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At least 883 records · Page 49

Large Game Distribution Camera Study at Los Alamos National Laboratory

The unique habitats at the Laboratory support a diverse community of wildlife. The habitat types that include Pinon Juniper, Ponderosa Pine, and Mixed-conifer forests each provide different resources important for a variety of species. Wildlife monitoring for large game animals can be challenging because they avoid interactions with humans, and prefer undeveloped areas. This study was conducted to analyze the distribution of predators and other game animals seasonally across the Laboratory. This research informs decisions regarding wildlife management recommendations for conservation and protection. This study utilized game cameras to remotely monitor wildlife. As camera technology has advanced, game cameras have become adequate for documenting individuals, and are commonly used in wildlife studies on predation, abundance, occupancy, diversity, and endangered species detection. Twenty cameras were placed across the LANL landscape using a modified systematic sampling design. They were deployed in February 2018 and retrieved in January 2019, thus each camera sampled for one full year. All images were reviewed and the species, number, age, and sex of all animals in the photo were recorded. Here we present data for the most abundant species encountered: deer, elk, coyote, bear, bobcat, mountain lion, and fox respectively. The data were summarized by species and season. Future work will include occupancy modelling for each species. This will allow the development of heat maps showing species distributions across the Laboratory.

59 BASIC BIOLOGICAL SCIENCES↗

Rapid and automated design of two-component protein nanomaterials using ProteinMPNN

The design of protein–protein interfaces using physics-based design methods such as Rosetta requires substantial computational resources and manual refinement by expert structural biologists. Deep learning methods promise to simplify protein–protein interface design and enable its application to a wide variety of problems by researchers from various scientific disciplines. Here, we test the ability of a deep learning method for protein sequence design, ProteinMPNN, to design two-component tetrahedral protein nanomaterials and benchmark its performance against Rosetta. ProteinMPNN had a similar success rate to Rosetta, yielding 13 new experimentally confirmed assemblies, but required orders of magnitude less computation and no manual refinement. The interfaces designed by ProteinMPNN were substantially more polar than those designed by Rosetta, which facilitated in vitro assembly of the designed nanomaterials from independently purified components. Crystal structures of several of the assemblies confirmed the accuracy of the design method at high resolution. Our results showcase the potential of deep learning–based methods to unlock the widespread application of designed protein–protein interfaces and self-assembling protein nanomaterials in biotechnology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Incubation Temperature Affects Duckling Body Size and Food Consumption Despite No Effect on Associated Feeding Behaviors

Synopsis Developmental conditions can have consequences for offspring fitness. For example, small changes (<1°C) in average avian incubation temperature have large effects on important post-hatch offspring phenotypes, including growth rate, thermoregulation, and behavior. Furthermore, average incubation temperatures differ among eggs within the same nest, to the extent (i.e., >1°C) that differences in offspring phenotypes within broods should result. A potential consequence of within-nest incubation temperature variation is inequality in behaviors that could cause differences in resource acquisition within broods. To investigate this, we incubated wood duck (Aix sponsa) eggs at one of two ecologically-relevant incubation temperatures (35°C or 36°C), formed mixed-incubation temperature broods after ducklings hatched, and conducted trials to measure duckling behaviors associated with acquisition of heat (one trial) or food (three trials). Contrary to our predictions, we found no effect of incubation temperature on duckling behaviors (e.g., time spent occupying heat source, frequency of feeding bouts). However, we found evidence that ducklings incubated at the higher temperature consumed more food during the 1-h feeding trials, and grew faster in body mass and structural size (culmen and tarsus) throughout the study, than those incubated at the lower temperature. Apparent food consumption during the trials was positively related to culmen length, suggesting that differences in food consumption may be driven by structural size. This could result in positive feedback, which would amplify size differences between offspring incubated at different temperatures. Thus, our study identifies incubation temperature as a mechanism by which fitness-related phenotypic differences can be generated and even amplified within avian broods.

59 BASIC BIOLOGICAL SCIENCES↗

Interactions among rooting traits for deep water and nitrogen uptake in upland and lowland ecotypes of switchgrass ( Panicum virgatum L.)

Abstract The response of plant growth and development to nutrient and water availability is an important adaptation for abiotic stress tolerance. Roots need to intercept both passing nutrients and water while foraging into new soil layers for further resources. Substantial amounts of nitrate can be lost in the field when leaching into groundwater, yet very little is known about how deep rooting affects this process. Here, we phenotyped root system traits and deep 15N nitrate capture across 1.5 m vertical profiles of solid media using tall mesocosms in switchgrass (Panicum virgatum L.), a promising cellulosic bioenergy feedstock. Root and shoot biomass traits, photosynthesis and respiration measures, and nutrient uptake and accumulation traits were quantified in response to a water and nitrate stress factorial experiment for switchgrass upland (VS16) and lowland (AP13) ecotypes. The two switchgrass ecotypes shared common plastic abiotic responses to nitrogen (N) and water availability, and yet had substantial genotypic variation for root and shoot traits. A significant interaction between N and water stress combination treatments for axial and lateral root traits represents a complex and shared root development strategy for stress mitigation. Deep root growth and 15N capture were found to be closely linked to aboveground growth. Together, these results represent the wide genetic pool of switchgrass and show that deep rooting promotes nitrate capture, plant productivity, and sustainability.

59 BASIC BIOLOGICAL SCIENCES↗

Structure-guided utilization of lignocellulose for catalysis, energy, and biomaterials

As a complex composite of cellulose, hemicellulose, and lignin, plant lignocellulose has long served as a major resource for biomass conversion, materials engineering, and bio-based product development. High-resolution structural insights enabled by solid-state nuclear magnetic resonance (ssNMR) now allow the mapping of polymer interfaces, identification of functional group accessibility, and tracking of molecular organization during processing, all of which are critical factors for optimizing catalytic strategies. These insights could drive transformative progress in lignocellulose-based applications, including selective depolymerization, improved pretreatment design, and efficient upcycling of lignin into resins, plastics, and biomedical materials. In industry-relevant contexts, such as biofuel generation and renewable material manufacturing, understanding the hydration dynamics, cross-linking patterns, and structural heterogeneity is also essential. The ability to visualize these features in native biomass presents a unique opportunity to develop new strategies for sustainability and performance. As the structural toolbox continues to expand, it is becoming a central enabler for innovations in renewable energy, green chemistry, and advanced bioproducts.

bioproduct↗

Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification

Competition between nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) for resources in anoxic environments is generally thought to be governed largely by thermodynamics. It is now recognized that intermediates of nitrogen and sulfur cycling (e.g., hydrogen sulfide, nitrite, etc.) can also directly impact NRB and SRB activities in freshwater, wastewater, and sediment and therefore may play important roles in competitive interactions. Here, through comparative transcriptomic and metabolomic analyses, we have uncovered mechanisms of hydrogen sulfide- and cysteine-mediated inhibition of nitrate respiratory growth for the NRB Intrasporangium calvum C5. Specifically, the systems analysis predicted that cysteine and hydrogen sulfide inhibit growth of I. calvum C5 by disrupting distinct steps across multiple pathways, including branched-chain amino acid (BCAA) biosynthesis, utilization of specific carbon sources, and cofactor metabolism. Here, we have validated these predictions by demonstrating that complementation with BCAAs and specific carbon sources relieves the growth inhibitory effects of cysteine and hydrogen sulfide. We discuss how these mechanistic insights give new context to the interplay and stratification of NRB and SRB in diverse environments.

59 BASIC BIOLOGICAL SCIENCES↗

Computational design and analysis of modular cells for large libraries of exchangeable product synthesis modules

Microbial metabolism can be harnessed to produce a large library of useful chemicals from renewable resources such as plant biomass. However, it is laborious and expensive to create microbial biocatalysts to produce each new product. To tackle this challenge, we have recently developed modular cell (ModCell) design principles that enable rapid generation of production strains by assembling a modular (chassis) cell with exchangeable production modules to achieve overproduction of target molecules. Previous computational ModCell design methods are limited to analyze small libraries of around 20 products. In this study, we developed a new computational method, named ModCell-HPC, that can design modular cells for large libraries with hundreds of products with a highly-parallel and multi-objective evolutionary algorithm and enable us to elucidate modular design properties. We demonstrated ModCell-HPC to design Escherichia coli modular cells towards a library of 161 endogenous production modules. From these simulations, we identified E. coli modular cells with few genetic manipulations that can produce dozens of molecules in a growth-coupled manner with different types of fermentable sugars. These designs revealed key genetic manipulations at the chassis and module levels to accomplish versatile modular cells, involving not only in the removal of major by-products but also modification of branch points in the central metabolism. We further found that the effect of various sugar degradation on redox metabolism results in lower compatibility between a modular cell and production modules for growth on pentoses than hexoses. To better characterize the degree of compatibility, we developed a method to calculate the minimal set cover, identifying that only three modular cells are all needed to couple with up 85 compatible production modules. By determining the unknown compatibility contribution metric, we further elucidated the design features that allow an existing modular cell to be re-purposed towards production of new molecules. Altogether, ModCell-HPC is a useful tool for understanding modularity of biological systems and guiding more efficient and generalizable design of modular cells that help reduce research and development cost in biocatalysis.

59 BASIC BIOLOGICAL SCIENCES↗

Utilizing digitized occurrence records of Midwestern feral Cannabis sativa to develop ecological niche models

Hemp (Cannabis sativa L.) has historically played a vital role in agriculture across the globe. Feral and wild populations have served as genetic resources for breeding, conservation, and adaptation to changing environmental conditions. However, feral populations of Cannabis, specifically in the Midwestern United States, remain poorly understood. This study aims to characterize the abiotic tolerances of these populations, estimate suitable areas, identify regions at risk of abiotic suitability change, and highlight the utility of ecological niche models (ENMs) in germplasm conservation. The Maxent algorithm was used to construct a series of ENMs. Validation metrics and MOP (Mobility-oriented Parity) analysis were used to assess extrapolation risk and model performance. We also projected the final projected under current and future climate scenarios (2021–2040 and 2061–2080) to assess how abiotic suitability changes with time. Climate change scenarios indicated an expansion of suitable habitat, with priority areas for germplasm collection in Indiana, Illinois, Kansas, Missouri, and Nebraska. This study demonstrates the application of ENMs for characterizing feral Cannabis populations and highlights their value in germplasm conservation and breeding efforts. Populations of feral C. sativa in the Midwest are of high interest, and future research should focus on utilizing tools to aid the collection of materials for the characterization of genetic diversity and adaptation to a changing climate.

59 BASIC BIOLOGICAL SCIENCES↗

Research progress on organic acid pretreatment of lignocellulose

Lignocellulosic biomass is a naturally occurring, renewable resource that is utilized to produce a variety of high–value-added products, such as fuels, acids, and building block chemicals. The pretreatment of lignocellulosic biomass is a crucial step in the deconstruction and fractionation of its components. Organic acids, such as formic, acetic, lactic, and maleic acids, have been widely studied for their effectiveness in lignocellulose pretreatment. Organic acid–based pretreatment techniques are gaining increased attention due to their ability to selectively separate hemicellulose and cellulose, promote oligomer formation, and minimize byproducts. This paper presents a comprehensive review of the various advancements in the science and application of organic acids for the pretreatment of lignocellulose. Furthermore, the significant challenges of organic acid recovery after pretreatment are highlighted, and different recovery methods are discussed. In conclusion, the future challenges related to utilizing organic acids for lignocellulose pretreatment are summarized, with a strong emphasis on adopting a sustainable approach to converting valuable bioresources into renewable products.

59 BASIC BIOLOGICAL SCIENCES↗

A census of the lung: CellCards from LungMAP

The human lung plays vital roles in respiration, host defense, and basic physiology. Recent technological advancements such as single-cell RNA sequencing and genetic lineage tracing have revealed novel cell types and enriched functional properties of existing cell types in lung. The time has come to take a new census. Initiated by members of the NHLBI-funded LungMAP Consortium and aided by experts in the lung biology community, we synthesized current data into a comprehensive and practical cellular census of the lung. Identities of cell types in the normal lung are captured in individual cell cards with delineation of function, markers, developmental lineages, heterogeneity, regenerative potential, disease links, and key experimental tools. This publication will serve as the starting point of a live, up-to-date guide for lung research at https://www.lungmap.net/cell-cards/. We hope that Lung CellCards will promote the community-wide effort to establish, maintain, and restore respiratory health.

COVID↗

The auxin efflux carrier PIN1a regulates vascular patterning in cereal roots

Barley (Hordeum vulgare) is an important global cereal crop and a model in genetic studies. Despite advances in characterising barley genomic resources, few mutant studies have identified genes controlling root architecture and anatomy, which plays a critical role in capturing soil resources. Our phenotypic screening of a TILLING mutant collection identified line TM5992 exhibiting a short-root phenotype compared with wild-type (WT) Morex background. Outcrossing TM5992 with barley variety Proctor and subsequent SNP array-based bulk segregant analysis, fine mapped the mutation to a cM scale. Exome sequencing pinpointed a mutation in the candidate gene HvPIN1a, further confirming this by analysing independent mutant alleles. Detailed analysis of root growth and anatomy in Hvpin1a mutant alleles exhibited a slower growth rate, shorter apical meristem and striking vascular patterning defects compared to WT. Expression and mutant analyses of PIN1 members in the closely related cereal brachypodium (Brachypodium distachyon) revealed that BdPIN1a and BdPIN1b were redundantly expressed in root vascular tissues but only Bdpin1a mutant allele displayed root vascular defects similar to Hvpin1a. We conclude that barley PIN1 genes have sub-functionalised in cereals, compared to Arabidopsis (Arabidopsis thaliana), where PIN1a sequences control root vascular patterning.

59 BASIC BIOLOGICAL SCIENCES↗

RNAi and genome editing of sugarcane: Progress and prospects

SUMMARY Sugarcane, which provides 80% of global table sugar and 40% of biofuel, presents unique breeding challenges due to its highly polyploid, heterozygous, and frequently aneuploid genome. Significant progress has been made in developing genetic resources, including the recently completed reference genome of the sugarcane cultivar R570 and pan‐genomic resources from sorghum, a closely related diploid species. Biotechnological approaches including RNA interference (RNAi), overexpression of transgenes, and gene editing technologies offer promising avenues for accelerating sugarcane improvement. These methods have successfully targeted genes involved in important traits such as sucrose accumulation, lignin biosynthesis, biomass oil accumulation, and stress response. One of the main transformation methods—biolistic gene transfer or Agrobacterium ‐mediated transformation—coupled with efficient tissue culture protocols, is typically used for implementing these biotechnology approaches. Emerging technologies show promise for overcoming current limitations. The use of morphogenic genes can help address genotype constraints and improve transformation efficiency. Tissue culture‐free technologies, such as spray‐induced gene silencing, virus‐induced gene silencing, or virus‐induced gene editing, offer potential for accelerating functional genomics studies. Additionally, novel approaches including base and prime editing, orthogonal synthetic transcription factors, and synthetic directed evolution present opportunities for enhancing sugarcane traits. These advances collectively aim to improve sugarcane's efficiency as a crop for both sugar and biofuel production. This review aims to discuss the progress made in sugarcane methodologies, with a focus on RNAi and gene editing approaches, how RNAi can be used to inform functional gene targets, and future improvements and applications.

Brant, Eleanor [Agronomy Department, Plant Molecul↗

Cellulose nanofibrils-based packaging films synergistically reinforced by lignin and tea polyphenols for strawberry preservation

Developing biomass-based food packaging materials could alleviate resource scarcity and environmental pollution. Here, this study successfully fabricated cellulose nanofibrils-based packaging films synergistically reinforced by lignin and tea polyphenols for fruit preservation. Thanks to the abundant carboxyl and hydroxyl groups in modified lignin and tea polyphenol, the composite film delivered the highest tensile strength and Young’s modulus of 230.7 MPa and 11.9 GPa, respectively. The water vapor permeability (WVP) and oxygen permeability (OP) of composite film were as low as 2.53 × 10 –11 gm –1 s –1 Pa –1 and 1.69 × 10 –16 cm m –2 s–1 Pa –1 , respectively, demonstrating excellent barrier performance. Furthermore, the composite film possessed remarkable antibacterial (100 % antibacterial activity against two types of bacteria), antioxidant (DPPH free radical scavenging activity of 90 %), and UV shielding properties (impressive UV shielding rate of 99.0 %). Strawberry preservation experiments showed that these composite films could significantly extend shelf life, owing to the excellent barrier and antimicrobial properties. Our research indicated that these composite films could be promising food packaging material compared with traditional plastic and showed great application potential in fruit preservation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Predominance of Methanomicrobiales and diverse hydrocarbon–degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome–resolved metabolisms

Coalbed deposits are a unique subsurface environment and represent an underutilized resource for methane generation. Microbial communities extant in coalbed deposits are responsible for key subsurface biogeochemical cycling and could be utilized to enhance methane production in areas where existing gas wells have depleted methane stores, or in coalbeds that are unmined, or conversely be utilized for mitigation of methane release. Here we utilize metagenomics and metagenome-assembled genomes to identify extant microbial lineages and genome-resolved microbial metabolisms of coalbed produced water, which has not yet been explored in the Appalachian Basin. Our analyses resulted in the recovery of over 40 metagenome-assembled genomes (MAGs) from eight coalbed methane wells. The most commonly identified taxa among samples were hydrogenotrophic methanogens from the order Methanomicrobiales and these dominant MAGs were highly similar to one another. Conversely, low-abundance coalbed bacterial populations were taxonomically and functionally diverse, mostly belonging to a variety of Proteobacteria classes, and encoding various hydrocarbon solubilization and degradation pathways. Further, the data presented herein provides novel insights into Appalachian Basin coalbed microbial ecology, and our findings provide new perspectives on underrepresented Methanocalculus species and low-relative abundance bacterial assemblages in coalbed environments, and their potential roles in stimulation or mitigation of methane release.

59 BASIC BIOLOGICAL SCIENCES↗

Fitness factors impacting survival of a subsurface bacterium in contaminated groundwater

Many factors contribute to the ability of a microbial species to persist when encountering complexly contaminated environments, including time of exposure, the nature and concentration of contaminants, availability of nutritional resources, and possession of a combination of appropriate molecular mechanisms needed for survival. Herein we sought to identify genes that are most important for survival of Gram-negative Enterobacteriaceae in contaminated groundwater environments containing high concentrations of nitrate and metals using the metal-tolerant Oak Ridge Reservation isolate, Pantoea sp. MT58 (MT58). Survival fitness experiments in which a randomly barcoded transposon insertion (RB-TnSeq) library of MT58 was exposed directly to contaminated Oak Ridge Reservation groundwater samples from across a nitrate and mixed metal contamination plume were used to identify genes important for survival with increasing exposure times and concentrations of contaminants, and availability of a carbon source. Genes involved in controlling and using carbon, encoding transcriptional regulators, and related to Gram-negative outer membrane processes were among those found to be important for survival in contaminated Oak Ridge Reservation groundwater. A comparative genomics analysis of 75 Pantoea genus strains allowed us to further separate the survival determinants into core and non-core genes in the Pantoea pangenome, revealing insights into the survival of subsurface microorganisms during contaminant plume intrusion.

59 BASIC BIOLOGICAL SCIENCES↗

Bacterial population-level trade-offs between drought tolerance and resource acquisition traits impact decomposition

Microbes drive fundamental ecosystem processes, such as decomposition. Environmental stressors are known to affect microbes, their fitness, and the ecosystem functions that they perform; yet, understanding the causal mechanisms behind this influence has been difficult. We used leaf litter on soil surface as a model in situ system to assess changes in bacterial genomic traits and decomposition rates for 18 months with drought as a stressor. We hypothesized that genome-scale trade-offs due to investment in stress tolerance traits under drought reduce the capacity for bacterial populations to carry out decomposition, and that these population-level trade-offs scale up to impact emergent community traits, thereby reducing decomposition rates. We observed drought tolerance mechanisms that were heightened in bacterial populations under drought, identified as higher gene copy numbers in metagenome-assembled genomes. A subset of populations under drought had reduced carbohydrate-active enzyme genes that suggested—as a trade-off—a decline in decomposition capabilities. These trade-offs were driven by community succession and taxonomic shifts as distinct patterns appeared in populations. We show that trait–trade-offs in bacterial populations under drought could scale up to reduce overall decomposition capabilities and litter decay rates. Using a trait-based approach to assess the population ecology of soil bacteria, we demonstrate genome-level trade-offs in response to drought with consequences for decomposition rates.

59 BASIC BIOLOGICAL SCIENCES↗

Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron

Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in early stages of development. Here, we describe the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created as a resource for the research community. We used flow cytometry to sort single cells from a pooled library, located mutants within this initial progenitor collection by applying a pooling strategy with barcode sequencing, and re-arrayed specific mutants to create a condensed collection with single-insertion strains covering >2500 genes. To demonstrate the potential of the condensed collection for phenotypic screening, we analyzed growth dynamics and cell morphology. We identified both growth defects and altered cell shape in mutants disrupting sphingolipid synthesis and thiamine scavenging. Finally, we analyzed the process of assembling the B. theta condensed collection to identify inefficiencies that limited coverage. We demonstrate as part of this analysis that the process of assembling an ordered collection can be accurately modeled using barcode sequencing data. We expect that utilization of this ordered collection will accelerate research into B. theta physiology and that lessons learned while assembling the collection will inform future efforts to assemble ordered mutant collections for an increasing number of gut microbiota members.

59 BASIC BIOLOGICAL SCIENCES↗

Hotter droughts alter resource allocation to chemical defenses in piñon pine

Abstract Heat and drought affect plant chemical defenses and thereby plant susceptibility to pests and pathogens. Monoterpenes are of particular importance for conifers as they play critical roles in defense against bark beetles. To date, work seeking to understand the impacts of heat and drought on monoterpenes has primarily focused on young potted seedlings, leaving it unclear how older age classes that are more vulnerable to bark beetles might respond to stress. Furthermore, we lack a clear picture of what carbon resources might be prioritized to support monoterpene synthesis under drought stress. To address this, we measured needle and woody tissue monoterpene concentrations and physiological variables simultaneously from mature piñon pines ( Pinus edulis ) from a unique temperature and drought manipulation field experiment. While heat had no effect on total monoterpene concentrations, trees under combined heat and drought stress exhibited ~ 85% and 35% increases in needle and woody tissue, respectively, over multiple years. Plant physiological variables like maximum photosynthesis each explained less than 10% of the variation in total monoterpenes for both tissue types while starch and glucose + fructose measured 1-month prior explained ~ 45% and 60% of the variation in woody tissue total monoterpene concentrations. Although total monoterpenes increased under combined stress, some key monoterpenes with known roles in bark beetle ecology decreased. These shifts may make trees more favorable for bark beetle attack rather than well defended, which one might conclude if only considering total monoterpene concentrations. Our results point to cumulative and synergistic effects of heat and drought that may reprioritize carbon allocation of specific non-structural carbohydrates toward defense.

59 BASIC BIOLOGICAL SCIENCES↗