bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atomic Force Microscopy Reveals Distinct Protofilament-scale Structural Dynamics in Depolymerizing Microtubule Arrays
Authors: Wijeratne Sithara S. , Marchan Michelle F. , Tresback Jason S. , Subramanian Radhika 
Published: December 2020

ABSTRACTThe dynamic reorganization of microtubule-based cellular structures, such as the spindle and the axoneme, fundamentally depends on the dynamics of individual polymers within multimicrotubule arrays. A major class of enzymes, implicated in both the complete demolition and fine size control of microtubule-based arrays, are depolymerizing kinesins. How different depolymerases differently remodel microtubule arrays is poorly understood. A major technical challenge in addressing this question is that existing optical or electron-microscopy methods lack the spatial-temporal resolution to observe the dynamics of individual microtubules within larger arrays. Here we use Atomic Force Microscopy (AFM) to image depolymerizing arrays at single microtubule and protofilament resolution. We discover previously unseen modes of microtubule array destabilization by conserved depolymerases. We find that the kinesin-13 MCAK mediates asynchronous protofilament depolymerization and lattice-defect propagation, whereas the kinesin-8 Kip3p promotes synchronous protofilament depolymerization. Unexpectedly, MCAK can depolymerize the highly stable axonemal doublets, but Kip3p cannot. We propose that distinct protofilament-level activities underlie the functional dichotomy of depolymerases, resulting in either large-scale destabilization or length regulation of microtubule arrays. Our work establishes AFM as a powerful strategy to visualize microtubule dynamics within arrays and reveals how nanometer-scale substrate specificity leads to differential remodeling of micron-sized cytoskeletal structures.SIGNIFICANCE STATEMENTOne cannot help but marvel at the precise organization of microtubule polymers in cellular structures such as the axoneme and the spindle. However, our understanding of the biochemical mechanisms that sculpt these arrays comes largely from in vitro experiments with a small number (one or two) of microtubules. This is somewhat akin to studying the architecture of multilane highways by studying one-lane streets. Here we directly visualize depolymerizing microtubule arrays at individual microtubule and protofilament resolution using Atomic Force Microscopy. Our results reveal differences in microtubule depolymerase activity and provide insights into how these differences in enzymatic activity on the nanometer scale can result in the differential remodeling of multi-microtubule arrays on the micron-length scale.
Identifying and testing marker-trait associations for growth and phenology in three pine species: implications for genomic prediction
Authors: Perry Annika , Wachowiak Witold , Beaton Joan , Iason Glenn , Cottrell Joan , Cavers Stephen 
Published: December 2020

AbstractIn tree species, genomic prediction offers the potential to forecast mature trait values in early growth stages, if robust marker-trait associations can be identified. Here we apply a novel multispecies approach using genotypes from a new genotyping array, based on 20,795 SNPs from three closely related pine species (Pinus sylvestris, Pinus uncinataandPinus mugo), to test for associations with growth and phenology data from a common garden study. Predictive models constructed using significantly associated SNPs were then tested and applied to an independent multisite field trial ofP. sylvestrisand the capability to predict trait values was evaluated. One hundred and eighteen SNPs showed significant associations with the traits in the pine species. Common SNPs (MAF > 0.05) associated with bud set were only found in genes putatively involved in growth and development, whereas those associated with growth and budburst were also located in genes putatively involved in response to environment and, to a lesser extent, reproduction. At one of the two independent sites, the model we developed produced highly significant correlations between predicted values and observed height data (YA, height 2020: r = 0.376,p< 0.001). Predicted values estimated with our budburst model were weakly but positively correlated with duration of budburst at one of the sites (GS, 2015: r = 0.204,p= 0.034; 2018: r = 0.205,p= 0.034-0.037) and negatively associated with budburst timing at the other (YA: r = -0.202,p= 0.046). Genomic prediction resulted in the selection of sets of trees whose mean height was taller than the average for each site. Our results provide tentative support for the capability of prediction models to forecast trait values in trees, while highlighting the need for caution in applying them to trees grown in different environments.
Coordinated hippocampal-thalamic-cortical communication crucial for engram dynamics underneath systems consolidation
Authors: Tomé Douglas Feitosa , Sadeh Sadra , Clopath Claudia 
Published: December 2020

AbstractSystems consolidation refers to the reorganization of memory over time across brain regions. Despite recent advancements in unravelling engrams and circuits essential for this process, the exact mechanisms behind engram cell dynamics and the role of associated pathways remain poorly understood. Here, we propose a computational model to address this knowledge gap that consists of a multi-region spiking recurrent neural network subject to biologically-plausible synaptic plasticity mechanisms. By coordinating the timescales of synaptic plasticity throughout the network and incorporating a hippocampus-thalamus-cortex circuit, our model is able to couple engram reactivations across these brain regions and thereby reproduce key dynamics of cortical and hippocampal engram cells along with their interdependencies. Decoupling hippocampal-thalamic-cortical activity disrupts engram dynamics and systems consolidation. Our modeling work also yields several testable predictions: engram cells in mediodorsal thalamus are activated in response to partial cues in recent and remote recall and are crucial for systems consolidation; hippocampal and thalamic engram cells are essential for coupling engram reactivations between subcortical and cortical regions; inhibitory engram cells have region-specific dynamics with coupled reactivations; inhibitory input to mediodorsal thalamus is critical for systems consolidation; and thalamocortical synaptic coupling is predictive of cortical engram dynamics and the retrograde amnesia pattern induced by hippocampal damage. Overall, our results suggest that systems consolidation emerges from concerted interactions among engram cells in distributed brain regions enabled by coordinated synaptic plasticity timescales in multisynaptic subcortical-cortical circuits.
In vivogenetic screen identifies a SLC5A3-dependent myo-inositol auxotrophy in acute myeloid leukemia
Authors: Wei Yiliang , Iyer Shruti V. , Costa Ana S. H. , Yang Zhaolin , Kramer Melissa , Adelman Emmalee R. , Klingbeil Olaf , Demerdash Osama E. , Polyanskaya Sofya , Chang Kenneth , Goodwin Sara , Hodges Emily , McCombie W. Richard , Figueroa Maria E. , Vakoc Christopher R. 
Published: December 2020

AbstractAn enhanced requirement for extracellular nutrients is a hallmark property of cancer cells. Here, we optimized anin vivogenetic screening strategy for evaluating dependencies in acute myeloid leukemia (AML), which led to the identification of the myo-inositol transporter SLC5A3 as a unique vulnerability in this disease. In accord with this transport function, we demonstrate that the SLC5A3 dependency reflects a myo-inositol auxotrophy in AML. Importantly, the commonality among SLC5A3-dependent AML lines is the transcriptional silencing ofISYNA1, which encodes the rate limiting enzyme for myoinositol biosynthesis, inositol-3-phosphate synthase 1. We used gain- and loss-of-function experiments to demonstrate a synthetic lethal genetic interaction betweenISYNA1andSLC5A3in AML, which function redundantly to sustain intracellular myo-inositol. Transcriptional silencing and DNA hypermethylation ofISYNA1occur in a recurrent manner in human AML patient samples, in association with the presence ofIDH1/IDH2andCEBPAmutations. Collectively, our findings reveal myo-inositol auxotrophy as a novel form of metabolic dysregulation in AML, which is caused by the aberrant silencing of a biosynthetic enzyme.Statement of significanceHere, we show how epigenetic silencing can provoke a nutrient dependency in AML by exploiting a synthetic lethality relationship between biosynthesis and transport of myo-inositol. Blocking the function of this solute carrier may have therapeutic potential in an epigenetically-defined subset of AML.
Rapid 40 kb genome construction from 52 parts
Authors: Pryor John M. , Potapov Vladimir , Pokhrel Nilisha , Lohman Gregory J. S. 
Published: December 2020

ABSTRACTLarge DNA constructs (>10 kb), including small genomes and artificial chromosomes, are invaluable tools for genetic engineering and vaccine development. However, the manufacture of these constructs is laborious. To address this problem, we applied new design insights and modified protocols to Golden Gate assembly. While this methodology is routinely used to assemble 5-10 DNA parts in one-step, we found that optimized assembly permitted >50 DNA fragments to be faithfully assembled in a single reaction. We applied these insights to genome construction, carrying out rapid assembly of the 40 kb T7 bacteriophage genome from 52 parts and recovering infectious phage particles after cellular transformation. The new Golden Gate assembly protocols and design principles described here can be applied to rapidly engineer a wide variety of large and complex assembly targets.
Bridging themes: short protein segments found in different architectures
Authors: Kolodny Rachel , Nepomnyachiy Sergey , Tawfik Dan S. , Ben-Tal Nir 
Published: December 2020

AbstractThe vast majority of theoretically possible polypeptide chains do not fold, let alone confer function. Hence, protein evolution from preexisting building blocks has clear potential advantages overab initioemergence from random sequences. In support of this view, sequence similarities between different proteins is generally indicative of common ancestry, and we collectively refer to such homologous sequences as ‘themes’. At the domain level, sequence homology is routinely detected. However, short themes which are segments, or fragments of intact domains, are particularly interesting because they may provide hints about the emergence of domains, as opposed to divergence of preexisting domains, or their mixing-and-matching to form multi-domain proteins. Here we identified 525 representative short themes, comprising 20-to-80 residues, that are unexpectedly shared between domains considered to have emerged independently. Among these ‘bridging themes’ are ones shared between the most ancient domains, e.g., Rossmann, P-loop NTPase, TIM-barrel, Flavodoxin, and Ferredoxin-like. We elaborate on several particularly interesting cases, where the bridging themes mediate ligand binding. Ligand binding may have contributed to the stability and the plasticity of these building blocks, and to their ability to invade preexisting domains or serve as starting points for completely new domains.
Multinucleation Associated DNA Damage causes quiescence despite compromised p53
Authors: Hart Madeleine , Adams Sophie D , Draviam Viji M 
Published: December 2020

ABSTRACTNuclear atypia is one of the earliest hallmarks of cancer progression. How distinct forms of nuclear atypia differently impact cell fate is not understood at the molecular level. Here, we perform single-cell tracking studies to determine the immediate and long-term impact of multinucleation or misshapen nuclei and reveal a significant difference between multinucleation and micronucleation, a catastrophic nuclear atypia known to promote genomic rearrangements and tumour heterogeneity. Tracking the fate of newborn cells exhibiting various nuclear atypia shows that multinucleation, unlike other forms of nuclear atypia, blocks proliferation in p53-compromised cells. Because compromised p53 is seen in over 50% of cancers, we explored how multinucleation blocks proliferation and promotes quiescence. Multinucleation increases 53BP1-decorated nuclear bodies (DNA damage repair platforms), along with a heterogeneous reduction in transcription and protein accumulation across the multi-nucleated compartments. Importantly, Multinucleation Associated DNA Damage (MADD) associated 53BP1-bodies remain unresolved for days, despite an intact NHEJ machinery that repairs laser-induced DNA damage within minutes. This persistent MADD signalling blocks the onset of DNA replication and is associated with driving proliferative G1 cells into quiescence, revealing a novel replication stress independent cell cycle arrest caused by mitotic lesions. These findings call for segregating protective and prohibitive nuclear atypia to inform therapeutic approaches aimed at limiting tumour heterogeneity.
Identification of the toxic 6mer seed consensus in human cancer cells
Authors: Patel Monal , Bartom Elizabeth T. , Paudel Bidur , Kocherginsky Masha , O’Shea Kaitlyn L. , Murmann Andrea E. , Peter Marcus E. 
Published: December 2020

Abstract6mer seed toxicity is a novel anti-cancer mechanism that kills cancer cells by triggering death induced by survival gene elimination (DISE). It is based on si- or shRNAs with a specific G-rich nucleotide composition in position 2-7 of their guide strand. An arrayed screen of 4096 6mer seeds on two human and two mouse cell lines identified a consensus GGGGGC as the most toxic seed. After testing two more cell lines, one human and one mouse, we found that the GGGGGC seed while also toxic to murine cells, is more toxic to human cells, suggesting that the evolution to use of Gs as part of the toxic seeds is still slowly evolving, with Gs more common in the human toxic seeds. While new RNA Seq and bioinformatics analyses suggest that the GGGGGC seed is toxic to cancer cells by targeting GCCCCC seed matches in the 3’ UTR of a set of genes critical for cell survival, we now directly confirm this by identifying a number of genes targeted by this seed. Furthermore, by using a luciferase reporter fused to the 3’ UTR of these genes we confirm direct and specific on-targeting of GCCCCC seed matches. Targeting is strongly attenuated after mutating the GCCCCC seed matches in these 3’ UTRs. Our data confirm that an siRNA containing the GGGGGC seed kills cancer cells through its miRNA like activity and points at artificial miRNAs, si- or shRNAs containing this seed as a potential new cancer therapeutics.
Neuronal Correlates of the Perceptual Invariance of Words and Other Sounds in the Supplementary Motor Area of Macaques
Authors: Melchor Jonathan , Morán Isaac , Vergara José , Figueroa Tonatiuh , Perez-Orive Javier , Lemus Luis 
Published: December 2020

ABSTRACTThe supplementary motor area (SMA) of the brain is critical for integrating memory and sensory signals into perceptual decisions. For example, in macaques, SMA activity correlates with decisions based on the comparison of sounds.1In humans, functional MRI shows SMA activation during the invariant recognition of words pronounced by different speakers.2Nevertheless, the neuronal correlates of perceptual invariance are unknown. Here we show that the SMA of macaques associates novel sounds with behaviors triggered by similar learned categories when recognizing sounds such as words. Notably, the neuronal activity at single and population levels correlates with the monkeys’ behaviors (e.g. hits and false alarms). Our results demonstrate that invariant recognitions of complex sounds involve premotor computations in areas other than the temporal and parietal speech areas. Therefore, we propose that perceptual invariance depends on motor predictions and not only sensory representations. We anticipate that studies on speech will observe sensory-motor transformations of acoustic information into motor skills.
Characterization of chitin deacetylase genes in theDiaphorina citrigenome
Authors: Miller Sherry , Shippy Teresa D. , Tamayo Blessy , Hosmani Prashant S , Flores-Gonzalez Mirella , Mueller Lukas A , Hunter Wayne B , Brown Susan J , D’elia Tom , Saha Surya 
Published: December 2020

AbstractChitin deacetylases (CDAs) are one of the least understood components of insect chitin metabolism. The partial deacetylation of chitin polymers appears to be important for the proper formation of higher order chitin structures, such as long fibers and bundles, that contribute to the integrity of the insect exoskeleton and other structures. Some CDAs may also play a role in bacterial defense. Here we report the characterization of four CDA genes from the Asian citrus psyllid,Diaphorina citri,laying the groundwork for future study of these genes.D. citriis the vector forCandidatusLiberibacter asiaticus (CLas), which is responsible for the global outbreak of Huanglongbing (citrus greening) disease. The manual annotation was done as part of a collaborative community annotation project (https://citrusgreening.org/annotation/index).
Effect of insider trading on stock characteristics
Authors: Nanda Sudipta Kumar , Barai Parama 
Published: December 2020

PurposeThis paper investigates if investors consider legal insider trading data while making investment decisions. If any investment decision is based on insider transactions, then it will result in abnormal stock characteristics. The purpose of this paper is to investigate if insider trading affects stock characteristics like price, return and volume. The paper further investigates the effect on stock characteristics after the trade of different types of insiders and the relationship between abnormal return and abnormal volume.Design/methodology/approachThe study uses the event study method to measure the abnormal price, return and volume. Two-stage least square regression is used to investigate the relationship between abnormal return and abnormal volume.FindingsThe insider trades affect price, return and volume. The results are identical for both buy and sell transactions. The trades of different types of insiders have diverse effects on stock characteristics. The trades of substantial shareholders give rise to the highest abnormal price and return, whereas the promoters' trades result in the highest abnormal volume. No relationship is detected between abnormal return and volume.Originality/valueA novel method to calculate the abnormal price is proposed. The effect of trading of all types of insiders on stock characteristics is analyzed. The relationship between abnormal return and abnormal volume, after an insider trade, is investigated.
Can R&D internationalization improve EMNES' innovation efficiency? The moderating effects of TMT human capital
Authors: Zhong Xi , Song Tiebo , Chen Weihong 
Published: December 2020

PurposeThe authors aim to discuss the impact of research and development (R&D) internationalization on emerging market enterprises' (EMNEs') innovation efficiency, as well as the moderating effects of top management team (TMT) human capital.Design/methodology/approachThe authors empirically tested the hypotheses based on Chinese listed manufacturing company data from 2008 to 2017.FindingsR&D internationalization helps to increase EMNEs' innovation efficiency. Incorporating TMT human capital into this framework, the authors found that international experience, education level and technical background would all strengthen the above relationship.Originality/valueFirst, the authors contribute to the R&D internationalization literature by providing the first empirical evidence that R&D internationalization will influence EMNEs' innovation efficiency. Second, this study enriches the research results on the driving factors of enterprise innovation efficiency and expands the related research results on the relationship between R&D internationalization and production efficiency. Third, the research highlights the prominent position of TMT human capital in the relationship between R&D internationalization and EMNEs' innovation efficiency, which strengthens the contextual characteristics of the “R&D internationalization-innovation performance” framework.
Empirical assessment on factors contributing to integrity practices of Malaysian public sector officers
Authors: Johari Razana Juhaida , Alam Md. Mahmudul , Said Jamaliah 
Published: December 2020

PurposeIntegrity-related issues are now endemic to public service bureaucracies. It is claimed that corruption in the public sector is very common in various departments/agencies. Lack of integrity will lead to failings in governance and proper oversight of procedures, and subsequently poor financial management and incidents of fraud. Based on the stakeholder theory perspective, this study examines the influences of accountability, risk management and managerial commitment on practices of integrity in the Malaysian public sector.Design/methodology/approachPrimary data were collected through both printed and online questionnaires given to 210 department heads operating within selected Malaysian federal ministries. Data were analysed via the partial least squares-structural equation modelling (PLS-SEM) approach to examine the research hypotheses.FindingsIt is evident that integrity practices in Malaysia's public sector are statistically significantly related to risk management, accountability and management commitment.Practical implicationsThe findings will help the Malaysian federal ministries to take the necessary steps to improve integrity so that dependability and efficiency are the hallmarks of public sector services.Originality/valueTo the best of the authors' knowledge, this study is one of the first to examine the role of accountability, risk management and managerial commitment to integrity in the public sector of a developing market economy.
Hyperspectral estimation of soil organic matter content using grey relational local regression model
Authors: Cao Xuesong , Li Xican , Ren Wenjing , Wu Yanan , Liu Jieya 
Published: December 2020

PurposeThis study aims to improve the accuracy of hyperspectral estimation of soil organic matter content.Design/methodology/approachBased on the uncertainty in spectral estimation, 76 soil samples collected in Zhangqiu District, Jinan City, Shandong Province, were studied in this paper. First, the spectral transformation of the spectral data after denoising was carried out by means of 11 transformation methods such as reciprocal and square, and the estimation factor was selected according to the principle of maximum correlation. Secondly, the grey weighted distance was used to calculate the grey relational degree between the samples to be estimated and the known patterns, and the local linear regression estimation model of soil organic matter content was established by using the pattern samples closest to the samples to be identified. Thirdly, the models were optimized by gradually increasing the number of modeling samples and adjusting the decision coefficient, and a comprehensive index was constructed to determine the optimal predicted value. Finally, the determination coefficient and average relative error are used to evaluate the validity of the model.FindingsThe results show that the maximum correlation coefficient of the seven estimated factors selected is 0.82; the estimation results of 14 test samples are of high accuracy, among which the determination coefficient R2 = 0.924, and the average relative error is 6.608%.Practical implicationsStudies have shown that it is feasible and effective to estimate the content of soil organic matter by using grey correlation local linear regression model.Originality/valueThe paper succeeds in realizing both the soil organic matter hyperspectral grey relation estimating pattern based on the grey relational theory and the estimating pattern by using the local linear regression.