bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why are amyloid-β plaques detected by X-ray phase-contrast imaging? Role of metals revealed through combined synchrotron infrared and X-ray fluorescence microscopies
Authors: Chourrout Matthieu , Sandt Christophe , Weitkamp Timm , Dučić Tanja , Meyronet David , Baron Thierry , Klohs Jan , Rama Nicolas , Boutin Hervé , Singh Shifali , Olivier Cécile , Wiart Marlène , Brun Emmanuel , Bohic Sylvain , Chauveau Fabien 
Published: September 2022

AbstractAmyloid-β (Aβ) plaques from Alzheimer’s Disease (AD) can be visualizedex vivoin label-free brain samples using synchrotron X-ray phase-contrast tomography (XPCT). However, for XPCT to be useful as a screening method for amyloid pathology, it is essential to understand which factors drive the detection of Aβ plaques. The current study was designed to test the hypothesis that Aβ-related contrast in XPCT could be caused by the Aβ fibrils and/or by metals trapped in the plaques. This study probed the fibrillar and elemental compositions of Aβ plaques in brain samples from different types of AD patients and AD models to establish a relationship between XPCT contrast and Aβ plaque characteristics. XPCT, micro-Fourier-Transform Infrared spectroscopy and micro-X-Ray Fluorescence spectroscopy were conducted on human samples (genetic and sporadic cases) and on four transgenic rodent strains (mouse: APPPS1, ArcAβ, J20; rat: TgF344). Aβ plaques from the genetic AD patient were visible using XPCT, and had higher β–sheet content and higher metal levels than the sporadic AD patient, which remained undetected by XPCT. Aβ plaques in J20 mice and TgF344 rats appeared hyperintense on XPCT images, while they were hypointense with an hyperintense core in the case of APPPS1 and ArcAβ mice. In all four transgenic strains, β-sheet content was similar, while metal levels were highly variable: J20 (zinc and iron) and TgF344 (copper) strains showed greater metal accumulation than APPPS1 and ArcAβ mice. Hence, a positive contrast formation of Aβ plaques in XPCT images appeared driven by biometal entrapment.Graphical AbstractHighlightsAmyloid-β plaques in the different forms of Alzheimer’s Disease have various contrasts in X-ray phase-contrast tomographyIn transgenic rodents, a core-restricted, positive contrast is driven by the level of metal entrapment within plaquesIn humans, greater and more diffuse metal accumulation lead to a positive contrast in a genetic case of AD
Shifts in mutation bias promote mutators by altering the distribution of fitness effects
Authors: Tuffaha Marwa , Varakunan Saranya , Castellano David , Gutenkunst Ryan N. , Wahl Lindi M. 
Published: September 2022

AbstractRecent experimental evidence demonstrates that shifts in mutational biases, for example increases in transversion frequency, can change the distribution of fitness effects of mutations (DFE). In particular, reducing or reversing a prevailing bias can increase the probability that ade novomutation is beneficial. It has also been shown that mutator bacteria are more likely to emerge if the beneficial mutations they generate have a larger effect size than observed in the wildtype. Here, we connect these two results, demonstrating that mutator strains that reduce or reverse a prevailing bias have a positively-shifted DFE, which in turn can dramatically increase their emergence probability. Since changes in mutation rate and bias are often coupled through the gain and loss of DNA repair enzymes, our results predict that the invasion of mutator strains will be facilitated by shifts in mutation bias that offer improved access to previously under-sampled beneficial mutations.
Bridging-mediated compaction of mitotic chromosomes
Authors: Forte Giada , Boteva Lora , Gilbert Nick , Cook Peter R. , Marenduzzo Davide 
Published: September 2022

SUMMARYEukaryotic chromosomes compact during mitosis and meiosis into elongated cylinders – and not the spherical globules expected of self-attracting long flexible polymers. This process is mainly driven by condensin-like proteins. Here, we present Brownian-dynamics simulations involving two types of such proteins. The first anchors topologically-stable and long-lived chromatin loops to create bottlebrush structures. The second forms multivalent bridges between distant parts of these loops without entrapping them. We show bridging factors lead to the formation of shorter and stiffer mitotic-like cylinders, without requiring any energy input. These cylinders have several features matching experimental observations. For instance, the axial condensin backbone breaks up into clusters as found by microscopy, and cylinder elasticity qualitatively matches that seen in chromosome pulling experiments. Additionally, simulating global condensin depletion or local faulty condensin loading gives phenotypes in agreement with experiments, and provides a mechanistic model to understand mitotic chromatin structure at common fragile sites.
Loss of the E3 ubiquitin ligases UBR-5 or HECD-1 restoresCaenorhabditis elegansdevelopment in the absence of SWI/SNF function
Authors: Lampersberger Lisa , Conte Francesca , Ghosh Subhanita , Xiao Yutong , Price Jonathan , Jordan David , Matus David Q , Sarkies Peter , Beli Petra , Miska Eric A , Burton Nicholas O 
Published: September 2022

AbstractSWItch/Sucrose Non-Fermenting (SWI/SNF) complexes are a family of chromatin remodellers that are conserved across eukaryotes. Mutations in subunits of SWI/SNF cause a multitude of different developmental disorders in humans, most of which have no current treatment options. Here we identify an alanine to valine causing mutation in the SWI/SNF subunitsnfc-5(SMARCB1in humans) that prevents embryonic lethality inC. elegansnematodes harbouring a loss-of-function mutation in the SWI/SNF subunitswsn-1(SMARCC1/2in humans). Furthermore, we found that the combination of this specific mutation insnfc-5and a loss-of-function mutation in either of the E3 ubiquitin ligasesubr-5(UBR5in humans) orhecd-1(HECTD1in humans) can restore development to adulthood inswsn-1loss-of-function mutants that otherwise die as embryos. Using these mutant models, we established a set of 335 genes that are dysregulated in SWI/SNF mutants that arrest their development embryonically but exhibit near wild-type levels of expression in the presence of suppressor mutations that prevent embryonic lethality, suggesting that SWI/SNF promotes development by regulating this specific subset of genes. In addition, we show that SWI/SNF protein levels are reduced inswsn-1; snfc-5double mutants and partly restored to wild-type levels inswsn-1; snfc-5; ubr-5triple mutants, consistent with a model in which UBR-5 regulates SWI/SNF levels by tagging the complex for proteasomal degradation. Our findings establish a link between two E3 ubiquitin ligases and SWI/SNF function and suggest that UBR5 and HECTD1 might be viable therapeutic targets for the many developmental disorders caused by missense mutations in SWI/SNF subunits.
Hybridisation has shaped a recent radiation of grass-feeding aphids
Authors: Mathers Thomas C. , Wouters Roland H. M. , Mugford Sam T. , Biello Roberto , Van Oosterhout Cock , Hogenhout Saskia A. 
Published: September 2022

AbstractAphids are common crop pests. These insects reproduce by facultative parthenogenesis involving several rounds of clonal reproduction interspersed with an occasional sexual cycle. Furthermore, clonal aphids give birth to live apterous or winged young that are already pregnant. Together, these qualities enable rapid population growth and have facilitated the colonisation of crops globally. In several cases so-called “super clones” have come to dominate agricultural systems. However, the extent to which the sexual stage of the aphid life cycle has shaped global pest populations has remained largely unclear, as have the origins of successful lineages. Here, we used chromosome-scale genome assemblies to disentangle the evolution of two of the most significant global pests of cereals – the English (Sitobion avenae) and Indian (Sitobion miscanthi) grain aphids. We found that genome-wide divergence betweenS. avenaeandS. miscanthiis low and thatS. avenae sensu strictois part of a larger cryptic species complex that includes multiple divergedS. miscanthilineages. Moreover, comparison of haplotype-resolved assemblies reveals that theS. miscanthiisolate used for genome sequencing is likely a hybrid, with one of its diploid genome copies being closely related toS. avenae(∼0.5% divergence) and the second being substantially more divergent (> 1%). Analyses of genotyping-by-sequencing (GBS) data of grain aphids from the UK and China revealed thatS. avenaeandS. miscanthiare part of a species complex with many highly differentiated lineages that predate the origins of agriculture. The complex consists of hybrid lineages that display a tangled history of hybridisation and genetic introgression. These data demonstrate that hybridisation has substantially contributed to grain aphid diversity, and hence, to the evolutionary potential of this important pest species.
Size and position dependent cytoplasm viscoelasticity through hydrodynamic interactions with the cell surface
Authors: Najafi Javad , Dmitrieff Serge , Minc Nicolas 
Published: September 2022

ABSTRACTMany studies of cytoplasm rheology have focused on small components in the sub-micrometer scale. However, the cytoplasm also baths large organelles like nuclei, microtubule asters or spindles that often take significant portions of cells and move across the cytoplasm to regulate cell division or polarization. Here, we translated passive components of sizes ranging from few up to ~50 percent of the cell diameter, through the vast cytoplasm of live sea urchin eggs, with calibrated magnetic forces. Creep and relaxation responses indicate that for objects larger than the micron size, the cytoplasm behaves as a Jeffreys’ material, viscoelastic at short time-scales and fluidizing at longer times. However, as components size approached that of cells, cytoplasm viscoelastic resistance increased in a non-monotonic manner. Flow analysis and simulations suggest that this size-dependent viscoelasticity emerges from hydrodynamic interactions between the moving object and the static cell surface. This effect also yields to position-dependent viscoelasticity with objects initially closer to the cell surface being harder to displace. These findings suggest that the cytoplasm hydrodynamically couples large organelles to the cell surface to restrain their motion, with important implications for cell shape sensing and cellular organization.Significance StatementLarge-sized organelles like nuclei or mitotic spindles typically translocate through the cytoplasm to regulate cell division or polarity, but their frictional interaction with the cytoplasm and the cell surface remain poorly addressed. We used in vivo magnetic tweezers, to move passive components in a range of size in the cytoplasm of living cells. We found that the mobility of objects with sizes approaching that of cells, can be largely reduced as a result of hydrodynamic interactions that couple objects and the cell surface through the cytoplasm fluid.
Alternative mRNA polyadenylation bridges mitochondrion-to-nucleus communication in Arabidopsis
Authors: Jia Huifang , Zeng Weike , Zhang Xiaoyan , Li Jiedi , Bao Xinyue , Zhao Yanming , Zhu Lingjun , Ma Chongyang , Wang Fengling , Guo Xiangqian , Song Chun-Peng , Ma Liuyin , Zhu Xiaohong 
Published: September 2022

AbstractMitochondria produce signals besides energy and metabolites that influence plant growth and fitness. However, how mitochondrial signals are relayed to other cellular compartments is largely unknown. By applying poly(A)-site RNA-sequencing (PAS-seq) to wildtype Arabidopsis seedlings and a mutant in the histone demethylase JMJ30 treated with the mitochondrial electron transfer chain inhibitor antimycin A (AA), we identified a previously undefined mitochondrion-to-nucleus communication pathway by which mitochondrial functional state regulates co-transcriptionally alternative polyadenylation (APA) of nuclear mRNA. We observed a global shortening of 3′ untranslated regions (UTRs) as a molecular signature of AA-activated mitochondrial retrograde response (MRR), which contributed in part to translational regulation of auxin response and cell wall biogenesis. JMJ30 regulated AA-induced 3′ UTR shortening, resulting in more transcripts with shortened 3′ UTRs upon AA treatment in a JMJ30 gain-of-function mutant and overexpression lines. We also report on the JMJ30-interacting protein CPSF30, a cleavage and polyadenylation specificity factor that recruits JMJ30 to modulate H3K27me3 status at its target loci. Our study illustrates how epigenetic modification and APA coordinate mitochondrion-to-nucleus communication to allow cells to rapidly respond to changes in mitochondrial functional state and shape plant growth and fitness.One-sentence summaryEpigenetic modification and APA coordinate mitochondrion-to-nucleus communication to allow cells to rapidly respond to changes in mitochondrial functional state and shape plant growth and fitness.
Titrating CD47 by mismatch CRISPRi reveals incomplete repression can eliminate IgG-opsonized tumors but CD47 heterogeneity limits induction of anti-tumor IgG
Authors: Hayes Brandon H. , Zhu Hui , Andrechak Jason C. , Discher Dennis E. 
Published: September 2022

AbstractPhagocytic elimination of solid tumors is an attractive mechanism for immunotherapy – particularly because of the possible induction of anti-cancer immunity. The phagocytic potential of macrophages is limited, however, by the CD47-SIRPα checkpoint, and how much CD47 disruption is needed for efficacy remains unclear, even when tumors are opsonized by a pro-phagocytic antibody. Here, CRISPR-interference (CRISPRi) is applied with a large set of sgRNAs to produce a broad range of CD47 knockdowns in B16F10 melanoma, which is generally found to be resistant to the heavily studied PD-1 blockade. Guided by 3D immuno-tumoroid results, we identify a critical CD47 density below which macrophage-mediated phagocytosis dominates proliferation in the presence of an otherwise ineffective pro-phagocytic antibody (anti-Tyrp1). Growing tumors and immuno-tumoroids generally show selection for CD47-positive cells, but some mice reject tumors having >97% mean repression of CD47 or even having 80% repression – unless mixed with 50% repressed cells. Interestingly, long-term survivors have de novo pro-phagocytic IgG antibodies that increase in titer with depth of repression and also with early accumulation of tumor macrophages. Given well-known limitations of antibody permeation into solid tumors, our studies set a benchmark for anti-CD47 blockade and suggest deep disruption favors acquired immunity.
Cellular proteomic profiling using proximity labelling by TurboID-NES in microglial and neuronal cell lines
Authors: Sunna Sydney , Bowen Christine , Zeng Hollis , Rayaprolu Sruti , Kumar Prateek , Bagchi Pritha , Guo Qi , Duong Duc M. , Bitarafan Sara , Natu Aditya , Wood Levi , Seyfried Nicholas T. , Rangaraju Srikant 
Published: September 2022

1.0ABSTRACTDifferent brain cell types play distinct roles in brain development and disease. Molecular characterization of cell-specific mechanisms using cell type-specific approaches at the protein (proteomic) level, can provide biological and therapeutic insights. To overcome the barriers of conventional isolation-based methods for cell type-specific proteomics,in vivoproteomic labeling with proximity dependent biotinylation of cytosolic proteins using biotin ligase TurboID, coupled with mass spectrometry (MS) of labeled proteins, has emerged as a powerful strategy for cell type-specific proteomics in the native state of cells without need for cellular isolation. To complementin vivoproximity labeling approaches,in vitrostudies are needed to ensure that cellular proteomes using the TurboID approach are representative of the whole cell proteome, and capture cellular responses to stimuli without disruption of cellular processes. To address this, we generated murine neuroblastoma (N2A) and microglial (BV2) lines stably expressing cytosolic TurboID to biotinylate the cellular proteome for downstream purification and analysis using MS. TurboID-mediated biotinylation captured 59% of BV2 and 65% of N2A proteomes under homeostatic conditions. TurboID expression and biotinylation minimally impacted homeostatic cellular proteomes of BV2 and N2A cells, and did not affect cytokine production or mitochondrial respiration in BV2 cells under resting or lipopolysaccharide (LPS)-stimulated conditions. These included endo-lysosome, translation, vesicle and signaling proteins in BV2 microglia, and synaptic, neuron projection and microtubule proteins in N2A neurons. The effect of LPS treatment on the microglial proteome was captured by MS analysis of biotinylated proteins (>500 differentially-abundant proteins) including increased canonical pro-inflammatory proteins (Il1a, Irg1, Oasl1) and decrease anti-inflammatory proteins (Arg1, Mgl2).
A scalable screening platform for phenotypic subtyping of ALS patient-derived fibroblasts
Authors: Kumbier Karl , Roth Maike , Li Zizheng , Lazzari-Dean Julia , Waters Christopher , Huang Ping , Korobeynikov Vlad ,   New York Genome Center ALS Consortium, Phatnani Hemali , Shneider Neil , Jacobson Matthew P. , Wu Lani , Altschuler Steven 
Published: September 2022

ABSTRACTA major challenge for understanding and treating Amyotrophic Lateral Sclerosis (ALS) is that most patients have no known genetic cause. Even within defined genetic subtypes, patients display considerable clinical heterogeneity. It is unclear how to identify subsets of ALS patients that share common molecular dysregulation or could respond similarly to treatment. Here, we developed a scalable microscopy and machine learning platform to phenotypically subtype readily available, primary patient-derived fibroblasts. Application of our platform identified robust signatures for the genetic subtype FUS-ALS, allowing cell lines to be scored along a spectrum from FUS-ALS to non-ALS. Our FUS-ALS phenotypic score negatively correlates with age of diagnosis and provides information that is distinct from transcript profiling. Interestingly, the FUS-ALS phenotypic score can be used to identify sporadic patient fibroblasts that have consistent pathway dysregulation with FUS-ALS. Further, we showcase how the score can be used to evaluate the effects of ASO treatment on patient fibroblasts. Our platform provides an approach to move from genetic to phenotypic subtyping and a first step towards rational selection of patient subpopulations for targeted therapies.
Distinct pathways of adaptive evolution inCryptococcus neoformansreveal a point mutation in adenylate cyclase with drastic tradeoffs for pathogenicity
Authors: Hilbert Zoë A. , Chung Krystal Y. , Bednarek Joseph M. , Schwiesow Mara W. , Brown Jessica C.S. , Elde Nels C. 
Published: September 2022

AbstractPathogenic fungi populate a wide range of environments and infect a diversity of host species. Despite this substantial biological flexibility, the impact of interactions between fungi and their hosts on the evolution of pathogenicity remains unclear. We studied how repeated interactions between the fungusCryptococcus neoformansand relevant environmental and mammalian host cells—amoeba and mouse macrophages—shape the evolution of this model fungal pathogen. First, using a collection of clinical and environmental isolates ofC. neoformans, we characterized a range of survival phenotypes for these strains when exposed to host cells of different species. We then performed serial passages of an environmentally isolatedC. neoformansstrain through either amoeba or macrophages for ~75 generations to observe how these interactions select for improved replication within hosts. In an adapted population, we identified a single point mutation in the adenylate cyclase gene,CAC1, that swept to fixation and confers a strong competitive advantage for growth inside of macrophages. Strikingly, this growth advantage in macrophages is inversely correlated with disease severity during mouse infections, suggesting that adaptations to specific host niches can markedly reduce the pathogenicity of these fungi. These results raise intriguing questions about the influence of cAMP signaling on pathogenicity and highlight the role of seemingly small adaptive changes in promoting fundamental shifts in the intracellular behavior and virulence of these important human pathogens.
Inter-gastruloid heterogeneity revealed by single cell transcriptomics time course: implications for organoid based perturbation studies
Authors: Rosen Leah U. , Stapel L. Carine , Argelaguet Ricard , Barker Charlie George , Yang Andrian , Reik Wolf , Marioni John C. 
Published: September 2022

AbstractRecent advances in organoid and genome editing technologies are allowing for perturbation experiments at an unprecedented scale. However, before doing such experiments it is important to understand the gene expression profile in each of the organoid’s cells, as well as how much heterogeneity there is between individual organoids. Here we characterise an organoid model of mouse gastrulation called gastruloids using single cell RNA-sequencing of individual organoids at half-day intervals between day 3 and day 5 of differentiation (roughly corresponding to E6.5-E8.75 in vivo). Our study reveals multiple differentiation trajectories that have hitherto not been characterised in gastruloids. Intriguingly, we observe that individual gastruloids displayed a strong bias towards producing either mesodermal (largely somitic) or ectodermal (specifically neural) cell types. This bifurcation is already seen at the earliest sampled time point, and is characterised by increased activity of WNT-associated pathways in mesodermally-biased gastruloids as compared to neurally-biased gastruloids. Notably, at day 5, mesodermal gastruloids show an increase in the proportion of neural cells, while neural gastruloids do not produce notably more mesodermal cells. This is in line with previous studies on how the balance between these cell types is regulated. We demonstrate using in silico simulations that without proper understanding of the inter-organoid heterogeneity, perturbation experiments have either very high false positive or negative rates, depending on the statistical model used. Thus in future studies, modelling of inter-organoid heterogeneity will be crucial when designing organoid-based perturbation studies.HighlightsA single cell RNA-sequencing time course of day 3 to day 5 mouse gastruloids reveals multiple mesodermal and neural differentiation trajectories hitherto uncharacterised in gastruloidsSingle gastruloid, single cell RNA-sequencing of mouse gastruloids reveals that gastruloids are either mesodermally- or neurally-biasedThe two classes of gastruloid arise from differences in response strength to the WNT-agonist chironAt day 5, mesodermal gastruloids start making more neural cells, while neural gastruloids do not make more mesodermal cells, aligning with previously studied in vivo feedback loopsWe show using simulations that understanding interorganoid heterogeneity is a crucial consideration in the design and analysis of well-powered organoid-based perturbation studies