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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Visualizing novel connections and genetic similarities across diseases using a network-medicine based approach

Understanding the genetic relationships between human disorders could lead to better treatment and prevention strategies, especially for individuals with multiple comorbidities. A common resource for studying genetic-disease relationships is the GWAS Catalog, a large and well curated repository of SNP-trait associations from various studies and populations. Some of these populations are contained within mega-biobanks such as the Million Veteran Program (MVP), which has enabled the genetic classification of several diseases in a large well-characterized and heterogeneous population. Here we aim to provide a network of the genetic relationships among diseases and to demonstrate the utility of quantifying the extent to which a given resource such as MVP has contributed to the discovery of such relations. We use a network-based approach to evaluate shared variants among thousands of traits in the GWAS Catalog repository. Our results indicate many more novel disease relationships that did not exist in early studies and demonstrate that the network can reveal clusters of diseases mechanistically related. Finally, we show novel disease connections that emerge when MVP data is included, highlighting methodology that can be used to indicate the contributions of a given biobank.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genome sequence and characterization of a novel Pseudomonas putida phage, MiCath

Abstract Pseudomonads are ubiquitous bacteria with importance in medicine, soil, agriculture, and biomanufacturing. We report a novel Pseudomonas putida phage, MiCath, which is the first known phage infecting P. putida S12, a strain increasingly used as a synthetic biology chassis. MiCath was isolated from garden soil under a tomato plant using P. putida S12 as a host and was also found to infect four other P. putida strains. MiCath has a ~ 61 kbp double-stranded DNA genome which encodes 97 predicted open reading frames (ORFs); functions could only be predicted for 48 ORFs using comparative genomics. Functions include structural phage proteins, other common phage proteins (e.g., terminase), a queuosine gene cassette, a cas4 exonuclease, and an endosialidase. Restriction digestion analysis suggests the queuosine gene cassette encodes a pathway capable of modification of guanine residues. When compared to other phage genomes, MiCath shares at most 74% nucleotide identity over 2% of the genome with any sequenced phage. Overall, MiCath is a novel phage with no close relatives, encoding many unique gene products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Novel usage of deep learning and high-performance computing in long-baseline neutrino oscillation experiments

Mención Internacional en el título de doctorDeep-learning methods are playing a crucial role in numerous scientific and industrialapplications. Over the past two decades, these techniques have helped in the collection,reconstruction, and analysis of large data samples in particle physics experiments. Themain topic of this PhD research is the study of deep-learning techniques in long-baselineneutrino oscillation experiments. Neutrinos are mysterious light elementary particles,and their investigation is essential to shed light on some of the remaining open questionsin physics. The work presented here describes an algorithm based on a convolutionalneural network developed to provide highly accurate and efficient selections of electronneutrino and muon neutrino interactions in the Deep Underground Neutrino Experiment(DUNE). With this algorithm, the electron neutrino (antineutrino) selection efficiencypeaks at 90% (94%) and exceeds 85% (90%) for reconstructed neutrino energies between2-5 GeV. The selection efficiency for muon neutrino (antineutrino) interactions is foundto have a maximum of 96% (97%) and exceeds 90% (95%) efficiency for reconstructedneutrino energies above 2 GeV. When considering all electron neutrino and antineutrinointeractions as signal (both those appearing from oscillations and those intrinsic tothe beam), a selection purity of 90% is achieved. These event selections are criticalto maximise the sensitivity of the experiment to CP-violating effects, key to furtherunderstand the matter-antimatter asymmetry of the Universe.In high-energy physics experiments, deep learning has also been explored for producingfast simulations and physically-motivated manipulations of simulated images. Some ofthose simulations, such as the light production and detection, are very computationallyexpensive and require novel methods to produce the necessary samples while controllingthe varied underlying physics model parameters. To do so, we invented the model-assistedgenerative adversarial network (MAGAN), first validated on simple generic case studiesand then successfully applied to the DUNE photon-detector simulation.Moreover, we also developed graph neural networks for 3D-voxel classification ofambiguities and optical crosstalk for a different particle physics experiment, most preciselyfor the proposed SuperFGD. This novel 3D-granular plastic-scintillator neutrino detectorwill be used to upgrade the near detector of the T2K neutrino oscillation experiment, and our method reports efficiencies and purities of 94-96% per event in the classificationof particle track voxels.Due to the growth and complexity of deep neural networks, researchers have beeninvestigating techniques to train those networks in a more computationally-efficient way.Many efforts have been made by the community to optimise deep-learning models byparallelising or distributing their training computation across multiple devices. In thisthesis, we study an approach based on data locality for those neural networks that cannotbenefit from scaling their computation due to a significant bottleneck in the data I/O.The research also includes a detailed study on the performance of deep neural networkson hardware accelerator boards.Los métodos de aprendizaje profundo son cada vez más utilizados en numerosas aplicacionescientíficas e industriales hoy en día. Durante las dos últimas décadas, estastécnicas se han empleado en la recolección, reconstrucción y análisis de la gran cantidadde datos generados por experimentos de física de partículas. El tema principal de estatesis doctoral es el uso de estos modelos de aprendizaje profundo en experimentos defísica de neutrinos, en concreto en los experimentos de larga distancia DUNE y T2K. Losneutrinos, partículas fundamentales neutras, de las más ligeras del Universo, pueden serclave para explicar algunas de las cuestiones todavía sin resolver en física fundamental.Entre las diferentes contribuciones que esta tesis ha hecho a su estudio, cabe destacar eldesarrollo de un algoritmo basado en una red de neuronas convolucional para seleccionarcon gran eficiencia y precisión las interacciones de neutrinos electrónicos y muónicos enel Deep Underground Neutrino Experiment (DUNE). La eficiencia de selección obtenidapara neutrinos (antineutrinos) electrónicos alcanza un máximo del 90% (94%) y supera el85% (90%) para neutrinos con energías reconstruidas en el rango 2-5 GeV. La selección deneutrinos (antineutrinos) muónicos tiene una eficiencia máxima del 96% (97%) y excedeel 90% (95%) para neutrinos con energías reconstruidas de más de 2 GeV. Considerandocomo señal todas las interacciones de neutrinos y antineutrinos electrónicos (procedentestanto de oscilaciones como intrínsecos en el haz inicial), se logra una pureza en la seleccióndel 90%. Dichas selecciones de eventos son fundamentales para maximizar la sensibilidaddel experimento a los efectos de violació...

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Novel Earned Value Management System Maturity Framework and Its Relation to Project Performance

Earned value management systems (EVMS) are used by industry practitioners to successfully manage projects and programs; however, there has been no past study to characterize and evaluate the impact of EVMS maturity on project performance. This paper introduces a novel framework, developed to measure the EVMS maturity, composed of 56 attributes arrayed across ten subprocesses, which together make up an integrated project/program management system. This paper describes how the framework was conceived and developed, based on literature review and data collected from industry workshops. Then, it examines the relationship between EVMS maturity and ten project performance metrics through statistical analyses. The study analyzed project data from 35 projects and programs worth over $21.8 billion in total cost. For this sample, results showed statistically significant differences between projects with high and low EVMS maturity; on average, projects exhibiting high EVMS maturity have 54% less cost overruns and 19% less change orders versus their performance measurement baseline. Higher maturity projects and programs also achieve better customer satisfaction, meet business objectives more often, and are more often in compliance with EVMS standards and guidelines. This paper contributes to the body of knowledge by providing a practical and novel framework for assessing the maturity of earned value management systems. Practitioners can use the framework to improve their integrated project and program management.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2022

Perspective on solid-phase epitaxy as a method for searching novel topological phases in pyrochlore iridate thin films

Pyrochlore iridates exhibit various novel topological phenomena due to their topology and electron correlation. Notably, pyrochlore iridate was the first proposed material system shown to host the time-reversal symmetry broken Weyl semimetal phase. After this profound theoretical proposal, extensive experimental attempts have been made to synthesize high-quality samples in both bulk and film forms. In particular, adjusting thin film geometry represents a practical way to tune the U/ t ( U: Coulomb interaction and t: for hopping parameter) and identify the various topological phases in the regime U ~ λ ( λ: spin–orbit interaction). However, the instability of pyrochlore iridates at high temperature and low oxygen pressure has long been a barrier to growing pyrochlore iridate thin films by conventional film growth methods. To overcome this, pyrochlore iridate films have often been grown by the solid-phase epitaxy method, which uses a metastable amorphous layer grown at low temperature. During a high temperature post-annealing process, the layer in contact with a single crystalline substrate will crystallize epitaxially in the solid state by rearranging atoms at the interface. Here, we present a perspective on the solid-phase epitaxy as a method to synthesize epitaxial pyrochlore iridate thin films and a way to search for novel correlated phenomena.

36 MATERIALS SCIENCE↗
DOE OSTI2023

A novel class of broad-spectrum active-site-directed 3C-like protease inhibitors with nanomolar antiviral activity against highly immune-evasive SARS-CoV-2 Omicron subvariants

Antivirals with broad coronavirus activity are important for treating high-risk individuals exposed to the constantly evolving SARS-CoV-2 variants of concern (VOCs) as well as emerging drug-resistant variants. We developed and characterized a novel class of active-site-directed 3-chymotrypsin-like protease (3CLpro) inhibitors (C2-C5a). Our lead direct-acting antiviral (DAA), C5a, is a non-covalent, non-peptide with a dissociation constant of 170 nM against recombinant SARS-CoV-2 3CLpro. The compounds C2-C5a exhibit broad-spectrum activity against Omicron subvariants (BA.5, BQ.1.1, and XBB.1.5) and seasonal human coronavirus-229E infection in human cells. Notably, C5a has median effective concentrations of 30-50 nM against BQ.1.1 and XBB.1.5 in two different human cell lines. X-ray crystallography has confirmed the unique binding modes of C2-C5a to the 3CLpro, which can limit virus cross-resistance to emerging Paxlovid-resistant variants. We tested the effect of C5a with two of our newly discovered host-directed antivirals (HDAs): N-0385, a TMPRSS2 inhibitor, and bafilomycin D (BafD), a human vacuolar H+-ATPase [V-ATPase] inhibitor. We demonstrated a synergistic action of C5a in combination with N-0385 and BafD against Omicron BA.5 infection in human Calu-3 lung cells. Our findings underscore that a SARS-CoV-2 multi-targeted treatment for circulating Omicron subvariants based on DAAs (C5a) and HDAs (N-0385 or BafD) can lead to therapeutic benefits by enhancing treatment efficacy. Furthermore, the high-resolution structures of SARS-CoV-2 3CLpro in complex with C2-C5a will facilitate future rational optimization of our novel broad-spectrum active-site-directed 3C-like protease inhibitors.

3CLpro inhibitor↗
DOE OSTI2026

Comparison of juvenile white sturgeon blade strike survival through a conventional and a novel hydropower turbine

Hydropower is a globally important renewable energy source with profound impacts on aquatic organisms, including direct injury and mortality to fish that move through hydropower facilities. While it is expected that the characteristics of turbine design and operation influence the type, frequency, and magnitude of injuries suffered by entrained fish, few direct comparisons exist to illustrate differences in fish survival outcomes for conventional and novel turbine designs. This study evaluated blade strike-associated injury and mortality rates for juvenile white sturgeon (Acipenser transmontanus) passed through a model-scale turbine equipped with a runner having conventional blade profiles (thin, straight leading edges) and the same turbine equipped with a runner designed for improved fish survival (thick, slanted leading edges). In both trials, head and turbine runner rotational speeds were matched to produce five blade peripheral speeds between 15.0 and 27.6 m/s. High-speed video was captured for all turbine passage events. Fish were assessed for injuries following passage, and mortalities were assessed immediately after passage and after 48 h. Conventional runner passage resulted in 42% to 78% survival after 48 h, with approximately one-third of all tested fish killed by severing. Under the same test conditions, immediate and 48 h survival rates through the novel runner were 100% except at the highest speed condition (95.6% survival at 48 h). These results clearly indicate that turbine design has a profound effect on fish survival, and suggest that thoughtful redesign of hydropower equipment could significantly ameliorate the risks of blade strike mortality.

13 HYDRO ENERGY↗
DOE OSTI2020

Novel tools and observables for jet physics in heavy-ion collisions

Abstract Studies of fully-reconstructed jets in heavy-ion collisions aim at extracting thermodynamical and transport properties of hot and dense QCD matter. Recently, a plethora of new jet substructure observables have been theoretically and experimentally developed that provide novel precise insights on the modifications of the parton radiation pattern induced by a QCD medium. This report, summarizing the main lines of discussion at the 5th Heavy Ion Jet Workshop and CERN TH institute ‘Novel tools and observables for jet physics in heavy-ion collisions’ in 2017, presents a first attempt at outlining a strategy for isolating and identifying the relevant physical processes that are responsible for the observed medium-induced jet modifications. These studies combine theory insights, based on the Lund parton splitting map, with sophisticated jet reconstruction techniques, including grooming and background subtraction algorithms.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance

Democratizing genomic data science, including bioinformatics, can diversify the STEM workforce and may, in turn, bring new perspectives into the space sciences. In this respect, the development of education and research programs that bridge genome science with “place” and world-views specific to a given region are valuable for Indigenous students and educators. Through a multi-institutional collaboration, we developed an ongoing education program and model that includes Illumina and Oxford Nanopore sequencing, free bioinformatic platforms, and teacher training workshops to address our research and education goals through a place-based science education lens. High school students and researchers cultivated, sequenced, assembled, and annotated the genomes of 13 bacteria from Mars analog sites with cultural relevance, 10 of which were novel species. Students, teachers, and community members assisted with the discovery of new, potentially chemolithotrophic bacteria relevant to astrobiology. This joint education-research program also led to the discovery of species from Mars analog sites capable of producing N-acyl homoserine lactones, which are quorum-sensing molecules used in bacterial communication. Whole genome sequencing was completed in high school classrooms, and connected students to funded space research, increased research output, and provided culturally relevant, place-based science education, with participants naming three novel species described here. Students at St. Andrew's School (Honolulu, Hawai‘i) proposed the name Bradyrhizobium prioritasuperba for the type strain, BL16A T , of the new species (DSM 112479 T = NCTC 14602 T ). The nonprofit organization Kauluakalana proposed the name Brenneria ulupoensis for the type strain, K61 T , of the new species (DSM 116657 T = LMG = 33184 T ), and Hawai‘i Baptist Academy students proposed the name Paraflavitalea speifideiaquila for the type strain, BL16E T , of the new species (DSM 112478 T = NCTC 14603 T ).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Novel symmetry-preserving neural network model for phylogenetic inference

Abstract Motivation Scientists world-wide are putting together massive efforts to understand how the biodiversity that we see on Earth evolved from single-cell organisms at the origin of life and this diversification process is represented through the Tree of Life. Low sampling rates and high heterogeneity in the rate of evolution across sites and lineages produce a phenomenon denoted “long branch attraction” (LBA) in which long nonsister lineages are estimated to be sisters regardless of their true evolutionary relationship. LBA has been a pervasive problem in phylogenetic inference affecting different types of methodologies from distance-based to likelihood-based. Results Here, we present a novel neural network model that outperforms standard phylogenetic methods and other neural network implementations under LBA settings. Furthermore, unlike existing neural network models in phylogenetics, our model naturally accounts for the tree isomorphisms via permutation invariant functions which ultimately result in lower memory and allows the seamless extension to larger trees. Availability and implementation We implement our novel theory on an open-source publicly available GitHub repository: https://github.com/crsl4/nn-phylogenetics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A novel polypeptide vaccine and adjuvant formulation of EV71

ABSTRACT Hand foot and mouth disease (HFMD) is an infectious disease mainly caused by Enterovirus 71 (EV 71). However, the effective treatment is limited currently. The aim of this study was to investigate the activity of the vaccine including the EV71 polypeptides mixed with a novel adjuvant containing CpG oligodeoxynucleotides (CpG ODNs). After collecting mouse sera, we determined the antibody concentration in serum by enzyme-linked immunosorbent assays (ELISA). Then, CD19+CD27+ B cells in the spleen were analysed by flow cytometry. The assay revealed that a substantial increase in antibody titers was achieved. This indicates a high level of immunogenicity for peptide vaccine and the good stability of adjuvant, also suggests that the combination of vaccine and adjuvant can stimulate the production of high-level antibodies and CD19+CD27+ B lymphocytes in mice. Furthermore, the antibody could effectively identify EV71 inactivated virus. The results demonstrated that the autonomous construction of EV71 polypeptide vaccine had a good immunogenicity. Moreover, the peptide vaccine injection with a novel adjuvant, which is easy to prepare, could cause a high antibody level of EV71 and shown a good application prospect.

Liu, Zhiang↗
DOE OSTI2023

Characterization of a novel polyextremotolerant fungus, Exophiala viscosa , with insights into its melanin regulation and ecological niche

Black yeasts are polyextremotolerant fungi that contain high amounts of melanin in their cell wall and maintain a primary yeast form. These fungi grow in xeric, nutrient depletes environments which implies that they require highly flexible metabolisms and have been suggested to contain the ability to form lichen-like mutualisms with nearby algae and bacteria. However, the exact ecological niche and interactions between these fungi and their surrounding community are not well understood. We have isolated 2 novel black yeasts from the genus Exophiala that were recovered from dryland biological soil crusts. Despite notable differences in colony and cellular morphology, both fungi appear to be members of the same species, which has been named Exophiala viscosa (i.e. E. viscosa JF 03-3 Goopy and E. viscosa JF 03-4F Slimy). A combination of whole genome sequencing, phenotypic experiments, and melanin regulation experiments have been performed on these isolates to fully characterize these fungi and help decipher their fundamental niche within the biological soil crust consortium. Our results reveal that E. viscosa is capable of utilizing a wide variety of carbon and nitrogen sources potentially derived from symbiotic microbes, can withstand many forms of abiotic stresses, and excretes melanin which can potentially provide ultraviolet resistance to the biological soil crust community. Besides the identification of a novel species within the genus Exophiala, our study also provides new insight into the regulation of melanin production in polyextremotolerant fungi.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Proteome-wide association study and functional validation identify novel protein markers for pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) remains a lethal malignancy, largely due to the paucity of reliable biomarkers for early detection and therapeutic targeting. Existing blood protein biomarkers for PDAC often suffer from replicability issues, arising from inherent limitations such as unmeasured confounding factors in conventional epidemiologic study designs. To circumvent these limitations, we use genetic instruments to identify proteins with genetically predicted levels to be associated with PDAC risk. Leveraging genome and plasma proteome data from the INTERVAL study, we established and validated models to predict protein levels using genetic variants. By examining 8,275 PDAC cases and 6,723 controls, we identified 40 associated proteins, of which 16 are novel. Functionally validating these candidates by focusing on 2 selected novel protein-encoding genes, GOLM1 and B4GALT1, we demonstrated their pivotal roles in driving PDAC cell proliferation, migration, and invasion. Furthermore, we also identified potential drug repurposing opportunities for treating PDAC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Novel Focused Ion Beam Liftouts for Spatial Characterization of Spherical Biominerals With Transmission Electron Microscopy

Abstract Focused ion beam (FIB) is frequently used to prepare electron- and X-ray-beam-transparent thin sections of samples, called lamellae. Typically, lamellae are prepared from only a subregion of a sample. In this paper, we present a novel approach for FIB lamella preparation of microscopic samples, wherein the entire cross-section of the whole sample can be investigated. The approach was demonstrated using spherical, porous, and often hollow microprecipitates of biologically precipitated calcium carbonate. The microprecipitate morphology made these biogenic samples more fragile and challenging than materials commonly investigated using FIB lamellae. Our method enables the appropriate orientation of the lamellae required for further electron/X-ray analyses after attachment to the transmission electron microscopy (TEM) grid post and facilitates more secure adhesion onto the grid post. We present evidence of autofluorescence in bacterially precipitated vaterite using this lamella preparation method coupled with TEM selected area diffraction. This innovative approach allows studying biomineralization at the micro to nano scales, which can provide novel insights into bacterial responses to microenvironmental conditions.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

A novel approach for calculating galaxy rotation curves using spaxel cross-correlation and iterative smoothing

ABSTRACT Precise measurements of the internal dynamics of galaxies have proven of great importance for understanding the internal dark matter distribution of galaxies. We present a novel method for measuring the line-of-sight (LOS) velocities across the face of galaxies by cross-correlation of spectral pixels (spaxels) and an iterative method of smoothing. On simulated data the method can accurately recover the input LOS velocities for different types of spectra (absorption-line dominated, emission-line dominated, and differing shapes of the continuum), and can handle stellar population radial gradients. Most important of all, it continues to provide reliable measurements of LOS velocities with reasonable uncertainties even when the spectra are very low signal-to-noise ratio (approaching ∼1), which is a challenge for traditional template-fitting approaches. We apply our method to data from a real MaNGA galaxy as a demonstration and find promising results with good precision. This novel approach can be complementary to existing methods primarily based on template fitting.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Tree-based solvers for adaptive mesh refinement code FLASH – III: a novel scheme for radiation pressure on dust and gas and radiative transfer from diffuse sources

Radiation is an important contributor to the energetics of the interstellar medium, yet its transport is difficult to solve numerically. We present a novel approach towards solving radiative transfer of diffuse sources via backwards ray tracing. Here, we focus on the radiative transfer of infrared radiation and the radiation pressure on dust. The new module, TREERAY/RADPRESSURE, is an extension to the novel radiative transfer method TREERAY implemented in the grid-based Magneto-Hydrodynamics code FLASH. In TREERAY/RADPRESSURE, every cell and every star particle is a source of infrared radiation. We also describe how gas, dust, and radiation are coupled via a chemical network. This allows us to compute the local dust temperature in thermal equilibrium, leading to a significantly improvement over the classical grey approximation. In several tests, we demonstrate that the scheme produces the correct radiative intensities as well as the correct momentum input by radiation pressure. Subsequently, we apply our new scheme to model massive star formation from a collapsing, turbulent core of 150 M ⊙ . We include the effects of both, ionizing and infrared radiation on the dynamics of the core. We find that the newborn massive star prevents fragmentation in its proximity due to radiative heating. Over time, dust and radiation temperature equalize, while the gas temperature can be either warmer due to shock heating or colder due to insufficient dust–gas coupling. Compared to gravity, the effects of radiation pressure are insignificant for the stellar mass on the simulated time-scale in this work.

(ISM:) HII regions↗
DOE OSTI2023

NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes

Abstract The Novel Metagenome Protein Families Database (NMPFamsDB) is a database of metagenome- and metatranscriptome-derived protein families, whose members have no hits to proteins of reference genomes or Pfam domains. Each protein family is accompanied by multiple sequence alignments, Hidden Markov Models, taxonomic information, ecosystem and geolocation metadata, sequence and structure predictions, as well as 3D structure models predicted with AlphaFold2. In its current version, NMPFamsDB hosts over 100 000 protein families, each with at least 100 members. The reported protein families significantly expand (more than double) the number of known protein sequence clusters from reference genomes and reveal new insights into their habitat distribution, origins, functions and taxonomy. We expect NMPFamsDB to be a valuable resource for microbial proteome-wide analyses and for further discovery and characterization of novel functions. NMPFamsDB is publicly available in http://www.nmpfamsdb.org/ or https://bib.fleming.gr/NMPFamsDB.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structure of the E. coli nucleoid-associated protein YejK reveals a novel DNA binding clamp

Abstract Nucleoid-associated proteins (NAPs) play central roles in bacterial chromosome organization and DNA processes. The Escherichia coli YejK protein is a highly abundant, yet poorly understood NAP. YejK proteins are conserved among Gram-negative bacteria but show no homology to any previously characterized DNA-binding protein. Hence, how YejK binds DNA is unknown. To gain insight into YejK structure and its DNA binding mechanism we performed biochemical and structural analyses on the E. coli YejK protein. Biochemical assays demonstrate that, unlike many NAPs, YejK does not show a preference for AT-rich DNA and binds non-sequence specifically. A crystal structure revealed YejK adopts a novel fold comprised of two domains. Strikingly, each of the domains harbors an extended arm that mediates dimerization, creating an asymmetric clamp with a 30 Å diameter pore. The lining of the pore is electropositive and mutagenesis combined with fluorescence polarization assays support DNA binding within the pore. Finally, our biochemical analyses on truncated YejK proteins suggest a mechanism for YejK clamp loading. Thus, these data reveal YejK contains a newly described DNA-binding motif that functions as a novel clamp.

Biochemistry & Molecular Biology↗