Reference Species Research Articles

Species identification of modern and archaeological shark and ray skeletal tissues using collagen peptide mass fingerprinting

IntroductionElasmobranchs, such as sharks and rays, are among the world’s most endangered vertebrates, with over 70% loss in abundance over the past 50 years due to human impacts. Zooarchaeological baselines of elasmobranch diversity, distribution, and exploitation hold great promise for contributing essential historical contexts in the assessment of contemporary patterns in their taxonomic diversity and vulnerability to human-caused extinction. Yet, the historical ecology of elasmobranchs receives relatively less archaeological attention compared to that of ray-finned fishes or marine mammals, largely due to issues of taxonomic resolution across zooarchaeological identifications.MethodsWe explore the use of Zooarchaeology by Mass Spectrometry (ZooMS) for species identification in this unstudied group, using an archaeological case study from the marine environments of the Florida Keys, a marine biodiversity hotspot that is home to an array of elasmobranch species and conservation efforts. By comparison with 39 modern reference species, we could distinguish 12 taxa within the zooarchaeological assemblage from the Clupper archaeological site (Upper Matecumbe Key) that included nine sharks, two rays and a sawfish.Results and discussionThe results indicate that, through additional complexity of the collagen peptide mass fingerprint, obtained due to the presence of the cartilaginous type II collagen, ZooMS collagen peptide mass fingerprinting provides exceptionally high taxonomic resolution in this group, yielding species-level identifications in all cases where sufficient reference material was used. This case study also highlights the added value of ZooMS for taxa that are more difficult to distinguish in zooarchaeological analyses, such as vertebrae of the Atlantic sharpnose shark (Rhizoprionodon terraenovae) and the hammerhead sharks (Sphyrna spp.) in the Florida Keys. Therefore, the application of collagen peptide mass fingerprinting to elasmobranchs offers great potential to improve our understanding of their archaeological past and historical ecology.

A nuclear phylogenomic tree of grasses (Poaceae) recovers current classification despite gene tree incongruence.

Grasses (Poaceae) comprise c. 11 800 species and are central to human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new reference species tree of the family. We inferred a comprehensive species tree of grasses by combining new and published sequences for 331 nuclear genes from genome, transcriptome, target enrichment and shotgun data. Our 1153-tip tree covers 79% of grass genera (including 21 genera sequenced for the first time) and all but two small tribes. We compared it to a newly inferred 910-tip plastome tree. We recovered most of the tribes and subfamilies previously established, despite pervasive incongruence among nuclear gene trees. The early diversification of the PACMAD clade could represent a hard polytomy. Gene tree-species tree reconciliation suggests that reticulation events occurred repeatedly. Nuclear-plastome incongruence is rare, with very few cases of supported conflict. We provide a robust framework for the grass tree of life to support research on grass evolution, including modes of reticulation, and genetic diversity for sustainable agriculture.

Evolution of g-type lysozymes in metazoa: insights into immunity and digestive adaptations.

Exploring the evolutionary dynamics of lysozymes is critical for advancing our knowledge of adaptations in immune and digestive systems. Here, we characterize the distribution of a unique class of lysozymes known as g-type, which hydrolyze key components of bacterial cell walls. Notably, ctenophores, and choanoflagellates (the sister group of Metazoa), lack g-type lysozymes. We reveal a mosaic distribution of these genes, particularly within lophotrochozoans/spiralians, suggesting the horizontal gene transfer events from predatory myxobacteria played a role in their acquisition, enabling specialized dietary and defensive adaptations. We further identify two major groups of g-type lysozymes based on their widespread distribution in gastropods. Despite their sequence diversity, these lysozymes maintain conserved structural integrity that is crucial for enzymatic activity, underscoring independent evolutionary pathways where g-type lysozymes have developed functionalities typically associated with different lysozyme types in other species. Specifically, using Aplysia californica as a reference species, we identified three distinct g-type lysozyme genes: two are expressed in organs linked to both feeding and defense, and the third exhibits broader distribution, likely associated with immune functions. These findings advance our understanding of the evolutionary dynamics shaping the recruitment and mosaic functional diversification of these enzymes across metazoans, offering new insights into ecological physiology and physiological evolution as emerging fields.

New Insights into the Antibacterial Activity of Hydroxytyrosol Extracted from Olive Leaves: Molecular Docking Simulations of its Antibacterial Mechanisms.

This study investigated the biological activities of a hydroxytyrosol-rich extract from Olea europaea leaves, particularly its ability to eradicate severe pathogenic bacteria producing Extended-Spectrum Beta-Lactamases (ESBLs). The latter bacteria are emerging microorganisms that pose significant challenges due to their resistance to a broad range of potent therapeutic drugs. The extract was prepared through an accessible acid hydrolysis method. In vitro and In silico analyses through MIC, MBC analysis and molecular docking were conducted to evaluate the antibacterial properties. The extract showed remarkable antioxidant activity and significant antibacterial potential against reference species and ESBL bacteria. MIC and MBC calculations confirmed the extract's capacity to kill bacteria rather than just inhibit their growth. Further in silico analyzes demonstrated the high binding affinity of HT to the active sites of the gyrase B subunit and the peptidoglycan DD-transpeptidase domain from proteins located in the cytoplasm and the cell wall of the bacteria, respectively. Results confirmed the structure-activity relationship and the ability of HT to disrupt essential bacterial functions. This study validates the debated antimicrobial potential of HT and highlights its importance as a potential therapeutic agent against resistant bacteria, which is a critical area of research given the global challenge of antibiotic resistance.

Making Neurobots and Chimerical Ctenophores.

Making living machines using biological materials (cells, tissues, and organs) is one of the challenges in developmental biology and modern biomedicine. Constraints in regeneration potential and immune self-defense mechanisms limit the progress in the field. Here, we present unanticipated features related to self-recognition and ancestral neuro-immune architectures of new emerging reference species - ctenophores or comb jellies. These are descendants of the earliest survival metazoan lineage with unique tissues, organs and independent origins of major animal traits such as neurons, muscles, mesoderm, and through-gut. Thus, ctenophores convergently evolved complex organization, compared to bilaterians. Nevertheless, their neural and immune systems are likely functionally coupled, enabling designs and experimental construction of hybrid neural systems and even entire animals. This report illustrates impressive opportunities to build both chimeric animals and neurobots using ctenophores as models for bioengineering. The obtained neurobots and chimeric animals from three ctenophore species (Bolinopsis, Mnemiopsis, and Pleurobrachia) were able to be autonomous and survive for days. In sum, the unification of biodiversity, cell biology, and neuroscience opens unprecedented opportunities for experimental synthetic biology.

Detailed Profiling of 17-Hydroxygeranyllinalool Diterpene Glycosides from Nicotiana Species Reveals Complex Reaction Networks of Conjugation Isomers.

Specialised anti-herbivory metabolites are abundant in the solanaceous genus Nicotiana. These metabolites include the large family of 17-hydroxygeranyllinalool diterpene glycosides (HGL-DTGs). Many HGL-DTGs occur exclusively within the Nicotiana genus, but information from the molecular model species N. tabacum, N. benthamiana, and the tree tobacco N. glauca is limited. We studied HGL-DTG occurrence and complexity in these species with the aim of providing in-depth reference annotations and comprehensive HGL-DTG inventories. We analysed polar metabolite extracts in comparison to the previously investigated wild reference species N. attenuata using positive ESI(+) and negative ESI(-) mode electrospray ionisation LC-MS and MS/MS. We provide annotations of 66 HGL-DTGs with in-source and MS/MS fragmentation spectra for selected HGL-DTGs with exemplary fragment interpretations of ESI(+) as well as less studied ESI(-) spectra. We assemble a potential biosynthesis pathway comparing the presence of HGL-DTGs in N. tabacum, N. glauca, and N. benthamiana to N. attenuata. Approximately one-third of HGL-DTGs are chromatographically resolved isomers of hexose, deoxyhexose, or malonate conjugates. The number of isomers is especially high for conjugates with low numbers of deoxyhexose moieties. We extend the number of known HGL-DTGs with a focus on Nicotiana model species and demonstrate that the HGL-DTG family of N. tabacum plants can be surprisingly complex. Our study provides an improved basis with detailed references to previous studies of wild Nicotiana species and enables inference of HGL-DTG pathways with required enzymes for the biosynthesis of this important family of specialised defence metabolites.

POTENTIAL USE OF Pinus patula WOOD FOR THE PRODUCTION OF PURE AND IN COMBINATION WITH Eucalyptus PLYWOOD PANELS

Plywood panels are products of great importance in the global market, and Brazil is a large producer of conifer plywood, which boosts industrial activities in the south of the country and consequently contributes to the Brazilian GDP. Pinus patula is an unconventional species that requires study for this purpose. Thus, this research aimed to evaluate the potential for using Pinus patula wood for the production of pure plywood panels and in combination with Eucalyptus grandis and Eucalyptus dunnii. 8 treatments were produced, pure and in combination of species, which were glued with phenol formaldehyde adhesive, in a grammage of 180 g/m2 and a solids content from the adhesive formulation of 34%, and pressed at a temperature of 140°C for 13 minutes at a specific pressure of 11 kgf/cm2. Pinus taeda was used as a reference species. The physical and mechanical properties were evaluated according to the ABNT NBR 17002 and ABNT ISO 12466 standards. The results demonstrated that, for the majority of the properties evaluated, the Pinus patula panels were statistically equal or superior in relation to Pinus taeda. The “combi” type panels showed that the Eucalyptus species contributed to improving the static bending property. It is concluded, therefore, that Pinus patula has potential for the production of plywood panels, allowing an increase in the availability and diversity of raw materials for industrial processes, and that the static bending property can be improved with the production of panels of the “combi'' type using Eucalyptus veneers.

Analysis of fauna of mollusks, pollen assemblages and sedimentary environments in the Taganrog Bay of the Sea of Azov

The paper presents the results of a comprehensive study of well sections drilled on the coastal spits of the Taganrog Gulf of the Sea of Azov and bottom sediment columns selected in the water area. A detailed analysis of the early malacological communities, an important participant in the sedimentary process, made it possible to trace changes in their living conditions in the Holocene. Based on determining the absolute age (14C) from the valves of mollusk shells buried in situ, it is shown that at the beginning of the Phanagorian regression, in the area of the distal part of the Dolgaya Spit, there was a sea reservoir with an Azov-Black Sea complex of reference species. Based on the results of palynological analysis, changes in the natural conditions of the Azov region over the past few thousand years have been reconstructed and arid and humid climatic phases have been identified.

Aspergillus aureoterreus, A. pseudonomiae, A. siamensis, and A. flocculosus-ochraceopetaliformis as Four New Pathogens of Eye Infection in DNA Barcoding Markers

Background: The use of a morphological method to determine Aspergillus species in routine laboratory investigation has always been challenged with low sensitivity and low specificity. Time-consuming specimen preparation and insufficient expertise are the crucial reasons. DNA barcoding markers have been introduced for identification as another gold standard method. Objective: To investigate DNA barcoding markers in identifying Aspergillus strains isolated from patients with eye infection. Methods: This study extracted 12 DNA samples of 12 Aspergillus strains. DNA barcoding genes, i.e., ITS, betatubulin (BT2), calmodulin (CAL), and actin (ACT) genes, were amplified and sequenced by polymerase chain reaction and Sanger's sequencing methods. All gene sequences were compared to those of the type or reference species collected from public databases. The species were identified with phylogenetic analyses in free applications from public websites. Results: ITS, BT2 and CAL, and ACT identified 5, 6, and 3 species and 3, 2, and 1 species complex of Aspergillus, respectively. DNA barcoding with multi-locus sequence typing revealed four new pathogens of human eye infection, including A. aureoterreus, A. pseudonomiae, A. siamensis, and A. flocculosus-ochraceopetaliformis. Conclusion: The DNA barcoding markers identified Aspergillus species with better specificity than the conventional method. The markers and techniques need to be used as tools for routine Aspergillus identification.

Assessing new microalgae species as potential feed for bivalve spat in nursery culture

ABSTRACT Microalgae remains a primary food source for hatchery and nursery culture of juvenile bivalves. However, there is a mismatch between the characteristics of the microalgae currently used in nursery culture and the feeding abilities and nutritional requirements of juveniles of some bivalve species, such as the green-lipped mussel, Perna canaliculus. Therefore, there is a need to identify new species of microalgae for this purpose that have favourable cell size, good growth performance under culture conditions and appropriate nutritional content for juvenile bivalves by using these characteristics as primary selection criteria. In this study, the growth performance under standard culture conditions of four microalgae species (Chrysochromulina camella, Gymnodinium simplex, Pyramimonas parkeae and Stephanodiscus niagarae) which are of a sufficiently large cell size to meet the needs of juvenile mussels (i.e. 10–20 µm size range) were tested in comparison to three commonly cultured commercial species (Chaetoceros muelleri, Diacronema lutheri and Tisochrysis lutea). Results show that G. simplex, S. niagarae and the two strains of P. parkeae (P. parkeae (C) and P. parkeae (I)) can achieve similar biomass as the reference species in the intermediate (1 L) culture stages despite the large difference in cell densities. The poor growth of C. camella in F/2 media indicates a necessity of determining its appropriate culture conditions before further assessing its suitability as a nursery feed for juvenile bivalves. The proximate analysis of S. niagarae, G. simplex and P. parkeae (I) reveals nutritional profiles conducive to spat development. However, the P. parkeae (C) strain contained low carbohydrate content, suggesting inferior nutritional value compared to the P. parkeae (I) strain, showing that variants of the same species can have different biochemical composition and suggesting the former might have limited suitability for feeding in nursery culture. The findings indicate that G. simplex, S. niagarae and P. parkeae (C) hold sufficient promise as spat feed in nursery culture to warrant further testing to confirm their efficacy as live microalgal feed for bivalve spat.

Development of a Multiplex Real-Time PCR Assay for the Simultaneous Detection of Two Fungal Pathogens Causing Pneumonia.

Infectious diseases caused by fungal sources are of great interest owing to their increasing prevalence. Invasive fungal infections, including invasive pulmonary aspergillosis caused by Aspergillus fumigatus, and Pneumocystis pneumonia caused by Pneumocystis jirovecii, are significant causes of morbidity and mortality among immunocompromised patients. The accurate and timely detection of these pathogens in this high-risk population is crucial for effective patient management. We developed a multiplex real-time polymerase chain reaction (PCR) assay, RF2 mRT-PCR, specifically designed to detect two respiratory fungi, P. jirovecii and A. fumigatus, and evaluated its performance in specimens of patients with lower respiratory tract infection. The performance was evaluated using 731 clinical samples, 55 reference species, and one synthetic DNA. The reproducibility test yielded a probit curve with a lower limit of detection of 19.82 copies/reaction for P. jirovecii and 64.20 copies/reaction for A. fumigatus. The RF2 mRT-PCR assay did not cross-react with non-A. fumigatus Aspergillus species or other common bacterial and viral species, and showed 100% in vitro sensitivity and specificity with reference assays. Additionally, it simultaneously detected A. fumigatus and P. jirovecii in co-infected samples. Therefore, the RF2 mRT-PCR assay is an efficient and reliable tool for in vitro diagnosis of A. fumigatus and P. jirovecii pulmonary infections.

Molecular Identification Validates Morphological Identification of Javanese Cardamom from Banyumas in Central Java, Indonesia

Cardamom is one of the prominent plants with significant economic value in the Banyumas Regency, Central Java, Indonesia. Although Javanese cardamom is traditionally categorized under Amomum compactum, the morphological variations observed create ambiguity about its exact species status. DNA barcoding using the maturase K (matK) and ribulose-bisphosphate carboxylase (rbcL) genes is proven as a reliable technique to elucidate the taxonomic status of morphological variable plant cultivars. This study aimed to characterize cardamom from Banyumas Regency using morphological and molecular approaches for taxonomic status identification and genetic diversity evaluation. The matK and rbcL genes were selected as genetic markers and sequenced using a bidirectional sequencing technique. Morphological examination showed significant color variations at the cardamom stem base. All samples had high genetic identities to reference species in databases and were supported by high query cover and zero e-values. Therefore, molecular characterization, alongside geographic distribution assessment, established that this plant belongs to a single species, Amomum compactum. Additionally, the analysis conducted showed a low level of genetic diversity, as evidenced by haplotype and nucleotide diversity. Low-level genetic diversity provides additional data to convince that cardamon in Banyumas Regency belongs to a single species. These results are essential data in seed selection for further cultivation.

LAFL Factors in Seed Development and Phase Transitions.

Development is a chain reaction in which one event leads to another until the completion of a life cycle. Phase transitions are milestone events in the cycle of life. LEAFY COTYLEDON1 (LEC1), ABA INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2 proteins, collectively known as LAFL, are master transcription factors (TFs) regulating seed and other developmental processes. Since the initial characterization of the LAFL genes, more than three decades of active research has generated tremendous amounts of knowledge about these TFs, whose roles in seed development and germination have been comprehensively reviewed. Recent advances in cell biology with genetic and genomic tools have allowed the characterization of the LAFL regulatory networks in previously challenging tissues at a higher throughput and resolution in reference species and crops. In this review, we provide a holistic perspective by integrating advances at the epigenetic, transcriptional, posttranscriptional, and protein levels to exemplify the spatiotemporal regulation of the LAFL networks in Arabidopsis seed development and phase transitions, and we briefly discuss the evolution of these TF networks.

Mass calibration of Rosetta’s ROSINA/DFMS mass spectrometer

The Double Focusing Mass Spectrometer (DFMS) onboard the Rosetta spacecraft employs an electrostatic and a magnet sector for energy and mass discrimination, resulting in a high mass resolution. A built-in feedback loop uses the measured magnet temperature to compensate for the temperature dependence of the magnet’s field strength. Still, large onboard temperature variations and other effects cause any given mass peak to move over a range of 30 pixels or more on the detector during the mission. The present paper discusses the various factors that contribute to the time variations in the mass calibration relation. A technique is developed to evaluate and correct for these factors. A mass calibration relation that is valid for the DFMS neutral high mass resolution mode measurements throughout the entire mission for the mass range m/z=13–69 is established and its accuracy is evaluated. The 1σ precision turns out to be less than a single pixel, which is excellent as full peak width at half height is about 12 pixels. The proposed approach provides an a posteriori mass calibration and is useful for all magnet-based mass spectrometers where experimental mass calibration by comparison to reference species, temperature stabilization, and/or electrostatic compensation, are not possible or fail to deliver a mass scale precision that is comparable to the mass resolution of the instrument.

Baseline study of biomarkers of exposure to metal and polycyclic aromatic hydrocarbon in wild Mugil cephalus from the coastal waters of Fiji

The indirect exposure and effects of marine pollutants such as metals and polycyclic aromatic hydrocarbons, present significant health concerns for human coastal communities that rely on fish consumption as a regular nutritional source. This study verified Mugil cephalus (“mullet”) as an adequate sentinel species for biomonitoring environmental health and conducting risk assessments using biomarkers in Fiji. A non-parametric Kruskall Wallis Test was employed at a 5 % significant difference level to test sample group differences. Sampling was performed over five months in two Fijian study areas, i.e., Laucala Bay and the Ba River Delta by local fishers based on Fiji’s wet season (Nov-Mar). The K factor and hepatosomatic index (HSI) were relatively lower in mullet from Laucala Bay compared to the Ba River Delta, with HSI having a significant difference (χ2= 3.64, d.f. = 1, p-value = 0.057). No significant differences were observed for metals (Pb and Cr) at an instrumental limit of detection of 0.05 mg kg−1, but an important finding was that the levels of Cr in edible tissues of mullet from both study sites exceeded the permissible limits for human consumption set by the World Health Organisation (0.05–0.15 mg kg−1) by approximately 2-fold in Laucala Bay and 3-fold in Ba River Delta. The levels of Hg and Cd in the two sample groups were determined to be below the instrumental limit of detection of 0.1 mg kg−1. Total biliary polycyclic aromatic hydrocarbons (PAHs) were significantly higher in mullet from the Ba River Delta (χ2 = 21.14, d.f. = 1, p-value < 0.001), particularly for phenanthrene (χ2 = 24.678, d.f. = 1, p-value < 0.001). No statistical variations were observed in phase I biotransformation (ethoxyresorufin O-deethylase); however, phase II biotransformation activity (glutathione S-transferase) was found to be significantly higher in mullet from the Ba River Delta compared to Laucala Ba (χ2 = 35.85, d.f. = 1, p-value < 0.001). Similarly, no remarkable variations were observed in glutathione peroxidase activity, but glutathione reductase activity was significantly higher in mullet (χ2 = 5.05, d.f. = 1, p-value = 0.025) from Laucala Bay compared to Ba River Delta. Considering biological damages from oxidative stress, levels of lipid peroxidation were significantly higher (χ2= 4.10, d.f. = 1, p-value = 0.043) in mullet from Ba River Delta, including higher occurrences of micronuclei (χ2= 12.66, d.f. = 1, p-value = <0.001) and other abnormal erythrocyte nuclei (χ2= 26.67, d.f. = 2, p-value < 0.001), suggesting genotoxic damage. These findings 1) support the use of mullet as a suitable reference species for future ecotoxicology studies in Fiji, 2) are essential to take informed health and safety considerations regarding mullet consumption, 3) provide a baseline to compare future monitoring results and, 4) underscore the importance of incorporating biomonitoring practices in future environmental risk assessments.

Photobacterium pectinilyticum sp. nov., a novel bacterium isolated from surface seawater of Qingdao offshore.

A Gram-staining-negative, facultative aerobic, motile strain, designated strain ZSDE20T, was isolated from the surface seawater of Qingdao offshore. Phylogenetic analysis of the 16S rRNA gene of strain ZSDE20T, affiliated it to the genus Photobacterium. It was closely related to Photobacterium lutimaris DF-42T (98.92% 16S rRNA gene sequence similarity). Growth occurred at 4-28ºC (optimum 28ºC), pH 1.0-7.0 (optimum 7.0) and in the presence of 1-7% (w/v) NaCl (optimum 3%). The dominant fatty acids were summed feature 3 (C16:1 ω7c or/and C16:1 ω6c, 34.23%), summed feature 8 (C18:1 ω7c and C18:1 ω6c, 10.36%) and C16:0 (20.05%). The polar lipids of strain ZSDE20T comprised phosphatidylethanolamine, phosphatidylcholine, lyso-phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol dimannoside, phosphatidylinositol mannosides and two unknown lipids. The major respiratory quinone was ubiquinone-8 (Q-8). The DNA G + C content of strain ZSDE20T was 45.6mol%. Average nucleotide identity (ANI) values between ZSDE20T and its reference species were lower than the threshold for species delineation (95-96%); in silico DNA-DNA hybridization further showed that strain ZSDE20T had less than 70% similarity to its relatives. Based on the polyphasic evidences, strain ZSDE20T is proposed as representing a novel species of the genus Photobacterium, for which the name Photobacterium pectinilyticum sp. nov. is proposed. The type strain is ZSDE20T (= MCCC 1K06283T = KCTC 82885T).

Efficient Reaction‐Based Approaches for Gas‐Phase Enthalpy of Formation Prediction and their Application to Large (C32) Polycyclic Aromatic Hydrocarbons

AbstractIn this work, an efficient and generally applicable scheme for the automatic generation of the minimal set of independent model reactions to be used for the calculation of enthalpies of formation is presented. A post‐processing procedure targeting the selection of the most suitable model reactions by assigning them larger weights is suggested. The developed computational protocol exploiting high‐level ab initio calculations and accurate reference enthalpies of formation retrieved from the Active Thermochemical Tables reproduces with chemical accuracy well‐established enthalpies of formation of 15 relatively small (C10–C24) polycyclic aromatic hydrocarbons (PAHs). A promising alternative single‐reaction strategy encompassing all reference species is outlined. Both methods are then applied to predict for the set of 43 larger (C32) PAHs, and revealed significant deviation (Mean Unsigned Error, MUE = 23.2 kJ mol−1) compared to the earlier theoretical results obtained from B3LYP calculations with subsequent group‐based empirical corrections. In the absence of the experimental data, these evaluations of are expected to be more realistic as the approach employed in this work demonstrated better performance on the benchmarking set of 15 smaller PAHs with the MUE of 1.3–1.5 versus 6.2 kJ mol−1.

Root carboxylate release is common in phosphorus-limited forest ecosystems in China: using leaf manganese concentration as a proxy

Abstract Background and aims Certain plant species release root carboxylates in response to phosphorus (P) limitation; however, the prevalence of root exudate release in species in P-limited forest ecosystems remains unexplored due to challenges in field assessment. Methods Manganese (Mn) accumulation in mature leaves can indicate the presence of root carboxylate exudates in rhizosphere soil. To account for environmental factors such as soil pH, a negative reference species that does not release carboxylates is used for comparison. In this study, we assessed multiple forest stands across soil types and different levels of P availability in northern (Gansu) and southern (Guangxi) China. Leaf and soil samples were collected from 188 plant families representing various life forms, and leaf Mn concentration ([Mn]) was analyzed as a proxy for root carboxylate exudation patterns, using Dryopteridaceae as a negative reference. Results The results supported our hypotheses that leaf [Mn] was higher in P-limited forests of southern China compared to P-richer forests of northern China, even though the soil [Mn] was higher in the forests of northern China. Additionally, we observed a higher prevalence of species with high leaf [Mn] across various plant families in Guangxi (82%) than in Gansu (42%). Conclusion Our findings suggest a potential common strategy among plants in Guangxi forests, where root exudates are released in response to P limitation, possibly due to ineffective mycorrhizal symbiosis for nutrient acquisition. The diverse forest systems in China exhibit varying soil P availability, leading to the evolution of plant species with distinct P-acquisition strategies.

Influence of Donor-Acceptor Interactions on MLCT Hole Reconfiguration in {Ru(bpy)} Chromophores.

In MLCT chromophores, internal conversion (IC) in the form of hole reconfiguration pathways (HR) is a major source of dissipation of the absorbed photon energy. Therefore, it is desirable to minimize their impact in energy conversion schemes by slowing them down. According to previous findings on {Ru(bpy)} chromophores, donor-acceptor interactions between the Ru ion and the ligand scaffold might allow to control HR/IC rates. Here, a series of [Ru(tpm)(bpy)(R-py)]2+ chromophores, where tpm is tris(1-pyrazolyl)methane, bpy is 2,2'-bipyridine and R-py is a 4-substituted pyridine, were prepared and fully characterized employing electrochemistry, spectroelectrochemistry, steady-state absorption/emission spectroscopy and electronic structure computations based on DFT/TD-DFT. Their excited-state decay was monitored using nanosecond and femtosecond transient absorption spectroscopy. HR/IC lifetimes as slow as 568 ps were obtained in DMSO at room temperature, twice as slow as in the reference species [Ru(tpm)(bpy)(NCS)]+.

Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES.

Inference of species trees plays a crucial role in advancing our understanding of evolutionary relationships and has immense significance for diverse biological and medical applications. Extensive genome sequencing efforts are currently in progress across a broad spectrum of life forms, holding the potential to unravel the intricate branching patterns within the tree of life. However, estimating species trees starting from raw genome sequences is quite challenging, and the current cutting-edge methodologies require a series of error-prone steps that are neither entirely automated nor standardized. In this paper, we present ROADIES, a novel pipeline for species tree inference from raw genome assemblies that is fully automated, easy to use, scalable, free from reference bias, and provides flexibility to adjust the tradeoff between accuracy and runtime. The ROADIES pipeline eliminates the need to align whole genomes, choose a single reference species, or pre-select loci such as functional genes found using cumbersome annotation steps. Moreover, it leverages recent advances in phylogenetic inference to allow multi-copy genes, eliminating the need to detect orthology. Using the genomic datasets released from large-scale sequencing consortia across three diverse life forms (placental mammals, pomace flies, and birds), we show that ROADIES infers species trees that are comparable in quality with the state-of-the-art approaches but in a fraction of the time. By incorporating optimal approaches and automating all steps from assembled genomes to species and gene trees, ROADIES is poised to improve the accuracy, scalability, and reproducibility of phylogenomic analyses.