bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early regional lymph node activation drives influenza vaccine responses in an ancestrally diverse cohort
Authors: Siu Jacqueline HY , Coelho Sofia , Palomeras Aime , Belij-Rammerstorfer Sandra , Lee Chloe H , Strobel Tamara , Thorpe Christopher , Kaur Charandeep , Cole Tom , Remmert Nico , Fowler Jamie , Pledger Sam , Dooley Kyla B , Opoka Daniel , Szommer Tamas , Vanderslott Samantha , Kaleebu Pontiano , Milicic Anita , Palmer Donald B , Lambe Teresa , Marsden Brian D , Koohey Hashem , Coles Mark , Dendrou Calliope A , Pollock Katrina M 
Published: November 2024

AbstractEarlyin vivodynamics of human immune-cell activation across regionally activated lymphoid tissue sites upon immunisation are poorly characterised in ancestrally diverse individuals. Here, we profiled draining and non-draining axillary lymph nodes (dLNs and ndLNs) by ultrasound-guided fine-needle aspiration (FNA) in 13 Black and Asian ancestry individuals, before and 3-7 days after vaccination with adjuvanted influenza vaccine. Draining but not ndLNs rapidly increased in size post-vaccination, by day 3, with distinct cellular dynamics determined through single cell multiomics. Dissecting LN cellular diversity into 42 lymphoid and non-lymphoid cell states, post-vaccination cell abundance changes were observed across all LNs, but dLNs were specifically characterised by CD4+T follicular helper (CD4+Tfh) cell expansion. Gene expression analysis revealed a dLN post-vaccination hub of multicellular activity defined by CD4+Tfh signalling, cross-compartmental activation, translation, and enhanced antigen-presentation capacity. Thus, robust responses to intramuscular immunisation transcending ancestral inter-individual variation are elicited through temporal, anatomical and cellular lymphatic co-ordination with implications for vaccine design in ancestrally diverse populations.SummaryIn this study of ancestrally diverse young adults, the temporarily co-ordinated response to an adjuvanted influenza vaccine at lymph nodes local to (draining) and distal from (non-draining) the injection site, reveals early regulation of cellular kinetics and anatomical hierarchy of the innate and adaptive immune responses.
BC-Design: A Biochemistry-Aware Framework for Highly Accurate Inverse Protein Folding
Authors: Tang Xiangru , Ye Xinwu , Wu Fang , Shao Daniel , Fang Yin , Chen Siming , Xu Dong , Gerstein Mark 
Published: November 2024

AbstractInverse protein folding, which aims to design amino acid sequences for desired protein structures, is fundamental to protein engineering and therapeutic development. While recent deep-learning approaches have made remarkable progress in addressing this challenge, they typically represent biochemical properties as discrete features associated with individual residues. Here, we present BC-Design, an approach that explicitly represents these properties as decorations on randomly sampled points on exterior surfaces and within internally bound regions representing the complete molecular extent of the protein. This provides a more natural way to capture the spatial distribution of properties. We demonstrate that BC-Designsignificantly outperforms all current methods, improving sequence recovery from 67% to88.37%over the state-of-the-art methods (a21.32%absolute improvement) and reducing perplexity from 2.4 to1.47(a39.51%relative improvement) on the CATH 4.2 benchmark. Notably, our model exhibits robust generalization across diverse protein characteristics, achieving consistently high performance on proteins of varying sizes (50-500 residues), structural complexity (measured by contact order), and all major CATH fold classes. Through ablation tests, we compare the relative contribution of both structure encoding information and the encoded property information, and we show that both substantially contribute equally to this strong performance. Overall, this opens new avenues for computational protein engineering and drug discovery.
Pathophysiological Implications of Nucleotide Self-Assembly: Adenine-Derived Nucleotides Aggregation in Disease Mechanisms
Authors: Dave Raj , Singh Ankur , Pandey Kshipra , Patel Ritu , Gour Nidhi , Bhatia Dhiraj 
Published: November 2024

AbstractAdenine nucleotides, including adenosine monophosphate, adenosine diphosphate, and adenosine triphosphate, play pivotal roles in cellular bioenergetics, nucleic acid metabolism, and signal transduction. However, their propensity to undergo self-assembly and form supramolecular aggregates under certain conditions is not well-characterized. In this study, we examined the self-assembly, aggregation, and cytotoxicity of AMP, ADP, and ATP in both fresh and aged conditions. Utilizing advanced microscopy techniques, Thioflavin T (ThT) fluorescence assays, and cross-seeding experiments, we identified oligomer formation in freshly prepared nucleotide solutions, which progressed to larger, more stable aggregates over time. The cytotoxic potential of these nucleotide aggregates was assessed using in vitro models, including human retinal pigment epithelial (RPE-1) and colorectal carcinoma (HCT-116) cell lines. Our findings demonstrate that nucleotide aggregation induces significant cytotoxic effects, particularly in aged conditions. Further investigations into bacterial toxicity models revealed similar deleterious impacts, indicating a broad-spectrum biological stress response to nucleotide aggregates. These results suggest that nucleotide self-assembly and aggregation may contribute to cellular dysfunction, offering new insights into their non-canonical roles in disease pathophysiology, potentially analogous to protein misfolding disorders.
RvD1 and LXA4 inhibitory effects on cardiac voltage-gated potassium channels
Authors: De la Cruz Alicia , Ronchi Carlotta , Bartolucci Chiara , Socuéllamos Paula G , Benito-Bueno Angela de , Severi Stefano , Zaza Antonio , Valenzuela Carmen 
Published: November 2024

AbstractAimsThe resolution of inflammation is modulated by specialized pro-resolving lipid mediators (SPMs), which can be modified in some cardiovascular diseases. Among them, RvD1 and LXA4prevent atrial fibrillation (AF) remodeling in the atria and cardiac hypertrophy, respectively in animal models. However, little is known about their electrophysiological effects on cardiac voltage-gated (VG) ion channels.Methods and resultsWe used the patch-clamp technique in heterologous systems and cardiomyocytes to assess the acute effect of RvD1, and LXA4, on VG potassium currents.In silicosimulations were used to predict the effect of current modulation on the atrial and ventricular action potentials (AP). RvD1 and LXA4reducedIKs(channel KV7.1/KCNE1) in COS-7 cells and guinea-pig cardiomyocytes without modifying its voltage dependence; RvD1 was more potent than LXA4. In heterologous systems, RvD1 was also tested onIKur(channel KV1.5),Ito(channel KV4.3/KChIP2),IKr(channel KV11.1), andIK1(channel Kir2.1) with the largest inhibitory effect onIKsandIKr. In simulations RvD1 prolonged repolarization significantly in both atrial and ventricular myocytes.ConclusionThe results provide a comprehensive evaluation of RvD1 and LXA4on cardiac human potassium channels, at pathophysiological relevant concentrations, being RvD1 more potent than LXA4. The predicted effects on the action potential suggest that, along with their antiinflammatory action, RvD1 may reverse AF-induced electrical remodeling in the atria by direct modulation of K+currents. The same action might instead contribute to ventricular functional remodeling; however, direct evidence for this is missing.
Intestinal stem cells enhance local mucosal immunity through apoptotic body phagocytosis
Authors: Zhou Julie Y. , Lu Qiuhe , Hu Yujia , Fujii Satoru , Espenschied Scott T. , Engelhart Morgan J. , Lewis Kelsey J. , Karell Paul E. , Han Yi , Shin Heaji , Schmidt Robert E. , Silver Daniel J. , Ivanov Andrei I. , Yilmaz Omer H. , Stappenbeck Thaddeus S. 
Published: November 2024

ABSTRACTModulation of immune tone at mucosal surfaces is critical to maintain homeostasis while facilitating the handling of emerging threats. One dynamic component of immune modulation is the phagocytosis and clearance of apoptotic bodies known as efferocytosis that inhibits inflammation by promoting its resolution. Here, we evaluated the effects of apoptotic body phagocytosis by intestinal epithelial stem and progenitor cells (ISCs). Unexpectedly, instead of immunomodulation through efferocytosis, this process elevated local immune system activity. To achieve this result, ISCs actively engaged apoptotic bodies in a unique fashion, leading to their engulfment and ultimate delivery to lysosomes for processing. We found that ISCs were capable of actively recruiting inert material such as apoptotic bodies by using actin-based intrinsic biomechanical processes. Uptake of apoptotic bodies was facilitated by complement factor C3 produced by apoptotic bodies themselves. ISCs in turn generated signals heightening T cell activity that was driven in part by ISC-generated TNF. Taken together, uptake of apoptotic bodies by ISCs produced a local inflammatory alert to specific immune cells. This altered paradigm for the response to phagocytosed apoptotic bodies fits the needs of active mucosal surfaces and demonstrates that efferocytosis as currently defined is not a universal response of all cell types.
Drosophila melanogasteremploys nuclear architecture for recruitment of dosage compensation
Authors: Sneideman Maggie P. Lauria , Meller Victoria H. 
Published: November 2024

ABSTRACTDrosophila melanogastermales increase expression from their single X chromosome to match the expression from two female X chromosomes. Increased expression involves recruitment of the Male Specific Lethal (MSL) complex to X-linked genes and modification of chromatin by this complex. How X-linked genes are selectively identified remains unclear, butcis-acting recruiting elements are involved. Chromatin Entry Sites (CES) bind an adapter protein that directly recruits the MSL complex. In addition, a class of AT-rich satellites, the 1.688Xrepeats, are enriched on the X and facilitate compensation of nearby genes. How these elements cooperate to identify the X is unknown. Nuclear architecture influences dosage compensation in many organisms. In this study we test the idea that factors involved in nuclear architecture participate in recruitment by the CES and 1.688Xrepeats. We find genetic interactions between mutations that reduce X recognition and factors that govern chromatin structure, silencing, remodeling and insulation, suggesting roles in X recognition. A reporter for recruitment revealed that Heterochromatin Protein 2 (HP2) and Scaffold Attachment Factor-A (SAF-A) disrupt compensation but do not selectively influence recruitment by either element. In contrast, Imitation switch (ISWI), D1 and Nucleoporin 153kD (Nup153) contribute to recruitment by the CES and Centrosomal protein 190kD (Cp190) exerts a striking influence on recruitment by 1.688Xrepeats. These findings reveal that recruitment by the CES and 1.688Xrepeats involves nuclear organization. We propose that the use ofcis-acting elements that engage complementary aspects of nuclear organization ensures robust X recognition.
Genomic prediction by modelling genotype by environment interaction for yield in groundnut
Authors: Lubanga Nelson , Okaron Velma , Gimode Davis M. , Persa Reyna , Mwololo James , Okello David K. , Ssemakula Mildred Ochwo , Odong Thomas L. , Odeny Damaris A. , Jarquin Diego 
Published: November 2024

AbstractMulti-environment trials (METs) are routinely conducted in plant breeding to capture the genotype-by-environment (G×E) interaction effects. We assessed the potential of using genomic prediction (GP) in four groundnut traits (pod yield[PY], shelling percentage[SP], seed weight[SW] and seed weight of 100 seeds[SW100]) observed in four environments. Three prediction models (M1: Environment + Line, M2: Environment + Line + Genomic, and M3: Environment + Line + Genomic + Genomic × Environment) were evaluated under four cross-validation (CV) schemes that simulate realistic problems that breeders face at different stages of their programs. CV2 predicts lines tested in sparse multi-location trials; CV1 predicts newly developed lines; CV0 predicts tested lines in unobserved environments by leaving one environment out; CV00 predicts untested lines in unobserved environments. Under CV2, the average predictive ability (PA) range was 0.6-0.68 (PY), -0.26-0.05 (SP), 0.5-0.59 (SW) and 0.79-0.86 (SW100). For CV1, the PA range was -0.12-0.51 (PY), -0.08-0.35 (SP), -0.10-0.47 (SW) and -0.05-0.47 (SW100). In CV0, the PA range was 0.27-0.35 (PY), -0.18--0.17 (SP), 0.24-0.32 (SW) and 0.59-0.66 (SW100). In CV00, the PA range was 0.01-0.23 (PY), -0.03-0.07 (SP), 0.01-0.19 (SW) and -0.02-0.38 (SW100). In all the four CV schemes, including marker data improved the PA. Incorporating G×E in M3 model improved PA in CV2 and CV1 schemes and also reduced the residual and environment variances. The high PA in CV2 imply that sparse testing could be implemented. The low PA recorded in CV00 shows that it is difficult to predict untested lines in new environments.
The Xanthophyll Cycle balances Photoprotection and Efficiency in the seawater alga Nannochloropsis oceanica
Authors: Michelberger Tim , Mezzadrelli Eleonora , Bellan Alessandra , Perin Giorgio , Morosinotto Tomas 
Published: November 2024

AbstractPhotosynthetic reactions require continuous modulation to respond to highly dynamic environmental conditions. Regulation of photosynthesis involves various mechanisms, which differ across phylogenetic groups. One such mechanism, found widespread in photosynthetic eukaryotes, is the xanthophyll cycle, which involves the reversible light-dependent conversion between the carotenoids violaxanthin, antheraxanthin, and zeaxanthin.In this study, we investigated the impact of the xanthophyll cycle inNannochloropsis oceanica, a seawater microalga member of Eustigmatophyta that features a peculiarly high content of xanthophylls. We generated and characterized lines with increased levels of the enzymes involved in the xanthophyll cycle, i.e. violaxanthin de-epoxidase (VDE) and zeaxanthin epoxidase (ZEP) and demonstrated that their content is a main factor in controlling the overall reaction rates and the dynamics of the xanthophyll cycle. Subsequent differences in the xanthophyll profile affect the activation of photoprotection mechanisms such as non-photochemical quenching and tolerance to reactive oxygen species. Interestingly, overexpression of VDE expands the limits of high light tolerance, whereas the increased content of ZEP facilitates faster recovery after exposure to light but also heightened photosensitivity under some conditions.These findings underscore the critical role of the xanthophyll cycle in the regulation of photosynthesis inNannochloropsis,where it is not simply a mechanism to respond to excess illumination, but plays a central role in modulating photosynthesis, fulfilling the complex task of balancing photoprotection and light-use efficiency under different environmental conditions.
Development of an ELISA assay for EV quantification to assist the large-scale EV manufacture
Authors: Zhou Xin , Wang Wenli , Zhang Lei , Yang Shiyi , Peng Xincheng , Zhang Xin , Zhao Jinxiu , He Xinjun , Xu Ke 
Published: November 2024

AbstractAccurate EV quantitation is essential for ensuring quality, consistency, and safety during large-scale extracellular vesicle (EV) manufacturing. In the upstream phase, EV quantitation allows for the monitoring of cell culture conditions that impact EV yield and quality, while in the downstream phase, it helps to control the efficiency and purity of EV purification. Nanoparticle Tracking Analysis is the most commonly used method for EV quantification, while it faces significant limitations due to interference from nanosize contaminants like protein aggregates, especially in crude samples (e.g. cell culture media). To address this issue, we developed a highly specific and accurate ELISA assay that quantifies EVs even in crude samples. With ultra-pure EV standard samples, this assay showed reliable quantitative result of EV detection to support method development as well as in-process control of large-scale EV manufacture. The detection range of this assay is from 4.1E7 to 3E10 EVs/mL, with an LOD of 1.04E7 EVs/mL and an LOQ of 3.21E7 EVs/mL. We therefore developed this assay into a testing kit and demonstrated that this EV quantification ELISA kit is capable of ensuring minimal interference from impurities and supporting the process development and in-process control in EV production.
The spliceosomal component GAMETOPHYTIC FACTOR 1 (GFA1) regulates a key photoperiodic switch
Authors: Tiedemann Sebastian , Sterck Lieven , Becker Hanna , Nielsen Nicola , Blohm Cordula , Blum Daniel , Lanz Christa , Maedler Kathrin , Weigel Detlef , Van de Peer Yves , Groß-Hardt Rita 
Published: November 2024

AbstractPlants have evolved sophisticated mechanisms to perceive and interpret daytime in order to flower at an optimal time point. Here we show that the spliceosomal componentGAMETOPHYTIC FACTOR 1(GFA1) constitutes a previously unrecognized key photoperiodic switch, that is essential for flowering in long days. We show thatgfa1hypomorphic (gfa1hyp) plants fail to initiate flowering in long-days (LD), which correlates with ectopic activation of the short-day (SD) flowering repressorARABIDOPSIS THALIANA CENTRORADIALIS (ATC). Accordingly, flowering is restored upon inactivation ofATCingfa1hypmutants. A novel tissue-specificin-plantasplice assay and comprehensive RNAseq profiling ofgfa1hypmutants indicate that GFA1 mediated pre-mRNA splicing is substrate specific, as previously suggested for GFA1 orthologs. Furthermore, we show thatgfa1hypmutants accumulate nonsense transcripts of the photoreceptor componentsPHYBandRRC1, suggesting inappropriate photoreceptor signaling as a potential cause for the ectopic activation of the SD characteristic profile ingfa1hyp. In fact, known downstream targets of the phytochrome system such asRS31, SR34a, SRp30accumulate reduced amounts of light-dependent splice isoforms. Together, our data reveal a link between spliceosome composition and long-day flowering, based on complex transcriptional readouts in response to day length.
DNA replication fork stabilization and restart mechanisms revealed by biochemical reconstitution
Authors: Canal Berta , Bertolin Agostina P. , Lee Giselle C. , Minamino Masashi , Diffley John F.X. 
Published: November 2024

SummaryUnderstanding how DNA replication forks stall and restart and how the DNA damage checkpoint prevents irreversible fork collapse in molecular detail are crucial for understanding how cells maintain stable genomes and how they prevent the genetic instability that drives cancer. Here we describe the reconstitution of fork stalling and restart with purified budding yeast proteins. After nucleotide depletion, leading strand DNA synthesis quickly stops but CMG helicase continues to unwind and Okazaki fragments continue to initiate on the lagging strand. Incomplete Okazaki fragments sequester PCNA, RFC and DNA polymerases δ and ε which prevents normal DNA synthesis restart and exposes nascent DNA to nuclease attack. The DNA damage checkpoint limits this sequestration by restraining fork progression, which protects stalled forks from collapse and ensures restart.
Tethering ferredoxin-NADP+reductase to photosystem I promotes photosynthetic cyclic electron transfer
Authors: Emrich-Mills Thomas Z. , Proctor Matthew S. , Degen Gustaf E. , Jackson Philip J. , Richardson Katherine H. , Hawkings Frederick R. , Buchert Felix , Hitchcock Andrew , Hunter C. Neil , Mackinder Luke C.M. , Hippler Michael , Johnson Matthew P. 
Published: November 2024

AbstractFixing CO2via photosynthesis requires ATP and NADPH. Linear electron transfer (LET) supplies both metabolites, yet depending on environmental conditions, additional ATP is required which can be generated by cyclic electron transfer (CET). How the balance between LET and CET is set remains largely unknown. Ferredoxin(FD)-NADP+reductase (FNR) has been suggested to act as the switch, channelling photosynthetic electrons to LET when it is bound to photosystem I (PSI) or CET when bound to cytochromeb6f. The essential role of FNR in LET precludes the use of a direct gene knock-out to test this hypothesis. We circumvented this problem by using CRISPR-Cas9 gene editing inChlamydomonas reinhardtiito create a chimeric form of FNR tethered to PSI via PSAF. Chimeric FNR mutants exhibited impaired photosynthetic growth relative to the wild type, and decreased LET and non-photochemical quenching (NPQ) under high CO2conditions. However, higher rates of CET and increased NPQ were found in the mutants under low CO2or low O2conditions where CET is normally up-regulated. Thus, rather than PSI-FNR interactions promoting LET, tethering FNR to PSI promotes CET at the expense of LET and CO2fixation.
Insights into the Translational Activation Mechanisms of theCOX1mRNA in Yeast Mitochondria
Authors: Zamudio-Ochoa Angelica , Camacho-Villasana Yolanda , García-Guerrero Aldo E. , Pérez-Martínez Xochitl 
Published: November 2024

ABSTRACTMitochondrial translation is a critical regulatory step in mitochondrial genome expression. InSaccharomyces cerevisiae, translational activators are believed to bind to the 5’ UTRs of their target mRNAs to position the mitochondrial ribosome at the start codon. Pet309 and Mss51 are translational activators ofCOX1mRNA, which encodes subunit one of cytochromecoxidase. Pet309 physically interacts withCOX1mRNA, but no direct interaction of Mss51 with its target mRNA has been detected. Currently, the mechanisms underlying translational activation ofCOX1, or any other mitochondrial gene, remain poorly understood.To explore in depth the mechanism ofCOX1mRNA translational activation, we studied the association of Pet309 and Mss51 with the mitochondrial ribosome. Both Pet309 and Mss51 interact with the mitoribosome regardless of the presence ofCOX1mRNA or of each other. Pet309’s association with the ribosome and withCOX1mRNA depends on its N-terminal domain. These findings indicate that Pet309 and Mss51 stably interact with the mitoribosome independently of an active translation. By integrating our data with previously published research, we propose a new mechanism ofCOX1mRNA translation activation.SUMMARY STATEMENTYeast mitochondrial mRNAs require translational activators by an almost unknown mechanism. Based on our findings on Mss51 and Pet309 function, we present a new model for translation of theCOX1mRNA