bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual-AAV split prime editor corrects the mutation and phenotype in mice with inherited retinal degeneration
Authors: She Kaiqin , Liu Yi , Zhao Qinyu , Jin Xiu , Yang Yiliu , Su Jing , Li Ruiting , Song Li , Xiao Jianlu , Yao Shaohua , Lu Fang , Wei Yuquan , Yang Yang 
Published: February 2023

AbstractThe prime editor (PE) can edit genomes with almost any intended changes, including all 12 possible types of base substitutions, small insertions and deletions, and their combinations, without the requirement for double strand breaks or exogenous donor templates. PE demonstrates the possibility of correcting a variety of disease-causing mutations and might expand the therapeutic application of gene editing. In this study, PE was optimized based on a dual-adeno-associated virus (AAV) split-intein system in vitro by screening different split sites and split inteins. We found that splitting PE before amino acid 1105(Ser) of SpCas9 with Rma intein resulted in the highest on-target editing. The orientations of pegRNA and nicking sgRNA in the AAV vector were further optimized. To test the in vivo performance of the optimized dual-AAV split-PE3, it was delivered by subretinal injection in rd12 mice with inherited retinal disease Leber congenital amaurosis. The prime editors corrected the pathogenic mutation with up to 16% efficiency in a precise way, with no detectable off-target edits, restored RPE65 expression, rescued retinal and visual function, and preserved photoceptors. Our findings establish a framework for the preclinical development of PE and motivate further testing of PE for the treatment of inherited retinal diseases caused by various mutations.
Restoration of lipid homeostasis between TG and PE by the LXRα-ATGL/EPT1 axis ameliorates hepatosteatosis
Authors: Chen Yulian , Jiang Huanguo , Zhan Zhikun , Lu Jindi , Gu Tanwei , Yu Ping , Liang Weimin , Zhang Xi , Liu Shuwen , Bi Huichang , Zhong Shilong , Tang Lan 
Published: February 2023

AbstractConverting lipid disturbances in response to energy oversupply into healthy lipid homeostasis is a promising therapy to alleviate hepatosteatosis. Our clinical studies found that a further elevation of triglyceride (TG) in obese patients with the body mass index (BMI) greater than 28 was accompanied by a further reduction of phosphatidylethanolamine (PE). Shorter survival and poor prognosis were shown for the patients with high TG and low PE levels. Liver X receptor alpha (LXRα) knockout mice aggravated high-fat diet (HFD)-induced obesity and lipid disorders, making the TG enrichment and the PE decrease more pronounced according to the liver lipidomics analysis. The RNA-seq from mice liver exhibited that these metabolism disorders were attributed to the decline of Atgl (encoding the TG metabolism enzyme ATGL) and Ept1 (encoding the PE synthesis enzyme EPT1) expression. Mechanistic studies uncovered that LXRα activated the ATGL and EPT1 gene via direct binding to a LXR response element (LXRE) in the promoter. Moreover, both the supplement of PE in statin or fibrate therapy, and the LXRα inducer (oridonin) ameliorated cellular lipid deposition and lipotoxicity. Altogether, restoration of lipid homeostasis of TG and PE via the LXRα-ATGL/EPT1 axis may be a potential approach for the management of hepatosteatosis and metabolic syndrome.
FcγRIIIA activation-mediated up-regulation of glycolysis alters MDSCs modulation in CD4+ T cell subsets of Sjögren syndrome
Authors: Qi Jingjing , Zhou Xinyang , Bai Ziran , Lu Zhimin , Zhu Xiaolu , Liu Jiaqing , Wang Junli , Jin Minli , Liu Chang , Li Xia 
Published: February 2023

AbstractOur and other researchers’ previous studies found that myeloid-derived suppressor cells (MDSCs) were increased, and these MDSCs, supposed to play immunosuppressive roles, showed significant pro-inflammatory effects in Sjögren’s syndrome (SS). However, the key factors and potential mechanisms leading MDSCs to be inflammatory remain unclear. In this study, we found that MDSCs from SS patients were positively correlated with the percentages of Th17 cells, disease activity and serum autoantibodies, and showed higher levels of Fc gamma receptor (FcγR) IIIA and glycolysis. Most importantly, SS MDSCs or heat-aggregated IgG (HAIG)-treated MDSCs down-regulated Th1/Th2 ratio and up-regulated Th17/Treg ratio, which could be obviously rescued by IgG monomer or glycolysis inhibitor 2-DG. As well, the levels of FcγRIV and glycolysis in MDSCs and the ratio of Th17/Treg were increased, and the ratio of Th1/Th2 was decreased in SS-like NOD mice. Our study indicated that MDSCs showed pro-inflammatory phenotypes by disturbing CD4+ T-cell balances in SS. The pro-inflammatory effects of MDSCs might be directly linked to the enhanced glycolysis mediated by FcγRIIIA activation.
Dendritiform immune cells with reduced antigen-capture capacity persist in the cornea during the asymptomatic phase of allergic conjunctivitis
Authors: Tajbakhsh Zahra , Jalbert Isabelle , Stapleton Fiona , Alghamdi Ali , Gray Paul E. , Briggs Nancy , Altavilla Betina , Mobeen Rabia , Golebiowski Blanka 
Published: February 2023

Abstract
Background
Increased density and altered morphology of dendritic cells (DC) in the cornea and conjunctiva occur during active allergic conjunctivitis. This study investigated whether inflammation (characterised by altered DC density and morphology) persists during the symptom-free phase of allergic conjunctivitis.

Methods
Twenty participants (age 43.3 ± 14.3 years, 55% female) assessed during their active (symptomatic) phase of allergic conjunctivitis were re-examined during the asymptomatic phase. Ocular allergy symptoms and signs were evaluated during both phases, and five ocular surface locations (corneal centre, inferior whorl, corneal periphery, corneal limbus, and bulbar conjunctiva) were examined using in vivo confocal microscopy (HRT III). DC were counted manually, and their morphology was assessed for cell body size, presence of dendrites, presence of long dendrites and presence of thick dendrites using a grading system. Mixed model analysis (DC density) and non-parametric tests (DC morphology) were used to examine differences between phases.

Results
DC density at corneal locations did not change between the active and asymptomatic phases (p ≥ 0.22). However, corneal DC body size was smaller and fewer DC presented with long dendrites during the asymptomatic phase (p ≤ 0.02). In contrast, at the bulbar conjunctiva, DC density was reduced during the asymptomatic phase compared to the active phase (p = 0.01), but there were no changes in DC morphology.

Conclusions
Dendritiform immune cell numbers persist in the cornea during the symptom-free phase of allergic conjunctivitis, whereas conjunctival DC appear to return to a baseline state. The morphology of these persisting corneal DC suggests their antigen-capture capacity is reduced during the asymptomatic phase.
Direct digital sensing of protein biomarkers in solution
Authors: Krainer Georg , Saar Kadi L. , Arter William E. , Welsh Timothy J. , Czekalska Magdalena A. , Jacquat Raphaël P. B. , Peter Quentin , Traberg Walther C. , Pujari Arvind , Jayaram Akhila K. , Challa Pavankumar , Taylor Christopher G. , van der Linden Lize-Mari , Franzmann Titus , Owens Roisin M. , Alberti Simon , Klenerman David , Knowles Tuomas P. J. 
Published: February 2023

AbstractThe detection of proteins is of central importance to biomolecular analysis and diagnostics. Typical immunosensing assays rely on surface-capture of target molecules, but this constraint can limit specificity, sensitivity, and the ability to obtain information beyond simple concentration measurements. Here we present a surface-free, single-molecule microfluidic sensing platform for direct digital protein biomarker detection in solution, termed digital immunosensor assay (DigitISA). DigitISA is based on microchip electrophoretic separation combined with single-molecule detection and enables absolute number/concentration quantification of proteins in a single, solution-phase step. Applying DigitISA to a range of targets including amyloid aggregates, exosomes, and biomolecular condensates, we demonstrate that the assay provides information beyond stoichiometric interactions, and enables characterization of immunochemistry, binding affinity, and protein biomarker abundance. Taken together, our results suggest a experimental paradigm for the sensing of protein biomarkers, which enables analyses of targets that are challenging to address using conventional immunosensing approaches.
Conformation-dependent dynamic organic phosphorescence through thermal energy driven molecular rotations
Authors: Wei Juan , Liu Chenyuan , Duan Jiayu , Shao Aiwen , Li Jinlu , Li Jiangang , Gu Wenjie , Li Zixian , Liu Shujuan , Ma Yun , Huang Wei , Zhao Qiang 
Published: February 2023

AbstractOrganic room-temperature phosphorescent (RTP) materials exhibiting reversible changes in optical properties upon exposure to external stimuli have shown great potential in diverse optoelectronic fields. Particularly, dynamic manipulation of response behaviors for such materials is of fundamental significance, but it remains a formidable challenge. Herein, a series of RTP polymers were prepared by incorporating phosphorescent rotors into polymer backbone, and these materials show color-tunable persistent luminescence upon excitation at different wavelengths. Experimental results and theoretical calculations revealed that the various molecular conformations of monomers are responsible for the excitation wavelength-dependent (Ex-De) RTP behavior. Impressively, after gaining insights into the underlying mechanism, dynamic control of Ex-De RTP behavior was achieved through thermal energy driven molecular rotations of monomers. Eventually, we demonstrate the practical applications of these amorphous polymers in anti-counterfeiting areas. These findings open new opportunities for the control of response behaviors of smart-responsive RTP materials through external stimuli rather than conventional covalent modification method.
Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin
Authors: Geller-McGrath David , Mara Paraskevi , Taylor Gordon T. , Suter Elizabeth , Edgcomb Virginia , Pachiadaki Maria 
Published: February 2023

AbstractSecondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds. Here, we use metagenomics and metatranscriptomics to analyze BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela. We recovered 565 bacterial and archaeal metagenome-assembled genomes (MAGs) and identified 1154 diverse BGCs. We show that differences in water redox potential and microbial lifestyle (particle-associated vs. free-living) are associated with variations in the predicted composition and production of secondary metabolites. Our results indicate that microbes, including understudied clades such as Planctomycetota, potentially produce a wide range of secondary metabolites in these anoxic/euxinic waters.
Dearomative triple elementalization of quinolines driven by visible light
Authors: Ishigaki Shiho , Nagashima Yuki , Yukimori Daiki , Tanaka Jin , Matsumoto Takashi , Miyamoto Kazunori , Uchiyama Masanobu , Tanaka Ken 
Published: February 2023

AbstractOrganoboron and organosilicon compounds are used not only as synthetic building blocks but also as functional materials and pharmaceuticals, and compounds with multiple boryl and silyl groups are beginning to be used for these purposes. Especially in drug discovery, methodology providing easy stereoselective access to aliphatic nitrogen heterocycles bearing multiple boryl or silyl groups from readily available aromatic nitrogen heterocycles would be attractive. However, such transformations remain challenging, and available reactions have been mostly limited to dearomative hydroboration or hydrosilylation reactions. Here, we report the dearomative triple elementalization (carbo-sila-boration) of quinolines via the addition of organolithium followed by photo-boosted silaboration, affording the desired products with complete chemo-, regio-, and stereoselectivity. The reaction proceeds via the formation of silyl radicals instead of silyl anions. We also present preliminary studies to illustrate the potential of silaboration products as synthetic platforms.
Isoform- and ligand-specific modulation of the adhesion GPCR ADGRL3/Latrophilin3 by a synthetic binder
Authors: Kordon Szymon P. , Dutka Przemysław , Adamska Justyna M. , Bandekar Sumit J. , Leon Katherine , Erramilli Satchal K. , Adams Brock , Li Jingxian , Kossiakoff Anthony A. , Araç Demet 
Published: February 2023

AbstractAdhesion G protein-coupled receptors (aGPCRs) are cell-surface proteins with large extracellular regions that bind to multiple ligands to regulate key biological functions including neurodevelopment and organogenesis. Modulating a single function of a specific aGPCR isoform while affecting no other function and no other receptor is not trivial. Here, we engineered an antibody, termed LK30, that binds to the extracellular region of the aGPCR ADGRL3, and specifically acts as an agonist for ADGRL3 but not for its isoform, ADGRL1. The LK30/ADGRL3 complex structure revealed that the LK30 binding site on ADGRL3 overlaps with the binding site for an ADGRL3 ligand – teneurin. In cellular-adhesion assays, LK30 specifically broke the trans-cellular interaction of ADGRL3 with teneurin, but not with another ADGRL3 ligand – FLRT3. Our work provides proof of concept for the modulation of isoform- and ligand-specific aGPCR functions using unique tools, and thus establishes a foundation for the development of fine-tuned aGPCR-targeted therapeutics.
Small-molecule-mediated OGG1 inhibition attenuates pulmonary inflammation and lung fibrosis in a murine lung fibrosis model
Authors: Tanner L. , Single A. B. , Bhongir R. K. V. , Heusel M. , Mohanty T. , Karlsson C. A. Q. , Pan L. , Clausson C-M. , Bergwik J. , Wang K. , Andersson C. K. , Oommen R. M. , Erjefält J. S. , Malmström J. , Wallner O. , Boldogh I. , Helleday T. , Kalderén C. , Egesten A. 
Published: February 2023

AbstractInterstitial lung diseases such as idiopathic pulmonary fibrosis (IPF) are caused by persistent micro-injuries to alveolar epithelial tissues accompanied by aberrant repair processes. IPF is currently treated with pirfenidone and nintedanib, compounds which slow the rate of disease progression but fail to target underlying pathophysiological mechanisms. The DNA repair protein 8-oxoguanine DNA glycosylase-1 (OGG1) has significant roles in the modulation of inflammation and metabolic syndromes. Currently, no pharmaceutical solutions targeting OGG1 have been utilized in the treatment of IPF. In this study we show Ogg1-targeting siRNA mitigates bleomycin-induced pulmonary fibrosis in male mice, highlighting OGG1 as a tractable target in lung fibrosis. The small molecule OGG1 inhibitor, TH5487, decreases myofibroblast transition and associated pro-fibrotic gene expressions in fibroblast cells. In addition, TH5487 decreases levels of pro-inflammatory mediators, inflammatory cell infiltration, and lung remodeling in a murine model of bleomycin-induced pulmonary fibrosis conducted in male C57BL6/J mice. OGG1 and SMAD7 interact to induce fibroblast proliferation and differentiation and display roles in fibrotic murine and IPF patient lung tissue. Taken together, these data suggest that TH5487 is a potentially clinically relevant treatment for IPF but further study in human trials is required.
High-throughput single-molecule quantification of individual base stacking energies in nucleic acids
Authors: Abraham Punnoose Jibin , Thomas Kevin J. , Chandrasekaran Arun Richard , Vilcapoma Javier , Hayden Andrew , Kilpatrick Kacey , Vangaveti Sweta , Chen Alan , Banco Thomas , Halvorsen Ken 
Published: February 2023

AbstractBase stacking interactions between adjacent bases in DNA and RNA are important for many biological processes and in biotechnology applications. Previous work has estimated stacking energies between pairs of bases, but contributions of individual bases has remained unknown. Here, we use a Centrifuge Force Microscope for high-throughput single molecule experiments to measure stacking energies between adjacent bases. We found stacking energies strongest between purines (G|A at −2.3 ± 0.2 kcal/mol) and weakest between pyrimidines (C|T at −0.5 ± 0.1 kcal/mol). Hybrid stacking with phosphorylated, methylated, and RNA nucleotides had no measurable effect, but a fluorophore modification reduced stacking energy. We experimentally show that base stacking can influence stability of a DNA nanostructure, modulate kinetics of enzymatic ligation, and assess accuracy of force fields in molecular dynamics simulations. Our results provide insights into fundamental DNA interactions that are critical in biology and can inform design in biotechnology applications.
Establishment and validation of a plasma oncofetal chondroitin sulfated proteoglycan for pan-cancer detection
Authors: Zhang Pei-Fen , Wu Zi-Yi , Zhang Wen-Bin , He Yong-Qiao , Chen Kexin , Wang Tong-Min , Li Haixin , Zheng Hong , Li Dan-Hua , Yang Da-Wei , Zhou Ting , Deng Chang-Mi , Liao Ying , Xue Wen-Qiong , Cao Lian-Jing , Li Xi-Zhao , Zhang Jiang-Bo , Dong Si-Qi , Wang Fang , Zheng Mei-Qi , Zhang Wen-Li , Mu Jianbing , Jia Wei-Hua 
Published: February 2023

AbstractVarious biomarkers targeting cell-free DNA (cfDNA) and circulating proteins have been tested for pan-cancer detection. Oncofetal chondroitin sulfate (ofCS), which distinctively modifies proteoglycans (PGs) of most cancer cells and binds specifically to the recombinant Plasmodium falciparum VAR2CSA proteins (rVAR2), is explored for its potential as a plasma biomarker in pan-cancer detection. To quantitate the plasma ofCS/ofCSPGs, we optimized an ELISA using different capture/detection pairs (rVAR2/anti-CD44, -SDC1, and -CSPG4) in a case-control study with six cancer types. We show that the plasma levels of ofCS/ofCSPGs are significantly higher in cancer patients (P values, 1.2 × 10−2 to 4.4 × 10−10). Validation studies are performed with two independent cohorts covering 11 malignant tumors. The individuals in the top decile of ofCS-CD44 have more than 27-fold cancer risk (OR = 27.8, 95%CI = 18.8–41.4, P = 2.72 × 10−62) compared with the lowest 20%. Moreover, the elevated plasma ofCS-CD44 could be detected at the early stage of pan-cancer with strong dose-dependent odds risk prediction.
Thermal expansion and the glass transition
Authors: Lunkenheimer Peter , Loidl Alois , Riechers Birte , Zaccone Alessio , Samwer Konrad 
Published: February 2023

AbstractMelting is well understood in terms of the Lindemann criterion, which essentially states that crystalline materials melt when the thermal vibrations of their atoms become so vigorous that they shake themselves free of the binding forces. This picture does not necessarily have to hold for glasses, where the nature of the solid–liquid cross-over is highly debated. The Lindemann criterion implies that the thermal expansion coefficients of crystals are inversely proportional to their melting temperatures. Here we find that, in contrast, the thermal expansion coefficient of glasses decreases more strongly with increasing glass temperature, which marks the liquid–solid cross-over in this material class. However, this proportionality returns when the thermal expansion coefficient is scaled by the fragility, a measure of particle cooperativity. Therefore, for a glass to become liquid, it is not sufficient to simply overcome the interparticle binding energies. Instead, more energy must be invested to break up the typical cooperative particle network that is common to glassy materials. The thermal expansion coefficient of the liquid phase reveals similar anomalous behaviour and is universally enhanced by a constant factor of approximately 3. These universalities allow the estimation of glass temperatures from thermal expansion and vice versa.
The volatile organic compounds and palatability of mixed ensilage of marigold (Tagetes erecta L.) crop residues
Authors: Hou Zhijiang , Liu Jianyong , Cai Ming , Liu Yanpei , Zhang Meiyan , Wang Ling , Yang Wengao , Huang Bizhi 
Published: February 2023

AbstractWith increasing acreage of cash crops, the use of their by-products as supplements for livestock feed becomes an important factor. Marigold (Tagetes erecta L.) account for more than half of the world’s loose flower production. However, there is no precedent for the abundantly available marigold crop residue (MCR) being used as feed in agricultural production, probably because of its strong pungent taste. This study aimed to evaluate the biotransformation of the volatile organic compounds (VOCs) of MCR by mixed ensilage and assess its palatability by cattle. Caryophyllene, the most prevalent VOC in MCR, decreased by 29.11% (P < 0.05), 38.85% (P < 0.05), 37.15% (P < 0.05), and 28.36% (P < 0.05) ensilage with corn meal (CM), bran (BR), crop corn (CC), and straw (ST), respectively. The acetic acid content increased by 686.05% (P < 0.05), 1337.21% (P < 0.05), 1244.19% (P < 0.05), and 1795.34% (P < 0.05) after mixed ensilage with CM, BR, CC, and ST, respectively. The total amount of alcoholic VOCs followed an overall increasing trend during mixed storage and 10 new alcohols were obtained. Over seven days, feed intake of mixed ensilage MCR by cattle differed significantly (P < 0.05) among treatments compared with MCR and was highest in MCRCM. Combined with palatability trials, the best MCR feed intake was achieved with MCRCM. The findings shed light on how feed odor can be improved and how degradation of terpenes can be enhanced in practical applications by mixed ensilage.
Simultaneous detection of omicron and other SARS-CoV-2 variants by multiplex PCR MassARRAY technology
Authors: Wacharapluesadee Supaporn , Hirunpatrawong Piyapha , Petcharat Sininat , Torvorapanit Pattama , Jitsatja Anusara , Thippamom Nattakarn , Ninwattana Sasiprapa , Phanlop Chanchanit , Buathong Rome , Tangwangvivat Ratanaporn , Klungthong Chonticha , Chinnawirotpisan Piyawan , Hunsawong Taweewun , Suthum Krairerk , Komolsiri Suparerk , Jones Anthony R. , Fernandez Stefan , Putcharoen Opass 
Published: February 2023

AbstractThe rapid emergence of SARS-CoV-2 variants with high severity and transmutability adds further urgency for rapid and multiplex molecular testing to identify the variants. A nucleotide matrix-assisted laser-desorption-ionization time-of-flight mass spectrophotometry (MALDI-TOF MS)-based assay was developed (called point mutation array, PMA) to identify four major SARS-CoV-2 variants of concern (VOCs) including Alpha, Beta, Delta, and Omicron (namely PMA-ABDO) and differentiate Omicron subvariant (namely PMA-Omicron). PMA-ABDO and PMA-Omicron consist of 24 and 28 mutation sites of the spike gene. Both PMA panels specifically identified VOCs with as low as 10 viral copies/µl. The panel has shown a 100% concordant with the Next Generation Sequencing (NGS) results testing on 256 clinical specimens with real-time PCR cycle threshold (Ct) values less than 26. It showed a higher sensitivity over NGS; 25/28 samples were positive by PMA but not NGS in the clinical samples with PCR Ct higher than 26. Due to the mass of nucleotide used to differentiate between wild-type and mutation strains, the co-infection or recombination of multiple variants can be determined by the PMA method. This method is flexible in adding a new primer set to identify a new emerging mutation site among the current circulating VOCs and the turnaround time is less than 8 h. However, the spike gene sequencing or NGS retains the advantage of detecting newly emerged variants.