Controlling Crystal Texture in Programmable Atom Equivalent Thin Films
Abstract not provided
Gabrys, Paul A.↗
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Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity
DNA polymerases catalyze DNA synthesis with high efficiency, which is essential for all life. Extensive kinetic and structural efforts have been executed in exploring mechanisms of DNA polymerases, surrounding their kinetic pathway, catalytic mechanisms, and factors that dictate polymerase fidelity. Recent time-resolved crystallography studies on DNA polymerase η (Pol η) and β have revealed essential transient events during the DNA synthesis reaction, such as mechanisms of primer deprotonation, separated roles of the three metal ions, and conformational changes that disfavor incorporation of the incorrect substrate. DNA-embedded ribonucleotides (rNs) are the most common lesion on DNA and a major threat to genome integrity. While kinetics of rN incorporation has been explored and structural studies have revealed that DNA polymerases have a steric gate that destabilizes ribonucleotide triphosphate binding, the mechanism of extension upon rN addition remains poorly characterized. Using steady-state kinetics, static and time-resolved X-ray crystallography with Pol η as a model system, we showed that the extra hydroxyl group on the primer terminus does alter the dynamics of the polymerase active site as well as the catalysis and fidelity of DNA synthesis. During rN extension, Pol η error incorporation efficiency increases significantly across different sequence contexts. Finally, our systematic structural studies suggest that the rN at the primer end improves primer alignment and reduces barriers in C2'-endo to C3'-endo sugar conformational change. Overall, our work provides further mechanistic insights into the effects of rN incorporation on DNA synthesis.
59 BASIC BIOLOGICAL SCIENCES↗
Opening options for material transfer
Material-transfer agreements (MTAs) underlie the legal frameworks within which biotechnology practitioners define the terms and conditions for sharing biomaterials ranging, for example, from plasmid DNA to patient samples. If MTAs are easy to use and well adapted to the needs of individual researchers, institutions, and broader communities, then more sharing, innovation, and translation can occur. However, the MTA frameworks currently in place were developed in the 1990s—before widespread adoption of the World Wide Web, genome sequencing, and gene synthesis—and are not always well adapted for contemporary research and translation practices or aligned with social objectives.
Kahl, Linda↗
Omega: an Overlap-graph de novo Assembler for Meta-genomics
Motivation: Metagenomic sequencing allows reconstruction of mi-crobial genomes directly from environmental samples. Omega (overlap-graph metagenome assembler) was developed here for assembling and scaffolding Illumina sequencing data of microbial communities. Results: Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming small branches. Unitigs were generat-ed based on minimum cost flow analysis of the overlap graph. Obtained unitigs were merged to contigs and scaffolds using mate-pair information. Omega was compared with two de Bruijn graph assemblers, SOAPdenovo and IDBA-UD, using a publically-available Illumina sequencing dataset of a 64-genome mock com-munity. The assembly results were verified by their alignment with reference genomes. The overall performances of the three assem-blers were comparable and each assembler provided best results for a subset of genomes.
Haider, Bahlul↗
Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina
A novel yeast species was isolated from the sugar-rich stromata of Cyttaria hariotii collected from two different Nothofagus tree species in the Andean forests of Patagonia, Argentina. Phylogenetic analyses of the concatenated sequence of the rRNA gene sequences and the protein-coding genes for actin and translational elongation factor-1α indicated that the novel species belongs to the genus Hanseniaspora. De novo genome assembly of the strain CRUB 1928 T yielded a 10.2-Mbp genome assembly predicted to encode 4452 protein-coding genes. The genome sequence data were compared to the genomes of other Hanseniaspora species using three different methods, an alignment-free distance measure, K r , and two model-based estimations of DNA-DNA homology values, of which all provided indicative values to delineate species of Hanseniaspora. Given its potential role in a rare indigenous alcoholic beverage in which yeasts ferment sugars extracted from the stromata of Cytarria sp., we searched for the genes that may suggest adaptation of novel Hanseniaspora species to fermenting communities. The SSU1-like gene encoding a sulfite efflux pump, which, among Hanseniaspora, is present only in close relatives to the new species, was detected and analyzed, suggesting that this gene might be one factor that characterizes this novel species. We also discuss several candidate genes that likely underlie the physiological traits used for traditional taxonomic identification. Based on these results, a novel yeast species with the name Hanseniaspora gamundiae sp. nov. is proposed with CRUB 1928 T (ex-types: ZIM 2545 T = NRRL Y-63793 T = PYCC 7262 T ; MycoBank number MB 824091) as the type strain. Furthermore, we propose the transfer of the Kloeckera species, K. hatyaiensis, K. lindneri and K. taiwanica to the genus Hanseniaspora as Hanseniaspora hatyaiensis comb. nov. (MB 828569), Hanseniaspora lindneri comb. nov. (MB 828566) and Hanseniaspora taiwanica comb. nov. (MB 828567).
59 BASIC BIOLOGICAL SCIENCES↗
High-Density Single Nucleotide Polymorphism Linkage Maps of Lowland Switchgrass using Genotyping-by-Sequencing
Switchgrass (Panicum virgatum L.) is a warm-season perennial grass with promising potential as a bioenergy crop in the United States. However, the lack of genomic resources has slowed the development of plant lines with optimal characteristics for sustainable feedstock production. We generated high-density single nucleotide polymorphism (SNP) linkage maps using a reduced-representation sequencing approach by genotyping 231 F 1 progeny of a cross between two parents of lowland ecotype from the cultivars Kanlow and Alamo. Over 350 million reads were generated and aligned, which enabled identification and ordering of 4611 high-quality SNPs. The total lengths of the resulting framework maps were 1770 cM for the Kanlow parent and 2059 cM for the Alamo parent. These maps show collinearity with maps generated with polymerase chain reaction (PCR)-based simple-sequence repeat (SSR) markers, and new SNP markers were identified in previously unpopulated regions of the genome. Transmission segregation distortion affected all linkage groups (LGs) to differing degrees, and ordering of distorted markers highlighted several regions of unequal inheritance. Framework maps were adversely affected by the addition of distorted markers with varying severity, but distorted maps were of higher marker density and provided additional information for analysis. Alignment of these linkage maps with a draft version of the switchgrass genome assembly demonstrated high levels of collinearity and provides greater confidence in the validity of both resources. This methodology has proven to be a rapid and cost-effective way to generate high-quality linkage maps of an outcrossing species.
59 BASIC BIOLOGICAL SCIENCES↗
CAHS: Context-Aware Homology Search
Protein homology search is foundational to bioinformatics: it supports annotation transfer, structure/function inference, and evolutionary analysis over rapidly expanding sequence repositories (e.g., UniProtKB). Profile hidden Markov models (pHMMs), as implemented in HMMER, remain the most widely trusted approach because they provide statistically calibrated E-values; however, their gap behavior is fixed once a profile is trained, despite biological evidence that insertion/deletion tolerance varies across flexible loops and intrinsically disordered regions. We present CAHS (Context-Aware Homology Search), a lightweight query-time adapter for pHMM search that incorporates learned and biologically motivated signals without changing HMMER's downstream search pipeline or its calibrated E-value reporting. Given a query sequence, CAHS computes per-residue representations from a protein language model and a disorder predictor, maps these to profile coordinates, and modulates only match-state transition rows (gap-open and gap-extension probabilities) while preserving Plan7 constraints. We comprehensively evaluate CAHS across six structurally diverse protein families and multi-domain architectures against a 570k-sequence target corpus. CAHS expands detection capability, retrieving thousands of additional remote homologs at relaxed thresholds by maintaining alignment quality through flexible regions. For multi-domain proteins, context-aware modulation resolves 94% of fragmented alignments. Crucially, CAHS preserves hit-set invariance at stringent operating points (E<10-10), demonstrating increased statistical confidence without inflating false positives. Furthermore, sharper statistical distinction between homologs and background noise during early filter stages yields up to a 3.87× acceleration in end-to-end wall-clock time on high-performance computing clusters. Overall, CAHS illustrates a practical AI-for-science design pattern: augmenting a trusted probabilistic model with query-specific learned signals to improve interpretable, reproducible inference in data-rich biology.
Bhattaram, Swethasree [Georgia Institute of Techno↗
Astrophysical tests of modified gravity: the morphology and kinematics of dwarf galaxies
This paper is the third in a series on tests of gravity using observations of stars and nearby dwarf galaxies. We carry out four distinct tests using published data on the kinematics and morphology of dwarf galaxies, motivated by the theoretical work of Hui et al. (2009) and Jain and Vanderplas (2011). In a wide class of gravity theories a scalar field couples to matter and provides an attractive fifth force. Due to their different self-gravity, stars and gas may respond differently to the scalar force leading to several observable deviations from standard gravity. HI gas, red giant stars and main sequence stars can be displaced relative to each other, and the stellar disk can display warps or asymmetric rotation curves aligned with external potential gradients. To distinguish the effects of modified gravity from standard astrophysical phenomena, we use a control sample of galaxies that are expected to be screened from the fifth force. In all cases we find no significant deviation from the null hypothesis of general relativity. The limits obtained from dwarf galaxies are not yet competitive with the limits from cepheids obtained in our first paper, but can be improved to probe regions of parameter space that are inaccessible using other tests. We discuss how our methodology can be applied to new radio and optical observations of nearby galaxies.
79 ASTRONOMY AND ASTROPHYSICS↗
Phase diagram of the SU(2) Kondo lattice
We examine the SU(2) Kondo Lattice Model, for simple cubic lattices with various magnitudes of the localized spins j and numbers of conduction electrons, nc. For j=1/2, the system undergoes transitions from the paramagnetic to magnetically ordered states. The sequence of low-temperature magnetic states found on increasing n c is symmetric about half-filling and exhibits a preference for commensurate phases over incommensurate phases. On increasing nc from small values, the sequence of magnetic orderings consists of: ferromagnetic phases, planes of ferromagnetically spins which are sequentially twisted by nc-dependent angles, ferromagnetic planes of spins that are aligned antiferromagnetically, antiferromagnetic planes of spins in which the Neel order parameters are twisted through incommensurate angles. Neel order is most stable around half-filling. Magnetic ordered phases are found to be more stable than the Kondo phase for j=1/2, but larger j values may stabilize the Kondo phase. For j=3/2 the sequence of magnetic ordering with increasing nc is the same but, depending on the value of the strength of the Kondo interaction, the Kondo phase may be stabilized in a window 4 ≥ n c ≥ 2. In accordance with Nozieres’s arguments, we find that magnetic ordering is dominant for almost filled and almost empty bands.
36 MATERIALS SCIENCE↗
k-merSNP discovery: Software for alignment-and reference-free scalable SNP discovery, phylogenetics, and annotation for hundreds of microbial genomes
With the flood of whole genome finished and draft microbial sequences, we need faster, more scalable bioinformatics tools for sequence comparison. An algorithm is described to find single nucleotide polymorphisms (SNPs) in whole genome data. It scales to hundreds of bacterial or viral genomes, and can be used for finished and/or draft genomes available as unassembled contigs or raw, unassembled reads. The method is fast to compute, finding SNPs and building a SNP phylogeny in minutes to hours, depending on the size and diversity of the input sequences. The SNP-based trees that result are consistent with known taxonomy and trees determined in other studies. The approach we describe can handle many gigabases of sequence in a single run. The algorithm is based on k-mer analysis.
Source record↗
Predicting Antimicrobial Resistance Using Partial Genome Alignments
Antimicrobial resistance (AMR) is an important global health threat that impacts millions of people worldwide each year. Developing methods that can detect and predict AMR phenotypes can help to mitigate the spread of AMR by informing clinical decision making and appropriate mitigation strategies. Many bioinformatic methods have been developed for predicting AMR phenotypes from whole-genome sequences and AMR genes, but recent studies have indicated that predictions can be made from incomplete genome sequence data. In order to more systematically understand this, we built random forest-based machine learning classifiers for predicting susceptible and resistant phenotypes for Klebsiella pneumoniae (1,640 strains), Mycobacterium tuberculosis (2,497 strains), and Salmonella enterica (1,981 strains). We started by building models from alignments that were based on a reference chromosome for each species. We then subsampled each chromosomal alignment and built models for the resulting subalignments, finding that very small regions, representing approximately 0.1 to 0.2% of the chromosome, are predictive. In K. pneumoniae, M. tuberculosis, and S. enterica, the subalignments are able to predict multiple AMR phenotypes with at least 70% accuracy, even though most do not encode an AMR-related function. We used these models to identify regions of the chromosome with high and low predictive signals. Finally, subalignments that retain high accuracy across larger phylogenetic distances were examined in greater detail, revealing genes and intergenic regions with potential links to AMR, virulence, transport, and survival under stress conditions. IMPORTANCE Antimicrobial resistance causes thousands of deaths annually worldwide. Understanding the regions of the genome that are involved in antimicrobial resistance is important for developing mitigation strategies and preventing transmission. Machine learning models are capable of predicting antimicrobial resistance phenotypes from bacterial genome sequence data by identifying resistance genes, mutations, and other correlated features. They are also capable of implicating regions of the genome that have not been previously characterized as being involved in resistance. In this study, we generated global chromosomal alignments for Klebsiella pneumoniae, Mycobacterium tuberculosis, and Salmonella enterica and systematically searched them for small conserved regions of the genome that enable the prediction of antimicrobial resistance phenotypes. In addition to known antimicrobial resistance genes, this analysis identified genes involved in virulence and transport functions, as well as many genes with no previous implication in antimicrobial resistance.
59 BASIC BIOLOGICAL SCIENCES↗
Ultrahigh-Resolution Differential Ion Mobility Separations of Conformers for Proteins above 10 kDa: Onset of Dipole Alignment?
Biomacromolecules tend to assume numerous structures in solution or the gas phase. It has been possible to resolve disparate conformational families but not unique geometries within each, and drastic peak broadening has been the bane of protein analyses by chromatography, electrophoresis, and ion mobility spectrometry (IMS). The new differential IMS (FAIMS) approach using hydrogen-rich gases was recently found to separate conformers of a small protein ubiquitin with same peak width and resolving power up to ~400 as for peptides. Present work explores the reach of this approach for larger proteins, exemplified by cytochrome c and myoglobin. Resolution similar to that for ubiquitin was largely achieved with longer separations, while the onset of peak broadening and coalescence with shorter separations suggests the limitation of present technique to proteins under ~20 kDa. This capability may enable distinguishing whole proteins with differing residue sequences or localizations of posttranslational modifications. Small features at negative compensation voltages that markedly grow from cytochrome c to myoglobin indicate the dipole alignment of rare conformers in accord with theory, further supporting the concept of pendular macroions in FAIMS.
Environmental Molecular Sciences Laboratory↗
A novel strategy to improve the thermostability of Penicillium camembertii mono- and di-acylglycerol lipase
Highlights: • A new protein engineering method has been developed to tailor enzyme with high thermostability. • The optimum catalytic temperature of mutant D25R was increased by 5 °C. • Tm value of mutant D25R was increase by 3 °C. • Mutant D25R showed the increase in t{sub 1/2} with a nearly 4-fold. Penicillium camembertii (PCL), a mono- and di-acylglycerol lipase (DGL), has the vital potential in the oil chemistry for food industry. However, known DGLs are mesophilic enzymes which restricts its application in the industry. To improve thermostability of PCL, we used amino acid substitution by comparison of amino acids compositions of PCL and protein sequences from typical thermophilic bacteria. Then, some conservative residues around active center were avoided to mutate according to homologous alignment analyses. Furthermore, the list was narrowed down to 28 candidate mutational sites of PCL by analyzing the hydrophobic interaction of amino acids in the structure. And among them only the mutant PCL-D25R had formed an additional salt bridge between R25-D32 and increased more hydrogen bonds interaction. Therefore, mutant PCL-D25R were constructed and expressed. Thermal inactivation assay showed that the half-life of mutant PCL-D25R at 45 °C increased 4-fold compared to that of PCL-WT. Melting temperature of mutant PCL-D25R increased to 49.5 °C from 46.5 °C by fluorescence-based thermal stability assay. This study provides a valuable strategy for engineering DGL thermostability.
60 APPLIED LIFE SCIENCES↗
Phase-dependent shear-induced order of nanorods in isotropic and nematic wormlike micelle solutions
Small angle X-ray scattering with in situ shear was employed to study the assembly and ordering of dispersions of gold nanorods within wormlike micelle solutions formed by the surfactant cetylpyridinium chloride (CPyCl) and counter-ion sodium salicylate (NaSal). Above a threshold CPyCl concentration but below the isotropic-to-nematic transition of the micelles, the nanorods self-assembled under quiescent conditions into isotropically oriented domains with hexagonal order. Under steady shear at rates between 0.5 and 7.5 s -1 , the nanorod assemblies acquired macroscopic orientational order in which the hexagonal planes were coincident with the flow-vorticity plane. The nanorods could be re-dispersed by strong shear but re-assembled following cessation of the shear. In the nematic phase of the micelles at higher surfactant concentration, the nanorods did not acquire hexagonal order but instead formed smectic-like layers in the gradient–vorticity plane under shear. Finally, at still higher surfactant concentration, where the micelles form a hexagonal phase, the nanorods showed no translational ordering but did acquire nematic-like order under shear due to alignment in the flow. Depletion forces mediated by the wormlike micelles are identified as the driving mechanism for this sequence of nanorod ordering behaviors, suggesting a novel mechanism for controlled, reconfigurable assembly of nanoparticles in solution.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Post-Modification of Crystalline Peptoid Nanomembranes with Active Nanoparticles for Efficient Photooxidation of a Mustard Gas Simulant
Peptoids (or poly-N-substituted glycines) hold immense potential for assembling into hierarchically structured functional materials via controlled molecular interactions. To create self-assembled materials with tailored functionalities, peptoid sequences are often conjugated with reactive or recognition motifs to enable applications including specific binding, biomimetic catalysis, and fluorescence imaging. However, the direct integration of bulky functional motifs into peptoid sequences can disrupt assembly processes and structural outcomes. Herein, we present a post-modification strategy for functionalizing pre-formed 2D crystalline assemblies. Through introducing clickable active sites, such as azide, alkyne, or thiol groups into a peptoid sequence, site-specific conjugation is achieved post-assembly via efficient “click”-type reactions. This strategy enables the ordered alignment of functional groups and gold nanoparticles (Au NPs) on the surface of 2D peptoid nanomaterials with controlled density, while preserving their high crystallinity and structural integrity. Furthermore, we demonstrated that nanomembranes functionalized with both Au NPs and porphyrins enhance the efficiency and selectivity of the photooxidation of 2-chloroethyl ethyl sulfide, a simulant of sulfur mustard. This innovative strategy lays the groundwork for advancing peptoid-based functional materials across diverse applications, from catalysis to biomedicine.
Chemistry↗
First report of barley root-knot nematode, Meloidogyne naasi from turfgrass in Idaho, with multigene molecular characterization
Barley root-knot nematode, Meloidogyne naasi Franklin, 1965, is one of the most important pest nematodes infecting monocots (Franklin, 1965). Two-inch core soil samples collected from a golf course in Ada County, Idaho were submitted for identification in November of 2019. A high number of Meloidogyne sp. juveniles were recovered from both soil samples using sieving and decantation followed by the sugar centrifugal flotation method. They were examined by light microscopy, morphometric measurements, and multiple molecular markers, including the ribosomal 28S D2–D3 and intergenic spacer 2 (IGS-2) regions, mitochondrial markers cytochrome oxidase I (COI) and the interval from COII to 16S, and the protein-coding gene Hsp90. Morphometrics as well as BlastN comparisons with other root-knot nematode sequences from GenBank were consistent with identification as M. naasi. Phylogenetic trees inferred from 28S, IGS-2, COI, or Hsp90 alignments each separated the Idaho population into a strongly supported clade with other populations of M. naasi, while the COII-16S interval could not resolve M. naasi from M. minor. This report represents the first morphological and molecular characterization of Meloidogyne naasi from turfgrass in Idaho.
59 BASIC BIOLOGICAL SCIENCES↗
Effects of Size and Shape on the Tolerances for Misalignment and Probabilities for Successful Oriented Attachment of Nanoparticles
Oriented attachment (OA) of nanoparticles is an important pathway of crystal growth, but tools for quantitatively modeling OA are lacking. Here we present several simple models that relate the probability of achieving OA to basic geometric parameters such as particle size, shape, and lattice periodicity. A Moiré-domain model is applied to understand twist-misorientations between parallel surfaces, and it predicts that the range of twist angles yielding perfect OA is inversely related to the width of the contact area. This is confirmed and further developed using a surface functional model, which predicts how crystallographic registration forces drive the emergence of complex orientational energy landscapes. The energy landscapes are predicted to possess local minima that can trap particles in imperfect alignments, and these local minima become deeper and more numerous as the contact area increases, making OA more challenging for large particles. Further, a second set of models is presented to understand the sequence of events by which two crystallographic faces become co-planer after collision. We use a ‘central force approximation’ to quantitatively predict the odds of attaining coalignment between various faces when particles collide with random misalignments, and we show that in the absence of biasing forces, the probability of attaining alignment on a given face is roughly proportional to its solid angle as viewed from the center of the particle. The model predicts that OA is most favorable between well-faceted particles and becomes exceedingly unlikely for large spherical particles that express many microfacets.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
UAE6 - Wind Tunnel Tests Data - UAE6 - Sequence 8 - Raw Data
Sequences 8 and 9: Downwind Sonics (F,P) and Downwind Sonics Parked (P) This test sequence used an upwind, rigid turbine with a 0° cone angle. The wind speed ranged from 5 m/s to 25 m/s. Yaw angles of 0° to 60° were achieved. The blade tip pitch was 3°. The rotor rotated at 72 RPM during Sequence 8, but it was parked during Sequence 9. Blade pressure measurements were collected. The five-hole probes were removed and the plugs were installed. Plastic tape 0.03-mm-thick was used to smooth the interface between the plugs and the blade. The teeter dampers were replaced with rigid links, and these two channels were flagged as not applicable by setting the measured values in the data file to –99999.99 Nm. The teeter link load cell was pre-tensioned to 40,000 N. During post-processing, the probe channels were set to read -99999.99. Sonic anemometers were mounted on a strut downwind of the turbine. The strut was mounted to the T-frame, which was rotated to align the anemometers aft of the 9% and 49% radius locations at hub height. Because of this configuration, the tunnel balance data are considered invalid. Sequence 9 was designed to compare the downwind sonic anemometer readings with the upwind sonic anemometers without interference from the turbine. The rotor was parked with the instrumented blade at 0° azimuth. All pressure measurements obtained in Sequence 9 are invalid because sufficient time for temperature stabilization did not occur, thus all associated data values were flagged as not applicable by setting the measured values in the data file to 0.0000 Pa. This test is further described in Appendix G.
17 WIND ENERGY↗