bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel microRNA-455-3p mouse models to study Alzheimer’s disease pathogenesis
Authors: Kumar Subodh , Mortan Hallie , Sawant Neha , Orlov Erika , Bunquin Lloyd , Pradeepkiran Jangampalli Adi , Reddy P. Hemachandra 
Published: September 2021

AbstractMicroRNA-455-3p is one of the highly conserved miRNAs involved in several human diseases but newly explored by our lab in Alzheimer’s disease (AD). Our past studies unveiled the biomarker and therapeutic potentials of miR-455-3p in AD. Our in vitro study exhibited the protective role of miR-455-3p against AD toxicities in reducing full-length APP and amyloid-β (Aβ) protein levels, and also reducing defective mitochondrial biogenesis, impaired mitochondrial dynamics and synaptic deficiencies. Next, we sought to determine the essential roles of miR-455-3p in AD using mouse models. Therefore, for the first time we generated both transgenic (TG) and knockout (KO) mouse models of miR-455-3p. We determined the positive and negative effects of miR-455-3p on mice cognitive function, mitochondrial biogenesis, mitochondrial dynamics, mitochondrial number & length, dendritic spine density, synapse numbers and synaptic activity in 12-month-old miR-455-3p TG and KO mice. MiR-455-3p TG mice lived 5 months longer than wild-type (WT) mice, whereas KO mice lived 4 months shorter than their WT counter parts. Morris water maze test showed improved cognitive behavior, spatial learning and memory in miR-455-3p TG mice relative to age-matched WT mice and miR-455-3p KO mice. Further, mitochondrial biogenesis, dynamics and synaptic activities were enhanced in miR-455-3p TG mice, while these were reduced in KO mice. Overall, miR-455-3p TG mice displayed protective effects and miR-455-3p KO mice exhibited deleterious effects in relation to AD pathogenesis. Both mouse models could be ideal research tools to understand the molecular mechanism of miR-455-3p in AD and other human diseases.
Towards a system-level causative knowledge of pollinator communities
Authors: Saavedra Serguei , Bartomeus Ignasi , Godoy Oscar , Rohr Rudolf P. , Zu Penguan 
Published: September 2021

AbstractPollination plays a central role both in the maintenance of biodiversity and in crop production. However, habitat loss, pesticides, invasive species, and larger environmental fluctuations are contributing to a dramatic decline of numerous pollinators world-wide. This has increased the need for interventions to protect the composition, functioning, and dynamics of pollinator communities. Yet, how to make these interventions successful at the system level remains extremely challenging due to the complex nature of species interactions and the various unknown or unmeasured confounding ecological factors. Here, we propose that this knowledge can be derived by following a probabilistic causal analysis of pollinator communities. This analysis implies the inference of interventional expectations from the integration of observational and synthetic data. We propose that such synthetic data can be generated using theoretical models that can enable the tractability and scalability of unseen confounding ecological factors affecting the behavior of pollinator communities. We discuss a road map for how this probabilistic causal analysis can be accomplished to increase our system-level causative knowledge of natural communities.
Concurrent tau pathologies in frontotemporal lobar degeneration with TDP-43 pathology
Authors: Koga Shunsuke , Zhou Xiaolai , Murakami Aya , De Castro Cristhoper Fernandez , Baker Matthew C. , Rademakers Rosa , Dickson Dennis W. 
Published: September 2021

AbstractAimsAccumulating evidence suggests that patients with frontotemporal lobar degeneration (FTLD) can have pathologic accumulation of multiple proteins, including tau and TDP-43. This study aimed to determine the frequency and characteristics of concurrent tau pathology in FTLD with TDP-43 pathology (FTLD-TDP).MethodsThe study included 146 autopsy-confirmed cases of FTLD-TDP and 55 cases of FTLD-TDP with motor neuron disease (FTLD-MND). Sections from the basal forebrain were screened for tau pathology with phospho-tau immunohistochemistry. For cases with tau pathology on the screening section, additional brain sections were studied to establish a diagnosis. Genetic analysis of C9ORF72, GRN, and MAPT was performed on select cases.ResultsAmong 201 cases, we found 72 cases (36%) with primary age-related tauopathy (PART), 85 (42%) with aging-related tau astrogliopathy (ARTAG), 45 (22%) with argyrophilic grain disease (AGD), and 2 cases (1%) with corticobasal degeneration (CBD). Patients with ARTAG or AGD were significantly older than those without these comorbidities. One of the patients with FTLD-TDP and CBD had C9ORF72 mutation and relatively mild tau pathology, consistent with incidental CBD.ConclusionThe coexistence of TDP-43 and tau pathologies was relatively common, particularly PART and ARTAG. Although rare, individual patients with FTLD can have multiple concurrent proteinopathies. The absence of TDP-43-positive astrocytic plaques may suggest that CBD and FTLD-TDP were independent disease processes in the two patients with both tau and TDP-43 pathologies. It remains to be determined if mixed cases represent a unique disease process or two concurrent disease processes in an individual.
The structural basis of huntingtin (Htt) fibril polymorphism, revealed by cryo-EM of exon 1 Htt fibrils
Authors: Nazarov Sergey , Chiki Anass , Boudeffa Driss , Lashuel Hilal A. 
Published: September 2021

AbstractThe lack of detailed insight into the structure of aggregates formed by the huntingtin protein has hampered efforts to develop therapeutics and diagnostics targeting pathology formation in the brain of patients with Huntington’s disease. To address this knowledge gap, we investigated the structural properties of in vitro generated fibrils from exon1 of the huntingtin protein by electron cryo-microscopy and single-particle analysis. We show that wildtype and mutant exon1 of the huntingtin protein form non-helical fibrils with a polygultamine amyloid core composed of β-hairpins with unique characteristics that have not been previously observed with other amyloid filaments. The stacks of β-hairpins form long planar β- sheets (protofilaments) with variable stacking angle and occasional out-of-register state of individual β-hairpins. These features and the propensity of protofilament to undergo lateral association results in a high degree of fibril polymorphism, including fibrils composed of varying numbers of protofilaments. Our results also represent the first direct observation of how the flanking domains are organized around the polyglutamine core of the fibril and provide insight into how they might affect huntingtin fibril structure, polymorphism, and stacking of β-hairpins within its core structure. Removal of the first 17 amino acids at the N-terminus resulted in surprising intra-fibril structural heterogeneity and reduced fibril’s propensity to lateral associations. Overall, this work provides valuable insights that could guide future mechanistic studies to elucidate the sequence and structural determinants of huntingtin aggregation, as well as cryo-EM and structural studies of fibrils derived from huntingtin proteins and other disease-associated polyglutamine-containing proteins.
FAIR enough? A perspective on the status of nucleotide sequence data and metadata on public archives
Authors: Hassenrück Christiane , Poprick Tobias , Helfer Véronique , Molari Massimiliano , Meyer Raissa , Kostadinov Ivaylo 
Published: September 2021

AbstractKnowledge derived from nucleotide sequence data is increasing in importance in the life sciences, as well as decision making (mainly in biodiversity policy). Metadata standards have been established to facilitate sustainable sequence data management according to the FAIR principles (Findability, Accessibility, Interoperability, Reusability). Here, we review the status of metadata available for raw read Illumina amplicon and whole genome shotgun sequencing data derived from ecological metagenomic material that are accessible at the European Nucleotide Archive (ENA), as well as the compliance of the primary sequence data (fastq files) with data submission requirements. While overall basic metadata, such as geographic coordinates, were retrievable in 98% of the cases for this type of sequence data, interoperability was not always ensured and other (mainly conditionally) mandatory parameters were often not provided at all. Metadata standards, such as the ‘Minimum Information about any(x) Sequence (MIxS)’, were only infrequently used despite a demonstrated positive impact on metadata quality. Furthermore, the sequence data itself did not meet the prescribed requirements in 31 out of 39 studies that were manually inspected. To tackle the most immediate needs to improve FAIR sequence data management, we provide a list of minimal suggestions to researchers, research institutions, funding agencies, reviewers, publishers, and databases, that we believe might have a potentially large positive impact on sequence data and metadata FAIRness, which is crucial for further research and its derived applications.
Active Translation Control of CD4 T Cell Activation by Regulatory T Cells
Authors: So Lomon , Obata-Ninomiya Kazushige , Hu Alex , Muir Virginia , Takamori Ayako , Song Jing , Buckner Jane H. , Savan Ram , Ziegler Steven F. 
Published: September 2021

SUMMARYIncreased protein synthesis is a hallmark of lymphocyte activation. Regulatory T cells (Tregs) suppress the activation and subsequent effector functions of CD4 effector T cells (Teffs). However, molecular mechanisms that enforce Treg-mediated suppression in CD4 Teff are not fully clear. Control of CD4 Teff activation by Tregs has largely been defined at the transcriptional level, which does not reflect changes in post-transcriptional control. We found that Tregs suppressed activation-induced global protein synthesis in CD4 Teffs prior to cell division. We analyzed genome-wide changes in the transcriptome and translatome of activated CD4 Teffs using two independent approaches. We show that mRNAs encoding for the protein synthesis machinery are regulated at the level of translation in activated Teffs. Strikingly, Tregs suppressed global protein synthesis of CD4 Teffs by specifically inhibiting mRNAs of the translation machinery at the level of mTORC1-mediated translation control. Lastly, we found that the RNA helicase eIF4A inhibitor rocaglamide A (RocA) can suppress CD4 Teff activation in vitro to alleviate inflammatory CD4 Teff activation caused by acute Treg depletion in vivo. These data provide evidence that peripheral tolerance is enforced by Tregs through mRNA translational control in CD4 Teffs. Therefore, therapeutic targeting of the protein synthesis machinery can be expected to mitigate inflammatory responses invoked by Treg loss of function.
Tracking extracellular vesicle (EV) cargo as a platform for studying EVomics, signaling, and targeting in vivo
Authors: Nikonorova Inna A. , Wang Juan , Cope Alexander L. , Tilton Peter , Power Kaiden M. , Walsh Jonathon D. , Akella Jyothi S. , Krauchunas Amber R. , Shah Premal , Barr Maureen M. 
Published: September 2021

AbstractExtracellular vesicle (EV)-based signaling is a challenge to study, due to EV small size, heterogeneity, and limited information on cargo content in vivo. We present Caenorhabditis elegans as a discovery platform that allows single EV tracking from source to target tissue in living animals. We enriched ciliary EVs using GFP-tagged PKD-2 cargo followed by mass spectrometry analysis to identify 2,888 cargo candidates. By integrating our dataset with single-cell transcriptomic data, we identified EV cargo produced by individual neurons and other cell and tissue types. A single cilium produces multiple EVs with distinct protein content. Ciliary EVs carry nucleic acid binding proteins. We observed transfer of EV cargo from the male reproductive tract to the hermaphrodite uterus during mating, a direct demonstration of animal-to-animal EV targeting.One-Sentence SummaryHere we present a discovery platform for studying animal extracellular vesicle composition and biogenesis.
DuoxandJak/Statsignalling influence disease tolerance in Drosophila duringPseudomonas entomophilainfection
Authors: Prakash Arun , Monteith Katy M. , Bonnet Mickael , Vale Pedro F. 
Published: September 2021

AbstractDisease tolerance describes an infected host’s ability to maintain health independently of the ability to clear microbe loads. The Jak/Stat pathway plays a pivotal role in humoral innate immunity by detecting tissue damage and triggering cellular renewal, making it a candidate tolerance mechanism. Here, we find that inDrosophila melanogasterinfected withPseudomonas entomophiladisruptingROS-producingdual oxidase (duox) or the negative regulator of Jak/StatSocs36E, render male flies less tolerant. Another negative regulator of Jak/Stat,G9a- which has previously been associated with variable tolerance of viral infections – did not affect the rate of mortality with increasing microbe loads compared to flies with functionalG9a, suggesting it does not affect tolerance of bacterial infection as in viral infection. Our findings highlight that ROS production and Jak/Stat signalling influence the ability of flies to tolerate bacterial infection sex-specifically and may therefore contribute to sexually dimorphic infection outcomes inDrosophila.
Mice With Monoallelic GNAO1 Loss Exhibit Reduced Inhibitory Synaptic Input To Cerebellar Purkinje Cells
Authors: Feng Huijie , Yuan Yukun , Williams Michael R. , Roy Alex J. , Leipprandt Jeffery , Neubig Richard R. 
Published: September 2021

AbstractGNAO1 encodes Gαo, a heterotrimeric G protein alpha subunit in the Gi/o family. In this report, we used a Gnao1 mouse model “G203R” previously described as a “gain-of-function” Gnao1 mutant with movement abnormalities and enhanced seizure susceptibility. Here, we report an unexpected second mutation resulting in a loss-of-function Gαo protein and describe alterations in central synaptic transmission.Whole cell patch clamp recordings from Purkinje cells (PCs) in acute cerebellar slices from Gnao1 mutant mice showed significantly lower frequencies of spontaneous and miniature inhibitory postsynaptic currents (sIPSCs and mIPSCs) compared to WT mice. There was no significant change in sEPSCs or mEPSCs. Whereas mIPSC frequency was reduced, mIPSC amplitudes were not affected, suggesting a presynaptic mechanism of action. A modest decrease in the number of molecular layer interneurons was insufficient to explain the magnitude of IPSC suppression. Paradoxically, Gi/o inhibitors (pertussis toxin), enhanced the mutant-suppressed mIPSC frequency and eliminated the difference between WT and Gnao1 mice. While GABAB receptor regulates mIPSCs, neither agonists nor antagonists of this receptor altered function in the mutant mouse PCs. This study is the first electrophysiological investigation of the role of Gi/o protein in cerebellar synaptic transmission using an animal model with a loss-of-function Gi/o protein.Significance StatementThis is the first report on the electrophysiological mechanisms of a movement disorder animal model with monoallelic Gnao1 loss. This study illustrates the role of Gαo protein in regulating GABA release in mouse cerebellum. This study could also facilitate the discovery of new drugs or drug repurposing for GNAO1-associated disorders. Moreover, since GNAO1 shares pathways with other genes related to movement disorders, developing drugs for the treatment of GNAO1-associated movement disorders could further the pharmacological intervention for other monogenic movement disorders.
CHEK2 SIGNALING IS THE KEY REGULATOR OF OOCYTE SURVIVAL AFTER CHEMOTHERAPY
Authors: Emori Chihiro , Boucher Zachary , Bolcun-Filas Ewelina 
Published: September 2021

ABSTRACTRadiation and chemotherapy can damage the primordial follicle reserve in female cancer patients leading to ovarian failure and infertility. Preservation of ovarian function requires treatment strategies that prevent loss of immature oocytes in primordial follicles during cancer therapy. Checkpoint kinase 2 (CHEK2) inhibition prevents loss of primordial oocytes caused by DNA damage and thus is a promising target for ovoprotective treatment against genotoxic agents. To determine which cancer treatments could benefit from ovoprotective activity of CHEK2 inhibition we investigated oocyte survival inChek2-/- mice exposed to different chemotherapy drugs. Here, we show that loss of CHEK2 function prevents elimination of primordial oocytes damaged by cisplatin, cyclophosphamide, mafosfamide, doxorubicin, and etoposide, suggesting it could be used to reduce ovarian damage caused by wide range of drugs. Using genetic knockouts we reveal a critical role for TRP53 in oocyte response to chemotherapy drugs and show that both targets of CHEK2—TAp63 and TRP53— are activated by cisplatin and cyclophosphamide. Furthermore, we show that checkpoint kinase inhibitor and radiation- and chemotherapy sensitizer AZD7762 reduces oocyte elimination after radiation and chemotherapy treatments, despite its cytotoxic effect on ovarian somatic cells. Altogether, these findings demonstrate the role for CHEK2 as the master regulator of primordial oocyte survival or death and credential its targeting for ovoprotective treatments.SIGNIFICANCEChemotherapy and radiation are ovotoxic and increase the risk of premature ovarian insufficiency and infertility in women cancer survivors. Development of treatment strategies preserving ovarian function and ensuring future reproductive health of female cancer patients depends on better understanding of the mechanisms underlying ovarian toxicity caused by different chemotherapy treatments. Preservation of long-term ovarian function can only be achieved by preventing the loss of immature oocytes in primordial follicles during toxic cancer therapies. Checkpoint kinase 2 (CHEK2) inhibition is an attractive strategy for protecting ovarian reserve with a potential additional benefit of sensitizing cancer cells to radiation and chemotherapy. Using a genetic approach, we show that blocking CHEK2 function is sufficient to prevent elimination of primordial oocytes damaged by chemotherapy drugs such as cisplatin, cyclophosphamide, mafosfamide, doxorubicin and etoposide. Many chemotherapy drugs are used in combination (e.g. cyclophosphamide with doxorubicin), thus the protective effect of CHEK2 inhibition is likely to be beneficial for a broad spectrum of patient treatments.
Satellite glia are essential modulators of sympathetic neuron survival, activity, and autonomic function
Authors: Mapps Aurelia A. , Boehm Erica , Beier Corrine , Keenan William T. , Langel Jennifer , Liu Michael , Hattar Samer , Zhao Haiqing , Tampakakis Emmanouil , Kuruvilla Rejji 
Published: September 2021

AbstractSatellite glia are the major glial cells in sympathetic ganglia, enveloping neuronal cell bodies. Despite this intimate association, how satellite glia contribute to sympathetic functions remain unclear. Here, we show that satellite glia are critical for metabolism, survival, and activity of sympathetic neurons and modulate autonomic behaviors in mice. Adult ablation of satellite glia results in impaired mTOR signaling, soma atrophy, reduced noradrenergic enzymes, and loss of sympathetic neurons. However, persisting neurons have elevated activity, and satellite glia-ablated mice show increased pupil dilation and heart rate, indicative of enhanced sympathetic tone. Satellite glia-specific deletion of Kir4.1, an inward-rectifying potassium channel, largely recapitulates the cellular defects observed in glia-ablated mice, suggesting that satellite glia act in part via extracellular K+buffering. These findings highlight neuron-satellite glia as functional units in regulating sympathetic output, with implications for disorders linked to sympathetic hyper-activity such as cardiovascular disease and hypertension.
High-throughput functionalization of theToxoplasmakinome uncovers a novel regulator of invasion and egress
Authors: Smith Tyler A. , Lopez-Perez Gabriella S. , Shortt Emily , Lourido Sebastian 
Published: September 2021

ABSTRACTProtein kinases regulate fundamental aspects of cell biology in all eukaryotes, making them attractive chemotherapeutic targets in Apicomplexan parasites such as the causative agents of malaria (Plasmodiumspp.) and toxoplasmosis (Toxoplasma gondii). However, the precise roles of individual parasite kinases cannot be inferred simply from sequence identity, due to rewiring of signaling pathways and the shifting repertoire of kinases across species. To systematically examine the parasite kinome, we developed a high-throughput (HiT) CRISPR-mediated tagging strategy to endogenously label all predicted cytosolic protein kinases with a synthetic sequence encoding the minimal auxin-inducible degron (mAID) linked to a fluorophore and epitope tag. The system enables the assembly of thousands of tagging vectors from synthetic sequences in a single reaction and the pooled generation of mutants to examine kinase localization and function. We examined the phenotypes associated with kinase knock-down in 1,160 arrayed clones by replica-plating in the presence or absence of auxin and found broad defects across the lytic cycle for 109 clonal isolates, assigning localizations to 39 proteins, and associating 15 kinases within 6 distinct morphological phenotypes. The relative fitness of tagged alleles was also examined by tracking the relative abundance of individual guide RNAs as parasite populations progressed through the lytic cycle, in the presence or absence of auxin. Pooled screening had a high predictive value and differentiated between delayed and acute death. Demonstrating the value of this resource, we identified a novel kinase associated with delayed death as a novel regulator of invasion and egress. We call the previously unstudied kinase Store Potentiating/Activating Regulatory Kinase (SPARK), based on its impact on intracellular Ca2+stores at key moments during the lytic cycle. Despite having a similar kinase domain to the mammalian PDK1, SPARK lacks the canonical lipid-binding domain and we find no indication SPARK positively regulates other AGC kinases, suggesting a rewiring of signaling pathways to accommodate parasite adaptations. The HiT vector screening system extends the applications of genome-wide screens into complex cellular phenotypes, providing a scalable and versatile platform for the dissection of apicomplexan cell biology.