Disentangling microbial coupled fillers mechanisms for the permeable layer optimization process in multi-soil-layering systems.

The multi-soil-layering (MSL) systems is an emerging solution for environmentally-friendly and cost-effective treatment of decentralized rural domestic wastewater. However, the role of the seemingly simple permeable layer has been overlooked, potentially holding the breakthroughs or directions to addressing suboptimal nitrogen removal performance in MSL systems. In this paper, the mechanism among diverse substrates (zeolite, green zeolite and biological ceramsite) coupled microorganisms in different systems (activated bacterial powder and activated sludge) for rural domestic wastewater purification was investigated. The removal efficiencies performed by zeolite coupled with microorganisms within 3 days were 93.8% for COD, 97.1% for TP, and 98.8% for NH4+-N. Notably, activated sludge showed better nitrification and comprehensive performance than specialized nitrifying bacteria powder. Zeolite attained an impressive 89.4% NH4+-N desorption efficiency, with a substantive fraction of NH4+-N manifesting as exchanged ammonium. High-throughput 16S rRNA gene sequencing revealed that aerobic and parthenogenetic anaerobic bacteria dominated the reactor, with anaerobic bacteria conspicuously absent. And the heterotrophic nitrification-aerobic denitrification (HN-AD) process was significant, with the presence of denitrifying phosphorus-accumulating organisms (DPAOs) for simultaneous nitrogen and phosphorus removal. This study not only raises awareness about the importance of the permeable layer and enhances comprehension of the HN-AD mechanism in MSL systems, but also provides valuable insights for optimizing MSL system construction, operation, and rural domestic wastewater treatment.

From the cauldron of conflict: Endogenous gene regulation by piRNA and other modes of adaptation enabled by selfish transposable elements.

Transposable elements (TEs) provide a prime example of genetic conflict because they can proliferate in genomes and populations even if they harm the host. However, numerous studies have shown that TEs, though typically harmful, can also provide fuel for adaptation. This is because they code functional sequences that can be useful for the host in which they reside. In this review, I summarize the "how" and "why" of adaptation enabled by the genetic conflict between TEs and hosts. In addition, focusing on mechanisms of TE control by small piwi-interacting RNAs (piRNAs), I highlight an indirect form of adaptation enabled by conflict. In this case, mechanisms of host defense that regulate TEs have been redeployed for endogenous gene regulation. I propose that the genetic conflict released by meiosis in early eukaryotes may have been important because, among other reasons, it spurred evolutionary innovation on multiple interwoven trajectories - on the part of hosts and also embedded genetic parasites. This form of evolution may function as a complexity generating engine that was a critical player in eukaryotic evolution.

Magnesium-promoted rapid self-reconstruction of NiFe-based electrocatalysts toward efficient oxygen evolution.

The acceleration of active sites formation through surface reconstruction is widely acknowledged as the crucial factor in developing high-performance oxygen evolution reaction (OER) catalysts for water splitting. Herein, a simple one-step corrosion method and magnesium (Mg)-promoted strategy are reported to develop the NiFe-based catalyst with enhanced OER performance. The Mg is introduced in NiFe materials to preparate a "pre-catalyst" Mg-Ni/Fe2O3. In-situ Raman shows that Mg doping would accelerate the self-reconstruction of Ni/Fe2O3 to form active NiOOH species during OER. In-situ infrared indicates that Mg doping benefits the formation of *OOH intermediate. Theoretical analysis further confirms that Mg doping can optimize the adsorption of oxygen intermediates, accelerating the OER kinetics. Accordingly, the Mg-Ni/Fe2O3 catalyst exhibits excellent OER performance with overpotential of 168 mV at 10 mA cm-2. The anion exchange membrane water electrolyzer achieved 200 mA cm-2 at voltage of 1.53 V, showing excellent stability over 500 h as well. This work demonstrates the potential of Mg-promoted strategy in regulating the activity of transition metal-based OER electrocatalysts.

An ancient role for CYP73 monooxygenases in phenylpropanoid biosynthesis and embryophyte development.

The phenylpropanoid pathway is one of the plant metabolic pathways most prominently linked to the transition to terrestrial life, but its evolution and early functions remain elusive. Here, we show that activity of the t-cinnamic acid 4-hydroxylase (C4H), the first plant-specific step in the pathway, emerged concomitantly with the CYP73 gene family in a common ancestor of embryophytes. Through structural studies, we identify conserved CYP73 residues, including a crucial arginine, that have supported C4H activity since the early stages of its evolution. We further demonstrate that impairing C4H function via CYP73 gene inactivation or inhibitor treatment in three bryophyte species-the moss Physcomitrium patens, the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis-consistently resulted in a shortage of phenylpropanoids and abnormal plant development. The latter could be rescued in the moss by exogenous supply of p-coumaric acid, the product of C4H. Our findings establish the emergence of the CYP73 gene family as a foundational event in the development of the plant phenylpropanoid pathway, and underscore the deep-rooted function of the C4H enzyme in embryophyte biology.

Direct Identification of O─O Bond Formation Through Three-Step Oxidation During Water Splitting by Operando Soft X-ray Absorption Spectroscopy.

Anionic redox allows the direct formation of O─O bonds from lattice oxygens and provides higher catalytic in the oxygen evolution reaction (OER) than does the conventional metal ion mechanism. While previous theories have predicted and experiments have suggested the possible O─O bond, it has not yet been directly observed in the OER process. In this study, operando soft X-ray absorption spectroscopy (sXAS) at the O K-edge and the operando Raman spectra is performed on layered double CoFe hydroxides (LDHs) after intercalation with [Cr(C2O4)3]3-, and revealed a three-step oxidation process, staring from Co2+ to Co3+, further to Co4+ (3d6L), and ultimately leading to the formation of O─O bonds and O2 evolution above a threshold voltage (1.4 V). In contrast, a gradual oxidation of Fe is observed in CoFe LDHs. The OER activity exhibits a significant enhancement, with the overpotential decreasing from 300 to 248 mV at 10 mA cm-2, following the intercalation of [Cr(C2O4)3]3- into CoFe LDHs, underscoring a crucial role of anionic redox in facilitating water splitting.

Population bottlenecks and sexual recombination shape diatom microevolution.

Diatoms are single-celled organisms that contribute approximately 20% of the global primary production and play a crucial role in biogeochemical cycles and trophic chains. Despite their ecological importance, our knowledge of microevolution is limited. We developed a model using the SLiM evolutionary framework to address this knowledge gap. As a reference, we used the diatom Pseudo-nitzschia multistriata, which has been extensively studied in the Gulf of Naples. Our model recapitulates what we observe in natural populations, with microevolutionary processes that occur annually during a three-stage bloom phase. Interestingly, we found that non-bloom phases allow the population to maintain sex-generated diversity produced during blooms. This finding suggests that non-bloom phases are critical to counteract bloom-related pressures and mitigate genetic divergence at the species level. Moreover, our model showed that despite the consistent genetic differentiation during bloom phases, the population tends to return to pre-bloom states. While our model is limited to neutral dynamics, our study provides valuable insights into diatoms' microevolution, paving the way to explore the ecological implications of the life history dynamics of these organisms.

Spatial and temporal evolution characteristics and factors of heat vulnerability in the Pearl River Delta urban agglomeration from 2001 to 2022.

To explore the spatiotemporal evolution characteristics of heat vulnerability in the Pearl River Delta urban agglomeration during heatwave disasters, this research employs the Entropy Weight Method (EWM) to calculate the heat vulnerability assessment results for nine cities in the region spanning from 2001 to 2022. Through the application of kernel density estimation, Moran's I, and the Geographically and Temporally Weighted Regression (GTWR) model, which is proven to be superior to traditional model such as OLS, this study analyzes the dynamic distribution patterns of heat vulnerability in the study area and dissect the trends of influencing factors. The results reveal that from 2001 to 2022, the overall heat vulnerability index in the study area demonstrates a fluctuating downward trend. Key contributors to heat vulnerability include high-frequency and long-duration heatwaves, population sensitivity, and changes in residents' consumption levels. Throughout this period of development, the disparity in heat vulnerability among cities has gradually widened, indicating an overall pattern of uneven development in the region. Future attention should be focused on formulating heat adaptation strategies in areas with high vulnerability to enhance the overall sustainability of the study area.

Adaptation of turnip mosaic virus to Arabidopsis thaliana involves rewiring of VPg-host proteome interactions.

The outcome of a viral infection depends on a complex interplay between the host physiology and the virus, mediated through numerous protein-protein interactions. In a previous study, we used high-throughput yeast two-hybrid (HT-Y2H) to identify proteins in Arabidopsis thaliana that bind to the proteins encoded by the turnip mosaic virus (TuMV) genome. Furthermore, after experimental evolution of TuMV lineages in plants with mutations in defense-related or proviral genes, most mutations observed in the evolved viruses affected the VPg cistron. Among these mutations, D113G was a convergent mutation selected in many lineages across different plant genotypes, including cpr5-2 with constitutive expression of systemic acquired resistance. In contrast, mutation R118H specifically emerged in the jin1 mutant with affected jasmonate signaling. Using the HT-Y2H system, we analyzed the impact of these two mutations on VPg's interaction with plant proteins. Interestingly, both mutations severely compromised the interaction of VPg with the translation initiation factor eIF(iso)4E, a crucial interactor for potyvirus infection. Moreover, mutation D113G, but not R118H, adversely affected the interaction with RHD1, a zinc-finger homeodomain transcription factor involved in regulating DNA demethylation. Our results suggest that RHD1 enhances plant tolerance to TuMV infection. We also discuss our findings in a broad virus evolution context.

The ancient Z-DNA and Z-RNA specific Zα fold has evolved modern roles in immunity and transcription through the natural selection of flipons.

The Zα fold specifically binds to both Z-DNA and Z-RNA, left-handed nucleic acid structures that form under physiological conditions and are encoded by flipons. I trace the Zα fold back to unicellular organisms representing all three domains of life and to the realm of giant nucleocytoplasmic DNA viruses (NCVs). The canonical Zα fold is present in the earliest known holozoan unicellular symbiont Capsaspora owczarzaki and persists in vertebrates and some invertebrates, but not in plants or fungi. In metazoans, starting with porifera, Zα is incorporated into the double-stranded RNA editing enzyme ADAR and reflects an early symbiont relationship with NCV. In vertebrates, Zα is also present in ZBP1 and PKZ proteins that recognize host-derived Z-RNAs to defend against modern-day viruses. A related Zα fold, also likely to bind Z-DNA, is present in proteins thought to modulate gene expression, including a subset of prokaryote arsR proteins and the p15 (PC4) family present in algae. Other Zα variants that probably play a more general role in the reinitiation of transcription include the archaeal and human transcription factor E and the human RNA polymerase 3 subunit C proteins. The roles in immunity and transcription underlie the natural selection of flipons.

Adaptive radiation without independent stages of trait evolution in a group of Caribbean anoles.

Adaptive radiation involves diversification along multiple trait axes, producing phenotypically diverse, species-rich lineages. Theory generally predicts that multi-trait evolution occurs via a 'stages' model, with some traits saturating early in a lineage's history, and others diversifying later. Despite its multidimensional nature, however, we know surprisingly little about how different suites of traits evolve during adaptive radiation. Here, we investigated the rate, pattern, and timing of morphological and physiological evolution in the anole lizard adaptive radiation from the Caribbean island of Hispaniola. Rates and patterns of morphological and physiological diversity are largely unaligned, corresponding to independent selective pressures associated with structural and thermal niches. Cold tolerance evolution reflects parapatric divergence across elevation, rather than niche partitioning within communities. Heat tolerance evolution and the preferred temperature evolve more slowly than cold tolerance, reflecting behavioral buffering, particularly in edge-habitat species (a pattern associated with the Bogert effect). In contrast to the nearby island of Puerto Rico, closely related anoles on Hispaniola do not sympatrically partition thermal niche space. Instead, allopatric and parapatric separation across biogeographic and environmental boundaries serves to keep morphologically similar close relatives apart. The phenotypic diversity of this island's adaptive radiation accumulated largely as a by-product of time, with surprisingly few exceptional pulses of trait evolution. A better understanding of the processes that guide multidimensional trait evolution (and nuance therein) will prove key in determining whether the stages model should be considered a common theme of adaptive radiation.

ZnMn2(PO4)2·nH2O: An H2O-Imbedding-Activated Cathode for Robust Aqueous Zinc-Ion Batteries.

Component modulation endows Mn-based electrodes with prominent energy storage properties due to their adjustable crystal structure characteristics. Herein, ZnMn2(PO4)2·nH2O (ZMP·nH2O) was obtained by a hydration reaction from ZnMn2(PO4)2 (ZMP) during an electrode-aging evolution. Benefiting from the introduction of lattice H2O molecules into the ZMP structure, the ion transmission path has been expanded along with the extended d-spacing, which will further facilitate the ZMP → ZMP·nH2O phase evolution and electrochemical reaction kinetics. Meanwhile, the hydrogen bond can be generated between H2O and O in PO43-, which strengthens the structure stability of ZMP·nH2O and lowers the conversion barrier from ZMP to ZMP·4H2O during the Zn2+ uptake/removal process. Thereof, ZMP·nH2O delivers enhanced electrochemical reaction kinetics with robust structure tolerance (106.52 mA h g-1 at 100 mA g-1 over 620 cycles). This high-energy aqueous Zn||ZMP·nH2O battery provides a facile strategy for engineering and exploration of high-performance ZIBs to realize the practical application of Mn-based cathodes.

Population diversity control based differential evolution algorithm using fuzzy system for noisy multi-objective optimization problems.

The objective measurements of the real-world optimization problems are mostly subject to noise which occurs due to several reasons like human measurement or environmental factors. The performance of the optimization algorithm gets affected if the effect of noise is higher than the negligible limit. The previous noise handling optimization algorithms use a large population size or multiple sampling at same region which increases the total count of function evaluations, and few methods work for a particular problem type. To address the above challenges, a Differential Evolution based Noise handling Optimization algorithm (NDE) to solve and optimize noisy bi-objective optimization problems is proposed. NDE is a Differential Evolution (DE) based optimization algorithm where the strategies for trial vector generation and the control parameters of DE algorithm are self-adapted using fuzzy inference system to improve the population diversity along the evolution process. In NDE, explicit averaging based method for denoising is used when the noise level is higher than negligible limit. Extending noise handling method enhances the performance of the optimization algorithm in solving real world optimization problems. To improve the convergence characteristics of the proposed algorithm, a restricted local search procedure is proposed. The performance of NDE algorithm is experimented using DTLZ and WFG problems, which are benchmark bi-objective optimization problems. The obtained results are compared with other SOTA algorithm using modified Inverted Generational Distance and Hypervolume performance metrics, from which it is confirmed that the proposed NDE algorithm is better in solving noisy bi-objective problems when compared to the other methods. To further strengthen the claim, statistical tests are conducted using the Wilcoxon and Friedman rank tests, and the proposed NDE algorithm shows significance over the other algorithms rejecting the null hypothesis.

Convergent expansions of keystone gene families drive metabolic innovation in a major eukaryotic clade.

Many remarkable innovations have repeatedly occurred across vast evolutionary distances. When convergent traits emerge on the tree of life, they are sometimes driven by the same underlying gene families, while other times many different gene families are involved. Conversely, a gene family may be repeatedly recruited for a single trait or many different traits. To understand the general rules governing convergence at both genomic and phenotypic levels, we systematically tested associations between 56 binary metabolic traits and gene count in 14,710 gene families from 993 species of Saccharomycotina yeasts. Using a recently developed phylogenetic approach that reduces spurious correlations, we discovered that gene family expansion and contraction was significantly linked to trait gain and loss in 45/56 (80%) of traits. While 601/746 (81%) of significant gene families were associated with only one trait, we also identified several 'keystone' gene families that were significantly associated with up to 13/56 (23%) of all traits. These results indicate that metabolic innovations in yeasts are governed by a narrow set of major genetic elements and mechanisms.

Evolutionary changes in cognition due to fisheries mortality?

Fish experiencing harvest mortality often evolve a fast life-history that prioritizes investment in current versus future reproduction, thereby potentially limiting energetic investment in the brain. Fisheries may also select for shy fish that are less willing to learn, or directly select fish with poor cognitive ability. The resulting evolutionary changes can alter the cognitive performance of individuals and affect fish populations and fisheries quality.

Transcriptomic responses and evolutionary insights of deep-sea and shallow-water mussels under high hydrostatic pressure condition.

Marine mussels inhabit a wide range of ocean depths, necessitating unique adaptations to cope with varying hydrostatic pressures. This study investigates the transcriptomic responses and evolutionary adaptations of the deep-sea mussel Gigantidas platifrons and the shallow-water mussel Mytilus galloprovincialis to high hydrostatic pressure (HHP) conditions. By exposing atmospheric pressure (AP) acclimated G. platifrons and M. galloprovincialis to HHP, we aim to simulate extreme environmental challenges and assess their adaptive mechanisms. Through comparative transcriptomic analysis, we identified both conserved and species-specific mechanisms of adaptation, with a notable change in gene expression associated with immune system, substance transport, protein ubiquitination, apoptosis, lipid metabolism and antioxidant processes in both species. G. platifrons demonstrated an augmented lipid metabolism, whereas M. galloprovincialis exhibited a dampened immune function. Additionally, the expressed pattern of deep-sea mussel G. platifrons were more consistent than shallow-water mussel M. galloprovincialis under hydrostatic pressures changed conditions which corresponding the long-term living stable deep-sea environment. Moreover, evolutionary analysis pinpointed positively selected genes in G. platifrons that are linked to transmembrane transporters, DNA repair and replication, apoptosis, ubiquitination which are important to cell structural integrity, substances transport, and cellular growth regulation. This indicates a specialized adaptation strategy in G. platifrons to cope with the persistent HHP conditions of the deep sea. These results offer significant insights into the molecular underpinnings of mussel adaptation to varied hydrostatic conditions and enhance our comprehension of the evolutionary forces driving their depth-specific adaptations.

Molecular epidemiology and phylogenetic analysis of influenza viruses A (H3N2) and B/Victoria during the COVID-19 pandemic in Guangdong, China.

BACKGROUND: Non-pharmaceutical measures and travel restrictions have halted the spread of coronavirus disease 2019 (COVID-19) and influenza. Nonetheless, with COVID-19 restrictions lifted, an unanticipated outbreak of the influenza B/Victoria virus in late 2021 and another influenza H3N2 outbreak in mid-2022 occurred in Guangdong, southern China. The mechanism underlying this phenomenon remains unknown. To better prepare for potential influenza outbreaks during COVID-19 pandemic, we studied the molecular epidemiology and phylogenetics of influenza A(H3N2) and B/Victoria that circulated during the COVID-19 pandemic in this region. METHODS: From January 1, 2018 to December 31, 2022, we collected throat swabs from 173,401 patients in Guangdong who had acute respiratory tract infections. Influenza viruses in the samples were tested using reverse transcription-polymerase chain reaction, followed by subtype identification and sequencing of hemagglutinin (HA) and neuraminidase (NA) genes. Phylogenetic and genetic diversity analyses were performed on both genes from 403 samples. A rigorous molecular clock was aligned with the phylogenetic tree to measure the rate of viral evolution and the root-to-tip distance within strains in different years was assessed using regression curve models to determine the correlation. RESULTS: During the early period of COVID-19 control, various influenza viruses were nearly undetectable in respiratory specimens. When control measures were relaxed in January 2020, the influenza infection rate peaked at 4.94% (39/789) in December 2021, with the influenza B/Victoria accounting for 87.18% (34/39) of the total influenza cases. Six months later, the influenza infection rate again increased and peaked at 11.34% (255/2248) in June 2022; influenza A/H3N2 accounted for 94.51% (241/255) of the total influenza cases in autumn 2022. The diverse geographic distribution of HA genes of B/Victoria and A/H3N2 had drastically reduced, and most strains originated from China. The rate of B/Victoria HA evolution (3.11 × 10-3, P < 0.05) was 1.7 times faster than before the COVID-19 outbreak (1.80 × 10-3, P < 0.05). Likewise, the H3N2 HA gene's evolution rate was 7.96 × 10-3 (P < 0.05), which is 2.1 times faster than the strains' pre-COVID-19 evolution rate (3.81 × 10-3, P < 0.05). CONCLUSIONS: Despite the extraordinarily low detection rate of influenza infection, concealed influenza transmission may occur between individuals during strict COVID-19 control. This ultimately leads to the accumulation of viral mutations and accelerated evolution of H3N2 and B/Victoria viruses. Monitoring the evolution of influenza may provide insights and alerts regarding potential epidemics in the future.

Constructing Co4(SO4)4 Clusters within Metal-Organic Frameworks for Efficient Oxygen Electrocatalysis.

Multinuclear metal clusters are ideal candidates to catalyze small molecule activation reactions involving the transfer of multiple electrons. However, synthesizing active metal clusters is a big challenge. Herein, on constructing an unparalleled Co4(SO4)4 cluster within porphyrin-based metal-organic frameworks (MOFs) and the electrocatalytic features of such Co4(SO4)4 clusters for the oxygen evolution reaction (OER) and oxygen reduction reaction (ORR) is reported. The reaction of CoII sulfate and metal complexes of tetrakis(4-pyridyl)porphyrin under solvothermal conditions afforded Co4-M-MOFs (M═Co, Cu, and Zn). Crystallographic studies revealed that these Co4-M-MOFs have the same framework structure, having the Co4(SO4)4 clusters connected by metalloporphyrin units through Co─Npyridyl bonds. In the Co4(SO4)4 cluster, the four CoII ions are chemically and symmetrically equivalent and are each coordinated with four sulfate O atoms to give a distorted cube-like structure. Electrocatalytic studies showed that these Co4-M-MOFs are all active for electrocatalytic OER and ORR. Importantly, by regulating the activity of the metalloporphyrin units, it is confirmed that the Co4(SO4)4 cluster is active for oxygen electrocatalysis. With the use of Co porphyrins as connecting units, Co4-Co-MOF displays the highest electrocatalytic activity in this series of MOFs by showing a 10 mA cm-2 OER current density at 357 mV overpotential and an ORR half-wave potential at 0.83 V versus reversible hydrogen electrode (RHE). Theoretical studies revealed the synergistic effect of two proximal Co atoms in the Co4(SO4)4 cluster in OER by facilitating the formation of O─O bonds. This work is of fundamental significance to present the construction of Co4(SO4)4 clusters in framework structures for oxygen electrocatalysis and to demonstrate the cooperation between two proximal Co atoms in such clusters during the O─O bond formation process.

In Situ Synthesis of High-Entropy (Oxy)Hydroxides Via Electrochemical Reconfiguration As Catalysts For Efficient Water Oxidation.

Surface reconstruction plays a pivotal role in enhancing the activity of the oxygen evolution reaction (OER), particularly in terms of the structural transformation from metal oxides to (oxy)hydroxides. Herein, a novel (oxy)hydroxide (FeCoNiCuMoOOH) with high entropy is developed by the electrochemical reconstitution of corresponding oxide (FeCoNiCuMoOx). Significantly, the FeCoNiCuMoOOH exhibits much higher OER electrocatalytic activity and durability with an overpotential as low as 201 mV at a current density of 10 mA cm-2, and with a Tafel slope of 39.4 mV dec-1. The FeCoNiCuMoOOH/NF presents high stability when testing under a constant current at 100 mA cm-2 within 1000 h. The surface reconstruction is a process of dissolution-reprecipitation of Cu and Mo species and co-hydroxylation of five metal species, which ultimately leads to the formation of FeCoNiCuMoOOH from FeCoNiCuMoOx. This study holds great significance in the realm of designing high-entropy (oxy)hydroxides catalysts with exceptional activity and stability for OER.