1
|
Duckett DJ, Calder K, Sullivan J, Tank DC, Carstens BC. Reduced representation approaches produce similar results to whole genome sequencing for some common phylogeographic analyses. PLoS One 2023; 18:e0291941. [PMID: 38032899 PMCID: PMC10688678 DOI: 10.1371/journal.pone.0291941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 09/09/2023] [Indexed: 12/02/2023] Open
Abstract
When designing phylogeographic investigations researchers can choose to collect many different types of molecular markers, including mitochondrial genes or genomes, SNPs from reduced representation protocols, large sequence capture data sets, and even whole genomes. Given that the statistical power and accuracy of various analyses are expected to differ depending on both the type of marker and the amount of data collected, an exploration of the variance across methodological results as a function of marker type should provide valuable information to researchers. Here we collect mitochondrial Cytochrome b sequences, whole mitochondrial genomes, single nucleotide polymorphisms (SNP)s isolated using a genotype by sequencing (GBS) protocol, sequences from ultraconserved elements, and low-coverage nuclear genomes from the North American water vole (Microtus richardsoni). We estimate genetic distances, population genetic structure, and historical demography using data from each of these datasets and compare the results across markers. As anticipated, the results exhibit differences across marker types, particularly in terms of the resolution offered by different analyses. A cost-benefit analysis indicates that SNPs collected using a GBS protocol are the most cost-effective molecular marker, with inferences that mirror those collected from the whole genome data at a fraction of the cost per sample.
Collapse
Affiliation(s)
- Drew J. Duckett
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, United States of America
| | - Kailee Calder
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States of America
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
| | - David C. Tank
- Department of Botany, University of Wyoming, Laramie, WY, United States of America
| | - Bryan C. Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, United States of America
| |
Collapse
|
2
|
Podlesny B, Hinkle KR, Hayashi K, Niidome Y, Shiraki T, Janas D. Highly-Selective Harvesting of (6,4) SWCNTs Using the Aqueous Two-Phase Extraction Method and Nonionic Surfactants. Adv Sci (Weinh) 2023; 10:e2207218. [PMID: 36856265 DOI: 10.1002/advs.202207218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/26/2023] [Indexed: 05/18/2023]
Abstract
Monochiral single-walled carbon nanotubes (SWCNTs) are indispensable for advancing the technology readiness level of nanocarbon-based concepts. In recent times, many separation techniques have been developed to obtain specific SWCNTs from raw unsorted materials to catalyze the development in this area. This work presents how the aqueous two-phase extraction (ATPE) method can be enhanced for the straightforward isolation of (6,4) SWCNTs in one step. Introducing nonionic surfactant into the typically employed mixture of anionic surfactants, which drive the partitioning, is essential to increasing the ATPE system's resolution. A thorough analysis of the parameter space by experiments and modeling reveals the underlying interactions between SWCNTs, surfactants, and phase-forming agents, which drive the partitioning. Based on new insight gained on this front, a separation mechanism is proposed. Notably, the developed method is highly robust, which is proven by isolating (6,4) SWCNTs from several raw SWCNT materials, including SWCNT waste generated over the years in the laboratory.
Collapse
Affiliation(s)
- Blazej Podlesny
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, Gliwice, 44-100, Poland
| | - Kevin R Hinkle
- Department of Chemical and Materials Engineering, University of Dayton, Dayton, OH, 45469, USA
| | - Keita Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yoshiaki Niidome
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Tomohiro Shiraki
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Dawid Janas
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, Gliwice, 44-100, Poland
| |
Collapse
|
3
|
Fonseca EM, Duckett DJ, Almeida FG, Smith ML, Thomé MTC, Carstens BC. Assessing model adequacy for Bayesian Skyline plots using posterior predictive simulation. PLoS One 2022; 17:e0269438. [PMID: 35877611 PMCID: PMC9312427 DOI: 10.1371/journal.pone.0269438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 05/23/2022] [Indexed: 11/30/2022] Open
Abstract
Bayesian skyline plots (BSPs) are a useful tool for making inferences about demographic history. For example, researchers typically apply BSPs to test hypotheses regarding how climate changes have influenced intraspecific genetic diversity over time. Like any method, BSP has assumptions that may be violated in some empirical systems (e.g., the absence of population genetic structure), and the naïve analysis of data collected from these systems may lead to spurious results. To address these issues, we introduce P2C2M.Skyline, an R package designed to assess model adequacy for BSPs using posterior predictive simulation. P2C2M.Skyline uses a phylogenetic tree and the log file output from Bayesian Skyline analyses to simulate posterior predictive datasets and then compares this null distribution to statistics calculated from the empirical data to check for model violations. P2C2M.Skyline was able to correctly identify model violations when simulated datasets were generated assuming genetic structure, which is a clear violation of BSP model assumptions. Conversely, P2C2M.Skyline showed low rates of false positives when models were simulated under the BSP model. We also evaluate the P2C2M.Skyline performance in empirical systems, where we detected model violations when DNA sequences from multiple populations were lumped together. P2C2M.Skyline represents a user-friendly and computationally efficient resource for researchers aiming to make inferences from BSP.
Collapse
Affiliation(s)
- Emanuel M. Fonseca
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States of America
- Museum of Biological Diversity, The Ohio State University, Columbus, OH, United States of America
| | - Drew J. Duckett
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States of America
- Museum of Biological Diversity, The Ohio State University, Columbus, OH, United States of America
| | - Filipe G. Almeida
- Department of Zoology, Federal University at Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Megan L. Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN, United States of America
| | - Maria Tereza C. Thomé
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States of America
- Museum of Biological Diversity, The Ohio State University, Columbus, OH, United States of America
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States of America
- Museum of Biological Diversity, The Ohio State University, Columbus, OH, United States of America
- * E-mail:
| |
Collapse
|
4
|
Gregory AC, Gerhardt K, Zhong ZP, Bolduc B, Temperton B, Konstantinidis KT, Sullivan MB. MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations. Microbiome 2022; 10:49. [PMID: 35287721 PMCID: PMC8922842 DOI: 10.1186/s40168-022-01231-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 11/29/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Microbes and their viruses are hidden engines driving Earth's ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed. RESULTS Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro- and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity (π and θ), and selective pressures (pN/pS and Tajima's D) within and fixation indices (FST) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available) that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity (π) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better "bet hedge" in changing environments. Further, comparisons of microdiversity pre- and post-FMT in autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro level alone can miss important biological differences. CONCLUSIONS These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro- and microdiversity across microbial communities. Video abstract.
Collapse
Affiliation(s)
- Ann C Gregory
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Present Address: Department of Microbiology and Immunology, Rega Institute for Medical Research, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Kenji Gerhardt
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Zhi-Ping Zhong
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, UK
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA.
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA.
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
5
|
Grossman EF, Daramola DA, Botte GG. Comparing B3LYP and B97 Dispersion-corrected Functionals for Studying Adsorption and Vibrational Spectra in Nitrogen Reduction. ChemistryOpen 2021; 10:316-326. [PMID: 33434349 PMCID: PMC7953478 DOI: 10.1002/open.202000158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 12/20/2020] [Indexed: 11/10/2022] Open
Abstract
Electrochemical ammonia synthesis is being actively studied as a low temperature, low pressure alternative to the Haber-Bosch process. This work studied pure iridium as the catalyst for ammonia synthesis, following promising experimental results of Pt-Ir alloys. The characteristics studied include bond energies, bond lengths, spin densities, and free and adsorbed vibrational frequencies for the molecules N2 , N, NH, NH2 , and NH3 . Overall, these descriptive characteristics explore the use of dispersion-corrected density functional theory methods that can model N2 adsorption - the key reactant for electrochemical ammonia synthesis via transition metal catalysis. Specifically, three methods were tested: hybrid B3LYP, a dispersion-corrected form B3LYP-D3, and semi-empirical B97-D3. The latter semi-empirical method was explored to increase the accuracy obtained in vibrational analysis as well as reduce computational time. Two lattice surfaces, (111) and (100), were compared. The adsorption energies are stronger on (100) and follow the trend EB3LYP >EB3LYP-D3 >EB97-D3 on both surfaces.
Collapse
Affiliation(s)
- Esther F. Grossman
- Department of Physics and AstronomyCenter for Electrochemical Engineering ResearchOhio UniversityAthensOH 45701USA
| | - Damilola A. Daramola
- Department of Chemical and Biomolecular EngineeringOhio UniversityAthensOH 45701USA
| | - Gerardine G. Botte
- Department of Chemical EngineeringTexas Tech UniversityLubbockTX 79409USA
| |
Collapse
|
6
|
Killian JA, Topiwala TM, Pelletier AR, Frankhouser DE, Yan PS, Bundschuh R. FuSpot: a web-based tool for visual evaluation of fusion candidates. BMC Genomics 2018; 19:139. [PMID: 29439649 PMCID: PMC5812216 DOI: 10.1186/s12864-018-4486-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 01/17/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Gene fusions often occur in cancer cells and in some cases are the main driver of oncogenesis. Correct identification of oncogenic gene fusions thus has implications for targeted cancer therapy. Recognition of this potential has led to the development of a myriad of sequencing-based fusion detection tools. However, given the same input, many of these detectors will find different fusion points or claim different sets of supporting data. Furthermore, the rate at which these tools falsely detect fusion events in data varies greatly. This discrepancy between tools underscores the fact that computation algorithms still cannot perfectly evaluate evidence; especially when provided with small amounts of supporting data as is typical in fusion detection. We assert that when evidence is provided in an easily digestible form, humans are more proficient in identifying true positives from false positives. RESULTS We have developed a web tool that, given the genomic coordinates of a candidate fusion breakpoint, will extract fusion and non-fusion reads adjacent to the fusion point from partner transcripts, and color code reads by transcript origin and read orientation for ease of intuitive inspection by the user. Fusion partner transcript read alignments are performed using a novel variant of the Smith-Waterman algorithm. CONCLUSIONS Combined with dynamic filtering parameters, the visualization provided by our tool introduces a powerful new investigative step that allows researchers to comprehensively evaluate fusion evidence. Additionally, this allows quick identification of false positives that may deceive most fusion detectors, thus eliminating unnecessary gene fusion validation. We apply our visualization tool to publicly available datasets and provide examples of true as well as false positives reported by open source fusion detection tools.
Collapse
Affiliation(s)
- Jackson A. Killian
- Department of Physics, The Ohio State University, Columbus, OH USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH USA
| | - Taha M. Topiwala
- Department of Physics, The Ohio State University, Columbus, OH USA
| | | | - David E. Frankhouser
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH USA
| | - Pearlly S. Yan
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH USA
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH USA
| | - Ralf Bundschuh
- Department of Physics, The Ohio State University, Columbus, OH USA
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH USA
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH USA
| |
Collapse
|
7
|
Gorelenkova Miller O, Cole KS, Emerson CC, Allimuthu D, Golczak M, Stewart PL, Weerapana E, Adams DJ, Mieyal JJ. Novel chloroacetamido compound CWR-J02 is an anti-inflammatory glutaredoxin-1 inhibitor. PLoS One 2017; 12:e0187991. [PMID: 29155853 PMCID: PMC5695812 DOI: 10.1371/journal.pone.0187991] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/30/2017] [Indexed: 12/29/2022] Open
Abstract
Glutaredoxin (Grx1) is a ubiquitously expressed thiol-disulfide oxidoreductase that specifically catalyzes reduction of S-glutathionylated substrates. Grx1 is known to be a key regulator of pro-inflammatory signaling, and Grx1 silencing inhibits inflammation in inflammatory disease models. Therefore, we anticipate that inhibition of Grx1 could be an anti-inflammatory therapeutic strategy. We used a rapid screening approach to test 504 novel electrophilic compounds for inhibition of Grx1, which has a highly reactive active-site cysteine residue (pKa 3.5). From this chemical library a chloroacetamido compound, CWR-J02, was identified as a potential lead compound to be characterized. CWR-J02 inhibited isolated Grx1 with an IC50 value of 32 μM in the presence of 1 mM glutathione. Mass spectrometric analysis documented preferential adduction of CWR-J02 to the active site Cys-22 of Grx1, and molecular dynamics simulation identified a potential non-covalent binding site. Treatment of the BV2 microglial cell line with CWR-J02 led to inhibition of intracellular Grx1 activity with an IC50 value (37 μM). CWR-J02 treatment decreased lipopolysaccharide-induced inflammatory gene transcription in the microglial cells in a parallel concentration-dependent manner, documenting the anti-inflammatory potential of CWR-J02. Exploiting the alkyne moiety of CWR-J02, we used click chemistry to link biotin azide to CWR-J02-adducted proteins, isolating them with streptavidin beads. Tandem mass spectrometric analysis identified many CWR-J02-reactive proteins, including Grx1 and several mediators of inflammatory activation. Taken together, these data identify CWR-J02 as an intracellularly effective Grx1 inhibitor that may elicit its anti-inflammatory action in a synergistic manner by also disabling other pro-inflammatory mediators. The CWR-J02 molecule provides a starting point for developing more selective Grx1 inhibitors and anti-inflammatory agents for therapeutic development.
Collapse
Affiliation(s)
- Olga Gorelenkova Miller
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Kyle S. Cole
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Corey C. Emerson
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Dharmaraja Allimuthu
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Marcin Golczak
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Phoebe L. Stewart
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Drew J. Adams
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - John J. Mieyal
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
| |
Collapse
|
8
|
Abstract
Riblet structures found on fast-swimming shark scales, such as those found on a mako shark, have been shown to reduce fluid drag. In previous experimental and modelling studies, riblets have been shown to provide drag reduction by lifting vortices formed in turbulent flow, decreasing overall shear stresses. Skimmer birds (Rynchops) are the only birds to catch fish in flight by flying just above the water surface with a submerged beak to fish for food. Because they need to quickly catch prey, reducing drag on their beak is advantageous. For the first time, riblet structures found on the beak of the skimmer bird have been studied experimentally and computationally for low fluid drag properties. In this study, skimmer replicas were studied for drag reduction through pressure drop in closed-channel, turbulent water flow. Pressure drop measurements are compared for black and yellow skimmer beaks in two configurations, and mako shark skin. In addition, two configurations of skimmer beak were modelled to compare drag properties and vortex structures. Results are discussed, and a conceptual model is presented to explain a possible drag reduction mechanism in skimmers.This article is part of the themed issue 'Bioinspired hierarchically structured surfaces for green science'.
Collapse
Affiliation(s)
- Samuel Martin
- Nanoprobe Laboratory for Bio and Nanotechnology and Biomimetics (NLBB), The Ohio State University, 201 West 19th Avenue, Columbus, OH 43210-1142, USA
| | - Bharat Bhushan
- Nanoprobe Laboratory for Bio and Nanotechnology and Biomimetics (NLBB), The Ohio State University, 201 West 19th Avenue, Columbus, OH 43210-1142, USA
| |
Collapse
|