bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci
Authors: Rodriguez Oscar L. , Sharp Andrew J. , Watson Corey T. 
Published: July 2021

AbstractLymphoblastoid cell lines (LCLs) have been critical to establishing genetic resources for biomedical science. They have been used extensively to study human genetic diversity, genome function, and inform the development of tools and methodologies for augmenting disease genetics research. While the validity of variant callsets from LCLs has been demonstrated for most of the genome, previous work has shown that DNA extracted from LCLs is modified by V(D)J recombination within the immunoglobulin (IG) loci, regions that harbor antibody genes critical to immune system function. However, the impacts of V(D)J on data generated from LCLs has not been extensively investigated. In this study, we used LCL-derived short read sequencing data from the 1000 Genomes Project (n=2,504) to identify signatures of V(D)J recombination. Our analyses revealed sample-level impacts of V(D)J recombination that varied depending on the degree of inferred monoclonality. We showed that V(D)J associated somatic deletions impacted genotyping accuracy, leading to adulterated population-level estimates of allele frequency and linkage disequilibrium. These findings illuminate limitations of using LCLs for building genetic resources in the IG loci, with implications for interpreting previous disease association studies in these regions.Author summaryLymphoblastoid cell lines (LCLs) are cells that have been manipulated to proliferate indefinitely in order to provide a replenishable source of DNA. However, because these cell lines are derived from B cells which have undergone V(D)J recombination they contain somatic deletions within regions of the genome that encode antibody genes. Although several large collaborative projects have utilized DNA from LCLs to generate invaluable genomic resources for the scientific community, the negative impacts of cell line artifacts in these regions of the genome have not been fully appreciated. In this study, we used newly released sequencing data from a large collection of LCLs to determine that the non-inherited artificial deletions within the antibody gene loci can have detrimental effects on downstream genetic analyses.
Inactivation effects of plasma-activated water on Fusarium graminearum
Authors: Guo Jian , Wang Jiaoyu , Xie Hui , Jiang Junlong , Li Chunyuan , Li Wanting , Li Ling , Liu Xingquan , Lin Fucheng 
Published: July 2021

AbstractThe continuous usage of fungicides poses a potential threat to the environment, ranging from mere irritation to being very toxic to human beings and organisms. Plasma-activated water (PAW) has recently gained much interest as a promising candidate to inactivate fungi. However, the inactivation mechanisms of PAW are still not well understood. In this study, the effect of PAW on the viability and the cellular responses of Fusarium graminearum in PAW inactivation were investigated. The results showed that microbial activity of spores was significantly inhibited by PAW treatment (P < 0.05). The symptoms caused by F. graminearum were significantly reduced on the spikelets. Our data indicated that PAW could induce cell wall sculpturing, membrane permeability changes, and mitochondrial dysfunction. Differential gene expression analysis also confirmed that the cell membrane, the cell wall and the mitochondria were the organelles most affected by PAW. The results from this study facilitate the understanding of the mechanisms underlying the responses of F. graminearum to PAW and the development of PAW as a potential fungicidal agent or an effective supplement to fungicides.HighlightsThe viability of F. graminearum is notably inhibited by PAWThe symptoms caused by F. graminearum were significantly reduced on the spikeletsOxidative stress induce cell wall sculpturing, membrane permeability changePAW can cause the mitochondrial dysfunctionCell wall, membrane and mitochondria are the most affected organelles by PAW
Comparative Genome Analysis Reveals Human Pathogenic Potential of ESBL-Escherichia coli Isolated from Swine Microbiomes
Authors: Founou Luria Leslie , Founou Raspail Carrel , Allam Mushal , Ismail Arshad , Essack Sabiha Yusuf 
Published: July 2021

AbstractBackgroundExtended-spectrum β-lactamase-producing E. coli (ESBL-Ec) harbouring virulence genes in the microbiome of food animals could likely threaten human health but is poorly understood in Cameroon and South Africa. Here, we assessed the resistome, virulome and mobilome of ESBL-Ec isolated from swine microbiomes in these countries, using whole genome sequencing (WGS).Materials/methodsEleven clonally-related phenotypic ESBL-Ec isolates were subjected to WGS. The isolates were de novo assembled using the CLC Genomics Workbench and SPAdes while RAST and PROKKA were used for annotation of the assembled contigs. Prediction of antibiotic resistance genes, virulence factors and plasmids was performed using ResFinder, VirulenceFinder and PlasmidFinder, respectively.ResultsDiverse STs were detected with sequence types ST2144 and ST88 predominating and blaCTX-M-15 (55%) as principal ESBL genes. Although the isolates belonged mainly to commensal phylogroups A/B1 (45/28.3%) and C (18.18%), all harboured at least three extraintestinal pathogenic E. coli (ExPEC) VFs with one isolate harbouring up to 18 ExPEC VFs.ConclusionThe resistance and pathogenic potential of ESBL-Ec colonizing the gut microbiota of swine in both countries demonstrate the urgent need to implement effective strategies to contain the dissemination of virulent ESBL-Ec through the food chain in Cameroon and South Africa.
The role of the first transmembrane helix in bacterial YidC: Insights from the crystal structure and molecular dynamics simulations
Authors: Nass Karol J. , Ilie Ioana M. , Saller Manfred J. , Driessen Arnold J.M. , Caflisch Amedeo , Kammerer Richard A. , Li Xiaodan 
Published: July 2021

AbstractThe evolutionary conserved YidC is a unique dual-function protein that adopts insertase and chaperone conformations. The TM1 helix of Escherichia coli YidC mediates the interaction between the YidC chaperone and the Sec translocon. Here, we report the first crystal structure of Thermotoga maritima YidC (TmYidC) including the TM1 helix (PDB ID: 6Y86). The TM1 helix lies on the periplasmic side of the bilayer forming an angle of about 15 degrees with the membrane surface. Our functional studies suggest a role of TM1 for the species-specific interaction with the Sec translocon. The reconstitution data and the superimposition of TmYidC with known YidC structures suggest an active insertase conformation for YidC. Molecular dynamics (MD) simulations of TmYidC provide evidence that the TM1 helix acts as a membrane anchor for the YidC insertase and highlight the flexibility of the C1 region underlining its ability to switch between insertase and chaperone conformations. A structure-based model is proposed to rationalize how YidC performs the insertase and chaperone functions by re-positioning of the TM1 helix and the other structural elements.
Ammonium regulates the development of pine roots through hormonal crosstalk and differential expression of transcription factors in the apex
Authors: Ortigosa Francisco , Lobato-Fernández César , Shikano Hitomi , Ávila Concepción , Taira Shu , Cánovas Francisco M. , Cañas Rafael A. 
Published: July 2021

ABSTRACTAmmonium is a prominent source of inorganic nitrogen for plant nutrition, but excessive amounts can be toxic for many species. However, most conifers are tolerant to ammonium, a relevant physiological feature of this ancient evolutionary lineage. For a better understanding of the molecular basis of this trait, ammonium-induced changes in the transcriptome of maritime pine (Pinus pinasterAit.) root apex have been determined by laser capture microdissection and RNA sequencing. Ammonium promoted changes in the transcriptional profiles of multiple transcription factors, such asSHORT-ROOT, and phytohormone-related transcripts, such asACO, involved in the development of the root meristem. Nano-PALDI-MSI and transcriptomic analyses showed that the distributions of IAA and CKs were altered in the root apex in response to ammonium nutrition. Taken together, the data suggest that this early response is involved in the increased lateral root branching and principal root growth, which characterize the long-term response to ammonium supply in pine. All these results suggest that ammonium induces changes in the root system architecture through the IAA-CK-ET phytohormone crosstalk and transcriptional regulation.
SMC complexes can traverse physical roadblocks bigger than their ring size
Authors: Pradhan Biswajit , Barth Roman , Kim Eugene , Davidson Iain F. , Bauer Benedikt , van Laar Theo , Yang Wayne , Ryu Je-Kyung , van der Torre Jaco , Peters Jan-Michael , Dekker Cees 
Published: July 2021

AbstractThe ring-shaped structural-maintenance-of-chromosomes (SMC) complexes condensin and cohesin extrude loops of DNA as a key motif in chromosome organization. It remains, how ever, unclear how these SMC motor proteins can extrude DNA loops in chromatin that is bound with proteins. Here, using in vitro single-molecule visualization, we show that nucleosomes, RNA polymerase, and dCas9 pose virtually no barrier to DNA loop extrusion by yeast condensin. Strikingly, we find that even DNA-bound nanoparticles as large as 200 nm, much bigger than the SMC ring size, can be translocated into DNA loops during condensin-driven extrusion. Similarly, human cohesin can pass 200 nm particles during loop extrusion, which even occurs for a single-chain version of cohesin in which the ring-forming subunits are covalently linked and cannot open up to entrap DNA. These findings disqualify all common loop-extrusion models where DNA passes through the SMC rings (pseudo)topologically, and instead point to a nontopological mechanism for DNA loop extrusion.One-sentence summaryHuge DNA-bound roadblocks can be incorporated into SMC-extruded DNA loops, pointing to a nontopological mechanism for loop extrusion.
Experience-Driven Rate Modulation is Reinstated During Hippocampal Replay
Authors: Tirole M. , Huelin Gorriz M. , Takigawa M. , Kukovska L. , Bendor D. 
Published: July 2021

SUMMARYReplay, the sequential reactivation within a neuronal ensemble, is a central hippocampal mechanism postulated to drive memory processing. While both rate and place representations are used by hippocampal place cells to encode behavioral episodes, replay has been largely defined by only the latter – based on the fidelity of sequential activity across neighboring place fields. Here we show that dorsal CA1 place cells in rats can modulate their firing rate between replay events of two different contexts. This experience-dependent phenomenon mirrors the same pattern of rate modulation observed during behavior and can be used independently from place information within replay sequences to discriminate between contexts. Our results reveal the existence of two complementary neural representations available for memory processes.
Minimizing the ex vivo confounds of cell-isolation techniques on transcriptomic -profiles of purified microglia
Authors: Ocañas Sarah R. , Pham Kevin D. , Blankenship Harris E. , Machalinski Adeline H. , Chucair-Elliott Ana J. , Freeman Willard M. 
Published: July 2021

AbstractModern molecular neuroscience studies require analysis of specific cellular populations derived from brain tissue samples to disambiguate cell-type specific events. This is particularly true in the analysis of minority glial populations in the brain, such as microglia, which may be obscured in whole tissue analyses. Microglia have central functions in development, aging, and neurodegeneration and are a current focus of neuroscience research. A long-standing concern for glial biologists using in vivo models is whether cell isolation from CNS tissue could introduce ex vivo artifacts in microglia, which respond quickly to changes in the environment. Mouse microglia were purified by magnetic-activated cell sorting (MACS), as well as cytometer- and cartridge-based fluorescence-activated cell sorting (FACS) approaches to compare and contrast performance. The Cx3cr1-NuTRAP mouse model was used here to provide an endogenous fluorescent microglial marker and a microglial-specific translatome profile as a baseline comparison lacking cell isolation artifacts. All methods performed similarly for microglial purity with main differences being in cell yield and time of isolation. Ex vivo activation signatures occurred principally during the initial tissue dissociation and cell preparation and not the microglial cell sorting. Utilizing transcriptional and translational inhibitors during the cell preparation prevented the activational phenotype. These data demonstrate that a variety of microglial isolation approaches can be used, depending on experimental needs, and that inhibitor cocktails are effective at reducing cell preparation artifacts.Table of Contents ImageMain PointsMACS, cytometer-FACS, and cartridge-FACS give equivalent and sufficient yield/purity for microglial analyses. Ex vivo microglial activation is prevented by supplementation with transcription/translation inhibitors during cell preparation.
Gambling environment exposure increases temporal discounting but improves model-based control in regular slot-machine gamblers
Authors: Wagner Ben , Mathar David , Peters Jan 
Published: July 2021

AbstractGambling disorder is a behavioral addiction that negatively impacts personal finances, work, relationships and mental health. In this pre-registered study (https://osf.io/5ptz9/?view_only=62956a2afcd1495984db4be18c54b50a) we investigated the impact of real-life gambling environments on two computational markers of addiction, temporal discounting and model-based reinforcement learning. Gambling disorder is associated with increased temporal discounting and reduced model-based learning. Regular gamblers (n = 30, DSM-5 score range 3-9) performed both tasks in a neutral (café) and a gambling-related environment (slot-machine venue) in counterbalanced order. Data were modeled using drift diffusion models for temporal discounting and reinforcement learning via hierarchical Bayesian estimation. Replicating previous findings, gamblers discounted rewards more steeply in the gambling-related context. This effect was positively correlated with gambling related cognitive distortions (pre-registered analysis). In contrast to our pre-registered hypothesis, model-based reinforcement learning was improved in the gambling context. Here we show that temporal discounting and model-based reinforcement learning are modulated in opposite ways by real-life gambling cue exposure. Results challenge aspects of habit theories of addiction, and reveal that laboratory-based computational markers of psychopathology are under substantial contextual control.
Antagonists targeting eEF2 kinase rescue multiple aspects of pathophysiology in Alzheimer’s disease model mice
Authors: Kasica Nicole P , Zhou Xueyan , Wang Xin , Yang Wenzhong , Zimmermann Helena R , Holland Caroline E , Koscielniak Elizabeth , Wu Hanzhi , Cox Anderson O , Lee Jingyun , Ryazanov Alexey G , Furdui Cristina M. , Ma Tao 
Published: July 2021

AbstractIt is imperative to develop novel therapeutic strategies for Alzheimer’s disease (AD) and related dementia syndromes based on solid mechanistic studies. Maintenance of memory and synaptic plasticity relies on de novo protein synthesis, which is partially regulated by phosphorylation of eukaryotic elongation factor 2 (eEF2) via its kinase eEF2K. Abnormally increased eEF2 phosphorylation and impaired mRNA translation have been linked to AD. We recently reported that prenatal genetic suppression of eEF2K is able to prevent aging-related cognitive deficits in AD model mice, suggesting the therapeutic potential of targeting eEF2K/eEF2 signaling in AD. Here, we tested two structurally distinct small-molecule eEF2K inhibitors in two different lines of AD model mice after onset of cognitive impairments. Our data revealed that treatment with eEF2K inhibitors improved AD-associated synaptic plasticity impairments and cognitive dysfunction, without altering brain amyloid β (Aβ) and tau pathology. Furthermore, eEF2K inhibition alleviated AD-associated defects in dendritic spine morphology, postsynaptic density formation, protein synthesis, and dendritic polyribosome assembly. Our results may offer critical therapeutic implications for AD, and the proof-of-principle study indicates translational implication of inhibiting eEF2K for AD and related dementia syndromes.One Sentence SummaryTreatment with eEF2K inhibitors and genetic eEF2K knockout improved cognitive deficits in Alzheimer’s disease model mice.
Feedbacks between size and density determine rapid eco-phenotypic dynamics
Authors: Gibert Jean Philippe , Han Ze-Yi , Wieczynski Daniel J , Votzke Samantha , Yammine Andrea 
Published: July 2021

ABSTRACTBody size is a fundamental trait linked to many ecological processes—from individuals to ecosystems. Although the effects of body size on metabolism are well-known, the potential reciprocal effects of body size and density are less clear. Specifically, 1) whether changes in body size or density more strongly influence the other and 2) whether coupled rapid changes in body size and density are due to plasticity, rapid evolutionary change, or a combination of both.Here, we address these two issues by experimentally tracking population density and mean body size in the protistTetrahymena pyriformisas it grows from low density to carrying capacity. We then useConvergent Cross Mappingtime series analyses to infer the direction, magnitude, and causality of the link between body size and ecological dynamics. We confirm the results of our analysis by experimentally manipulating body size and density while keeping the other constant. Last, we fit mathematical models to our experimental time series that account for purely plastic change in body size, rapid evolution in size, or a combination of both, to gain insight into the processes that most likely explain the observed dynamics.Our results indicate that changes in body size more strongly influence changes in density than the other way around, but also show that there is reciprocity in this effect (i.e., afeedback). We show that a model that only accounts for purely plastic change in size most parsimoniously explains observed, coupled phenotypic and ecological dynamics.Together, these results suggest 1) that body size can shift dramatically through plasticity, well within ecological timescales, 2) that rapid changes in body size may have a larger effect on ecological dynamics than the reverse, but 3) phenotypic and ecological dynamics influence each as populations grow. Overall, we show that rapid plastic changes in functional traits like body size may play a fundamental –but currently unrecognized– role in familiar ecological processes such as logistic population growth.
Segmenting and Predicting Musical Phrase Structure Exploits Neural Gain Modulation and Phase Precession
Authors: Teng Xiangbin , Larrouy-Maestri Pauline , Poeppel David 
Published: July 2021

SummaryMusic, like language, is characterized by hierarchically organized structure that unfolds over time. Music listening therefore requires not only the tracking of notes and beats but also internally constructing high-level musical structures or phrases and anticipating incoming contents. Unlike for language, mechanistic evidence for online musical segmentation and prediction at a structural level is sparse. We recorded neurophysiological data from participants listening to music in its original forms as well as in manipulated versions with locally or globally reversed harmonic structures. We discovered a low-frequency neural component that modulated the neural rhythms of beat tracking and reliably parsed musical phrases. We next identified phrasal phase precession, suggesting that listeners established structural predictions from ongoing listening experience to track phrasal boundaries. The data point to brain mechanisms that listeners use to segment continuous music at the phrasal level and to predict abstract structural features of music.
Time cell encoding in deep reinforcement learning agents depends on mnemonic demands
Authors: Lin Dongyan , Richards Blake A. 
Published: July 2021

AbstractThe representation of “what happened when” is central to encoding episodic and working memories. Recently discovered hippocampal time cells are theorized to provide the neural substrate for such representations by forming distinct sequences that both encode time elapsed and sensory content. However, little work has directly addressed to what extent cognitive demands and temporal structure of experimental tasks affect the emergence and informativeness of these temporal representations. Here, we trained deep reinforcement learning (DRL) agents on a simulated trial-unique nonmatch-to-location (TUNL) task, and analyzed the activities of artificial recurrent units using neuroscience-based methods. We show that, after training, representations resembling both time cells and ramping cells (whose activity increases or decreases monotonically over time) simultaneously emerged in the same population of recurrent units. Furthermore, with simulated variations of the TUNL task that controlled for (1) memory demands during the delay period and (2) the temporal structure of the episodes, we show that memory demands are necessary for the time cells to encode information about the sensory stimuli, while the temporal structure of the task only affected the encoding of “what” and “when” by time cells minimally. Our findings help to reconcile current discrepancies regarding the involvement of time cells in memory-encoding by providing a normative framework. Our modelling results also provide concrete experimental predictions for future studies.
A coordinated function of lncRNA HOTTIP and miRNA-196b underpinning leukemogenesis by targeting Fas signaling
Authors: Singh Ajeet P. , Luo Huacheng , Matur Meghana , Eshelman Melanie , Sharma Arati , Huang Suming 
Published: July 2021

AbstractMicroRNAs (miRNAs) may modulate more than 60% of human coding genes and act as negative regulators, while long non-coding RNAs (lncRNAs) regulate gene expression on multiple levels by interacting with chromatin, functional proteins, and RNAs such as mRNAs and microRNAs. However, the crosstalk between lncRNA HOTTIP and miRNAs in leukemogenesis remains elusive. Using combined integrated analyses of global miRNA expression profiling and state-of-the-art genomic analyses of chromatin such as ChIRP-seq., (genome wide HOTTIP binding analysis), ChIP-seq., and ATAC-seq., we found that miRNA genes are directly controlled by HOTTIP. Specifically, the HOX cluster miRNAs (miR-196a, miR-196b, miR-10a and miR-10b), located cis & trans, were most dramatically regulated and significantly decreased in HOTTIP-/- AML cells. HOTTIP bound to the miR-196b promoter, and HOTTIP deletion reduced chromatin accessibility and enrichment of active histone modifications at HOX cluster associated miRNAs in AML cells, while reactivation of HOTTIP restored miR gene expression and chromatin accessibility in the CTCF-boundary-attenuated AML cells. Inactivation of HOTTIP or miR-196b promotes apoptosis by altering the chromatin signature at the FAS promoter and increasing FAS expression. Transplantation of miR-196b knockdown MOLM13 cells in NSG mice increased overall survival compared to wild-type cells. Thus, HOTTIP remodels the chromatin architecture around miRNAs to promote their transcription, consequently repressing tumor suppressors and promoting leukemogenesis.