bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of machine learning and complex network measures to an EEG dataset from ayahuasca experiments
Authors: Alves Caroline L. , Cury Rubens Gisbert , Roster Kirstin , Pineda Aruane M. , Rodrigues Francisco A. , Thielemann Christiane , Ciba Manuel 
Published: June 2022

Ayahuasca is made from a mixture of Amazonian herbs and has been used for a few hundred years by the people of this region for traditional medicine. In addition, this plant has been shown to be a potential treatment for various neurological and psychiatric disorders.EEG experiments have found specific brain regions that changed significantly due to ayahuasca. Here, we used an EEG dataset to investigate the ability to automatically detect changes in brain activity using machine learning and complex networks. Machine learning was applied at three different levels of data abstraction: (A) the raw EEG time series, (B) the correlation of the EEG time series, and (C) the complex network measures calculated from (B).As a result, the machine learning method was able to automatically detect changes in brain activity, with case (B) showing the highest accuracy (92%), followed by (A) (88%) and (C) (83%), indicating that connectivity changes between brain regions are more important than connectivity changes within brain regions. The most activated areas were the frontal and temporal lobe, which is consistent with the literature.In terms of brain connections, the correlation between F3 and PO4 was the most important. This connection may point to a cognitive process similar to face recognition in individuals during ayahuasca-mediated visual hallucinations.Furthermore, closeness centrality and assortativity were the most important complex network measures. These two measures are also associated with diseases such as Alzheimer’s disease, indicating a possible therapeutic mechanism.Overall, our results showed that machine learning methods were able to automatically detect changes in brain activity during ayahuasca consumption. The results also suggest that the application of machine learning and complex network measurements are useful methods to study the effects of ayahuasca on brain activity and medical use.
Mast cells impair melanoma cell homing and metastasis by inhibiting HMGA1 secretion
Authors: Benito-Martin Alberto , Hergueta-Redondo Marta , Nogués Laura , Castellano-Sanz Elena , Garvin Eduardo , Cioffi Michele , Sola-Castrillo Paloma , Buehring Weston , Ximénez-Embún Pilar , Muñoz Javier , Matei Irina , Villanueva Josep , Peinado Héctor 
Published: June 2022

AbstractMetastatic disease is the major cause of death from cancer. From the primary tumor, cells remotely prepare the environment of the future metastatic sites by secreted factors and extracellular vesicles. During this process, known as pre-metastatic niche formation, immune cells play a crucial role. Mast cells are hematopoietic bone marrow-derived innate immune cells whose function in lung immune response to invading tumors remains to be defined. We found reduced melanoma lung metastasis in mast cell deficient mouse models (Wsh and MCTP5-Cre-RDTR), supporting a pro-metastatic role for mast cells in vivo. However, due to evidence pointing to their antitumorigenic role, we studied the impact of mast cells in melanoma cell function in vitro. Surprisingly, in vitro co-culture of bone-marrow derived mast cells with melanoma cells showed that they have an intrinsic anti-metastatic activity. Mass spectrometry analysis of melanoma-mast cell co-cultures secretome showed that HMGA1 secretion by melanoma cells was significantly impaired. Consistently, HMGA1 knock down in B16-F10 cells reduced their metastatic capacity in vivo. Importantly, analysis of HMGA1 expression in human melanoma tumors showed that metastatic tumors with high HMGA1 expression are associated with reduced overall and disease-free survival. Moreover, we show that HMGA1 is reduced in the nuclei and enriched in the cytoplasm of melanoma metastatic lesions when compared to primary tumors. These data suggest that high HMGA1 expression and secretion from melanoma cells promotes metastatic behavior. Targeting HMGA1 expression intrinsically or extrinsically by mast cells actions reduce melanoma metastasis. Our results pave the way to the use of HMGA1 as anti-metastatic target in melanoma as previously suggested in other cancer types.
The lupus susceptibility alleleDRB1*03:01encodes a disease-driving epitope
Authors: Scavuzzi Bruna Miglioranza , van Drongelen Vincent , Kaur Bhavneet , Fox Jennifer Callahan , Liu Jianhua , Mesquita-Ferrari Raquel A. , Kahlenberg J. Michelle , Farkash Evan A. , Benavides Fernando , Miller Frederick W. , Sawalha Amr H. , Holoshitz Joseph 
Published: June 2022

ABSTRACTTheHLA-DRB1*03:01allele is a major genetic risk factor in systemic lupus erythematosus (SLE), but the mechanistic basis of the association is unclear. Here we show that in the presence of interferon gamma (IFN-γ), a shortDRB1*03:01-encoded allelic epitope activates a characteristic lupus transcriptome in mouse and human macrophages. It also triggers a cascade of SLE-associated cellular aberrations, including endoplasmic reticulum stress, unfolded protein response, mitochondrial dysfunction, necroptotic cell death, and production of pro-inflammatory cytokines. Parenteral administration of IFN-γ to naïveDRB1*03:01transgenic mice causes increased serum levels of anti-double stranded DNA antibodies, glomerular immune complex deposition and histopathological renal changes that resemble human lupus nephritis. This study provides evidence for a noncanonical, antigen presentation-independent mechanism of HLA-disease association in SLE and could lay new foundations for our understanding of key molecular mechanisms that trigger and propagate this devastating autoimmune disease.
A remodeled RNA polymerase II complex catalyzing viroid RNA-templated transcription
Authors: Dissanayaka Mudiyanselage Shachinthaka D. , Ma Junfei , Pechan Tibor , Pechanova Olga , Liu Bin , Wang Ying 
Published: June 2022

AbstractViroids, a group of plant pathogens, are mysterious subviral agents composed of single-stranded circular noncoding RNAs. Nuclear-replicating viroids exploit host RNA polymerase II (Pol II) activity for transcription from circular RNA genome to minus-strand intermediates, a classic example illustrating the intrinsic RNA-dependent RNA polymerase activity of Pol II. The mechanism for Pol II to accept single-stranded RNAs as templates for transcription remains poorly understood. Here, we reconstituted a robust in vitro transcription system and demonstrated that Pol II also accepts the minus-strand viroid RNA template to generate plus-strand RNAs. Based on this reconstituted system, we purified the Pol II complex on RNA templates for nano-liquid chromatography-tandem mass spectrometry analysis. We identified a remodeled Pol II missing Rpb4, Rpb5, Rpb6, Rpb7, and Rpb9, which contrasts to the canonical 12-subunit Pol II or the 10-subunit Pol II core on DNA templates. This remodeled Pol II is active in transcription with the aid of TFIIIA-7ZF. Interestingly, this remodeled Pol II appears not to require other canonical general transcription factors (such as TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and TFIIS), indicating a different mechanism/machinery regulating RNA-templated transcription. Transcription elongation factors, such as FACT complex, PAF1 complex, and SPT6, were also absent in the transcription complex on RNA templates. We further analyzed the critical zinc finger domains in TFIIIA-7ZF for aiding Pol II activity on RNA template and revealed the first three zinc finger domains pivotal for template binding. Collectively, our data illustrated a distinct organization of Pol II complex on viroid RNA templates, providing new insights into the evolution of transcription machinery, the mechanism of RNA-templated transcription, as well as viroid replication.
Nuclear position modulates long-range chromatin interactions
Authors: Finn Elizabeth H. , Misteli Tom 
Published: June 2022

AbstractThe human genome is non-randomly organized within the cell nucleus. Spatial mapping of genome folding by biochemical methods and imaging has revealed extensive variation in locus interaction frequencies between cells in a population and between homologs within an individual cell. Commonly used mapping approaches typically examine either the relative position of genomic sites to each other or the position of individual loci relative to nuclear landmarks. Whether the frequency of specific chromatin-chromatin interactions is affected by where in the nuclear space a locus is located is unknown. Here, we have simultaneously mapped at the single cell level the interaction frequencies and radial position of more than a hundred locus pairs using high-throughput imaging to ask whether the location within the nucleus affects interactions frequency. We find strong enrichment of many interactions at specific radial positions. Position-dependency of interactions was cell-type specific, correlated with local chromatin type, and cell-type-specific enriched associations were marked by increased variability, sometimes without a significant decrease in mean spatial distance. These observations demonstrate that genome organization relative to itself and relative to nuclear landmarks are closely interwoven.Significance StatementA gene’s nuclear environment is defined by its distance to other genes as well as its distance to nuclear structures such as the nuclear periphery. While both of these features have been shown to be important for gene function, they are often studied separately. We performed the first systematic analysis comparing these two features. We determined that at the level of single chromosomes they are correlated, suggesting that genome organization relative to itself and relative to nuclear landmarks are closely interwoven.
Mechanism of PEX5-mediated protein import into peroxisomes
Authors: Skowyra Michael L. , Rapoport Tom A. 
Published: June 2022

SummaryPeroxisomes are ubiquitous organelles, whose dysfunction causes fatal human diseases. Most peroxisomal enzymes are imported from the cytosol by the receptor PEX5, which interacts with a docking complex in the peroxisomal membrane, and then returns to the cytosol after monoubiquitination by a membrane-embedded ubiquitin ligase. The mechanism by which PEX5 shuttles between cytosol and peroxisomes, and releases cargo inside the lumen, is unclear. Here, we use Xenopus egg extract to demonstrate that PEX5 accompanies cargo completely into the lumen, utilizing WxxxF/Y motifs near its N-terminus that bind a lumenal domain of the docking complex. PEX5 recycling is initiated by an amphipathic helix that binds to the lumenal side of the ubiquitin ligase. The N-terminus then emerges in the cytosol for monoubiquitination. Finally, PEX5 is extracted from the lumen, resulting in unfolding of the receptor and cargo release. Our results reveal the unique mechanism by which PEX5 ferries proteins into peroxisomes.
Reconstitution of an N-AChR from Brugia malayi
Authors: Noonan Jennifer D. , Beech Robin N. 
Published: June 2022

AbstractNeurotransmission is an important target for anthelmintic drugs, where receptor characteristics and response can be examined through reconstitution ex vivo in Xenopus laevis oocytes. The homomeric ACR-16 nicotine sensitive acetylcholine receptors (N-AChRs) of several helminth species have been characterized in this way. Our efforts to reconstitute the N-AChR from the clade III filarial parasite, Brugia malayi using similar conditions, initially produced no detectable response. A robust response to acetylcholine is obtained from the closely related clade III parasite Ascaris suum, suggesting that specific changes have occurred between Ascaris and Brugia. N-AChRs from three species intermediate between A. suum and B. malayi were characterized to provide information on the cause. Maximal current to acetylcholine did not change abruptly, consistent with a discrete event, but rather decreased progressively from A. suum through Dracunculus medinensis, Gonglylonema pulchrum and Thelazia callipaeda. Receptor responses to the characteristic nicotine, and other agonists were generally similar. The decrease in maximal current did correlate with a delayed time to maximal response. Together, this suggested that the failure to reconstitute the B. malayi N-AChR was one extreme of a progressive decrease and that synthesis of the receptor in oocytes was responsible. Addition of accessory proteins EMC-6, NRA-2 and NRA-4, in addition to RIC-3, produced a small, but measurable B. malayi N-AChR response. Pharmacological properties of a chimeric B. malayi N-AChR were equivalent to the other species, confirming the receptor response remains unchanged while its production is increasingly dependent on accessory proteins. One possibility is that loss of many subunits for acetylcholine receptors from the filarial nematode genome is linked to such a dependence. This novel phylogenetic approach allowed the first characterization of a B. malayi AChR ex vivo and in doing so, provides a framework for the successful characterization of other receptors that have yet to be reconstituted.
Opto-MASS: a high-throughput engineering platform for genetically encoded fluorescent sensors enabling all-optical in vivo detection of monoamines and opioids
Authors: Rappleye Michael , Gordon-Fennel Adam , Castro Daniel C. , Matarasso Avi K. , Zamorano Catalina A. , Stine Carrie , Wait Sarah J. , Lee Justin D. , Siebart Jamison C. , Suko Azra , Smith Netta , Muster Jeanot , Matreyek Kenneth A , Fowler Douglas M. , Stuber Garrett D. , Bruchas Michael R. , Berndt Andre 
Published: June 2022

AbstractFluorescent sensor proteins are instrumental for detecting biological signals in vivo with high temporal accuracy and cell-type specificity. However, engineering sensors with physiological ligand sensitivity and selectivity is difficult because they need to be optimized through individual mutagenesis in vitro to assess their performance. The vast mutational landscape proteins constitute an obstacle that slows down sensor development. This is particularly true for sensors that require mammalian host systems to be screened. Here, we developed a novel high-throughput engineering platform that functionally tests thousands of variants simultaneously in mammalian cells and thus allows the screening of large variant numbers. We showcase the capabilities of our platform, called Optogenetic Microwell Array Screening System (Opto-MASS), by engineering novel monoamine and neuropeptide in vivo capable sensors with distinct physiological roles at high-throughput.
SUBATOMIC: a SUbgraph BAsed mulTi-OMIcs Clustering framework to analyze integrated multi-edge networks
Authors: Loers Jens Uwe , Vermeirssen Vanessa 
Published: June 2022

AbstractRepresenting the complex interplay between different types of biomolecules across different omics layers in multi-omics networks bears great potential to gain a deep mechanistic understanding of gene regulation and disease. However, multi-omics networks easily grow into giant hairball structures that hamper biological interpretation. Module detection methods can decompose these networks into smaller interpretable modules. However, these methods are not adapted to deal with multi-omics data nor consider topological features. When deriving very large modules or ignoring the broader network context, interpretability remains limited. To address these issues, we developed a subgraph based multi-omics clustering framework (SUBATOMIC), which infers small and interpretable modules with a specific topology while keeping track of connections to other modules and regulators.SUBATOMIC groups specific molecular interactions in composite network subgraphs of two and three nodes and clusters them into topological modules. These are functionally annotated, visualized and overlaid with expression profiles to go from static to dynamic modules. To preserve the larger network context, SUBATOMIC investigates statistically the connections in between modules as well as between modules and regulators such as miRNAs and transcription factors. We applied SUBATOMIC to analyze a composite Homo sapiens network containing transcription factor-target gene, miRNA-target gene, protein-protein, homologous and co-functional interactions from different databases. We derived and annotated 5586 modules with diverse topological, functional and regulatory properties. We created novel functional hypotheses for unannotated genes. Furthermore, we integrated modules with condition specific expression data to study the influence of hypoxia in three cancer cell lines. We developed two prioritization strategies to identify the most relevant modules in specific biological contexts: one considering GO term enrichments and one calculating an activity score reflecting the degree of differential expression. Both strategies yielded modules specifically reacting to low oxygen levels.In conclusion, we developed the SUBATOMIC framework that generates interpretable modules from multi-omics networks and applied it to hypoxia in cancer. SUBATOMIC can infer and contextualize modules, explore condition or disease specific modules, identify regulators and functionally related modules, and derive novel gene functions for uncharacterized genes. The software is available at https://github.com/CBIGR/SUBATOMIC.
Large-scale brain correlates of sweet versus cocaine reward in rats
Authors: Lenoir Magalie , Navailles Sylvia , Vandaele Youna , Vouillac-Mendoza Caroline , Guillem Karine , Ahmed Serge H. 
Published: June 2022

AbstractCocaine induces many supranormal changes in neuronal activity in the brain, notably in learning- and reward-related regions, in comparison to nondrug rewards - a difference that is thought to contribute to its relatively high addictive potential. However, when facing a choice between cocaine and a nondrug reward (e.g., water sweetened with saccharin), most rats do not choose cocaine, as one would expect from the extent and magnitude of its global activation of the brain, but instead choose the nondrug option. We recently showed that cocaine, though larger in magnitude, is also an inherently more delayed reward than sweet water, thereby explaining why it has less value during choice and why rats opt for the more immediate nondrug option. Here we used a large-scale fos brain mapping approach to measure brain responses to each option in saccharin-preferring rats, with the hope to identify brain regions whose activity may explain the preference for the nondrug option. In total, fos expression was measured in 142 brain levels corresponding to 52 brain subregions and composing 5 brain macrosystems. Overall, our findings confirm in rats with a preference for saccharin that cocaine induces more global brain activation than the preferred nondrug option does. Only very few brain regions were uniquely activated by saccharin. They included regions involved in taste processing (i.e., anterior gustatory cortex) and also regions involved in processing reward delay and intertemporal choice (i.e., some components of the septohippocampal system and its connections with the lateral habenula).
Conditional termination of transcription is shaped by Rho and translated uORFS inMycobacterium tuberculosis
Authors: D’Halluin Alexandre , Polgar Peter , Kipkorir Terry , Patel Zaynah , Cortes Teresa , Arnvig Kristine B. 
Published: June 2022

SUMMARYLittle is known about the decisions behind transcription elongationversustermination in the human pathogenMycobacterium tuberculosis. By applying Term-seq toM. tuberculosiswe found that the majority of transcription termination is premature and associated with translated regions, i.e. within previously annotated or newly identified open reading frames. Computational predictions and Term-seq analysis upon depletion of termination factor Rho suggests that Rho-dependent transcription termination dominates all TTS including those associated with regulatory 5’ leaders. Moreover, our results suggest that tightly coupled translation, in the form of overlapping stop and start codons, may suppress Rho-dependent termination. This study provides detailed insights into novelM. tuberculosis cis-regulatory elements, where Rho-dependent, conditional termination of transcription and translational coupling together play major roles in gene expression control. Our findings contribute to a deeper understanding of the fundamental regulatory mechanisms that enableM. tuberculosisadaptation to the host environment offering novel potential points of intervention.
ssDNA is not superior to dsDNA as long HDR donors for CRISPR-mediated endogenous gene tagging in human diploid cells
Authors: Mabuchi Akira , Hata Shoji , Genova Mariya , Tei Chiharu , Ito Kei K , Hirota Masayasu , Komori Takuma , Fukuyama Masamitsu , Chinen Takumi , Toyoda Atsushi , Kitagawa Daiju 
Published: June 2022

AbstractRecent advances in CRISPR technology have enabled us to perform gene knock-in in various species and cell lines. CRISPR-mediated knock-in requires donor DNA which serves as a template for homology-directed repair (HDR). For knock-in of short sequences or base substitutions, ssDNA donors are frequently used among various other forms of HDR donors, such as linear dsDNA. However, for insertion of long transgenes such as fluorescent reporters in human cells, the optimal type of HDR donors remains unclear. In this study, we established a simple and efficient CRISPR-mediated knock-in method for long transgenes using linear dsDNA and ssDNA donors, and systematically compared the performance of these two donors for endogenous gene tagging in human non-transformed diploid cells. Quantification using flow cytometry revealed higher efficiency of fluorescent tagging with dsDNA donors than with ssDNA. By analyzing knock-in outcomes using long-read amplicon sequencing and a classification framework, a variety of mis-integration events were detected regardless of the donor type. Importantly, the ratio of precise insertion was higher with dsDNA donors than with ssDNA. Moreover, in off-target integration analyses, dsDNA and ssDNA were comparably prone to non-homologous integration. These results indicate that ssDNA is not superior to dsDNA as long HDR donors for gene knock-in in human cells.
Color Constant Representations in Early Visual Cortex
Authors: Albers Anke Marit , Baumgartner Elisabeth , Gegenfurtner Karl R. 
Published: June 2022

AbstractThe light entering our eyes is the product of the illumination and the surface reflectance of an object. Although this light changes considerably when the illumination changes, we are usually able to perceive objects as stable in color. To investigate how the brain achieves color constancy, we measured BOLD fMRI while 19 participants either observed patches of light that appear colored (yellow, blue) under a spectrally neutral illuminant, or spectrally neutral gray patches that appear colored under simulated blue and yellow illumination conditions. Under bluish illumination, the neutral gray patches appeared yellow; under yellowish illumination, the same gray patches appeared blue. We successfully trained a classifier to discriminate between the blue- and yellow-colored patches in V1-V4. Crucially, we then tested whether this same classifier could also distinguish between the apparent blue and yellow induced by the illuminants. The neural representations for apparent blue and yellow resembled colorimetric blue and yellow in V1, V3 and V4. A control experiment showed that apparent lightness cannot explain these effects. These findings suggest that not only colorimetric, but also apparent color is represented to some degree in retinotopic visual cortex, as early as in V1. Furthermore, a small frontal region, the Rolandic operculum, showed activation for apparent color, possibly playing a role in color constancy.