Salty chemical cocktails as water quality signatures: Longitudinal trends and breakpoints along different U.S. streams
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Environmental Sciences & Ecology↗
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Nonlinear drought plasticity reveals intraspecific diversity in a dominant grass species
Abstract Intraspecific diversity of dominant species in native plant communities can modulate ecosystem function under both optimal and stressful conditions. Yet, few genotype by environment interaction studies quantify differences in the shape of plasticity functions or phenotypic breakpoints across genotypes in natural populations. Using three genotypes with a history of drought selection, we performed a greenhouse study on the dominant tallgrass prairie species Andropogon gerardii . We investigated phenotypic plasticity and recovery differences among genotypes across a water availability gradient, measuring growth‐related, instantaneous and cumulative phenotypes. To further understand genotype by environment effects, we quantified plasticity functions and breakpoints among genotypes. Like other studies, we found strong evidence for phenotypic and plasticity differences among genotypes. However, we also found nonlinear plasticity functions and breakpoints were common across phenotypes, especially relative growth rates, biomass allocation and root architecture. Drought selected genotypes were also more likely to flower during recovery, but all genotypes were resilient to drought across treatments. We demonstrate that plasticity functions may help explain intraspecific diversity, patterns of selection and nonlinear community responses to more variable rainfall within an experimental population. In particular, plasticity functions can help disentangle drought/variability tolerance versus acquisitive strategies. A better understanding of intraspecific diversity in this grass species will provide more mechanistic insight into its ability to buffer ecosystem changes and provide resiliency in the tallgrass prairie under future droughts. A free Plain Language Summary can be found within the Supporting Information of this article.
Hoffman, Ava M.↗
Comprehensive Genetic Characterization of Four Novel HIV-1 Circulating Recombinant Forms (CRF129_56G, CRF130_A1B, CRF131_A1B, and CRF138_cpx): Insights from Molecular Epidemiology in Cyprus
Molecular investigations of the HIV-1 pol region (2253–5250 in the HXB2 genome) were conducted on sequences obtained from 331 individuals infected with HIV-1 in Cyprus between 2017 and 2021. This study unveiled four distinct HIV-1 putative transmission clusters, encompassing 19 previously unidentified HIV-1 recombinants. These recombinants, each comprising eight, three, four, and four sequences, respectively, did not align with previously established Circulating Recombinant Forms (CRFs). To characterize these novel HIV-1 recombinants, near-full-length genome sequences were successfully obtained for 16 of the 19 recombinants (790–8795 in the HXB2 genome) using an in-house-developed RT-PCR assay. Phylogenetic analyses, employing MEGAX and Cluster-Picker, along with confirmatory neighbor-joining tree analyses of subregions, were conducted to identify distinct clusters and determine subtypes. The uniqueness of the HIV-1 recombinants was evident in their exclusive clustering within generated maximum likelihood trees. Recombination analyses highlighted the distinct chimeric nature of these recombinants, with consistent mosaic patterns observed across all sequences within each of the four putative transmission clusters. Conclusive genetic characterization identified four novel HIV-1 CRFs: CRF129_56G, CRF130_A1B, CRF131_A1B, and CRF138_cpx. CRF129_56G exhibited two recombination breakpoints and three fragments of subtypes CRF56_cpx and G. Both CRF130_A1B and CRF131_A1B featured seven recombination breakpoints and eight fragments of subtypes A1 and B. CRF138_cpx displayed five recombination breakpoints and six fragments of subtypes CRF22_01A1 and F2, along with an unclassified fragment. Additional BLAST analyses identified a Unique Recombinant Form (URF) of CRF138_cpx with three additional recombination sites, involving subtype F2, a fragment of unknown subtype origin, and CRF138_cpx. Post-identification, all putative transmission clusters remained active, with CRF130_A1B, CRF131_A1B, and CRF138_cpx clusters exhibiting further growth. Furthermore, international connections were identified through BLAST analyses, linking one sequence from the USA to the CRF130_A1B strain, and three sequences from Belgium and Cameroon to the CRF138_cpx strain. This study contributes valuable insights into the dynamic landscape of HIV-1 diversity and transmission patterns, emphasizing the need for ongoing molecular surveillance and global collaboration in tracking emerging viral variants.
60 APPLIED LIFE SCIENCES↗
Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments
Although biodiversity and ecosystem functions are strongly shaped by contemporary environments, such as climate and local biotic and abiotic attributes, relatively little is known about how they depend on long-term geological processes. Here, along a 3000-m elevational gradient with tectonic faults on the Tibetan Plateau (that is, Galongla Mountain in Medog County, China), we study the joint effects of geological and contemporary environments on biological communities, such as the diversity and community composition of plants and soil bacteria, and ecosystem functions. We find that these biological communities and ecosystem functions generally show consistent elevational breakpoints at 2000–2800 m, which coincide with Indus-Yalu suture zone fault and are similar to the elevational breakpoints of soil bacteria on another mountain range 1000 km away. Mean annual temperature, soil pH and moisture are the primary contemporary determinants of biodiversity and ecosystem functions, which support previous findings. However, compared with the models excluding geological processes, inclusion of geological effects, such as parent rock and weathering, increases 67.9 and 35.9% of the explained variations in plant and bacterial communities, respectively. Such inclusion increases 27.6% of the explained variations in ecosystem functions. The geological processes thus provide additional links to ecosystem properties, which are prominent but show divergent effects on biodiversity and ecosystem functions: parent rock and weathering exert considerable direct effects on biodiversity, whereas indirectly influence ecosystem functions via interactions with biodiversity and contemporary environments. Thus, the integration of geological processes with environmental gradients could enhance our understanding of biodiversity and, ultimately, ecosystem functioning across different climatic zones.
54 ENVIRONMENTAL SCIENCES↗
Impact analysis of DERs on bulk power system stability through the parameterization of aggregated DER_a model for real feeders
With an ever increasing percentage of distributed energy resources (DERs) connected behind the meter in the distribution system, it is becoming increasingly important to equip transmission planners with the visibility of DER dynamic performance in distribution system. Not having visibility of the disconnection of DERs with the occurrence of transmission events, could result in an erroneous view of the stability of bulk power system. Here, in this paper, a parameterized aggregated model (DER_a) serves as a representation of the distribution-level dynamics of real residential feeders, which is used for analysis of bulk power system stability. The parameters are obtained by executing dynamic Monte Carlo simulations. Faults are then induced at the substation level causing the DERs to trip which subsequently enables the parameterization of the low and high voltage breakpoints (v l0 , v l1 , v h0 , and v h1 ) of the DER_a model’s partial voltage trip block. These parameters are then utilized to study the effectiveness of the DER_a model to represent the behavior of the aggregated DERs’ response and their impact on the bulk power system. The case study shows the ability of the positive-sequence DER_a model to provide an accurate estimation of DERs that are susceptible to trip due to 3-$\phi$ and 1-$\phi$ faults of transmission.
14 SOLAR ENERGY↗
Restricted Rotational Flexibility of the C5α-Methyl-Substituted Carbapenem NA-1-157 Leads to Potent Inhibition of the GES-5 Carbapenemase
Carbapenem antibiotics are used as a last-resort treatment for infections caused by multidrug-resistant bacteria. The wide spread of carbapenemases in Gram-negative bacteria has severely compromised the utility of these drugs and represents a serious public health threat. To combat carbapenemase-mediated resistance, new antimicrobials and inhibitors of these enzymes are urgently needed. Here, we describe the interaction of the atypically C5α-methyl-substituted carbapenem, NA-1-157, with the GES-5 carbapenemase. MICs of this compound against Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii producing the enzyme were reduced 4–16-fold when compared to MICs of the commercial carbapenems, reaching clinically sensitive breakpoints. When NA-1-157 was combined with meropenem, a strong synergistic effect was observed. Kinetic and ESI-LC/MS studies demonstrated that NA-1-157 is a potent inhibitor of GES-5, with a high inactivation efficiency of (2.9 ± 0.9) × 105 M –1 s –1 . Acylation of GES-5 by NA-1-157 was biphasic, with the fast phase completing within seconds, and the slow phase taking several hours and likely proceeding through a reversible tetrahedral intermediate. Deacylation was extremely slow (k 3 = (2.4 ± 0.3) × 10 –7 s –1 ), resulting in a residence time of 48 ± 6 days. MD simulation of the GES-5-meropenem and GES-5-NA-1-157 acyl-enzyme complexes revealed that the C5α-methyl group in NA-1- 157 sterically restricts rotation of the 6α-hydroxyethyl group preventing ingress of the deacylating water into the vicinity of the scissile bond of the acyl-enzyme intermediate. Furthermore, these data demonstrate that NA-1-157 is a potent irreversible inhibitor of the GES-5 carbapenemase.
60 APPLIED LIFE SCIENCES↗
Multilayer DNA Origami with Terminal Interfaces That Are Flat and Wide-Area
DNA origami is a popular nanofabrication strategy that employs self-assembly of a long single scaffold strand, typically less than 10 kilobases in length, with hundreds of shorter staple strands into a desired shape. In particular, origami arranged as a single-layer rectangle has proven popular as flat pegboards that can display functionalities at staple-strand breakpoints, off the sides of the constituent double helices, with a ~5.3 nm rhombic-lattice spacing. For applications that demand tighter spacing, functionalities can be displayed instead on the termini of helices of multilayer DNA origami. However, pegboards with the greatest addressable surface area are often found to be the most versatile. Given the practical limitations of the length of the scaffold that can be easily realized, designs that minimize the length of each helix would have advantages for maximizing the number of helices and therefore the number of addressable pixels on each terminal surface. Here we present an architecture for multilayer DNA origami displaying flush terminal interfaces from over 200 helices that each are only 5.3 turns in length. As a result, we characterize an example using cryo-EM imaging paired with single-particle analysis for further analysis of the global structure.
59 BASIC BIOLOGICAL SCIENCES↗
The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole
Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change.
59 BASIC BIOLOGICAL SCIENCES↗
$\mathrm{COBRA}$ improves the completeness and contiguity of viral genomes assembled from metagenomes
Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of huge phages, whiB-encoding phages and cysC- and cysH-encoding phages. COBRA improves viral genome assembly contiguity and completeness, thus the accuracy and reliability of analyses of gene content, diversity and evolution.
54 ENVIRONMENTAL SCIENCES↗
Characterization of a novel HIV-1 circulating recombinant form, CRF91_cpx, comprising CRF02_AG, G, J, and U, mostly among men who have sex with men
Prospective molecular studies of HIV-1 pol region (2253–5250 in HXB2 genome) sequences from sequenced samples of 269 HIV-1-infected patients in Cyprus (2017–2021) revealed a transmission cluster of 14 unknown HIV-1 recombinants that were not classified as previously established CRFs. The earliest recombinant was collected in September 2017, and the transmission cluster continued to grow until November 2020. Near full-length HIV-1 genome sequences of the 11 of the 14 recombinants were successfully obtained (790–8795 in HXB2 genome) and aligned against a reference dataset of HIV-1 subtypes and CRFs. We employed MEGAX for maximum-likelihood tree construction (GTR model, 1000 bootstrap replicates), Cluster-Picker for phylogenetic clustering analysis (genetic distance ≤0.045, bootstrap support value ≥70%), and REGA-3.0 for subtype determination. Bootscan and similarity plot analyses (sliding window of 400 nucleotides overlapped by 40 nucleotides) were conducted using SimPlot-v3.5.1, and subregion confirmatory neighbour-joining tree analyses were conducted using MEGAX (Kimura two-parameter model, 1000 bootstrap replicates, ≥70% bootstrap-support value). Exclusive clustering of the HIV-1 recombinants revealed their uniqueness. The recombination analyses illustrated the same unique mosaic pattern with six putative intersubtype recombination breakpoints, seven fragments of subtypes CRF02_AG, G, J and an unclassified fragment. We conclusively characterized the mosaic structure of the novel HIV-1 CRF, named CRF91_cpx, by the Los Alamos HIV Sequence Database. Additionally, we identified a URF of CRF91_cpx with two additional recombination sites, generated by a recombination event between subtype B and CRF91_cpx. Since the identification of CRF91_cpx, two additional patient samples have been entered into the CRF91_cpx transmission cluster, demonstrating active growth.
60 APPLIED LIFE SCIENCES↗
Cristae formation is a mechanical buckling event controlled by the inner mitochondrial membrane lipidome
Cristae are high–curvature structures in the inner mitochondrial membrane (IMM) that are crucial for ATP production. While cristae–shaping proteins have been defined, analogous lipid–based mechanisms have yet to be elucidated. Here, we combine experimental lipidome dissection with multi–scale modeling to investigate how lipid interactions dictate IMM morphology and ATP generation. When modulating phospholipid (PL) saturation in engineered yeast strains, we observed a surprisingly abrupt breakpoint in IMM topology driven by a continuous loss of ATP synthase organization at cristae ridges. We found that cardiolipin (CL) specifically buffers the inner mitochondrial membrane against curvature loss, an effect that is independent of ATP synthase dimerization. To explain this interaction, we developed a continuum model for cristae tubule formation that integrates both lipid and protein–mediated curvatures. This model highlighted a snapthrough instability, which drives IMM collapse upon small changes in membrane properties. We also showed that cardiolipin is essential in low–oxygen conditions that promote PL saturation. These results demonstrate that the mechanical function of cardiolipin is dependent on the surrounding lipid and protein components of the IMM.
59 BASIC BIOLOGICAL SCIENCES↗
Identification of a new circulating recombinant form of human immunodeficiency virus type 1, CRF124_cpx involving subtypes A, G, H, and CRF27_cpx in Angola
Angola, located in Central Africa, has around 320,000 (270,000–380,000) people living with human immunodeficiency virus (HIV)/AIDS, equivalent to 1% of the country’s population at the end of 2021. A previous study conducted in 2012, using Angolan samples collected between 2008 and 2010 revealed a high prevalence of HIV-1 recombinants, around 42% of sequences, with 21% showing the same UH profile in partial pol region which were grouped into a monophyletic cluster with high bootstrap support. Thus, the objective of the present work was to obtain complete genomes of those sequences and characterize them, aiming at a description of a new circulating recombinant form (CRF). Whole blood from nine HIV-1 UH pol -infected individuals had their genomic DNA extracted, and nested PCR was used to amplify seven overlapping fragments targeting the full-length HIV-1 genome. The final classification was based on maximum likelihood trees, and recombination analyses were performed using a bootscan from the Simplot program. BLAST and Los Alamos Database inspections were used to search other similar H-like pol sequences. Complete genome amplification was possible for three samples, partial genomes were obtained for the other three, and only pol was available for the remaining three sequences. Bootscan analysis of the two whole-genome and three partial genome sequences retrieved from people living with HIV/AIDS (PLHIVA) without epidemiological linkage showed the same complex recombination profile involving HIV-1 subtypes A/G/H/CRF27_cpx, with a total of six recombinant breakpoints, aiming to classify a new HIV-1 CRF124_cpx. We found no other full-length HIV-1 genomes with the same mosaic profile; however, we identified 33 partial pol sequences, mainly sampled from Angola between 2001 to 2019, with the same H-like profile. Bayesian analysis of H and H-like pol sequences indicates that CRF124_cpx probably originated in Angola at mid-1970s, indicating that this CRF has been circulating in the country for a long time. In summary, our study describes a new CRF circulating principally in Angola and highlights the importance of continuing molecular surveillance studies, especially in countries with high molecular diversity of HIV.
60 APPLIED LIFE SCIENCES↗
Planning Amidst Uncertainty: Identifying Core CCS Infrastructure Robust to Storage Uncertainty
Carbon Capture and Storage (CCS) is a critical technology for reducing anthropogenic CO2 emissions, but its large-scale deployment is complicated by uncertainties in geological storage performance. These uncertainties pose significant financial and operational risks, as underperforming storage sites can lead to costly infrastructure modifications, inefficient pipeline routing, and economic shortfalls. To address this challenge, we propose a novel optimization workflow that is based on mixed-integer linear programming and explicitly integrates probabilistic modeling of storage uncertainty into CCS infrastructure design. This workflow generates multiple infrastructure scenarios by sampling storage capacity distributions, optimally solving each scenario using a mixed-integer linear programming model, and aggregating results into a heatmap to identify core infrastructure components that have a low likelihood of underperforming. A risk index parameter is introduced to balance trade-offs between cost, CO2 processing capacity, and risk of underperformance, allowing stakeholders to quantify and mitigate uncertainty in CCS planning. Applying this workflow to a CCS dataset from the US Department of Energy’s Carbon Utilization and Storage Partnership project reveals key insights into infrastructure resilience. Reducing the risk index from 15% to 0% is observed to lead to an 83.7% reduction in CO2 processing capacity and a 77.1% decrease in project profit, quantifying the trade-off between risk tolerance and project performance. Furthermore, our results highlight critical breakpoints, where small adjustments in the risk index produce disproportionate shifts in infrastructure performance, providing actionable guidance for decision-makers. Unlike prior approaches that aimed to cheaply repair underperforming infrastructure, our workflow constructs robust CCS networks from the ground up, ensuring cost-effective infrastructure under storage uncertainty. These findings demonstrate the practical relevance of incorporating uncertainty-aware optimization into CCS planning, equipping decision-makers with a tool to make informed project planning decisions.
Olson, Daniel↗
A Robust Segmented Mixed Effect Regression Model for Baseline Electricity Consumption Forecasting
Renewable energy production has been surging around the world in recent years. To mitigate the increasing uncertainty and intermittency of the renewable generation, proactive demand response algorithms and programs are proposed and developed to further improve the utilization of load flexibility and increase the efficiency of power system operation. One of the biggest challenges to efficient control and operation of demand response resources is how to forecast the baseline electricity consumption and estimate the load impact from demand response resources accurately. In this paper, we propose a mixed effect segmented regression model and a new robust estimate for forecasting the baseline electricity consumption in Southern California, USA, by combining the ideas of random effect regression model, segmented regression model, and the least trimmed squares estimate. Since the log-likelihood of the considered model is not differentiable at breakpoints, we propose a new backfitting algorithm to estimate the unknown parameters. The estimation performance of the new estimation procedure has been demonstrated with both simulation studies and the real data application for the electric load baseline forecasting in Southern California.
42 ENGINEERING↗
Ion Acceleration and the Development of a Power-law Energy Spectrum in Magnetic Reconnection
How charged particles are accelerated efficiently and form a power-law energy spectrum in magnetic reconnection is a problem that is not well understood. In a previous paper, it was shown that the electron Kelvin–Helmholtz instability (EKHI) in force-free magnetic reconnection generates fast-expanding vortices that can accelerate electrons in a few tens of ion gyroperiods (less than 1 ms in the solar corona) to form a power-law energy distribution. In this paper, we present a particle-in-cell (PIC) simulation study of ion acceleration in force-free magnetic reconnection in the presence of the EKHI-induced turbulence. We find that ions are not significantly accelerated by the EKHI-induced stochastic electric field until the magnetic vortices expand to sizes comparable to the ion gyroradius. The Alfvén waves generated by the EKHI couple with the magnetic vortices, leading to resonance between the ions inside the magnetic vortices and Alfvén waves and enhanced ion heating. The induced Alfvén wave resonance results in a broken power-law energy spectrum with a breakpoint at $\sim {m}_{i}{v}_{A}^{2}$, where v A is the Alfvén velocity. Here, we show that the process that forms the nonthermal tail is a second-order Fermi mechanism and the mean spectral index is α = (1 + 4 a 2 D/R) /2, where D is the spatial scale of the inductive electric field, R is that of vortices, and a = B g /B 0 , with ratio of guide field B g and asymptotic B 0 .
79 ASTRONOMY AND ASTROPHYSICS↗