Apoptotic cell fragments locally activate tingible body macrophages in the germinal center.

Germinal centers (GCs) that form within lymphoid follicles during antibody responses are sites of massive cell death. Tingible body macrophages (TBMs) are tasked with apoptotic cell clearance to prevent secondary necrosis and autoimmune activation by intracellular self antigens. We show by multiple redundant and complementary methods that TBMs derive from a lymph node-resident, CD169-lineage, CSF1R-blockade-resistant precursor that is prepositioned in the follicle. Non-migratory TBMs use cytoplasmic processes to chase and capture migrating dead cell fragments using a "lazy" search strategy. Follicular macrophages activated by the presence of nearby apoptotic cells can mature into TBMs in the absence of GCs. Single-cell transcriptomics identified a TBM cell cluster in immunized lymph nodes which upregulated genes involved in apoptotic cell clearance. Thus, apoptotic B cells in early GCs trigger activation and maturation of follicular macrophages into classical TBMs to clear apoptotic debris and prevent antibody-mediated autoimmune diseases.

Osteoclasts recycle via osteomorphs during RANKL-stimulated bone resorption.

Osteoclasts are large multinucleated bone-resorbing cells formed by the fusion of monocyte/macrophage-derived precursors that are thought to undergo apoptosis once resorption is complete. Here, by intravital imaging, we reveal that RANKL-stimulated osteoclasts have an alternative cell fate in which they fission into daughter cells called osteomorphs. Inhibiting RANKL blocked this cellular recycling and resulted in osteomorph accumulation. Single-cell RNA sequencing showed that osteomorphs are transcriptionally distinct from osteoclasts and macrophages and express a number of non-canonical osteoclast genes that are associated with structural and functional bone phenotypes when deleted in mice. Furthermore, genetic variation in human orthologs of osteomorph genes causes monogenic skeletal disorders and associates with bone mineral density, a polygenetic skeletal trait. Thus, osteoclasts recycle via osteomorphs, a cell type involved in the regulation of bone resorption that may be targeted for the treatment of skeletal diseases.

Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs.

The multi-subunit bacterial RNA polymerase (RNAP) and its associated regulators carry out transcription and integrate myriad regulatory signals. Numerous studies have interrogated RNAP mechanism, and RNAP mutations drive Escherichia coli adaptation to many health- and industry-relevant environments, yet a paucity of systematic analyses hampers our understanding of the fitness trade-offs from altering RNAP function. Here, we conduct a chemical-genetic analysis of a library of RNAP mutants. We discover phenotypes for non-essential insertions, show that clustering mutant phenotypes increases their predictive power for drawing functional inferences, and demonstrate that some RNA polymerase mutants both decrease average cell length and prevent killing by cell-wall targeting antibiotics. Our findings demonstrate that RNAP chemical-genetic interactions provide a general platform for interrogating structure-function relationships in vivo and for identifying physiological trade-offs of mutations, including those relevant for disease and biotechnology. This strategy should have broad utility for illuminating the role of other important protein complexes.

The UDP-Glycosyltransferase (UGT) Superfamily: New Members, New Functions, and Novel Paradigms.

UDP-glycosyltransferases (UGTs) catalyze the covalent addition of sugars to a broad range of lipophilic molecules. This biotransformation plays a critical role in elimination of a broad range of exogenous chemicals and by-products of endogenous metabolism, and also controls the levels and distribution of many endogenous signaling molecules. In mammals, the superfamily comprises four families: UGT1, UGT2, UGT3, and UGT8. UGT1 and UGT2 enzymes have important roles in pharmacology and toxicology including contributing to interindividual differences in drug disposition as well as to cancer risk. These UGTs are highly expressed in organs of detoxification (e.g., liver, kidney, intestine) and can be induced by pathways that sense demand for detoxification and for modulation of endobiotic signaling molecules. The functions of the UGT3 and UGT8 family enzymes have only been characterized relatively recently; these enzymes show different UDP-sugar preferences to that of UGT1 and UGT2 enzymes, and to date, their contributions to drug metabolism appear to be relatively minor. This review summarizes and provides critical analysis of the current state of research into all four families of UGT enzymes. Key areas discussed include the roles of UGTs in drug metabolism, cancer risk, and regulation of signaling, as well as the transcriptional and posttranscriptional control of UGT expression and function. The latter part of this review provides an in-depth analysis of the known and predicted functions of UGT3 and UGT8 enzymes, focused on their likely roles in modulation of levels of endogenous signaling pathways.

Two-Coordinate Thermally Activated Delayed Fluorescence Coinage Metal Complexes: Molecular Design, Photophysical Characters, and Device Application.

Since the emergence of the first green light emission from a fluorescent thin-film organic light emitting diode (OLED) in the mid-1980s, a global consumer market for OLED displays has flourished over the past few decades. This growth can primarily be attributed to the development of noble metal phosphorescent emitters that facilitated remarkable gains in electrical conversion efficiency, a broadened color gamut, and vibrant image quality for OLED displays. Despite these achievements, the limited abundance of noble metals in the Earth's crust has spurred ongoing efforts to discover cost-effective electroluminescent materials. One particularly promising avenue is the exploration of thermally activated delayed fluorescence (TADF), a mechanism with the potential to fully harness excitons in OLEDs. Recently, investigations have unveiled TADF in a series of two-coordinate coinage metal (Cu, Ag, and Au) complexes. These organometallic TADF materials exhibit distinctive behavior in comparison to their organic counterparts. They offer benefits such as tunable emissive colors, short TADF emission lifetimes, high luminescent quantum yields, and reasonable stability. Impressively, both vacuum-deposited and solution-processed OLEDs incorporating these materials have achieved outstanding performance. This review encompasses various facets on two-coordinate TADF coinage metal complexes, including molecular design, photophysical characterizations, elucidation of structure-property relationships, and OLED applications.

Modeling for COVID-19 college reopening decisions: Cornell, a case study.

We consider epidemiological modeling for the design of COVID-19 interventions in university populations, which have seen significant outbreaks during the pandemic. A central challenge is sensitivity of predictions to input parameters coupled with uncertainty about these parameters. Nearly 2 y into the pandemic, parameter uncertainty remains because of changes in vaccination efficacy, viral variants, and mask mandates, and because universities' unique characteristics hinder translation from the general population: a high fraction of young people, who have higher rates of asymptomatic infection and social contact, as well as an enhanced ability to implement behavioral and testing interventions. We describe an epidemiological model that formed the basis for Cornell University's decision to reopen for in-person instruction in fall 2020 and supported the design of an asymptomatic screening program instituted concurrently to prevent viral spread. We demonstrate how the structure of these decisions allowed risk to be minimized despite parameter uncertainty leading to an inability to make accurate point estimates and how this generalizes to other university settings. We find that once-per-week asymptomatic screening of vaccinated undergraduate students provides substantial value against the Delta variant, even if all students are vaccinated, and that more targeted testing of the most social vaccinated students provides further value.

Spns1 is a lysophospholipid transporter mediating lysosomal phospholipid salvage.

The lysosome is central to the degradation of proteins, carbohydrates, and lipids and their salvage back to the cytosol for reutilization. Lysosomal transporters for amino acids, sugars, and cholesterol have been identified, and the metabolic fates of these molecules in the cytoplasm have been elucidated. Remarkably, it is not known whether lysosomal salvage exists for glycerophospholipids, the major constituents of cellular membranes. By using a transport assay screen against orphan lysosomal transporters, we identified the major facilitator superfamily protein Spns1 that is ubiquitously expressed in all tissues as a proton-dependent lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE) transporter, with LPC and LPE being the lysosomal breakdown products of the most abundant eukaryotic phospholipids, phosphatidylcholine and phosphatidylethanolamine, respectively. Spns1 deficiency in cells, zebrafish embryos, and mouse liver resulted in lysosomal accumulation of LPC and LPE species with pathological consequences on lysosomal function. Flux analysis using stable isotope-labeled phospholipid apolipoprotein E nanodiscs targeted to lysosomes showed that LPC was transported out of lysosomes in an Spns1-dependent manner and re-esterified back into the cytoplasmic pools of phosphatidylcholine. Our findings identify a phospholipid salvage pathway from lysosomes to the cytosol that is dependent on Spns1 and critical for maintaining normal lysosomal function.

Airway wall extracellular matrix changes induced by bronchial thermoplasty in severe asthma.

BACKGROUND: Airway remodeling is a prominent feature of asthma, which involves increased airway smooth muscle mass and altered extracellular matrix composition. Bronchial thermoplasty (BT), a bronchoscopic treatment for severe asthma, targets airway remodeling. OBJECTIVE: We sought to investigate the effect of BT on extracellular matrix composition and its association with clinical outcomes. METHODS: This is a substudy of the TASMA trial. Thirty patients with severe asthma were BT-treated, of whom 13 patients were treated for 6 months with standard therapy (control group) before BT. Demographic data, clinical data including pulmonary function, and bronchial biopsies were collected. Biopsies at BT-treated and nontreated locations were analyzed by histological and immunohistochemical staining. Associations between histology and clinical outcomes were explored. RESULTS: Six months after treatment, it was found that the reticular basement membrane thickness was reduced from 7.28 µm to 5.74 µm (21% relative reduction) and the percentage area of tissue positive for collagen increased from 26.3% to 29.8% (13% relative increase). Collagen structure analysis revealed a reduction in the curvature frequency of fibers. The percentage area positive for fibulin-1 and fibronectin increased by 2.5% and 5.9%, respectively (relative increase of 124% and 15%). No changes were found for elastin. The changes in collagen and fibulin-1 negatively associated with changes in FEV1 reversibility. CONCLUSIONS: Besides reduction of airway smooth muscle mass, BT has an impact on reticular basement membrane thickness and the extracellular matrix arrangement characterized by an increase in tissue area occupied by collagen with a less dense fiber organization. Both collagen and fibulin-1 are negatively associated with the change in FEV1 reversibility.

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.

Airway smooth muscle and long-term clinical efficacy following bronchial thermoplasty in severe asthma.

The mechanism of action of bronchial thermoplasty (BT) treatment for patients with severe asthma is incompletely understood. This study investigated the 2.5-year impact of BT on airway smooth muscle (ASM) mass and clinical parameters by paired data analysis in 22 patients. Our findings demonstrate the persistence of ASM mass reduction of >50% after 2.5 years. Furthermore, sustained improvement in asthma control, quality of life and exacerbation rates was found, which is in line with previous reports. An association was found between the remaining ASM and both the exacerbation rate (r=0.61, p=0.04 for desmin, r=0.85, p<0.01 for alpha smooth muscle actin (SMA)) and post-bronchodilator forced expiratory volume in 1 s predicted percentage (r=-0.69, p=0.03 for desmin, r=-0.58, p=0.08 for alpha SMA). This study provides new insight into the long-term impact of BT.

ENTRAIN: integrating trajectory inference and gene regulatory networks with spatial data to co-localize the receptor-ligand interactions that specify cell fate.

MOTIVATION: Cell fate is commonly studied by profiling the gene expression of single cells to infer developmental trajectories based on expression similarity, RNA velocity, or statistical mechanical properties. However, current approaches do not recover microenvironmental signals from the cellular niche that drive a differentiation trajectory. RESULTS: We resolve this with environment-aware trajectory inference (ENTRAIN), a computational method that integrates trajectory inference methods with ligand-receptor pair gene regulatory networks to identify extracellular signals and evaluate their relative contribution towards a differentiation trajectory. The output from ENTRAIN can be superimposed on spatial data to co-localize cells and molecules in space and time to map cell fate potentials to cell-cell interactions. We validate and benchmark our approach on single-cell bone marrow and spatially resolved embryonic neurogenesis datasets to identify known and novel environmental drivers of cellular differentiation. AVAILABILITY AND IMPLEMENTATION: ENTRAIN is available as a public package at https://github.com/theimagelab/entrain and can be used on both single-cell and spatially resolved datasets.

Activation of Cryptic Donor Splice Sites within the UDP-Glucuronosyltransferase (UGT)1A First-Exon Region Generates Variant Transcripts That Encode UGT1A Proteins with Truncated Aglycone-Binding Domains.

The human UDP-glucuronosyltransferases (UGTs) have crucial roles in metabolizing and clearing numerous small lipophilic compounds. The UGT1A locus generates nine UGT1A mRNAs, 65 spliced transcripts, and 34 circular RNAs. In this study, our analysis of published UGT-RNA capture sequencing (CaptureSeq) datasets identified novel splice junctions that predict 24 variant UGT1A transcripts derived from ligation of exon 2 to unique sequences within the UGT1A first-exon region using cryptic donor splice sites. Of these variants, seven (1A1_n1, 1A3_n3, 1A4_n4, 1A5_n1, 1A8_n2, 1A9_n2, 1A10_n7) are predicted to encode UGT1A proteins with truncated aglycone-binding domains. We assessed their expression profiles and deregulation in cancer using four RNA sequencing (RNA-Seq) datasets of paired normal and cancerous drug-metabolizing tissues from large patient cohorts. Variants were generally coexpressed with their canonical counterparts with a higher relative abundance in tumor than in normal tissues. Variants showed tissue-specific expression with high interindividual variability but overall low abundance. However, 1A8_n2 showed high abundance in normal and cancerous colorectal tissues, with levels that approached or surpassed canonical 1A8 mRNA levels in many samples. We cloned 1A8_n2 and showed expression of the predicted protein (1A8_i3) in human embryonic kidney (HEK)293T cells. Glucuronidation assays with 4-methylumbelliferone (4MU) showed that 1A8_i3 had no activity and was unable to inhibit the activity of 1A8_i1 protein. In summary, the activation of cryptic donor splice sites within the UGT1A first-exon region expands the UGT1A transcriptome and proteome. The 1A8_n2 cryptic donor splice site is highly active in colorectal tissues, representing an important cis-regulatory element that negatively regulates the function of the UGT1A8 gene through pre-mRNA splicing. SIGNIFICANT STATEMENT: The UGT1A locus generates nine canonical mRNAs, 65 alternately spliced transcripts, and 34 different circular RNAs. The present study reports a series of novel UDP-glucuronosyltransferase (UGT)1A variants resulting from use of cryptic donor splice sites in both normal and cancerous tissues, several of which are predicted to encode variant UGT1A proteins with truncated aglycone-binding domains. Of these, 1A8_n2 shows exceptionally high abundance in colorectal tissues, highlighting its potential role in the first-pass metabolism in gut through the glucuronidation pathway.

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.

Blue carbon sink capacity of mangroves determined by leaves and their associated microbiome.

Mangroves play a globally significant role in carbon capture and storage, known as blue carbon ecosystems. Yet, there are fundamental biogeochemical processes of mangrove blue carbon formation that are inadequately understood, such as the mechanisms by which mangrove afforestation regulates the microbial-driven transfer of carbon from leaf to below-ground blue carbon pool. In this study, we addressed this knowledge gap by investigating: (1) the mangrove leaf characteristics using state-of-the-art FT-ICR-MS; (2) the microbial biomass and their transformation patterns of assimilated plant-carbon; and (3) the degradation potentials of plant-derived carbon in soils of an introduced (Sonneratia apetala) and a native mangrove (Kandelia obovata). We found that biogeochemical cycling took entirely different pathways for S. apetala and K. obovata. Blue carbon accumulation and the proportion of plant-carbon for native mangroves were high, with microbes (dominated by K-strategists) allocating the assimilated-carbon to starch and sucrose metabolism. Conversely, microbes with S. apetala adopted an r-strategy and increased protein- and nucleotide-biosynthetic potentials. These divergent biogeochemical pathways were related to leaf characteristics, with S. apetala leaves characterized by lower molecular-weight, C:N ratio, and lignin content than K. obovata. Moreover, anaerobic-degradation potentials for lignin were high in old-aged soils, but the overall degradation potentials of plant carbon were age-independent, explaining that S. apetala age had no significant influences on the contribution of plant-carbon to blue carbon. We propose that for introduced mangroves, newly fallen leaves release nutrient-rich organic matter that favors growth of r-strategists, which rapidly consume carbon to fuel growth, increasing the proportion of microbial-carbon to blue carbon. In contrast, lignin-rich native mangrove leaves shape K-strategist-dominated microbial communities, which grow slowly and store assimilated-carbon in cells, ultimately promoting the contribution of plant-carbon to the remarkable accumulation of blue carbon. Our study provides new insights into the molecular mechanisms of microbial community responses during reforestation in mangrove ecosystems.

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.

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.

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.

Plastic Paradox in Blue Carbon Ecosystems.

Plastics are rapidly accumulating in blue carbon ecosystems, i.e., mangrove forests, tidal marshes, and seagrass meadows. Accumulated plastic is diverted from the ocean, but the extent and nature of impacts on blue carbon ecosystem processes, including carbon sequestration, are poorly known. Here, we explore the potential positive and negative consequences of plastic accumulation in blue carbon ecosystems. We highlight the effects of plastic accumulation on organic carbon stocks and sediment biogeochemistry through microbial metabolism. The notion of beneficial plastic accumulation in blue carbon ecosystems is controversial, yet considering the alternative impacts of plastics on oceanic and aboveground environments, this may be the "lesser of evils". Using environmental life cycle impact assessment, we propose a research framework to address the potential positive and negative impacts of plastic accumulation in blue carbon ecosystems. Considering the multifaceted benefits, we prioritize expanding and managing blue carbon ecosystems, which may help with ecosystem conservation, as well as mitigating the negative effects of plastic.

Bis-oxazoline derivatives as ancillary ligands for bis-cyclometalated iridium complexes.

Organometallic iridium complexes with two cyclometalated ligands (CN) and one bis-oxazoline derived ancillary ligand (L^X), i.e. (CN)2Ir(L^X), are reported. The CN ligands are 1-phenylpyrazoline (ppz), 2-(4,6-difluorophenyl)pyridine (F2ppy), 2-phenylpyridine (ppy), 1-phenylisoquinoline (piq). The box ligand is (4S)-(+)-phenyl-α-[(4S)-phenyloxazolidin-2-ylidene]-2-oxazoline-2-acetonitrile. The emission of these complexes span across the visible and into the near-ultraviolet region of the electromagnetic spectrum with moderate to high photoluminescence quantum yields (ΦPL = 0.45-1.0). These complexes were found to emit from a metal-ligand to ligand charge transfer (ML'LCT) state and have lifetimes (1.3-2.1 µs), radiative rates (105 s-1), and nonradiative rates (104-105 s-1) comparable to state-of-the-art iridium emitters. The (ppy)2Ir(BOX-CN) complexes were resolved into the Δ- and Λ- diastereomers using differences in their solubility and additionally characterized by x-ray crystallography, stability, and chiroptic studies. The high ΦPL of these isomers results in the best to date brightness for circularly polarized luminescence (CPL) from iridium complexes (7.0 M-1 cm-1), with dissymmetry factors of -0.57 × 10-3 and +1.9 × 10-3 for 3Δ and 3Λ, respectively. The significant difference in CPL magnitude between 3Δ and 3Λ likely arises from interligand interactions (edge-to-face arrangement versus strong π-π interaction) for the pendant phenyl ring of the BOX-CN ligand which differ for the two isomers.