bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network structure of the mouse brain connectome with voxel resolution
Authors: Coletta Ludovico , Pagani Marco , Whitesell Jennifer D. , Harris Julie A. , Bernhardt Boris , Gozzi Alessandro 
Published: March 2020

AbstractFine-grained descriptions of brain connectivity are fundamental for understanding how neural information is processed and relayed across spatial scales. Prior investigations of the mouse brain connectome have employed discrete anatomical parcellations, limiting spatial resolution and potentially concealing network attributes critical to the organization of the mammalian connectome. Here we provide a voxel-level description of the network and hierarchical structure of the directed mouse connectome, unconstrained by regional partitioning. We show that integrativehubregions can be directionally segregated into neural sinks and sources, defining a hierarchical axis. We describe a set of structural communities that spatially reconstitute previously described fMRI networks of the mouse brain, and document that neuromodulatory nuclei are strategically wired as critical orchestrators of inter-modular and network communicability. Notably, like in primates, the directed mouse connectome is organized along two superimposed cortical gradients reflecting unimodal-transmodal functional processing and a modality-specific sensorimotor axis. These structural features can be related to patterns of intralaminar connectivity and to the spatial topography of dynamic fMRI brain states, respectively. Together, our results reveal a high-resolution structural scaffold linking mesoscale connectome topography to its macroscale functional organization, and create opportunities for identifying targets of interventions to modulate brain function in a physiologically-accessible species.
Targeting the water network in cyclin G associated kinase (GAK) with 4-anilino-quin(az)oline inhibitors
Authors: Asquith Christopher R. M. , Tizzard Graham J. , Bennett James M. , Wells Carrow I. , Elkins Jonathan M. , Willson Timothy M. , Poso Antti , Laitinen Tuomo 
Published: March 2020

AbstractWater networks within kinase inhibitor design and more widely within drug discovery are generally poorly understood. The successful targeting of these networks prospectively has great promise for all facets of inhibitor design, including potency and selectivity on target. Here we describe the design and testing of a targeted library of 4-anilinoquinolines for use as inhibitors of cyclin G associated kinase (GAK). The GAK cellular target engagement assays, ATP binding site modelling and extensive water mapping provide a clear route to access potent inhibitors for GAK and beyond.
Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites
Authors: Kang Sisi , Yang Mei , Hong Zhongsi , Zhang Liping , Huang Zhaoxia , Chen Xiaoxue , He Suhua , Zhou Ziliang , Zhou Zhechong , Chen Qiuyue , Yan Yan , Zhang Changsheng , Shan Hong , Chen Shoudeng 
Published: March 2020

AbstractThe outbreak of coronavirus disease (COVID-19) in China caused by SARS-CoV-2 virus continually lead to worldwide human infections and deaths. It is currently no specific viral protein targeted therapeutics yet. Viral nucleocapsid protein is a potential antiviral drug target, serving multiple critical functions during the viral life cycle. However, the structural information of SARS-CoV-2 nucleocapsid protein is yet to be clear. Herein, we have determined the 2.7 Å crystal structure of the N-terminal RNA binding domain of SARS-CoV-2 nucleocapsid protein. Although overall structure is similar with other reported coronavirus nucleocapsid protein N-terminal domain, the surface electrostatic potential characteristics between them are distinct. Further comparison with mild virus type HCoV-OC43 equivalent domain demonstrates a unique potential RNA binding pocket alongside the β-sheet core. Complemented byin vitrobinding studies, our data provide several atomic resolution features of SARS-CoV-2 nucleocapsid protein N-terminal domain, guiding the design of novel antiviral agents specific targeting to SARS-CoV-2.
Long-read error correction: a survey and qualitative comparison
Authors: Morisse Pierre , Lecroq Thierry , Lefebvre Arnaud 
Published: March 2020

AbstractThird generation sequencing technologies Pacific Biosciences and Oxford Nanopore Technologies were respectively made available in 2011 and 2014. In contrast with second generation sequencing technologies such as Illumina, these new technologies allow the sequencing of long reads of tens to hundreds of kbp. These so called long reads are particularly promising, and are especially expected to solve various problems such as contig and haplotype assembly or scaffolding, for instance. However, these reads are also much more error prone than second generation reads, and display error rates reaching 10 to 30%, according to the sequencing technology and to the version of the chemistry. Moreover, these errors are mainly composed of insertions and deletions, whereas most errors are substitutions in Illumina reads. As a result, long reads require efficient error correction, and a plethora of error correction tools, directly targeted at these reads, were developed in the past ten years. These methods can adopt a hybrid approach, using complementary short reads to perform correction, or a self-correction approach, only making use of the information contained in the long reads sequences. Both these approaches make use of various strategies such as multiple sequence alignment, de Bruijn graphs, Hidden Markov Models, or even combine different strategies. In this paper, we describe a complete survey of long-read error correction, reviewing all the different methodologies and tools existing up to date, for both hybrid and self-correction. Moreover, the long reads characteristics, such as sequencing depth, length, error rate, or even sequencing technology, have huge impacts on how well a given tool or strategy performs, and can thus drastically reduce the correction quality. We thus also present an in-depth benchmark of available long-read error correction tools, on a wide variety of datasets, composed of both simulated and real data, with various error rates, coverages, and read lengths, ranging from small bacterial to large mammal genomes.
Long-term T cell fitness and proliferation is driven by AMPK-dependent regulation of oxygen reactive species
Authors: Lepez Anouk , Pirnay Tiphène , Denanglaire Sébastien , Perez-Morga David , Vermeersch Marjorie , Leo Oberdan , Andris Fabienne 
Published: March 2020

AbstractThe AMP-activated kinase (AMPK) is a major energy sensor metabolic enzyme that is activated early during T cell immune responses but its role in the generation of effector T cells is still controversial.Using bothin vitroandin vivomodels of T cell proliferation, we show herein that AMPK is dispensable for early TCR signaling and short-term proliferation but required for sustained long-term T cell proliferation and effector / memory T cell survival. In particular, AMPK promoted accumulation of effector / memory T cells in competitive homeostatic proliferation settings. Transplantation of AMPK-deficient hematopoïetic cells into allogeneic host recipients led to a reduced graft-versus-host disease, further bolstering a role for AMPK in the expansion and pathogenicity of effector T cells.Mechanistically, AMPK expression enhances the mitochondrial membrane potential of T cells, limits reactive oxygen species (ROS) production, and resolves ROS-mediated toxicity. Moreover, dampening ROS production alleviates the proliferative defect of AMPK-deficient T cells, therefore indicating a role for an AMPK-mediated ROS control of T cell fitness.
Repeatable differences in exploratory behaviour predict tick infestation probability in wild great tits
Authors: Rollins Robert E. , Mouchet Alexia , Margos Gabriele , Fingerle Volker , Becker Noémie S. , Dingemanse Niels J. 
Published: March 2020

AbstractTicks are parasites that feed on the blood of various vertebrate hosts, including many species of bird. Birds can disperse ticks over short and long distances, therefore impacting tick population dynamics. The likelihood that birds attract ticks should depend on their behaviour and the environment. We studied various key ecological variables (breeding density, human disturbance) and phenotypic traits (exploratory behaviour; body condition) proposed to predict tick burden in great tits (Parus major). Our study spanned over three years and 12 human-recreated plots, equipped with nest-boxes in southern Germany. Adult breeders were assessed for exploratory behaviour, tick burden, and body condition. For each plot, human disturbance was quantified as a human recreational pressure index during biweekly nest box inspections by scoring the number of recreants using the plots. Infestation probability but not tick burden increased with exploratory behaviour. We also found moderate support for a positive effect of recreational pressure on infestation probability. Further, body condition negatively predicted tick burden. Individuals were repeatable in tick burden across years. Our study implies that infestation probability and tick burden are governed by distinct ecological and phenotypic drivers. Our findings also highlight the importance of incorporating ecological and individual variation in host phenotypes to predict spatiotemporal distributions of ticks in nature. (207/250-word limit)Lay SummaryTicks use many birds as hosts, but why do some individuals have more or fewer ticks? Using a data collected over three years on great tit adults inhabiting 12 different nest-box plots, we showed that more explorative birds and those in highly recreated habitats were more likely to be infested with ticks. Exploratory behaviour and human disturbance could modify great tit habitat choice and, therefore, impact how often a birds and ticks encounter each other.
Dynamics of protein binding to sites of nascent unscheduled DNA repair synthesis in non-proliferating cells
Authors: Scalera Claudia , Dutto Ilaria , Barbazza Francesca , Abou Khouzam Raefa , Ticli Giulio , Cazzalini Ornella , Stivala Lucia A. , Prosperi Ennio 
Published: March 2020

ABSTRACTThe analysis of DNA repair mechanisms is of fundamental importance to understand how cells remove DNA damage and maintain their genome stability. Investigating the dynamic association of proteins at sites of active DNA synthesis has been successfully performed at DNA replication forks, providing important information on the process, and allowing the identification of new players acting at these sites. However, the applicability of these studies to DNA repair events at sites of nascent unscheduled DNA synthesis (UDS) in non-proliferating cells has been never tested. Here, we describe the analysis of dynamics association of protein participating in nucleotide excision repair (NER), and in other DNA repair processes, at sites of nascent UDS in non-proliferating cells, to avoid interference by DNA replication. Labeling with 5-ethynyl-2’-deoxyuridine (EdU) after DNA damage, followed by click reaction to biotinylate these sites, permits the analysis of dynamic association of proteins, such as DNA polymerases δ and κ, as well as PCNA, to active DNA repair synthesis sites. The suitability of this technique to identify new factors present at active UDS sites is illustrated by two examples of proteins previously unknown to participate in the UV-induced DNA repair process.
Homologous organization of cerebellar pathways to sensory, motor, and associative forebrain
Authors: Pisano Thomas J. , Dhanerawala Zahra M. , Kislin Mikhail , Bakshinskaya Dariya , Engel Esteban A. , Hansen Ethan J. , Hoag Austin T. , Lee Junuk , de Oude Nina L. , Venkataraju Kannan Umadevi , Verpeut Jessica L. , Hoebeek Freek E. , Richardson Ben D. , Boele Henk-Jan , Wang Samuel S.-H. 
Published: March 2020

AbstractCerebellar outputs take polysynaptic routes to reach the rest of the brain, impeding conventional tracing. Here we quantify pathways between cerebellum and forebrain using transsynaptic tracing viruses and a whole-brain quantitative analysis pipeline. Retrograde tracing found a majority of descending paths originating from somatomotor cortex. Anterograde tracing of ascending paths encompassed most thalamic nuclei, especially ventral posteromedial, lateral posterior, mediodorsal, and reticular nuclei; in neocortex, sensorimotor regions contained the most labeled neurons, but higher densities were found in associative areas, including orbital, anterior cingulate, prelimbic, and infralimbic cortex. Patterns of ascending expression correlated with c-Fos expression after optogenetic inhibition of Purkinje cells. Our results reveal homologous networks linking single areas of cerebellar cortex to diverse forebrain targets. We conclude that shared areas of cerebellum are positioned to provide sensory-motor information to regions implicated in both movement and nonmotor function.Graphical Abstract
Mechanosensing through direct binding of tensed F-actin by LIM domains
Authors: Sun Xiaoyu , Phua Donovan Y. Z. , Axiotakis Lucas , Smith Mark A. , Blankman Elizabeth , Gong Rui , Cail Robert C. , Espinosa de Los Reyes Santiago , Beckerle Mary C. , Waterman Clare M. , Alushin Gregory M. 
Published: March 2020

SummaryMechanical signals transmitted through the cytoplasmic actin cytoskeleton must be relayed to the nucleus to control gene expression. LIM domains are protein-protein interaction modules found in cytoskeletal proteins and transcriptional regulators; however, it is unclear if there is a direct link between these two functions. Here we identify three LIM protein families (zyxin, paxillin, and FHL) whose members preferentially localize to the actin cytoskeleton in mechanically-stimulated cells through their tandem LIM domains. A minimal actin-myosin reconstitution system reveals that representatives of all three families directly bind F-actin only in the presence of mechanical force. Point mutations at a site conserved in each LIM domain of these proteins selectively disrupt tensed F-actin bindingin vitroand cytoskeletal localization in cells, demonstrating a common, avidity-based mechanism. Finally, we find that binding to tensed F-actin in the cytoplasm excludes the cancer-associated transcriptional co-activator FHL2 from the nucleus in stiff microenvironments. This establishes direct force-activated F-actin binding by FHL2 as a mechanosensing mechanism. Our studies suggest that force-dependent sequestration of LIM proteins on the actin cytoskeleton could be a general mechanism for controlling nuclear localization to effect mechanical signaling.
A method for large scale implantation of 3D microdevice ensembles into brain and soft tissue
Authors: Sigurdsson Stefan A. , Yu Zeyang , Lee Joonhee , Nurmikko Arto 
Published: March 2020

AbstractWireless networks of implantable electronic sensors and actuators on the microscale (sub-mm) are being explored for monitoring and modulation of physiological activity for medical diagnostics and therapeutic purposes. Beyond the requirement of integrating multiple electronic or chemical functions within small device volumes, a key challenge is the development of high-throughput methods for implantation of large numbers of microdevices into soft tissues with minimal damage. To that end, we have developed a method for high-throughput implantation of ∼100-200 μm size devices which are here simulated by proxy microparticle ensembles. While generally applicable to subdermal tissue, our main focus and experimental testbed is the implantation of microparticles into the brain. The method deploys a scalable delivery tool composed of a 2-dimensional array of polyethylene glycol tipped microneedles which confine the microparticle payloads. Upon dissolution of the bioresorbable polyethylene glycol, the supporting array structure is retrieved and the microparticles remain embedded in the tissue, distributed spatially and geometrically according to the design of the microfabricated delivery tool. We first evaluated the method in an agarose testbed in terms of spatial precision and throughput for up to 1000 passive spherical and planar microparticles acting as proxy devices. We then performed the same evaluations of particles implanted into the rat cortex under acute conditions and assessed the tissue injury produced by our method of implantation under chronic conditions.
Frequency-dependent interactions determine outcome of competition between two breast cancer cell lines
Authors: Freischel Audrey R. , Damaghi Mehdi , Cunningham Jessica J. , Ibrahim-Hashim Arig , Gillies Robert J. , Gatenby Robert A. , Brown Joel S. 
Published: March 2020

ABSTRACTTumors are highly dynamic ecosystems in which diverse cancer cell subpopulations compete for space and resources. These complex, often non-linear interactions govern continuous spatial and temporal changes in the size and phenotypic properties of these subpopulations. Because intra-tumoral blood flow is often chaotic, competition for resources may be a critical selection factor in progression and prognosis. Here, we quantify resource competition using 3D spheroid cultures with MDA-MB-231 and MCF-7 breast cancer cells. We hypothesized that MCF-7 cells, which primarily rely on efficient aerobic glucose metabolism, would dominate the population under normal pH and low glucose conditions; and MDA-MB-231 cells, which exhibit high levels of glycolytic metabolism, would dominate under low pH and high glucose conditions. In spheroids with single populations, MCF-7 cells exhibited equal or superior intrinsic growth rates (density-independent measure of success) and carrying capacities (density-dependent measure of success) when compared to MDA-MB-231 cells under all pH and nutrient conditions. Despite these advantages, when grown together, MCF-7 cells do not always outcompete MDA-MB-231 cells. MDA-MB-231 cells outcompete MCF-7 cells in low glucose conditions and coexistence is achieved in low pH conditions. Under all conditions, MDA-MB-231 has a stronger competitive effect (frequency-dependent interaction) on MCF-7 cells than vice-versa. This, and the inability of growth rate or carrying capacity when grown individually to predict the outcome of competition, suggests a reliance on frequency-dependent interactions and the need for competition assays. We frame these results in a game-theoretic (frequency-dependent) model of cancer cell interactions and conclude that competition assays can demonstrate critical density-independent, density-dependent and frequency-dependent interactions that likely contribute toin vivooutcomes.HighlightsDemonstrate how mixed-culture spheroids must be used to characterize competition between two cancer cell lines.Competition alters growth dynamics of cancer cells.Competition growth models can be used to quantify density-independent, density-dependent and frequency-dependent effects on competition.Competition affects tumor progression and structure, making it key to understanding tumor development and evolution.
HumanMETTL7BEncodes an Alkyl Thiol Methyltransferase that Methylates Hydrogen Sulfide
Authors: Maldonato Benjamin J. , Totah Rheem A. 
Published: March 2020

Summary Paragraph/AbstractMethyltransferase-like protein 7B (METTL7B) is implicated in tumor growth and progression while gene expression is upregulated in several different disease states such as rheumatoid arthritis and breast cancer. Yet, the catalytic function of METTL7B has not been characterized. Here we demonstrate thatMETTL7Bencodes a protein that catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (SAM) to hydrogen sulfide (H2S) to form methanethiol (CH3SH). Several exogenous aliphatic thiols were also identified as substrates. Modulation ofMETTL7Bgene expression in HepG2 and HeLa cell culture directly alters the methylation of captopril, a marker reaction of alkyl thiol methyltransferase (TMT) activity(1, 2). Furthermore, cloned and recombinantly expressed and purified METTL7B full length protein methylates several thiol compounds, including hydrogen sulfide, 7α-thiospironolactone, captopril, and L-penicillamine in a concentration dependent manner. Endogenous thiols such as glutathione and cysteine or classic probe substrates of other known small moleculeS-,N-, andO- methyltransferases were not substrates for METTL7B. Our results unequivocally demonstrate, and for the first time, that METTL7B, a protein implicated in several disease states, is an alkyl thiol methyltransferase(3–5). Identifying the catalytic function of METTL7B will enable future pharmacological research in disease pathophysiology whereMETTL7Bexpression and H2S levels can potentially alter the redox state and growth cycle of cells.
Adhesion-mediated mechanosignaling forces mitohormesis
Authors: Tharp Kevin M. , Higuchi-Sanabria Ryo , Timblin Greg A. , Ford Breanna , Garzon-Coral Carlos , Schneider Catherine , Muncie Jonathon M. , Stashko Connor , Daniele Joseph R. , Moore Andrew S. , Frankino Phillip A. , Manoli Sagar S. , Shao Hao , Richards Alicia L. , Chen Kuei-Ho , Ku Gregory M. , Hellerstein Marc , Nomura Daniel K. , Saijo Karou , Gestwicki Jason , Dunn Alexander R. , Krogan Nevan J. , Swaney Danielle L. , Dillin Andrew , Weaver Valerie M. 
Published: March 2020

AbstractMitochondria control eukaryotic cell fate by producing the energy needed to support life and the signals required to execute programmed cell death. The biochemical milieu is known to affect mitochondrial function and contribute to the dysfunctional mitochondrial phenotypes implicated in cancer and the morbidities of ageing. However, the physical characteristics of the extracellular matrix are also altered in cancer and in aging tissues. We demonstrate that cells sense the physical properties of the extracellular matrix and activate a mitochondrial stress response that adaptively tunes mitochondrial functionviaSLC9A1-dependent ion exchange and HSF1-dependent transcription. Overall, our data indicate that adhesion-mediated mechanosignaling may play an unappreciated role in the altered mitochondrial functions observed in aging and cancer.Graphical Abstract
A validated quantitative method for the assessment of neuroprotective barrier impairment in neurodegenerative disease models
Authors: Kumar Vinod , Lee John D. , Coulson Elizabeth J. , Woodruff Trent M. 
Published: March 2020

AbstractThe blood brain barrier (BBB) and blood spinal cord barrier (BSCB) are highly specialised structures that limit molecule entry from the blood and maintain homeostasis within the central nervous system (CNS). BBB and BSCB breakdown are associated with multiple neurodegenerative diseases. Given the key role of neuroprotective barrier impairment in neurodegeneration, it is important to identify an effective quantitative method to assess barrier integrity in animal models. In the present study, we developed and validated a quantitative method for assessing BBB and BSCB integrity using sodium fluorescein, a compound that outperformed other fluorescent dyes. We demonstrated using this method that multiple CNS regions progressively increase in permeability in models of Huntington’s disease and amyotrophic lateral sclerosis, while biphasic disruption occurred in a mouse model of Alzheimer’s disease with disease progression. Collectively, we report a quantitative fluorometric marker with validated reproducible experimental methods, that allows the effective assessment of BBB and BSCB integrity in animal models. This method could be useful to further the understanding of the contribution of these neuroprotective barriers to neurodegeneration processes.