bluuebunny/crossref_metadata_2025_split huggingface dataset:
The biological consequences of knockout of genes involved in the synthesis and metabolism of H2S inDrosophila melanogaster
Authors: Shilova V.Y. , Chuvakova L.N. , Garbuz D.G. , Rezvykh A.P. , Funikov S.Y. , Davletshin A.I. , Sorokina S. , Nikitina E.A. , Gorenskaya O. , Evgen’ev M.B. , Zatsepina O.G. 
Published: October 2024

AbstractHere, we describe the effect of knockout (KO) of two key genes (cbs,cse) responsible for H2S synthesis in the transsulfuration pathway as well as the inactivation of sulfurtransferase gene (dtst1) encoding single domain rhodanese onDrosophila melanogastergenome expression and several life-history traits. The analysis of H2S production in the KO flies showed its minimal level in the strain with double KO (CBS-/-; CSE-/-) while flies with triple KO (CBS-/-;CSE-/-;dTST1-/-) exhibited higher H2S level and improvements in lifespan. The transcriptomic analysis of fly bodies from the double KO strain with maximum disturbances of fitness components revealed a profound increase in the expression of genes involved in the functioning of the excretory system. Besides, double and triple KO flies exhibited drastic changes in Malpighian tubules’ appearance. Inactivation of genes related to H2S metabolism resulted in altered expression of numerous loci involved in mitochondrial function. While KO of thedtst1gene did not affect the genome expression, the triple KO flies exhibited more changes in the whole-body transcriptome than double KO flies. Reduced fecundity in double knockouts correlates with pronounced changes in ovarian transcriptome data. Surprisingly, the knockout of thedtst1gene affected the flies’ memory.
2.6-Å resolution cryo-EM structure of a class Ia ribonucleotide reductase trapped with mechanism-based inhibitor N3CDP
Authors: Westmoreland Dana E. , Feliciano Patricia R. , Kang Gyunghoon , Cui Chang , Kim Albert , Stubbe JoAnne , Nocera Daniel G. , Drennan Catherine L. 
Published: October 2024

AbstractRibonucleotide reductases (RNRs) reduce ribonucleotides to deoxyribonucleotides using radical-based chemistry. For class Ia RNRs, the radical species is stored in a separate subunit (β2) from the subunit housing the active site (α2), requiring the formation of a short-lived α2β2 complex and long-range radical transfer (RT). RT occurs via proton-coupled electron transfer (PCET) over a long distance (~32-Å) and involves the formation and decay of multiple amino acid radical species. Here, we use cryogenic-electron microscopy and a mechanism-based inhibitor 2′-azido-2′-deoxycytidine-5′-diphosphate (N3CDP) to trap a wild-type α2β2 complex ofE. coliclass Ia RNR. We find that one α subunit has turned over and that the other is trapped, bound to β in a mid-turnover state. Instead of N3CDP in the active site, forward RT has resulted in N2loss, migration of the third nitrogen from the ribose C2′ to C3′ positions, and attachment of this nitrogen to the sulfur of cysteine-225. To the best of our knowledge, this is the first time an inhibitor has been visualized as an adduct to an RNR. Additionally, this structure reveals the positions of PCET residues following forward RT, complementing the previous structure that depicted a pre-turnover PCET pathway and suggesting how PCET is gated at the α–β interface. This N3CDP-trapped structure is also of sufficient resolution (2.6 Å) to visualize water molecules, allowing us to evaluate the proposal that water molecules are proton acceptors and donors as part of the PCET process.Significance StatementSeveral FDA-approved cancer drugs target human ribonucleotide reductase (RNR), a radical enzyme that produces the requisite deoxyribonucleotides for DNA biosynthesis and repair. Human RNR is a class Ia enzyme that requires radical transfer (RT) from a β2 subunit to an α2 subunit on every round of turnover. Long-range RT is both a remarkable feature and an Achilles heel, given that inhibitors can intercept the radical species. Here we present a cryogenic electron microscopy (cryo-EM) structure of the best studied class Ia RNR, the enzyme fromE. coli, in which α2 and β2 subunits have been trapped together using a mechanism-based inhibitor. This structure provides insight into both the mechanism of RNR inhibition and the mechanism of long-range RT.
Unprecedented sighting of coral populations and associated fauna in the High Sedimentation Waters of Puerto Velero, Atlántico, Colombia
Authors: Moreno-Tilano Jorge , Sanabria Ramirez Irene Lucia , Neme Rafik 
Published: October 2024

AbstractThe marine coastal zone of Atlántico, Colombia, faces significant anthropogenic impact due to sediment and organic matter from the Magdalena River. This study reports the presence of two distinct coral patches in Puerto Velero, Atlántico, an area previously considered unfavorable for coral growth. Located at depths of 1-6 meters, these patches harbor a variety of marine species, extending the known distribution of 15 species in the Colombian Caribbean. Despite high sedimentation rates, the larger coral colonies show resilience, surviving mass mortality events and diseases. These findings highlight the adaptive capacity of corals in adverse conditions, emphasizing the importance of systematic monitoring and conservation efforts to understand their response to environmental changes and support marine biodiversity in the Colombian Caribbean.
Associations between Neonicotinoid, Pyrethroid, and Organophosphate Insecticide Metabolites and Neurobehavioral Performance in Ecuadorian Adolescents
Authors: Yen Jessica , Yang Kun , Tu Xin M. , Kayser Georgia , Skomal Ana , Gahagan Sheila , Suarez-Torres Jose , Hong Suzi , Moore Raeanne C. , Suarez-Lopez Jose R. 
Published: October 2024

AbstractBackgroundOrganophosphate and pyrethroid insecticides can affect children’s neurodevelopment and increase inflammation. Limited evidence exists among adolescents and on whether inflammation may mediate pesticide–neurobehavior associations. We examined the associations between insecticide metabolite concentrations and neurobehavior among adolescents in Ecuadorian agricultural communities.MethodsWe included 520 participants aged 11-17 years. We measured urinary insecticide metabolites (mass spectrometry) and neurobehavior (NEPSY-II). Associations were adjusted for socio-demographic and anthropometric characteristics. The associations of insecticide mixtures with neurobehavior were evaluated using PLS regression, and mediation by inflammatory biomarkers (TNF-α, IL-6, CRP, SAA, sICAM-1, sVCAM-1 and sCD-14) was conducted.ResultsAmong organophosphates, para-nitrophenol (PNP) and 3,5,6-Trichloro-2-pyridinol (TCPy) were inversely associated with Social Perception (score difference per 50% increase [β50%] = -0.26 [95%CI: - 1.07, -0.20] and -0.10 [-0.22, 0.01], respectively). PNP and TCPy also had significant inverse associations with Attention/Inhibitory Control at concentrations >60thpercentile (β50%= -0.26 [95%CI: -0.51, -0.01] and β50%= -0.22 [95%CI: -0.43, -0.00], respectively). The pyrethroid, 3-phenoxybenzoic acid (3-PBA), was inversely associated with Language (β50%= -0.13 [95%CI: -0.19, -0.01]) and had a negative quadratic association with Attention/Inhibitory Control. The neonicotinoid 5-Hydroxy imidacloprid (OHIM) was positively associated with Memory/Learning (β50%= 0.20 [95%CI: 0.04, 0.37]). Mixtures of all insecticides were significantly negatively related to all domains, except for Memory/Learning, which was positively associated. No mediation by inflammatory markers on these associations was observed.ConclusionsConcurrent organophosphate, pyrethroid, and the mixtures of all metabolites were associated with lower performance in all domains except for Memory/Learning. Neonicotinoids were positively associated with Memory/Learning and Social Perception scores.
EXploring the journeys of Patients who End their Calls prior to Triage by NHS111: The EXPECT study
Authors: Pilbery Richard , Lewis Jen , Simpson Rebecca 
Published: October 2024

AbstractBackgroundThe English National Health Service (NHS) 111 telephone service aims to assist members of the public with urgent medical care needs. However, each year nearly 18% of the 20.6 million calls to 111 are abandoned prior to speaking to a health advisor. There are concerns that callers who are not triaged may not appropriately seek the correct level of care for their needs.The aim of this study was to explore the patient journey for callers who contact NHS 111 but end the call prior to speaking to a health advisor. The primary objective was to determine whether callers to NHS 111 who end the call prior to triage attend an ED with a non-avoidable cause sooner than who are triaged by an NHS 111 health advisor.MethodsWe obtained routine data pertaining to all NHS 111 calls made by adult patients registered with a General Practitioner (GP) in the Bradford region of Yorkshire, UK, between the 1st January 2022 and 30th June 2023. Subsequent healthcare access in the 72 hours following each caller’s first (index) call was identified using the Connected Yorkshire research database.We conducted a time-to-event analysis comparing the two cohorts: those whose index call was triaged by an NHS 111 health advisor vs. callers who ended the index call prior to triage. The ‘event’ was defined as an Emergency Department (ED) attendance within 72 hours for a non-avoidable cause.We utilised Kaplan–Meier (KM) curves and conducted log-rank tests to compare the time to first non-avoidable ED attendance between cohorts, and a Cox proportional hazards model adjusted for baseline characteristics. From this, we calculated the adjusted hazard ratio (aHR) of attending an ED with a non-avoidable cause.ResultsThere were 19,056 index non-triaged and 168,609 triaged calls made to NHS 111 by an adult registered with a Bradford GP. A lower proportion of ED attendances in the non-triaged call cohort were non-avoidable compared with the triaged cohort (80.0% compared to 84.6% for triaged calls). In addition, callers in the non-triaged call cohort attended ED later than the triaged call cohort (median 10 vs 8 hours, p<0.001 by log rank test). The time-to-attend ED aHR for non-triaged calls vs triaged calls was 0.32 (95%CI 0.30–0.34).ConclusionThe time-to-event analysis found that callers to NHS 111 who do not wait to be triaged, are slower to attend ED with a non-avoidable cause than those who are triaged, and are more likely to attend ED with an avoidable cause than triaged callers. This suggests that, for patients with a serious health problem that would be considered non-avoidable at ED, triaging by NHS 111 supports those patients to seek appropriate help more quickly. In turn, patients with such health conditions who end the call before triage may delay seeking appropriate levels of healthcare.
Cardiovascular and non-cardiovascular risks among female breast cancer survivors in Japan: A matched cohort study
Authors: Kawamura Chitose , Bhaskaran Krishnan , Konishi Takaaki , Sagara Yasuaki , Bando Hiroko , Shinozaki Tomohiro , Nojiri Shuko , Adomi Motohiko , Wong Angel YS , Tamiya Nanako , Iwagami Masao 
Published: October 2024

AbstractBackgroundThe number of breast cancer (BC) survivors has increased worldwide, but the landscape of their non-cancer disease risks remains unclear, especially among Asian women.MethodsIn the JMDC claims database, which covers company employees and their family members in Japan, women aged 18–74 years with and without an incident BC were matched in a 1:4 ratio for age and entry timing to the database between January 2005 and December 2019. The risks for six cardiovascular diseases (myocardial infarction, heart failure, atrial fibrillation/flutter, ischemic stroke, intracranial hemorrhage, and pulmonary embolism) and six non-cardiovascular diseases (major osteoporotic fractures, other fractures, gastrointestinal bleeding, urinary tract infection, infectious pneumonia, and anxiety/depression) were compared between the groups.FindingsComparing 24,017 BC survivors and 96,068 matched women (mean age, 50·5 years), the incidence rates of heart failure, atrial fibrillation/flutter, and all non-cardiovascular diseases were higher in the BC survivor group. The highest adjusted hazard ratio (HR) was noted for heart failure (4·09 [95% confidence interval 2·58–6·50]), followed by gastrointestinal bleeding (3·55 [3·10–4·06]), and anxiety/depression (3·06 [2·86–3·27]). The HRs in the first year were larger than those for 1–10 years for most outcomes, whereas the HRs for fracture outcomes were larger in the 1–10 years group.InterpretationBC survivors in Japan showed an increased risk of many non-cancer diseases compared to women without BC. Most risks increased more steeply during the first year following diagnosis, whereas the risk of fractures increased later.FundingCompetitive research funding from Pfizer Health Research Foundation in Japan.
Chemical circularization of in vitro transcribed RNA opens new avenues for circular mRNA design
Authors: Mamot Adam , Wasinska-Kalwa Malgorzata , Czubak Karol , Frankowska Katarzyna , Spiewla Tomasz , Warminski Marcin , Nowis Dominika , Golab Jakub , Kowalska Joanna , Jemielity Jacek 
Published: October 2024

ABSTRACTCircularization is at the frontier of therapeutic messenger RNA (mRNA) enhancements. Currently available enzymatic and ribozymatic methods for generating circular RNAs (circRNAs) face several challenges related to sequence limitations, purification, and sub-optimal biological activity. The chemical circularization of synthetic RNA fragments potentially overcomes these limitations but is applicable only to extremely short sequences. Here, we report a novel approach for accessing circular RNAs based on the chemical circularization of in vitro transcribed RNA. We efficiently accessed chemically circularized RNAs (chem-circRNAs) by making in vitro transcribed precursor RNAs modified at the 5′ end with an ethylenediamine moiety, which undergoes an intramolecular reaction with the periodate-oxidized RNA 3′ end under reductive amination conditions. We demonstrate that this method is modification-compatible and applicable to various sequences. Additionally, we report methods for the effective separation of chem-circRNAs from their linear precursors. Using this approach, we prepared multiple chemically-obtained circular RNAs (chem-circRNAs; 35–1500 nt long) with circularization efficiencies reaching up to 60%. We show that protein-coding chem-circRNAs are translationally active in living cells and exhibit increased durability, similar to enzymatically circularized mRNAs. We also demonstrate that this approach enables unprecedented access to chemically modified circRNAs, such as circ-mRNAs incorporating a functional endocyclic N7-methylguanosine cap or modified with N1-methylpseudouridine within the RNA body. Notably, circRNAs containing an endocyclic cap structure engage in the most efficient, cap-dependent mechanism of translation. Our approach makes chemically-modified circularized full-length protein-coding RNAs easily accessible, thereby opening new avenues for the design, modification, and functionalization of circular mRNAs.
The role of GPR87 in Pulmonary Fibrosis
Authors: Khoury Johad , Ahangari Farida , Adams Taylor , Justet Aurelien , Manning Edward , McDonough John , Barnthaler Thomas , Anderson Sabina , Nikola Fadi , Beermann Mary Lou , Gomez Jose L , Kaminski Naftali 
Published: October 2024

AbstractRationaleG- protein coupled receptor 87 (GPR87), an alternative lysophosphatidic acid (LPA) receptor previously implicated in cancer, is highly expressed in basal and aberrant basaloid cells in idiopathic pulmonary fibrosis (IPF). We sought to determine whether signaling through GPR87 is important to the development of pulmonary fibrosis.MethodsReanalysis of bulk and single cell RNA sequencing dataset was performed to confirm the increased expression of GPR87 in pulmonary fibrosis. The role of GPR87 in fibrosisin-vivowas assessed using global GPR87 knockout (GPR87-/-) and wildtype mice in the bleomycin model of pulmonary fibrosis,in-vitroin induced pluripotent stem cells (iPSCs) derived airway basal cells (iBC) using GPR87 siRNAs, andex-vivoin human precision cut slices using disease free tissues in the fibrotic cocktail model as well as IPF tissues treated with GPR87 siRNA.ResultsGPR87 is highly expressed in IPF lungs, and its expression correlates with disease severity. Furthermore, It is highly expressed in basal and aberrant basaloid cells. GPR87-/-mice are protected against bleomycin induced pulmonary fibrosis. GPR87 knockdown is protective against fibrosis development in normal PCLS treated with fibrotic cocktail and leads to fibrosis regression in IPF PCLS. In iBC, GPR87 knockdown leads to decreased expression of fibrosis related genes, proteins and microRNAs. GPR87 stimulation with LPA leads to the opposite results. The main downstream pathways are PI3K, mTOR, and TNF/NFkB; stimulation or inhibition of PI3K pathway mimics GPR87 stimulation or inhibition responses, respectively.ConclusionGPR87 is highly expressed in basal and aberrant basaloid cells in IPF lungs and seems to mediate profibrotic effects based onin-vivo, ex-vivoandin-vitromodels of disease, suggesting that it should be studied as a potential epithelial specific therapeutic target in pulmonary fibrosis.
Diffusion and Viscosity in Mixed Protein Solutions
Authors: Wozniak Spencer , Feig Michael 
Published: October 2024

ABSTRACTThe viscosity and diffusion properties of crowded protein systems were investigated with molecular dynamics simulations of SH3 mixtures with different crowders, and results were compared with experimental data. The simulations accurately reproduced experimental trends across a wide range of protein concentrations, including highly crowded environments up to 300 g/L. Notably, viscosity increased with crowding but varied little between different crowder types, while diffusion rates were significantly reduced depending on protein-protein interaction strength. Analysis using the Stokes-Einstein relation indicated that the reduction in diffusion exceeded what was expected from viscosity changes alone, with the additional slow-down attributable to transient cluster formation driven by weakly attractive interactions. Contact kinetics analysis further revealed that longer-lived interactions contributed more significantly to reduced diffusion rates than short-lived interactions. This study also highlights the accuracy of current computational methodologies for capturing the dynamics of proteins in highly concentrated solutions and provides insights into the molecular mechanisms affecting protein mobility in crowded environments.
Modulation of SpyCatcher Ligation Kinetics by SpyTag Thioamide Substitution
Authors: Fiore Kristen E. , Francis Denver Y. , Casimir Sobrielle M. , Perez Ryann M. , Petersson E. James 
Published: October 2024

AbstractThioamide substitutions have been shown to impart valuable properties on peptides for biophysical experiments as well as cell or in vivo studies, but a rational understanding of thioamide effects on protein structure and protein-protein interactions is lacking. To elucidate their effects in β-sheet structures, we have used SpyCatcher003-SpyTag003 as a host-guest system to study individual thioamide incorporation at eight different positions in the SpyTag peptide. We have demonstrated that incorporating thioamides into SpyTag at specific positions can result in a ∼2-fold faster ligating complex, as well as >2000-fold slower ligating complex. Biophysical analysis and structural modeling provide a reasonable explanation for most of the thioamide effects, altering hydrogen bond networks as well as modulating an n→π* interaction within the SpyTag peptide. Our findings have important implications for potential applications of thioamide SpyTag variants, where the thioamide could impart protease stability in cells while also controlling the rate of ligation to SpyCatcher. These SpyCatcher-SpyTag host-guest experiments will also help to build a database for predicting thioamide effects on protein structure and function.
Full-length Cryptochrome 1 in the outer segments of the retinal blue cone photoreceptors in humans and great apes suggests a role beyond transcriptional repression
Authors: Bartölke Rabea , Nießner Christine , Reinhard Katja , Wolfrum Uwe , Meimann Sonja , Bolte Petra , Feederle Regina , Mouritsen Henrik , Dedek Karin , Peichl Leo , Winklhofer Michael 
Published: October 2024

AbstractMammalian cryptochrome 1 (CRY1) is a central player in the circadian transcription-translation feedback loop, crucial for maintaining a roughly 24-hour rhythm. CRY1 was suggested to also function as blue-light photoreceptor in humans and has been found to be expressed at the mRNA level in various cell types of the inner retina. However, attempts to detect CRY1 at the protein level in the human retina have remained unsuccessful so far. Using various C-terminal specific antibodies recognizing full-length CRY1 protein, we consistently detected selective labelling in the outer segments of short wavelength-sensitive (SWS1, “blue”) cone photoreceptor cells across human, bonobo, and gorilla retinae. No other retinal cell types were stained, which is in contrast to what would be expected of a ubiquitous clock protein. Subcellular fractionation experiments in transfected HEK cells using a C-terminal specific antibody located full-length CRY1 in the cytosol and membrane fractions. Our findings indicate that human CRY1 has several different functions including at least one non-clock function. Our results also raise the likely possibility that several different versions of CRY1 exists in humans. We suggest that truncation of the C-terminal tail, maybe to different degrees, may affect the localization and function of human CRY1.
Spheroplasted cells: a game changer for DNA delivery to diatoms
Authors: Walker E.J.L. , Pampuch M. , Tran G. , Karas B.J.K. 
Published: October 2024

ABSTRACTDiatoms, vital to global carbon fixation and climate change mitigation, produce 20% of the world’s fixed organic carbon annually. Their potential as cell factories for biofuels, proteins, and other high value chemicals remains underutilized due to a lack of genetic engineering tools, with DNA delivery being the biggest challenge. Here, we present an optimized, highly efficient electroporation method for delivering DNA constructs as large as 55.6 kb toPhaeodactylum tricornutum, a model diatom species and emerging chassis for algal biotechnology. We also demonstrate that with this optimized protocol, episomes can be assembledde novo, forgoing the need for time-consuming traditional cloning steps inEscherichia coliandSaccharomyces cerevisiae. By incorporating other technologies, such as CRISPR genome editing, this method will accelerate diatom-based synthetic biology projects and, therefore, the development of sustainable technologies. This method should also be applicable to other diatom species.