Publications by Colleges and Departments (MSU - Bozeman)
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Item Hydrogen Adsorption in Ultramicroporous Metal–Organic Frameworks Featuring Silent Open Metal Sites(American Chemical Society, 2023-11) Chiu, Nan Chieh; Compton, Dalton; Gładysiak, Andrzej; Simrod, Scott; Khivantsev, Konstantin; Woo, Tom K.; Stadie, Nicholas P.; Stylianou, Kyriakos C.In this study, we utilized an ultramicroporous metal–organic framework (MOF) named [Ni3(pzdc)2(ade)2(H2O)4]·2.18H2O (where H3pzdc represents pyrazole-3,5-dicarboxylic acid and ade represents adenine) for hydrogen (H2) adsorption. Upon activation, [Ni3(pzdc)2(ade)2] was obtained, and in situ carbon monoxide loading by transmission infrared spectroscopy revealed the generation of open Ni(II) sites. The MOF displayed a Brunauer–Emmett–Teller (BET) surface area of 160 m2/g and a pore size of 0.67 nm. Hydrogen adsorption measurements conducted on this MOF at 77 K showed a steep increase in uptake (up to 1.93 mmol/g at 0.04 bar) at low pressure, reaching a H2 uptake saturation at 2.11 mmol/g at ∼0.15 bar. The affinity of this MOF for H2 was determined to be 9.7 ± 1.0 kJ/mol. In situ H2 loading experiments supported by molecular simulations confirmed that H2 does not bind to the open Ni(II) sites of [Ni3(pzdc)2(ade)2], and the high affinity of the MOF for H2 is attributed to the interplay of pore size, shape, and functionality.Item Prominent Structural Dependence of Quantum Capacitance Unraveled by Nitrogen‐Doped Graphene Mesosponge(Wiley, 2023-12) Tang, Rui; Aziz, Alex; Yu, Wei; Pan, Zheng‐Ze; Nishikawa, Ginga; Yoshii, Takeharu; Nomura, Keita; Taylor, Erin E.; Stadie, Nicholas P.; Inoue, Kazutoshi; Kotani, Motoko; Kyotani, Takashi; Nishihara, HirotomoPorous carbons are important electrode materials for supercapacitors. One of the challenges associated with supercapacitors is improving their energy density without relying on pseudocapacitance, which is based on fast redox reactions that often shorten device lifetimes. A possible solution involves achieving high total capacitance (Ctot), which comprises Helmholtz capacitance (CH) and possibly quantum capacitance (CQ), in high-surface carbon materials comprising minimally stacked graphene walls. In this work, a templating method is used to synthesize 3D mesoporous graphenes with largely identical pore structures (≈2100 m2 g−1 with an average pore size of ≈7 nm) but different concentrations of oxygen-containing functional groups (0.3–6.7 wt.%) and nitrogen dopants (0.1–4.5 wt.%). Thus, the impact of the heteroatom functionalities on Ctot is systematically investigated in an organic electrolyte excluding the effect of pore structures. It is found that heteroatom functionalities determine Ctot, resulting in the cyclic voltammetry curves being rectangular or butterfly-shaped. The nitrogen functionalities are found to significantly enhance Ctot owing to increased CQ.Item Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea(Public Library of Science, 2023-09) Murali, Ranjani; Yu, Hang; Speth, Daan R.; Wu, Fabai; Metcalfe, Kyle S.; Crémière, Antoine; Laso-Pèrez, Rafael; Malmstrom, Rex R.; Goudeau, Danielle; Woyke, Tanja; Hatzenpichler, Roland; Chadwick, Grayson L.; Connon, Stephanie A.; Orphan, Victoria J.Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.Item Fe protein docking transduces conformational changes to MoFe nitrogenase active site in a nucleotide-dependent manner(Springer Science and Business Media LLC, 2023-11) Tokmina-Lukaszewska, Monika; Huang, Qi; Berry, Luke; Kallas, Hayden; Peters, John W.; Seefeldt, Lance C.; Raugei, Simone; Bothner, BrianThe reduction of dinitrogen to ammonia catalyzed by nitrogenase involves a complex series of events, including ATP hydrolysis, electron transfer, and activation of metal clusters for N2 reduction. Early evidence shows that an essential part of the mechanism involves transducing information between the nitrogenase component proteins through conformational dynamics. Here, millisecond time-resolved hydrogen-deuterium exchange mass spectrometry was used to unravel peptide-level protein motion on the time scale of catalysis of Mo-dependent nitrogenase from Azotobacter vinelandii. Normal mode analysis calculations complemented this data, providing insights into the specific signal transduction pathways that relay information across protein interfaces at distances spanning 100 Å. Together, these results show that conformational changes induced by protein docking are rapidly transduced to the active site, suggesting a specific mechanism for activating the metal cofactor in the enzyme active site.Item Genome sequence, phylogenetic analysis, and structure-based annotation reveal metabolic potential of Chlorella sp. SLA-04(Elsevier BV, 2023-01) Goemann, Calvin L.C.; Wilkinson, Royce; Henriques, William; Bui, Huyen; Goemann, Hannah M.; Carlson, Ross P.; Viamajala, Sridhar; Gerlach, Robin; Wiedenheft, BlakeAlgae are a broad class of photosynthetic eukaryotes that are phylogenetically and physiologically diverse. Most of the phylogenetic diversity has been inferred from 18S rDNA sequencing since there are only a few complete genomes available in public databases. Here we use ultra-long-read Nanopore sequencing to determine a gapless, telomere-to-telomere complete genome sequence of Chlorella sp. SLA-04, previously described as Chlorella sorokiniana SLA-04. Chlorella sp. SLA-04 is a green alga that grows to high cell density in a wide variety of environments – high and neutral pH, high and low alkalinity, and high and low salinity. SLA-04's ability to grow in high pH and high alkalinity media without external CO2 supply is favorable for large-scale algal biomass production. Phylogenetic analysis performed using ribosomal DNA and conserved protein sequences consistently reveal that Chlorella sp. SLA-04 forms a distinct lineage from other strains of Chlorella sorokiniana. We complement traditional genome annotation methods with high throughput structural predictions and demonstrate that this approach expands functional prediction of the SLA-04 proteome. Genomic analysis of the SLA-04 genome identifies the genes capable of utilizing TCA cycle intermediates to replenish cytosolic acetyl-CoA pools for lipid production. We also identify a complete metabolic pathway for sphingolipid anabolism that may allow SLA-04 to readily adapt to changing environmental conditions and facilitate robust cultivation in mass production systems. Collectively, this work clarifies the phylogeny of Chlorella sp. SLA-04 within Trebouxiophyceae and demonstrates how structural predictions can be used to improve annotation beyond sequence-based methods.Item Soluble CD4 and low molecular weight CD4-mimetic compounds sensitize cells to be killed by anti-HIV cytotoxic immunoconjugates(American Society for Microbiology, 2023-09) Pincus, Seth H.; Stackhouse, Megan; Watt, Connie; Ober, Kelli; Cole, Frances M.; Chen, Hung-Ching; Smith III, Amos B.; Peters, TamiThe reservoir of HIV-infected cells that persist in the face of effective anti-retroviral therapy (ART) is the barrier to curing HIV infection. These long-lived CD4+ cells carry a functional provirus that can become activated upon immune stimulation. When ART is stopped, this leads to a rapid rebound in viremia. A variety of approaches are proposed to eliminate these cells, many dependent upon the expression of virus proteins. We are examining the use of cytotoxic immunoconjugates targeting the HIV envelope protein (Env) as a method to eradicate cells producing virus and have demonstrated that soluble CD4 enhances the cytotoxic effect of gp41-targeted immunoconjugates. Mechanisms include increased antigen exposure and greater internalization of the immunoconjugate. Here we have tested different protein forms of CD4 and the small molecule CD4-mimetic BNM-III-170 for their effects on cells expressing cell-surface Env. Effects studied include sensitization to immunoconjugate killing, cell surface antigen expression, viability, and virus secretion. The CD4 proteins and BNM-III-170 produced comparable effects in these Env-expressing cell lines, each sensitizing cells to cytotoxicity by anti-gp41 immunoconjugates. The results provide further evidence that low molecular weight CD4 mimetics produce biologic effects similar to those caused by soluble CD4 itself and suggest additional therapeutic uses for these molecules.Item Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment(Frontiers Media SA, 2023-09) Frates, Erin S.; Lange Spietz, Rachel K.; Silverstein, Michael R.; Girguis, Peter; Hatzenpichler, Roland; Marlow, Jeffrey J.Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways.Item Yeast Rad52 is a homodecamer and possesses BRCA2-like bipartite Rad51 binding modes(Springer Science and Business Media LLC, 2023-10) Deveryshetty, Jaigeeth; Chadda, Rahul; Mattice, Jenna R.; Karunakaran, Simrithaa; Rau, Michael J.; Basore, Katherine; Pokhrel, Nilisha; Englander, Noah; Fitzpatrick, James A. J.; Bothner, Brian; Antony, EdwinHomologous recombination (HR) is an essential double-stranded DNA break repair pathway. In HR, Rad52 facilitates the formation of Rad51 nucleoprotein filaments on RPA-coated ssDNA. Here, we decipher how Rad52 functions using single-particle cryo-electron microscopy and biophysical approaches. We report that Rad52 is a homodecameric ring and each subunit possesses an ordered N-terminal and disordered C-terminal half. An intrinsic structural asymmetry is observed where a few of the C-terminal halves interact with the ordered ring. We describe two conserved charged patches in the C-terminal half that harbor Rad51 and RPA interacting motifs. Interactions between these patches regulate ssDNA binding. Surprisingly, Rad51 interacts with Rad52 at two different bindings sites: one within the positive patch in the disordered C-terminus and the other in the ordered ring. We propose that these features drive Rad51 nucleation onto a single position on the DNA to promote formation of uniform pre-synaptic Rad51 filaments in HR.Item Viruses of the Turriviridae: an emerging model system for studying archaeal virus-host interactions(Frontiers Media SA, 2023-09) Overton, Michael S.; Manuel, Robert D.; Lawrence, C. Martin; Snyder, Jamie C.Viruses have played a central role in the evolution and ecology of cellular life since it first arose. Investigations into viral molecular biology and ecological dynamics have propelled abundant progress in our understanding of living systems, including genetic inheritance, cellular signaling and trafficking, and organismal development. As well, the discovery of viral lineages that infect members of all three domains suggest that these lineages originated at the earliest stages of biological evolution. Research into these viruses is helping to elucidate the conditions under which life arose, and the dynamics that directed its early development. Archaeal viruses have only recently become a subject of intense study, but investigations have already produced intriguing and exciting results. STIV was originally discovered in Yellowstone National Park and has been the focus of concentrated research. Through this research, a viral genetic system was created, a novel lysis mechanism was discovered, and the interaction of the virus with cellular ESCRT machinery was revealed. This review will summarize the discoveries within this group of viruses and will also discuss future work.Item Metabolic Phenotypes Reflect Patient Sex and Injury Status: A Cross-Sectional Analysis of Human Synovial Fluid(Elsevier BV, 2023-09) Welhaven, Hope D.; Welfley, Avery H.; Pershad, Prayag; Satalich, James; O'Connell, Robert; Bothner, Brian; Vap, Alexander R.; June, Ronald K.Objective. Osteoarthritis is a heterogeneous disease. The objective was to compare differences in underlying cellular mechanisms and endogenous repair pathways between synovial fluid (SF) from male and female participants with different injuries to improve the current understanding of the pathophysiology of downstream post-traumatic osteoarthritis (PTOA). Design. SF from n = 33 knee arthroscopy patients between 18 and 70 years with no prior knee injuries was obtained pre-procedure and injury pathology assigned post-procedure. SF was extracted and analyzed via liquid chromatography-mass spectrometry metabolomic profiling to examine differences in metabolism between injury pathologies (ligament, meniscal, and combined ligament and meniscal) and patient sex. Samples were pooled and underwent secondary fragmentation to identify metabolites. Results. Different knee injuries uniquely altered SF metabolites and downstream pathways including amino acid, lipid, and inflammatory-associated metabolic pathways. Notably, sexual dimorphic metabolic phenotypes were examined between males and females and within injury pathology. Cervonyl carnitine and other identified metabolites differed in concentrations between sexes. Conclusions. These results suggest that different injuries and patient sex are associated with distinct metabolic phenotypes. Considering these phenotypic associations, a greater understanding of metabolic mechanisms associated with specific injuries, sex, and PTOA development may yield data regarding how endogenous repair pathways differ between male and female injury types. Ongoing metabolomic analysis of SF in injured male and female patients can be performed to monitor PTOA development and progression.