bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure basis for recognition of 26RFa by the pyroglutamylated RFamide peptide receptor
Authors: Jin Sanshan , Li Xin , Xu Youwei , Guo Shimeng , Wu Canrong , Pan Benxun , Xin Wenwen , Zhang Heng , Hu Wen , Yin Yuling , Zhang Tianwei , Wu Kai , Yuan Qingning , Eric Xu H. , Xie Xin , Jiang Yi
Published: December 2023

The neuropeptide 26RFa, a member of the RF-amide peptide family, activates the pyroglutamylated RF-amide peptide receptor (QRFPR), a class A GPCR. The 26RFa/QRFPR system plays critical roles in energy homeostasis, making QRFPR an attractive drug target for treating obesity, diabetes, and eating disorders. However, the lack of structural information has hindered our understanding of the peptide recognition and regulatory mechanism of QRFPR, impeding drug design efforts. In this study, we determined the cryo-EM structure of the Gq-coupled QRFPR bound to 26RFa. The structure reveals a unique assembly mode of the receptor extracellular regions and the peptide N-terminus and elucidates the recognition mechanism of the C-terminal heptapeptide of 26RFa within the transmembrane binding pocket of QRFPR. The study also clarifies the similarities and distinctions in the binding pattern of the RF-amide moiety in five RF-amide peptides and the RY-amide segment in neuropeptide Y. These findings deepen our understanding of the RF-amide peptides recognition, aiding in the rational design of drugs targeting QRFPR and other RF-amide receptors.
Evolution of threat response-related polymorphisms at theSLC6A4locus in callitrichid primates
Authors: Twyman Hanlu , Heywood India , Barros Marília , Zeredo Jorge , Mundy Nicholas I. , Santangelo Andrea
Published: December 2023

Variation in an upstream repetitive region at theSLC6A4locus, which encodes a serotonin transporter, is associated with anxiety-related behaviour in a few primate species, including humans and rhesus macaques. In this study we investigate evolution ofSLC6A4polymorphisms associated with anxiety-related behaviour in common marmosets (Callithrix jacchus). Assaying variation in theSLC6A4repeat region across 14 species in 8 genera of callitrichid primates (marmosets and tamarins) we find large interspecific variation in the number of repeats present (24-43). The black tufted-ear marmoset (C. penicillata) has sequence polymorphisms similar to those found in the common marmoset, which is its sister species, and no other species has intraspecific variation at these sites. We conclude that, similar to humans and rhesus macaques, the functional polymorphism atSLC6A4in common marmosets has a recent evolutionary origin, and that the anxiety-related allele is evolutionarily derived. Common/black tufted-ear marmosets and rhesus macaques share high ecological adaptability and behavioural flexibility that we propose may be related to the maintenance of the polymorphism.
Intestinal epithelialAtg16l1influences pregnancy-induced fecal microbiota shifts in mice
Authors: López-Agudelo Víctor A. , Falk-Paulsen Maren , Rehman Ateequr , Bharti Richa , Sommer Felix , Wacker Eike Matthias , Ellinghaus David , Luzius Anne , Sievers Laura , Kaser Arthur , Rosenstiel Philip
Published: December 2023

Throughout gestation, the female body undergoes a series of transformations, including profound alterations in intestinal microbial communities. Changes gradually increase towards the end of pregnancy and comprise reduced α-diversity of microbial communities and an increased propensity for energy harvest. Despite the importance of the intestinal microbiota for the pathophysiology of inflammatory bowel diseases, very little is known about the relationship between these microbiota shifts and pregnancy-associated complications of the disease. Here, we explored the longitudinal dynamics of gut microbiota composition and functional potential during pregnancy and after lactation inAtg16l1ΔIECmice carrying an intestinal epithelial deletion of the Crohńs disease risk geneAtg16l1.Using 16S rRNA amplicon and shotgun metagenomic sequencing, we demonstrated divergent temporal shifts in microbial composition betweenAtg16l1wildtype andAtg16l1ΔIECpregnant mice in trimester 3, which was validated in an independent experiment. Observed differences included microbial genera implicated in IBD such asLachnospiraceae,Roseburia,Ruminococcus, andTuricibacter. Changes partially recovered after lactation. In addition, functional inference of metagenomic data suggest a reduced potential to biosynthesize mucosal protective polyamines and reduced capacity to metabolize acidic polysaccharides (ketogluconate metabolism).

On the host side, we found that the immunological response ofAtg16l1ΔIECmice is characterized by higher colonic mRNA levels of TNFA, and CXCL1 in trimester 3 and a lower weight of offspring at birth. Understanding pregnancy-dependent microbiome changes in the context of IBD may constitute the first step in the identification of fecal microbial biomarkers and microbiota-directed therapies that could help improving precision care for managing pregnancies in IBD patients.
DSMBind: SE(3) denoising score matching for unsupervised binding energy prediction and nanobody design
Authors: Jin Wengong , Chen Xun , Vetticaden Amrita , Sarzikova Siranush , Raychowdhury Raktima , Uhler Caroline , Hacohen Nir
Published: December 2023

Modeling the binding between proteins and other molecules is pivotal to drug discovery. Geometric deep learning is a promising paradigm for protein-ligand/protein-protein binding energy prediction, but its accuracy is limited by the size of training data as high-throughput binding assays are expensive. Herein, we propose an unsupervised binding energy prediction framework, named DSMBind, which does not need experimental binding data for training. DSMBind is an energy-based model that estimates the likelihood of a protein complex via SE(3) denoising score matching (DSM). This objective, applied at both backbone and side-chain levels, builds on a novel equivariant rotation prediction network derived from Euler’s Rotation Equations. We find that the learned log-likelihood of protein complexes is highly correlated with experimental binding energy across multiple benchmarks, even matching the performance of supervised models trained on experimental data. We further demonstrate DSMBind’s zero-shot binder design capability through a PD-L1 nanobody design task, where we randomize all three complementarity-determining regions (CDRs) and select the best CDR sequences based on DSMBind score. We experimentally tested the designed nanobodies with ELISA binding assay and successfully discovered a novel PD-L1 binder. In summary, DSMBind offers a versatile framework for binding energy prediction and binder design. Our code is publicly available atgithub.com/wengong-jin/DSMBind.
Restriction of intercellular communication is required for organ regeneration
Authors: Cohen Itay , Hak Hagit , Perez-Sancho Jessica , Spiegelman Ziv , Efroni Idan
Published: December 2023

The excision of the root tip, including the stem cell niche, triggers rapid regeneration from remnant cells in the stump. In plants, cell identity relies on positional information transported through cytoplasmatic bridges known as plasmodesmata. However, how such information is reset to allow the regeneration of lost identities is unknown. Here, we show that the movement of mobile signals is temporarily restricted near the incision site and that regeneration-induced members of the LATERAL ORGAN DOMAIN (LBD) plant-specific developmental regulators are necessary and sufficient for this restriction. Regeneration was disrupted in high-orderlbdmutants but was restored by transient localized plasmodesmata closure. We propose that LBD-mediated modulation of intercellular connectivity is crucial for plant regeneration and may have widespread roles inde novopattern formation.

One Sentence Summary

Plant-specific DNA binding genes mediate a transient restriction of intercellular communication to allow root regeneration
Rapid and Quantitative Functional Interrogation of Human Enhancer Variant Activity in Live Mice
Authors: Hollingsworth Ethan W. , Liu Taryn A. , Jacinto Sandra H. , Chen Cindy X. , Alcantara Joshua A. , Kvon Evgeny Z.
Published: December 2023

Functional analysis of non-coding variants associated with human congenital disorders remains challenging due to the lack of efficientin vivomodels. Here we introduce dual-enSERT, a robust Cas9-based two-color fluorescent reporter system which enables rapid, quantitative comparison of enhancer allele activities in live mice of any genetic background. We use this new technology to examine and measure the gain- and loss-of-function effects of enhancer variants linked to limb polydactyly, autism, and craniofacial malformation. By combining dual-enSERT with single-cell transcriptomics, we characterize variant enhancer alleles at cellular resolution, thereby implicating candidate molecular pathways in pathogenic enhancer misregulation. We further show that independent, polydactyly-linked enhancer variants lead to ectopic expression in the same cell populations, indicating shared genetic mechanisms underlying non-coding variant pathogenesis. Finally, we streamline dual-enSERT for analysis in F0 animals by placing both reporters on the same transgene separated by a synthetic insulator. Dual-enSERT allows researchers to go from identifying candidate enhancer variants to analysis of comparative enhancer activity in live embryos in under two weeks.
Targeting PrfA from Listeria monocytogenes: a computational drug repurposing approach
Authors: Arias Moreno Xabier
Published: December 2023

Humans can develop listeriosis by ingestion of foods contaminated withListeria monocytogenes,an opportunistic gram-positive ubiquitous bacterium. Whilst the non-invasive form of listeriosis may be asymptomatic or cause mild flu-like symptoms, the invasive form of listeriosis is life-threatening and is associated with high hospitalization and fatality rates. Current antibiotic-based therapies are still effective against listeriosis. However, multi-drug resistantListeria monocytogenesstrains have already been identified, which represents a new risk in the treatment of invasive listeriosis. Therefore, it is increasingly urgent to identify new compounds that do not target the conventional biochemical pathways disrupted by current antibiotics. Positive Regulatory Factor A (PrfA) is a well-studied transcriptional factor inListeria monocytogenesthat is responsible for activating a plethora of virulence factors. Targeting virulence factors is a promising strategy that is being considered to combat bacterial infections, hence targeting PrfA is both logical and attractive. In the present computational drug repurposing approach, a complete FDA-approved drugs dataset of more than 700 compounds was virtually screened by docking the drugs against the structure of PrfA. Three of the most promising top-scored FDA drug candidates were then simulated complexed to PrfA. Data from Molecular docking and Molecular Dynamics simulations suggest that Dutasteride and Solifenacin may bind PrfA, and as a result, might exhibit inhibitory activity againstListeria monocytogenes. The use of Dutasteride and Solifenacin is safe in humans since they have been used in the treatment of benign prostatic hyperplasia and androgenic alopecia, and urinary incontinence respectively for decades. Their unique chemical scaffolds may represent valuable starting points for the rapid development of disruptive novel listeria-specific drugs that will be soon needed to combat multi-drug resistantListeria monocytogenesstrains.
Free-floating Bacteria Transcriptionally Respond to Shear Flow
Authors: Ramachandran Ashwin , Stone Howard A. , Gitai Zemer
Published: December 2023

Planktonic (free-floating) cells are typically assumed to be oblivious to any flow that carries them. Here we discover that planktonic bacteria can sense flow to induce gene expression changes that are beneficial in flow. Specifically, planktonicP. aeruginosainduce shear-rate-dependent genes that promote growth in low oxygen environments. Untangling this mechanism revealed that in flow, motileP. aeruginosaspatially redistribute, leading to cell density changes that activate quorum sensing, which in turn enhances oxygen uptake rate. In diffusion-limited environments, including those commonly encountered by bacteria, flow-induced cell density gradients also independently generate oxygen gradients that alter gene expression. Mutants deficient in this newly-discovered flow sensing mechanism exhibit decreased fitness in flow, suggesting that this dynamic coupling of biological and mechanical processes can be physiologically significant.

One-Sentence Summary

Free-floating bacteria integrate biological and mechanical responses to adaptively alter gene expression in flow environments
Skeletal Muscle Satellite Cells Co-Opt the Tenogenic GeneScleraxisto Instruct Regeneration
Authors: Bai Yun , Harvey Tyler , Bilyou Colin , Hu Minjie , Fan Chen-Ming
Published: December 2023

Skeletal muscles connect bones and tendons for locomotion and posture. Understanding the regenerative processes of muscle, bone and tendon is of importance to basic research and clinical applications. Despite their interconnections, distinct transcription factors have been reported to orchestrate each tissue’s developmental and regenerative processes. Here we show thatScxexpression is not detectable in adult muscle stem cells (also known as satellite cells, SCs) during quiescence.Scxexpression begins in activated SCs and continues throughout regenerative myogenesis after injury. By SC-specificScxgene inactivation (ScxcKO), we show thatScxfunction is required for SC expansion/renewal and robust new myofiber formation after injury. We combined single-cell RNA-sequencing and CUT&RUN to identify direct Scx target genes during muscle regeneration. These target genes help explain the muscle regeneration defects of ScxcKO, and are not overlapping withScx-target genes identified in tendon development. Together with a recent finding of a subpopulation ofScx-expressing connective tissue fibroblasts with myogenic potential during early embryogenesis, we propose that regenerative and developmental myogenesis co-opt theScxgene via different mechanisms.
The Salmon Microbial Genome Atlas enables novel insights into bacteria-host interactions via functional mapping
Authors: de León Arturo Vera-Ponce , Hoetzinger Matthias , Hensen Tim , Gupta Shashank , Weston Bronson , Johnsen Sander M. , Rasmussen Jacob A. , Clausen Cecilie Grønlund , Pless Louisa , Veríssimo Ana Raquel Andrade , Rudi Knut , Snipen Lars , Karlsen Christian René , Limborg Morten T. , Bertilsson Stefan , Thiele Ines , Hvidsten Torgeir R. , Sandve Simen R. , Pope Phillip B. , La Rosa Sabina Leanti
Published: December 2023

The essential role of the gut microbiota for host health and nutrition is well established for many terrestrial animals, while its importance for fish and particularly Atlantic salmon is unclear. Here, we present the Salmon Microbial Genome Atlas (SMGA) originating from wild and farmed fish both in freshwater and seawater, and consisting of 211 high-quality bacterial genomes, recovered by cultivation (n=131) and gut metagenomics (n=80). Bacterial genomes were taxonomically assigned into 14 different orders, including 28 distinctive genera and 31 potentially novel species. Benchmarking the SMGA, we functionally characterized key populations in the salmon gut that were detectedin vivo. This included the ability to degrade diet-derived fibers and release vitamins and other exo-metabolites with known beneficial effects, which were validated byin vitrocultivation and untargeted metabolomics. Together, the SMGA enables high resolution functional insight into salmon gut microbiota with relevance for salmon nutrition and health.
The molecular principles underlying diverse functions of the SLC26 family of proteins
Authors: Takahashi Satoe , Homma Kazuaki
Published: December 2023

Mammalian SLC26 proteins are membrane-based anion transporters that belong to the large SLC26/SulP family, and many of their variants are associated with hereditary diseases. Recent structural studies revealed a strikingly similar homodimeric molecular architecture for several SLC26 members, implying a shared molecular principle. Now a new question emerges as to how these structurally similar proteins execute diverse physiological functions. In this study we sought to identify the common vs. distinct molecular mechanism among the SLC26 proteins using both naturally occurring and artificial missense changes introduced to SLC26A4, SLC26A5, and SLC26A9. We found: (i) the basic residue at the anion binding site is essential for both anion antiport of SLC26A4 and motor functions of SLC26A5, and its conversion to a nonpolar residue is crucial but not sufficient for the fast uncoupled anion transport in SLC26A9; (ii) the conserved polar residues in the N- and C-terminal cytosolic domains are likely involved in dynamic hydrogen-bonding networks and are essential for anion antiport of SLC26A4 but not for motor (SLC26A5) and uncoupled anion transport (SLC26A9) functions; (iii) the hydrophobic interaction between each protomer’s last transmembrane helices, TM14, is not of functional significance in SLC26A9 but crucial for the functions of SLC26A4 and SLC26A5, likely contributing to optimally orient the axis of the relative movements of the core domain with respect to the gate domains within the cell membrane. These findings advance our understanding of the molecular mechanisms underlying the diverse physiological roles of the SLC26 family of proteins.
High-density sampling reveals volume growth in human tumours
Authors: Angaji Arman , Owusu Michel , Velling Christoph , Dick Nicola , Weghorn Donate , Berg Johannes
Published: December 2023

In growing cell populations such tumours, mutations can serve as markers that allow tracking the past evolution from current samples. The genomic analyses of bulk samples and samples from multiple regions have shed light on the evolutionary forces acting on tumours. However, little is known empirically on the spatio-temporal dynamics of tumour evolution. Here, we leverage published data from resected hepatocellular carcinomas, each with several hundred samples taken in two and three dimensions. Using spatial metrics of evolution, we find that tumour cells grow predominantly uniformly within the tumour volume instead of at the surface. We determine how mutations and cells are dispersed throughout the tumour and how cell death contributes to the overall tumour growth. Our methods shed light on the early evolution of tumours in vivo and can be applied to high-resolution data in the emerging field of spatial biology.
Evolutionary and Developmental Specialization of Foveal Cell Types in the Marmoset
Authors: Zhang Lin , Cavallini Martina , Wang Junqiang , Xin Ruiqi , Zhang Qiangge , Feng Guoping , Sanes Joshua R. , Peng Yi-Rong
Published: December 2023

In primates, high-acuity vision is mediated by the fovea, a small specialized central region of the retina. The fovea, unique to the anthropoid lineage among mammals, undergoes notable neuronal morphological changes during postnatal maturation. However, the extent of cellular similarity across anthropoid foveas and the molecular underpinnings of foveal maturation remain unclear. Here, we used high throughput single cell RNA sequencing to profile retinal cells of the common marmoset (Callithrix jacchus), an early divergent in anthropoid evolution from humans, apes, and macaques. We generated atlases of the marmoset fovea and peripheral retina for both neonates and adults. Our comparative analysis revealed that marmosets share almost all its foveal types with both humans and macaques, highlighting a conserved cellular structure among primate foveas. Furthermore, by tracing the developmental trajectory of cell types in the foveal and peripheral retina, we found distinct maturation paths for each. In-depth analysis of gene expression differences demonstrated that cone photoreceptors and Müller glia, among others, show the greatest molecular divergence between these two regions. Utilizing single-cell ATAC-seq and gene-regulatory network inference, we uncovered distinct transcriptional regulations differentiating foveal cones from their peripheral counterparts. Further analysis of predicted ligand-receptor interactions suggested a potential role for Müller glia in supporting the maturation of foveal cones. Together, these results provide valuable insights into foveal development, structure, and evolution.

Significance statement

The sharpness of our eyesight hinges on a tiny retinal region known as the fovea. The fovea is pivotal for primate vision and is susceptible to diseases like age-related macular degeneration. We studied the fovea in the marmoset–a primate with ancient evolutionary ties. Our data illustrated the cellular and molecular composition of its fovea across different developmental ages. Our findings highlighted a profound cellular consistency among marmosets, humans, and macaques, emphasizing the value of marmosets in visual research and the study of visual diseases.
A super-resolution compatible workflow for highly multiplexed immunofluorescence of routinely processed kidney tissue
Authors: Siegerist Florian , Kitzel Svenja , Telli Nihal , Dikou Juan Saydou , Drenić Vedran , Chadjichristos Christos E. , Chatziantoniou Christos , Endlich Nicole
Published: December 2023

Deep insights into the complex cellular and molecular changes occurring during different (patho-)physiological conditions are essential for understanding the interactions and regulation of different proteins. This understanding is crucial for both research and diagnostics. However, the effectiveness of conventional immunofluorescence, an effective tool for visualizing the spatial distribution of cells or proteins, is limited in complex tissues. This is mainly due to challenges such as the spectral overlap of fluorophore wavelengths, a limited range of antibody types, and the inherent variability of samples.

Multiplex immunofluorescence imaging offers a solution to these limitations by enabling precise localization of proteins and identification of different cell types in a single tissue sample. In this study, we demonstrate the cyclic staining and de-staining of paraffin kidney sections, making it suitable for routine use and compatible with super-resolution microscopy for podocyte ultrastructural studies. We have further developed a computerized workflow for data processing which is accessible to all researchers through commercially available reagents and open-access image analysis codes.

As a proof of principle, we identified CDH2 as a marker for cellular lesions of sclerotic glomeruli in the nephrotoxic serum nephritis mouse model and cross-validated this finding with a human Nephroseq dataset indicating its translatability.

In summary, our work represents a significant advance in multiplex imaging, which is crucial for understanding the localization of numerous proteins in a single FFPE kidney section and the compatibility with super-resolution microscopy to study ultrastructural changes of podocytes.
The novel bacterial effector proteinCbEPF1 mediates ER-LD membrane contacts to regulate host lipid droplet metabolism
Authors: Angara Rajendra Kumar , Sadi Arif , Gilk Stacey D.
Published: December 2023

Effective intracellular communication between cellular organelles is pivotal for maintaining cellular homeostasis. Tether proteins, which are responsible for establishing membrane contact sites between cell organelles, enable direct communication between organelles and ultimately influence organelle function and host cell homeostasis. While recent research has identified tether proteins in several bacterial pathogens, their functions have predominantly been associated with mediating inter-organelle communication specifically between the bacteria containing vacuole (BCV) and the host endoplasmic reticulum (ER). However, this study reveals a novel bacterial effector protein,CbEPF1, which acts as a molecular tether beyond the confines of the BCV and facilitates interactions between host cell organelles.Coxiella burnetii, an obligate intracellular bacterial pathogen, encodes the FFAT motif-containing proteinCbEPF1 which localizes to host lipid droplets (LDs).CbEPF1 establishes inter-organelle contact sites between host LDs and the ER through its interactions with VAP family proteins. Intriguingly,CbEPF1 modulates growth of host LDs in a FFAT motif-dependent manner. These findings highlight the potential for bacterial effector proteins to impact host cellular homeostasis by manipulating inter-organelle communication beyond conventional BCVs.
Longitudinal profiling of the pregnancy plasma proteome through organic solvent precipitation and nano LC-MS/MS
Authors: George A.L , Cook E , Smith G.C.S , Charnock-Jones D.S , O’Rahilly S , Reimann F , Gribble F.M , Kay R.G
Published: December 2023

Proteins secreted from maternal, fetal, and placental tissue are vital for processes like placental development, immunotolerance, and fetal growth, and are associated with pregnancy complications, necessitating predictive biomarkers. In this study, we introduce an acetonitrile-based precipitation coupled with solid-phase extraction that addresses limitations of current low throughput blood-based biomarker discovery workflows. Our method is efficient and cost-effective, and identified 433 protein groups, showing specific tissue associations and enrichment in reproductive tissues such as the placenta, breast, and endometrium. Significant alterations in proteins related to hormonal regulation, immune modulation, and placental development throughout gestation were observed. This approach offers comprehensive insights into the circulating pregnancy proteome, but also provides a scalable solution for larger studies for biomarker discovery in the context of pregnancy complications.

TOC
Mechanism of connexin channel inhibition by mefloquine and 2-aminoethoxydiphenyl borate
Authors: Lavriha Pia , Han Yufei , Ding Xinyue , Qi Chao , Vaithia Anand , Korkhov Volodymyr M.
Published: December 2023

Gap junction intercellular communication (GJIC) between two adjacent cells involves direct exchange of cytosolic ions and small molecules via connexin gap junction channels (GJCs). Connexin GJCs have emerged as drug targets, with small molecule connexin inhibitors considered a viable therapeutic strategy in several diseases. The molecular mechanisms of GJC inhibition by known small molecule connexin inhibitors remain unknown, preventing the development of more potent and connexin-specific therapeutics. Here we show that two GJC inhibitors, mefloquine (MFQ) and 2-aminoethoxydiphenyl borate (2APB) bind to Cx32 and block dye permeation across Cx32 hemichannels (HCs) and GJCs. Cryo-EM analysis shows that 2APB binds to “site A”, close to the N-terminal gating helix of Cx32 GJC, restricting the entrance to the channel pore. In contrast, MFQ binds to a distinct “site M”, deeply buried within the pore. MFQ binding to this site modifies the electrostatic properties of Cx32 pore. Mutagenesis of V37, a key residue located in the site M, renders Cx32 HCs and GJCs insensitive to MFQ-mediated inhibition. Moreover, our cryo-EM analysis, mutagenesis and activity assays show that MFQ targets the M site in Cx43 GJC similarly to Cx32. Taken together, our results point to a conserved inhibitor binding site in connexin channels, opening a new route for development of specific drugs targeting connexins.

One-Sentence Summary

Inhibition of Cx32 and Cx43 channels via functionally relevant drug binding sites
Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase
Authors: Chen Boning , MacAlpine Heather K. , Hartemink Alexander J. , MacAlpine David M.
Published: December 2023

Proper maintenance of epigenetic information after replication is dependent on the rapid assembly and maturation of chromatin. Chromatin Assembly Complex 1 (CAF-1) is a conserved histone chaperone that deposits (H3-H4)2tetramers as part of the replication-dependent chromatin assembly process. Loss of CAF-1 leads to a delay in chromatin maturation, albeit with minimal impact on steady-state chromatin structure. However, the mechanisms by which CAF-1 mediates the deposition of (H3-H4)2tetramers and the phenotypic consequences of CAF-1-associated assembly defects are not well understood. We used nascent chromatin occupancy profiling to track the spatiotemporal kinetics of chromatin maturation in both wild-type (WT) and CAF-1 mutant yeast cells. Our results show that loss of CAF-1 leads to a heterogeneous rate of nucleosome assembly, with some nucleosomes maturing at near WT kinetics and others showing significantly slower maturation kinetics. The slow-to-mature nucleosomes are enriched in intergenic and poorly transcribed regions, suggesting that transcription-dependent assembly mechanisms can reset the slow-to-mature nucleosomes following replication. Nucleosomes with slow maturation kinetics are also associated with poly(dA:dT) sequences, which implies that CAF-1 deposits histones in a manner that counteracts resistance from the inflexible DNA sequence, promoting the formation of histone octamers as well as ordered nucleosome arrays. In addition, we show that the delay in chromatin maturation is accompanied by a transient and S-phase-specific loss of gene silencing and transcriptional regulation, revealing that the DNA replication program can directly shape the chromatin landscape and modulate gene expression through the process of chromatin maturation.
Deepening the disciplinary cognition and constructing the theoretical system of socialist political economy with Chinese characteristics
Authors: Liu Can
Published: December 2023

Purpose

The socialist political economy with Chinese characteristics is a systematic economic discipline, which theoretically summarises the socialist economic system and the path of economic development with Chinese characteristics. It is a systematic economic theory of adapting Marxism to the Chinese context. The theoretical system construction for the discipline of socialist political economy with Chinese characteristics is currently a major task.

Design/methodology/approach

From the perspective of disciplinary cognition, the theoretical system of the discipline of socialist political economy with Chinese characteristics includes the disciplinary attributes and connotations, theoretical basis, the origin of thoughts, major principles, logical starting point, main logic and problem-based study of major theoretical and practical issues.

Findings

Developing the discipline and building the theoretical system of the socialist political economy with Chinese characteristics, several major principles should be adhered to, including building the socialist political economy with Chinese characteristics on the basis of historical materialism; building the theoretical paradigm of socialist political economy with Chinese characteristics around the analysis of production relations; adhering to the people-centred principle; taking common prosperity as the main logic of the socialist political economy with Chinese characteristics; studying the major theoretical and practical issues of building the socialism with Chinese characteristics in the new era based on problems; and reflecting the innovative development of the discipline in the textbook, The Socialist Political Economy with Chinese Characteristics.

Originality/value

Disciplinary cognition involves the connotations, attributes, mission and development path of the discipline, which is related to how to construct the discipline system and is a significant part of the disciplinary construction.
Impostorization in the ivory tower: less discussed but more vexing than impostor syndrome
Authors: Gutiérrez Angélica S. , Cole Jean Lee
Published: December 2023

Purpose

Given the lack of research on the lived experiences of racially minoritized women in academia, this paper provides primary accounts of their experience with impostorization. Impostorization refers to the policies, practices and seemingly innocuous interactions that make or intend to make individuals (i.e. women of color) question their intelligence, competence and sense of belonging.

Design/methodology/approach

To explore experiences with impostorization and identify effective coping strategies to counter the debilitating effects of impostorization, 17 semi-structured interviews were conducted with women of color PhD students and faculty at universities throughout the USA and across disciplines.

Findings

While impostor syndrome, which refers to feelings of inadequacy that individuals experience and a fear that they will be discovered as fraud, has garnered much attention, the present accounts suggest that the more vexing issue in academia is impostorization, not impostor syndrome. Forms of impostorization include microaggressions, grateful guest syndrome, invisibility and inclusion taxation.

Originality/value

The interviews reveal the implicit and explicit ways in which academia impostorizes racially minoritized women scholars and the coping strategies that they use to navigate and survive within academia. The accounts demonstrate the pernicious effects of labeling feelings of inadequacy and unbelonging as impostor syndrome rather than recognizing that the problem is impostorization. This is a call to change the narrative and go from a fix-the-individual to a fix-the-institution approach.
Asset redeployability, sustainability, and managerial prudence: evidence from economic policy uncertainty
Authors: Chatjuthamard Pattanaporn , Papangkorn Suwongrat , Jiraporn Pornsit , Phiromswad Piyachart
Published: December 2023

Purpose

The purpose of this study is to shed light on the impact of economic policy uncertainty (EPU) on asset redeployability. Capitalizing on a novel measure of asset redeployability, the authors explore the effect of economic policy uncertainty (EPU) on redeployable assets using a unique text-based measure of EPU. Asset redeployability is an important aspect of sustainability that has been largely overlooked. More redeployable assets can be repurposed for a variety of uses, lessening the necessity for new products and thus conserving natural resources.

Design/methodology/approach

In addition to the standard regression analysis, the authors execute a variety of robustness checks, i.e. propensity score matching, entropy balancing, instrumental-variable analysis, GMM dynamic panel data analysis and use Oster’s (2019) approach for testing coefficient stability. Importantly, the authors incorporate firm fixed effects in the analysis, which helps mitigate endogeneity due to unobservable firm characteristics.

Findings

Based on an immense sample of over 200,000 observations over three decades, the results reveal that greater uncertainty raises asset redeployability significantly. The findings corroborate the managerial prudence hypothesis. The future deployment of assets is less predictable in times of increased uncertainty. Consequently, during uncertain times, it is more prudent to have assets that can be redeployed for multiple purposes.

Originality/value

To the best of the authors’ knowledge, this is the first study to explore the impact of EPU on asset redeployability, which is a critical aspect of sustainability that has rarely been investigated in the literature. The authors fill this important void in the literature. The authors extend the literature in EPU, asset redeployability as well as sustainability.
Health and health care in Australian immigration detention: a comparison between onshore and offshore data
Authors: Kalocsányiová Erika , Essex Ryan
Published: December 2023

Purpose

This study aims to compare the impact of Australian onshore and offshore immigration detention centres (IDCs) on detainees’ health and health-care events.

Design/methodology/approach

It uses data extracted from the Australian Government’s quarterly health reports from 2014 to 2017. These reports contain a range of data about the health and well-being of detainees, including complaints/presenting symptoms and number of appointments and hospitalisations. To compare onshore and offshore data sets, the authors calculated the rate of health events per quarter against the estimated quarterly onshore and offshore detention population. They ran a series of two-proportion z-tests for each matched quarter to calculate median z- and p-values for all quarters. These were used as an indicator as to whether the observed differences between onshore and offshore events were statistically significant.

Findings

The results suggest that adults detained onshore and offshore have substantial health needs, however, almost all rates were far higher in offshore detention, with people more likely to raise a health-related complaint, access health services and be prescribed medications, often at two to three times the rate of those onshore.

Originality/value

This paper adds to a modest body of literature that explains the health of people detained in Australian IDCs. To the best of the authors’ knowledge, this is the first paper to explore health service utilisation and a range of other variables found in the Australian Government’s quarterly health reports. These findings bolster the evidence which suggests that detention, and particularly offshore detention is particularly harmful to health.
Overcoming the “tenant-owner dilemma” to foster energy efficiency in residential private rented housing
Authors: Garcia-Teruel Rosa M.
Published: December 2023

Purpose

The Recast Energy Efficiency Directive 2023 has defined the concept of “split incentive,” also known as “tenant-owner dilemma.” This dilemma refers to the situation where neither landlords nor tenants have incentives to invest in energy efficiency upgrades. Although the Energy Efficiency Directive calls Member States to overcome legal barriers to remove split incentives and to encourage retrofits, the list of possible measures is too vague. This paper aims to discuss tenancy law measures designed to increase the energy efficiency of residential housing and to detect which Member States have already addressed this phenomenon.

Design/methodology/approach

This paper analyses, from a civil legal perspective, the possible private law barriers arising from the tenant-owner dilemma when performing energy efficiency works in selected countries and proposes legal reforms in tenancy law and related policies to overcome them. To do so, this paper follows a legal-dogmatic and comparative law methodology.

Findings

This paper concludes that some tenancy law provisions, such as the possibility to increase the rent after energy efficiency renovations and long-term leases, may challenge the tenant-owner dilemma in private rented markets, thus promoting renovations and retrofitting for energy efficiency purposes. It also proposes other policies intended to increase parties’ willingness to undertake works.

Research limitations/implications

More research on the economic and legal efficiency to regulate some of the civil law measures to challenge the tenant-owner dilemma should be necessary.

Practical implications

The civil law measures included in this paper may help national policymakers meet the energy efficiency targets, according to what is established in the Recast Energy Efficiency Directive 2023.

Originality/value

Based on the economic theory of the tenant-owner dilemma, this paper investigates the elements of tenancy law that may contribute to less energy-efficient homes, proposing policies for those countries interested in addressing the energy-efficiency challenge from a private law point of view.
Fitness benefits of alternated chick provisioning in cooperatively breeding carrion crows
Authors: Trapote Eva , Moreno‐González Víctor , Canestrari Daniela , Rutz Christian , Baglione Vittorio
Published: December 2023

In most bird species, parents raise offspring cooperatively. In some cases, this cooperation extends to helpers‐at‐the‐nest who assist the breeders with a range of tasks.

While cooperative food provisioning might merely arise incidentally, as a result of the efforts of carers that act independently from each other, recent studies suggest that birds may coordinate by taking turns in visiting the nest. However, evidence that such coordination emerges because individuals actively respond to each other's behaviour is controversial, and the potential benefits of carers' alternation remain unknown.

We addressed this knowledge gap by analysing a multiyear dataset for cooperatively breeding carrion crows Corvus corone, comprising 8693 nest visits across 50 groups.

Our results reveal that turn‐taking does occur in this species and that all group members, regardless of their sex and social role (breeder/helper), tend to alternate at the nest with other carers rather than to make repeat visits.

Importantly, we found that the body mass of nestlings increased significantly with the degree of carers' alternation, possibly because well‐coordinated groups provided food at more regular intervals.

Using earlier monitoring data, the observed increase in body mass is predicted to substantially boost postfledging survival rates. Our analyses demonstrate that alternation in nestling provisioning has measurable fitness benefits in this study system.

This raises the possibility that cooperatively breeding carrion crows, as well as other bird species with similarly coordinated brood provisioning, exhibit specialized behavioural strategies that enable effective alternation.
Genome‐Scale Model of Rhizopus microsporus: Metabolic integration of a fungal holobiont with its bacterial and viral endosymbionts
Authors: Valadez‐Cano Cecilio , Olivares‐Hernández Roberto , Espino‐Vázquez Astrid N. , Partida‐Martínez Laila P.
Published: December 2023

Rhizopus microsporus often lives in association with bacterial and viral symbionts that alter its biology. This fungal model represents an example of the complex interactions established among diverse organisms in functional holobionts. We constructed a Genome‐Scale Model (GSM) of the fungal‐bacterial‐viral holobiont (iHol). We employed a constraint‐based method to calculate the metabolic fluxes to decipher the metabolic interactions of the symbionts with their host. Our computational analyses of iHol simulate the holobiont's growth and the production of the toxin rhizoxin. Analyses of the calculated fluxes between R. microsporus in symbiotic (iHol) versus asymbiotic conditions suggest that changes in the lipid and nucleotide metabolism of the host are necessary for the functionality of the holobiont. Glycerol plays a pivotal role in the fungal‐bacterial metabolic interaction, as its production does not compromise fungal growth, and Mycetohabitans bacteria can efficiently consume it. Narnavirus RmNV‐20S and RmNV‐23S affected the nucleotide metabolism without impacting the fungal‐bacterial symbiosis. Our analyses highlighted the metabolic stability of Mycetohabitans throughout its co‐evolution with the fungal host. We also predicted changes in reactions of the bacterial metabolism required for the active production of rhizoxin. This iHol is the first GSM of a fungal holobiont.
Vacuum‐steam pulsed blanching: An emerging method to enhance texture softening, drying behavior and physicochemical properties of Cornus officinalis
Authors: Zhang An‐An , Ha Bu‐Er , Chen Chang , Xu Ming‐Qiang , Wang Qing‐Hui , Xie Long , Zheng Zhi‐An , Zhang Jing‐Shou , Lv Wei‐Qiao , Xiao Hong‐Wei
Published: December 2023

Vacuum steam pulsed blanching (VSPB) was employed as a novel blanching technology on Cornus officinalis to soften the tissue for subsequent coring and dehydration. The current work aims to explore its effect on mass transfer behavior, PPO inactivation, drying characteristics, physicochemical properties, antioxidant capacity, and microstructure of C. officinalis. Results showed that VSPB increased water loss, decreased solid gain, and increased weight reduction with increased blanching cycles. Besides, VSPB significantly changed physical properties and extensively reduced drying time which was attributed to the cell wall components dissolving and cell turgor pressure decreasing, also verified by observing microstructure alteration. PPO was completely denatured after blanching in 6 cycles, but phenolic compounds were still diffused or degraded. Notably, the content of flavonoids and antioxidant capacity significantly increased compared to fresh samples probably due to increased extractability caused by the disrupting cell structure. Besides, the carotenoids and ascorbic acid could be well preserved.
Cross‐protection against pepino mosaic virus, more than a decade of efficient disease control
Authors: Hernando Yolanda , Aranda Miguel A.
Published: December 2023

Cross‐protection was first described a century ago. In practical terms, cross‐protection consists of the pre‐inoculation of plants with mild or attenuated viral isolates that protect the plants from subsequent infections with aggressive isolates. Experimentally, cross‐protection has been shown to apply to numerous virus and viroid species infecting numerous plant hosts, but the number of cases in which it has been successfully used for the control of the damage caused by viruses in crops is rather limited. Significant examples include citrus tristeza virus and zucchini yellow mosaic virus, and more recently, pepino mosaic virus (PepMV). PepMV is a pandemic virus affecting tomato crops worldwide. During the first decade of the current century, a number of mild PepMV isolates useful in cross‐protection were identified and characterized. Soon after, cross‐protection programs against PepMV were implemented in the Netherlands, Belgium, Morocco, and Spain. These programs were easily adopted by farmers, as no other efficient control methods were available and the losses caused by PepMV were unbearable for tomato producers. PepMV cross‐protection has been working exceedingly well during this time, although the potential interaction of the PepMV mild isolates with the recently emerging tomato brown rugose fruit virus (ToBRFV) may be threatening its viability. In this review, we describe our experience in deploying cross‐protection against PepMV in Spain. In our view, this is an underexploited technology that holds promise, but when it is used and how it is used requires careful thinking and preparation, as not all situations are as favourable for the use of cross‐protection as the PepMV pandemic has been.