bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rescue of secretion of a rare-disease associated mis-folded mutant glycoprotein inUGGT1knock-out mammalian cells
Authors: Tax Gábor , Guay Kevin P. , Soldà Tatiana , Hitchman Charlie J. , Hill Johan C. , Vasiljević Snežana , Lia Andrea , Modenutti Carlos P. , Straatman Kees R. , Santino Angelo , Molinari Maurizio , Zitzmann Nicole , Hebert Daniel N. , Roversi Pietro , Trerotola Marco 
Published: May 2023

AbstractEndoplasmic reticulum (ER) retention of mis-folded glycoproteins is mediated by the ER- localised eukaryotic glycoprotein secretion checkpoint, UDP-glucose glycoprotein glucosyl-transferase (UGGT). The enzyme recognises a mis-folded glycoprotein and flags it for ER retention by reglucosylating one of its N-linked glycans. In the background of a congenital mutation in a secreted glycoprotein gene, UGGT-mediated ER retention can cause rare disease even if the mutant glycoprotein retains activity (“responsive mutant”). Here, we investigated the subcellular localisation of the human Trop-2 Q118E variant, which causes gelatinous drop- like corneal dystrophy (GDLD). Compared with the wild type Trop-2, which is correctly localised at the plasma membrane, the Trop-2-Q118E variant is found to be heavily retained in the ER. Using Trop-2-Q118E, we tested UGGT modulation as a rescue-of-secretion therapeutic strategy for congenital rare disease caused by responsive mutations in genes encoding secreted glycoproteins. We investigated secretion of a EYFP-fusion of Trop-2-Q118E by confocal laser scanning microscopy. As a limiting case of UGGT inhibition, mammalian cells harbouring CRISPR/Cas9-mediated inhibition of theUGGT1and/orUGGT2gene expressions were used. The membrane localisation of the Trop-2-Q118E-EYFP mutant was successfully rescued inUGGT1-/-andUGGT1/2-/-cells. UGGT1 also efficiently reglucosylated Trop-2-Q118E-EYFPin cellula. The study supports the hypothesis that UGGT1 modulation constitutes a novel therapeutic strategy for the treatment of Trop-2-Q118E associated GDLD, and it encourages the testing of modulators of ER glycoprotein folding Quality Control (ERQC) as broad-spectrum rescue- of-secretion drugs in rare diseases caused by responsive secreted glycoprotein mutants.SynopsisDeletion of theUGGT1andUGGT1/2genes in HEK 293T cells rescues secretion of an EYFP-fusion of the human Trop-2-Q118E glycoprotein mutant. The mutant is retained in the secretory pathway in wild type cells and it localises to the cell membrane inUGGT1-/-single andUGGT1/2-/-double knock-out cells. The Trop-2-Q118E glycoprotein disease mutant is efficiently glucosylated by UGGT1 in human cells demonstrating that it is abona fidecellular UGGT1 substrate.
Reconstructing stochastic cell population trajectories reveals regulators and heterogeneity of endothelial flow-migration coupling driving vascular remodelling
Authors: Giese Wolfgang , Rosa André , Baumann Elisabeth , Oppenheim Olya , Akmeric Emir B. , Andrade Santiago , Hollfinger Irene , Bartels-Klein Eireen , Alt Silvanus , Gerhardt Holger 
Published: May 2023

AbstractEmerging concepts of developmental vascular remodelling recently identified that selectively labelled sprouting tip cells and/or venous endothelial cells (ECs) accumulate in developing arteries, suggesting directional migration of specific ECs drives artery formation. However, a general population analysis and detailed quantitative investigation of migratory mechanisms is so far lacking. Here, we developed a universally applicable quantitative approach and a computational model allowing to track and simulate stochastically labelled EC populations irrespective of labelling density and origin. Dynamic mapping of EC distributions in a bespoke coordinate system revealed how ECs move during the most active remodelling phases in the mouse retina. Simulation and parameter sensitivity analysis illustrated that the population shift from veins to arteries cannot be explained by random walk, but best fits to a tuneable dual force-field between shear-force induced directionality against blood flow, and hypoxia mediated VEGFA-gradients. High migration rates require only weak flow-migration coupling, whereas low migration rates require strong coupling to the flow direction. Functional analysis identified Cdc42 as the critical mediator of overall population movement from veins to arteries, yet with surprising heterogeneity suggesting the existence of distinct cell populations. This new quantitative understanding will enable future tailored intervention and tuning of the remodelling process.
Structural evidence for MADS-box type I family expansion seen in new assemblies ofA. arenosaandA. lyrata
Authors: Bramsiepe Jonathan , Krabberød Anders K. , Bjerkan Katrine N. , Alling Renate M. , Johannessen Ida M. , Hornslien Karina S. , Miller Jason R. , Brysting Anne K. , Grini Paul E. 
Published: May 2023

SummaryArabidopsis thalianadiverged fromA. arenosaandA. lyrataat least 6 million years ago and are identified by genome-wide polymorphisms or morphological traits. The species are to a high degree reproductively isolated, but hybridization barriers are incomplete. A special type of hybridization barrier is based in the triploid endosperm of the seed, where embryo lethality is caused by endosperm failure to support the developing embryo. The MADS-box type I family of transcription factors are specifically expressed in the endosperm and has been proposed to play a role in endosperm-based hybridization barriers. The gene family is well known for a high evolutionary duplication rate, as well as being regulated by genomic imprinting. Here we address MADS-box type I gene family evolution and the role of type I genes in the context of hybridization. Using twode-novoassembled and annotated chromosome-level genomes ofA. arenosaandA. lyratassp.petraeawe analyzed the MADS-box type I gene family inArabidopsisto predict orthologs, copy number and structural genomic variation related to the type I loci. Our findings were compared to gene expression profiles sampled before and after the transition to endosperm cellularization in order to investigate the involvement of MADS-box type I loci in endosperm-based hybridization barriers. We observed substantial differences in type-I expression betweenA. arenosaandA. lyratassp.petraeain the endosperm, suggesting a genetic cause for the endosperm-based hybridization barrier inA. arenosaandA. lyratassp.petraeahybrid seeds.
OAS3 and RNase L integrate into higher-order antiviral condensates
Authors: Cusic Renee , Burke James M. 
Published: May 2023

ABSTRACTOligoadenylate synthetase 3 (OAS3) and Ribonuclease L (RNase L) are components of a mammalian RNA decay pathway that is critical for combating viral infection. Nevertheless, the subcellular localization of OAS3 and RNase L during the antiviral response has remained elusive. Herein, we show that upon activation in response to double-stranded RNA or viral infection, OAS3 and RNase L integrate into higher-order cytoplasmic assemblies distinct from stress granules (SGs), RNase L-induced bodies (RLBs), or processing bodies (P-bodies). We identified these assemblies as double-stranded RNA-induced foci (dRIF), which also contain activated protein kinase R (PKR). We observed incorporation of RNase L, OAS3, and PKR in dRIFs during Zika virus and dengue virus infection. Our data support that condensation of dsRNA, OAS3 and RNase L at dRIFs promotes the homodimerization and oligomerization of RNase L required for its rapid activation, demonstrating a fundamental role for biological condensates in activating antiviral signaling.
In-cell structural insight into the stability of sperm microtubule doublet
Authors: Tai Linhua , Yin Guoliang , Huang Xiaojun , Zhu Yun , Sun Fei 
Published: May 2023

AbstractThe propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. However, the intricate molecular architecture of sperm DMT remains elusive. Here, byin situcryo-electron tomography, we solved the in-cell structure of mouse sperm DMT up to 3.6 Å resolution and built its model with 36 kinds of MIPs in 48 nm periodicity. We identified multiple copies of Tektin5 that reinforce Tektin bundle, and multiple MIPs with different periodicities that anchor the Tektin bundle to tubulin wall. This architecture contributes to a superior stability of A-tubule than B-tubule of DMT, which was revealed by structural comparison of DMTs from the intact and deformed axonemes. Our work provides an overall molecular picture of sperm DMT that is essential to understand the molecular mechanism of sperm motility as well as the related ciliopathies.
The variation and evolution of complete human centromeres
Authors: Logsdon Glennis A. , Rozanski Allison N. , Ryabov Fedor , Potapova Tamara , Shepelev Valery A. , Mao Yafei , Rautiainen Mikko , Koren Sergey , Nurk Sergey , Porubsky David , Lucas Julian K. , Hoekzema Kendra , Munson Katherine M. , Gerton Jennifer L. , Phillippy Adam M. , Alexandrov Ivan A. , Eichler Evan E. 
Published: May 2023

ABSTRACTWe completely sequenced and assembled all centromeres from a second human genome and used two reference sets to benchmark genetic, epigenetic, and evolutionary variation within centromeres from a diversity panel of humans and apes. We find that centromere single-nucleotide variation can increase by up to 4.1-fold relative to other genomic regions, with the caveat that up to 45.8% of centromeric sequence, on average, cannot be reliably aligned with current methods due to the emergence of new α-satellite higher-order repeat (HOR) structures and two to threefold differences in the length of the centromeres. The extent to which this occurs differs depending on the chromosome and haplotype. Comparing the two sets of complete human centromeres, we find that eight harbor distinctly different α-satellite HOR array structures and four contain novel α-satellite HOR variants in high abundance. DNA methylation and CENP-A chromatin immunoprecipitation experiments show that 26% of the centromeres differ in their kinetochore position by at least 500 kbp—a property not readily associated with novel α-satellite HORs. To understand evolutionary change, we selected six chromosomes and sequenced and assembled 31 orthologous centromeres from the common chimpanzee, orangutan, and macaque genomes. Comparative analyses reveal nearly complete turnover of α-satellite HORs, but with idiosyncratic changes in structure characteristic to each species. Phylogenetic reconstruction of human haplotypes supports limited to no recombination between the p- and q-arms of human chromosomes and reveals that novel α-satellite HORs share a monophyletic origin, providing a strategy to estimate the rate of saltatory amplification and mutation of human centromeric DNA.
Exogenous Recombinant N-Acetylgalactosamine-4-Sulfatase (Arylsulfatase B; ARSB) Inhibits Progression of B16F10 Cutaneous Melanomas and Modulates Cell Signaling
Authors: Bhattacharyya Sumit , O-Sullivan Insug , Tu Jieqi , Chen Zhengjia , Tobacman Joanne K. 
Published: May 2023

AbstractIn the syngeneic, subcutaneous B16F10 mouse model of malignant melanoma, treatment with exogenous ARSB markedly reduced tumor size and extended survival.In vivoexperiments showed that local treatment with exogenous N-acetylgalactosamine-4-sulfatase (Arylsulfatase B; ARSB) led to reduced tumor growth over time (p<0.0001) and improved the probability of survival up to 21 days (p=0.0391). Tumor tissue from the treated mice had lower chondroitin 4-sulfate (C4S) content and lower sulfotransferase activity. The free galectin-3 declined, and the SHP2 activity increased, due to altered binding with chondroitin 4-sulfate. These changes induced effects on transcription, which were mediated by Sp1, phospho-ERK1/2, and phospho-p38 MAPK. Reduced mRNA expression of chondroitin sulfate proteoglycan 4 (CSPG4), chondroitin sulfotransferase 15 (N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase), and matrix metalloproteinases 2 and 9 resulted. Experiments in the human melanoma cell line A375 demonstrated similar responses to exogenous ARSB as in the tumors, and inverse effects followed RNA silencing. ARSB, which removes the 4-sulfate group at the non-reducing end of C4S, acts as a tumor suppressor, and treatment with exogenous ARSB impacts on vital cell signaling and reduces the expression of critical genes associated with melanoma progression.Highlights:Exogenous ARSB reduced tumor size and increased survivalChondroitin 4-sulfate increased, leading to increased free galectin-3mRNA expression of CSPG4 and CHST15 declined following ARSB treatmentmRNA expression of MMP9 and pro-MMP2 declined following ARSB treatmentActive SHP2 increased, leading to declines in phospho-ERK1/2 and phospho-p38 MAPK
Human amygdala volumetric patterns convergently evolved in cooperatively breeding and domesticated species
Authors: Cerrito Paola , Burkart Judith M. 
Published: May 2023

AbstractPurposeThe amygdala is a hub in brain networks that supports social life and fear processing. Compared to other apes, humans have a relatively larger lateral nucleus of the amygdala, which is consistent with both the self-domestication and the cooperative breeding hypothesis of human evolution.MethodsHere, we take a comparative approach to the evolutionary origin of the relatively larger lateral amygdala nucleus in humans. We carry out phylogenetic analysis on a sample of 17 mammalian species for which we acquired single amygdala nuclei volumetric data.ResultsOur results indicate that there has been convergent evolution toward larger lateral amygdala nuclei in both domesticated and cooperatively breeding mammals.ConclusionThese results suggest that changes in processing fearful stimuli to reduce fear-induced aggression, which are necessary for domesticated and cooperatively breeding species alike, tap into the same neurobiological proximate mechanism. However, humans show not only changes in processing fearful stimuli but also in prosociality. Since cooperative breeding, but not domestication, is also associated with prosociality, a prominent role of the former during human evolution is more parsimonious, whereas self-domestication may have been involved as an additional stepping stone.
Bioluminescence imaging ofCyp1a1-luciferase reporter mice demonstrates prolonged activation of the aryl hydrocarbon receptor in the lung
Authors: Veland Nicolas , Gleneadie Hannah J , Brown Karen E , Sardini Alessandro , Pombo Joaquim , Dimond Andrew , Burns Vanessa , Sarkisyan Karen , Schiering Chris , Webster Zoe , Merkenschlager Matthias , Fisher Amanda G 
Published: May 2023

AbstractAryl hydrocarbon receptor (AHR) signalling integrates biological processes that sense and respond to environmental, dietary, and metabolic challenges to ensure tissue homeostasis. AHR is a transcription factor that is inactive in the cytosol but upon encounter with ligand translocates to the nucleus and drives the expression of AHR targets, including genes of the cytochrome P4501 family of enzymes such asCyp1a1. To dynamically visualise AHR activityin vivo,we generated reporter mice in which firefly luciferase (Fluc) was non-disruptively targeted into the endogenousCyp1a1locus. Exposure of these animals to FICZ, 3-MC or to dietary I3C induced strong bioluminescence signal andCyp1a1expression in many organs including liver, lung and intestine. Longitudinal studies revealed that AHR activity was surprisingly long-lived in the lung, with sustainedCyp1a1expression evident in discrete populations of cells including columnar epithelia around bronchioles. Our data link diet to lung physiology and also reveal the power of bespokeCyp1a1-Flucreporters to longitudinally monitor AHR activityin vivo.
Single Cell Transcriptomics Identifies Distinct Choroid Cell Populations Involved in Visually Guided Eye Growth
Authors: Summers Jody A. , Jones Kenneth L. 
Published: May 2023

ABSTRACTPostnatal ocular growth is regulated by a vision-dependent mechanism, termed emmetropization, which acts to minimize refractive error through coordinated growth of the ocular tissues. Many studies suggest that the ocular choroid participates in the emmetropization process via the production of scleral growth regulators that control ocular elongation and refractive development. To elucidate the role of the choroid in emmetropization, we used single-cell RNA sequencing (scRNA-seq) to characterize the cell populations in the chick choroid and compare gene expression changes in these cell populations during conditions in which the eye is undergoing emmetropization. UMAP clustering analysis identified 24 distinct cell clusters in all chick choroids. 7 clusters were identified as fibroblast subpopulations; 5 clusters represented different populations of endothelial cells; 4 clusters were CD45+ macrophages, T cells and B cells; 3 clusters were Schwann cell subpopulations; and 2 clusters were identified as melanocytes. Additionally, single populations of RBCs, plasma cells and neuronal cells were identified. Significant changes in gene expression between control and treated choroids were identified in 17 cell clusters, representing 95% of total choroidal cells. The majority of significant gene expression changes were relatively small (< 2 fold). The highest changes in gene expression were identified in a rare cell population (0.11% - 0.49% of total choroidal cells). This cell population expressed high levels of neuron-specific genes as well as several opsin genes suggestive of a rare neuronal cell population that is potentially light sensitive. Our results, for the first time, provide a comprehensive profile of the major choroidal cell types and their gene expression changes during the process of emmetropization as well as insights into the canonical pathways and upstream regulators that coordinate postnatal ocular growth.
Retracing the evolution of a modern periplasmic binding protein
Authors: Michel Florian , Romero-Romero Sergio , Höcker Birte 
Published: May 2023

AbstractInvestigating the evolution of structural features in modern multidomain proteins helps to understand their immense diversity and functional versatility. The class of periplasmic binding proteins (PBPs) offers an opportunity to interrogate one of the main processes driving diversification: the duplication and fusion of protein sequences to generate new architectures. The symmetry of their two-lobed topology, their mechanism of binding, and the organization of their operon structure led to the hypothesis that PBPs arose through a duplication and fusion event of a single common ancestor. To investigate this claim, we set out to reverse the evolutionary process and recreate the structural equivalent of a single-lobed progenitor using ribose-binding protein (RBP) as our model. We found that this modern PBP can be deconstructed into its lobes, producing two proteins that represent possible progenitor halves. The isolated halves of RBP are well folded and monomeric proteins, albeit with a lower thermostability, and do not retain the original binding function. However, the two entities readily form a heterodimerin vitroandin-cell. The X-ray structure of the heterodimer closely resembles the parental protein. Moreover, the binding function is fully regained upon formation of the heterodimer with a ligand affinity similar to that observed in the modern RBP. This highlights how a duplication event could have given rise to a stable and functional PBP-like fold and provides insights into how more complex functional structures can evolve from simpler molecular components.
The oncogene cyclin D1 promotes bipolar spindle integrity under compressive force
Authors: Sutanto Renaldo , Neahring Lila , Marques Andrea Serra , Kilinc Seda , Goga Andrei , Dumont Sophie 
Published: May 2023

AbstractThe mitotic spindle is the bipolar, microtubule-based structure that segregates chromosomes at each cell division. Aberrant spindles are frequently observed in cancer cells, but how oncogenic transformation affects spindle mechanics and function, particularly in the mechanical context of solid tumors, remains poorly understood. Here, we constitutively overexpress the oncogene cyclin D1 in human MCF10A cells to probe its effects on spindle architecture and response to compressive force. We find that cyclin D1 overexpression increases the incidence of spindles with extra poles, centrioles, and chromosomes. However, it also protects spindle poles from fracturing under compressive force, a deleterious outcome linked to multipolar cell divisions. Our findings suggest that cyclin D1 overexpression may adapt cells to increased compressive stress, contributing to its prevalence in cancers such as breast cancer by allowing continued proliferation in mechanically challenging environments.
Visual deprivation during mouse critical period reorganizes network-level functional connectivity
Authors: Chen Siyu , Rahn Rachel M. , Bice Annie R. , Bice Seana H. , Padawer-Curry Jonah A. , Hengen Keith B. , Dougherty Joseph D. , Culver Joseph P. 
Published: May 2023

AbstractA classic example of experience-dependent plasticity is ocular dominance (OD) shift, in which the responsiveness of neurons in the visual cortex is profoundly altered following monocular deprivation (MD). It has been postulated that OD shifts also modify global neural networks, but such effects have never been demonstrated. Here, we used longitudinal wide-field optical calcium imaging to measure resting-state functional connectivity during acute (3-day) MD in mice. First, delta GCaMP6 power in the deprived visual cortex decreased, suggesting that excitatory activity was reduced in the region. In parallel, interhemispheric visual homotopic functional connectivity was rapidly reduced by the disruption of visual drive through MD and was sustained significantly below baseline state. This reduction of visual homotopic connectivity was accompanied by a reduction in parietal and motor homotopic connectivity. Finally, we observed enhanced internetwork connectivity between visual and parietal cortex that peaked at MD2. Together, these findings support the hypothesis that early MD induces dynamic reorganization of disparate functional networks including association cortices.Significance StatementMonocular deprivation during the visual critical period triggers several plasticity mechanisms that collaborate to shift the excitability of neurons in the visual cortex. However, little is known about the impacts of MD on cortex-wide functional networks. Here, we measured cortical functional connectivity during short-term critical period MD. We demonstrate that critical period MD has immediate effects on functional networks beyond the visual cortex, and identify regions of substantial functional connectivity reorganization in response to MD.