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Clathrate nanostructures for mass spectrometry

Trent R. Northen, Oscar Yanes, Michael T. Northen, Dena Marrinucci, Winnie Uritboonthai, Junefredo Apon, Stephen L. Golledge, Anders Nordström, Gary Siuzdak
2007 Nature  
The ability of mass spectrometry to generate intact biomolecular ions efficiently in the gas phase has led to its widespread application in metabolomics 1 , proteomics 2 , biological imaging 3 , biomarker discovery 4 and clinical assays (namely neonatal screens 5 ). Matrix-assisted laser desorption/ionization 6,7 (MALDI) and electrospray ionization 8 have been at the forefront of these developments. However, matrix application complicates the use of MALDI for cellular, tissue, biofluid and
more » ... array analysis and can limit the spatial resolution because of the matrix crystal size 9 (typically more than 10 mm), sensitivity and detection of small compounds (less than 500 Da). Secondary-ion mass spectrometry 10 has extremely high lateral resolution (100 nm) and has found biological applications 11,12 although the energetic desorption/ionization is a limitation owing to molecular fragmentation. Here we introduce nanostructure-initiator mass spectrometry (NIMS), a tool for spatially defined mass analysis. NIMS uses 'initiator' molecules trapped in nanostructured surfaces or 'clathrates' to release and ionize intact molecules adsorbed on the surface. This surface responds to both ion and laser irradiation. The lateral resolution (ion-NIMS about 150 nm), sensitivity, matrix-free and reduced fragmentation of NIMS allows direct characterization of peptide microarrays, direct mass analysis of single cells, tissue imaging, and direct characterization of blood and urine. A diagram of the main applications of NIMS is provided in Supplementary Fig. 1 . Conceptually, NIMS reverses the system of desorption/ionization developed by Tanaka 7 , which uses ,30-nm nanoparticles suspended in glycerol, where desorption/ionization is thought to occur by a thermally driven process for nanoparticles larger than 3 nm (ref. 13). As illustrated in Fig. 1a , b, NIMS uses a nanostructured surface composed of roughly 10-nm pores (Fig. 1c) to trap 'initiator' materials such as fluorinated siloxanes. The analyte is adsorbed on top of the NIMS surface and laser irradiation results in rapid surface heating causing initiator vaporization from many clathrates, triggering the desorption of adsorbed materials. Scanning electron microscopy (SEM) images of a laser-irradiated NIMS surface suggest that rapid surface heating results in a violent expansion of initiator, as indicated by bulk surface destruction and deformation (Fig. 1a) . Ion irradiation also results in intact ion formation; however, SEM imaging (not shown) of ion-irradiated surfaces does not reveal any changes in surface nanostructure, indicating a more localized process. The large amounts of trapped initiators are found to migrate reversibly into and out of the NIMS surface with slight heating and cooling (Supplementary Movie 1), indicating that the initiator is highly ordered within the nanostructured surface. In these ways NIMS is very different from existing surface desorption/ ionization techniques such as desorption-ionization on silicon 14 (DIOS), which is limited to small molecules and peptides, and laser irradiation. In addition, NIMS is characterized by robustness, reproducibility, ease of preparation and minimal training for newcomers (Supplementary Methods), all of which have limited the application of DIOS. NIMS is flexible as regards irradiation source, surface, and initiator composition: NIMS activity has been found to be compatible with a variety of irradiation including a nitrogen laser and ion sources (
doi:10.1038/nature06195 pmid:17960240 fatcat:nmykhwt245atjkt7fprcyyikau

Exometabolomic Analysis of Cross-Feeding Metabolites

Andrea Lubbe, Benjamin Bowen, Trent Northen
2017 Metabolites  
Microbial consortia have the potential to perform complex, industrially important tasks. The design of microbial consortia requires knowledge of the substrate preferences and metabolic outputs of each member, to allow understanding of potential interactions such as competition and beneficial metabolic exchange. Here, we used exometabolite profiling to follow the resource processing by a microbial co-culture of two biotechnologically relevant microbes, the bacterial cellulose degrader
more » ... s fimi, and the oleaginous yeast Yarrowia lipolytica. We characterized the substrate preferences of the two strains on compounds typically found in lignocellulose hydrolysates. This allowed prediction that specific sugars resulting from hemicellulose polysaccharide degradation by C. fimi may serve as a cross-feeding metabolites to Y. lipolytica in co-culture. We also showed that products of ionic liquid-treated switchgrass lignocellulose degradation by C. fimi were channeled to Y. lipolytica in a co-culture. Additionally, we observed metabolites, such as shikimic acid accumulating in the co-culture supernatants, suggesting the potential for producing interesting co-products. Insights gained from characterizing the exometabolite profiles of individual and co-cultures of the two strains can help to refine this interaction, and guide strategies for making this an industrially viable co-culture to produce valuable products from lignocellulose material.
doi:10.3390/metabo7040050 pmid:28976938 pmcid:PMC5746730 fatcat:b2nmc7zgcvbp5ljn3e5g4z43g4

Cyanobacteria as Biocatalysts for Carbonate Mineralization

Nina Kamennaya, Caroline Ajo-Franklin, Trent Northen, Christer Jansson
2012 Minerals  
Microbial carbonate mineralization is widespread in nature and among microorganisms, and of vast ecological and geological importance. However, our understanding of the mechanisms that trigger and control processes such as calcification, i.e., mineralization of CO 2 to calcium carbonate (CaCO 3 ), is limited and literature on cyanobacterial calcification is oftentimes bewildering and occasionally controversial. In cyanobacteria, calcification may be intimately associated with the carbon
more » ... (CO 2 ) concentrating mechanism (CCM), a biochemical system that allows the cells to raise the concentration of CO 2 at the site of the carboxylating enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) up to 1000-fold over that in the surrounding medium. A comprehensive understanding of biologically induced carbonate mineralization is important for our ability to assess its role in past, present, and future carbon cycling, interpret paleontological data, and for evaluating the process as a means for biological carbon capture and storage (CCS). In this review we summarize and discuss the metabolic, physiological and structural features of cyanobacteria that may be involved in the reactions leading to mineral formation and precipitation, present a conceptual model of cyanobacterial calcification, and, finally, suggest practical applications for cyanobacterial carbonate mineralization.
doi:10.3390/min2040338 fatcat:hsio66b2mzckxgugfiuneq3ica

SIMILE enables alignment of fragmentation mass spectra with statistical significance [article]

Daniel GC Treen, Trent R Northen, Ben Bowen
2021 bioRxiv   pre-print
Interrelating compounds according to their aligned fragmentation spectra is central to tandem mass spectrometry-based metabolomics. However, current alignment algorithms do not provide statistical significance and compounds that have multiple delocalized structural differences often fail to have their fragment ions aligned. Significant Interrelation of MS/MS Ions via Laplacian Embedding (SIMILE) is a new tool inspired by protein sequence alignment for aligning fragmentation spectra with
more » ... cal significance and allowance for multiple chemical differences. We found SIMILE yields 550% more pairs of structurally similar compounds than commonly used cosine-based scoring algorithms, and anticipate SIMILE will fill an important role by also providing p-values for fragmentation spectra alignments to explore structural relationships between compounds.
doi:10.1101/2021.02.24.432767 fatcat:c2xrfueryfh65hhev4gepo2i6e

High-throughput platforms for metabolomics

Markus de Raad, Curt R Fischer, Trent R Northen
2016 Current Opinion in Chemical Biology  
Silva LP, Northen TR: Exometabolomics and MSI: deconstructing how cells interact to transform their small molecule environment. Curr Opin Biotechnol 2015, 34:209-216. 10.  ...  Mass spectrometry based high-throughput platforms de Raad, Fischer and Northen 9 Sample throughput vs metabolite coverage High-throughput approaches usually improve sample throughput at the expense  ... 
doi:10.1016/j.cbpa.2015.10.012 pmid:26544850 fatcat:4cpidoec2bgo5k6ubphcbxeqgi

Localizing metabolic synthesis in microbial cultures with kinetic mass spectrometry imaging (kMSI) [article]

Katherine Louie, Benjamin Bowen, Rebecca Lau, Trent Northen
2016 bioRxiv   pre-print
Mass spectrometry imaging (MSI) has emerged as a powerful technique enabling spatially defined imaging of metabolites within microbial biofilms. Here, we extend this approach to enable differentiation of newly synthesized versus pre-existing metabolites across a co-culture. This is accomplished by MS imaging two soil microbes, Shewanella oneidensis MR1 and Pseudomonas stutzeri RCH2, that were administered heavy water (D2O) during growth on agar plates. For two species-specific diglyceride (DG)
more » ... ipids, isotopic analysis was performed on each spectra collected across the co-culture to determine the relative amount of newly synthesized versus pre-existing lipid. Here, highest levels of new synthesis of RCH2 lipid was localized to border regions adjacent to S. oneidensis MR1, while the MR1 lipid showed highest levels in regions further from RCH2. Interestingly, regions of high lipid abundance did not correspond to the regions with highest new lipid biosynthesis. Given the simplicity and generality of using D2O as a stable isotopic probe combined with the accessibility of kMSI to a range of MSI instrumentation, this approach has broad application for improving our understanding of how microbial interactions influence metabolite biosynthesis.
doi:10.1101/050658 fatcat:rlhityfch5bdlfyyncu3a66f5i

Combinatorial Screening of Biomimetic Protein Affinity Materials

Trent R. Northen, Matthew P. Greving, Neal W. Woodbury
2008 Advanced Materials  
doi:10.1002/adma.200800567 fatcat:jyxf3d3s7rdk7gekrf72y22xia

Linking soil biology and chemistry using bacterial isolate exometabolite profiles [article]

Tami L Swenson, Ulas Karaoz, Joel M Swenson, Benjamin P Bowen, Trent R Northen
2017 bioRxiv   pre-print
Sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites displayed the
more » ... ed relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 78% were negatively correlated with the abundance of in situ isolate phylotypes whereas for released metabolites, 73% were positively correlated. Our results demonstrate that metabolite profiling, sequencing and exometabolomics can be successfully integrated to functionally link metagenomes and microbial community structure with environmental chemistry.
doi:10.1101/109330 fatcat:36nxxzagvnasfc67463vcx44aa

A New Method to Correct for Habitat Filtering in Microbial Correlation Networks [article]

Vanessa Brisson, Jennifer Schmidt, Trent R Northen, John P Vogel, Amelie Gaudin
2018 bioRxiv   pre-print
Amplicon sequencing of 16S, ITS, and 18S regions of microbial genomes is a commonly used first step toward understanding microbial communities of interest for human health, agriculture, and the environment. Correlation network analysis is an emerging tool for investigating the interactions within these microbial communities. However, when data from different habitats (e.g sampling sites, host genotype, etc.) are combined into one analysis, habitat filtering (co-occurrence of microbes due to
more » ... tat sampled rather than biological interactions) can induce apparent correlations, resulting in a network dominated by habitat effects and masking correlations of biological interest. We developed an algorithm to correct for habitat filtering effects in microbial correlation network analysis in order to reveal the true underlying microbial correlations. This algorithm was tested on simulated data that was constructed to exhibit habitat filtering. Our algorithm significantly improved correlation detection accuracy for these data compared to Spearman and Pearson correlations. We then used our algorithm to analyze a real data set of 16S-V4 amplicon sequences that was expected to exhibit habitat filtering. Our algorithm was found to effectively reduce habitat effects, enabling the construction of consensus correlation networks from data sets combining multiple related sample habitats.
doi:10.1101/467365 fatcat:6ayukoggxnbjjkdlq2mxizrrji

High surface area of porous silicon drives desorption of intact molecules

Trent R. Northen, Hin-Koon Woo, Michael T. Northen, Anders Nordström, Winnie Uritboonthail, Kimberly L. Turner, Gary Siuzdak
2007 Journal of the American Society for Mass Spectrometry  
The surface structure of porous silicon used in desorption/ionization on porous silicon (DIOS) mass analysis is known to play a primary role in the desorption/ionization (D/I) process. In this study, mass spectrometry and scanning electron microscopy (SEM) are used to examine the correlation between intact ion generation with surface ablation and surface morphology. The DIOS process is found to be highly laser energy dependent and correlates directly with the appearance of surface ions (Si n ϩ
more » ... nd OSiH ϩ ). A threshold laser energy for DIOS is observed (10 mJ/cm 2 ), which supports that DIOS is driven by surface restructuring and is not a strictly thermal process. In addition, three DIOS regimes are observed that correspond to surface restructuring and melting. These results suggest that higher surface area silicon substrates may enhance DIOS performance. A recent example that fits into this mechanism is the surface of silicon nanowires, which has a high surface energy and concomitantly requires lower laser energy for analyte desorption. (J Am Soc Mass Spectrom 2007, 18, 1945-1949
doi:10.1016/j.jasms.2007.08.009 pmid:17881245 pmcid:PMC2080661 fatcat:pdygdlkvbjdrdllks5lhb76i4e

Mass spectrometry–based metabolomics, analysis of metabolite-protein interactions, and imaging

Do Lee, Benjamin Bowen, Trent Northen
2010 BioTechniques  
Our understanding of biology has been greatly improved through recent developments in mass spectrometry, which is providing detailed information on protein and metabolite composition as well as protein-metabolite interactions. The high sensitivity and resolution of mass spectrometry achieved with liquid or gas chromatography allows for detection and quantification of hundreds to thousands of molecules in a single measurement. Where homogenization-based sample preparation and extraction methods
more » ... esult in a loss of spatial information, mass spectrometry imaging technologies provide the in situ distribution profiles of metabolites and proteins within tissues. Mass spectrometry-based analysis of metabolite abundance, protein-metabolite interactions, and spatial distribution of compounds facilitates the high-throughput screening of biochemical reactions, the reconstruction of metabolic networks, biomarker discovery, determination of tissue compositions, and functional annotation of both proteins and metabolites.
doi:10.2144/000113451 pmid:20701590 pmcid:PMC2967016 fatcat:uwhcbsndxbew3j4atxi2ygjgmq

Dynamic substrate preferences and predicted metabolic properties of a simple microbial consortium [article]

Onur Erbilgin, Benjamin P Bowen, Suzanne M Kosina, Stefan Jenkins, Rebecca K Lau, Trent R Northen
2016 bioRxiv   pre-print
. & Northen, T. R. Exometabolomics and MSI: deconstructing how 577 cells interact to transform their small molecule environment.  ... 
doi:10.1101/053777 fatcat:4d7x5vxcbveipnula5ucjvrlla

Deciphering microbial interactions in synthetic human gut microbiome communities [article]

Ophelia S Venturelli, Alex C Carr, Garth Fisher, Ryan H Hsu, Rebecca Lau, Benjamin P Bowen, Trent Northen, Adam P Arkin
2017 bioRxiv   pre-print
The human gut microbiota comprises a dynamic ecological system that contributes significantly to human health and disease. The ecological forces that govern community assembly and stability in the gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-order consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse 12-member human gut microbiome synthetic
more » ... . We show that microbial growth parameters and pairwise interactions are the major drivers of multi-species community dynamics, as opposed to context-dependent (conditional) interactions. The inferred microbial interaction network as well as a top-down approach to community assembly pinpointed both ecological driver and responsive species that were significantly modulated by microbial inter-relationships. Our model demonstrated that negative pairwise interactions could generate history-dependent responses of initial species proportions on physiological timescales that frequently does not originate from bistability. The model elucidated a topology for robust coexistence in pairwise assemblages consisting of a negative feedback loop that balances disparities in monospecies fitness levels. Bayesian statistical methods were used to evaluate the constraint of model parameters by the experimental data. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis for competitive and cooperative interactions in the community. However, these data failed to predict influential organisms shaping community assembly. In sum, these methods defined the ecological roles of key species shaping community assembly and illuminated network design principles of microbial communities.
doi:10.1101/228395 fatcat:tydbjenwjjh7jjzrmjvx7rkdbq

High throughput screening of enzyme activity with mass spectrometry imaging

Tristan de Rond, Megan Danielewicz, Trent Northen
2015 Current Opinion in Biotechnology  
This was put into practice by Northen et al. [50] , who were able to detect glycosylhydrolase activity in lysate prepared from a complex microbial community. This technology was titled "Nimzyme".  ... 
doi:10.1016/j.copbio.2014.07.008 pmid:25129648 fatcat:sptlpviud5hwneijzytroaqvbe

Calcifying cyanobacteria—the potential of biomineralization for carbon capture and storage

Christer Jansson, Trent Northen
2010 Current Opinion in Biotechnology  
doi:10.1016/j.copbio.2010.03.017 pmid:20456936 fatcat:6yfarxdekfas5lkzz4jv5g3ebu
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