bluuebunny/crossref_metadata_2025 huggingface dataset:
Differentiating Macrovascular and Microvascular Ischemia Using Fractal Analysis of Dynamic Myocardial Perfusion Stress-CT
Authors: Michallek Florian , Nakamura Satoshi , Kurita Tairo , Ota Hideki , Nishimiya Kensuke , Ogawa Ryo , Shizuka Takehito , Nakashima Hitoshi , Wang Yi-Ning , Ito Tatsuro , Sakuma Hajime , Dewey Marc , Kitagawa Kakuya
Published: October 2023

Objectives

Fractal analysis of dynamic myocardial stress computed tomography perfusion imaging (4D-CTP) has shown potential to noninvasively differentiate obstructive coronary artery disease (CAD) and coronary microvascular disease (CMD). This study validates fractal analysis of 4D-CTP in a multicenter setting and assesses its diagnostic accuracy in subgroups with ischemia and nonobstructed coronary arteries (INOCA) and with mild to moderate stenosis.

Materials and Methods

From the AMPLIFiED multicenter trial, patients with suspected or known chronic myocardial ischemia and an indication for invasive coronary angiography were included. Patients underwent dual-source CT angiography, 4D-CTP, and CT delayed-enhancement imaging. Coronary artery disease, CMD, and normal perfusion were defined by a combined reference standard comprising invasive coronary angiography with fractional flow reserve, and absolute or relative CT-derived myocardial blood flow. Nonobstructed coronary arteries were defined as ≤25% stenosis and mild to moderate stenosis as 26%–80%.

Results

In 127 patients (27% female), fractal analysis accurately differentiated CAD (n = 61, 23% female), CMD (n = 23, 30% female), and normal perfusion (n = 34, 35% female) with a multiclass area under the receiver operating characteristic curve (AUC) of 0.92 and high agreement (multiclass κ = 0.89). In patients with ischemia (n = 84), fractal analysis detected CAD (n = 61) over CMD (n = 23) with sensitivity of 95%, specificity of 74%, accuracy of 89%, and AUC of 0.83. In patients with nonobstructed coronary arteries (n = 33), INOCA (n = 15) was detected with sensitivity of 100%, specificity of 78%, accuracy of 88%, and AUC of 0.94. In patients with mild to moderate stenosis (n = 27), fractal analysis detected CAD (n = 19) over CMD with sensitivity of 84%, specificity of 100%, accuracy of 89%, and AUC of 0.95.

Conclusions

In this multicenter study, fractal analysis of 4D-CTP accurately differentiated CAD and CMD including subgroups with INOCA and with mild to moderate stenosis.
SARS-CoV-2 N protein-induced Dicer, XPO5, SRSF3, and hnRNPA3 downregulation causes pneumonia
Authors: Luo Yu-Wei , Zhou Jiang-Peng , Ji Hongyu , Zheng Anqi , Wang Xin , Dai Zhizheng , Luo Zhicheng , Cao Fang , Wang Xing-Yue , Bai Yunfang , Chen Di , Chen Yueming , Wang Qi , Yang Yaying , Zhang Xinghai , Chiu Sandra , Huang Ai-Long , Tang Kai-Fu
Published: October 2023

Age is a major risk factor for coronavirus disease (COVID-19)-associated severe pneumonia and mortality; however, the underlying mechanism remains unclear. Herein, we investigated whether age-related deregulation of RNAi components and RNA splicing factors affects COVID-19 severity. Decreased expression of RNAi components (Dicer and XPO5) and splicing factors (SRSF3 and hnRNPA3) correlated with increased severity of COVID-19 and SARS-CoV-2 nucleocapsid (N) protein-induced pneumonia. N protein induced autophagic degradation of Dicer, XPO5, SRSF3, and hnRNPA3, repressing miRNA biogenesis and RNA splicing and inducing DNA damage, proteotoxic stress, and pneumonia. Dicer, XPO5, SRSF3, and hnRNPA3 were downregulated with age in mouse lung tissues. Older mice experienced more severe N protein-induced pneumonia than younger mice. However, treatment with a poly(ADP-ribose) polymerase inhibitor (PJ34) or aromatase inhibitor (anastrozole) relieved N protein-induced pneumonia by restoring Dicer, XPO5, SRSF3, and hnRNPA3 expression. These findings will aid in developing improved treatments for SARS-CoV-2-associated pneumonia.
Utilizing an acute hyperthermia-induced seizure test and pharmacokinetic studies to establish optimal dosing regimens in a mouse model of Dravet syndrome
Authors: Mensah Jeffrey A. , Johnson Kristina , Freeman Tia , Reilly Christopher A. , Rower Joseph E. , Metcalf Cameron S. , Wilcox Karen S.
Published: October 2023

Objective

The current standard of care for Dravet Syndrome includes polytherapy after inadequate seizure control with one or more monotherapy approaches. Treatment guidelines are often based on expert opinions, and finding an optimal balance between seizure control and adverse drug effects can be challenging. This study utilizes efficacy and pharmacokinetic analysis of a second-line treatment regimen that combines clobazam and sodium valproate with an add-on drug as a proof-of-principle approach to establish an effective therapeutic regimen in a preclinical mouse model of Dravet Syndrome.

Method

We evaluated the efficacy of add-on therapies stiripentol, cannabidiol, lorcaserin, or fenfluramine to clobazam and sodium valproate against hyperthermia-induced seizures inScn1aA1783V/WTmice. Clobazam, N-desmethyl clobazam (an active metabolite of clobazam), sodium valproate, stiripentol, and cannabidiol concentrations were quantified in plasma and brain using liquid chromatography-tandem mass spectrometry for the combinations deemed effective against hyperthermia-induced seizures. The concentration data were used to calculate pharmacokinetic parameters via non-compartmental analysis in Phoenix WinNonLin.

Results

Higher doses of stiripentol or cannabidiol, in combination with clobazam and sodium valproate, were effective against hyperthermia-induced seizures inScn1aA1783V/WTmice. InScn1aWT/WTmice, brain clobazam and N-desmethyl clobazam concentrations were higher in the triple-drug combinations than in the clobazam monotherapy. Stiripentol and cannabidiol brain concentrations were greater in the triple-drug therapy than when given alone.

Interpretation

A polypharmacy strategy may be a practical preclinical approach to identifying efficacious compounds for Dravet Syndrome. The drug-drug interactions between compounds used in this study may explain the potentiated efficacy of some combination therapies.

Graphical Abstract

Key findings

The hyperthermia-induced seizure assay inScn1aA1783V/WTmice can identify efficacious antiseizure medications. A triple-drug administration paradigm was designed that mimics clinical standards for add-on therapies in DS. Stiripentol and cannabidiol were effective against hyperthermia-induced seizures when co-administered with clobazam and sodium valproate. Potential drug-drug interactions between compounds may explain the potentiated antiseizure effect in triple-drug therapies. The triple-drug “add-on” therapy approach may be a valuable preclinical strategy for screening investigational compounds for DS, an assay offered at the ETSP.
Sequence-based Protein-Protein Interaction Prediction Using Multi-kernel Deep Convolutional Neural Networks with Protein Language Model
Authors: Dang Thanh Hai , Vu Tien Anh
Published: October 2023

Predicting protein-protein interactions (PPIs) using only sequence information represents a fundamental problem in biology. In the past five years, a wide range of state-of-the-art deep learning models have been developed to address the computational prediction of PPIs based on sequences. Convolutional neural networks (CNNs) are widely adopted in these model architectures; however, the design of a deep and wide CNN architecture that comprehensively extracts interaction features from pairs of proteins is not well studied. Despite the development of several protein language models that distill the knowledge of evolutionary, structural, and functional information from gigantic protein sequence databases, no studies have integrated the amino acid embeddings of the protein language model for encoding protein sequences.In this study, we introduces a novel hybrid classifier, xCAPT5, which combines the deep multi-kernel convolutional accumulated pooling siamese neural network (CAPT5) and the XGBoost model (x) to enhance interaction prediction. The CAPT5 utilizes multi-deep convolutional channels with varying kernel sizes in the Siamese architecture, enabling the capture of small- and large-scale local features. By concatenating max and average pooling features in a depth-wise manner, CAPT5 effectively learns crucial features with low computational cost. This study is the first to extract information-rich amino acid embedding from a protein language model by a deep convolutional network, through training to obtain discriminant representations of protein sequence pairs that are fed into XGBoost for predicting PPIs. Experimental results demonstrate that xCAPT5 outperforms several state-of-the-art methods on binary PPI prediction, including generalized PPI on intra-species, cross-species, inter-species, and stringent similarity tasks. The implementation of our framework is available athttps://github.com/anhvt00/MCAPS
SCUBE-1 in The Diagnosis and Follow-Up Of Subclinical Atherosclerosis in The Experimental Diabetes Mellitus and Obesity Model
Authors: KÖK Mehmet , ASLANKOÇ Rahime , ÖZMEN Özlem , DORA Devrim , ELLIDAG Hamit Yasar
Published: October 2023

ABSCTRACT

BACKGROUND

Obesity and diabetes mellitus (DM) is a metabolic disease that is a global problem, the most crucial complication of which is atherosclerotic cardiovascular disease resulting from endothelial dysfunction and accompanying platelet hyperactivity. The presence of the SCUBE-1 protein has been observed within vascular endothelial cells and platelets, both recognized for their pivotal involvement in the arterial thrombosis mechanism. The objective of this research is to examine the utility of serum SCUBE-1 levels in diagnosing and monitoring subclinical atherosclerosis in experimentally induced DM and obese rats.

METHODS

The study comprised a cohort of 28 male Sprague‒Dawleyrats, which encompassed the following groups: the obese group subjected to a high-fat diet (HFD), the TII-DM group administered HFD in combination with a single dose of streptozocin (STZ), the TI-DM group treated solely with STZ, and the control group. Serum SCUBE1 was analyzed using the enzyme-linked immunosorbent assay method, and caspase-3 (Cas-3), interleukin-6 (IL-6), interferon-gamma (INF-gamma) and superoxide dismutase (SOD) expression in the liver and pancreas of rats were evaluated using immunohistochemical methods.

RESULTS

Serum SCUBE1 levels were significantly higher in the obese and DM groups than in the control group, but there was no significant difference among the obese, TI-DM and TII-DM groups. The study identified a significant relationship between serum SCUBE1 level and hepatic CAS3, IL-6 and SOD expression and pancreatic SOD expression.

CONCULISON

SCUBE1 can be used as a promising novel marker for the diagnosis and monitoring of subclinical atherosclerosis in individuals with obesity, TI-DM, and TII-DM
How tool combinations in different pipeline versions affect the outcome in RNA-seq analysis
Authors: Perelo Louisa Wessels , Gabernet Gisela , Straub Daniel , Nahnsen Sven
Published: October 2023

Data analysis tools are continuously changed and improved over time. In order to test how these changes influence the comparability between analyses, the output of different workflow options of the nf-core/rnaseq pipeline were compared. Five different pipeline settings (STAR+Salmon, STAR+RSEM, STAR+featureCounts, HiSAT+featureCounts, pseudoaligner Salmon) were run on three datasets (human, Arabidopsis, zebrafish) containing spike-ins of the External RNA Control Consortium (ERCC). Fold change ratios and differential expression of genes and spike-ins were used for comparative analyses of the different tools and versions settings of the pipeline. An overlap of 85% for differential gene classification between pipelines could be shown. Genes interpreted with a bias were mostly those present at lower concentration. Also, the number of isoforms and exons per gene were determinants. Previous pipeline versions using featureCounts showed a higher sensitivity to detect one-isoform genes like ERCC. To ensure data comparability in long-term analysis series it would be recommendable to either stay with the pipeline version the series was initialized with or to run both versions during a transition time in order to ensure that the target genes are addressed the same way.
LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening
Authors: Ritzau-Jost Andreas , Gsell Felix , Sell Josefine , Sachs Stefan , Montanaro Jacqueline , Kirmann Toni , Maaß Sebastian , Irani Sarosh R. , Werner Christian , Geis Christian , Sauer Markus , Shigemoto Ryuichi , Hallermann Stefan
Published: October 2023

Background and Objectives

Autoantibodies against the neuronally secreted protein leucine-rich glioma inactivated 1 (LGI1) cause the most common subtype of autoimmune limbic encephalitis associated with seizures and memory deficits. LGI1 and its receptor ADAM22 are part of a transsynaptic protein complex that includes several proteins involved in presynaptic neurotransmitter release and postsynaptic glutamate sensing. Autoantibodies against LGI1 increase excitatory synaptic strength, but studies that genetically disrupt the LGI1-ADAM22 complex report a reduction in postsynaptic glutamate receptor-mediated responses. Thus, the mechanisms underlying the increased synaptic strength induced by LGI1 autoantibodies remain elusive, and the contributions of presynaptic molecules to the LGI1-transsynaptic complex remain unclear. We therefore investigated the presynaptic mechanisms that mediate autoantibody-induced synaptic strengthening.

Methods

We studied the effects of patient-derived purified polyclonal LGI1 autoantibodies on synaptic structure and function by combining direct patch-clamp recordings from presynaptic boutons and somata of hippocampal neurons with super-resolution light and electron microscopy of hippocampal cultures and acute brain slices. We also identified the protein domain mediating the presynaptic effect using domain-specific patient-derived monoclonal antibodies.

Results

LGI1 autoantibodies dose-dependently increased short-term depression during high-frequency transmission, consistent with increased release probability. The increased neurotransmission was not related to presynaptic calcium channels, as presynaptic Cav2.1 channel density, calcium current amplitude, and calcium channel gating were unaffected by LGI1 autoantibodies. In contrast, application of LGI1 autoantibodies homogeneously reduced Kv1.1 and Kv1.2 channel density on the surface of presynaptic boutons. Direct presynaptic patch-clamp recordings revealed that LGI1 autoantibodies cause a pronounced broadening of the presynaptic action potential. Domain-specific effects of LGI1 autoantibodies were analysed at the soma, where polyclonal LGI1 autoantibodies and patient-derived monoclonal autoantibodies targeting the Epitempin-domain but not the Leucin rich repeat-domain induced action potential broadening.

Discussion

Our results indicate that LGI1 autoantibodies do not affect calcium channel density or function, but reduce the density of both Kv1.1 and Kv1.2 on presynaptic boutons, thereby broadening the presynaptic action potential and increasing neurotransmitter release. This study provides a molecular explanation for the neuronal hyperactivity induced by LGI1 autoantibodies.
Natural malaria infection elicits rare but potent neutralizing antibodies to the blood-stage antigen RH5
Authors: Wang Lawrence T. , Cooper Andrew J.R. , Farrell Brendan , Miura Kazutoyo , Diouf Ababacar , Müller-Sienerth Nicole , Crosnier Cécile , Purser Lauren , Maciuszek Maciej , Barrett Jordan R. , McHugh Kirsty , Tucker Courtney , Li Shanping , Doumbo Safiatou , Doumtabe Didier , Pyo Chul-Woo , Nielsen Carolyn M. , Silk Sarah E. , Kayentao Kassoum , Ongoiba Aissata , Zhao Ming , Nguyen Doan C. , Lee F. Eun-Hyung , Minassian Angela M. , Geraghty Daniel E. , Traore Boubacar , Seder Robert A. , Crompton Peter D. , Wright Gavin J. , Long Carole A. , Draper Simon J. , Higgins Matthew K. , Tan Joshua
Published: October 2023

Plasmodium falciparumRH5 is the most advanced blood-stage malaria vaccine candidate and is under evaluation for efficacy in endemic regions, emphasizing the need to study the underlying antibody response to RH5 during natural infection. Here, we found that RH5-reactive B cells were rare in malaria-exposed individuals despite repeated infections over multiple years. RH5-specific monoclonal antibodies isolated from these individuals were extensively mutated but mostly targeted non-neutralizing epitopes, in contrast to antibodies from RH5-vaccinated, malaria-naive individuals. However, infection-derived MAD8-151 and MAD8-502 were among the most potent neutralizers out of 186 antibodies isolated from both cohorts and target the same epitopes as the most effective vaccine-induced antibodies. Binding to basigin receptor-proximal epitopes was the primary factor governing the potency of RH5-specific antibodies from both natural infection and vaccination, followed by the strength of binding. These results indicate a clear strategy for the development of next-generation RH5 vaccines for use in malaria-endemic regions.
Recurrent duplication and diversification of a vital DNA repair gene family across Drosophila
Authors: Brand Cara L. , Oliver Genevieve T. , Farkas Isabella Z. , Levine Mia T.
Published: October 2023

Maintaining genome integrity is vital for organismal survival and reproduction. Essential, broadly conserved DNA repair pathways actively preserve genome integrity. However, many DNA repair proteins evolve adaptively. Ecological forces like UV exposure are classically cited as drivers of DNA repair evolution. Intrinsic forces like repetitive DNA, which can also imperil genome integrity, have received less attention. We recently reported that aDrosophila melanogaster-specific DNA satellite array triggered species-specific, adaptive evolution of a DNA repair protein called Spartan/MH. The Spartan family of proteases cleave hazardous, covalent crosslinks that form between DNA and proteins (“DNA-protein crosslink repair”). Appreciating that DNA satellites are both ubiquitous and universally fast-evolving, we hypothesized that satellite DNA turnover spurs evolution of DNA-protein crosslink repair beyondD. melanogaster. This hypothesis predicts pervasive Spartan gene family diversification across the Drosophila phylogeny. To study the evolutionary history of the Drosophila Spartan gene family, we conducted population genetic, molecular evolution, phylogenomic, and tissue-specific expression analyses. We uncovered widespread signals of positive selection across multiple Spartan family genes and across multiple evolutionary timescales. We also detected recurrent Spartan family gene duplication, divergence, and gene loss. Finally, we found that ovary-enriched parent genes consistently birthed testis-enriched daughter genes. To account for Drosophila-wide, Spartan family diversification, we introduce a mechanistic model of antagonistic coevolution that links DNA satellite evolution and adaptive regulation of Spartan protease activity. This framework, combined with a recent explosion of genome assemblies that encompass repeat-rich genomic regions, promises to accelerate our understanding of how DNA repeats drive recurrent evolutionary innovation to preserve genome integrity.
Differences in binding preferences for XIST partners are observed in mammals with different early pregnancy morphologies
Authors: Tsagakis Ioannis , Tinning Haidee , Malo-Estepa Irene , Whitehouse Adrian , O’Connell Mary J. , Forde Niamh , Aspden Julie L
Published: October 2023

In comparison to protein-coding genes, long non-coding RNAs (lncRNAs) are poorly conserved between species at the sequence level yet they often perform conserved and essential regulatory roles. The lncRNAXISTmediates X chromosome inactivation (XCI) through the interaction of numerous proteins, most of which bind to its repeat regions. WhilstXISTis present across placental mammals, its sequence is divergent. In addition, the timing and mechanistic details of the process of XCI also vary across placental mammals. Here, we sought to determine whetherXISTinteractor proteins previously identified in a model mammalian species (mouse) also bind in other mammals which exhibit divergent timing of XCI (human and bovine) and differing pre-implantation embryo morphology. We show thatXISTand its putative protein partners are coordinately expressed in the endometria of mammals with different pre-implantation embryo morphologies. RNA immunoprecipitations revealed that human WTAP, SPEN, hnRNPK and CIZ1 proteins bind humanXIST. CIZ1-XISTbinding was also detected in bovine. In both human and cow, we found CIZ1 binds to the repeat E element ofXIST. However, human CIZ1 protein is not able to bind bovine repeat E, indicating a species-specific binding interaction. Together these data indicate that several of the key RNA-protein interactions withXISTare common across placental mammals, even though we observe divergence in both the RNA sequence ofXIST, and early embryo morphologies. This work sheds light upon the evolution of RNA-protein binding interactions, revealing that the binding events can be conserved even when the precise mechanism of binding has changed.

Statements and Declarations

Authors have no financial or non-financial interests that are directly or indirectly related to the work submitted for publication.
Wireless electrocochleography in awake chinchillas: a model to study multimodal modulations at the peripheral level
Authors: Pérez-Valenzuela Catherine , Vicencio-Jiménez Sergio , Memmel Mia , Delano Paul H. , Elgueda Diego
Published: October 2023

The discovery and development of electrocochleography (ECochG) in animal models has been fundamental for its implementation in clinical audiology and neurotology. In our laboratory, the use of round-window ECochG recordings in chinchillas has allowed a better understanding of auditory efferent functioning. In previous works, we gave evidence of the corticofugal modulation of auditory-nerve and cochlear responses during visual attention and working memory. However, whether these cognitive top-down mechanisms to the most peripheral structures of the auditory pathway are also active during audiovisual crossmodal stimulation is unknown. Here, we introduce a new technique, wireless ECochG to record compound-action potentials of the auditory nerve (CAP), cochlear microphonics (CM), and round-window noise (RWN) in awake chinchillas during a paradigm of crossmodal (visual and auditory) stimulation. A total of four chinchillas were successfully recorded during the experimental protocol. There were non-significant differences in CAP, CM, and RWN amplitudes in response to auditory stimulation alone (clicks and tones) as compared to audio-visual crossmodal stimulation. These results suggest that cognition, such as attention or working memory, is needed for the corticofugal modulation of auditory-nerve and cochlear responses. In addition, we introduce the use of wireless ECochG in animal models as a useful tool for translational research.
Hog1 acts in a Mec1-independent manner to counteract oxidative stress following telomerase inactivation
Authors: Zeinoun Bechara , Teixeira Maria Teresa , Barascu Aurélia
Published: October 2023

Replicative senescence is triggered when telomeres reach critically short length and activate permanent DNA damage checkpoint-dependent cell cycle arrest. Mitochondrial dysfunction and increase in oxidative stress are both features of replicative senescence in mammalian cells. Here, we show that reactive oxygen species (ROS) levels increase in the telomerase-negative cells ofSaccharomyces cerevisiaeduring replicative senescence, and that this coincides with the activation of Hog1, a mammalian p38 mitogen-activated protein kinase (MAPK) ortholog. Hog1 activation is dependent on Pbs2, the MAPK kinase (MAPKK) in its canonical pathway, and counteracts increased ROS levels during replicative senescence. While Hog1 deletion accelerates replicative senescence, we found this could stem from decreased telomere length and reduced cell viability prior to telomerase inactivation. ROS levels also increase upon telomerase inactivation when Mec1, the yeast ortholog of ATR, is mutated, suggesting that oxidative stress is not simply a consequence of DNA damage checkpoint activation in budding yeast. We speculate that oxidative stress is a conserved hallmark of telomerase-negative eukaryote cells, and that its sources and consequences can be dissected inS. cerevisiae.
Proximal protein landscapes of the type I interferon signaling cascade reveal negative regulation by the E3 ubiquitin ligase PJA2
Authors: Schiefer Samira , Hale Benjamin G.
Published: October 2023

Deciphering the intricate dynamic events governing type I interferon (IFN) signaling is critical to unravel key regulatory mechanisms in host antiviral defense. Here, we leveraged TurboID-based proximity labeling coupled with affinity purification-mass spectrometry to comprehensively map the proximal proteomes of all seven canonical human type I IFN signaling cascade members under basal and IFN-stimulated conditions. This established a network of 103 proteins in close proximity to the core members IFNAR1, IFNAR2, JAK1, TYK2, STAT1, STAT2, and IRF9. We validated several known constitutive protein assemblies, while also revealing novel stimulus-dependent and -independent associations between key signaling molecules. Functional screening further identified PJA2 as a negative regulator of IFN signaling via its E3 ubiquitin ligase activity. Mechanistically, PJA2 interacts with the Janus kinases, TYK2 and JAK1, and promotes their non-lysine and non-degradative ubiquitination, resulting in restrained downstream STAT signaling. Our high-resolution proximal protein landscapes provide global insights into the type I IFN signaling network, and serve as a valuable resource for future exploration of its functional complexities.
Impairment of the glial phagolysosomal system drives prion-like propagation in aDrosophilamodel of Huntington’s disease
Authors: Davis Graham H. , Zaya Aprem , Panning Pearce Margaret M.
Published: October 2023

Protein misfolding, aggregation, and spread through the brain are primary drivers of neurodegenerative diseases pathogenesis. Phagocytic glia are responsible for regulating the load of pathogenic protein aggregates in the brain, but emerging evidence suggests that glia may also act as vectors for aggregate spread. Accumulation of protein aggregates could compromise the ability of glia to eliminate toxic materials from the brain by disrupting efficient degradation in the phagolysosomal system. A better understanding of phagocytic glial cell deficiencies in the disease state could help to identify novel therapeutic targets for multiple neurological disorders. Here, we report that mutant huntingtin (mHTT) aggregates impair glial responsiveness to injury and capacity to degrade neuronal debris in male and female adultDrosophilaexpressing the gene that causes Huntington’s disease (HD). mHTT aggregate formation in neurons impairs engulfment and clearance of injured axons and causes accumulation of phagolysosomes in glia. Neuronal mHTT expression induces upregulation of key innate immunity and phagocytic genes, some of which were found to regulate mHTT aggregate burden in the brain. Finally, a forward genetic screen revealed Rab10 as a novel component of Draper-dependent phagocytosis that regulates mHTT aggregate transmission from neurons to glia. These data suggest that glial phagocytic defects enable engulfed mHTT aggregates to evade lysosomal degradation and acquire prion-like characteristics. Together, our findings reveal new mechanisms that enhance our understanding of the beneficial and potentially harmful effects of phagocytic glia in HD and potentially other neurodegenerative diseases.

SIGNIFICANCE STATEMENT

Deposition of amyloid aggregates is strongly associated with neurodegenerative disease progression and neuronal cell loss. Many studies point to glial cells as dynamic mediators of disease, capable of phagocytosing toxic materials, but also promoting chronic inflammation and proteopathic aggregate spread. Thus, glia have emerged as promising therapeutic targets for disease intervention. Here, we demonstrate in aDrosophilamodel of Huntington’s disease that neuronal mHTT aggregates interfere with glial phagocytic engulfment, phagolysosomal processing, and innate immunity transcriptional responses. We also identify Rab10 as a novel modifier of prion-like transmission of mHTT aggregates. Our findings add to a growing narrative of glia as double-edged players in neurodegenerative diseases.
The role of location propagation for translocon complex relocation during eukaryogenesis
Authors: Carilo Isaac , Senju Yosuke , Robinson Robert C.
Published: October 2023

In all domains of life, the translationally-active ribosome-translocon complex inserts nascent transmembrane proteins into, and processes and transports signal peptide-containing proteins across, membranes1,2. Eukaryotic translocons are anchored in the endoplasmic reticulum, while the prokaryotic complexes reside in cell membranes. DNA sequence analyses indicate that the eukaryotic Sec61/OST/TRAP translocon is inherited from an Asgard archaea ancestor3,4. However, the mechanism for translocon migration from a peripheral membrane to an internal cellular compartment (the proto-endoplasmic reticulum) during eukaryogenesis is unknown. Here we show that Asgard and eukaryotic ribosome-translocon complexes are intercompatible. We find that fluorescently-tagged Asgard translocon proteins fromCandidatusPrometheoarchaeum syntrophicum strain MK-D15, a Lokiarchaeon confirmed to contain no internal cellular membranes, are targeted to the eukaryotic endoplasmic reticulum on ectopic expression. Our data demonstrate that the location of existing ribosome-translocon complexes, at the protein level, determines the future placement of yet to be translated translocon subunits. This principle predicts that during eukaryogenesis, under positive selection pressure, the relocation of a few translocon complexes to the proto-endoplasmic reticulum will have propagated the new translocon location, leading to their loss from the cell membrane.
Chimpanzees and bonobos reinstate an interrupted triadic game
Authors: Heesen Raphaela , Bangerter Adrian , Zuberbühler Klaus , Iglesias Katia , Rossano Federico , Guéry Jean-Pascal , Genty Emilie
Published: October 2023

When humans engage in joint action, they seem to so with an underlying sense of joint commitment, a feeling of mutual obligation towards their partner and a shared goal. Whether our closest living relatives, bonobos and chimpanzees, experience and understand joint commitment in the same way is subject to debate. Crucial evidence concerns how participants respond to interruptions of joint actions, particularly if they protest or attempt to reengage their reluctant or distracted partners. During dyadic interactions, bonobos and chimpanzees appear to have some sense of joint commitment, according to recent studies. Yet, data are inconsistent for triadic games with objects. We addressed this issue by engagingN=23 apes (5 adult chimpanzees, 5 infant bonobos, 13 adult bonobos) in a “tug-of-war” game with a human experimenter who abruptly stopped playing. Adult apes readily attempted to reengage the experimenter (>60% of subjects on first trial), with no group differences in the way of reengagement. Infant bonobos rarely reengaged and never did so on their first trial. Importantly, when infants reengaged passive partners, they mostly deployed (tactile) signals, yet rarely game-related behaviours (GRBs) as commonly observed in adults. These findings might explain negative results of earlier research. Bonobos and chimpanzees may thus have motivational foundations for joint commitment, although this capacity might develop over lifetime. We discuss this finding in relation to evolutionary and developmental theories on joint commitment.
The Chaperone NASP Contributes toDe NovoDeposition of the Centromeric Histone Variant CENH3 inArabidopsisEarly Embryogenesis
Authors: Takeuchi Hidenori , Nagahara Shiori , Higashiyama Tetsuya , Berger Frédéric
Published: October 2023

The centromere is an essential chromosome region where the kinetochore is formed to control equal chromosome distribution during cell division. The centromere-specific histone H3 variant CENH3 (also called CENP-A) is a prerequisite for the kinetochore formation. Since CENH3 evolves rapidly, associated factors, including histone chaperones mediating the deposition of CENH3 on the centromere, are thought to act through species-specific amino-acid sequences. The functions and interaction networks of CENH3 and histone chaperons have been well-characterized in animals and yeasts. However, molecular mechanisms involved in recognition and deposition of CENH3 are still unclear in plants. Here, we used a swapping strategy between domains of CENH3 ofArabidopsis thalianaand the liverwortMarchantia polymorphato identify specific regions of CENH3 involved in targeting the centromeres and interacting with the general histone H3 chaperone, NASP (nuclear autoantigenic sperm protein). CENH3’s LoopN-α1 region was necessary and sufficient for the centromere targeting in cooperation with the α2 region and was involved in interaction with NASP in cooperation with αN, suggesting a species-specific CENH3 recognition. In addition, by generating anArabidopsis naspknockout mutant in the background of a fully fertileGFP-CENH3/cenh3-1line, we found that NASP was implicated forde novoCENH3 deposition after fertilization and thus for early embryo development. Our results imply that the NASP mediates the supply of CENH3 in the context of the rapidly evolving centromere identity in land plants.
A supernumerary synthetic chromosome inKomagataella phaffiias a repository for extraneous genetic material
Authors: Abramczyk Dariusz , Sanchez Olmos Maria del Carmen , Ramirez Rojas Adan Andres , Schindler Daniel , Robertson Daniel , McColm Stephen , Marston Adele L. , Barlow Paul N.
Published: October 2023

Background

Komagataella phaffii (Pichia pastoris) is a methylotropic commercially important non-conventional species of yeast that grows in a fermentor to exceptionally high densities on simple media and secretes recombinant proteins efficiently. Genetic engineering strategies are being explored in this organism to facilitate cost-effective biomanufacturing. Small, stable artificial chromosomes inK. phaffiicould offer unique advantages by accommodating multiple integrations of extraneous genes and their promoters without accumulating perturbations of native chromosomes or exhausting the availability of selection markers.

Results

Here, we describe a linear “nano”chromosome (of 15-25 kb) that, according to whole-genome sequencing, persists inK. phaffiiover many generations with a copy number per cell of one, provided non-homologous end joining is compromised (byKU70-knockout). The nanochromosome includes a copy of the centromere fromK. phaffiichromosome 3, aK. phaffii-derived autonomously replicating sequence on either side of the centromere, and a pair ofK. phaffii-like telomeres. It contains, within its q arm, a landing zone in which genes of interest alternate with long (approx. 1-kb) non-coding DNA chosen to facilitate homologous recombination and serve as spacers. The landing zone can be extended along the nanochromosome, in an inch-worming mode of sequential gene integrations, accompanied by recycling of just two antibiotic-resistance markers. The nanochromosome was used to expressPDI, a gene encoding protein disulfide isomerase. Co-expression withPDIallowed the production, from a genomically integrated gene, of secreted murine complement factor H, a plasma protein containing 40 disulfide bonds. As further proof-of-principle, we co-expressed, from a nanochromosome, bothPDIand a gene for GFP-tagged human complement factor H under the control ofPAOX1and demonstrated that the secreted protein was active as a regulator of the complement system.

Conclusions

We have addedK. phaffiito the list of organisms that can produce human proteins from genes carried on a stable, linear, artificial chromosome. We envisage using nanochromosomes as repositories for numerous extraneous genes, allowing intensive engineering ofK. phaffiiwithout compromising its genome or weakening the resulting strain.
A comparative approach for selecting orthologous candidate genes in genome-wide association studies across multiple species
Authors: Whitt Lauren , Mahood Elizabeth H. , Ziegler Greg , Luebbert Collin , Gillman Jason D. , Norton Gareth J. , Price Adam H. , Salt David E. , Dilkes Brian P. , Baxter Ivan
Published: October 2023

Advances in quantitative genetics have enabled researchers to identify genomic regions associated with changes in phenotype. However, genomic regions can contain hundreds to thousands of genes, and progressing from genomic regions to causative genes is still challenging. In genome-wide association studies (GWAS) measuring elemental accumulation (ionomic) traits, only 5% of loci overlap genes known to control the ionome - indicating that many causal genes are still unknown. To identify candidates for the remaining 95% loci, we developed a method that uses GWAS studies across multiple species to identify conserved causative genes. By Filtering the Results of Multi-species, Analogous, GWAS Experiments (FiREMAGE) we were able to take the GWAS of 19 ionomic traits in Arabidopsis, soybean, rice, maize, and sorghum, and identify alleles affecting trait variation at conserved genes. Permutation testing demonstrated that GWAS loci affecting the same trait contained homologs more often than expected by chance. Most of the top 10% most significant conserved candidate sets encoded alleles in all five species, highlighting the conservation of ionomic genetic regulators in flowering plants. The candidates include proteins with known biochemical functions that regulate the ionome, validating the approach. In addition to genes with known functions, this approach also identified many conserved genes underlying GWAS loci affecting the same trait in multiple species that have no previously identified function in regulating the ionome, providing a path to discover the as yet unknown mechanisms of element accumulation in plants. This method enables the identification of conserved genes of previously unknown function via GWAS.

Author summary

Quantitative genetics identifies a genomic region of interest but not the causal gene. We developed an approach to narrow these gene lists using genetic loci affecting elemental (i.e., calcium, iron, zinc) accumulation. Comparative genomics and GWAS demonstrates that alleles at evolutionarily conserved genes alter the same phenotype in multiple species. This produced a list of conserved candidate genes including previously known elemental regulators and genes whose elemental accumulation mechanism has yet to be determined. Combining datasets across species boosted the signal at these loci. This approach accelerates the discovery of new functional roles of genes.
Identification and characterization of interactions between Influenza A Virus NS1 protein and the human ubiquitin proteasome system
Authors: Lamotte Laurie-Anne , Kindylides Samuel , Gaupin Chloé , Demeret Caroline , Tafforeau Lionel
Published: October 2023

As a key player involved in various cellular pathways, including innate immune response activation, the human ubiquitin-proteasome system (UPS) is particularly targeted by viral proteins upon infection. Indeed, most viruses have evolved to counteract and hijack this system, as it is the case for the influenza A virus (IAV). The non-structural protein 1 (NS1) is described as the main IAV virulence factor, which is known to interact with several cellular proteins, including some UPS factors that are important for the viral escape of the immune cell response. In this study, we profiled the overall interplay between the NS1 proteins of multiple IAV strains and the human UPS. We identified 98 UPS factors directly interacting with NS1 of all or a subset of the studied strains, and we functionally studied 18 of them. We highlighted the involvement of these UPS factors in the IAV life cycle by performing viral titrations, minigenome replicon assays and an ISRE-luc (IFN pathway) assays. Furthermore, we analyzed the expression and subcellular localizations of FZR1, MKRN3, RC3H2 and SHKBP1 upon IAV infection. This interactomics approach allows for an improved understanding of the interplay between NS1 and UPS pathway in the context of an IAV-mediated inhibition of cellular anti-viral responses.

Importance

Influenza A viruses (IAV) are pathogens responsible for annual flu epidemics causing up to 650,000 deaths each year, resulting in a significant impact in public health and global economy. IAV are also responsible of occasionally pandemic outbreaks in human population, such as in 1918 that caused the death of 50-100 million people. Non-structural protein 1 (NS1) is the main IAV virulence factor; it acts by direct interactions with several cellular proteins, leading to the host shut-off and to the inhibition of the host cell innate immune response. Since the ubiquitin-proteasome system (UPS) plays a crucial role in the innate immune response activation, it is a designated target for NS1 upon infection. Our research thus focused on the identification of interactions between NS1 of 6 different IAV strains and the UPS, to better understand the interplay between this viral protein and the UPS upon viral infection.
Ectopic adipogenesis in response to injury and material implantation in an autoimmune mouse model
Authors: Ngo Tran B. , Josyula Aditya , DeStefano Sabrina , Fertil Daphna , Faust Mondreakest , Lokwani Ravi , Sadtler Kaitlyn
Published: October 2023

Due to the limited capacity of mammals to regenerate complex tissues, researchers have worked to understand the mechanisms of tissue regeneration in organisms that maintain that capacity. One example is the MRL/MpJ mouse strain with unique regenerative capacity in ear pinnae that is absent from other strains, such as the common C57BL/6 strain. The MRL/MpJ mouse has also been associated with an autoimmune phenotype even in the absence of the mutantFasgene described in its parent strain MRL/lpr. Due to these findings, we evaluated the differences between the responses of MRL/MpJ versus C57BL/6 strain in traumatic muscle injury and subsequent material implantation. One salient feature of the MRL/MpJ response to injury was a robust adipogenesis within the muscle. This was associated with a decrease in M2-like polarization in response to biologically derived extracellular matrix scaffolds. In pro-fibrotic materials, such as polyethylene, there were fewer foreign body giant cells in the MRL/MpJ mice. As there are reports of both positive and negative influences of adipose tissue and adipogenesis on wound healing, this model could provide an important lens to investigate the interplay between stem cells, adipose tissue, and immune responses in trauma and materials implantation.
Cadherin-dependent adhesion is required for muscle stem cell niche anchorage and maintenance
Authors: Hung Margaret , Lo Hsiao-Fan , Beckmann Aviva G. , Demircioglu Deniz , Damle Gargi , Hasson Dan , Radice Glenn L. , Krauss Robert S.
Published: October 2023

Adhesion between stem cells and their niche provides stable anchorage and signaling cues to sustain properties such as quiescence. Skeletal muscle stem cells (MuSCs) directly adhere to an adjacent myofiber via cadherin-catenin complexes. Previous studies on N- and M-cadherin function in MuSCs revealed that while N-cadherin is required for quiescence, they are collectively dispensable for MuSC niche localization and regenerative activity. While additional cadherins are expressed at low levels, these findings raise the possibility that cadherins are unnecessary for MuSC anchorage to the niche. To address this question, we conditionally removed from MuSCs β- and γ-catenin and, separately, αE- and αT-catenin, factors essential for cadherin-dependent adhesion. Catenin-deficient MuSCs break quiescence similarly to N-/M-cadherin-deficient MuSCs, but exit the niche, and are depleted. A combination of in vivo, ex vivo, and single cell RNA sequencing approaches reveal that MuSC attrition occurs via a single fate: precocious differentiation, reentry to the niche, and fusion to myofibers. These findings indicate that cadherin-catenin–dependent adhesion is required for anchorage of MuSCs to their niche and preservation of the stem cell compartment. Furthermore, separable, cadherin-regulated functions govern niche localization, quiescence, and stem cell maintenance in MuSCs.

SUMMARY STATEMENT

Genetic ablation of cadherin-based adhesion in skeletal muscle stem cells triggers activation, niche exit, precocious differentiation, and subsequent depletion of the stem cell pool.
Neural signatures of competition between voluntary and involuntary influences over the focus of attention in visual working memory
Authors: Ding Yun , Postle Bradley R. , van Ede Freek
Published: October 2023

Adaptive behaviour relies on the selection and prioritisation of relevant sensory inputs from the external environment as well as from among internal sensory representations held in working memory. Recent behavioural evidence suggests that the classic distinction between voluntary (goal-driven) and involuntary (stimulus-driven) influences over attentional allocation also applies to the selection of internal representations held in working memory. In the current EEG study, we set out to investigate the neural dynamics associated with the competition between voluntary and involuntary control over the focus of attention in visual working memory. We show that when voluntary and involuntary factors compete for the internal focus of attention, prioritisation of the appropriate item is delayed – as reflected both in delayed gaze biases that track internal selection and in delayed neural beta (15-25 Hz) dynamics that track the planning for the upcoming memory-guided manual action. We further show how this competition is paralleled – possibly resolved – by an increase in frontal midline theta (4-8 Hz) activity that, moreover, predicts the speed of ensuing memory-guided behaviour. Finally, because theta increased following retrocues that effectively reduced working-memory load, our data unveil how frontal theta activity during internal attentional focusing tracks demands on cognitive control over and above working-memory load. Together, these data yield new insight into the neural dynamics that govern the focus of attention in visual working memory, and disentangles the contributions of frontal midline theta activity to the processes of control versus retention in working memory.