bluuebunny/crossref_metadata_2025 huggingface dataset:
DREAMS: Deep Read-level Error Model for Sequencing data applied to low-frequency variant calling and circulating tumor DNA detection
Authors: Christensen Mikkel H. , Drue Simon , Rasmussen Mads H. , Frydendahl Amanda , Lyskjær Iben , Demuth Christina , Nors Jesper , Gotschalck Kåre A. , Iversen Lene H. , Andersen Claus L. , Pedersen Jakob Skou
Published: September 2022

Circulating tumor DNA detection using Next-Generation Sequencing (NGS) data of plasma DNA is promising for cancer identification and characterization. However, the tumor signal in the blood is often low and difficult to distinguish from errors. We present DREAMS (Deep Read-level Modelling of Sequencing-errors) for estimating error rates of individual read positions. Using DREAMS, we developed statistical methods for variant calling (DREAMS-vc) and cancer detection (DREAMS-cc).

For evaluation, we generated deep targeted NGS data of matching tumor and plasma DNA from 85 colorectal cancer patients. The DREAMS approach performed better than state-of-the-art methods for variant calling and cancer detection.
Machine learning and hypothesis driven optimization of bull semen cryopreservation media
Authors: Tu Frankie , Bhat Maajid , Blondin Patrick , Vincent Patrick , Sharafi Mohsen , Benson James D
Published: September 2022

Cryopreservation provides a critical tool for dairy herd genetics management. Due to widely varying inter- and within-bull post thaw fertility, recent research on cryoprotectant extender medium has not dramatically improved suboptimal post-thaw recovery in industry. This progress is stymied by the interactions between samples and the many components of extender media and is often compounded by industry irrelevant sample sizes. To address these challenges, here we demonstrate blank-slate optimization of bull sperm cryopreservation media by supervised machine learning. We considered two supervised learning models: artificial neural networks and Gaussian process regression (GPR). Eleven media components and initial concentrations were identified from publications in bull semen cryopreservation, and an initial 200 extender-post-thaw motility pairs were used to train and 32 extender-post-thaw motility pairs to test the machine learning algorithms. The median post-thaw motility after coupling differential evolution with GPR the increased from 52.6 ± 6.9% to 68.3 ± 6.0% at generations 7 and 17 respectively, with several media performing dramatically better than control media counterparts. This is the first study in which machine learning was used to determine the best combination of constituents to optimize bull sperm cryopreservation media, and provides a template for optimization in other cell types.
Vascular-water-exchange MRI (VEXI) enables the detection of subtle BBB breakdown in Alzheimer’s disease without MRI contrast agent
Authors: Zhang Yifan , Wang Yue , Li Zhaoqing , Wang Zejun , Cheng Juange , Bai Xiaoyan , Hsu Yi-Cheng , Sun Yi , Li Shiping , Shi Jiong , Sui Binbin , Bai Ruiliang
Published: September 2022

Blood-brain barrier (BBB) impairment is an important pathophysiological process in Alzheimer’s disease (AD) and a potential biomarker for early diagnosis of AD. However, most current neuroimaging methods assessing BBB function need the injection of exogenous contrast agents (or tracers), which limits the application of these methods in a large population. In this study, we aim to explore the feasibility of vascular water exchange MRI (VEXI), a diffusion-MRI-based method to assess the BBB permeability to water molecules without using a contrast agent, in the detection of the BBB breakdown in AD. We tested VEXI on a 3T MRI scanner on three groups: AD patients (AD group), mild cognitive impairment (MCI) patients due to AD (MCI group), and the age-matched normal cognition subjects (NC group). Interestingly, we find that VEXI can detect the BBB permeability to water molecules increase in MCI and this BBB breakdown happens specifically in the hippocampus. This BBB breakdown gets worse and extends to more brain regions (orbital frontal cortex and thalamus) from MCI group to the AD group. Furthermore, we find that the BBB breakdown of these three regions detected by VEXI is correlated significantly with impairment of respective cognitive domains independent of age, sex and education. These results suggest VEXI is a promising method to assess the BBB breakdown in AD.

Highlights

The vascular water exchange MRI (VEXI) is a contrast-agent-free method to assess BBB permeability

BBB breakdown happens specifically in the hippocampus, orbital frontal cortex, and thalamus in AD

BBB breakdown detected by VEXI is significantly correlated with cognitive dysfunction
Trends in Self-citation Rates in High-impact Neurology, Neuroscience, and Psychiatry Journals
Authors: Rosenblatt Matthew , Mehta Saloni , Peterson Hannah , Dadashkarimi Javid , Rodriguez Raimundo X , Foster Maya L , Adkinson Brendan D , Liang Qinghao , Kimble Violet M , Ye Jean , McCusker Marie C , Farruggia Michael C , Rolison Max , Westwater Margaret L , Jiang Rongtao , Noble Stephanie , Scheinost Dustin
Published: September 2022

Citation metrics influence academic reputation and career trajectories. Recent works have highlighted flaws in citation practices in the Neurosciences, such as the under-citation of women. However, self-citation rates--or how much authors cite themselves--have not yet been comprehensively investigated in the Neurosciences. This work characterizes self-citation rates in basic, translational, and clinical Neuroscience literature by collating 100,347 articles from 63 journals between the years 2000-2020. In analyzing over five million citations, we demonstrate four key findings: 1) increasing self-citation rates of Last Authors relative to First Authors, 2) lower self-citation rates in low- and middle-income countries, 3) gender differences in self-citation stemming from differences in the number of previously published papers, and 4) variations in self-citation rates by field. Our characterization of self-citation provides insight into citation practices that shape the perceived influence of authors in the Neurosciences, which in turn may impact what type of scientific research is done and who gets the opportunity to do it.
The RNA binding proteins ZFP36L1 and ZFP36L2 modulate transcriptional and post-transcriptional genome-wide effects of glucocorticoids
Authors: Rynne Jennifer , Ortiz-Zapater Elena , Khooshemehri Paniz , Ponde Nicole O. , Bucca Giselda , Hesketh Andrew , Platé Manuela , Chambers Rachel , Smith Colin , Martinez-Nunez Rocio T.
Published: September 2022

Glucocorticoids (GCs) are one of the most used anti-inflammatory drugs worldwide. Despite their widespread use, our understanding of their post-transcriptional effects remains poorly understood. The tristetraprolin (TTP) RNA binding protein (RBP) family (ZFP36, ZFP36L1 and ZFP36L2) has been implicated in inflammation regulation via binding to AU-rich elements (ARE) in mRNAs, with TTP being implicated in GC modulation. We hypothesised that ZFP36L1 and ZFP36L2 are part of the GC pathway and tested this hypothesis in bronchial epithelium, which commonly encounters GC in vivo upon inhalation. Our data show that dexamethasone, a commonly used GC, modulated the levels, subcellular localisation and RNA binding of ZFP36L1/L2. Employing Frac-seq (subcellular fractionation and RNA-sequencing), we show that GC modulated distinct subsets of RNAs in a subcellular-dependent manner. In addition to their mostly known transcriptional effects (116 differentially expressed genes, DEGs), GCs modified the binding to monosomes of myriad mRNAs (83 differentially bound genes, DBGs). We also demonstrate that ZFP36L1/L2 modulated gene expression mainly at the total cytoplasmic and polyribosome binding levels. ZFP36L1/L2 down-regulation led to an increase in ARE-containing mRNAs and a pronounced modification of the effects of GC on gene expression. We observed a small overlap of genes modulated by GCs when comparing control and ZFP36L1/L2 knockdown cells, in a subcellular-dependent manner Our data also suggest a novel role for these RBPs and GCs in epithelial biology via regulation of mRNAs encoding proteins important for epithelial cell function including cellular structure. We believe that our data has further implications in how we investigate gene expression. We show the power of employing sub-cellular fractionation when analysing genome-wide effects for known ‘transcriptional modulators’ such as GCs, as well as a tool to demonstrate the extent of the effect of RBPs on gene expression modulation beyond total RNA levels.
KaryoCreate: a new CRISPR-based technology to generate chromosome-specific aneuploidy by targeting human centromeres
Authors: Bosco Nazario , Goldberg Aleah , Johnson Adam F , Zhao Xin , Mays Joseph C , Cheng Pan , Bianchi Joy J , Toscani Cecilia , Katsnelson Lizabeth , Annuar Dania , Mei Sally , Faitelson Roni E , Pesselev Ilan Y , Mohamed Kareem S , Mermerian Angela , Camacho-Hernandez Elaine M , Gionco Courtney A , Manikas Julie , Tseng Yi-Shuan , Sun Zhengxi , Fani Somayeh , Keegan Sarah , Lippman Scott M , Fenyö David , Santaguida Stefano , Davoli Teresa
Published: September 2022

Aneuploidy, the presence of chromosome gains or losses, is a hallmark of cancer and congenital syndromes. Here, we describe KaryoCreate (Karyotype CRISPR Engineered Aneuploidy Technology), a system that enables generation of chromosome-specific aneuploidies by co-expression of a sgRNA targeting chromosome-specific CENPA-binding ɑ-satellite repeats together with dCas9 fused to a mutant form of KNL1. We designed unique and highly specific sgRNAs for 19 out of 24 chromosomes. Expression of these sgRNAs with KNL1Mut-dCas9 leads to missegregation and induction of gains or losses of the targeted chromosome in cellular progeny with an average efficiency of 8% and 12% for gains and losses, respectively (up to 20%), tested and validated across 9 chromosomes. Using KaryoCreate in colon epithelial cells, we show that chromosome 18q loss, a frequent occurrence in gastrointestinal cancers, promotes resistance to TGFβ, likely due to synergistic hemizygous deletion of multiple genes. Altogether, we describe a novel technology to create and study chromosome missegregation and aneuploidy in the context of cancer and beyond.

Highlights

We designed sgRNAs targeting chromosome-specific centromeres across 19 human chromosomes

KaryoCreate combines chromosome-specific centromeric sgRNAs with dCas9 fused to a mutant form of KNL1.

KaryoCreate allows engineering gains and losses of specific human chromosomes.

Engineered Chromosome 18q loss promotes tumor-associated phenotypes in colon-derived cells.

KaryoCreate is a CRISPR-based technology to foster the study of centromere biology and aneuploidy.
Edaphic specialization onto bare, rocky outcrops as a factor in the evolution of desert angiosperms
Authors: Lichter Marck Isaac H. , Baldwin Bruce G.
Published: September 2022

Understanding the processes that enable organisms to shift into more arid environments as they emerge is critical for gauging resilience to climate change, yet these forces remain poorly known. In a comprehensive clade-based study, we investigate recent shifts into North American deserts in the rock daisies (Perityleae), a diverse tribe of desert sunflowers (Compositae). We sample Perityleae across two separate contact zones between tropical deciduous forest and desert biomes in western North America and infer a time-calibrated phylogeny based on target capture sequence data. We reconstruct biome shifts using Bayesian inference with paleobiome-informed models and find evidence for seven independent shifts into desert habitats since the onset of aridification in the late Miocene epoch. The earliest shift occurred out of tropical deciduous forests and led to an extensive radiation throughout North American deserts that accounts for the majority of extant desert Perityleae. Reconstructions of life history and micro-habitat in Perityleae reveal a correlation between a suffrutescent perennial life history and edaphic endemism onto rocky outcrops, an ecological specialization that evolved prior to establishment and diversification in deserts. That the insular radiation of desert rock daisies stemmed from ancestors pre-adapted for dry conditions as edaphic endemics in otherwise densely vegetated tropical deciduous forests in northwest Mexico underscores the crucial role of exaptation and dispersal for shifts into arid environments.

Significance Statement

The environmentally stressful conditions found in desert regions have often been implicated as the main factor in the evolution of drought tolerance in desert plants. Yet many iconic desert plant lineages evolved prior to the recent emergence of widespread arid climates, suggesting an important role for pre-adaptation (exaptation). In the desert rock daisies (Perityleae), we provide empirical support for this view by showing that life history evolution associated with their ecological specialization onto rock outcrops was a precursor to their establishment and extensive diversification in North American deserts. We caution against assuming the presence of ancient dry biomes based on time-calibrated phylogenies and we emphasize the fundamental roles that exaptation and dispersal play during community assembly in novel environments.
Specific connectivity optimizes learning in thalamocortical loops
Authors: Lakshminarasimhan Kaushik , Xie Marjorie , Cohen Jeremy , Sauerbrei Britton , Hantman Adam , Litwin-Kumar Ashok , Escola Sean
Published: September 2022

1

Cortico-thalamo-cortical loops have a central role in cognition and motor control, but precisely how thalamus contributes to these processes is unclear. Recent studies showing evidence of plasticity in thalamocortical synapses indicate a role for thalamus in shaping cortical dynamics – and thus behavior – through learning. Since corticothalamic projections compress cortical activity into a lower-dimensional thalamic activity space, we hypothesized that the computational role of thalamus would depend critically on the structure of corticothalamic connectivity. To test this, we identified the optimal corticothalamic structure that promotes biologically plausible learning in thalamocortical synapses. We found that corticothalamic structures specialized to carry an efference copy of the cortical output benefit motor control, while corticothalamic connections that communicate the directions of highest variance in cortical activity are optimal for working memory tasks. We analyzed neural recordings from mice performing grasping and delayed discrimination, and found corticothalamic interactions consistent with these predictions. These results suggest that thalamus orchestrates cortical dynamics in a functionally precise manner through structured connectivity.
Caveolin-1 protects endothelial cells from extensive expansion of transcellular tunnel by stiffening the plasma membrane
Authors: Morel Camille , Lemerle Eline , Tsai Feng-Ching , Obadia Thomas , Srivastava Nishit , Marechal Maud , Salles Audrey , Albert Marvin , Stefani Caroline , Benito Yvonne , Vandenesch François , Lamaze Christophe , Vassilopoulos Stéphane , Piel Matthieu , Bassereau Patricia , Gonzalez-Rodriguez David , Leduc Cécile , Lemichez Emmanuel
Published: September 2022

Large transcellular pores elicited by bacterial mono-ADP-ribosyltransferase (mART) exotoxins inhibiting the small RhoA GTPase compromise the endothelial barrier. Recent advances in biophysical modeling point towards membrane tension and bending rigidity as the minimal set of mechanical parameters determining the nucleation and maximal size of transendothelial cell macroaperture (TEM) tunnels induced by bacterial RhoA-targeting mART exotoxins. We report that cellular depletion of caveolin-1, the membrane-embedded building block of caveolae, and depletion of cavin-1, the master regulator of caveolae invaginations, increase the number of TEMs per cell. The enhanced occurrence of TEM nucleation events correlates with a reduction of cell height, due to the increase of cell spreading and decrease of cell volume, which, together with the disruption of RhoA-driven F-actin meshwork, favor membrane apposition for TEM nucleation. Strikingly, caveolin-1 specifically controls the opening speed of TEMs leading to their dramatic 5.4-fold larger widening. Consistent with the increase of TEM density and width in siCAV1 cells, we record a higher lethality in caveolin-1-deficient mice subjected to a catalytically active mART exotoxin targeting RhoA during staphylococcal bloodstream infection. Combined theoretical modeling with independent biophysical measurements of plasma membrane bending rigidity point toward a specific contribution of caveolin-1 to membrane stiffening in addition to the role of cavin-1/caveolin-1-dependent caveolae in the control of membrane tension homeostasis.
The TBX20-TLE Interaction is Essential for the Second Heart Field
Authors: Edwards Whitney , Bussey Olivia K. , Conlon Frank L.
Published: September 2022

Tbx20 plays a multifaceted role in cardiac morphogenesis and controls a broad gene regulatory network. However, the mechanism by which Tbx20 activates and represses target genes in a tissue-specific and temporal manner remains unclear. Studies show that Tbx20 directly interacts with the Transducin-like Enhancer of Split (TLE) family of proteins to mediate transcriptional repression of downstream target genes. However, a functional role for the Tbx20-TLE transcriptional repression complex during heart development is not established. To this end, we generated a mouse model with a two-amino acid substitution in the Tbx20 EH1 domain, thereby disrupting the Tbx20-TLE interaction (Tbx20EH1mut). We demonstrate that disruption of this interaction impairs critical morphogenic events, including cardiac looping and chamber formation, and ultimately leads to embryonic lethality. Transcriptional profiling of Tbx20EH1mut hearts and analysis of putative Tbx20 direct targets reveals misexpression of the retinoic acid pathway and cardiac progenitor genes, demonstrating that the Tbx20-TLE interaction serves to inhibit cardiac progenitor programs in the developing heart. We find that loss of this interaction also results in perturbations of the second heart field progenitor population, implying that altered cardiac progenitor function may underly the observed cardiac defects in our model. Our studies indicate that TLE-mediated repression is a primary mechanism by which Tbx20 systematically controls gene expression.
Analysis of the abomasal transcriptome of LDA affected cattle
Authors: Gál Zoltán , Biró Bálint , Nagy Zsófia , Kontra Levente , Horváth András , Hoffmann Orsolya Ivett
Published: September 2022

Left displacement of the abomasum (LDA) is a common condition in Holstein population mainly occur around the time of parturition. The entrapped abomasum located between the rumen and the abdominal wall caused by the abomasal hypomotility. The heritability of LDA estimated higher than for other bovine diseases but a number of management and nutritional conditions are also affecting the disease appearance. Genome studies revealed many significant genomic regions associated with LDA, although an RNA sequencing analysis of abomasum is missing from the literature. Within the framework of this research, we tried to patch up this area missing from the literature and to reveal the genetic causes and a complex interaction between the endocrine and neuromuscular pathways behind the symptoms of the disease with the help of transcriptomic analysis.
Small-molecule Polθ inhibitors provide safe and effective tumor radiosensitization in preclinical models
Authors: Rodriguez-Berriguete Gonzalo , Ranzani Marco , Prevo Remko , Puliyadi Rathi , Machado Nicole , Bolland Hannah R. , Millar Val , Ebner Daniel , Boursier Marie , Cerutti Aurora , Cicconi Alessandro , Galbiati Alessandro , Grande Diego , Grinkevich Vera , Majithiya Jayesh , Piscitello Desiree , Rajendra Eeson , Stockley Martin , Boulton Simon J. , Hammond Ester M. , Heald Robert , Smith Graeme C. M. , Robinson Helen , Higgins Geoff S.
Published: September 2022

DNA polymerase theta (Polθ) is a DNA repair enzyme critical for microhomology mediated end joining (MMEJ). Polθ has limited expression in normal tissues but is frequently overexpressed in cancer cells and, therefore, represents an ideal target for tumor-specific radiosensitization. Here, we show that ART558 and ART899, two novel and specific allosteric inhibitors of the Polθ DNA polymerase domain, potently radiosensitize tumor cells, particularly when combined with fractionated radiation. Importantly, normal fibroblasts are not radiosensitized by Polθ inhibition. Mechanistically, we show that the radiosensitization caused by Polθ inhibition is most effective in replicating cells and is due to impaired DNA damage repair. We also show that radiosensitization is still effective under hypoxia, suggesting that these inhibitors may help overcome hypoxia-induced radioresistance. In addition, we describe for the first time ART899 and characterize it as a potent and specific Polθ inhibitor with improved metabolic stability. In vivo, the combination of Polθ inhibition using ART899 with fractionated radiation is well tolerated and results in a significant reduction in tumor growth compared to radiation alone. These results pave the way for future clinical trials of Polθ inhibitors in combination with radiotherapy.
Single cell transcriptomics delineates the immune-cell landscape in equine lower airways and reveals upregulation of the FKBP5 gene in horses with asthma
Authors: Riihimäki Miia , Fegraeus Kim , Nordlund Jessica , Waern Ida , Wernersson Sara , Akula Srinivas , Hellman Lars , Raine Amanda
Published: September 2022

Background

Equine asthma (EA) is a heterogenous, complex disease with a significant negative impact on horse welfare and performance. EA and human asthma have fundamental similarities, making EA a useful large animal disease model. Bronchoalveolar lavage (BAL) fluid provides a snapshot sample of the immune cells occupying the alveolar space and is one of the most relevant sample types for studies of chronic inflammation in the lung. In this study, we sequenced single equine BAL-cells in order to study the immune cell landscape of the respiratory tract of horses diagnosed with mild-to-moderate EA and healthy controls.

Results

ScRNA-seq analysis of ~63,000 cells from eleven horses diagnosed with mild-moderate asthma (mEA) and eight healthy controls were performed using the Drop-Seq technology. We identified five major immune cell populations in equine BAL; alveolar macrophages (AM), T cells, neutrophils, mast cells and dendritic cells, as well as subtypes thereof. The cellular subtypes demonstrated herein have previously not been characterized in horses. Differential gene expression analysis revealed upregulation of genes in mEA horses, including FKBP5 and CCL24, which have previously been associated with asthma in other species. The most significantly upregulated gene across the cell types in EA was FKBP5, a chaperone protein involved in regulating the assembly, activity, and sensitivity of the glucocorticoid receptor

Conclusion

Herein we demonstrate the first comprehensive scRNA-seq map of the immune-cell populations in BAL from horses with asthma and healthy individuals. The glucocorticoid receptor associated protein FKBP5 was identified as a potential biomarker for EA.
Deep Learning from Phylogenies for Diversification Analyses
Authors: Lambert Sophia , Voznica Jakub , Morlon Hélène
Published: September 2022

Birth-death models are widely used in combination with species phylogenies to study past diversification dynamics. Current inference approaches typically rely on likelihood-based methods. These methods are not generalizable, as a new likelihood formula must be established each time a new model is proposed; for some models such formula is not even tractable. Deep learning can bring solutions in such situations, as deep neural networks can be trained to learn the relation between simulations and parameter values as a regression problem. In this paper, we adapt a recently developed deep learning method from pathogen phylodynamics to the case of diversification inference, and we extend its applicability to the case of the inference of state-dependent diversification models from phylogenies associated with trait data. We demonstrate the accuracy and time efficiency of the approach for the time constant homogeneous birth-death model and the Binary-State Speciation and Extinction model. Finally, we illustrate the use of the proposed inference machinery by reanalyzing a phylogeny of primates and their associated ecological role as seed dispersers. Deep learning inference provides at least the same accuracy as likelihood-based inference while being faster by several orders of magnitude, offering a promising new inference approach for deployment of future models in the field.
The development of compulsive coping behaviors depends on the engagement of dorsolateral striatum dopamine-dependent mechanisms
Authors: Giuliano Chiara , Marti-Prats Lucia , Domi Ana , Puaud Mickaël , Pena-Oliver Yolanda , McKenzie Colin , Everitt Barry J. , Belin David
Published: September 2022

Humans greatly differ in how they cope with stress, a natural behavior learnt through negative reinforcement. Some individuals engage in displacement activities, others in exercise or comfort eating, and others still in alcohol use. Across species, adjunctive behaviors, such as polydipsic drinking, are used as a form of displacement activity that reduces distress. Some individuals, in particular those that use alcohol to self-medicate, tend to lose control over such coping behaviors, which become excessive and compulsive. However, the psychological and neural mechanisms underlying this individual vulnerability have not been elucidated. Here we tested the hypothesis that the development of compulsive adjunctive behaviors stems from the functional engagement of the dorsolateral striatum (DLS) dopamine-dependent habit system after a prolonged history of adjunctive responding. We measured in longitudinal studies in male Sprague Dawley rats the sensitivity of early established vs compulsive polydipsic water or alcohol drinking to a bilateral infusion of the dopamine receptor antagonist α-flupentixol into the anterior DLS (aDLS). While most rats acquired a polydipsic drinking response with water, others only did so with alcohol. Whether reliant on water or alcohol, the acquisition of this coping response was insensitive to aDLS dopamine receptor blockade. In contrast, after prolonged experience, adjunctive drinking became dependent on the aDLS dopamine-dependent habit system at a time it was compulsive in vulnerable individuals. These data suggest that habits may develop out of negative reinforcement and that the engagement of their underlying striatal system is necessary for the manifestation of adjunctive behaviors.

Significance statement

Harnessing the individual variability that rodents, like humans, show to engage in adaptive or maladaptive coping strategies, which can result in the development of compulsive disorders, here we demonstrate that the functional engagement of the dorsolateral striatum-dependent habit system precipitates the transition to compulsion in rats that have acquired a polydipsic adjunctive drinking response with water or alcohol as a means to cope with distress. The results of this study not only provide evidence for the emergence of instrumental habits under negative reinforcement, but they also reveal that compulsive behaviors that originate from the loss of control over coping strategies are mediated by the dorsolateral striatum-dependent habit system.
The Uniqueness of Human Vulnerability to Brain Aging in Great Ape Evolution
Authors: Vickery Sam , Patil Kaustubh R. , Dahnke Robert , Hopkins William D. , Sherwood Chet C. , Caspers Svenja , Eickhoff Simon B. , Hoffstaedter Felix
Published: September 2022

Aging is associated with robust decline of the brain’s gray matter. This spatially specific, morphological change in humans has recently been found in chimpanzees. Direct comparison of age-related brain deterioration between these great ape species can provide a unique evolutionary perspective on human brain aging. Here, we present a data-driven, cross-species comparative framework to explore the relationship between gray matter atrophy with age and cross-species cerebral expansion in chimpanzees and humans. In humans, we found a positive relationship between cerebral aging and cortical expansion, whereas, in chimpanzees no such relationship was found. The greater aging and expansion effects in higher-order cognitive regions like the orbito-frontal cortex were observed to be unique to humans. This resembles the last in, first out hypothesis for neurodevelopment and may represent a biological cost for recent evolutionary developments of human faculties.
The human MRS2 magnesium binding domain is a regulatory feedback switch for channel activity
Authors: Uthayabalan Sukanthathulse , Vishnu Neelanjan , Madesh Muniswamy , Stathopulos Peter B.
Published: September 2022

Mitochondrial RNA splicing protein 2 (MRS2) forms a major magnesium (Mg2+) entry channel into the matrix. While MRS2 contains two transmembrane domains that constitute a pore, most of the protein resides within the matrix. Yet, the precise structural and functional role of this obtrusive amino terminal domain (NTD) in human MRS2 function is unknown. Here, we show that the MRS2 NTD self-associates into a homodimer, contrasting the pentameric assembly of CorA, an orthologous bacterial channel. Mg2+and calcium suppress lower and higher order oligomerization of MRS2 NTD, while cobalt has no effect on the NTD but disassembles full-length MRS2. Mutating pinpointed residues mediating Mg2+binding to the NTD, not only selectively decreases Mg2+binding affinity ∼7-fold but also abrogates Mg2+binding-induced changes in secondary, tertiary and quaternary structures. Disruption of NTD Mg2+binding strikingly potentiates mitochondrial Mg2+uptake in wild-type and Mrs2 knockout cells. Our work exposes a mechanism for human MRS2 autoregulation by negative feedback from the NTD and identifies a novel gain of function mutant with broad applicability to future Mg2+signaling research.
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

Amyloid-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 Abstract

Highlights

Amyloid-β plaques in the different forms of Alzheimer’s Disease have various contrasts in X-ray phase-contrast tomography

In transgenic rodents, a core-restricted, positive contrast is driven by the level of metal entrapment within plaques

In 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

Recent 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

Eukaryotic 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

SWItch/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

Aphids 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

Many 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 Statement

Large-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

Mitochondria 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 summary

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.
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

Phagocytic 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

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Different 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).