bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aplp1 and the Aplp1-Lag3 Complex facilitates transmission of pathologic α-synuclein
Authors: Mao Xiaobo , Gu Hao , Kim Donghoon , Kimura Yasuyoshi , Wang Ning , Xu Enquan , Wang Haibo , Chen Chan , Zhang Shengnan , Jia Chunyu , Liu Yuqing , Bian Hetao , Karuppagounder Senthilkumar S. , Jia Longgang , Ke Xiyu , Chang Michael , Li Amanda , Yang Jun , Rastegar Cyrus , Sriparna Manjari , Ge Preston , Brahmachari Saurav , Kim Sangjune , Zhang Shu , Shimoda Yasushi , Saar Martina , Workman Creg J. , Vignali Dario A. A. , Muller Ulrike C. , Liu Cong , Ko Han Seok , Dawson Valina L. , Dawson Ted M. 
Published: May 2021

AbstractPathologic α-synuclein (α-syn) spreads from cell-to-cell, in part, through binding to the lymphocyte-activation gene 3 (Lag3). Here we report that amyloid β precursor-like protein 1 (Aplp1) forms a complex with Lag3 that facilitates the binding, internalization, transmission, and toxicity of pathologic α-syn. Deletion of both Aplp1 and Lag3 eliminates the loss of dopaminergic neurons and the accompanying behavioral deficits induced by α-syn preformed fibrils (PFF). Anti-Lag3 prevents the internalization of α-syn PFF by disrupting the interaction of Aplp1 and Lag3, and blocks the neurodegeneration induced by α-syn PFFin vivo. The identification of Aplp1 and the interplay with Lag3 for α-syn PFF induced pathology advances our understanding of the molecular mechanism of cell-to-cell transmission of pathologic α-syn and provides additional targets for therapeutic strategies aimed at preventing neurodegeneration in Parkinson’s disease and related α-synucleinopathies.One Sentence SummaryAplp1 forms a complex with Lag3 that facilitates the binding, internalization, transmission, and toxicity of pathologic α-synuclein.Graphical AbstractAplp1 and the Aplp1-Lag3 complex facilitates transmission of pathologic α-synuclein.Aplp1 is a receptor that drives pathologic α-syn transmission, and genetic depletion of Aplp1 can significantly reduce the α-synuclein pathogenesis. Aplp1 and Lag3 forms an Aplp1-Lag3 complex that accounts for substantial binding of pathologic α-syn to cortical neurons. Together Aplp1 and Lag3 play a major role in pathologic α-syn internalization, transmission and toxicity. Double knockout of Aplp1 and Lag3 and or a Lag3 antibody that disrupts the Aplp1 and Lag3 complex almost completely blocks α-syn PFF-induced neurodegeneration.
Activation of extrasynaptic kainate receptors drives hilar mossy cell activity
Authors: Ramos Czarina , Lutzu Stefano , Yamasaki Miwako , Yanagawa Yuchio , Sakimura Kenji , Tomita Susumu , Watanabe Masahiko , Castillo Pablo E. 
Published: May 2021

AbstractMossy cells (MCs) of the dentate gyrus (DG) are key components of an excitatory associative circuit established by reciprocal connections with dentate granule cells (GCs). MCs are implicated in place field encoding, pattern separation and novelty detection, as well as in brain disorders such as temporal lobe epilepsy and depression. Despite their functional relevance, little is known about the determinants that control MC activity. Here, we examined whether MCs express functional kainate receptors (KARs), a subtype of glutamate receptors involved in neuronal development, synaptic transmission and epilepsy. Using mouse hippocampal slices, we found that bath application of submicromolar and micromolar concentrations of the KAR agonist kainic acid induced inward currents and robust MC firing. These effects were abolished inGluK2KO mice, indicating the presence of functional GluK2-containing KARs in MCs. In contrast to CA3 pyramidal cells, which are structurally and functionally similar to MCs, and express synaptic KARs at mossy fiber (MF) inputs (i.e., GC axons), we found no evidence for KAR-mediated transmission at MF-MC synapses, indicating that most KARs at MCs are extrasynaptic. Immunofluorescence and immunoelectron microscopy analyses confirmed the extrasynaptic localization of GluK2-containing KARs in MCs. Finally, blocking glutamate transporters, a manipulation that increases extracellular levels of endogenous glutamate, was sufficient to induce KAR-mediated inward currents in MCs, suggesting that MC-KARs can be activated by increases in ambient glutamate. Our findings provide the first direct evidence of functional extrasynaptic KARs at a critical excitatory neuron of the hippocampus.Significance StatementHilar mossy cells (MCs) are an understudied population of hippocampal neurons that form an excitatory loop with dentate granule cells. MCs have been implicated in pattern separation, spatial navigation, and epilepsy. Despite their importance in hippocampal function and disease, little is known about how MC activity is recruited. Here, we show for the first time that MCs express extrasynaptic kainate receptors (KARs), a subtype of glutamate receptors critically involved in neuronal function and epilepsy. While we found no evidence for synaptic KARs in MCs, KAR activation induced strong action potential firing of MCs, raising the possibility that extracellular KARs regulate MC excitabilityin vivoand may also promote dentate gyrus hyperexcitability and epileptogenesis.
Linked machine learning classifiers improve species classification of fungi when using error-prone long-reads on extended metabarcodes
Authors: Eenjes Tavish , Hu Yiheng , Irinyi Laszlo , Vi Hoang Minh Thuy , Smith Leon M. , Linde Celeste C. , Milgate Andrew W. , Meyer Wieland , Stone Eric A. , Rathjen John P. , Mashford Benjamin , Schwessinger Benjamin 
Published: May 2021

ABSTRACTBackgroundThe increased usage of error-prone long-read sequencing for metabarcoding of fungi has not been matched with adequate public databases and concomitant analysis approaches. We address this gap and present a proof-of-concept study for classifying fungal taxa using linked machine learning classifiers. We demonstrate the capability of linked machine learning classifiers to accurately classify species and strains using real-world and simulated fungal ribosomal DNA datasets, including plant and human pathogens. We benchmark our new approach in comparison to current alignment and k-mer based methods based on synthetic mock communities. We also assess real world applications of species identification in complex unlabelled datasets.ResultsOur machine learning approach assigned individual nanopore long-read amplicon sequences to fungal species with high recall rates and low false positive rates. Importantly, our approach successfully distinguished between closely-related species and strains when individual read errors were higher than the genetic distance between individual taxa, which the alignment and k-mer methods could not do. The machine learning approach showed an ability to identify key species with high recall rates, even in complex samples of unknown species composition.ConclusionsA proof of concept machine learning approach using a tree-descent approach on a decision tree of classifiers can identify known taxa with high accuracy, and precisely detect known target species from complex samples with high recall rates. We propose this approach is suitable for detecting the known knowns of pathogens or invasive species in any environment of mostly unknown composition, including agriculture and wild ecosystems.
PAM-interacting domain swapping is extensively utilized in nature to evolve CRISPR-Cas9 nucleases with altered PAM specificities
Authors: Wang Qiuyan , Bian Xiaomeng , Du Jinli , Lv Yawen , Tao Lin , Xie Tian 
Published: May 2021

AbstractIt has been anticipated that protospacer adjacent motif (PAM) specificity of the CRISPR-Cas9 nucleases protospacer appears to be modular. Here we present the finding that naturally occurring domain swapping has been extensively involved in altering its PAM specificities. Sequence analysis of streptococcal Cas9 sequences revealed conservation of three distinct PAM-interacting motifs, with phylogenetic analysis of full-length Cas9 and the PID demonstrating that PAM-interacting domain (PID) domain swapping was extensively utilized to diversify its PAM specificity. An extended analysis of 582 representative Cas9 sequences revealed that this PID swapping was broadly present in most of the investigated genera. Mimicking the natural PID domain swapping, a functional chimeric enzyme, based on the scaffold of compact Staphylococcus aureus Cas9, with novel NNAAAA PAM specificity was developed. In summary, our findings shed new light on a rich source of exchangeable PID domains in Cas9 genes, which can be mined for domain swapping aiming to an effective PAM refinement.
Evaluation of Antibiotic Tolerance inPseudomonas aeruginosafor Aminoglycosides and its Predicted Gene Regulations Through In-silico Transcriptomic Analysis
Authors: Kumar Abishek , Thankappan Bency , Jayaraman Angayarkanni , Gupta Akshita 
Published: May 2021

AbstractPseudomonas aeruginosacauses chronic infections like cystic fibrosis, endocarditis, bacteremia and sepsis, which are life-threatening and difficult to treat. The lack of antibiotic response inP. aeruginosais due to adaptive resistance mechanism, which prevents the entry of antibiotics into cytosol of the cell to achieve tolerance. Among different groups of antibiotics, aminoglycosides are used as a parental antibiotic for treatment ofP. aeruginosa. This study aims to determine the kinetics of antibiotic tolerance and gene expression changes inP. aeruginosaexposed to amikacin, gentamicin, and tobramycin. These antibiotics were exposed toP. aeruginosaat their MICs and the experimental setup was monitored till 72 hours, followed by the measurement of optical density in the interval of every 12 hours. The growth ofP. aeruginosain MICs of antibiotics represents the kinetics of antibiotic tolerance in amikacin, gentamicin, and tobramycin. Transcriptomic profile of antibiotic exposedP. aeruginosaPA14 was taken from Gene Expression Omnibus (GEO), NCBI as microarray datasets. The gene expressions of two datasets were compared by test versus control. Tobramycin exposedP. aeruginosafailed to develop tolerance in MICs 0.5µg/mL, 1µg/mL and 1.5µg/mL. Whereas amikacin and gentamicin treatedP. aeruginosadeveloped tolerance in MICs. This depicts the superiorin vitroresponse of tobramycin over the gentamicin and amikacin. Further,in silicotranscriptomic analysis of tobramycin treatedP. aeruginosaresulted in low expression of 16s rRNA Methyltransferase E, B & L, alginate biosynthesis genes and several proteins of Type 2 Secretory System (T2SS) and Type 3 Secretory System (T3SS). The Differentially Expressed Genes (DEGs) of alginate biosynthesis, and RNA Methyltransferases suggests increased antibiotic response and low probability of developing resistance. The use of tobramycin as a parental antibiotic with its synergistic combination might combatP. aeruginosawith increased response.
Fractions of traditionally brewed rice beverage ameliorate anxiety and improve spatial memory in mice
Authors: Bhaskar Bhuwan , Adak Atanu , Khan Mojibur R. 
Published: May 2021

AbstractRice beverages are traditionally prepared and consumed popularly by the different ethnic groups of North East India. To investigate its effects on behavior, mice were treated with different fractions of rice beverage that included the beverage as a whole, insoluble and soluble fractions. Intragastric treatments of these fractions were given to the mice (n=6 per group) for 30 days and behavioral studies were performed on elevated plus and Y maze to evaluate anxiety and spatial memory, respectively. Next generation sequencing of metagenomic DNA of the beverage indicated presence of 157 OTUs and 26 bacterial genera were dominant with an abundance of 0.1%. The insoluble fraction treated animals showed lowest anxiety like symptoms. Spatial memory improved in all the treatments compared to the control, of which the rice beverage treatment showed the highest levels (p<0.05). Gas chromatography and mass spectroscopy-based metabolite profiling of the beverage revealed 10 alcohols, 29 sachharides, 43 acids and 13 amino acids. Findings of this study suggest a positive effect of rice beverage components on anxiety and spatial memory of mice.
Frizzled BRET sensors based on bioorthogonal labeling of unnatural amino acids reveal WNT-induced dynamics of the cysteine-rich domain
Authors: Kowalski-Jahn Maria , Schihada Hannes , Turku Ainoleena , Huber Thomas , Sakmar Thomas P. , Schulte Gunnar 
Published: May 2021

AbstractFrizzleds (FZD1-10) comprise a class of G protein-coupled receptors containing an extracellular cysteine-rich domain (CRD) that binds lipoglycoproteins of the Wingless/Int-1 family (WNTs). Despite the prominent role of the WNT/FZD system in health and disease, our understanding of how WNT binding to the FZD CRD is translated into receptor activation and transmembrane signaling remains limited. Current hypotheses dispute the roles for conformational dynamics and the involvement of the linker domain connecting the CRD with the seven-helical transmembrane core of FZD. To clarify the mechanism of WNT binding to FZD and to elucidate how WNT/FZD complexes achieve signaling pathway specificity, we devised conformational FZD-CRD biosensors based on bioluminescence-resonance-energy-transfer (BRET). Using FZD engineered with N-terminal nanoluciferase and fluorescently-labeled unnatural amino acids in the linker domain and extracellular loop 3, we show that WNT-3A and WNT-5A induce similar CRD conformational rearrangements despite promoting distinct downstream signaling pathways, and that CRD dynamics are not required for WNT/β-catenin signaling. Thus, the novel FZD-CRD biosensors we report provide insights into the stepwise binding, activation and signaling processes in FZDs. The sensor design is broadly applicable to explore fundamental events in signal transduction mediated by other membrane receptors.
Targetron-assisted delivery of exogenous DNA sequences intoPseudomonas putidathrough CRISPR-aided counterselection
Authors: Velázquez Elena , Al-Ramahi Yamal , Tellechea Jonathan , Krasnogor Natalio , de Lorenzo Víctor 
Published: May 2021

ABSTRACTGenome editing methods based on Group II introns (known as Targetron technology) have been long used as a gene knock-out strategy in a wide range of organisms in a fashion independent of homologous recombination. Yet, their utility as delivery systems has been typically suboptimal because of their reduced efficiency of insertion when they carry exogenous sequences. We show that this limitation can be tackled and Targetron adapted as a general tool in Gram-negative bacteria. To this end, a set of broad host range standardized vectors were designed for conditional expression of the Ll.LtrB intron. After testing the correct functionality of these plasmids inEscherichia coliandPseudomonas putida, we created a library of Ll.LtrB variants carrying cargo DNA sequences of different lengths to benchmark the capacity of intron-mediated delivery in these bacteria. Next, we combined CRISPR/Cas9-facilitated counterselection to increase the chances of finding genomic sites inserted with the thereby engineered introns. By following this pipeline, we were able to insert exogenous sequences of up to 600 bp at specific genomic locations in wild-typeP. putidaKT2440 and its ΔrecAderivative. Finally, we were able to apply this technology to successfully tag this strain with an orthogonal short sequence (barcode) that acts as a unique identifier for tracking this microorganism in biotechnological settings. The results withP. putidaexemplified the value of the Targetron approach for unrestricted delivery of small DNA fragments to the genomes of Gram-negative bacteria for a suite of genome editing endeavours.
Protein secondary structure affects glycan clustering in native mass spectrometry
Authors: Yan Hao , Lockhauserbäumer Julia , Szekeres Gergo Peter , Mallagaray Alvaro , Creutznacher Robert , Taube Stefan , Peters Thomas , Pagel Kevin , Uetrecht Charlotte 
Published: May 2021

AbstractInfection with human noroviruses (hNoV) for the vast majority of strains requires attachment of the viral capsid to histo blood group antigens (HBGA). The HBGA binding pocket is formed by dimers of the protruding domain (P dimers) of the capsid protein VP1. Several studies have focused on HBGA binding to P dimers, reporting binding affinities and stoichiometries. However, nuclear magnetic resonance spectroscopy (NMR) and native mass spectrometry (MS) analyses yielded incongruent dissociation constants (KD) for binding of HBGAs to P dimers and, in some cases, disagreed whether glycans bind at all. We hypothesized that glycan clustering during electrospray ionization in native MS critically depends on the physicochemical properties of the protein studied. It follows that the choice of the reference protein is crucial. We analyzed carbohydrate clustering using various P dimers and eight non-glycan binding proteins serving as possible references. Data from native and ion mobility MS indicate that the mass fraction of β-sheet has a strong influence on the degree of glycan clustering. Therefore, the determination of specific glycan binding affinities from native MS must be interpreted cautiously.
Organophosphate intoxication inC. elegansreveals a new route to mitigate poisoning through the modulation of determinants responsible for nicotinic acetylcholine receptor function
Authors: Izquierdo Patricia G. , Charvet Claude L. , Neveu Cedric , Green A. Christopher , Tattersall John E.H. , Holden-Dye Lindy , O’Connor Vincent 
Published: May 2021

AbstractPlasticity is a reactive mechanism that allows the adaptation of organisms to changing environmental cues. The exploitation of this physiological process has a clear benefit to promote the recovery from a wide range of neurological disorders. Here, we show that plasticity-promoting regimes provide candidate mechanisms to supplement the classically used antidotes for anti-cholinesterase poisoning. These neurotoxins inhibit acetylcholinesterase, causing the overstimulation of cholinergic transmission at synapses and neuromuscular junctions. The model organismC. elegansexhibits organophosphate-induced mitigating plasticity that impacts on the recovery of neuromuscular phenotypes, initially impaired by the drug. This is underpinned by overstimulation of nicotinic receptors at the neuromuscular junction. Intrinsic determinants of receptor’s location and sensitivity modulate the extent of plasticity in the context of persistent cholinergic stimulation. Our results indicate that pharmacological intervention of nicotinic receptors and/or scaffolding proteins that support receptor function might provide a novel treatment route for anti-cholinesterase poisoning.
Dyrk1agene dosage in glutamatergic neurons has key effects in cognitive deficits observed in mouse models of MRD7 and Down syndrome
Authors: Brault Véronique , Nguyen Thu Lan , Flores-Gutiérrez Javier , Iacono Giovanni , Birling Marie-Christine , Lalanne Valérie , Méziane Hamid , Manousopoulou Antigoni , Pavlovic Guillaume , Lindner Loïc , Selloum Mohammed , Sorg Tania , Yu Eugene , Garbis Spiros D. , Hérault Yann 
Published: May 2021

AbstractPerturbation of the excitation/inhibition (E/I) balance leads to neurodevelopmental diseases including to autism spectrum disorders, intellectual disability, and epilepsy. Mutation in theDYRK1Agene located on human chromosome 21 (Hsa21) leads to an intellectual disability syndrome associated with microcephaly, epilepsy, and autistic troubles (MRD7). Overexpression of DYRK1A, on the other hand, has been linked with learning and memory defects observed in people with Down syndrome (DS).Dyrk1ais expressed in both glutamatergic and GABAergic neurons, but its impact on each neuronal population has not yet been elucidated. Here we investigated the impact ofDyrk1agene copy number variation in glutamatergic neurons using a conditional knockout allele ofDyrk1acrossed with the Tg(Camk2-Cre)4Gsc transgenic mouse. We explored this genetic modification in homozygotes, heterozygotes and combined with the Dp(16Lipi-Zbtb21)1Yey trisomic mouse model to unravel the consequence ofDyrk1adosage from 0 to 3, to understand its role in normal physiology, and in MRD7 and DS. Overall,Dyrk1adosage in glutamatergic neurons did not impact locomotor activity, working memory or epileptic susceptibility, but revealed thatDyrk1ais involved in long-term explicit memory. Molecular analyses pointed at a deregulation of transcriptional activity through immediate early genes and a role of DYRK1A at the glutamatergic post-synapse by deregulating and interacting with key post-synaptic proteins implicated in mechanism leading to long-term enhanced synaptic plasticity. Altogether, our work gives important information to understand the action of DYRK1A inhibitors and have a better therapeutic approach.Author summaryThe Dual Specificity Tyrosine Phosphorylation Regulated Kinase 1A, DYRK1A, drives cognitive alterations with increased dose in Down syndrome (DS) or with reduced dose in mental retardation disease 7 (MRD7). Here we report that specific and complete loss ofDyrk1ain glutamatergic neurons induced a range of specific cognitive phenotypes and alter the expression of genes involved in neurotransmission in the hippocampus. We further explored the consequences ofDyrk1adosage in glutamatergic neurons on the cognitive phenotypes observed respectively in MRD7 and DS mouse models and we found specific roles in long-term explicit memory with no impact on motor activity, short-term working memory, and susceptibility to epilepsy. Then we demonstrated that DYRK1A is a component of the glutamatergic post-synapse and interacts with several component such as NR2B and PSD95. Altogether our work describes a new role of DYRK1A at the glutamatergic synapse that must be considered to understand the consequence of treatment targeting DYRK1A in disease.
Predicting drug concentrations in PDMS microfluidic organ chips
Authors: Grant Jennifer , Özkan Alican , Oh Crystal , Mahajan Gautam , Prantil-Baun Rachelle , Ingber Donald E. 
Published: May 2021

ABSTRACTMicrofluidic organ-on-a-chip (Organ Chip) cell culture devices are often fabricated using polydimethylsiloxane (PDMS) because it is biocompatible, transparent, elastomeric, and oxygen permeable; however, hydrophobic small molecules can absorb to PDMS, which makes it challenging to predict drug responses. Here, we describe a combined simulation and experimental approach to predict the spatial and temporal concentration profile of a drug under continuous dosing in a PDMS Organ Chip containing two parallel channels separated by a porous membrane that is lined with cultured cells, without prior knowledge of its log P value. First, a three-dimensional finite element simulation of drug loss into the chip was developed that incorporates absorption, adsorption, convection, and diffusion, which predicts changes in drug levels over time and space as a function of potential PDMS diffusion coefficients and log P values. By then experimentally measuring the diffusivity of the compound in PDMS and determining its partition coefficient through mass spectrometric analysis of the drug concentration in the channel outflow, it is possible to estimate the effective log P range of the compound. The diffusion and partition coefficients were experimentally derived for the antimalarial drug and potential SARS-CoV-2 therapeutic, amodiaquine, and incorporated into the model to quantitatively predict the drug-specific concentration profile over time measured in human Lung Airway Chips lined with bronchial epithelium interfaced with pulmonary microvascular endothelium. The same strategy can be applied to any device geometry, surface treatment, orin vitromicrofluidic model to predict the spatial and temporal gradient of a drug in 3D without prior knowledge of the partition coefficient or the rate of diffusion in PDMS. Thus, this approach may expand the use of PDMS Organ Chip devices for various forms of drug testing.