in the field-scale case, the SRU model offers good prediction accuracy, the overall relative error of the phase production rates at most producers ranges from 10% to 30%. It is shown that the dominant connections identified by the data-driven method and streamline method are in close agreement. This significantly improves confidence in our data-driven procedure. The novelty of this work is that it is purely data-driven method and can directly interpret routine surface measurements to intuitive subsurface knowledge. Furthermore, the streamline-based validation procedure provides physics-based backing to the results obtained from data analytics. This study results in a reliable and efficient data analytics framework that is well-suited for large field applications.

42 ENGINEERING↗

NASA NTRS2013

Forward-Looking IED Detector Ground Penetrating Radar

There have been many developments of mine or metal detectors based on ground penetrating radar techniques, usually in hand-held or rover-mounted devices. In most mine or metal detector applications, conditions are in a stationary mode and detection speed is not an important factor. A novel, forward-looking, stepped-frequency ground penetrating radar (GPR) has been developed with a capability to detect improvised explosive devices (IEDs) at vehicular speeds of 15 to 20 mph (24 to 32 km/h), 10 to 20 m ahead of the vehicle, to ensure adequate time for response. The GPR system employs two horn antennas (1.7 to 2.6 GHz, 20 dBi) as transmit and receive. The detector system features a user-friendly instantaneous display on a laptop PC and is a low-power-consumption (3 W) compact system with minimal impact on vehicle operations. In practice, the whole GPR system and a laptop PC can be powered by plugging into a cigarette lighter of a vehicle. The stepped-frequency continuous-wave (CW) radar scans frequency from 1.7 to 2.6 GHz in 1,000 steps of 0.9 MHz, with the full frequency scan in 60 ms. The GPR uses a bi-static configuration with one horn antenna used as a transmitter and the other used as a receiver so that isolation between transmitter and receiver is improved. Since the horn antennas (20 dBi) are mounted on the roof of a vehicle at a shallow inclination angle (15 to 25 with respect to horizontal), there is a first-order reduction in ground reflection so that a significant amount of the total reflected power received by the GPR comes from the scattering of RF energy off of buried objects. The stepped-frequency technique works by transmitting a tone at a particular frequency, while the received signal is mixed with the transmitted tone. As a result, the output of the mixer produces a signal that indicates the strength of the received signal and the extent to which it is in phase or out of phase with the transmitted tone. By taking measurements of the phase relationship between the transmitted and received signals over a wide frequency range, an interference pattern is produced showing all target reflections. When a Fourier transform is performed on this pattern, the result is a time-domain representation of targets. Among the advantages of this technique over impulse radar is the ability to transmit and receive much more total energy, and to use non-damped, highly focused horn antennas. The novelty of the IED detector GPR has been achieved by miniaturization of GPR electronics (single electronics board, 10x5x2 cm), low power consumption (3 W), faster signal processing capability, and minimal impact on vehicle operations.

Kim, Soon Sam↗

DOE OSTI2022

Selective Detection of Diglycolamide Diastereomers By Metal-Ligand Cluster Formation

Introduction (120 words): Differentiation of isomers using mass spectrometry is a challenge, as these species tend to produce ions of identical mass-to-charge ratio. Therefore, separation with mass spectrometry must rely on chemical differences between isomeric species. Separation of stereoisomers is especially challenging, as these species often have very similar chemistry. However, recent investigations of the solvent extraction behavior of diastereomers of diglycolamide molecules have shown that different stereoisomers can have significantly different lanthanide extraction efficiencies. These studies showed that the R,S stereoisomer of 2,2'-oxybis(N,N-dioctylpropanamide efficiently extracts lanthanides, while the S,S stereoisomer does not. Thus, gas-phase metal complexation may provide a pathway for differentiating these species using mass spectrometry. Methods (120 words): Europium, samarium, and holmium clusters with the R,S, and the S,S diastereomers of 2,2'-oxybis(N,N-didecylpropanamide (trivially tetradecyl diglycolamide, or mTDDGA) were generated in gas-phase using the electrospray ionization source of a Bruker (Billerica, MA, USA) micrOTOF-Q II quadrupole time-of-flight mass spectrometer. Solutions of aqueous lanthanide nitrate and diglycolamide ligands in 2-propanol were added to 50%:50% by volume acetonitrile:2-propanol to generate the spray solutions. Ligand concentration was maintained at approximately 6 µM, while lanthanide concentration was maintained at either 6 µM or 30 µM . High resolution, high mass accuracy spectra were recorded using the time-of-flight. Mass accuracy was ensured using external calibration with Agilent (Santa Clara, CA, USA) ESI-L Low Concentration tuning mix. Preliminary data (300 words): Electrospray of solutions containing only R,S-mTDDGA or S,S-m-TDDGA yield abundant peaks at m/z= 721.7, corresponding to [mTDDGA+H]+1, m/z = 743.7, corresponding to [mTDDGA+Na]+1, and m/z = 1464.4, corresponding to the sodium-bound dimer, [Na(mTDDGA)2]+1. Spray of solutions containing 6 µM europium (Eu) with 3 µM R,S-mTDDGA produced an abundant cluster ion with an isotopic envelope centered at m/z=772.0, corresponding to [Eu(R,S-mTDDGA)3]3+. Europium-containing cluster ions with isotopic envelopes apexing at m/z = 1012.3 and 1189.0 correspond to the [Eu(R,S-mTDDGA)4]3+ and [Eu(R,S-mTDDGA)5]3+ cluster ions, respectively. Protonated and sodiated R,S-mTDDGA are present as well, along with the sodium-bound dimer. In contrast, spray of solutions containing 6 µM europium (Eu) with 3 µM S,S-mTDDGA diastereomer yielded only protonated and sodiated ligand ions; no Eu- S,S-mTDDGA ions were present. This mirrors the solution-phase behavior, where the S,S diestereomer extracts lanthanides with significantly less efficiency than the R,S diestereomer. Experiments with holmium and samarium yielded the same results. Increasing the lanthanide concentration to 30 µM resulted in limited formation of lanthanide-S,S-mTDDGA clusters. However, the abundance of the [Ln(S,S-mTDDGA)3]3+ clusters remained low compared to the abundance of the protonated and sodiated ligand. Additionally, the abundance of the [Ln(R,S-mTDDGA)3]3+ cluster ion was significantly higher than that of the protonated and sodiated ligand in experiments with spray solutions containing 30 µM lanthanide with R,S-mTDDA, supporting the hypothesis that R,S-mTDDGA has a higher intrinsic affinity for the lanthanides than S,S-mTDDGA. Thus, the intrinsic complexation with lanthanides appears to offer a route to differentiate diglycolamide diestereomers in the gas-phase. Novelty (20): Stereoisomers can be differentiated in the gas phase by exploitation of differences in metal complexation chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗