bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA transcripts suppress G-quadruplex structures through G-loop formation
Authors: Sato Koichi , Hendrikx Aiko G.M. , Knipscheer Puck 
Published: March 2023

AbstractThe eukaryotic genome contains numerous guanine-rich sequences that regulate DNA replication and transcription by folding into non-canonical structures called G-quadruplexes (G4s)1. Compromised G4 resolution causes genomic instability and diseases linked to cancer susceptibility and aging2. However, how G4s are resolved is poorly understood. G4 structures are found in genomic regions containing DNA:RNA hybrids, also referred to as R-loops3, 4. When an R-loop and G4 structure form exactly opposite to each other, a G-loop structure is formed. G-loops have been observed directly in prokaryotes5but their function is unknown. Using theXenopusegg extract system, we show that G-loop structures act in suppressing mutagenic G4 structures thereby preventing genomic instability. Mechanistically, the RAD51 recombinase binds to the G4-opposing strand and promotes hybridization of RNA transcripts supplied by the hnRNPA1 ribonucleoprotein complex independently of ongoing transcription. The resulting G-loop then induces FANCI-FANCD2 monoubiquitination that triggers site-specific incision of the hybrid strand by the SLX4-XPF-ERCC1 complex. G-loop incision requires prior G4 unwinding by the DHX36 and FANCJ helicases and allows immediate DNA synthesis past the G4 motif. This resynthesis step impacts local chromatin states. This work establishes a G-loop-dependent mechanism that prevents mutagenic consequences of both G4 and R-loop structures.
Individual similarities and differences in eye-movement-related eardrum oscillations (EMREOs)
Authors: King Cynthia D , Lovich Stephanie N , Murphy David LK , Landrum Rachel , Kaylie David , Shera Christopher A , Groh Jennifer M 
Published: March 2023

AbstractWe recently discovered a unique type of low-frequency otoacoustic emission (OAE) time-locked to the onset (and offset) of saccadic eye movements and occurring in the absence of external sound (Gruters et al., 2018). How and why these eye-movement-related eardrum oscillations (EMREOs) are generated is unknown, with a role in visual-auditory integration being the likeliest candidate. Clues to both the drivers of EMREOs and their purpose can be gleaned by examining responses in normal hearing human subjects. Do EMREOs occur in all individuals with normal hearing? If so, what components of the response occur most consistently? Understanding which attributes of EMREOs are similar across participants and which show more variability will provide the groundwork for future comparisons with individuals with hearing abnormalities affecting the ear’s various motor components. Here we report that in subjects with normal hearing thresholds and normal middle ear function, all ears show (a) measurable EMREOs (mean: 58.7 dB SPL; range 45-67 dB SPL for large contralateral saccades), (b) a phase reversal for contra-versus ipsilaterally-directed saccades, (c) a large peak in the signal occurring soon after saccade onset, (d) an additional large peak time-locked to saccade offset and (e) evidence that saccade duration is encoded in the signal. We interpret the attributes of EMREOs that are most consistent across subjects as the ones that are most likely to play an essential role in their function. The individual differences likely reflect normal variation in individuals’ auditory system anatomy and physiology, much like traditional measures of auditory function such as auditory-evoked OAEs, tympanometry and auditory-evoked potentials. Future work will compare subjects with different types of auditory dysfunction to population data from normal hearing subjects. Overall, these findings provide important context for the widespread observations of visual-and eye-movement related signals found in cortical and subcortical auditory areas of the brain.
Diverse mutant selection windows shape spatial heterogeneity in evolving populations
Authors: King Eshan S. , Pierce Beck , Hinczewski Michael , Scott Jacob G. 
Published: March 2023

ABSTRACTMutant selection windows (MSWs), the range of drug concentrations that select for drug-resistant mutants, have long been used as a model for predicting drug resistance and designing optimal dosing strategies in infectious disease. The canonical MSW model offers comparisons between two subtypes at a time: drug-sensitive and drug-resistant. In contrast, the fitness landscape model withNalleles, which maps genotype to fitness, allows comparisons betweenNgenotypes simultaneously, but does not encode continuous drug response data. In clinical settings, there may be a wide range of drug concentrations selecting for a variety of genotypes. Therefore, there is a need for a more robust model of the pathogen response to therapy to predict resistance and design new therapeutic approaches. Fitness seascapes, which model genotype-by-environment interactions, permit multiple MSW comparisons simultaneously by encoding genotype-specific dose-response data. By comparing dose-response curves, one can visualize the range of drug concentrations where one genotype is selected over another. In this work, we show howN-allele fitness seascapes allow forN ∗2N−1unique MSW comparisons. In spatial drug diffusion models, we demonstrate how fitness seascapes reveal spatially heterogeneous MSWs, extending the MSW model to more accurately reflect the selection fo drug resistant genotypes. Furthermore, we find that the spatial structure of MSWs shapes the evolution of drug resistance in an agent-based model. Our work highlights the importance and utility of considering dose-dependent fitness seascapes in evolutionary medicine.Author SummaryDrug resistance in infectious disease and cancer is a major driver of mortality. While undergoing treatment, the population of cells in a tumor or infection may evolve the ability to grow despite the use of previously effective drugs. Researchers hypothesize that the spatial organization of these disease populations may contribute to drug resistance. In this work, we analyze how spatial gradients of drug concentration impact the evolution of drug resistance. We consider a decades-old model called the mutant selection window (MSW), which describes the drug concentration range that selects for drug-resistant cells. We show how extending this model with continuous dose-response data, which describes how different types of cells respond to drug, improves the ability of MSWs to predict evolution. This work helps us understand how the spatial organization of cells, such as the organization of blood vessels within a tumor, may promote drug resistance. In the future, we may use these methods to optimize drug dosing to prevent resistance or leverage known vulnerabilities of drug-resistant cells.
Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an Integer Programming framework
Authors: Loyer Gabriel , Reinharz Vladimir 
Published: March 2023

AbstractMotivationThe prediction of RNA structure canonical base pairs from a single sequence, especially pseudoknotted ones, remains challenging in a thermodynamic models that approximates the energy of the local 3D motifs joining canonical stems. It has become more and more apparent in recent years that the structural motifs in the loops, composed of non-canonical interactions, are essential for the final shape of the molecule enabling its multiple functions. Our capacity to predict accurate 3D structures is also limited when it comes to the organization of the large intricate network of interactions that form inside those loops.ResultsWe previously developed the integer programming framework RNAMoIP (RNA Motifs over Integer Programming) to reconcile RNA secondary structure and local 3D motif information available in databases. We further develop our model to now simultaneously predict the canonical base pairs (with pseudoknots) from base pair probability matrices with or without alignment. We benchmarked our new method over the all non-redundant RNAs below 150 nucleotides. We show that the joined prediction of canonical base pairs structure and local conserved motifs (i) improves the ratio of well-predicted interactions in the secondary structure, (ii) predicts well canonical and Wobble pairs at the location where motifs are inserted, (iii) is greatly improved with evolutionary information and (iv) non-canonical motifs at kink-turn locations.AvailabilityThe source code of the framework is available athttps://gitlab.info.uqam.ca/cbe/RNAMoIPand an interactive web server athttps://rnamoip.cbe.uqam.ca/
ATF4 Expression in Thermogenic Adipocytes is Required for Cold-Induced Thermogenesis in Mice via FGF21-Independent Mechanisms
Authors: Bjorkman Sarah H. , Marti Alex , Jena Jayashree , Garcia Pena Luis M , Weatherford Eric T. , Kato Kevin , Koneru Jivan , Chen Jason , Sood Ayushi , Potthoff Matthew J. , Adams Christopher M. , Abel E. Dale , Pereira Renata O. 
Published: March 2023

AbstractIn brown adipose tissue (BAT), short-term cold exposure induces the activating transcription factor 4 (ATF4), and its downstream target fibroblast growth factor 21 (FGF21). Induction of ATF4 in BAT in response to mitochondrial stress is required for thermoregulation, partially via upregulation of FGF21. In the present study, we tested the hypothesis thatAtf4andFgf21induction in BAT are both required for BAT thermogenesis by generating mice selectively lacking eitherAtf4 (ATF4 BKO)orFgf21(FGF21 BKO) in UCP1-expressing adipocytes. After 3 days of cold exposure, core body temperature was significantly reduced inad-libitum-fed ATF4 BKO mice, which correlated withFgf21downregulation in brown and beige adipocytes, and impaired browning of white adipose tissue (WAT). Conversely, despite having reduced browning, FGF21 BKO mice had preserved core body temperature after cold exposure. Mechanistically, ATF4, but not FGF21, regulates amino acid import and metabolism in response to cold, likely contributing to BAT thermogenic capacity underad libitum-fed conditions. Importantly, under fasting conditions, both ATF4 and FGF21 were required for thermogenesis in cold-exposed mice. Thus, ATF4 regulates BAT thermogenesis by activating amino acid metabolism in BAT in a FGF21-independent manner.Graphical Abstract
Knockout of cardiolipin synthase disrupts postnatal cardiac development by inhibiting the maturation of mitochondrial cristae
Authors: Ren Mindong , Xu Yang , Phoon Colin K. L. , Erdjument-Bromage Hediye , Neubert Thomas A. , Schlame Michael 
Published: March 2023

ABSTRACTBackgroundCardiomyocyte maturation requires a massive increase in respiratory enzymes and their assembly into long-lived complexes of oxidative phosphorylation (OXPHOS). The molecular mechanisms underlying the maturation of cardiac mitochondria have not been established.MethodsTo determine whether the mitochondria-specific lipid cardiolipin is involved in cardiac maturation, we created a cardiomyocyte-restricted knockout (KO) of cardiolipin synthase (Crls1) in mice and studied the postnatal development of the heart. We also measured the turnover rates of proteins and lipids in cardiolipin-deficient flight muscle from Drosophila, a tissue that has mitochondria with high OXPHOS activity like the heart.ResultsCrls1KOmice survived the prenatal period but failed to accumulate OXPHOS proteins during postnatal maturation and succumbed to heart failure at the age of 2 weeks. Turnover measurements showed that the exceptionally long half-life of OXPHOS proteins is critically dependent on cardiolipin.ConclusionsCardiolipin is essential for the postnatal maturation of cardiomyocytes because it allows mitochondrial cristae to accumulate OXPHOS proteins to a high concentration and to shield them from degradation.
Functional diversity of theTP53mutome revealed by saturating CRISPR mutagenesis
Authors: Funk Julianne , Klimovich Maria , Pavlakis Evangelos , Neumann Michelle , Drangenstein Daniel , Noeparast Maxim , Hunold Pascal , Borowek Anna , Balourdas Dimitrios-Ilias , Kochhan Katharina , Merle Nastasja , Bullwinkel Imke , Wanzel Michael , Elmshäuser Sabrina , Nist Andrea , Procida Tara , Bartkuhn Marek , Humpert Katharina , Mernberger Marco , Savai Rajkumar , Joerger Andreas C. , Stiewe Thorsten 
Published: March 2023

AbstractThe tumor suppressor geneTP53is the most frequently mutated gene in various cancers. Unlike other tumor suppressors,TP53is mostly hit by missense mutations, of which more than 2,000 have been described in cancer patients. To take advantage ofTP53mutation status for personalized therapy, a deeper knowledge of the functional ramifications of specific mutations is required as evidence of the functional heterogeneity of mutant p53 proteins mounts. Here, we report on a CRISPR-based saturation mutagenesis screen of 9,225 variants expressed from the endogenousTP53gene locus of a cancer cell. By tracking changes in the abundance of individual variants in response to specific p53-pathway stimulation, we were able to construct high-resolution functional activity maps of theTP53mutome, covering ∼94.5% of all cancer-associated missense mutations. The results demonstrate the impact of individual mutations on tumor cell fitness with unprecedented precision and coverage, even revealing underlying mechanisms such as apoptosis. The high discriminatory power also resolves subtle loss-of-function phenotypes and highlights a subset of mutants as particularly promising targets for pharmacological reactivation. Moreover, the data offer intriguing insight into the role of aberrant splicing and nonsense-mediated mRNA decay in clearing truncated proteins due to not only nonsense, frameshift, and splice-site mutations but also missense and synonymous mutations. Surprisingly, no missense mutation provided an immediate proliferative advantage over a null mutation. Nonetheless, cells with a missense, but not null mutations, acquired pro-metastatic properties after prolonged growth in mice, emphasizing the significance of mutant p53-directed clonal evolution in the progression of tumors towards metastasis.
Comparative 3D ultrastructure ofPlasmodium falciparumgametocytes
Authors: Evers Felix , Roverts Rona , Boshoven Cas , Kea-te Lindert Mariska , Verhoef Julie M.J. , Sinden Robert E. , Akiva Anat , Kooij Taco W.A. 
Published: March 2023

AbstractDespite the enormous significance of malaria parasites for global health, some basic features of their ultrastructure remain obscure. In this study, we apply high-resolution volumetric electron microscopy to examine and compare the ultrastructure ofPlasmodium falciparumgametocytes of both genders and in different stages of development as well as the more intensively studied asexual blood stages revisiting previously described phenomena in 3D. In doing so, we challenge the widely accepted notion of a single mitochondrion by demonstrating the presence of multiple mitochondria in gametocytes. We also provide evidence for a gametocyte-specific cytostome variant. Furthermore, we generate, among other organelles, the first 3D reconstructions of endoplasmic reticulum (ER), Golgi apparatus, and extraparasitic structures in gametocytes. Assessing interconnectivity between organelles, we find frequent structural appositions between the nucleus, mitochondria, and apicoplast. We provide evidence that the ER is a promiscuous interactor with numerous organelles and the trilaminar membrane of the gametocyte. Public availability of these volumetric electron microscopy resources of wild-type asexual and sexual blood-stage malaria parasites will facilitate reinterrogation of this global dataset with different research questions and expertise. Taken together, we reconstruct the 3D ultrastructure ofP. falciparumgametocytes in high detail and shed light on the unique organellar biology of these deadly parasites.
Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease
Authors: Sullivan Patrick F. , Meadows Jennifer R. S. , Gazal Steven , Phan BaDoi N. , Li Xue , Genereux Diane P. , Dong Michael X. , Bianchi Matteo , Andrews Gregory , Sakthikumar Sharadha , Nordin Jessika , Roy Ananya , Christmas Matthew J. , Marinescu Voichita D. , Wallerman Ola , Xue James R. , Li Yun , Yao Shuyang , Sun Quan , Szatkiewicz Jin , Wen Jia , Huckins Laura M. , Lawler Alyssa J. , Keough Kathleen C. , Zheng Zhili , Zeng Jian , Wray Naomi R. , Johnson Jessica , Chen Jiawen ,   Zoonomia Consortium, Paten Benedict , Reilly Steven K. , Hughes Graham M. , Weng Zhiping , Pollard Katherine S. , Pfenning Andreas R. , Forsberg-Nilsson Karin , Karlsson Elinor K. , Lindblad-Toh Kerstin 
Published: March 2023

AbstractAlthough thousands of genomic regions have been associated with heritable human diseases, attempts to elucidate biological mechanisms are impeded by a general inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function that is agnostic to cell type or disease mechanism. Here, single base phyloP scores from the whole genome alignment of 240 placental mammals identified 3.5% of the human genome as significantly constrained, and likely functional. We compared these scores to large-scale genome annotation, genome-wide association studies (GWAS), copy number variation, clinical genetics findings, and cancer data sets. Evolutionarily constrained positions are enriched for variants explaining common disease heritability (more than any other functional annotation). Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.
Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores
Authors: Stuber Annina , Douaki Ali , Hengsteler Julian , Buckingham Denis , Momotenko Dmitry , Garoli Denis , Nakatsuka Nako 
Published: March 2023

AbstractAptamers that undergo conformational changes upon small-molecule recognition have been shown to gate the ionic flux through nanopores by rearranging charge density within the aptamer-occluded orifice. However, mechanistic insight into such systems where biomolecular interactions are confined in nanoscale spaces, is limited. To understand the fundamental mechanisms that facilitate the detection of small-molecule analytes inside structure-switching aptamer-modified nanopores, we correlated experimental observations to theoretical models. We developed a dopamine aptamer-functionalized nanopore sensor with femtomolar detection limits and compared the sensing behavior with a serotonin sensor fabricated with the same methodology. When sensing these two neurotransmitters with comparable mass and equal charge, the sensors showed an opposite electronic behavior. This distinctive phenomenon was extensively studied using complementary experimental techniques such as quartz crystal microbalance with dissipation monitoring, in combination with theoretical assessment by the finite element method and molecular dynamic simulations. Taken together, our studies demonstrate that the sensing behavior of aptamer-modified nanopores in detecting specific small-molecule analytes correlates to the structure-switching mechanisms of individual aptamers. We believe that such investigations not only improve our understanding of the complex interactions occurring in confined nanoscale environments, but will also drive further innovations in biomimetic nanopore technologies.
Loss of MC1R signaling implicates TBX3 in pheomelanogenesis and melanoma predisposition
Authors: Berns H. Matthew , Watkins-Chow Dawn E. , Lu Sizhu , Louphrasitthiphol Pakavarin , Zhang Tongwu , Brown Kevin M. , Moura-Alves Pedro , Goding Colin R. , Pavan William J. 
Published: March 2023

AbstractThe human Red Hair Color (RHC) trait is caused by increased pheomelanin (red-yellow) and reduced eumelanin (black-brown) pigment in skin and hair due to diminished melanocortin 1 receptor (MC1R) function. In addition, individuals harboring the RHC trait are predisposed to melanoma development. WhileMC1Rvariants have been established as causative of RHC and are a well-defined risk factor for melanoma, it remains unclear mechanistically why decreased MC1R signaling alters pigmentation and increases melanoma susceptibility. Here, we use single-cell RNA-sequencing (scRNA-seq) of melanocytes isolated from RHC mouse models to reveal a Pheomelanin Gene Signature (PGS) comprising genes implicated in melanogenesis and oncogenic transformation. We show that TBX3, a well-known anti-senescence transcription factor implicated in melanoma progression, is part of the PGS and binds both E-box and T-box elements to regulate genes associated with melanogenesis and senescence bypass. Our results provide key insights into mechanisms by which MC1R signaling regulates pigmentation and how individuals with the RHC phenotype are predisposed to melanoma.
EEG reveals brain network alterations in chronic aphasia during natural speech listening
Authors: Mehraram Ramtin , Kries Jill , Clercq Pieter De , Vandermosten Maaike , Francart Tom 
Published: March 2023

AbstractAphasia is a common consequence of a stroke which affects language processing. In search of an objective biomarker for aphasia, we used EEG to investigate how functional network patterns in the cortex are affected in persons with post-stroke chronic aphasia (PWA) compared to healthy controls (HC) while they are listening to a story.EEG was recorded from 22 HC and 27 PWA while they listened to a 25-min-long story. Functional connectivity between scalp regions was measured with the weighted phase lag index. The Network- Based Statistics toolbox was used to detect altered network patterns and to investigate correlations with behavioural tests within the aphasia group. Differences in network geometry were assessed by means of graph theory and a targeted node-attack approach. Group-classification accuracy was obtained with a support vector machine classifier.PWA showed stronger inter-hemispheric connectivity compared to HC in the theta-band (4.5-7 Hz), whilst a weaker subnetwork emerged in the low-gamma band (30.5-49 Hz). Two subnetworks correlated with semantic fluency in PWA respectively in delta- (1-4 Hz) and low-gamma-bands. In the theta-band network, graph alterations in PWA emerged at both local and global level, whilst only local changes were found in the low-gamma-band network. As assessed with the targeted node-attack, PWA exhibit a more scale-free network compared to HC. Network metrics effectively discriminated PWA and HC (AUC = 83%).Overall, we showed for that EEG-network metrics are effective biomarkers to assess natural speech processing in chronic aphasia. We hypothesize that the detected alterations reflect compensatory mechanisms associated with recovery.