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At least 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Initial Stage of Nanoscale Imaging in Positive Tone Extreme UV Photoresists: The Influence of the Polymer Sequence

Photolithographic patterning using extreme ultraviolet (EUV, 92.5 eV) light is a radiolytic process that initially forms electrons, radical cations, anions, and neutral radicals in the polymeric photoresist matrix. These species may participate in the chemical reactions that define the ultimate resolution of the printed image, and their concentrations and nanometer-scale stochastic variations in their formation influence printed image quality. Proposals have been made that polymer chain uniformity may be advantageous in reducing stochastics due to spatial inhomogeneities, and this aspect of radiolysis is examined in this work. We have simulated the initial subpicosecond stages of the imaging process for a series of photoresist films that are identical in composition but vary in their polymer chain structures. We use detailed, physically accurate stochastic reaction-diffusion calculations to evaluate the influence of defined sequence and random copolymer structures on radiolytic spur formation, i.e., a cluster of species formed by electron-polymer interactions that defines the initial spatial characteristic of the imaging process. Predictions of electron thermalization in the present work are shown to be consistent with the literature, indicating that our overall computational approach for ultrafast nanoscale processes is sound. The computational results show that the polymer sequence has no significant effect on the spur composition. This suggests that any potential imaging improvements to be gained by sequence control must originate from postimaging lithographic process steps.

Absorption↗
DOE OSTI2026

Polymorphism in Self-Assembly of Short Peptoid Sequences

Due to various applications enabled by diverse morphologies of self-assembled sequence-defined polymers, controlling the self-assembly of synthetic peptidomimetics into designed morphologies has emerged as a promising route for the development of bioinspired functional materials. Herein, we report morphological control over the assembly of a series of short peptoids, or poly-N-substituted glycines, that contain asymmetric hydrophobic domains. We demonstrate that the inherent flexibility of amphiphilic peptoid bilayers drives assembly polymorphism, resulting in the coexistence of nanosheets, twisted ribbons, and nanofibers three distinct morphologies. By tuning peptoid molecular interactions through variations in sequence design, solution pH, and temperature, we demonstrate precise control over the twisting and folding of peptoid bilayers, enabling the formation of well-defined nanosheets and nanohelices. Molecular dynamics simulations further unravel how the introduction of asymmetric hydrophobic domains enables the flexibility of peptoid bilayers and results in peptoid assembly polymorphism. By tuning peptoid molecular interactions through heating, we further demonstrate the transformation of nanosheets into nanohelices. We envision that our mechanistic investigation of peptoid assembly polymorphism provides a strong foundation for leveraging peptoid sequences and chemistries to achieve controlled molecular interactions, driving the creation of biomimetic materials with tailored morphologies and functionalities.

assembly polymorphism↗
DOE OSTI2025

Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing

Microglia, the innate immune cells of the central nervous system, have been genetically implicated in multiple neurodegenerative diseases. Mapping the genetics of gene expression in human microglia has identified several loci associated with disease-associated genetic variants in microglia-specific regulatory elements. However, identifying genetic effects on splicing is challenging because of the use of short sequencing reads. Here, we present the isoform-centric microglia genomic atlas (isoMiGA), which leverages long-read RNA sequencing to identify 35,879 novel microglia isoforms. We show that these isoforms are involved in stimulation response and brain region specificity. We then quantified the expression of both known and novel isoforms in a multi-ancestry meta-analysis of 555 human microglia short-read RNA sequencing samples from 391 donors, and found associations with genetic risk loci in Alzheimer’s and Parkinson’s disease. We nominate several loci that may act through complex changes in isoform and splice-site usage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

THE INTERIOR STRUCTURE CONSTANTS AS AN AGE DIAGNOSTIC FOR LOW-MASS, PRE-MAIN-SEQUENCE DETACHED ECLIPSING BINARY STARS

We propose a novel method for determining the ages of low-mass, pre-main-sequence stellar systems using the apsidal motion of low-mass detached eclipsing binaries. The apsidal motion of a binary system with an eccentric orbit provides information regarding the interior structure constants of the individual stars. These constants are related to the normalized stellar interior density distribution and can be extracted from the predictions of stellar evolution models. We demonstrate that low-mass, pre-main-sequence stars undergoing radiative core contraction display rapidly changing interior structure constants (greater than 5% per 10 Myr) that, when combined with observational determinations of the interior structure constants (with 5%-10% precision), allow for a robust age estimate. This age estimate, unlike those based on surface quantities, is largely insensitive to the surface layer where effects of magnetic activity are likely to be most pronounced. On the main sequence, where age sensitivity is minimal, the interior structure constants provide a valuable test of the physics used in stellar structure models of low-mass stars. There are currently no known systems where this technique is applicable. Nevertheless, the emphasis on time domain astronomy with current missions, such as Kepler, and future missions, such as LSST, has the potential to discover systems where the proposed method will be observationally feasible.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

STELLAR AGES AND CONVECTIVE CORES IN FIELD MAIN-SEQUENCE STARS: FIRST ASTEROSEISMIC APPLICATION TO TWO KEPLER TARGETS

Using asteroseismic data and stellar evolution models we obtain the first detection of a convective core in a Kepler field main-sequence star, putting a stringent constraint on the total size of the mixed zone and showing that extra mixing beyond the formal convective boundary exists. In a slightly less massive target the presence of a convective core cannot be conclusively discarded, and thus its remaining main-sequence lifetime is uncertain. Our results reveal that best-fit models found solely by matching individual frequencies of oscillations corrected for surface effects do not always properly reproduce frequency combinations. Moreover, slightly different criteria to define what the best-fit model is can lead to solutions with similar global properties but very different interior structures. We argue that the use of frequency ratios is a more reliable way to obtain accurate stellar parameters, and show that our analysis in field main-sequence stars can yield an overall precision of 1.5%, 4%, and 10% in radius, mass, and age, respectively. We compare our results with those obtained from global oscillation properties, and discuss the possible sources of uncertainties in asteroseismic stellar modeling where further studies are still needed.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

STELLAR DIAMETERS AND TEMPERATURES. III. MAIN-SEQUENCE A, F, G, AND K STARS: ADDITIONAL HIGH-PRECISION MEASUREMENTS AND EMPIRICAL RELATIONS

Based on CHARA Array measurements, we present the angular diameters of 23 nearby, main-sequence stars, ranging from spectral types A7 to K0, 5 of which are exoplanet host stars. We derive linear radii, effective temperatures, and absolute luminosities of the stars using Hipparcos parallaxes and measured bolometric fluxes. The new data are combined with previously published values to create an Angular Diameter Anthology of measured angular diameters to main-sequence stars (luminosity classes V and IV). This compilation consists of 125 stars with diameter uncertainties of less than 5%, ranging in spectral types from A to M. The large quantity of empirical data is used to derive color-temperature relations to an assortment of color indices in the Johnson (BVR{sub J} I{sub J} JHK), Cousins (R{sub C} I{sub C}), Kron (R{sub K} I{sub K}), Sloan (griz), and WISE (W{sub 3} W{sub 4}) photometric systems. These relations have an average standard deviation of {approx}3% and are valid for stars with spectral types A0-M4. To derive even more accurate relations for Sun-like stars, we also determined these temperature relations omitting early-type stars (T{sub eff} > 6750 K) that may have biased luminosity estimates because of rapid rotation; for this subset the dispersion is only {approx}2.5%. We find effective temperatures in agreement within a couple of percent for the interferometrically characterized sample of main-sequence stars compared to those derived via the infrared flux method and spectroscopic analysis.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Magnetic inhibition of convection and the fundamental properties of low-mass stars. II. Fully convective main-sequence stars

We examine the hypothesis that magnetic fields are inflating the radii of fully convective main-sequence stars in detached eclipsing binaries (DEBs). The magnetic Dartmouth stellar evolution code is used to analyze two systems in particular: Kepler-16 and CM Draconis. Magneto-convection is treated assuming stabilization of convection and also by assuming reductions in convective efficiency due to a turbulent dynamo. We find that magnetic stellar models are unable to reproduce the properties of inflated fully convective main-sequence stars, unless strong interior magnetic fields in excess of 10 MG are present. Validation of the magnetic field hypothesis given the current generation of magnetic stellar evolution models therefore depends critically on whether the generation and maintenance of strong interior magnetic fields is physically possible. An examination of this requirement is provided. Additionally, an analysis of previous studies invoking the influence of star spots is presented to assess the suggestion that star spots are inflating stars and biasing light curve analyses toward larger radii. From our analysis, we find that there is not yet sufficient evidence to definitively support the hypothesis that magnetic fields are responsible for the observed inflation among fully convective main-sequence stars in DEBs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

A turnover in the galaxy main sequence of star formation at M{sub *} ∼ 10{sup 10}M{sub ☉} for Redshifts z < 1.3

The relationship between galaxy star formation rates (SFRs) and stellar masses (M {sub *}) is reexamined using a mass-selected sample of ∼62,000 star-forming galaxies at z ≤ 1.3 in the COSMOS 2 deg{sup 2} field. Using new far-infrared photometry from Herschel-PACS and SPIRE and Spitzer-MIPS 24 μm, along with derived infrared luminosities from the NRK method based on galaxies' locations in the restframe color-color diagram (NUV – r) versus (r – K), we are able to more accurately determine total SFRs for our complete sample. At all redshifts, the relationship between median SFR and M {sub *} follows a power law at low stellar masses, and flattens to nearly constant SFR at high stellar masses. We describe a new parameterization that provides the best fit to the main sequence and characterizes the low mass power-law slope, turnover mass, and overall scaling. The turnover in the main sequence occurs at a characteristic mass of about M {sub 0} ∼ 10{sup 10} M {sub ☉} at all redshifts. The low mass power-law slope ranges from 0.9-1.3 and the overall scaling rises in SFR as a function of (1 + z){sup 4.12 ± 0.10}. A broken power-law fit below and above the turnover mass gives relationships of SFR∝M{sub ∗}{sup 0.88±0.06} below the turnover mass and SFR∝M{sub ∗}{sup 0.27±0.04} above the turnover mass. Galaxies more massive than M {sub *} ≳ 10{sup 10} M {sub ☉} have a much lower average specific star formation rate (sSFR) than would be expected by simply extrapolating the traditional linear fit to the main sequence found for less massive galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

INTRINSIC COLORS, TEMPERATURES, AND BOLOMETRIC CORRECTIONS OF PRE-MAIN-SEQUENCE STARS

We present an analysis of the intrinsic colors and temperatures of 5-30 Myr old pre-main-sequence (pre-MS) stars using the F0- through M9-type members of nearby, negligibly reddened groups: the η Cha cluster, the TW Hydra Association, the β Pic Moving Group, and the Tucana-Horologium Association. To check the consistency of spectral types from the literature, we estimate new spectral types for 52 nearby pre-MS stars with spectral types F3 through M4 using optical spectra taken with the SMARTS 1.5 m telescope. Combining these new types with published spectral types and photometry from the literature (Johnson-Cousins BVI{sub C} , 2MASS JHK{sub S} and WISE W1, W2, W3, and W4), we derive a new empirical spectral type-color sequence for 5-30 Myr old pre-MS stars. Colors for pre-MS stars match dwarf colors for some spectral types and colors, but for other spectral types and colors, deviations can exceed 0.3 mag. We estimate effective temperatures (T {sub eff}) and bolometric corrections (BCs) for our pre-MS star sample through comparing their photometry to synthetic photometry generated using the BT-Settl grid of model atmosphere spectra. We derive a new T {sub eff} and BC scale for pre-MS stars, which should be a more appropriate match for T Tauri stars than often-adopted dwarf star scales. While our new T {sub eff} scale for pre-MS stars is within ≅100 K of dwarfs at a given spectral type for stars <G5, for G5 through K6, the pre-MS stars are ∼250 K cooler than their MS counterparts. Lastly, we present (1) a modern T {sub eff}, optical/IR color, and BC sequence for O9V-M9V MS stars based on an extensive literature survey, (2) a revised Q-method relation for dereddening UBV photometry of OB-type stars, and (3) introduce two candidate spectral standard stars as representatives of spectral types K8V and K9V.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

On the Impact of Widening Vector Registers on Sequence Alignment

Vector extensions, such as SSE, have been part of the x86 since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. In this paper, we demonstrate that the trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. We present a practically efficient SIMD implementation of a parallel scan based sequence alignment algorithm that can better exploit wider SIMD units. We conduct comprehensive workload and use case analyses to characterize the relative behavior of the striped and scan approaches and identify the best choice of algorithm based on input length and SIMD width.

Needleman-Wunsch↗
DOE OSTI2017

Universal Human Papillomavirus Typing Assay: Whole-Genome Sequencing following Target Enrichment

We designed a universal human papillomavirus (HPV) typing assay based on target enrichment and whole-genome sequencing (eWGS). The RNA bait included 23,941 probes targeting 191 HPV types and 12 probes targeting beta-globin as a control. We used the Agilent SureSelect XT2 protocol for library preparation, Illumina HiSeq 2500 for sequencing, and CLC Genomics Workbench for sequence analysis. Mapping stringency for type assignment was determined based on 8 (6 HPV-positive and 2 HPV-negative) control samples. Using the optimal mapping conditions, types were assigned to 24 blinded samples. eWGS results were 100% concordant with Linear Array (LA) genotyping results for 9 plasmid samples and fully or partially concordant for 9 of the 15 cervical-vaginal samples, with 95.83% overall type-specific concordance for LA genotyping. eWGS identified 7 HPV types not included in the LA genotyping. Since this method does not involve degenerate primers targeting HPV genomic regions, PCR bias in genotype detection is minimized. With further refinements aimed at reducing cost and increasing throughput, this first application of eWGS for universal HPV typing could be a useful method to elucidate HPV epidemiology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

RNA Sequencing Identifies New RNase III Cleavage Sites in Escherichia coli and Reveals Increased Regulation of mRNA

ABSTRACT Ribonucleases facilitate rapid turnover of RNA, providing cells with another mechanism to adjust transcript and protein levels in response to environmental conditions. While many examples have been documented, a comprehensive list of RNase targets is not available. To address this knowledge gap, we compared levels of RNA sequencing coverage of Escherichia coli and a corresponding RNase III mutant to expand the list of known RNase III targets. RNase III is a widespread endoribonuclease that binds and cleaves double-stranded RNA in many critical transcripts. RNase III cleavage at novel sites found in aceEF , proP , tnaC , dctA , pheM , sdhC , yhhQ , glpT , aceK , and gluQ accelerated RNA decay, consistent with previously described targets wherein RNase III cleavage initiates rapid degradation of secondary messages by other RNases. In contrast, cleavage at three novel sites in the ahpF , pflB , and yajQ transcripts led to stabilized secondary transcripts. Two other novel sites in hisL and pheM overlapped with transcriptional attenuators that likely serve to ensure turnover of these highly structured RNAs. Many of the new RNase III target sites are located on transcripts encoding metabolic enzymes. For instance, two novel RNase III sites are located within transcripts encoding enzymes near a key metabolic node connecting glycolysis and the tricarboxylic acid (TCA) cycle. Pyruvate dehydrogenase activity was increased in an rnc deletion mutant compared to the wild-type (WT) strain in early stationary phase, confirming the novel link between RNA turnover and regulation of pathway activity. Identification of these novel sites suggests that mRNA turnover may be an underappreciated mode of regulating metabolism. IMPORTANCE The concerted action and overlapping functions of endoribonucleases, exoribonucleases, and RNA processing enzymes complicate the study of global RNA turnover and recycling of specific transcripts. More information about RNase specificity and activity is needed to make predictions of transcript half-life and to design synthetic transcripts with optimal stability. RNase III does not have a conserved target sequence but instead recognizes RNA secondary structure. Prior to this study, only a few RNase III target sites in E. coli were known, so we used RNA sequencing to provide a more comprehensive list of cleavage sites and to examine the impact of RNase III on transcript degradation. With this added information on how RNase III participates in transcript regulation and recycling, a more complete picture of RNA turnover can be developed for E. coli . Similar approaches could be used to augment our understanding of RNA turnover in other bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Whole-Genome Sequencing of Human Clinical Klebsiella pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae

Klebsiella pneumoniae is a major threat to public health, causing significant morbidity and mortality worldwide. The emergence of highly drug-resistant strains is particularly concerning. There has been a recognition and division of Klebsiella pneumoniae into three distinct phylogenetic groups: Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. K. variicola and K. quasipneumoniae have often been described as opportunistic pathogens that have less virulence in humans than K. pneumoniae does. We recently sequenced the genomes of 1,777 extended-spectrum-beta-lactamase (ESBL)-producing K. pneumoniae isolates recovered from human infections and discovered that 28 strains were phylogenetically related to K. variicola and K. quasipneumoniae. Whole-genome sequencing of 95 additional non-ESBL-producing K. pneumoniae isolates recovered from patients found 12 K. quasipneumoniae strains. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) analysis initially identified all patient isolates as K. pneumoniae, suggesting a potential pitfall in conventional clinical microbiology laboratory identification methods. Whole-genome sequence analysis revealed extensive sharing of core gene content and plasmid replicons among the Klebsiella species. For the first time, strains of both K. variicola and K. quasipneumoniae were found to carry the Klebsiella pneumoniae carbapenemase (KPC) gene, while another K. variicola strain was found to carry the New Delhi metallo-beta-lactamase 1 (NDM-1) gene. K. variicola and K. quasipneumoniae infections were not less virulent than K. pneumoniae infections, as assessed by in-hospital mortality and infection type. We also discovered evidence of homologous recombination in one K. variicola strain, as well as one strain from a novel Klebsiella species, which challenge the current understanding of interrelationships between clades of Klebsiella.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Whole-Genome Sequencing Identifies a Rice Grain Shape Mutant, gs9–1

Breeding for genes controlling key agronomic traits is an important goal of rice genetic improvement. To gain insight into genes controlling grain morphology, we screened M 3 plants derived from 1,000 whole-genome sequenced (WGS) M 2 Kitaake mutants to identify lines with altered grain size. RESULTS:In this study, we isolated a mutant, named fast-neutron (FN) 60-4, which exhibits a significant reduction in grain size. We crossed FN60-4 with the parental line Kitaake and analyzed the resulting backcross population. Segregation analysis of 113 lines from the BC 2 F 2 population revealed that the mutant phenotype is controlled by a single semi-dominant locus. Mutant FN60-4 is reduced 20% in plant height and 8.8% in 1000-grain weight compared with Kitaake. FN60-4 also exhibits an 8% reduction in cell number and a 9% reduction in cell length along the vertical axis of the glume. We carried out whole-genome sequencing of DNA pools extracted from segregants with long grains or short grains, and revealed that one gene, LOC_Os09g02650, cosegregated with the grain size phenotype in the BC 1 F 2 and BC 2 F 2 populations. This mutant allele was named grain shape 9-1 (gs9-1). gs9-1 carries a 3-bp deletion that affects two amino acids. This locus is a new allele of the BC12/GDD1/MTD1 gene that encodes a kinesin-like protein involved in cell-cycle progression, cellulose microfibril deposition and gibberellic acid (GA) biosynthesis. The GA biosynthesis-related gene KO2 is down-regulated in gs9-1 . The dwarf phenotype of gs9-1 can be rescued by adding exogenous GA3. In contrast to the phenotypes for the other alleles, the gs9-1 is less severe, consistent with the nature of the mutation, which does not disrupt the open reading frame as observed for the other alleles. In this study, we isolated a mutant, which exhibits altered grain shape and identified the mutated gene, gs9-1 . Our study reveals that gs9-1 is a semi-dominant gene that carries a two-amino acid mutation. gs9-1 is allelic to the BC12/GDD1/MTD1 gene involved in GA biosynthesis. These results demonstrate the efficiency and convenience of cloning genes from the whole-genome sequenced Kitaake mutant population to advance investigations into genes controlling key agronomic traits in rice.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

ADEPT, a dynamic next generation sequencing data error-detection program with trimming

Illumina is the most widely used next generation sequencing technology and produces millions of short reads that contain errors. These sequencing errors constitute a major problem in applications such as de novo genome assembly, metagenomics analysis and single nucleotide polymorphism discovery. In this study, we present ADEPT, a dynamic error detection method, based on the quality scores of each nucleotide and its neighboring nucleotides, together with their positions within the read and compares this to the position-specific quality score distribution of all bases within the sequencing run. This method greatly improves upon other available methods in terms of the true positive rate of error discovery without affecting the false positive rate, particularly within the middle of reads. We conclude that ADEPT is the only tool to date that dynamically assesses errors within reads by comparing position-specific and neighboring base quality scores with the distribution of quality scores for the dataset being analyzed. The result is a method that is less prone to position-dependent under-prediction, which is one of the most prominent issues in error prediction. The outcome is that ADEPT improves upon prior efforts in identifying true errors, primarily within the middle of reads, while reducing the false positive rate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Genome sequence of the model rice variety KitaakeX

Abstract Background The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficiencies, which limits their usefulness as model organisms for functional genomics studies. In contrast, the rice variety Kitaake has a rapid life cycle (9 weeks seed to seed) and is easy to transform and propagate. For these reasons, Kitaake has emerged as a model for studies of diverse monocotyledonous species. Results Here, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica ), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica ). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics. Conclusions The high quality, de novo assembly of the KitaakeX genome will serve as a useful reference genome for rice and will accelerate functional genomics studies of rice and other species.

Nipponbare↗
DOE OSTI2019

Benchmarking of alignment-free sequence comparison methods

Background: Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. Results: Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference, and reconstruction of species trees under horizontal gene transfer and recombination events. Conclusion: The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

BMC Caller: a webtool to identify and analyze bacterial microcompartment types in sequence data

Bacterial microcompartments (BMCs) are protein-based organelles found across the bacterial tree of life. They consist of a shell, made of proteins that oligomerize into hexagonally and pentagonally shaped building blocks, that surrounds enzymes constituting a segment of a metabolic pathway. The proteins of the shell are unique to BMCs. They also provide selective permeability; this selectivity is dictated by the requirements of their cargo enzymes. We have recently surveyed the wealth of different BMC types and their occurrence in all available genome sequence data by analyzing and categorizing their components found in chromosomal loci using HMM (Hidden Markov Model) protein profiles. To make this a “do-it yourself” analysis for the public we have devised a webserver, BMC Caller (https://bmc-caller.prl.msu.edu), that compares user input sequences to our HMM profiles, creates a BMC locus visualization, and defines the functional type of BMC, if known. Shell proteins in the input sequence data are also classified according to our function-agnostic naming system and there are links to similar proteins in our database as well as an external link to a structure prediction website to easily generate structural models of the shell proteins, which facilitates understanding permeability properties of the shell. Additionally, the BMC Caller website contains a wealth of information on previously analyzed BMC loci with links to detailed data for each BMC protein and phylogenetic information on the BMC shell proteins. Our tools greatly facilitate BMC type identification to provide the user information about the associated organism’s metabolism and enable discovery of new BMC types by providing a reference database of all currently known examples.

59 BASIC BIOLOGICAL SCIENCES↗