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Primary production by the purple nonsulfur bacterium Rhodopila globiformis in an acidic, moderately sulfidic warm spring
(American Society for Microbiology, 2025-09)
Fecteau, Kristopher M.
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Weeks, Katelyn M.
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Debes II, R. Vincent
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Barnes Tanner J.
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Robinson, Kirtland J.
Populations of the acidophilic purple nonsulfur bacterium Rhodopila globiformis were identified in two geographically distinct thermal areas in Yellowstone National Park (Wyoming, USA), as confirmed by 16S rRNA gene sequencing and detection of characteristic methoxylated ketocarotenoids. Microcosm-based carbon uptake assays where oxygenic photosynthesis was excluded via addition of 3-(3,4-dichlorophenyl)-1,1-dimethylurea yielded a light-driven dissolved inorganic carbon (DIC) assimilation rate (7 ± 2 mg C g C−1 h−1) comparable to those of highly productive algal mats in acidic hot springs, suggesting that R. globiformis may be performing photoautotrophy at the time of the assay. Rates of acetate assimilation were more than two orders of magnitude lower than DIC assimilation and did not differ between light and dark treatments, indicating photoheterotrophic use of acetate was not occurring, though photoheterotrophic assimilation of other organic compounds cannot be excluded. The tepid (35°C) spring waters are acidic (pH = 3.7) with moderate dissolved hydrogen sulfide (0.2 mM) and abundant DIC (11 mM), an apparently rare set of conditions thought to arise from extremely shallow mixing of oxygenated meteoric water and volcanic gases. Though originally isolated and cultured photoheterotrophically, in nature, R. globiformis may grow photoautotrophically under the normal conditions of its habitat, utilizing a stable supply of DIC afforded by the injection of CO2-rich volcanic gases. To our knowledge, these are the most acidic conditions under which light-driven DIC assimilation has been observed in the domain Bacteria.
Dynamics of a state-dependent delay-differential equation
(University of Szeged, 2025-01)
Gedeon, Tomáš
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Humphries, Antony R.
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Mackey, Michael C.
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Walther, Hans-Otto
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Wang, Zhao
We present a detailed study of a scalar differential equation with threshold state-dependent delayed feedback. This equation arises as a simplification of a gene regulatory model. There are two monotone nonlinearities in the model: one describes the dependence of delay on state, and the other is the feedback nonlinearity. Both increasing and decreasing nonlinearities are considered. Our analysis is exhaustive both analytically and numerically as we examine the bifurcations of the system for various combinations of increasing and decreasing nonlinearities. We identify rich bifurcation patterns including Bautin, Bogdanov–Takens, cusp, fold, homoclinic, and Hopf bifurcations whose existence depend on the derivative signs of nonlinearities. Our analysis confirms many of these patterns in the limit where the nonlinearities are switch-like and change their value abruptly at a threshold. Perhaps one of the most surprising findings is the existence of a Hopf bifurcation to a periodic solution when the nonlinearity is monotone increasing and the time delay is a decreasing function of the state variable.
Securing the Future of NMR Metabolomics Reproducibility: A Call for Standardized Reportin
(ACS Publications, 2025-09)
Andersson, Erik R.
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Bayless, Amanda L.
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Brua, Robert B.
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Casu, Fabio
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Cheng, Leo L.
Metabolomics is a rapidly growing multidisciplinary field with ever increasing demand and usability, which is attracting a surge of new researchers. While their varied skill sets, scientific questions, and approaches enrich the field with fresh perspectives and innovation, individual investigators also bring wide-ranging levels of metabolomics-specific experience and diverse areas of interest. These factors introduce considerable variability and inconsistency in both the methodology and reporting. A recent comparative literature review of nuclear magnetic resonance (NMR) metabolomics from studies published in 2010 and 2020 revealed significant shortcomings in the reporting of experimental details necessary for evaluating both the scientific rigor and the reproducibility of NMR-based metabolomics experiments. Each stage of metabolomics research contains multiple methodological choices and various optimization parameters, all of which can introduce experimental bias and alter the study results. This emphasizes the need for proper reporting to enhance reproducibility, data reusability, and study comparability. To address these concerns, the NMR Special Interest Group within the Metabolomics Association of North America presents reporting recommendations focused on fundamental aspects of NMR metabolomics research identified from the detailed literature review report. These include specifics with respect to study design, sample preparation, data acquisition, data processing and analysis, data accessibility, and comparability to previous studies. Also presented is a complementary list of seminal papers in the field to guide the study design and implementation of NMR metabolomics experiments. This initiative seeks to enhance the long-term impact of NMR metabolomics by supporting high-quality, reproducible, and impactful data collected from well-executed and thoroughly reported studies.
On the origin of the late-flowering ppd-H1 allele in barley
(Springer Science and Business Media LLC, 2025-09)
Sharma, Rajiv
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Shaaf, Salar
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Neumann, Kerstin
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Civan, Peter
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Guo, Yu
To breed for climate resilient crops, an understanding of the genetic and environmental factors influencing adaptation is critical. Barley provides a model species to study adaptation to climate change. Here we present a detailed analysis of genetic variation at a major photoperiod response locus and relate this to the domestication history and dispersal of barley. The PPD-H1 locus (a PSEUDO-RESPONSE REGULATOR 7) promotes flowering under long-day conditions, and a natural mutation at this locus resulted in a recessive, late-flowering ppd-H1 allele. This mutation proved beneficial in high-latitude environments such as Northern Europe, where it allows extended vegetative growth during long spring days. We infer the origin of the mutated late-flowering ppd-H1 allele by re-sequencing a large geo-referenced collection of 942 Hordeum spontaneum, 5 Hordeum agriocrithon and 1110 domesticated (Hordeum vulgare) barleys. We demonstrate that the late-flowering phenotype originated from Desert-type wild barley in the Southern Levant and present evidence suggesting a post-domestication origin of the mutated ppd-H1 allele.
Evaluation of Hydrophobic, Hydrophilic, and Water Adsorption Properties of Microporous Metal–Organic Framework Materials by Unified Isotherm Analysis
(American Chemical Society, 2025-09)
Rutherford, Steven W.
Global challenges posed by freshwater scarcity and the water–energy nexus drive demand for novel macromolecular design of tailored nanostructures endowed with a variety of hydrophilic and hydrophobic features. Offering potential to meet this demand, metal–organic framework (MOF) materials are synthesized from coordinated formations that create versatile reticular structures with variable water adsorption affinities. However, advances in the fundamental understanding of water interactions within these structures are impeded by the failure of classical analyses to identify mechanisms of interaction, connect fundamental isotherm types, and provide appropriate benchmarks for assessment. Proposed herein is a novel definition of hydrophobicity that is coherently coupled with a unified isotherm analysis to connect a wide array of rigorous equilibrium isotherm types bounded by asymptotic limits dictated by hydrophilic rectangular Type I and hydrophobic stepwise Type V (unimodal Type VI). Moreover, distinct forms of hydrophobicity, associated benchmarks and discrete classes of material behavior are introduced to characterize hydrophobic to hydrophilic transitions. Simplification of the analysis for application to microporous MOF materials displaying nominally stepwise water adsorption isotherms yields Ising-Model-Modified-Kelvin-Analysis (IMMKA) that is delivered in a simple, rigorous, analytic form. Mechanisms of pore filling are characterized, allowing verification of widely accepted protocols and “rules of thumb” for the prediction of micropore filling pressures. The analysis successfully captures the foundational features of water in extreme confinement, including the role of pore morphology in directing the molecular and fluidic interactions that underpin the pseudocondensation mechanism of water in micropores.