Characterization of Mobility-Dependent Ion Confinement in Rotating Electric Fields
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Lee, Jung Yun [Biological Sciences Division; Pacif↗
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Analysis of RNA viral function from metatranscriptomic reads in drought simulated soils
Soil viruses have received increased interest in recent years because of their abundance and unelucidated potential as drivers for organic carbon derived from fungal and bacterial necromass. With decreasing levels of rainfall and climbing instances of unseasonal conditions, it becomes crucial to our goals for negative carbon emissions to understand how soil carbon flux is affected. Here we leveraged metatranscriptomic data from a section of research plot of Hopland Research and Extension in northern California with a suite of viral detection tools: VirSorter, DRAMv, and VContact2. We aimed to cross analyze moisture regiments with viral populations. We find that viral diversity is driven by site, like bacteria. We found that viral diversity at face value showed some differentiation but did not significantly differ by legacy moisture content. Additionally, there was detection of auxiliary metabolic genes in a viral sequence which may further support virus’s direct input into the soil carbon pool.
54 ENVIRONMENTAL SCIENCES↗
Protocol to detect dilution cycles in chemostat experiments and estimate growth rate slopes with linear modeling with R software chemostat_regression
Chemostat growth chambers measure optical density over time and require manual calculation of growth rates. Here, we present chemostat_regression, R software that enables users to automatically identify chemostat cycles and estimate growth rate using a linear regression approach. We describe steps for creating requisite software environment(s), formatting input data, executing the software via command line/RStudio/R-Shiny, interpreting results, assessing the validity of results, and modifying input parameters.
59 BASIC BIOLOGICAL SCIENCES↗
Single‐Cell Nanodroplet Processing Proteomics Pipeline for Analysis of Human‐Derived Microglia
Single-cell omics tools provide unique insights into heterogeneous cell populations and their responses to stimuli. For example, single-cell RNA sequencing has identified several transcriptionally distinct populations of microglia, which are resident immune cells of the central nervous system (CNS) that are responsive to CNS injury, infection, and neurodegeneration. To date, single-cell studies of microglia have focused on RNA-sequencing or cytometry by time of flight (CyTOF), which provide indirect readouts of protein abundance or quantification of a limited number of targets. Herein, we present a workflow based on FACS-assisted isolation, cryopreservation, and nanodroplet-based processing for single-cell mass spectrometry proteomics analysis of the postmortem human brain cortex-derived microglia. From a single microglial cell, 1039 proteins could be identified on average. As a proof-of-principle, we applied single-cell proteomics for exploring the heterogeneity of brain microglia at the cellular level. This pilot proteomics data partially recapitulates the prior microglia subtypes. Specifically, we determined that mitochondrial proteins, in particular members of NADH dehydrogenase (Complex I), cytochrome b-c1 (Complex III), cytochrome c oxidase (Complex IV), F1-ATPase (Complex V), and Na+/K+-ATPase complex, drive variation across microglia. This pipeline offers the potential for identifying functionally and analytically relevant protein targets for microglia in Alzheimer's disease and other neurological disorders.
59 BASIC BIOLOGICAL SCIENCES↗
A periplasmic zinc capture protein enhances the resistance of Neisseria gonorrhoeae to nutritional immunity
During microbial infection, mammalian hosts reduce the availability of free metals such as zinc in a process known as nutritional immunity. Pathogens counteract nutritional immunity by expressing gene products that enhance growth in metal-limited conditions. One of the most transcriptionally induced genes in zinc-limited Neisseria gonorrhoeae , ngo1049, encodes a DUF4198 family protein we have named Zcp. This family of proteins is widely distributed in Gram-negative bacteria. Here, we provide the first structural, biochemical, and functional characterization of a DUF4198 protein. Zcp is a periplasmic, homodimeric substrate-binding protein (SBP), which binds one zinc ion per subunit with submicromolar affinity. We identified a zinc binding pocket in each subunit, composed of three histidine residues. Zcp enables maximal growth of N. gonorrhoeae in zinc-limited conditions but is dispensable for zinc uptake, in contrast to the cluster A-I SBP ZnuA, which is required for zinc import. The growth defect of zcp mutant N. gonorrhoeae is rescued by zinc supplementation. Zcp associates with proteins with roles in maintaining cell envelope integrity, and N. gonorrhoeae lacking zcp is more sensitive to envelope-targeting antimicrobials. Zcp enables infectivity of human epithelial cells and neutrophils by zinc-limited N. gonorrhoeae . We conclude that N. gonorrhoeae produces Zcp to buffer periplasmic zinc, which enables ZnuA to balance import of different metals and ensures the bioavailability of zinc for extracytoplasmic zinc-requiring proteins, as part of the coordinated response to host-imposed nutritional immunity.
Liyayi, Ian K. [Department of Microbiology, Immuno↗
Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Human SIRT5 variants with reduced stability and activity do not cause neuropathology in mice
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
A trait syndrome ties cell morphology to glycolysis across the yeast subphylum
Co-variation of traits provides fundamental insights into constraints governing their evolution. An inverse correlation between glucose uptake rates (GURs) and cell surface area-to-volume (SA:V) ratios across 11 yeast species was recently reported. Here, we expand the analysis to 282 species to assess the generalizability of this correlation across Saccharomycotina yeasts and the contribution of shared evolutionary history to the co-variation of these traits. Using phylogenetic regression models, we found extracellular acidification rates (ECARs, used as a proxy for GURs) were weakly, but significantly, correlated with SA:V across Saccharomycotina. ECARs were also correlated with genome sizes and growth rates. Our findings support the reported correlation between GURs and SA:V ratios, but suggest other associated traits, including genome sizes. Specifically, yeasts that consume glucose faster tend to have lower SA:V, faster growth rates, and larger genomes, suggesting a trait syndrome governing several metabolic, genomic, and morphological traits across the yeast subphylum.
biological sciences↗
Desiccated Cyanobacteria Serve As Efficient Plasmid DNA Carriers in Space Flight
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days
In May and June of 2021, marine microbial samples were collected for DNA sequencing in East Sound, WA, USA every 4 hours for 22 days. This high temporal resolution sampling effort captured the last 3 days of a Rhizosolenia sp. bloom, the initiation and complete bloom cycle of Chaetoceros socialis (8 days), and the following bacterial bloom (2 days). Metagenomes were completed on the time series, and the dataset includes 128 size-fractionated microbial samples (0.22–1.2 µm), providing gene abundances for the dominant members of bacteria, archaea, and viruses. This dataset also has time-matched nutrient analyses, flow cytometry data, and physical parameters of the environment at a single point of sampling within a coastal ecosystem that experiences regular bloom events, facilitating a range of modeling efforts that can be leveraged to understand microbial community structure and their influences on the growth, maintenance, and senescence of phytoplankton blooms.
59 BASIC BIOLOGICAL SCIENCES↗
Hypermut 3: identifying specific mutational patterns in a defined nucleotide context that allows multistate characters
Abstract Motivation The detection of APOBEC3F- and APOBEC3G-induced mutations in virus sequences is useful for identifying hypermutated sequences. These sequences are not representative of viral evolution and can therefore alter the results of downstream sequence analyses if included. We previously published the software Hypermut, which detects hypermutation events in sequences relative to a reference. Two versions of this method are available as a webtool. Neither of these methods consider multistate characters or gaps in the sequence alignment. Results Here, we present an updated, user-friendly web and command-line version of Hypermut with functionality to handle multistate characters and gaps in the sequence alignment. This tool allows for straightforward integration of hypermutation detection into sequence analysis pipelines. As with the previous tool, while the main purpose is to identify G to A hypermutation events, any mutational pattern and context can be specified. Availability and implementation Hypermut 3 is written in Python 3. It is available as a command-line tool at https://github.com/MolEvolEpid/hypermut3 and as a webtool at https://www.hiv.lanl.gov/content/sequence/HYPERMUT/hypermutv3.html.
59 BASIC BIOLOGICAL SCIENCES↗
Corn stover variability drives differences in bisabolene production by engineered Rhodotorula toruloides
Microbial conversion of lignocellulosic biomass represents an alternative route for production of biofuels and bioproducts. While researchers have mostly focused on engineering strains such as Rhodotorula toruloides for better bisabolene production as a sustainable aviation fuel, less is known about the impact of the feedstock heterogeneity on bisabolene production. Critical material attributes like feedstock composition, nutritional content, and inhibitory compounds can all influence bioconversion. Further, the given feedstocks can have a marked influence on selection of suitable pretreatment and hydrolysis technologies, optimizing the fermentation conditions, and possibly even modifying the microorganism's metabolic pathways, to better utilize the available feedstock. Here, this work aimed to examine and understand how variations in corn stover batches, anatomical fractions, and storage conditions impact the efficiency of bisabolene production by R. toruloides. All of these represent different facets of feedstock heterogeneity. Deacetylation, mechanical refining, and enzymatic hydrolysis of these variable feedstocks served as the basis of this research. The resulting hydrolysates were converted to bisabolene via fermentation, a sustainable aviation fuel precursor, using an engineered R. toruloides strain. This study showed that different sources of feedstock heterogeneity can influence microbial growth and product titer in counterintuitive ways, as revealed through global analysis of protein expression. The maximum bisabolene produced by R. toruloides was on the stalk fraction of corn stover hydrolysate (8.89 ± 0.47 g/L). Further, proteomics analysis comparing the protein expression between the anatomic fractions showed that proteins relating to carbohydrate metabolism, energy production, and conversion as well as inorganic ion transport metabolism were either significantly upregulated or downregulated. Specifically, downregulation of proteins related to the iron–sulfur cluster in stalk fraction suggests a coordinated response by R. toruloides to maintain overall metabolic balance, and this was corroborated by the concentration of iron in the feedstocks.
09 BIOMASS FUELS↗
Ultrasonic deterrents provide no additional benefit over curtailment in reducing bat fatalities at an Ohio wind energy facility
Wind energy is important for achieving net-zero greenhouse gas emissions but also contributes to global bat mortality. Current strategies to minimize bat mortality due to collision with wind-turbine blades fall broadly into two categories: curtailment (limiting turbine operation during high-risk periods) and deterrence (discouraging bat activity near turbines). Recently, there has been interest in combining these strategies to achieve greater reductions in bat fatalities than either strategy might achieve in isolation. To investigate the effectiveness of combining curtailment with ultrasonic deterrent minimization strategies, we deployed six ultrasonic deterrents at nacelle height on 16 experimental turbines at Avangrid Renewables’ Blue Creek Wind Energy Facility. We rotated between four conditions (normal operations, curtailment only, deterrent only, curtailment and deterrent) randomly assigned to four wind turbines each night between 15 June and 3 October 2017. We found that bat mortality at wind turbines was independent of wind speed. The effectiveness of ultrasonic acoustic deterrents varied between high-frequency-calling species (eastern red bats) and low-frequency-calling species (hoary bats, silver-haired bats, and big brown bats). When deterrents were active, mortality was twice as high for eastern red bats compared to the control. Conversely, deterrents had a weak dampening effect on bat mortality for low-frequency species. We found no additive effects on mortality reduction for turbines operating both curtailment and deterrents compared to either approach in isolation. Our findings suggest that ultrasonic acoustic deterrents may not be effective for both high and low frequency echolocating bats. The increase in fatalities of eastern red bats is alarming and underscores the importance of considering site- and species-specific effects of minimization solutions.
60 APPLIED LIFE SCIENCES↗
A Comprehensive Overview of Postbiotics with a Special Focus on Discovery Techniques and Clinical Applications
The increasing interest in postbiotics, a term gaining recognition alongside probiotics and prebiotics, aligns with a growing number of clinical trials demonstrating positive outcomes for specific conditions. Postbiotics present several advantages, including safety, extended shelf life, ease of administration, absence of risk, and patentability, making them more appealing than probiotics alone. This review covers various aspects, starting with an introduction, terminology, classification of postbiotics, and brief mechanisms of action. It emphasizes microbial metabolomics as the initial step in discovering novel postbiotics. Commonly employed techniques such as NMR, GC-MS, and LC-MS are briefly outlined, along with their application principles and limitations in microbial metabolomics. The review also examines existing research where these techniques were used to identify, isolate, and characterize postbiotics derived from different microbial sources. The discovery section concludes by highlighting challenges and future directions to enhance postbiotic discovery. In the second half of the review, we delve deeper into numerous published postbiotic clinical trials to date. We provide brief overviews of system-specific trial applications, their objectives, the postbiotics tested, and their outcomes. The review concludes by highlighting ongoing applications of postbiotics in extended clinical trials, offering a comprehensive overview of the current landscape in this evolving field.
60 APPLIED LIFE SCIENCES↗
Seventh Oregon Climate Assessment
Consistent with its charge under Oregon House Bill 3543, the Oregon Climate Change Research Institute (OCCRI) conducts a biennial assessment of the state of climate change science, including biological, physical, and social science, as it relates to Oregon and the likely effects of climate change on Oregon. This seventh Oregon Climate Assessment, which builds on the previous assessments, is structured with the goal of supporting the state's mitigation planning for natural hazards and implementation of the Oregon Climate Change Adaptation Framework.
17 WIND ENERGY↗
Enabling Capabilities and Resources: 2024 Principal Investigator Meeting Proceedings
As a major supporter of basic genome-enabled research, BER’s Biological Systems Science Division (BSSD) fosters scientific discovery by funding - fundamental biological research across disciplines in conjunction with enabling investigational tools and computational capabilities that include world-class user facilities. The overarching goal of BSSD is to provide the necessary fundamental science to understand, predict, manipulate, and design biological systems that underpin innovations for bioenergy and bioproduct production and enhance understanding of natural, DOE-relevant environmental processes (Biological Systems Science Division Strategic Plan, 2021). To accelerate the U.S. bioeconomy, BSSD pursues innovative science underpinning advances in sustainable biofuels and bioproducts and the development of next-generation technologies and computational resources for systems biology research. The 2024 BSSD Enabling Capabilities and Resources (ECR) Principal Investigator (PI) meeting brought together PIs across the BSSD ECR portfolio to confer on shared interests and opportunities. The meeting was held concurrently with the Genomic Science program (GSP) PI meeting to optimize collaboration on research to advance bioenergy and the bioeconomy. Rick Stevens of Argonne National Laboratory gave a keynote on How Generative Artificial Intelligence Can Impact Biological Research (see Keynote: How Generative Artificial Intelligence Can Impact Biological Research, this page). Plenary presentations included several joint sessions that illuminated the integration and understanding of the larger BSSD mission. GSP’s objective is to provide systems-level understanding of plants, microbes, and their communities through its Bioenergy Research, Biosystems Design, and Environmental Microbiome Research portfolios. The objective of the ECR portfolio is to support development of computational and instrumental platforms to advance fundamental GSP research—and BER more broadly— toward the overall goal of understanding the functional principles of living systems and their response to environmental challenges.
59 BASIC BIOLOGICAL SCIENCES↗
Detection of non‐native species formed during fibrillization of the myocilin olfactomedin domain
Abstract Glaucoma is a group of neurodegenerative diseases that together are the leading cause of irreversible blindness worldwide. Myocilin‐associated glaucoma is an inherited form of this disease, caused by intracellular aggregation of misfolded mutant myocilin. In vitro, the myocilin C‐terminal olfactomedin domain (OLF), the relevant domain for glaucoma pathogenesis, can be driven to form amyloid‐like fibrils under mild conditions. Here we characterize a species present during in vitro fibrillization. Purified OLF was subjected to fibrillization at concentrations required for downstream electron microscopy imaging and NMR spectroscopy. Additional biophysical techniques, including analytical ultracentrifugation and X‐ray crystallography, were employed to further characterize the multicomponent mixture. Negative stain transmission electron microscopy (TEM) shows a non‐native species reminiscent of known prefibrillar oligomers from other amyloid systems, NMR indicates a minor population of partially misfolded species is present in solution, and cryo‐EM imaging shows two‐dimensional protein arrays. The predominant soluble species remaining in solution after the fibril reaction is natively folded, as evidenced by X‐ray crystallography. In summary, after incubating OLF under fibrillization‐promoting conditions, there is a heterogeneous mixture consisting of soluble folded protein, mature amyloid‐like fibrils, and partially misfolded intermediate species that at present belie additional molecular detail. The characterization of OLF fibrillar species illustrates the challenges associated with developing a comprehensive understanding of the fibrillization process for large, non‐model amyloidogenic proteins.
Scelsi, Hailee F. [School of Chemistry and Biochem↗
Reference-free structural variant detection in microbiomes via long-read co-assembly graphs
Motivation: The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining. Results: We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, particularly as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between successive time and temperature samples, suggesting host advantage. Our approach leverages previous work in assembly graph structural and coverage patterns to provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial gene flux.
59 BASIC BIOLOGICAL SCIENCES↗