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.

The state of parasitoid wasp genomics.

Parasitoid wasps represent a group of parasitic insects with high species diversity that have played a pivotal role in biological control and evolutionary studies. Over the past 20 years, developments in genomics have greatly enhanced our understanding of the biology of these species. Technological leaps in sequencing have facilitated the improvement of genome quality and quantity, leading to the availability of hundreds of parasitoid wasp genomes. Here, we summarize recent progress in parasitoid wasp genomics, focusing on the evolution of genome size (GS) and the genomic basis of several key traits. We also discuss the contributions of genomics in studying venom evolution and endogenization of viruses. Finally, we advocate for increased sequencing and functional research to better understand parasitoid biology and enhance biological control.

The Asymmetrical Fe-O-Se Bonds in Fe2O(SeO3)2 Boosting Bifunctional Oxygen Electrocatalytic Performance for Zinc-Air Battery.

Here Fe2O(SeO3)2/Fe3C@NC catalysts with high performance were fabricated for zinc-air batteries (ZABs). The experimental results confirmed that the existence of Fe-O-Se bonds in Fe2O(SeO3)2 crystal phase, and the Fe-O-Se bonds could obviously enhance ORR and OER catalytic performance of Fe2O(SeO3)2/Fe3C@NC. Density functional theoretical calculations (DFT) confirmed that the Fe2O(SeO3)2 in Fe2O(SeO3)2/Fe3C@NC had a higher d-band center of Fe atom and a lower p-orbital coupling degree with its own lattice O atom than Fe2O3, which leads to Fe site of Fe2O(SeO3)2 being more likely to adsorb external oxygen intermediates. The Fe-O-Se bonds in Fe2O(SeO3)2 results in the modification of coordination environment of Fe atoms and optimizes the adsorption energy of Fe site for oxygen intermediates. Compared with Fe2O3/Fe3C@NC, the Fe2O(SeO3)2/Fe3C@NC showed obvious enhancements of ORR/OER catalytic activities with a half-wave potential of 0.91 V for ORR in 0.1 M KOH electrolyte and a low overpotential of 345 mV for OER at 10 mA cm-2 in a 1.0 M KOH electrolyte. The peak power density and specific capacity of Fe2O(SeO3)2/Fe3C@NC-based ZABs are higher than those of Pt/C+RuO2-ZABs. The above results demonstrate that the asymmetrical Fe-O-Se bonds in Fe2O(SeO3)2 plays a key role in improving the bifunctional catalytic activities of ORR/OER for ZABs.

Fundamental patterns of structural evolution revealed by chromosome-length genomes of cactophilic Drosophila.

A thorough understanding of adaptation and speciation requires model organisms with both a history of ecological and phenotypic study as well as a complete set of genomic resources. In particular, high-quality genome assemblies of ecological model organisms are needed to assess the evolution of genome structure and its role in adaptation and speciation. Here, we generate new genomes of cactophilic Drosophila, a crucial model clade for understanding speciation and ecological adaptation in xeric environments. We generated chromosome-level genome assemblies and complete annotations for seven populations across D. mojavensis, D. arizonae, and D. navojoa. We use this data first to establish the most robust phylogeny for this clade to date, and to assess patterns of molecular evolution across the phylogeny, showing concordance with a priori hypotheses regarding adaptive genes in this system. We then show that structural evolution occurs at constant rate across the phylogeny, varies by chromosome, and is correlated with molecular evolution. These results advance the understanding of the D. mojavensis clade by demonstrating core evolutionary genetic patterns and integrating those patterns to generate new gene-level hypotheses regarding adaptation. Our data are presented in a new public database (cactusflybase.arizona.edu), providing one of the most in-depth resources for the analysis of inter- and intraspecific evolutionary genomic data. Furthermore, we anticipate that the patterns of structural evolution identified here will serve as a baseline for future comparative studies to identify the factors that influence the evolution of genome structure across taxa.

Corrigendum: The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics.

[This corrects the article DOI: 10.3389/ffunb.2023.1214537.].

Oxygen-doped FeP on Ti Foil with Ti3O Interlayer for Efficient and Durable Electrolysis.

The development of electrocatalysts with low cost, high efficiency, and long-term durability is crucial for advancing green hydrogen production. Transition metal phosphides (TMPs) have been proved to be efficient electrocatalyst, while the improvement in the performance and durability of the TMPs remains a big challenge. Employing atmospheric pressure chemical vapor deposition (APCVD) and phosphorization, FeP/Ti electrodes are fabricated featuring controllable oxygen ingredients (O-FeP/Ti). This manipulation of oxygen content fine-tunes the electronic structure of the catalyst, resulting in improved surface reaction kinetics and catalytic activity. The optimized O-FeP-400/Ti exhibits outstanding HER activity with overpotentials of 142 and 159 mV at -10 mA cm-2 in 0.5 M H2SO4 and 1 M KOH, respectively. Notably, the obtained O-FeP/Ti cathode also displays remarkable durability of up to 200 h in acidic electrolyte with surface topography remaining intact. For the first time, the low-valence titanium oxide (Ti3O) interlayer is identified in the composite electrode and ascribed for the superior connection between Ti substrate and the surface O-FeP catalyst, as supported by experimental results and density functional theory (DFT) analysis. This work has expanded the potential applications of transition metal phosphides (TMPs) as a cost-effective, highly efficient and durable catalyst for water splitting.

PTFE as a Multifunctional Binder for High-Current-Density Oxygen Evolution.

Binder plays a crucial role in constructing high-performance electrodes for water electrolysis. While most research has been focused on advancing electrocatalysts, the application of binders in electrode design has yet to be fully explored. Herein, the in situ incorporation of polytetrafluoroethylene (PTFE) as a multifunctional binder, which increases electrochemical active sites, enhances mass transfer, and strengthens the mechanical and chemical robustness of oxygen evolution reaction (OER) electrodes, is reported. The NiFe-LDH@PTFE/NF electrode prepared by co-deposition of PTFE with NiFe-layered double hydroxide onto nickel foam demonstrates exceptional long-term stability with a minimal potential decay rate of 0.034 mV h-1 at 500 mA cm-2 for 1000 h. The alkaline water electrolyzer utilizing NiFe-LDH@PTFE/NF requires only 1.584 V at 500 mA cm-2 and sustains high energy efficiency over 1000 h under industrial operating conditions. This work opens a new path for stabilizing active sites to obtain durable electrodes for OER as well as other electrocatalytic systems.

Introgression drives adaptation to the plateau environment in a subterranean rodent.

BACKGROUND: Introgression has repeatedly been shown to play an important role in the adaptation of species to extreme environments, yet how introgression enables rodents with specialized subterranean lifestyle to acclimatize to high altitudes is still unclear. Myospalacinae is a group of subterranean rodents, among which the high-altitude plateau zokors (Eospalax baileyi) and the low-altitude Gansu zokors (E. cansus) are sympatrically distributed in the grassland ecosystems of the Qinghai-Tibet Plateau (QTP). Together, they provide a model for the study of the role of introgression in the adaptation of low-altitude subterranean rodents to high altitudes. RESULTS: Applying low-coverage whole-genome resequencing and population genetics analyses, we identified evidence of adaptive introgression from plateau zokors into Gansu zokors, which likely facilitated the adaptation of the latter to the high-altitude environment of the QTP. We identified positively selected genes with functions related to energy metabolism, cardiovascular system development, calcium ion transport, and response to hypoxia which likely made critical contributions to adaptation to the plateau environment in both plateau zokors and high-altitude populations of Gansu zokors. CONCLUSIONS: Introgression of genes associated with hypoxia adaptation from plateau zokors may have played a role in the adaptation of Gansu zokors to the plateau environment. Our study provides new insights into the understanding of adaptive evolution of species on the QTP and the importance of introgression in the adaptation of species to high-altitude environments.

Peering through the hedge: Multiple datasets yield insights into the phylogenetic relationships and incongruences in the tribe Lilieae (Liliaceae).

The increasing use of genome-scale data has significantly facilitated phylogenetic analyses, contributing to the dissection of the underlying evolutionary mechanisms that shape phylogenetic incongruences, such as incomplete lineage sorting (ILS) and hybridization. Lilieae, a prominent member of the Liliaceae family, comprises four genera and approximately 260 species, representing 43% of all species within Liliaceae. They possess high ornamental, medicinal and edible values. Yet, no study has explored the validity of various genome-scale data in phylogenetic analyses within this tribe, nor have potential evolutionary mechanisms underlying its phylogenetic incongruences been investigated. Here, transcriptome, Angiosperms353, plastid and mitochondrial data, were collected from 50 to 93 samples of Lilieae, covering all four recognized genera. Multiple datasets were created and used for phylogenetic analyses based on concatenated and coalescent-based methods. Evolutionary rates of different datasets were calculated, and divergence times were estimated. Various approaches, including coalescence simulation, Quartet Sampling (QS), calculation of concordance factors (gCF and sCF), as well as MSCquartets and reticulate network inference, were carried out to infer the phylogenetic discordances and analyze their underlying mechanisms using a reduced 33-taxon dataset. Despite extensive phylogenetic discordances among gene trees, robust phylogenies were inferred from nuclear and plastid data compared to mitochondrial data, with lower synonymous substitution detected in mitochondrial genes than in nuclear and plastid genes. Significant ILS was detected across the phylogeny of Lilieae, with clear evidence of reticulate evolution identified. Divergence time estimation indicated that most of lineages in Lilieae diverged during a narrow time frame (ranging from 5.0 Ma to 10.0 Ma), consistent with the notion of rapid radiation evolution. Our results suggest that integrating transcriptomic and plastid data can serve as cost-effective and efficient tools for phylogenetic inference and evolutionary analysis within Lilieae, and Angiosperms353 data is also a favorable choice. Mitochondrial data are more suitable for phylogenetic analyses at higher taxonomic levels due to their stronger conservation and lower synonymous substitution rates. Significant phylogenetic incongruences detected in Lilieae were caused by both incomplete lineage sorting (ILS) and reticulate evolution, with hybridization and "ghost introgression" likely prevalent in the evolution of Lilieae species. Our findings provide new insights into the phylogeny of Lilieae, enhancing our understanding of the evolution of species in this tribe.

Cautionary tales on the use of proxies to estimate body size and form of extinct animals.

Body size is of fundamental importance to our understanding of extinct organisms. Physiology, ecology and life history are all strongly influenced by body size and shape, which ultimately determine how a species interacts with its environment. Reconstruction of body size and form in extinct animals provides insight into the dynamics underlying community composition and faunal turnover in past ecosystems and broad macroevolutionary trends. Many extinct animals are known only from incomplete remains, necessitating the use of anatomical proxies to reconstruct body size and form. Numerous limitations affecting the appropriateness of these proxies are often overlooked, leading to controversy and downstream inaccuracies in studies for which reconstructions represent key input data. In this perspective, we discuss four prominent case studies (Dunkleosteus, Helicoprion, Megalodon and Perucetus) in which proxy taxa have been used to estimate body size and shape from fragmentary remains. We synthesise the results of these and other studies to discuss nuances affecting the validity of taxon selection when reconstructing extinct organisms, as well as mitigation measures that can ensure the selection of the most appropriate proxy. We argue that these precautionary measures are necessary to maximise the robustness of reconstructions in extinct taxa for better evolutionary and ecological inferences.

Symbiosis between the Javan rhinoceros and slender-billed crow: A novel inferred cleaning mutualism.

Over the past century, the Javan rhinoceroses' (Rhinoceros sondaicus) secluded nature and low population size have led to a gap in knowledge of their ecology. With fewer than 80 individuals surviving in a single population in West Java, Indonesia, the Javan rhinoceros is one of the most critically endangered mammals in the world. As part of a pilot bioacoustics study of the Javan rhinoceros in 2019, we systematically reviewed camera trap footage from the core Javan rhinoceros range in Ujung Kulon National Park (UKNP). In doing so, we discovered a previously unknown interaction between the Javan rhinoceros and the slender-billed crow (Corvus enca), in which the crow finds and eats ectoparasites from the rhinoceros (Figure 1). We describe this interaction and suggest that it may represent a cleaning mutualism with benefits for both the crow and the rhinoceros.

Alkaline saline lakes: A chemical evolution experiment evaluating the stability of formaldehyde in an aqueous saline environment.

Formaldehyde condensation in the presence of a mineral catalyst and under alkaline conditions is considered to be a "messy" chemical system due to its dependence on the complex chemical equilibrium between the reaction intermediates, which has a significant impact on the final products. This chemical system is extremely important in prebiotic chemistry and has been proposed as a potential pathway for carbohydrate formation in the early Earth. Saline and soda lakes are alkaline systems that could concentrate and accumulate a wide variety of ions (such as phosphate) and clay minerals, which can catalyze prebiotic chemical reactions. These geological environments have recently been suggested as ideal environments in which prebiotic chemical reactions could have occurred. This study uses Lake Alchichica in Mexico as a physicochemical analog of an early Archean saline lake to examine the stability of formaldehyde in these aqueous saline environments. Formaldehyde decomposes into sugar-like and CHO molecules in alkaline, high-salinity environments depending on the minerals phases present. As phosphate ion (HPO4 2-) is available in the aqueous medium, the results of our experiments also imply that phosphorylation processes may have occurred in these natural settings.

Coffee arabica research (1932-2023): Performance, thematic evolution and mapping, global landscape, and emerging trends.

Background: Research on Coffea arabica focuses on various aspects, including genetics, breeding, climate change resilience, pest and disease management, agronomy, sensory analysis, and sustainability. This study aims to analyze the hotspots, conceptual map and dynamicity, global landscape, and emerging trends in Coffea arabica research (CA-R). Methods: A comprehensive dataset comprising data-driven articles (N = 3967) from 1932 to 2023 was extracted from Scopus using predefined search terms. VOSviewer and Bibliometrix applications were utilized to analyze the data. Thematic evolution was examined by identifying shifts in research focus over time. The global landscape was assessed by examining comparative productivity and collaborative dynamics. Highly-cited CA-R was identified to highlight key findings in specific research areas. Results: The analysis revealed a steady growth of CA-R (annual growth rate = 6.53 %), with strong international collaboration (international co-authorships = 29.35 %) and significant contributions from various countries. Brazil leads the way with 1601 publications, accounting for 28.55 % of the total. Recognizable CA-R focused on important areas such as pollination, shade management, nanotechnology applications, roasting effects, disease management, and environmental impacts. Thematic analysis identified five distinct clusters representing different CA-R themes: "coffee", "coffea," "fermentation," "Coffea arabica," and "climate change." Emerging themes such as "in vitro culture," "sustainable agriculture," "climate change," and "coffee berry borer" were also identified. Conclusion: The current findings enhance our understanding of CA-R and lay the groundwork for future studies in the coffee industry.

Integrating frontiers: a holistic, quantum and evolutionary approach to conquering cancer through systems biology and multidisciplinary synergy.

Cancer therapy is facing increasingly significant challenges, marked by a wide range of techniques and research efforts centered around somatic mutations, precision oncology, and the vast amount of big data. Despite this abundance of information, the quest to cure cancer often seems more elusive, with the "war on cancer" yet to deliver a definitive victory. A particularly pressing issue is the development of tumor treatment resistance, highlighting the urgent need for innovative approaches. Evolutionary, Quantum Biology and System Biology offer a promising framework for advancing experimental cancer research. By integrating theoretical studies, translational methods, and flexible multidisciplinary clinical research, there's potential to enhance current treatment strategies and improve outcomes for cancer patients. Establishing stronger links between evolutionary, quantum, entropy and chaos principles and oncology could lead to more effective treatments that leverage an understanding of the tumor's evolutionary dynamics, paving the way for novel methods to control and mitigate cancer. Achieving these objectives necessitates a commitment to multidisciplinary and interprofessional collaboration at the heart of both research and clinical endeavors in oncology. This entails dismantling silos between disciplines, encouraging open communication and data sharing, and integrating diverse viewpoints and expertise from the outset of research projects. Being receptive to new scientific discoveries and responsive to how patients react to treatments is also crucial. Such strategies are key to keeping the field of oncology at the forefront of effective cancer management, ensuring patients receive the most personalized and effective care. Ultimately, this approach aims to push the boundaries of cancer understanding, treating it as a manageable chronic condition, aiming to extend life expectancy and enhance patient quality of life.

The plastomes of Lepismium cruciforme (Vell.) Miq and Schlumbergera truncata (Haw.) Moran reveal tribe-specific rearrangements and the first loss of the trnT-GGU gene in Cactaceae.

BACKGROUND: Recent studies have revealed atypical features in the plastomes of the family Cactaceae, the largest lineage of succulent species adapted to arid and semi-arid regions. Most plastomes sequenced to date are from short-globose and cylindrical cacti, while little is known about plastomes of epiphytic cacti. Published cactus plastomes reveal reduction and complete loss of IRs, loss of genes, pseudogenization, and even degeneration of tRNA structures. Aiming to contribute with new insights into the plastid evolution of Cactaceae, particularly within the tribe Rhipsalideae, we de novo assembled and analyzed the plastomes of Lepismium cruciforme and Schlumbergera truncata, two South American epiphytic cacti. METHODS AND RESULTS: Our data reveal many gene losses in both plastomes and the first loss of functionality of the trnT-GGU gene in Cactaceae. The trnT-GGU is a pseudogene in L. cruciforme plastome and appears to be degenerating in the tribe Rhipsalideae. Although the plastome structure is conserved among the species of the tribe Rhipsalideae, with tribe-specific rearrangements, we mapped around 200 simple sequence repeats and identified nine nucleotide polymorphism hotspots, useful to improve the phylogenetic resolutions of the Rhipsalideae. Furthermore, our analysis indicated high gene divergence and rapid evolution of RNA editing sites in plastid protein-coding genes in Cactaceae. CONCLUSIONS: Our findings show that some characteristics of the Rhipsalideae tribe are conserved, such as plastome structure with IRs containing only the ycf2 and two tRNA genes, structural degeneration of the trnT-GGU gene and ndh complex, and lastly, pseudogenization of rpl33 and rpl23 genes, both plastid translation-related genes.

Origin and evolution of microvilli.

BACKGROUND INFORMATION: Microvilli are finger-like, straight, and stable cellular protrusions that are filled with F-actin and present a stereotypical length. They are present in a broad range of cell types across the animal tree of life and mediate several fundamental functions, including nutrient absorption, photosensation, and mechanosensation. Therefore, understanding the origin and evolution of microvilli is key to reconstructing the evolution of animal cellular form and function. Here, we review the current state of knowledge on microvilli evolution and perform a bioinformatic survey of the conservation of genes encoding microvillar proteins in animals and their unicellular relatives. RESULTS: We first present a detailed description of mammalian microvilli based on two well-studied examples, the brush border microvilli of enterocytes and the stereocilia of hair cells. We also survey the broader diversity of microvilli and discuss similarities and differences between microvilli and filopodia. Based on our bioinformatic survey coupled with carefully reconstructed molecular phylogenies, we reconstitute the order of evolutionary appearance of microvillar proteins. We document the stepwise evolutionary assembly of the "molecular microvillar toolkit" with notable bursts of innovation at two key nodes: the last common filozoan ancestor (correlated with the evolution of microvilli distinct from filopodia) and the last common choanozoan ancestor (correlated with the emergence of inter-microvillar adhesions). CONCLUSION AND SIGNIFICANCE: We conclude with a scenario for the evolution of microvilli from filopodia-like ancestral structures in unicellular precursors of animals.

Phylogeny, adaptive evolution, and taxonomy of Acronema (Apiaceae): evidence from plastid phylogenomics and morphological data.

Introduction: The genus Acronema, belonging to Apiaceae, includes approximately 25 species distributed in the high-altitude Sino-Himalayan region from E Nepal to SW China. This genus is a taxonomically complex genus with often indistinct species boundaries and problematic generic delimitation with Sinocarum and other close genera, largely due to the varied morphological characteristics. Methods: To explore the phylogenetic relationships and clarify the limits of the genus Acronema and its related genera, we reconstructed a reliable phylogenetic framework with high support and resolution based on two molecular datasets (plastome data and ITS sequences) and performed morphological analyses. Results: Both phylogenetic analyses robustly supported that Acronema was a non-monophyletic group that fell into two clades: Acronema Clade and East-Asia Clade. We also newly sequenced and assembled sixteen Acronema complete plastomes and performed comprehensively comparative analyses for this genus. The comparative results showed that the plastome structure, gene number, GC content, codon bias patterns were high similarity, but varied in borders of SC/IR and we identified six different types of SC/IR border. The SC/IR boundaries of Acronema chienii were significantly different from the other Acronema members which was consistent with the type VI pattern in the genus Tongoloa. We also identified twelve potential DNA barcode regions (ccsA, matK, ndhF, ndhG, psaI, psbI, rpl32, rps15, ycf1, ycf3, psaI-ycf4 and psbM-trnD) for species identification in Acronema. The molecular evolution of Acronema was relatively conservative that only one gene (petG) was found to be under positive selection (ω = 1.02489). Discussion: The gene petG is one of the genes involved in the transmission of photosynthetic electron chains during photosynthesis, which plays a crucial role in the process of photosynthesis in plants. This is also a manifestation of the adaptive evolution of plants in high-altitude areas to the environment. In conclusion, our study provides novel insights into the plastome adaptive evolution, phylogeny, and taxonomy of genus Acronema.

Gyrovirus: current status and challenge.

Gyrovirus (GyV) is small, single-stranded circular DNA viruses that has recently been assigned to the family Anelloviridae. In the last decade, many GyVs that have an apparent pan-tropism at the host level were identified by high-throughput sequencing (HTS) technology. As of now, they have achieved global distribution. Several species of GyVs have been demonstrated to be pathogenic to poultry, particularly chicken anemia virus (CAV), causing significant economic losses to the global poultry industry. Although GyVs are highly prevalent in various birds worldwide, their direct involvement in the etiology of specific diseases and the reasons for their ubiquity and host diversity are not fully understood. This review summarizes current knowledge about GyVs, with a major emphasis on their morphofunctional properties, epidemiological characteristics, genetic evolution, pathogenicity, and immunopathogenesis. Additionally, the association between GyVs and various diseases, as well as its potential impact on the poultry industry, have been discussed. Future prevention and control strategies have also been explored. These insights underscore the importance of conducting research to establish a virus culture system, optimize surveillance, and develop vaccines for GyVs.