bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intracellular binding pocket revealed in the human bitter taste receptor TAS2R14
Authors: Peri Lior , Matzov Donna , Huxley Dominic R. , Rainish Alon , Fierro Fabrizio , Sapir Liel , Pfeiffer Tara , Waterloo Lukas , Hübner Harald , Weikert Dorothee , Peleg Yoav , Gmeiner Peter , McCormick Peter J. , Niv Masha Y. , Shalev-Benami Moran 
Published: April 2024

AbstractBitter taste receptors (TAS2Rs), a subfamily of G-protein coupled receptors (GPCRs) expressed orally and extraorally, elicit signaling in response to a large set of ligands. Among the 25 functional TAS2Rs encoded in the human genome, TAS2R14 is the most promiscuous, and responds to hundreds of chemically diverse agonists. Here, we present the cryo–electron microscopy (cryo-EM) structure of the human TAS2R14 (hTAS2R14) in complex with its cognate signaling partner gustducin, and bound to flufenamic acid (FFA), a clinically approved nonsteroidal anti-inflammatory drug. The structure reveals an unusual binding mode for FFA, where two copies are bound at distinct binding pockets: one at the canonical GPCR site within the trans-membrane bundle, and the other in the intracellular facet, bridging the receptor with gustducin. Combined with site-directed mutagenesis and the design of a fluorescent FFA derivative for pocket-specific ligand binding BRET assays, our studies support a dual binding mode for FFA in TAS2R14. These results fill a gap in the understanding of bitter taste signaling and provide tools for guided design of TAS2R-targeted compounds.
Ovoselenol, a Selenium-containing Antioxidant Derived from Convergent Evolution
Authors: Kayrouz Chase M. , Ireland Kendra A. , Ying Vanessa , Davis Katherine M. , Seyedsayamdost Mohammad R. 
Published: April 2024

AbstractSelenium is an essential micronutrient, but its presence in biology has been limited to protein and nucleic acid biopolymers. The recent identification of the first biosynthetic pathway for selenium-containing small molecules suggests that there is a larger family of selenometabolites that remains to be discovered. Using a bioinformatic search strategy that relies on mapping of composite active site motifs, we identify a recently evolved branch of abundant and uncharacterized metalloenzymes that we predict are involved in selenometabolite biosynthesis. Biochemical studies confirm this prediction and show that these enzymes form an unusual C–Se bond onto histidine, thus giving rise to a novel selenometabolite and potent antioxidant that we have termed ovoselenol. Aside from providing insights into the evolution of this enzyme class and the structural basis of C–Se bond formation, our work offers a blueprint for charting the microbial selenometabolome in the future.
Multiple pathways for licensing human replication origins
Authors: Yang Ran , Hunker Olivia , Wise Marleigh , Bleichert Franziska 
Published: April 2024

SummaryThe loading of replicative helicases constitutes an obligatory step in the assembly of DNA replication machineries. In eukaryotes, the MCM2-7 replicative helicase motor is deposited onto DNA by the origin recognition complex (ORC) and co-loader proteins as a head-to-head MCM double hexamer to license replication origins. Although extensively studied in the budding yeast model system, the mechanisms of origin licensing in higher eukaryotes remain poorly defined. Here, we use biochemical reconstitution and electron microscopy (EM) to reconstruct the human MCM loading pathway. Unexpectedly, we find that, unlike in yeast, ORC’s Orc6 subunit is not essential for human MCM loading but can enhance loading efficiency. EM analyses identify several intermediatesen routeto MCM double hexamer formation in the presence and absence of Orc6, including an abundant DNA-loaded, closed-ring single MCM hexamer intermediate that can mature into a head-to-head double hexamer through different pathways. In an Orc6-facilitated pathway, ORC and a second MCM2-7 hexamer are recruited to the dimerization interface of the first hexamer through an MCM-ORC intermediate that is architecturally distinct from an analogous intermediate in yeast. In an alternative, Orc6-independent pathway, MCM double hexamer formation proceeds through dimerization of two independently loaded single MCM2-7 hexamers, promoted by a propensity of human MCM2-7 hexamers to dimerize without the help of other loading factors. This redundancy in human MCM loading pathways likely provides resilience against replication stress under cellular conditions by ensuring that enough origins are licensed for efficient DNA replication. Additionally, the biochemical reconstitution of human origin licensing paves the way to address many outstanding questions regarding DNA replication initiation and replication-coupled events in higher eukaryotes in the future.
Phage-Encoded Bismuth Bicycles: Instant Access to Targeted Bioactive Peptides
Authors: Ullrich Sven , Somathilake Upamali , Shang Minghao , Nitsche Christoph 
Published: April 2024

AbstractGenetically encoded libraries play a crucial role in discovering structurally rigid, high-affinity macrocyclic peptide ligands for therapeutic applications. This study represents the first genetic encoding of peptide-bismuth and peptide-arsenic bicyclic peptides in phage display. We introduce bismuth tripotassium dicitrate (gastrodenol) as a water-soluble Bi(III) reagent for phage library modification andin situbicyclic peptide preparation, eliminating the need for organic co-solvents. Additionally, we explore As(III) as an alternative thiophilic element used analogously to our previously introduced class of peptide-bismuth bicycles. The modification of phage libraries and peptides with these elements is instantaneous and entirely biocompatible, offering an advantage over conventional alkylation-based methods. In a pilot display screening campaign aimed at identifying ligands for the biotin-binding protein streptavidin, we demonstrate the enrichment of bicyclic peptides with dissociation constants two orders of magnitude lower than those of their linear counterparts, underscoring the impact of structural constraint on binding affinity.
Tissue-level integration overrides gradations of differentiating cell identity in beetle extraembryonic tissue
Authors: Mann Katie E. , Panfilio Kristen A. 
Published: April 2024

AbstractDuring animal embryogenesis, one of the earliest specification events distinguishes extraembryonic (EE) from embryonic tissue fates: the serosa in the case of the insects. While it is well established that the homeodomain transcription factor Zen1 is the critical determinant of the serosa, subsequent realization of the tissue’s identity has not been investigated. Here, we examine serosal differentiation in the beetleTribolium castaneumbased on quantification of morphological and morphogenetic features, comparing embryos from aTc-zen1RNAi dilution series, where complete knockdown results in amnion-only EE tissue identity. We assess features including cell density, tissue boundary morphology, and nuclear size as dynamic readouts for progressive tissue maturation. While some features exhibit an all-or-nothing outcome, other key features show dose-dependent phenotypic responses with trait-specific thresholds. Collectively, these findings provide nuance beyond the known status of Tc-Zen1 as a selector gene for serosal tissue patterning. Overall, our approach illustrates how analysis of tissue maturation dynamics from live imaging extends but also challenges interpretations based on gene expression data, refining our understanding of tissue identity and when it is achieved.
Multiplexed Assays of Human Disease-relevant Mutations Reveal UTR Dinucleotide Composition as a Major Determinant of RNA Stability
Authors: Su Jia-Ying , Wang Yun-Lin , Hsieh Yu-Tung , Chang Yu-Chi , Yang Cheng-Han , Kang YoonSoon , Huang Yen-Tsung , Lin Chien-Ling 
Published: April 2024

ABSTRACTUTRs contain crucial regulatory elements for RNA stability, translation and localization, so their integrity is indispensable for gene expression. Approximately 3.7% of genetic variants associated with diseases occur in UTRs, yet a comprehensive understanding of UTR variant functions remains limited due to inefficient experimental and computational assessment methods. To systematically evaluate the effects of UTR variants on RNA stability, we established a massively parallel reporter assay on 6,555 UTR variants reported in human disease databases. We examined the RNA degradation patterns mediated by the UTR library in two cell lines, and then applied LASSO regression to model the influential regulators of RNA stability. We found that UA dinucleotides and UA-rich motifs are the most prominent destabilizing element. Gain of UA dinucleotide outlined mutant UTRs with reduced stability. Studies on endogenous transcripts indicate that high UA-dinucleotide ratios in UTRs promote RNA degradation. Conversely, elevated GC content and protein binding on UA dinucleotides protect high-UA RNA from degradation. Further analysis reveals polarized roles of UA- dinucleotide-binding proteins in RNA protection and degradation. Furthermore, the UA- dinucleotide ratio of both UTRs is a common characteristic of genes in innate immune response pathways, implying a coordinated stability regulation through UTRs at the transcriptomic level. We also demonstrate that stability-altering UTRs are associated with changes in biobank-based health indices, underscoring the importance of precise UTR regulation for wellness. Our study highlights the importance of RNA stability regulation through UTR primary sequences, paving the way for further exploration of their implications in gene networks and precision medicine.
Multi-omic QTL mapping in early developmental tissues reveals phenotypic and temporal complexity of regulatory variants underlying GWAS loci
Authors: Arthur Timothy D. , Nguyen Jennifer P. , D’Antonio-Chronowska Agnieszka , Jaureguy Jeffrey , Silva Nayara , Henson Benjamin ,   iPSCORE Consortium, Panopoulos Athanasia D. , Belmonte Juan Carlos Izpisua , D’Antonio Matteo , McVicker Graham , Frazer Kelly A. 
Published: April 2024

AbstractMost GWAS loci are presumed to affect gene regulation, however, only ∼43% colocalize with expression quantitative trait loci (eQTLs). To address this colocalization gap, we identify eQTLs, chromatin accessibility QTLs (caQTLs), and histone acetylation QTLs (haQTLs) using molecular samples from three early developmental (EDev) tissues. Through colocalization, we annotate 586 GWAS loci for 17 traits by QTL complexity, QTL phenotype, and QTL temporal specificity. We show that GWAS loci are highly enriched for colocalization with complex QTL modules that affect multiple elements (genes and/or peaks). We also demonstrate that caQTLs and haQTLs capture regulatory variations not associated with eQTLs and explain ∼49% of the functionally annotated GWAS loci. Additionally, we show that EDev-unique QTLs are strongly depleted for colocalizing with GWAS loci. By conducting one of the largest multi-omic QTL studies to date, we demonstrate that many GWAS loci exhibit phenotypic complexity and therefore, are missed by traditional eQTL analyses.
The DNA Methyltransferase DMAP1 is Required for Tissue Maintenance and Planarian Regeneration
Authors: Rojas Salvador , Barghouth Paul G. , Karabinis Peter , Oviedo Néstor J. 
Published: April 2024

AbstractThe precise regulation of transcription is required for embryonic development, adult tissue turnover, and regeneration. Epigenetic modifications play a crucial role in orchestrating and regulating the transcription of genes. These modifications are important in the transition of pluripotent stem cells and their progeny. Methylation, a key epigenetic modification, influences gene expression through changes in histone tails and direct DNA methylation. Work in different organisms has shown that the DNA methyltransferase-1-associated protein (DMAP1) may associate with other molecules to repress transcription through DNA methylation. Thus, DMAP1 is a versatile protein implicated in a myriad of events, including pluripotency maintenance, DNA damage repair, and tumor suppression. While DMAP1 has been extensively studiedin vitro, its complex regulation in the context of the adult organism remains unclear. To gain insights into the possible roles of DMAP1 at the organismal level, we used planarian flatworms that possess remarkable regenerative capabilities driven by pluripotent stem cells called neoblast. Our findings demonstrate the evolutionary conservation of DMAP1 in the planarianSchmidtea mediterranea. Functional disruption of DMAP1 through RNA interference revealed its critical role in tissue maintenance, neoblast differentiation, and regeneration inS. mediterranea. Moreover, our analysis unveiled a novel function for DMAP1 in regulating cell death in response to DNA damage and influencing the expression of axial polarity markers. Our findings provide a simplified paradigm for studying DMAP1’s epigenetic regulation in adult tissues.HighlightsEpigenetic regulation through DMAP1 is evolutionarily conserved inSchmidtea mediterraneaand is crucial for tissue maintenance and regeneration.Neoblast differentiation into epithelial, muscle, digestive, and neural fate requires DMAP1.DMAP1 regulates DNA stability and cell death during adult cell turnover.DMAP1 regulates the spatial expression of axial polarity markers inS. mediterranea.
Disruption of Herpes Simplex Virus Type 2 pUL21 Phosphorylation Impairs Secondary Envelopment of Cytoplasmic Nucleocapsids
Authors: Finnen Renée L. , Muradov Jamil H. , Le Sage Valerie , Banfield Bruce W. 
Published: April 2024

AbstractThe multifunctional tegument protein pUL21 of HSV-2 is phosphorylated in infected cells. We have identified two residues in the unstructured linker region of pUL21, serine 251 and serine 253, as sites of phosphorylation. Both phosphorylation sites are absent in HSV-1 pUL21, which likely explains why phosphorylated pUL21 was not detected in cells infected with HSV-1. Cells infected with HSV-2 strain 186 viruses deficient in pUL21 phosphorylation exhibited reductions in both cell-cell spread of virus infection and virus replication. Defects in secondary envelopment of cytoplasmic nucleocapsids were also observed in cells infected with viruses deficient in pUL21 phosphorylation as well as in cells infected with multiple strains of HSV-2 and HSV-1 deleted for pUL21. These results confirm a role for HSV pUL21 in the secondary envelopment of cytoplasmic nucleocapsids and indicate that phosphorylation of HSV-2 pUL21 is required for this activity. Phosphorylation of pUL21 was not detected in cells infected with HSV-2 strain 186 mutants lacking the viral serine/threonine kinase pUL13, indicating a requirement for pUL13 in pUL21 phosphorylation.ImportanceIt is well known that post-translational modification of proteins by phosphorylation can regulate protein function. Here, we determined that phosphorylation of the multifunctional HSV-2 tegument protein pUL21 requires the viral serine/threonine kinase pUL13. Additionally, we identified serine residues within HSV-2 pUL21 that can be phosphorylated. Phenotypic analysis of mutant HSV-2 strains with deficiencies in pUL21 phosphorylation revealed reductions in both cell-cell spread of virus infection and virus replication. Deficiencies in pUL21 phosphorylation also compromised secondary envelopment of cytoplasmic nucleocapsids, a critical final step in the maturation of all herpes virions. Unlike HSV-2 pUL21, phosphorylation of HSV-1 pUL21 was not detected. This fundamental difference between HSV-2 and HSV-1 may underlie our previous observations that the requirements for pUL21 differ between HSV species.
Myogenic Anti-Nucleolin Aptamer iSN04 Inhibits Proliferation and Promotes Differentiation of Vascular Smooth Muscle Cells
Authors: Miyoshi Mana , Shimosato Takeshi , Takaya Tomohide 
Published: April 2024

AbstractDe-differentiation and subsequent increased proliferation and inflammation of vascular smooth muscle cells (VSMCs) is one of the mechanisms of atherogenesis. Maintaining VSMCs in a contractile differentiated state is therefore a promising therapeutic strategy for atherosclerosis. We have reported the 18-base myogenetic oligodeoxynucleotide, iSN04, which serves as an anti-nucleolin aptamer and promotes skeletal and myocardial differentiation. The present study investigated the effect of iSN04 on VSMCs because nucleolin has been reported to contribute to VSMC de-differentiation under pathophysiological conditions. Nucleolin was localized in the nucleoplasm and nucleoli of both rat and human VSMCs. iSN04 without carrier was spontaneously incorporated into VSMCs, indicating that iSN04 would serve as an anti-nucleolin aptamer. iSN04 treatment decreased the ratio of EdU+proliferating VSMCs and increased the expression of α-smooth muscle actin, a contractile marker of VSMCs. iSN04 also suppressed angiogenesis of mouse aortic rings ex vivo, which is a model of pathological angiogenesis involved in plaque formation, growth, and rupture. These results demonstrate that antagonizing nucleolin with iSN04 preserves VSMC differentiation, providing a nucleic acid drug candidate for the treatment of vascular disease.
Quantitative intra-Golgi transport and organization data suggest the stable compartment nature of the Golgi
Authors: Tie Hieng Chiong , Wang Haiyun , Mahajan Divyanshu , Sun Xiuping , Chen Bing , Lu Lei 
Published: April 2024

AbstractHow the intra-Golgi secretory transport works remains a mystery. The cisternal progression and the stable compartment models have been proposed and are under debate. Classic cisternal progression model posits that both the intra-Golgi transport and Golgi exit of secretory cargos should occur at a constant velocity dictated by the cisternal progression; furthermore, COPI-mediated intra-Golgi retrograde transport is essential for maintaining the Golgi organization. Leveraging our recently developed Golgi imaging tools in nocodazole-induced Golgi ministacks, we found that the intra-Golgi transport velocity of a secretory cargo decreases during their transition from the cis to the trans-side of the Golgi, and different cargos exhibit distinct velocities even within the same cisternae. We observed a vast variation in the Golgi residence times of different cargos. Remarkably, truncation of the luminal domain causes the Golgi residence time of Tac — a standard transmembrane secretory cargo without intra-Golgi recycling signals — to extend from 16 minutes to a notable 3.4 hours. Additionally, when COPI-mediated intra-Golgi retrograde transport was inhibited by brefeldin A, we found that nocodazole-induced Golgi can remain stacked for over 30 - 60 minutes. Therefore, our findings challenge the classical cisternal progression model and suggest the stable compartment nature of the Golgi.
Nonspreading relativistic electron wavepacket in a strong laser field
Authors: Campos Andre G. , Hatsagortsyan Karen Z. , Keitel Christoph H. 
Published: April 2024

A solution of the Dirac equation in a strong laser field presenting a nonspreading wave packet of the electron is derived. It consists of a generalization of the self-accelerating free electron wavepacket [I. Kaminer , ] to the case with the background of a strong laser field. Built upon the notion of nonspreading for an extended relativistic wavepacket, the concept of Born rigidity for accelerated motion in relativity is the key ingredient of the solution. At its core, the solution comes from the connection between the self-accelerated free electron wavepacket and the eigenstate of a Dirac electron in a constant and homogeneous gravitational field via the equivalence principle. The solution is an essential step towards the realization of the laser-driven relativistic collider [S. Meuren , ], where the large spreading of a common Gaussian wavepacket during the excursion in a strong laser field strongly limits the expectable yields.

Published by the American Physical Society
2024
Exploring access-based consumption in last-mile logistics: a customer foresight study
Authors: Komonen Pauli 
Published: April 2024

Purpose
Due to e-commerce growth, technological advancements and environmental concerns, developing a more nuanced service portfolio has become a critical issue for last-mile logistics service providers. Concurrently, consumers are adopting new modes of consumption. This paper aims to investigate the potential for last-mile logistics service providers to act as intermediaries in access-based consumption and to revitalise their service offerings through product-service systems – a pioneering strategy not executed in the market yet.

Design/methodology/approach
This strategic customer foresight study uses a quantitative survey of 1,000 respondents and an online focus group comprising 10 early adopter consumers to investigate emerging last-mile service models. Potential service concepts were identified through the survey, and two distinct concepts were subsequently selected for evaluation and co-development within the focus group. The research was conducted in partnership with an SME logistics company in Finland.

Findings
The consumers expressed selective interest in access-based consumption related to the proposed offering of essential household goods. Young adults and consumers in early middle age living in the city centre emerged as the most potential user groups. Economic reasons and short-term needs were the primary motivations for adopting access-based consumption.

Practical implications
The study showed that engaging consumers in a customer foresight process is viable for SMEs innovating their offerings and demonstrates how the process works in practice.

Originality/value
Documented cases of customer integration into foresight processes are rare in earlier research, and this paper extends the knowledge base through a multidisciplinary examination of future consumer behaviour in the last-mile logistics domain. The paper also expands the limited literature on the role of logistics in access-based consumption.
Perceptions of the freezing response of male and female rape victims, and the moderating role of rape myth beliefs
Authors: Ostermann Judith Christiane , Watson Steven James 
Published: April 2024

Purpose
The purpose of this study was to investigate whether indicating victims of sexual attacks actively resisted their attacker or froze during their assault affected perceptions of victim blame, perpetrator blame and seriousness of the crime. We also tested whether victim and perpetrator gender or participants’ rape myth endorsement moderated the outcomes.

Design/methodology/approach
This study was a cross-sectional, vignette survey study with a 2 × 2 between-participants experimental design. Participants read a mock police report describing an alleged rape with a female or male victim who either resisted or froze, while perpetrator gender was adjusted heteronormatively.

Findings
Freezing and male victims were blamed more than resisting and female victims. Perpetrators were blamed more when the victim resisted, but male and female perpetrators were blamed equally. Seriousness of the crime was higher for male perpetrators and when the victim resisted. Female, but not male, rape myth acceptance moderated the relationship between victim behaviour and outcome variables.

Originality/value
This study highlights the influence of expectations about victim behaviour on perceptions of rape victims and the pervasive influence of rape myths when evaluating female rape victims. The data is drawn from the German border region of the Netherlands, which is an especially valuable population given the evolving legal definitions of rape in both countries.