Evidence of nitrogen inputs affecting soil nitrogen purification by mediating root exudates of salt marsh plants.

Salt marsh has an important 'purification' role in coastal ecosystems by removing excess nitrogen that could otherwise harm aquatic life and reduce water quality. Recent studies suggest that salt marsh root exudates might be the 'control centre' for nitrogen transformation, but empirical evidence is lacking. Here we sought to estimate the direction and magnitude of nitrogen purification by salt marsh root exudates and gain a mechanistic understanding of the biogeochemical transformation pathway(s). To achieve this, we used a laboratory incubation to quantify both the root exudates and soil nitrogen purification rates, in addition to the enzyme activities and functional genes under Phragmites australis populations with different nitrogen forms addition (NO3-, NH4+ and urea). We found that NO3- and urea addition significantly stimulate P. australis root exudation of total acids, amino acids, total sugars and total organic carbon, while NH4+ addition only significantly increased total acids, amino acids and total phenol exudation. High total sugars, amino acids and total organic carbon concentrations enlarged nitrogen purification potential by stimulating the nitrogen purifying bacterial activities (including enzyme activities and related genes expression). Potential denitrification rates were not significantly elevated under NH4+ addition in comparison to NO3- and urea addition, which should be ascribed to total phenol self-toxicity and selective inhibition. Further, urea addition stimulated urease and protease activities with providing more NH4+ and NO2- substrates for elevated anaerobic ammonium oxidation rates among the nitrogen addition treatments. Overall, this study revealed that exogenous nitrogen could increase the nitrogen purification-associated bacterial activity through accelerating the root exudate release, which could stimulate the activity of nitrogen transformation, and then improve the nitrogen removal capacity in salt marsh.

Triphenylamine Sensitized 8-Dimethylaminoquinoline: An Efficient Two-Photon Caging Group for Intracellular Delivery.

Triphenylamine-sensitized 8-dimethylaminoquinoline (TAQ) probes showed fair two-photon absorption and fragmentation cross sections in releasing kainate and GABA ligands. The water-soluble PEG and TEG-analogs allowed cell internalization and efficient light-gated liberation of the rhodamine reporter under UV and two-photon (NIR) irradiation conditions.

Use of wound infusion catheters for delivery of local anesthetic following standing partial ostectomy of thoracolumbar vertebral spinous processes in horses is not associated with increased surgical site infections.

Background: Wound infusion catheters (WICs) have been used in humans and some veterinary species for post-operative local anesthetic administration following a variety of surgical procedures, aiming to reduce post-operative analgesia requirements and improve patient comfort. Benefit in reduction in pain, post-operative analgesia requirements and length of hospital stay are well documented in humans, but use of WICs may not have been widely adopted in veterinary species due to the concern of increased complications, such as dehiscence or surgical site infection (SSI), creating a barrier to their use. This study aimed to evaluate the use of WICs in horses undergoing standing partial ostectomy surgeries, document complications and investigate if the incidence of SSI was equivalent between those horses that did and did not have a WIC. Methods: Clinical records were searched between January 2010-December 2023 for horses undergoing standing partial ostectomy surgery of thoracolumbar vertebral spinous processes at one institution. Population variables (age, breed, bodyweight), placement of a WIC or not, post-operative complications, analgesia protocols and surgical time were recorded. Horses received up to 0.1 mg kg-1 bupivacaine (0.5 mg mL-1) every 6-8 h via the WIC where one was placed. To compare SSI complication incidence between using or not using a WIC, a proportional independent equivalence test was used. Results: There were 64 horses included in the final analysis with a WIC placed in 29/64 horses (45.3%) and 35/64 (54.7%) having no WIC placed at surgery. Incidence of short-term SSI was 11.4% (no WIC used) and 13.8% (WIC used), respectively. The difference in proportion of SSI between the presence or absence of a WIC was not significant [-0.024 (90% CI -0.181; 0.133); p = 0.94]. Conclusion: The incidence of SSIs was equivalent between groups whether a WIC was used or not. WICs should be considered as part of a multi-modal analgesic approach in the post-operative period. Further research into local anesthetic dosing and its impact on rescue analgesia requirements and pain-scores is warranted.

Simultaneous Thermally Stimulated Delayed Phosphorescence (TSDP) and Thermally Activated Delayed Fluorescence (TADF) in a Two-Coordinated Au(I) Bimetallic Complex Featuring a Tandem Carbene Structure.

A bimetallic, two-coordinated carbene-metal-amine (cMa) Au(I) complex featuring a twisted tandem carbene structure (NHC1-Au-NHC2-Au-carbazolyl) was synthesized. The molecular structure in single crystals revealed a large dihedral angle between the two carbene ligands, while the bridged carbene NHC2 and carbazolyl (Cz) ligands were coplanar. A bluish green thermally stimulated delayed phosphorescence (TSDP) was observed in crystals with an emission lifetime over 70 µs, which can be attributed to the spin allowed diabatic population of a high-lying emissive triplet state from the 3LE characterized low-lying ones. The small rotation energy barrier of Cz along the coordination bond allowed conformers with large dihedral angles between NHC2 and Cz. The ICT characterized S1 state was consequently stabilized to achieve a thermally accessible energy gap to facilitate ISC between triplets and the S1, leading to the thermally activated delayed fluorescence (TADF). Simultaneous TSDP and TADF dual emission can be recorded in its doped polymer film owing to the coexistence of these different conformers.

Drivers of wood-inhabiting fungal diversity in European and Oriental beech forests.

The hyperdiverse wood-inhabiting fungi play a crucial role in the global carbon cycle, but often are threatened by deadwood removal, particularly in temperate forests dominated by European beech (Fagus sylvatica) and Oriental beech (Fagus orientalis). To study the impact of abiotic drivers, deadwood factors, forest management and biogeographical patterns in forests of both beech species on fungal composition and diversity, we collected 215 deadwood-drilling samples in 18 forests from France to Armenia and identified fungi by meta-barcoding. In our analyses, we distinguished the patterns driven by rare, common, and dominant species using Hill numbers. Despite a broad overlap in species, the fungal composition with focus on rare species was determined by Fagus species, deadwood type, deadwood diameter, precipitation, temperature, and management status in decreasing order. Shifting the focus on common and dominant species, only Fagus species, both climate variables and deadwood type remained. The richness of species within the deadwood objects increased significantly only with decay stage. Gamma diversity in European beech forests was higher than in Oriental beech forests. We revealed the highest gamma diversity for old-growth forests of European beech when focusing on dominant species. Our results implicate that deadwood retention efforts, focusing on dominant fungi species, critical for the decay process, should be distributed across precipitation and temperature gradients and both Fagus species. Strategies focusing on rare species should additionally focus on different diameters and on the conservation of old-growth forests.

Bronchoscopy with and without needle-based confocal laser endomicroscopy for peripheral lung nodule diagnosis: protocol for a multicentre randomised controlled trial (CLEVER trial).

INTRODUCTION: Despite many technological advances, the diagnostic yield of bronchoscopic peripheral lung nodule analysis remains limited due to frequent mispositioning. Needle-based confocal laser endomicroscopy (nCLE) enables real-time microscopic feedback on needle positioning, potentially improving the sampling location and diagnostic yield. Previous studies have defined and validated nCLE criteria for malignancy, airway and lung parenchyma. Larger studies demonstrating the effect of nCLE on diagnostic yield are lacking. We aim to investigate if nCLE-imaging integrated with conventional bronchoscopy results in a higher diagnostic yield compared with conventional bronchoscopy without nCLE. METHODS AND ANALYSIS: This is a parallel-group randomised controlled trial. Recruitment is performed at pulmonology outpatient clinics in universities and general hospitals in six different European countries and one hospital in the USA. Consecutive patients with a for malignancy suspected peripheral lung nodule (10-30 mm) with an indication for diagnostic bronchoscopy will be screened, and 208 patients will be included. Web-based randomisation (1:1) between the two procedures will be performed. The primary outcome is diagnostic yield. Secondary outcomes include diagnostic sensitivity for malignancy, needle repositionings, procedure and fluoroscopy duration, and complications. Pathologists will be blinded to procedure type; patients and endoscopists will not. ETHICS AND DISSEMINATION: Primary approval by the Ethics Committee of the Amsterdam University Medical Center. Dissemination involves publication in a peer-reviewed journal. SUPPORT: Financial and material support from Mauna Kea Technologies. TRIAL REGISTRATION NUMBER: NCT06079970.

Red-shifted two-photon-sensitive phenanthridine photocages: synthesis and characterisation.

Herein we describe the rational design, synthesis and photophysical study of a novel class of phenanthridine-based, one- and two-photon sensitive, photoremovable protecting groups with absorption wavelengths extending beyond 400 nm. This design facilitated the development of scaffolds with enhanced uncaging quantum yield, paving the way for broader applications in controlled drug delivery and molecular manipulation.

The MUC2 Gene Product: Polymerisation and Post-Secretory Organisation-Current Models.

MUC2 mucin, the primary gel-forming component of intestinal mucus, is well researched and a model of polymerisation and post-secretory organisation has been published previously. Recently, several significant developments have been made which either introduce new ideas or challenge previous theories. New ideas include an overhaul of the MUC2 C-terminal globular structure which is proposed to harbour several previously unobserved domains, and include a site for an extra intermolecular disulphide bridge dimer between the cysteine 4379 of adjacent MUC2 C-termini. MUC2 polymers are also now thought to be secreted attached to the epithelial surface of goblet cells in the small intestine and removed following secretion via a metalloprotease meprin ß-mediated cleavage of the von Willebrand D2 domain of the N-terminus. It remains unclear whether MUC2 forms intermolecular dimers, trimers, or both, at the N-termini during polymerisation, with several articles supporting either trimer or dimer formation. The presence of a firm inner mucus layer in the small intestine is similarly unclear. Considering this recent research, this review proposes an update to the previous model of MUC2 polymerisation and secretion, considers conflicting theories and data, and highlights the importance of this research to the understanding of MUC2 mucus layers in health and disease.

Human Immunodeficiency Virus Type 1 Gag Polyprotein Modulates Membrane Physical Properties like a Surfactant: Potential Implications for Virus Assembly.

Human immunodeficiency virus (HIV) assembly at an infected cell's plasma membrane requires membrane deformation to organize the near-spherical shape of an immature virus. While the cellular expression of HIV Gag is sufficient to initiate budding of virus-like particles, how Gag generates membrane curvature is not fully understood. Using highly curved lipid nanotubes, we have investigated the physicochemical basis of the membrane activity of recombinant nonmyristoylated Gag-Δp6. Gag protein, upon adsorption onto the membrane, resulted in the shape changes of both charged and uncharged nanotubes. This shape change was more pronounced in the presence of charged lipids, especially phosphatidylinositol bisphosphate (PI(4,5)P2). We found that Gag modified the interfacial tension of phospholipid bilayer membranes, as judged by comparison with the effects of amphipathic peptides and nonionic detergent. Bioinformatic analysis demonstrated that a region of the capsid and SP1 domains junction of Gag is structurally similar to the amphipathic peptide magainin-1. This region accounts for integral changes in the physical properties of the membrane upon Gag adsorption, as we showed with the synthetic CA-SP1 junction peptide. Phenomenologically, membrane-adsorbed Gag could diminish the energetic cost of increasing the membrane area in a way similar to foam formation. We propose that Gag acts as a surface-active substance at the HIV budding site that softens the membrane at the place of Gag adsorption, lowering the energy for membrane bending. Finally, our experimental data and theoretical considerations give a lipid-centric view and common mechanism by which proteins could bend membranes, despite not having intrinsic curvature in their molecular surfaces or assemblies.

Seagrass decline weakens sediment organic carbon stability.

Seagrass meadows are globally recognized as critical natural carbon sinks, commonly known as 'blue carbon'. However, seagrass decline attributed to escalating human activities and climate change, significantly influences their carbon sequestration capacity. A key aspect in comprehending the impact of seagrass decline on carbon sequestration is understanding how degradation affects the stored blue carbon, primarily consisting of sediment organic carbon (SOC). While it is widely acknowledged that seagrass decline affects the input of organic carbon, little is known about its impact on SOC pool stability. To address this knowledge, we examined variations in total SOC and recalcitrant SOC (RSOC) at a depth of 15 cm in nine seagrass meadows located on the coast of Southern China. Our findings revealed that the ratio of RSOC to SOC (RSOC/SOC) ranged from 27 % to 91 % in the seagrass meadows, and the RSOC/SOC increased slightly with depth. Comparing different seagrass species, we observed that SOC and RSOC stocks were 1.94 and 3.19-fold higher under Halophila beccarii and Halophila ovalis meadows compared to Thalassia hemprichii and Enhalus acoroides meadows. Redundancy and correlation analyses indicated that SOC and RSOC content and stock, as well as the RSOC/SOC ratio, decreased with declining seagrass shoot density, biomass, and coverage. This implies that the loss of seagrass, caused by human activities and climate change, results in a reduction in carbon sequestration stability. Further, the RSOC decreased by 15 %, 29 %, and 40 % under unvegetated areas compared to adjacent Halophila spp., T. hemprichii and E. acoroides meadows, respectively. Given the anticipated acceleration of seagrass decline due to climate change and increasing coastal development, our study provides timely information for developing coastal carbon protection strategies. These strategies should focus on preserving seagrass and restoring damaged seagrass meadows, to maximize their carbon sequestration capacity.

It's time to broaden what we consider a 'blue carbon ecosystem'.

Photoautotrophic marine ecosystems can lock up organic carbon in their biomass and the associated organic sediments they trap over millennia and are thus regarded as blue carbon ecosystems. Because of the ability of marine ecosystems to lock up organic carbon for millennia, blue carbon is receiving much attention within the United Nations' 2030 Agenda for Sustainable Development as a nature-based solution (NBS) to climate change, but classically still focuses on seagrass meadows, mangrove forests, and tidal marshes. However, other coastal ecosystems could also be important for blue carbon storage, but remain largely neglected in both carbon cycling budgets and NBS strategic planning. Using a meta-analysis of 253 research publications, we identify other coastal ecosystems-including mud flats, fjords, coralline algal (rhodolith) beds, and some components or coral reef systems-with a strong capacity to act as blue carbon sinks in certain situations. Features that promote blue carbon burial within these 'non-classical' blue carbon ecosystems included: (1) balancing of carbon release by calcification via carbon uptake at the individual and ecosystem levels; (2) high rates of allochthonous organic carbon supply because of high particle trapping capacity; (3) high rates of carbon preservation and low remineralization rates; and (4) location in depositional environments. Some of these features are context-dependent, meaning that these ecosystems were blue carbon sinks in some locations, but not others. Therefore, we provide a universal framework that can evaluate the likelihood of a given ecosystem to behave as a blue carbon sink for a given context. Overall, this paper seeks to encourage consideration of non-classical blue carbon ecosystems within NBS strategies, allowing more complete blue carbon accounting.

Including Methane Emissions from Agricultural Ponds in National Greenhouse Gas Inventories.

Agricultural ponds are a significant source of greenhouse gases, contributing to the ongoing challenge of anthropogenic climate change. Nations are encouraged to account for these emissions in their national greenhouse gas inventory reports. We present a remote sensing approach using open-access satellite imagery to estimate total methane emissions from agricultural ponds that account for (1) monthly fluctuations in the surface area of individual ponds, (2) rates of historical accumulation of agricultural ponds, and (3) the temperature dependence of methane emissions. As a case study, we used this method to inform the 2024 National Greenhouse Gas Inventory reports submitted by the Australian government, in compliance with the Paris Agreement. Total annual methane emissions increased by 58% from 1990 (26 kilotons CH4 year-1) to 2022 (41 kilotons CH4 year-1). This increase is linked to the water surface of agricultural ponds growing by 51% between 1990 (115 kilo hectares; 1,150 km2) and 2022 (173 kilo hectares; 1,730 km2). In Australia, 16,000 new agricultural ponds are built annually, expanding methane-emitting water surfaces by 1,230 ha yearly (12.3 km2 year-1). On average, the methane flux of agricultural ponds in Australia is 0.238 t CH4 ha-1 year-1. These results offer policymakers insights into developing targeted mitigation strategies to curb these specific forms of anthropogenic emissions. For instance, financial incentives, such as carbon or biodiversity credits, can mobilize widespread investments toward reducing greenhouse gas emissions and enhancing the ecological and environmental values of agricultural ponds. Our data and modeling tools are available on a free cloud-based platform for other countries to adopt this approach.

Structural Diversity in 2-(2-Aminoethyl)pyridine-Based Lead Iodide Hybrids.

While 2D metal-organic hybrids have emerged as promising solar absorbers due to their improved moisture stability, their inferior transport properties limit their potential translation into devices. We report a new hybrid containing 2-(2-ammonioethyl)pyridine [(2-AEP)+], forming a 2D hybrid with the composition (2-AEP)2PbI4. The organic bilayer comprises of (2-AEP)+, which is arranged in a face-to-face stacking that promotes π-π interactions between neighboring pyridyl rings. We also demonstrate the structural diversity of 2-(2-aminoethyl)pyridine-based lead iodide hybrids in solution-processed films. This report highlights the importance of solution-processing conditions in trying to obtain single-phase films of hybrids containing dibasic organic species.

Back to the Basics of SARS-CoV-2 Biochemistry: Microvascular Occlusive Glycan Bindings Govern Its Morbidities and Inform Therapeutic Responses.

Consistent with the biochemistry of coronaviruses as well established over decades, SARS-CoV-2 makes its initial attachment to host cells through the binding of its spike protein (SP) to sialylated glycans (containing the monosaccharide sialic acid) on the cell surface. The virus can then slide over and enter via ACE2. SARS-CoV-2 SP attaches particularly tightly to the trillions of red blood cells (RBCs), platelets and endothelial cells in the human body, each cell very densely coated with sialic acid surface molecules but having no ACE2 or minimal ACE2. These interlaced attachments trigger the blood cell aggregation, microvascular occlusion and vascular damage that underlie the hypoxia, blood clotting and related morbidities of severe COVID-19. Notably, the two human betacoronaviruses that express a sialic acid-cleaving enzyme are benign, while the other three-SARS, SARS-CoV-2 and MERS-are virulent. RBC aggregation experimentally induced in several animal species using an injected polysaccharide caused most of the same morbidities of severe COVID-19. This glycan biochemistry is key to disentangling controversies that have arisen over the efficacy of certain generic COVID-19 treatment agents and the safety of SP-based COVID-19 vaccines. More broadly, disregard for the active physiological role of RBCs yields unreliable or erroneous reporting of pharmacokinetic parameters as routinely obtained for most drugs and other bioactive agents using detection in plasma, with whole-blood levels being up to 30-fold higher. Appreciation of the active role of RBCs can elucidate the microvascular underpinnings of other health conditions, including cardiovascular disease, and therapeutic opportunities to address them.

Transbronchial cryobiopsy followed by as-needed surgical lung biopsy versus immediate surgical lung biopsy for diagnosing interstitial lung disease (the COLD study): a randomised controlled trial.

BACKGROUND: An adequate diagnosis for interstitial lung disease (ILD) is important for clinical decision making and prognosis. In most patients with ILD, an accurate diagnosis can be made by clinical and radiological data assessment, but in a considerable proportion of patients, a lung biopsy is required. Surgical lung biopsy (SLB) is the most common method to obtain tissue, but it is associated with high morbidity and even mortality. More recently, transbronchial cryobiopsy has been introduced, with fewer adverse events but a lower diagnostic yield than SLB. The aim of this study is to compare two diagnostic strategies: a step-up strategy (transbronchial cryobiopsy, followed by SLB if the cryobiopsy is insufficiently informative) versus immediate SLB. METHODS: The COLD study was a multicentre, randomised controlled trial in six hospitals across the Netherlands. We included patients with ILD with an indication for lung biopsy as assessed by a multidisciplinary team discussion. Patients were randomly assigned in a 1:1 ratio to the step-up or immediate SLB strategy, with follow-up for 12 weeks from the initial procedure. Patients, clinicians, and pathologists were not masked to the study treatment. The primary endpoint was unexpected chest tube drainage, defined as requiring any chest tube after transbronchial cryobiopsy, or prolonged (>24 h) chest tube drainage after SLB. Secondary endpoints were diagnostic yield, in-hospital stay, pain, and serious adverse events. A modified intention-to-treat analysis was performed. This trial is registered with the Dutch Trial Register, NL7634, and is now closed. FINDINGS: Between April 8, 2019, and Oct 24, 2021, 122 patients with ILD were assessed for study participation; and 55 patients were randomly assigned to the step-up strategy (n=28) or immediate SLB (n=27); three patients from the immediate SLB group were excluded. Unexpected chest tube drainage occurred in three of 28 patients (11%; 95% CI 4-27%) in the step-up group, and the number of patients for whom the chest tube could not be removed within 24 h was 11 of 24 patients (46%; 95% CI 2-65%) in the SLB group, with an absolute risk reduction of 35% (11-56%; p=0·0058). In the step-up strategy, the multidisciplinary team diagnostic yield after transbronchial cryobiopsy alone was 82% (64-92%), which increased to 89% (73-96%) when subsequent SLB was performed after inconclusive transbronchial cryobiopsy. In the immediate surgery strategy, the multidisciplinary team diagnostic yield was 88% (69-97%). Total in-hospital stay was 1 day (IQR 1-1) in the step-up group versus 5 days (IQR 4-6) in the SLB group. One (4%) serious adverse event occurred in step-up strategy versus 12 (50%) in the immediate SLB strategy. INTERPRETATION: In ILD diagnosis, if lung tissue assessment is required, a diagnostic strategy starting with transbronchial cryobiopsy, followed by SLB when transbronchial cryobiopsy is inconclusive, appears to result in a significant reduction of patient burden and in-hospital stay with a similar diagnostic yield versus immediate SLB. FUNDING: Netherlands Organisation for Health Research and Development (ZonMW) and Amsterdam University Medical Centers.

Chemotherapy and the Extra-Tumor Immune Microenvironment: EXTRA-TIME.

SUMMARY: Understandably, conventional therapeutic strategies have focused on controlling primary tumors. We ask whether the cost of such strategies is actually an increased likelihood of metastatic relapse.

Clostridioides difficile infection is associated with differences in transcriptionally active microbial communities.

Clostridioides difficile infection (CDI) is responsible for around 300,000 hospitalizations yearly in the United States, with the associated monetary cost being billions of dollars. Gut microbiome dysbiosis is known to be important to CDI. To the best of our knowledge, metatranscriptomics (MT) has only been used to characterize gut microbiome composition and function in one prior study involving CDI patients. Therefore, we utilized MT to investigate differences in active community diversity and composition between CDI+ (n = 20) and CDI- (n = 19) samples with respect to microbial taxa and expressed genes. No significant (Kruskal-Wallis, p > 0.05) differences were detected for richness or evenness based on CDI status. However, clustering based on CDI status was significant for both active microbial taxa and expressed genes datasets (PERMANOVA, p ≤ 0.05). Furthermore, differential feature analysis revealed greater expression of the opportunistic pathogens Enterocloster bolteae and Ruminococcus gnavus in CDI+ compared to CDI- samples. When only fungal sequences were considered, the family Saccharomycetaceae expressed more genes in CDI-, while 31 other fungal taxa were identified as significantly (Kruskal-Wallis p ≤ 0.05, log(LDA) ≥ 2) associated with CDI+. We also detected a variety of genes and pathways that differed significantly (Kruskal-Wallis p ≤ 0.05, log(LDA) ≥ 2) based on CDI status. Notably, differential genes associated with biofilm formation were expressed by C. difficile. This provides evidence of another possible contributor to C. difficile's resistance to antibiotics and frequent recurrence in vivo. Furthermore, the greater number of CDI+ associated fungal taxa constitute additional evidence that the mycobiome is important to CDI pathogenesis. Future work will focus on establishing if C. difficile is actively producing biofilms during infection and if any specific fungal taxa are particularly influential in CDI.