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At least 73 records · Page 4

The microbiologist's guide to metaproteomics

Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state-of-the-art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.

bioinformatics↗

Bottom quark energy loss and hadronization with B + and ${\textrm{B}}_{\textrm{s}}^0$ nuclear modification factors using pp and PbPb collisions at $\sqrt{s_{\textrm{NN}}}$ = 5.02 TeV

The production cross sections of $ {\textrm{B}}_{\textrm{s}}^0 $ and B$^{+}$ mesons are reported in proton-proton (pp) collisions recorded by the CMS experiment at the CERN LHC with a center-of-mass energy of 5.02 TeV. The data sample corresponds to an integrated luminosity of 302 pb$^{−1}$. The cross sections are based on measurements of the $ {\textrm{B}}_{\textrm{s}}^0 $→ J/ψ(μ$^{+}$μ$^{−}$)ϕ(1020)(K$^{+}$K$^{−}$) and B$^{+}$→ J/ψ(μ$^{+}$μ$^{−}$)K$^{+}$ decay channels. Results are presented in the transverse momentum (p$_{T}$) range 7–50 GeV/c and the rapidity interval |y| < 2.4 for the B mesons. The measured p$_{T}$-differential cross sections of B$^{+}$ and $ {\textrm{B}}_{\textrm{s}}^0 $ in pp collisions are well described by fixed-order plus next-to-leading logarithm perturbative quantum chromodynamics calculations. Using previous PbPb collision measurements at the same nucleon-nucleon center-of-mass energy, the nuclear modification factors, R$_{AA}$, of the B mesons are determined. For p$_{T}$> 10 GeV/c, both mesons are found to be suppressed in PbPb collisions (with R$_{AA}$ values significantly below unity), with less suppression observed for the $ {\textrm{B}}_{\textrm{s}}^0 $ mesons. In this p$_{T}$ range, the R$_{AA}$ values for the B$^{+}$ mesons are consistent with those for inclusive charged hadrons and D$^{0}$ mesons. Below 10 GeV/c, both B$^{+}$ and $ {\textrm{B}}_{\textrm{s}}^0 $ are found to be less suppressed than either inclusive charged hadrons or D$^{0}$ mesons, with the $ {\textrm{B}}_{\textrm{s}}^0 $R$_{AA}$ value consistent with unity. The R$_{AA}$ values found for the B$^{+}$ and $ {\textrm{B}}_{\textrm{s}}^0 $ are compared to theoretical calculations, providing constraints on the mechanism of bottom quark energy loss and hadronization in the quark-gluon plasma, the hot and dense matter created in ultrarelativistic heavy ion collisions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Enhancing climate-smart crop performance in arid agrivoltaics systems: effects of photovoltaic shading and soil amendments on tepary bean growth, yield, and associated soil microbiome

As climate change expands the world’s arid and semiarid regions, sustainable systems that integrate food and energy production are becoming increasingly critical. Agrivoltaics—co-locating crops with photovoltaic (PV) panels—offers a dual land-use strategy that mitigates environmental stress by shading crops, conserving soil moisture, and enhancing PV efficiency. While climate-smart crops like the tepary bean ( Phaseolus acutifolius ) are well adapted to heat and drought, little is known about how these crops and their associated soil microbiomes respond to the unique microclimates created by PV shading. This study evaluated tepary bean performance and plant–microbial interactions under PV-shade vs. no shade across three soil amendment treatments at two experimental sites. We assessed plant traits including germination, phenology, biomass, height, as well as yield and bean morphology, alongside shifts in soil microbial composition and functional potential. Plants grown under PV-shade were generally taller, with extended reproductive periods and higher yields: 42% of shaded plants produced beans compared to only 8% under full sun. Shaded plants also produced rounder, higher-quality beans, whereas non-shaded plants yielded flatter, less developed beans. Microbial community composition was more strongly influenced by amendment and site conditions than by shading alone. Key microbial taxa (e.g., Glomeromycetes, Desulfobacterota ) and predicted functions (e.g., denitrification, nitrogen-respiration, sulfate reduction) were associated with differences in plant performance. Finally, combining agrivoltaic systems with targeted soil amendments can enhance crop yield and soil microbial functionality—offering a promising strategy for sustainable agriculture in arid landscapes.

14 SOLAR ENERGY↗

PERCEPTIVE: an R shiny $\underline{p}$ipelin$\underline{e}$ for the p$\underline{r}$edi$\underline{c}$tion of $\underline{ep}$igenetic modula$\underline{t}$ors $\underline{i}$n no$\underline{v}$el sp$\underline{e}$cies

Epigenetic processes are central to regulating gene expression, genome stability, and metabolic function across the tree of life; yet, their roles remain underexplored in microalgae, especially as new species continue to be identified and characterized. This is likely due to the cumbersome nature and species-dependent attributes of epigenetic wet-lab methodologies, which preclude the rapid identification of epigenetic modifications and modulators. However, there is high conservation of epigenetic processes from budding yeast to humans; in many cases, one may infer how behavior and function are epigenetically regulated in novel species by identifying epigenetic modulators, or the proteins responsible for conferring epigenetic modifications. Here, to this end, we have developed a graphical software package, titled PERCEPTIVE (pipeline for the prediction of epigenetic modulators in novel species). This platform solely uses the genomic sequence of an algal species, and preexisting information from other model organisms, to predict the epigenetic modulators and associated modifications in algae. Predictions are presented to the user in a graphical interface, which provides literature-based interpretation of results, enabling users to quickly understand potential epigenetic processes in their algal species of interest and plan follow-up experiments. To test PERCEPTIVE, we predicted epigenetic modulators in several feedstock candidate algae species. To validate these predictions, wet-lab studies were performed, including mass spectrometry; these results underscore the high accuracy of PERCEPTIVE predictions. Overall, PERCEPTIVE represents a powerful in silico tool for the research and manipulation of algal species, which does not require a priori knowledge of epigenetics and is accessible to a broad set of investigators.

59 BASIC BIOLOGICAL SCIENCES↗

Higher-order interaction effects among operating conditions and feedstocks shape reactor microbiomes and fatty acid production profiles

Arrested anaerobic digestion (AAD) offers a promising route for producing fatty acids (FAs) from organic residues, yet optimal conditions for selectively generating medium-chain fatty acids (MCFAs) remain poorly defined. Here, we systematically evaluated the main and interaction effects of pH (5, 7, 9), feedstock (food waste, manure), temperature (35 and 45 °C), and inoculum source on microbiome composition and FA production. Anaerobic digester sludge and a novel bison rumen inoculum were compared. Significant higher-order interactions among operating parameters governed FA profiles and microbiome structure. Butyric acid production was driven by a three-way interaction among pH, feedstock, and temperature (p < 0.001), with maximum concentrations achieved in food waste reactors at pH 5.0 and 35 °C (1.2 ± 0.1 g L −1 with sludge and 1.1 ± 0.3 g L −1 with rumen). MCFA production exhibited significant four-way interactions (p < 0.1 to p < 0.001). At 45 °C and pH 5.0, inoculum source tuned MCFA selectivity: sludge favored pentanoic acid (0.4 ± 0.1 g L −1 ), whereas rumen favored hexanoic and heptanoic acids (up to 0.4 ± 0.2 g L −1 ). Manure reactors produced < 0.2 g L −1 MCFAs under all conditions. Genera, including Megasphaera, Prevotella, and Lactobacillus, were associated with production of specific MCFAs. PICRUSt2-based pathway predictions were consistent with MCFA production patterns and suggested a potential role for lactic acid–driven chain elongation pathways. This study provides insights into how interacting operating conditions shape AAD microbiomes, their FA profiles, and advances the trajectory of research aimed at engineering robust and controllable microbiomes for waste valorization.

09 BIOMASS FUELS↗

Engineering PHL7 for Improved Poly(Ethylene Terephthalate) Depolymerization via Rational Design and Directed Evolution

Enzymatic depolymerization of poly(ethylene terephthalate) (PET) has emerged as a promising approach for polyester recycling, and, to date, many natural and engineered PET hydrolase enzymes have been reported. For industrial use, PET hydrolases must achieve high depolymerization extent and exhibit excellent thermostability. Here, we engineered a natural PET hydrolase, Polyester Hydrolase Leipzig #7 (PHL7), through rational design and directed evolution using a high-throughput screening platform. Four new enzymes were engineered with enhanced properties compared with the parent enzyme, wild-type PHL7 (PHL7-WT), and other benchmark PET hydrolases, under the tested conditions. In bioreactors, the exemplary engineered enzyme, PHL7-Jemez, exhibited improved ability to depolymerize amorphous PET film compared with PHL7-WT at 2.9% and 20% substrate loadings, with 37% and 270% higher hydrolysis, respectively, after 48 h. This study develops several state-of-the-art PET hydrolases and demonstrates a directed evolution platform to engineer high-performance enzymes, which can accelerate enzyme discovery toward improved biocatalytic recycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Determination of a suitable molar absorption coefficient (ε) for lignin analysis of fibrous plants using the CASA method

In this study, the benchmarking and applicability of the CASA method for the analysis of fibrous plants, such as flax, hemp, and jute, is evaluated. Lignin is a phenolic biopolymer present in plant cell walls and is composed of three primary monomeric units, designated G, S, and H. Various factors, such as the genetic variability, influence the relative proportions of these units in plant samples. Recently, the cysteine-assisted sulfuric acid (CASA) method has been introduced as a rapid method for the quantification of lignin in wood samples. The aim of this study is to establish a suitable molar absorption coefficient (ε, L·g –1 ·cm –1 ) to adapt the CASA method for use with annual plant fibers. This investigation was motivated by the technical advantages of the CASA method, including higher throughput, lower reaction temperatures, and ecological benefits due to the absence of carcinogenic, mutagenic, or reprotoxic (CMR) substances and the need for minimal sample quantities. In this method, lignin solubilization is facilitated by cysteine, which is an amino acid that enhances the reaction kinetics, using a one-hour incubation period. However, as with any spectrophotometric technique, the CASA method depends on a molar absorption coefficient (ε) that varies according to the ratio of the aromatic units within the polymer. To evaluate the suitability of CASA for quantifying lignin in economically significant plant fibers, we investigate the impact of the unit ratios on the accuracy of ε. The results are compared with those of two widely recognized lignin analytical methods: the Klason method, which is a gravimetric reference method, and the acetyl bromide soluble lignin method, which is the most commonly used spectrophotometric approach. The final ε obtained in this study reveals a relative difference in lignin content ranging from –8 % to +9 % based on a comparison between the CASA and Klason methods across different industrial hemp varieties. As a result, using known G:S ratios in annual fibrous plants, ε can be estimated from our results.

59 BASIC BIOLOGICAL SCIENCES↗

Regulatory helix plays a key role in genetic ON-OFF switching for the 2’-deoxyguanosine sensing mRNA element

Transcriptional riboswitches, noncoding mRNA elements that operate in cis to regulate gene expression, have a promising potential in medicine, synthetic biology and directed evolution. They bind to cellular metabolites or metal ions with high specificity, leading to conformational rearrangements that facilitate the activation or premature termination of transcription for downstream genes. This elegant mechanism for feedback regulation of metabolic pathways has been identified in prokaryotes and a few in eukaryotes. Our chemical probing of the 2’-deoxyguanosine (2’-dG)-sensing riboswitch demonstrates that the overall conformational state of the full-length riboswitch (dGsw-fl) is unresponsive to the 2’-dG. Although binding proceeds as expected, dGsw-fl exclusively populates an OFF state of transcriptional inhibition. We chemically probed the structure of a known dGsw transcriptional intermediate (dGsw-int) to evaluate the possibility of a cotranscriptional regulatory role. Interestingly, apo dGsw-int adopts an alternative conformation in which a stable anti-terminator helix is formed, leading to an ON state where transcription can proceed. In the presence of 2’-dG, this anti-terminator helix is destabilized to produce a conformation reminiscent of the full-length, OFF-state dGsw. Using a fluorescence quenching assay, we demonstrate that binding 2’-dG to early transcriptional intermediates can inhibit the formation of the anti-terminator helix, locking dGsw in an OFF state. These data suggest that metabolite sensing occurs during a brief window of time between the synthesis of two transcriptional intermediates. Our studies indicate that dGsw does not function as a binary ON−OFF switch, but instead fine-tunes the transcription of downstream genes during RNA synthesis using key intermediates.

59 BASIC BIOLOGICAL SCIENCES↗

A review of quantum imaging methods and enabling technologies

The field of quantum imaging has recently seen an explosion of new methods and techniques. At the heart of most quantum imaging approaches are three enabling technologies: the source of the quantum light, the detectors that turn sensing into imaging, and the method by which the quantum nature of light is leveraged to improve the desired measurement. This review addresses the dominant and emerging technologies in each of these components as well as details concerning the implementations of various quantum imaging methods.

36 MATERIALS SCIENCE↗

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↗

Challenges and Vision for Standardization of Biopolymer Data Sets for Machine Learning

Machine learning (ML) is transforming materials research, yet potential for biopolymer discovery remains constrained by fragmented data and nonstandardized reporting. Biopolymers differ significantly from synthetic polymers, requiring specialized approaches to represent their biosynthetic origins, hierarchical structures, and application-specific metrics. In this Perspective, we identify three core challenges limiting biopolymer representation: information encoding, data quality, and data sharing. We describe the most pressing issues and propose commensurate approaches to address each key challenge. Recommendations include the design and adoption of biopolymer-specific fingerprinting and representation frameworks, development of hybrid human-large language model (LLM) data extraction strategies, and expanding Findable, Accessible, Interoperable, Reusable (FAIR)-compliant repositories. We propose a robust foundation to define interoperable, high-quality data sets that capture the full context of biopolymer materials. Standardized metadata, shared ontologies, and community-driven infrastructure would enable scalable, reproducible workflows and accelerate the ML-driven development of biopolymers.

36 MATERIALS SCIENCE↗

Optimizing Cryo-Focused Pyrolysis GC/MS for Tracing Soil Organic Matter Across Diverse Ecosystems

The cycling of organic matter in terrestrial soils and sediments is central to a range of biogeochemical processes that regulate nutrient cycling, crop productivity, trace gas emissions, and contaminant transport. Pyrolysis-gas chromatography/mass spectrometry (py-GC/MS) is a powerful tool for characterizing bulk soil organic matter (SOM) at the molecular level. In this study, we used a cryo-focused py-GC/MS system to analyze soil samples from seven diverse ecosystems: vernal pool, prairie pothole, temperate forest, tropical forest, tundra, wildfire-affected boreal forest, and grassland. We addressed a key bottleneck in molecular-level SOM characterization by developing an automated data analysis pipeline to optimize py-GC/MS and complementary evolved gas analysis/mass spectrometry (EGA/MS) methods, incorporating advanced tools for peak deconvolution, developing a custom compound class library, and implementing fragmentation spectrum-based molecular networking for the first time. This improved workflow was applied to soil samples from all seven ecosystems, including multiple depths and density fractions. Our findings demonstrate that ecosystem type plays a dominant role in shaping compositional differences in SOM. We also identified trends in the source of SOM compounds (e.g., microbial vs plantderived) across soil depth and density fractions, which are critical for understanding persistence and turnover of SOM. Our molecular networking analysis indicated that although many compounds are widespread across ecosystems, others are restricted to specific environments, such as wetlands. This underscores the utility of molecular-level data in elucidating the complexity of SOM composition and the environmental drivers that shape it. Such molecular-level insights can deepen our knowledge of biogeochemical SOM cycles.

54 ENVIRONMENTAL SCIENCES↗

Nanodiamonds in Advancing Biomedical Sciences

Nanodiamonds (NDs), tetrahedral carbon frameworks with size ranging from 1 to 100 nanometers, have gained growing attention in recent years due to their distinct optical, thermal, and mechanical properties compared to other carbon nanomaterials (e.g., graphene, carbon nanotubes, carbon dots). Combined with a high surface-to-volume ratio and tunable and chemically versatile surfaces, these support broad applications across catalysis, electronics, and life sciences. Moreover, the biocompatible characteristics of NDs enable their controllable interfacial interactions with biological systems, positioning them as excellent candidates for advancing cutting-edge biomedical sciences, particularly through the engineering of efficient material-biointerfaces that facilitate optimal interactions with biological systems. Among various forms of NDs, fluorescent nanodiamonds (FNDs) have emerged as some of the most impactful and rapidly advancing materials, demonstrating strong potential in ultrasensitive spin-enhanced bioimaging, high-precision biosensing, traceable drug delivery, and quantum-enabled biomedical technologies. This Perspective introduces the key principles underlying NDs and FNDs, including their structural properties, synthesis methods, and surface functionalization strategies. It also highlights emerging biomedical applications of NDs and FNDs, with particular emphasis on neurological disorders. Last, the article discusses current challenges in advancing NDs as a multifunctional platform for neural therapies with translational potential toward clinical trials.

36 MATERIALS SCIENCE↗

Enhanced Electrocatalytic and Selective CO 2 -to-CO Reduction by a Rhenium(I) Complex Bearing 6,6′-Substituted 2,2′-Bipyridines

The electrochemical reduction of CO 2 (CO 2 RR) into value-added chemicals offers a promising route toward a circular carbon economy and reduced reliance on fossil fuels. A detailed understanding of the structural and electronic factors governing the performance of molecular CO 2 RR electrocatalysts is essential for the design of efficient, tunable systems. Here, in this study, we report a series of rhenium(I) complexes, fac-[Re I (6,6′-(R) 2 -bpy)(CO) 3 Cl] (bpy = 2,2′-bipyridine; R = mesityl (mes), 2,4,6-triisopropylphenyl (trip), or isophthalic acid (phth)) and evaluate their electrocatalytic activity. Among these, fac-[Re I (6,6′-(mes) 2 -bpy)(CO) 3 Cl] exhibited the highest performance, enabling selective CO 2 -to-CO conversion for 1 hour with Faradaic efficiency (FE) > 97%, representing an unprecedented activity level for a Re-bpy catalysts. Single-crystal X-ray diffraction and density functional theory (DFT) calculations indicated that favorable CO 2 binding could be promoted by the tilting of the 6,6′-(mes)2-bpy ligand (from the Re-CO coordination plane), providing mechanistic insight into the observed enhancement. The study consequently demonstrates a rational correlation between the CO 2 electrocatalytic performance of Re-bpy catalysts and their structural variations, as derived from X-ray data and corroborated by computational modeling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior

Lipid membranes are central to cellular life. Complementing experiments, computational modeling has been essential in unraveling complex lipid-biomolecule interactions, crucial in both academia and industry. The Martini model, a coarse-grained force field for efficient molecular dynamics simulations, is widely used to study membrane phenomena but has faced limitations, particularly in capturing realistic lipid phase behavior. Here, we present refined Martini 3 lipid models with a mapping scheme that distinguishes lipid tails that differ by just two carbon atoms, enhancing the structural resolution and thermodynamic accuracy of model membrane systems including ternary mixtures. The expanded Martini lipid library includes thousands of models, enabling simulations of complex and biologically relevant systems. These advancements establish Martini as a robust platform for lipid-based simulations across diverse fields.

Lipids↗

The Dynamical Role of Optical Phonons and Sublattice Screening in a Solid-State Ion Conductor

Solid-state electrolytes (SSEs) require ionic conductivities that are competitive with liquid electrolytes to realize applications in all-solid-state batteries. Although candidate SSEs have been discovered, the underlying mechanisms enabling superionic conduction (>1 mS cm –1 ) remain elusive. In particular, the role of ultrafast lattice dynamics in mediating ion migration, which involves couplings between ions, phonons, and electrons, is rarely explored experimentally at their corresponding time scales. To investigate the complex contributions of coupled lattice dynamics on ion migration, we modulate the charge density occupations within the crystal framework and then measure the time-resolved change in impedance on picosecond time scales for a candidate SSE, Li 0.5 La 0.5 TiO 3 (LLTO). Upon perturbation, we observe enhanced ion migration at ultrafast time scales. The respective transients match the time scales of optical and acoustic phonon vibrations, suggesting their involvement in ion migration. We further computationally evaluate the effect of a charge transfer from the O 2p to the Ti 3d band on the electronic and physical structure of LLTO. We hypothesize that the charge-transfer excitation distorts the TiO 6 polyhedra by altering the local charge density occupancy of the hopping site at the migration pathway saddle point, thereby causing a reduction in the migration barrier for the Li + hop. We rule out the contribution of photogenerated electron carriers and laser heating. Overall, our investigation introduces a new spectroscopic tool to probe fundamental ion hopping mechanisms transiently at ultrafast time scales, which has previously only been achieved in a time-averaged manner or solely via computational methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Highly multiplexed design of an allosteric transcription factor to sense new ligands

Allosteric transcription factors (aTF) regulate gene expression through conformational changes induced by small molecule binding. Although widely used as biosensors, aTFs have proven challenging to design for detecting new molecules because mutation of ligand-binding residues often disrupts allostery. Here, we develop Sensor-seq, a high-throughput platform to design and identify aTF biosensors that bind to non-native ligands. We screen a library of 17,737 variants of the aTF TtgR, a regulator of a multidrug exporter, against six non-native ligands of diverse chemical structures – four derivatives of the cancer therapeutic tamoxifen, the antimalarial drug quinine, and the opiate analog naltrexone – as well as two native flavonoid ligands, naringenin and phloretin. Sensor-seq identifies biosensors for each of these ligands with high dynamic range and diverse specificity profiles. The structure of a naltrexone-bound design shows shape-complementary methionine-aromatic interactions driving ligand specificity. To demonstrate practical utility, we develop cell-free detection systems for naltrexone and quinine. Sensor-seq enables rapid and scalable design of new biosensors, overcoming constraints of natural biosensors.

59 BASIC BIOLOGICAL SCIENCES↗

Multidrug-resistant Shigella flexneri outbreak affecting humans and non-human primates in New Mexico, USA

Shigellosis is a gastrointestinal infection caused by species of Shigella . A large outbreak of Shigella flexneri serotype 2a occurred in Albuquerque, New Mexico between May 2021 and November 2023 that involved humans and non-human primates (NHP) from a local zoo. We analyzed the genomes of 202 New Mexican isolates as well as 15 closely related isolates from other states, and four from NHP. The outbreak was initially detected within men who have sex with men but then predominantly affected people experiencing homelessness. Nearly 70% of cases were hospitalized and there was one human death. The outbreak extended into Albuquerque’s BioPark Zoo, causing high morbidity and six deaths in NHPs. All isolates were multidrug-resistant, including towards fluoroquinolones, a first line treatment option which led to treatment failures in human and NHP populations. We show the circulation of the same S. flexneri strain in humans and NHPs, causing fatalities in both populations. This study demonstrates the threat of antimicrobial resistant organisms to vulnerable human and NHP populations and emphasizes the value of genomic surveillance within a One Health framework.

59 BASIC BIOLOGICAL SCIENCES↗