bluuebunny/crossref_metadata_2025_split huggingface dataset:
Native Mass Spectrometry of Complexes Formed by Molecular Glues Reveals Stoichiometric Rearrangement of E3 Ligases
Authors: Jackson Cara , Beveridge Rebecca 
Published: February 2023

AbstractIn this application of native mass spectrometry (nMS) to investigate complexes formed by molecular glues (MGs), we have demonstrated its efficiency in delineating stoichiometric rearrangements of E3 ligases that occur during targeted protein degradation (TPD). MGs stabilise interactions between an E3 ligase and a protein of interest (POI) targeted for degradation, and these ternary interactions are challenging to characterise. We have shown that nMS can unambiguously identify complexes formed between the CRBN:DDB1 E3 ligase and the POI GSPT1 upon the addition of lenalidomide, pomalidomide or thalidomide. Ternary complex formation was also identified involving the DCAF15:DDA1:DDB1 E3 ligase in the presence of MG (E7820 or indisulam) and POI RBM39. Moreover, we uncovered that the DCAF15:DDA1:DDB1 E3 ligase self-associates into dimers and trimers when analysed alone at low salt concentrations (100 mM ammonium acetate) which dissociate into single copies of the complex at higher salt concentrations (500 mM ammonium acetate), or upon the addition of MG and POI, forming a 1:1:1 ternary complex. This work demonstrates the strength of nMS in TPD research, reveals novel binding mechanisms of the DCAF15 E3 ligase, and highlights the potential effect of salt concentrations on protein complexes during structural analysis.
An inhibitory circuit-based enhancer of Dyrk1a function reversesDyrk1a-associated impairment in social recognition
Authors: Shih Yu-Tzu , Alipio Jason Bondoc , Sahay Amar 
Published: February 2023

SUMMARYHeterozygous mutations in the Dual specificity tyrosine-phosphorylation-regulated kinase 1aDyrk1agene define a syndromic form of Autism Spectrum Disorder. The synaptic and circuit mechanisms mediating Dyrk1a functions in social cognition are unclear. Here, we identify a social experience-sensitive mechanism in hippocampal mossy fiber-parvalbumin interneuron (PV IN) synapses by which Dyrk1a recruits feedforward inhibition of CA3 and CA2 to promote social recognition. We employ genetic epistasis logic to identify a cytoskeletal protein, Ablim3, as a synaptic substrate of Dyrk1a. We demonstrate thatAblim3downregulation in dentate granule cells of adult hemizygousDyrk1amice is sufficient to restore PV IN mediated inhibition of CA3 and CA2 and social recognition. Acute chemogenetic activation of PV INs in CA3/CA2 of adult hemizygousDyrk1amice also rescued social recognition. Together, these findings illustrate how targeting Dyrk1a synaptic and circuit substrates as “enhancers of Dyrk1a function” harbors potential to reverseDyrk1ahaploinsufficiency-associated circuit and cognition impairments.HighlightsDyrk1a in mossy fibers recruits PV IN mediated feed-forward inhibition of CA3 and CA2Dyrk1a-Ablim3 signaling in mossy fiber-PV IN synapses promotes inhibition of CA3 and CA2DownregulatingAblim3restores PV IN excitability, CA3/CA2 inhibition and social recognition inDyrk1a+/-miceChemogenetic activation of PV INs in CA3/CA2 rescues social recognition inDyrk1a+/-mice
Reconfigurable pH-Responsive DNA Origami Lattices
Authors: Julin Sofia , Linko Veikko , Kostiainen Mauri A. 
Published: February 2023

AbstractDNA nanotechnology enables straightforward fabrication of user-defined and nano-meter-precise templates for a cornucopia of different uses. To date, most of these DNA assemblies have been static, but dynamic structures are increasingly coming into view. The programmability of DNA not only allows encoding of the DNA object shape, but it may be equally used in defining the mechanism of action and the type of stimuli-responsiveness of the dynamic structures. However, these "robotic" features of DNA nanostructures are usually demonstrated for only small, discrete and device-like objects rather than for collectively behaving higher-order systems. Here, we show how a large-scale, two-dimensional (2D) and pH-responsive DNA origami -based lattice can be assembled on a mica substrate and further reversibly switched between two distinct states upon the pH change of the surrounding solution. The control over these two configurations is achieved by equipping the arms of the lattice-forming DNA origami units with "pH-latches" that form Hoogsteen-type triplexes at low pH. In a nutshell, we demonstrate how the electrostatic control over the adhesion and mobility of the DNA origami units on the surface can be used both in the large lattice formation (with the help of directed polymerization) and in the conformational switching of the whole lattice on the substrate. To further emphasize the feasibility of the method, we also demonstrate the formation of reconfigurable 2D gold nanoparticle lattices. We believe this work serves as an important milestone in bridging the nanometer-precise DNA origami templates and higher-order large-scale systems with the stimuli-induced dynamicity.
Modulation of transcription burst amplitude underpins dosage compensation in theDrosophilaembryo
Authors: Forbes Beadle Lauren , Zhou Hongpeng , Rattray Magnus , Ashe Hilary L. 
Published: February 2023

SummaryDosage compensation, the balancing of X linked gene expression between sexes and to the autosomes, is critical to an organism’s fitness and survival. InDrosophila, dosage compensation involves hypertranscription of the male X chromosome. Here we use quantitative live imaging and modelling at single-cell resolution to determine the mechanism underlying X chromosome dosage compensation inDrosophila. We show that the four X chromosome genes studied undergo transcriptional bursting in male and female embryos. Mechanistically our data reveal that transcriptional upregulation of male X chromosome genes is primarily mediated by a higher RNA polymerase II initiation rate and burst amplitude across the expression domain. In contrast, burst frequency is spatially modulated in nuclei within the expression domain in response to different transcription factor concentrations to tune the transcriptional response. Together, these data show how the local and global regulation of distinct burst parameters establish the complex transcriptional outputs underpinning developmental patterning.
Long-term CRISPR array dynamics and stable host-virus co-existence in subsurface fractured shales
Authors: Amundson Kaela K. , Roux Simon , Shelton Jenna L. , Wilkins Michael J. 
Published: February 2023

AbstractViruses are the most ubiquitous biological entities on earth. Even so, elucidating the impact of viruses on microbial communities and associated ecosystem processes often requires identification of strong host-virus linkages – an undeniable challenge in many ecosystems. Subsurface fractured shales present a unique opportunity to first make these strong linkages and subsequently reveal complex long-term host-virus dynamics and trends in CRISPR array size and frequency. Here, we sampled two replicated sets of fractured shale wells for nearly 800 days (Denver-Julesburg Basin, Colorado, USA). We identified a relatively diverse microbial community with widely encoded CRISPR viral defense systems, which facilitated 2,110 CRISPR-based viral linkages across 90 host MAGs representing 25 phyla. Leveraging these linkages with timeseries data across differing well ages, we observed how patterns of host-virus co-existence develop and converge in this closed ecosystem through time. We observed a transition to smaller CRISPR arrays in older, more established wells, potentially reflecting a natural progression where CRISPR arrays harbor fewer, yet more effective spacers that target viral genes with fewer mutations. Together, our findings shed light on the complexities of host-virus temporal dynamics as well as possible drivers of spacer loss and acquisition within CRISPR arrays of diverse microbial populations through time.
Regulation of parvalbumin interneuron plasticity by neuropeptide-encoding genes
Authors: Selten Martijn , Bernard Clémence , Hamid Fursham , Hanusz-Godoy Alicia , Oozeer Fazal , Zimmer Christoph , Marín Oscar 
Published: February 2023

AbstractNeuronal activity is regulated in a narrow permissive band for the proper operation of neural networks. Changes in synaptic connectivity and network activity, for example, during learning, might disturb this balance, eliciting compensatory mechanisms to maintain network function. In the neocortex, excitatory pyramidal cells and inhibitory interneurons exhibit robust forms of stabilising plasticity. However, while neuronal plasticity has been thoroughly studied in pyramidal cells, little is known about how interneurons adapt to persistent changes in their activity. Here we uncover the critical cellular and molecular mechanisms through which cortical parvalbumin-expressing (PV+) interneurons adapt to changes in their activity levels. We found that changes in the activity of PV+ interneurons drive cell-autonomous, bi-directional compensatory adjustments of the number and strength of inhibitory synapses received by these cells, specifically from other PV+ interneurons. High-throughput profiling of ribosome-associated mRNA revealed that increasing the activity of PV+ interneurons leads to the cell-autonomous upregulation of two genes encoding multiple secreted neuropeptides,VgfandScg2. Functional experiments demonstrated that VGF is critically required for the activity-dependent scaling of inhibitory PV+ synapses onto PV+ interneurons. Our findings reveal an instructive role for neuropeptide-encoding genes in regulating synaptic connections among PV+ interneurons in the adult mouse neocortex.
Developmental and molecular contributions to contextual fear memory emergence in mice
Authors: Lanjewar Alexandra L. , Levitt Pat , Eagleson Kathie L. 
Published: February 2023

ABSTRACTCognitive impairment is a common phenotype of neurodevelopmental disorders, but how these deficits arise remains elusive. Determining the onset of discrete cognitive capabilities facilitates studies in probing mechanisms underlying their emergence. The present study analyzed the emergence of contextual fear memory persistence (7-day memory retention) and remote memory (30-day memory retention). There was a rapid transition from postnatal day (P) 20 to P21, in which memory persistence emerged in C57Bl/6J male and female mice. Remote memory was present at P23, but expression was not robust compared to pubertal and adult mice. Previous studies reported that following deletion of the MET receptor tyrosine kinase (MET), there are fear memory deficits in adult mice and the timing of critical period plasticity is altered in the developing visual cortex, positioning MET as a regulator for onset of contextual fear memory. SustainingMetpast the normal window of peak cortical expression or deletingMet, however, did not alter the timing of emergence of persistence or remote memory capabilities during development. Fear memory in young adults, however, was disrupted. Remarkably, compared to homecage controls, the number of FOS-expressing infragranular neurons in medial prefrontal cortex (mPFC) did not increase from contextual memory formation recall of fear conditioning at P35 but exhibited enhanced activation at P90 in male and female mice. Additionally, MET-expressing neurons were preferentially recruited at P90 compared to P35 during fear memory expression. The studies demonstrate a developmental profile of contextual fear memory capabilities. Further, developmental disruption ofMetleads to a delayed functional deficit that arises in young adulthood, correlated with an increase of mPFC neuron activation during fear memory recall.
Simulations predict preferred Mg2+coordination in a nonenzymatic primer extension reaction center
Authors: Mittal Shriyaa , Nisler Collin , Szostak Jack W. 
Published: February 2023

ABSTRACTThe mechanism by which genetic information was copied prior to the evolution of ribozymes is of great interest because of its importance to the origin of life. The most effective known process for the nonenzymatic copying of an RNA template is primer extension by a two-step pathway in which 2-aminoimidazole activated nucleotides first react with each other to form an imidazolium-bridged intermediate that subsequently reacts with the primer. Reaction kinetics, structure-activity relationships, and X-ray crystallography have provided insight into the overall reaction mechanism, but many puzzles remain. In particular, high concentrations of Mg2+are required for efficient primer extension, but the mechanism by which Mg2+accelerates primer extension remains unknown. By analogy with the mechanism of DNA and RNA polymerases, a role for Mg2+in facilitating the deprotonation of the primer 3′-hydroxyl is often assumed, but no catalytic metal ion is seen in crystal structures of the primer extension complex. To explore the potential effects of Mg2+binding in the reaction center, we performed atomistic molecular dynamics simulations of a series of modeled complexes in which a Mg2+ion was placed in the reaction center with inner sphere coordination to different sets of functional groups. Our simulations suggest that coordination of a Mg2+ion to both O3′ of the terminal primer nucleotide and the pro-Spnon- bridging oxygen of the reactive phosphate of an imidazolium-bridged dinucleotide would help to preorganize the structure of the primer/template substrate complex to favor the primer-extension reaction. Our results suggest that the catalytic metal ion may play an important role in overcoming electrostatic repulsion between a deprotonated O3′ and the reactive phosphate of the bridged dinucleotide. Our simulations lead to testable predictions of the mode of Mg2+binding that is most relevant to catalysis of primer extension.STATEMENT OF SIGNIFICANCEPrior to the evolution of complex enzymes, the replication of genetic material must have relied on nonenzymatic mechanisms. Nonenzymatic RNA template copying can be achieved through the extension of a primer by reaction with a 2-aminoimidazole (2AI) bridged dinucleotide in the presence of Mg2+. Despite progress in understanding the mechanism of this reaction, the catalytic role of Mg2+remains poorly understood. Here, we present a series of molecular dynamics simulations of a model RNA primer-extension complex in different potential reactive conformations. We find that one configuration of both the 2AI moiety and coordination state of the Mg2+promotes a geometry that is most favorable to reaction, suggesting a potential structural role for Mg2+and providing insights to guide future experiments.
The gag-like geneRTL8antagonizes PEG10-mediated virus like particles
Authors: Campodonico Will , Mohan Harihar M. , Black Holly H. , Lau Cristina I. , Paulson Henry L. , Sharkey Lisa M. , Whiteley Alexandra M. 
Published: February 2023

AbstractPEG10is a retroelement-derivedMart-family gene that is necessary for placentation and has been implicated in neurological disease. PEG10 resembles both retrotransposon and retroviral proteins and forms virus-like particles (VLPs) that can be purified using iodixanol ultracentrifugation. It is hypothesized that formation of VLPs is crucial to the biological roles of PEG10 in reproduction and neurological health. Here, we describe the regulation of PEG10 VLP formation and release in human cells with a role for the relatedMartgeneRTL8. RTL8 resembles a truncated form of PEG10 that shares homology with the N-terminal gag-like capsid domain. Alone, RTL8 is unable to form VLPs, but was incorporated into PEG10-derived particles. RTL8 co-expression decreased the abundance of PEG10 VLPs and increased intracellular levels of PEG10, suggesting a model where RTL8 inhibits PEG10 VLP formation or release. Consistent with this model, RTL8 bound to the N-terminal domain of PEG10 capsid, and modulation of RTL8 influenced PEG10-derived VLP abundance in naturally producing cells. RTL8 is broadly expressed in many of the same tissues as PEG10, including in human brain. Taken together, these results describe a novel antagonistic relationship between two human retroelement-derived genes and have implications for our understanding of PEG10 biology and disease.
Optogenetic recruitment of hypothalamic corticotrophin-releasing-hormone (CRH) neurons reduces motivational drive
Authors: Mitchell Caitlin S , Campbell Erin J , Fisher Simon D , Stanton Laura M , Burton Nicholas J , Pearl Amy J , McNally Gavan P , Bains Jaideep S , Füzesi Tamás , Graham Brett A , Manning Elizabeth E , Dayas Christopher V 
Published: February 2023

AbstractImpaired motivational drive is a key feature of depression. Chronic stress is a known antecedent to the development of depression in humans and depressive-like states in animals. Whilst there is a clear relationship between stress and motivational drive, the mechanisms underpinning this association remain unclear. One hypothesis is that the endocrine system, via corticotropin-releasing hormone (CRH) in the paraventricular nucleus of the hypothalamus (PVN; PVNCRH), initiates a hormonal cascade resulting in glucocorticoid release, and that excessive glucocorticoids change brain circuit function to produce depression-related symptoms. Another, mostly unexplored hypothesis is that the direct activity of PVNCRHneurons and their input to other stress- and reward-related brain regions drives these behaviours. To further understand the direct involvement of PVNCRHneurons in motivation, we used optogenetic stimulation to activate these neurons one hour/day for 5 consecutive days and showed increased acute stress-related behaviours and long-lasting deficits in the motivational drive for sucrose. This was associated with increased Fos-protein expression in the lateral hypothalamus (LH). Direct stimulation of the PVNCRHinputs in the LH produced a similar pattern of effects on sucrose motivation. Together, these data suggest that PVNCRHneuronal activity may be directly responsible for changes in motivational drive and that these behavioural changes may, in part, be driven by PVNCRHsynaptic projections to the LH.
Lean leadership: a bibliometric analysis
Authors: Santos Bruno B. , Sigahi Tiago F. A. C. , Rampasso Izabela Simon , Moraes Gustavo Hermínio Salati Marcondes De , Leal Filho Walter , Anholon Rosley 
Published: February 2023

PurposeThe present research aims to understand how the literature on lean leadership is currently structured. For this, the thematic subdivisions within the subject (thematic clusters) are analyzed as well as the networks between authors and the authors' countries and the chronological co-occurrence of terms over the years.Design/methodology/approachThe research strategy chosen was a bibliometric analysis conducted with documents collected from the Scopus scientific database. After screening, 192 documents were analyzed using the Vosviewer software.FindingsThe main result is related to identifying four thematic clusters. The first cluster is connected to the manufacturing and supply chain industry, and this showed an increasing concern with sustainability, agile manufacturing and digitalization. The second is related to small and medium-sized companies in which Lean concepts, often associated with Six Sigma ideas, present as differentials for competitive advantage. The third one is associated with the civil construction segment, in which there is a great need for cultural and organizational change. The fourth cluster focuses on health organizations. In all clusters, leadership plays a key role.Practical implicationsBesides the contributions to the literature on the theme, this study provides interesting insights for managers regarding the path the managers' sectors are taking in the Lean leadership context.Originality/valueThere are no studies that critically examine Lean leadership literature. This research identifies clusters on the theme, showing how Lean leadership is being addressed by international research.
Large displacement analysis of two-layer beam-columns taking into account slip and uplift
Authors: Oeng Thaileng , Keo Pisey , Guezouli Samy , Hjiaj Mohammed 
Published: February 2023

PurposeThis article presents a geometrically non-linear finite element formulation for the analysis of planar two-layer beam-columns taking into account the inter-layer slip and uplift.Design/methodology/approachThe co-rotational method is adopted, in which the motion of the element is decomposed into a rigid body motion and a small deformational one. The geometrically linear formulation can be used in the local frame and automatically be transformed into a geometrically nonlinear one. In co-rotational frame, both layers are assumed to be discretely connected at the element ends. Slips and uplifts are assumed to be small. Consequently, the condition of non interpenetration between the layers can be treated using a node-to-node contact algorithm. The resolution methods such as penalty (PM) and augmented Lagrangian method (ALM) with Uzawa updating scheme can be used.FindingsThe non-penetration condition between the layers of composite beams can be formulated by using contact law. It is found that despite a low convergence rate of augmented Lagrangian method compared to penalty method, the former prevents the unrealistic penetration. Besides, it is shown that the buckling load of the composite beam-column is largely affected by the uplift stiffness of the connectors.Originality/valueThe proposed finite element model is capable of simulating accurately the geometrically non-linear behavior of planar two-layer beam-columns taking into account the inter-layer slip and uplift. Regarding uplift, the non-penetration condition is strictly enforced by considering rigorous contact conditions at the interface. The constraint problem is solved using the penalty method or the augmented Lagrangian method with the Uzawa updating scheme.
Dependent self-employed individuals: are they different from paid employees?
Authors: Dvouletý Ondřej , Nikulin Dagmara 
Published: February 2023

PurposeThis study focusses on dependent self-employment, which covers a situation where a person works for the same employer as a typical worker whilst on a self-employment contractual basis, i.e. without a traditional employment contract and without certain rights granted to “regular” employees.Design/methodology/approachThe research exploits the individual-level dataset of 35 European countries extracted from the 2017 edition of the European Labour Force Survey (EU LFS) and compares the characteristics of employees and dependent self-employed individuals. Methodologically, the study relies on the estimation of a multivariate logistic regression model.FindingsThe main hypothesis assuming that dependent self-employed work most often in low-skilled occupations was empirically supported. There was also a non-linear (u-shaped) relationship between the years of accumulated experience (with a turning point at 35 years) and the likelihood of being dependent self-employed. Other results showed that dependent self-employed are less likely to be women and the dependent self-employed are more likely born outside of the countries where the dependent self-employed participate in the labour markets.Originality/valueThe study contributes to the field by adopting a comparable definition of dependent self-employment and exploiting the recent theoretical support of The Work Precarity Framework. The phenomenon should still be addressed by policymakers and labour office representatives, aiming to protect, primarily, vulnerable lower-skilled workers. The ongoing research should study the longitudinal dimension of dependent self-employment with a focus on motivational aspects.