bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating the Contribution of White Matter Hyperintensities and Cortical Thickness to Empathy in Neurodegenerative and Cerebrovascular Diseases
Authors: Ozzoude Miracle , Varriano Brenda , Beaton Derek , Ramirez Joel , Holmes Melissa F. , Scott Christopher J.M. , Gao Fuqiang , Sunderland Kelly M. , McLaughlin Paula , Rabin Jennifer , Goubran Maged , Kwan Donna , Roberts Angela , Bartha Robert , Symons Sean , Tan Brian , Swartz Richard H. , Abrahao Agessandro , Saposnik Gustavo , Masellis Mario , Lang Anthony E. , Marras Connie , Zinman Lorne , Shoesmith Christen , Borrie Michael , Fischer Corinne E. , Frank Andrew , Freedman Morris , Montero-Odasso Manuel , Kumar Sanjeev , Pasternak Stephen , Strother Stephen C. , Pollock Bruce G. , Rajji Tarek K. , Seitz Dallas , Tang-Wai David F. , Chum Marvin , Turnbull John , Dowlatshahi Dar , Hassan Ayman , Casaubon Leanne , Mandzia Jennifer , Sahlas Demetrios , Breen David P. , Grimes David , Jog Mandar , Steeves Thomas D.L. , Arnott Stephen R. , Black Sandra E. , Finger Elizabeth , Tartaglia Maria Carmela 
Published: August 2021

AbstractIntroduction: Change in empathy is an increasingly recognised symptom of neurodegenerative diseases and contributes to caregiver burden and patient distress. Empathy impairment has been associated with brain atrophy but its relationship to white matter hyperintensities (WMH) is unknown. We aimed to investigate the relationships amongst WMH, brain atrophy, and empathy deficits in neurodegenerative and cerebrovascular diseases.Methods: 513 participants with Alzheimer’s Disease/Mild Cognitive Impairment, Amyotrophic Lateral Sclerosis, Frontotemporal Dementia (FTD), Parkinson’s Disease, or Cerebrovascular Disease (CVD) were included. Empathy was assessed using the Interpersonal Reactivity Index. WMH were measured using a semi-automatic segmentation and FreeSurfer was used to measure cortical thickness.Results: A heterogeneous pattern of cortical thinning was found between groups, with FTD showing thinning in frontotemporal regions and CVD in left superior parietal, left insula, and left postcentral. Results from both univariate and multivariate analyses revealed that several variables were associated with empathy, particularly cortical thickness in the fronto-insulo-temporal and cingulate regions, sex(female), global cognition, and right parietal and occipital WMH.Conclusions: Our results suggest that cortical atrophy and WMH may be associated with empathy deficits in neurodegenerative and cerebrovascular diseases. Future work should consider investigating the longitudinal effects of WMH and atrophy on empathy deficits in neurodegenerative and cerebrovascular diseases.
Genome-wide DNA methylation and multi-omics study of human chondrocyte ontogeny and an epigenetic clock analysis of adult chondrocytes
Authors: Sarkar Arijita , Lee Siyoung , Shkhyan Ruzanna , Liu Nancy Q. , Handel Ben Van , Magallanes Jenny , Lee Youngjoo , Tao Litao , Segil Neil , Ernst Jason , Horvath Steve , Evseenko Denis 
Published: August 2021

AbstractArticular chondrocytes undergo functional changes and their regenerative potential declines with age. Although the molecular mechanisms guiding articular cartilage aging is poorly understood, DNA methylation is known to play a mechanistic role in aging. However, our understanding of DNA methylation in chondrocyte development across human ontogeny is limited. To better understand DNA methylome changes, methylation profiling was performed in human chondrocytes. This study reveals association between methylation of specific CpG sites and chondrocyte age. We also determined the putative binding targets of STAT3, a key age-patterned transcription factor in fetal chondrocytes and genetic ablation of STAT3 induced a global genomic hypermethylation. Moreover, an epigenetic clock built for adult human chondrocytes revealed that exposure of aged adult human chondrocytes to STAT3 agonist, decreased epigenetic age. Taken together, this work will serve as a foundation to understand development and aging of chondrocytes with a new perspective for development of rejuvenation agents for synovial joints.
Computational analysis of B cell receptor repertoires in COVID-19 patients using deep embedded representations of protein sequences
Authors: Kim Inyoung , Byun Sang Yoon , Kim Sangyeup , Choi Sangyoon , Noh Jinsung , Chung Junho , Kim Byung Gee 
Published: August 2021

AbstractAnalyzing B cell receptor (BCR) repertoires is immensely useful in evaluating one’s immunological status. Conventionally, repertoire analysis methods have focused on comprehensive assessments of clonal compositions, including V(D)J segment usage, nucleotide insertions/deletions, and amino acid distributions. Here, we introduce a novel computational approach that applies deep-learning-based protein embedding techniques to analyze BCR repertoires. By selecting the most frequently occurring BCR sequences in a given repertoire and computing the sum of the vector representations of these sequences, we represent an entire repertoire as a 100-dimensional vector and eventually as a single data point in vector space. We demonstrate that this new approach enables us to not only accurately cluster BCR repertoires of coronavirus disease 2019 (COVID-19) patients and healthy subjects but also efficiently track minute changes in immune status over time as patients undergo treatment. Furthermore, using the distributed representations, we successfully trained an XGBoost classification model that achieved a mean accuracy rate of over 87% given a repertoire of CDR3 sequences.
Functional characterization of two variants in the mitochondrial topoisomerase gene TOP1MT that impact regulation of the mitochondrial genome
Authors: Khatib Iman Al , Deng Jingti , Symes Andrew , Kerr Marina , Zhang Hongliang , Huang Sharyin , Pommier Yves , Khan Aneal , Shutt Timothy E 
Published: August 2021

AbstractTOP1MT encodes a mitochondrial topoisomerase that is important for mtDNA regulation, and that is involved in mitochondrial replication, transcription and translation. Two variants predicted to affect TOP1MT function (V1 - R198C and V2 - V338L) were identified by exome sequencing of a newborn with hypertrophic cardiomyopathy. As no pathogenic TOP1MT variants had been confirmed previously, we characterized these variants for their ability to rescue several TOP1MT functions in knockout cells. Consistent with these TOP1MT variants contributing to the patient phenotype, comprehensive characterization suggests that both variants had impaired activity. Critically, neither variant was able to restore steady state levels of mitochondrial-encoded proteins, nor reduced oxidative phosphorylation when re-expressed in TOP1MT knockout cells. However, the two variants behaved differently in some respects. While the V1 variant was better at restoring transcript levels, the V2 variant was able to restore mtDNA copy number and replication. These findings suggest that the different TOP1MT variants affect distinct TOP1MT functions. Altogether, these findings begin to provide insight into the many roles that TOP1MT plays in the maintenance and expression of the mitochondrial genome, and how impairments in this important protein may lead to human pathology.
Genomic remnants of ancestral hydrogen and methane metabolism in Archaea drive anaerobic carbon cycling
Authors: Adam Panagiotis S. , Kolyfetis George E. , Bornemann Till L.V. , Vorgias Constantinos E. , Probst Alexander J. 
Published: August 2021

AbstractMethane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Other than its two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), there exist other genes called “methanogenesis markers” that are believed to participate in methane metabolism. Many of them are Domains of Unknown Function. Here we show that these markers emerged together with methanogenesis. Even if Mcr is lost, the markers and Mtr can persist resulting in intermediate metabolic states related to the Wood-Ljungdahl pathway. Beyond the markers, the methanogenic ancestor was hydrogenotrophic, employing the anaplerotic hydrogenases Eha and Ehb. The selective pressures acting on Eha, Ehb, and Mtr partially depend on their subunits’ membrane association. Integrating the evolution of all these components, we propose that the ancestor of all methane metabolizers was an autotrophic H2/CO2 methanogen that could perhaps use methanol but not oxidize alkanes. Hydrogen-dependent methylotrophic methanogenesis has since emerged multiple times independently, both alongside a vertically inherited Mcr or from a patchwork of ancient transfers. Through their methanogenesis genomic remnants, Thorarchaeota and two newly reconstructed order-level lineages in Archaeoglobi and Bathyarchaeota act as metabolically versatile players in carbon cycling of anoxic environments across the globe.
Gene-dependent yeast cell death pathway requires AP-3 vesicle trafficking leading to vacuole membrane permeabilization
Authors: Stolp Zachary D. , Kulkarni Madhura , Liu Yining , Zhu Chengzhang , Jalisi Alizay , Lin Si , Casadevall Arturo , Cunningham Kyle W. , Pineda Fernando J. , Teng Xinchen , Hardwick J. Marie 
Published: August 2021

AbstractUnicellular eukaryotes are suggested to undergo self-inflicted destruction. However, molecular details are sparse by comparison to the mechanisms of cell death known for human cells and animal models. Here we report a molecular pathway inSaccharomyces cerevisiaeleading to vacuole/lysosome membrane permeabilization and cell death. Following exposure to heat-ramp conditions, a model of environmental stress, we observed that yeast cell death occurs over several hours, suggesting an ongoing molecular dying process. A genome-wide screen for death-promoting factors identified all subunits of the AP-3 adaptor complex. AP-3 promotes stress-induced cell death through its Arf1-GTPase-dependent vesicle trafficking function, which is required to transport and install proteins on the vacuole/lysosome membrane, including a death-promoting protein kinase Yck3. Time-lapse microscopy revealed a sequence of events where AP-3-dependent vacuole permeability occurs hours before the loss of plasma membrane integrity. An AP-3-dependent cell death pathway appears to be conserved in the human pathogenCryptococcus neoformans.
CRISPR/Cas9 screen for genome-wide interrogation of essential MYC binding sites in cancer cells
Authors: Kazimierska Marta , Podralska Marta , Żurawek Magdalena , Woźniak Tomasz , Kasprzyk Marta Elżbieta , Sura Weronika , Łosiewski Wojciech , Ziółkowska-Suchanek Iwona , Kluiver Joost , van den Berg Anke , Rozwadowska Natalia , Dzikiewicz-Krawczyk Agnieszka 
Published: August 2021

ABSTRACTThe transcription factor MYC is a proto-oncogene with a well-documented essential role in the pathogenesis and maintenance of several types of cancer. MYC binds to specific E-box sequences in the genome to regulate gene expression in a cell type- and developmental stage-specific manner. To date, a comprehensive analysis of direct MYC targets with essential roles in different types of cancer is missing. To enable identification of functional MYC binding sites and corresponding target genes, we designed a CRISPR/Cas9 library to destroy E-box sequences in a genome-wide fashion. In parallel, we used the Brunello library to knockout protein-coding genes. We performed high-throughput screens with these libraries in four MYC-dependent cancer cell lines: K562, ST486, HepG2 and MCF7, which revealed several essential E-boxes and genes. Among them we pinpointed crucial known and novel MYC-regulated genes involved in pathways associated with cancer development. Extensive validation of our approach in K562 cells confirmed that E-box disruption affects MYC binding, target genes expression and cell proliferation. Our unique, well-validated tool opens new possibilities to gain novel insights into MYC-dependent vulnerabilities in cancer cells.
Dissecting the import and export pathways of the human RNA helicase UPF1
Authors: Eberle Andrea B. , Schranz Karin , Nasif Sofia , Grollmus Lena , Mühlemann Oliver 
Published: August 2021

AbstractThe RNA helicase UPF1 is best known for its key role in mRNA surveillance but has been implicated in additional cellular processes both in the nucleus and in the cytoplasm. In human cells, the vast majority of UPF1 resides in the cytoplasm and only small amounts can be detected in the nucleus at steady state. It was previously shown that its export from the nucleus to the cytoplasm is Crm1-dependent, yet neither the nuclear export signal (NES) nor the nuclear localization signal (NLS) has been identified. Here, we provide evidence for a noncanonical NLS in UPF1, map the NES to amino acids 89-105 and show that L103 and F105 are essential for UPF1’s export to the cytoplasm. Examination of additional UPF1 mutants revealed that a functional helicase domain but not the association with RNA is crucial for the shuttling capacity of UPF1.
Concentration of intraflagellar transport proteins at the ciliary base is required for proper train injection
Authors: Jung Jamin , Santi-Rocca Julien , Fort Cécile , Tinevez Jean-Yves , Schietroma Cataldo , Bastin Philippe 
Published: August 2021

AbstractConstruction of cilia and flagella relies on Intraflagellar Transport (IFT). Although IFT proteins can be found in multiple locations in the cell, transport has only been reported along the axoneme. Here, we reveal that IFT concentration at the base of the flagellum of Trypanosoma brucei is required for proper assembly of IFT trains. Using live cell imaging at high resolution and direct optical nanoscopy with axially localized detection (DONALD) of fixed trypanosomes, we demonstrate that IFT proteins are localised around the 9 doublet microtubules of the proximal portion of the transition zone, just on top of the transition fibres. Super-resolution microscopy and photobleaching studies reveal that knockdown of the RP2 transition fibre protein results in reduced IFT protein concentration and turnover at the base of the flagellum. This in turn is accompanied by a 4- to 8-fold drop in the frequency of IFT train injection. We propose that the flagellum base provides a unique environment to assemble IFT trains.
Rapid Directed Molecular Evolution of Fluorescent Proteins in Mammalian Cells
Authors: Babakhanova Siranush , Jung Erica E. , Namikawa Kazuhiko , Zhang Hanbin , Wang Yangdong , Subach Oksana M. , Korzhenevskiy Dmitry A. , Rakitina Tatiana V. , Xiao Xian , Wang Wenjing , Shi Jing , Drobizhev Mikhail , Park Demian , Eisenhard Lea , Tang Hongyun , Köster Reinhard W. , Subach Fedor V. , Boyden Edward S. , Piatkevich Kiryl D. 
Published: August 2021

AbstractIn vivoimaging of model organisms is heavily reliant on fluorescent proteins with high intracellular brightness. Here we describe a practical method for rapid optimization of fluorescent proteins via directed molecular evolution in cultured mammalian cells. Using this method, we were able to perform screening of large gene libraries containing up to 2·107independent random genes of fluorescent proteins expressed in HEK cells completing one iteration directed evolution in a course of ∼8 days. We employed this approach to develop a set of green and near-infrared fluorescent proteins with enhanced intracellular brightness. The developed near-infrared fluorescent proteins demonstrated high performance for fluorescent labeling of neurons in culture andin vivoin model organisms such asC.elegans,Drosophila, zebrafish, and mice. Spectral properties of the optimized near-infrared fluorescent proteins enabled crosstalk-free multicolor imaging in combination with common green and red fluorescent proteins, as well as dual-color near-infrared fluorescence imaging. The described method has a great potential to be adopted by protein engineers due to its simplicity and practicality. We also believe that the new enhanced fluorescent proteins will find wide application forin vivomulticolor imaging of small model organisms.
Iron-loaded deferiprone can support full hemoglobinization of cultured red blood cells in the absence of transferrin
Authors: Gallego-Murillo Joan Sebastián , Yağcı Nurcan , Pinho Eduardo Machado , Abeijón-Valle Adrián , Wahl Aljoscha , van den Akker Emile , von Lindern Marieke 
Published: August 2021

AbstractIron is an essential nutrient in mammalian cell cultures, conventionally supplemented as iron-loaded transferrin (holotransferrin). The high cost of human transferrin represents a challenge for the large scale production of cell therapies, such as cultured red blood cells. We evaluated the use of deferiprone, a cell membrane-permeable drug for iron chelation therapy, as an iron carrier for erythroid cultures. Iron-loaded deferiprone (Def3·Fe3+) at a concentration of 52μmol/L could fully replace holotransferrin during erythroblast differentiation into reticulocytes, the erythroid differentiation stage with maximal iron requirements. Reticulocytes cultured in presence of Def3·Fe3+ or holotransferrin (1000μg/mL) were similar with respect to expression of cell-surface markers CD235a and CD49d, hemoglobin content, and oxygen association/dissociation. Def3·Fe3+ also supported expansion of the erythroid compartment in vitro, except for the first stage when hematopoietic stem cells committed to erythroblasts, in which a reduced erythroblasts yield was observed. This suggests that erythroblasts acquired the potential to process Def3·Fe3+ as iron source for biosynthesis pathways. Replacement of holotransferrin by Def3·Fe3+ was also successful in cultures of six myeloid cell lines (MOLM13, NB4, EOL1, K562, HL60, ML2). These results suggest that iron-loaded deferiprone can partially replace holotransferrin in chemically defined medium formulations for the production of cultured reticulocytes and proliferation of selected myeloid cell lines. This would lead to a significant decrease in medium cost that would improve the economic perspectives of the large scale production of red blood cells for transfusion purposes.Key pointsHolotransferrin limitations in erythroid cultures lead to lower erythroblast yields, impaired maturation and low enucleation efficiencies.Iron-loaded deferiprone can replace holotransferrin in erythroblast expansion and differentiation cultures.
Arabidopsis Mediator subunit 17 connects transcription with DNA repair after UV-B exposure
Authors: Giustozzi Marisol , Freytes Santiago Nicolás , Jaskolowski Aime , Lichy Micaela , Mateos Julieta , Ferreyra Maria Lorena Falcone , Rosano Germán L. , Cerdán Pablo , Casati Paula 
Published: August 2021

AbstractMediator 17 (MED17) is a subunit of the Mediator complex that regulates transcription initiation in eukaryotic organisms. In yeast and humans, MED17 also participates in DNA repair, physically interacting with proteins of the Nucleotide Excision DNA Repair system. We here analyzed the role of MED17 in Arabidopsis plants exposed to UV-B radiation, which role has not been previously described. Comparison of med17 mutant transcriptome to that of WT plants showed that almost one third of transcripts with altered expression in med17 plants are also changed by UV-B exposure in WT plants. To validate the role of MED17 in UV-B irradiated plants, plant responses to UV-B were analyzed, including flowering time, DNA damage accumulation and programmed cell death in the meristematic cells of the root tips. Our results show that med17 and OE MED17 plants have altered responses to UV-B; and that MED17 participates in various aspects of the DNA damage response (DDR). Increased sensitivity to DDR after UV-B in med17 plants can be due to altered regulation of UV-B responsive transcripts; but additionally MED17 physically interacts with DNA repair proteins, suggesting a direct role of this Mediator subunit during repair. Finally, we here also show that MED17 is necessary to regulate the DDR activated by ATR, and that PDCD5 overexpression reverts the deficiencies in DDR shown in med17 mutants. Together, the data presented demonstrates that MED17 is an important regulator of the DDR after UV-B radiation in Arabidopsis plants.One sentence summaryIn Arabidopsis, MED17 regulates the DNA damage response after UV-B exposure transcriptionally modulating the expression of genes and possibly also physically interacting with DNA repair proteins.
Small molecule photocatalysis enables drug target identification via energy transfer
Authors: Trowbridge Aaron D. , Seath Ciaran P. , Rodriguez-Rivera Frances P. , Li Beryl X. , Dul Barbara E. , Schwaid Adam G. , Geri Jacob B. , Oakley James V. , Fadeyi Olugbeminiyi O. , Oslund Rob C. , Ryu Keun Ah , White Cory , Reyes-Robles Tamara , Tawa Paul , Parker Dann L. , MacMillan David W. C. 
Published: August 2021

AbstractThe identification of cellular targets that can be exploited for therapeutic benefit, broadly known as target ID, remains a fundamental goal in drug discovery. In recent years, the application of new chemical and biological technologies that accelerate target ID has become commonplace within drug discovery programs, as a complete understanding of how molecules react in a cellular environment can lead to increased binding selectivity, improved safety profiles, and clinical efficacy. Established approaches using photoaffinity labelling (PAL) are often costly and time-consuming due to poor signal-to-noise coupled with extensive probe optimization. Such challenges are exacerbated when dealing with low abundance membrane proteins or multiple protein target engagement, typically rendering target ID unfeasible. Herein, we describe a general platform for photocatalytic small molecule target ID, which hinges upon the generation of high-energy carbene intermediates via visible light-mediated Dexter energy transfer. By decoupling the reactive warhead from the drug, catalytic signal amplification results in multiple labelling events per drug, leading to unprecedented levels of target enrichment. Through the development of cell permeable photo-catalyst conjugates, this method has enabled the quantitative target and off target identification of several drugs including (+)-JQ1, paclitaxel, and dasatinib. Moreover, this methodology has led to the target ID of two GPCRs – ADORA2A and GPR40 – a class of drug target seldom successfully uncovered in small molecule PAL campaigns.