bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of AsCas12a for combinatorial genetic screens in human cells
Authors: Sanson Kendall R , DeWeirdt Peter C , Sangree Annabel K , Hanna Ruth E , Hegde Mudra , Teng Teng , Borys Samantha M , Strand Christine , Joung J Keith , Kleinstiver Benjamin P , Pan Xuewen , Huang Alan , Doench John G 
Published: August 2019

ABSTRACTCas12a enzymes have attractive properties for scalable delivery of multiplexed perturbations, yet widespread usage has lagged behind Cas9-based strategies. Here we describe the optimization of Cas12a from Acidaminococcus (AsCas12a) for use in pooled genetic screens in human cells. By assaying the activity of thousands of guides, we confirm on-target design rules and extend them to an enhanced activity variant, enAsCas12a. We also develop the first comprehensive set of off-target rules for Cas12a, and demonstrate that we can predict and exclude promiscuous guides. Finally, to enable efficient higher-order multiplexing via lentiviral delivery, we screen thousands of direct repeat variants and identify 38 that outperform the wildtype sequence. We validate this optimized AsCas12a toolkit by targeting 12 synthetic lethal gene pairs with up to 400 guide pairs each, and demonstrate effective triple knockout via flow cytometry. These results establish AsCas12a as a robust system for combinatorial applications of CRISPR technology.
Visual working memory representations in visual and parietal cortex do not remap after eye movements
Authors: He Tao , Ekman Matthias , Vandenbroucke Annelinde R.E. , de Lange Floris P. 
Published: August 2019

ABSTRACTIt has been suggested that our visual system does not only process stimuli that are directly available to our eyes, but also has a role in maintaining information in VWM over a period of seconds. It remains unclear however what happens to VWM representations in the visual system when we make saccades. Here, we tested the hypothesis that VWM representations are remapped within the visual system after making saccades. We directly compared the content of VWM for saccade and no-saccade conditions using MVPA of delay-related activity measured with fMRI. We found that when participants did not make a saccade, VWM representations were robustly present in contralateral early visual cortex. When making a saccade, VWM representations degraded in contralateral V1-V3 after the saccade shifted the location of the remembered grating to the opposite visual field. However, contrary to our hypothesis we found no evidence for the representations of the remembered grating at the saccadic target location in the opposite visual field, suggesting that there is no evidence for remapping of VWM in early visual cortex. Interestingly, IPS showed persistent VWM representations in both the saccade and no-saccade condition. Together, our results indicate that VWM representations in early visual cortex are not remapped across eye movements, potentially limiting the role of early visual cortex in VWM storage.HighlightsVisual working memory (VWM) representations do not remap after making saccadesEye movement degrade VWM representations in early visual cortex, limiting the role of early visual cortex in VWM storageParietal cortex shows persistent VWM representations across saccades
A study of parietal-motor connectivity by intraoperative dual cortical stimulation
Authors: Cattaneo Luigi , Giampiccolo Davide , Meneghelli Pietro , Tramontano Vincenzo , Sala Francesco 
Published: August 2019

Abstractthe function of the primate’s posterior parietal cortex in sensorimotor transformations is well-established, though in humans its complexity is still challenging. Well-established models indicate that the posterior parietal cortex influences motor output indirectly, by means of connections to the premotor cortex, which in turn is directly connected to the motor cortex. The possibility that the posterior parietal cortex could be at the origin of direct afferents to M1 has been suggested in humans but has never been confirmed directly. In the present work we assessed during intraoperative monitoring of the corticospinal tract in brain tumour patients the existence of short-latency effects of parietal stimulation on corticospinal excitability to the upper limb. We identified several foci within the inferior parietal lobule that drove short-latency influences on cortical motor output. Active foci were distributed along the postcentral gyrus and clustered around the anterior intraparietal area and around the parietal operculum. For the first time in humans, the present data show direct evidence in favour of a distributed system of connections from the posterior parietal cortex to the ipsilateral primary motor cortex.
Why are children so distractible? Development of attention and motor control from childhood to adulthood
Authors: Hoyer R. S. , Elshafei H. , Hemmerlin J. , Bouet R. , Bidet-Caulet A. 
Published: August 2019

AbstractDistractibility is the propensity to behaviorally react to irrelevant information. Though children are more distractible the younger they are, the precise contribution of attentional and motor components to distractibility and their developmental trajectories have not been characterized yet. We used a new behavioral paradigm to identify the developmental dynamics of components contributing to distractibility in a large cohort of French participants balanced, between age groups, in gender and socio-economic status (N=352; age: 6-25). Results reveal that each measure of these components, namely voluntary attention, distraction, impulsivity and motor control, present a distinct maturational timeline. In young children, increased distractibility is mostly the result of reduced sustained attention capacities and enhanced distraction, while in teenagers, it is the result of decreased motor control and increased impulsivity.
Photo sensing and quorum sensing are integrated to control bacterial group behaviors
Authors: Mukherjee Sampriti , Jemielita Matthew , Stergioula Vasiliki , Tikhonov Mikhail , Bassler Bonnie L. 
Published: August 2019

ABSTRACTPseudomonas aeruginosatransitions between the free-swimming state and the sessile biofilm mode during its pathogenic lifestyle. We show that quorum sensing repressesP. aeruginosabiofilm formation and virulence by activating expression of genes encoding the KinB-AlgB two-component system. Phospho-AlgB represses biofilm and virulence genes, while KinB dephosphorylates, and thereby, inactivates AlgB. We discover that the photoreceptor BphP is the kinase that, in response to light, phosphorylates and activates AlgB. Indeed, exposingP. aeruginosato light represses biofilm formation and virulence gene expression. To our knowledge,P. aeruginosawas not previously known to detect light. The KinB-AlgB-BphP module is present in all Pseudomonads, and we demonstrate that AlgB is the cognate response regulator for BphP in diverse bacterial phyla. We propose that KinB-AlgB-BphP constitutes a “three-component” system and AlgB is the node at which varied sensory information is integrated. This study sets the stage for light-mediated control ofP. aeruginosainfectivity.
Convergence of DNA methylation profiles in a novel environment in the reef coral Porites astreoides
Authors: Dimond James L. , Roberts Steven B. 
Published: August 2019

AbstractPhenotypic acclimatization is an organismal response to environmental change that may be rooted in epigenetic mechanisms. In reef building corals, organisms that are severely threatened by environmental change, some evidence suggests that DNA methylation is an environmentally responsive mediator of acclimatization. We investigated changes in DNA methylation of the reef coral Porites astreoides in response to simulated environmental change. Coral colonies were sampled from a variety of habitats on the Belize Barrier Reef and transplanted to a common garden for one year. We used restriction site associated DNA sequencing, including a methylation-sensitive variant, to subsample the genome and assess changes in DNA methylation levels after a year in the common garden. Methylation changes among the 629 CpG loci we recovered were subtle, yet coral methylomes were more similar to each other after a year in the common garden together, indicating convergence of methylation profiles in the common environment. Differentially methylated loci showed matches with both coding and non-coding RNA sequences with putative roles in intracellular signaling, apoptosis, gene regulation, and epigenetic crosstalk. There was a weak but positive and significant relationship between genetic and epigenetic variation, providing evidence of methylation heritability. Altogether, our results suggest that DNA methylation in P. astreoides is at least somewhat responsive to environmental change, reflective of the environment, and heritable, characteristics necessary for methylation to be implicated as part of potential transgenerational acclimatization responses.
Regulation of defeat-induced social avoidance by medial amygdala DRD1 in male and female prairie voles
Authors: Tickerhoof Maria C. , Hale Luanne H. , Smith Adam S. 
Published: August 2019

ABSTRACTSocial interaction with unfamiliar individuals is necessary for species-preserving behaviors such as finding mates and establishing social groups. However, social conflict is a potential negative outcome to interaction with a stranger that can be distressing enough to cause an individual to later avoid interactions with other unfamiliar conspecifics. Unfortunately, stress research using a prominent model of social conflict, social defeat stress, has largely omitted female subjects. This has left a void in the literature regarding social strain on female stress biology and adequate comparison of the effect of sex in stress pathways. The prairie vole (Microtus ochrogaster) exhibits aggressive behavior in both sexes, making voles an attractive candidate to model social defeat in both sexes. This study sought to establish a model of social defeat stress in both male and female prairie voles, characterize behavioral changes in response to this stressor, and investigate the role of dopamine signaling in the response to social defeat stress. Defeated male and female prairie voles displayed social avoidance as well as an increase in expression of dopamine receptor D1 (DRD1) in the medial amygdala (MeA). Pharmacological manipulation of DRD1 signaling in the MeA revealed that increased DRD1 signaling is sufficient to induce a social avoidant state, and could be a necessary component in the defeat-induced social avoidance response. These findings provide the prairie vole as a model of social defeat in both sexes, and implicate the MeA in avoidance of unfamiliar conspecifics after a distressing social encounter.
Modeling the assessment of the upper limb motor function impairment in children with cerebral palsy using sEMG and IMU sensors
Authors: Raouafi S. , Raison M. , Sofiane A. 
Published: August 2019

AbstractSeveral rehabilitation approaches have shown that robot-assisted therapy (robot-AT) can improve the quality of upper limb movements in children with cerebral palsy (CP). However, there is still no method for assessing upper limb motor function impairment using a combination of surface electromyography (sEMG) and inertial measurement unit (IMU) sensors. The aim of this study was to develop a functional ability model to assess the effectiveness of robot-AT on improving upper limb function in children with CP. Fifteen healthy children and fifteen children with CP were included in this study. Children with CP performed eighteen robot-AT sessions and were evaluated twice, using EMG and three-axis IMU readings from accelerometer (IMU-ACC). Principal component analysis and the RELIEFF algorithm were used for dimensionality reduction of the feature space. The classification was performed by using support vector machines, linear discriminant analysis, and random forest. The proposed assessment method was evaluated by using leave-one-out cross validation. With this approach, it was possible to differentiate between healthy children and children with CP pre-robot-AT and post-robot-AT with an overall accuracy of 97.56%. This study suggests that there is potential for modeling the assessment of the upper limb motor function impairment in children with CP using sEMG and IMU-ACC sensors.
Local design principles at hippocampal synapses revealed by an energy-information trade-off
Authors: Mahajan Gaurang , Nadkarni Suhita 
Published: August 2019

AbstractSynapses across different brain regions display distinct structure-function relationships. We investigate the interplay of fundamental design principles that shape the transmission properties of the excitatory CA3-CA1 pyramidal cell connection, a prototypic synapse for studying the mechanisms of learning in the hippocampus. This small synapse is characterized by probabilistic release of transmitter, which is markedly facilitated in response to naturally occurring trains of action potentials. Based on a physiologically realistic computational model of the CA3 presynaptic terminal, we show how unreliability and short-term dynamics of vesicle release work together to regulate the trade-off of information transfer versus energy use. We propose that individual CA3-CA1 synapses are designed to operate at close to maximum possible capacity of information transfer in an efficient manner. Experimental measurements reveal a wide range of vesicle release probabilities at hippocampal synapses, which may be a necessary consequence of long-term plasticity and homeostatic mechanisms that manifest as presynaptic modifications of release probability. We show that the timescales and magnitude of short-term plasticity render synaptic information transfer nearly independent of differences in release probability. Thus, individual synapses transmit optimally while maintaining a heterogeneous distribution of presynaptic strengths indicative of synaptically-encoded memory representations. Our results support the view that organizing principles that are evident on higher scales of neural organization percolate down to the design of an individual synapse.
γ–Secretase controls the specification of astrocytes from oligodendrocyte precursor cells via Stat3
Authors: Hou Jinxing , Bi Huiru , Zou Gang , Ye Zhuoyang , Zhao Jing , Hu Yimin , Lu Jun , Chen Guiquan 
Published: August 2019

AbstractOligodendrocytes (OLs) and astrocytes play critical roles in a variety of brain functions. OL precursor cells (OPCs) are known to give rise to OLs as well as astrocytes. However, little is known about the mechanism by which OPCs determine their specification choice for OLs versus astrocytes in the central nervous system (CNS). Here we show that genetic inhibition of γ-secretase in OPCs reduces OL differentiation but enhances astrocyte specification. Mechanistic analysis reveals that inhibition of γ-secretase results in decreased levels of Hes1, and that Hes1 down-regulates the expression of signal transducer and activator of transcription3 (Stat3) via binding to specific regions of its promoter. We demonstrate that conditional inactivation of Stat3 in OL lineages restores the number of astrocytes in γ-secretase mutant mice. In summary, this study identifies a key mechanism which controls OPC’s specification choice for OL versus astrocyte during postnatal development. This γ-secretase-dependent machinery may be essential for the CNS to maintain the population balance between OLs and astrocytes.
The CDK Pef1 and Protein Phosphatase 4 oppose each other for regulating cohesin binding to fission yeast chromosomes
Authors: Birot Adrien , Tormos-Pérez Marta , Vaur Sabine , Feytout Amélie , Jaegy Julien , Gil Dácil Alonso , Vazquez Stéphanie , Ekwall Karl , Javerzat Jean-Paul 
Published: August 2019

ABSTRACTCohesin has essential roles in chromosome structure, segregation and repair. Cohesin binding to chromosomes is catalyzed by the cohesin loader, Mis4 in fission yeast. How cells fine tune cohesin deposition is largely unknown. Here we provide evidence that Mis4 activity is regulated by phosphorylation of its cohesin substrate. A genetic screen for negative regulators of Mis4 yielded a CDK called Pef1, whose closest human homologue is CDK5. Inhibition of Pef1 kinase activity rescued cohesin loader deficiencies. In an otherwise wild-type background, Pef1 ablation stimulated cohesin binding to its regular sites along chromosomes while ablating Protein Phosphatase 4 had the opposite effect. Pef1 and PP4 control the phosphorylation state of the cohesin kleisin Rad21. The CDK phosphorylates Rad21 on Threonine 262. Pef1 ablation, non phosphorylatable Rad21-T262 or mutations within a Rad21 binding domain of Mis4 alleviated the effect of PP4 deficiency. Such a CDK/PP4 based regulation of cohesin loader activity could provide an efficient mechanism for translating cellular cues into a fast and accurate cohesin response.
RUNX1-ETO induction rapidly alters chromatin landscape and growth of a specific sub-population of hESC-derived myeloid precursor cells by interfering with RUNX1 regulation
Authors: Nafria Monica , Keane Peter , Ng Elizabeth S. , Stanley Edouard G. , Elefanty Andrew G. , Bonifer Constanze 
Published: August 2019

SummaryAcute myeloid leukemia is a hematopoietic malignancy caused by recurrent mutations in genes encoding transcriptional, epigenetic and/or signaling regulators. The t(8;21) translocation generates the aberrant transcription factor RUNX1-ETO whose expression can be detectedin uterobut is insufficient to cause overt disease. Although patients harboring cells with the t(8;21) translocation have acquired additional mutations and show extensive epigenetic reprogramming, the effects directly attributable to RUNX1-ETO expression are unclear. To address this question, we used a human embryonic stem cell differentiation system capable of forming definitive human myeloid progenitor cells to express RUNX1-ETO in an inducible fashion. Induction of RUNX1-ETO causes extensive chromatin reprogramming by interfering with RUNX1 binding, blocks differentiation and arrests cellular growth, whereby growth arrest is reversible following RUNX1-ETO removal. Single cell gene expression analyses show that RUNX1-ETO induction alters the differentiation of a defined sub-population of progenitors, indicating that oncoprotein-mediated transcriptional reprogramming is highly target cell specific.
Neuron-glia interaction through Serotonin-BDNF-NGFR axis enables regenerative neurogenesis in Alzheimer’s model of adult zebrafish brain
Authors: Bhattarai Prabesh , Cosacak Mehmet Ilyas , Mashkaryan Violeta , Yilmaz Sevgican , Popova Stanislava Dimitrova , Govindarajan Nambirajan , Brandt Kerstin , Zhang Yixin , Kizil Caghan 
Published: August 2019

AbstractIt was recently suggested that supplying the brain with new neurons could counteract Alzheimer’s disease. This provocative idea requires further testing in experimental models where the molecular basis of disease-induced neuronal regeneration could be investigated. We previously found that zebrafish stimulates neural stem cell (NSC) plasticity and neurogenesis in Alzheimer’s disease and could help to understand the mechanisms to be harnessed for develop new neurons in diseased mammalian brains. Here, by performing single-cell transcriptomics, we found that Amyloid toxicity-induced Interleukin-4 induces NSC proliferation and neurogenesis by suppressing the tryptophan metabolism and reducing the production of Serotonin. NSC proliferation was suppressed by Serotonin via downregulation of BDNF-expression in Serotonin-responsive periventricular neurons. BDNF enhances NSC plasticity and neurogenesis via NGFRA/NFkB signaling in zebrafish but not in rodents. Collectively, our results suggest a complex neuron-glia interaction that regulates regenerative neurogenesis after Alzheimer’s disease conditions in zebrafish.Key findings-Amyloid-induced Interleukin-4 suppresses Serotonin (5-HT) production in adult zebrafish brain-5-HT affects htr1-expresing neurons and suppresses bdnf expression-BDNF enhances plasticity in neural stem cells via NGFRA/NFkB signaling-BDNF/NGFRA signaling is a neuro-regenerative mechanism in zebrafish but not in mammals.
High-throughput living-cell protein crosslinking analysis uncovers the physiological relevance of forming the “inserted” state of the ATP synthase ε-subunit
Authors: Liu Yang , Yu Jiayu , Wang Mengyuan , Zeng Qingfang , Fu Xinmiao , Chang Zengyi 
Published: August 2019

AbstractATP synthase, a highly conserved multi-subunit enzyme complex having a common stoichiometry of α3β3γδεab2c8-15, functions to supply ATP as the universal energy currency for cells. It comprises of the peripheral F1 sector (α3β3γδε) and the membrane-integrated Fo sector (ab2c8-15). In vitro structural analyses revealed that the C-terminal domain of the ε-subunit could adopt either an “inserted” or “non-inserted” state (with or without interacting with the α/β-subunits), with the former being viewed as inhibitory for the ATP hydrolysis activity of ATP synthase. Nevertheless, as common in current protein researches, the physiological relevance of such an “inserted” state for ATP synthase functioning is hardly known. To decipher this, designed an unnatural amino acid-mediated living-cell protein photocrosslinking analysis pipeline by developing the scarless genome-targeted site-directed mutagenesis and the high-throughput gel polyacrylamide gel electrophoresis (HT-PAGE) techniques. Employing this powerful approach, we systematically examined the interactions involving the C-terminal helix of the ε-subunit in cells living under a variety of experimental conditions. These studies enabled us to uncover that the “inserted” and “non-inserted” states of the ε-subunit exist as an equilibrium in cells cultured under common experimental conditions, shifting to the former upon the appearance of unfavorable conditions, acting as a low-gear state to strengthen the ATP synthesis function. Such a fine-tuning mechanism allows the ATP synthase to reversibly and instantly switch between two functional states. Further, the two powerful techniques that we developed here might be applied to many aspects of protein researches.