bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic signals of local adaptation and hybridization in Asian white birch
Authors: Nocchi Gabriele , Wang Jing , Yang Long , Ding Junyi , Gao Ying , Buggs Richard J. A. , Wang Nian 
Published: July 2022

AbstractDisentangling the numerous processes that affect patterns of genome-wide diversity in widespread tree species has important implications for taxonomy, conservation, and forestry. Here, we investigate the population genomic structure of Asian white birch (Betula platyphylla) in China and seek to explain it in terms of hybridization, demography and adaptation. We generate whole genome sequence data from 83 individuals across the species range in China. Combining this with an existing dataset for 79 European and Russian white birches, we show a clear distinction betweenB. pendulaandB. platyphylla, which have sometimes been lumped taxonomically. Genomic diversity ofB. platyphyllain north-western China and Central Russia is affected greatly by hybridization withB. pendula. Excluding these hybridized populations,B. platyphyllain China has a linear distribution from north-eastern to south-western China, along the edge of the inland mountainous region. Within this distribution, three genetic clusters are found, which we model as long diverged with subsequent episodes of gene flow. Patterns of co-variation between allele frequencies and environmental variables inB. platyphyllasuggest the role of natural selection in the distribution of diversity at 7,609 SNPs of which 3,767 were significantly differentiated among the genetic clusters. The putative adaptive SNPs are distributed throughout the genome and span 1,633 genic regions. Of these genic regions, 87 were previously identified as candidates for selective sweeps in EurasianB. pendula. We use the 7,609 environmentally associated SNPs to estimate the risk of non-adaptedness for each sequencedB. platyphyllaindividual under a scenario of future climate change, highlighting areas where populations may be under future threat from rising temperatures.
Development of nanobodies as theranostic agents against CMY-2-like class C β-lactamases
Authors: Frédéric Cawez , Mercuri Paola Sandra , Yanez Francisco Morales , Maalouf Rita , Vandevenne Marylène , Kerff Frederic , Guérin Virginie , Mainil Jacques , Thiry Damien , Saulmont Marc , Vanderplasschen Alain , Lafaye Pierre , Aymé Gabriel , Bogaerts Pierre , Dumoulin Mireille , Galleni Moreno 
Published: July 2022

ABSTRACTSoluble single-domain fragments derived from the unique variable region of camelid heavy-chain antibodies (VHHs) against enzymes may behave as potent inhibitors. The immunization of alpacas with the CMY-2 β-lactamase led to the isolation of three VHHs that specifically recognized and inhibited CMY-2. The structure of the complex VHH cAbCMY-2(254)/CMY-2 was determined by X-ray crystallography. We showed that the epitope is close to the active site and that the CDR3 of the VHH protrudes in the catalytic site. The β-lactamase inhibition was found to follow a mixed profile with a predominant non-competitive component. The three isolated VHHs recognized overlapping epitopes since they behaved as competitive binder. Our study identified a binding site that can be targeted by a new class of β-lactamase’s inhibitors designed with the help of a peptidomimetic approach. Furthermore, the use of mono or bivalent VHH and rabbit polyclonal anti-CMY-2 antibodies enable the development of the first generation of ELISA test for the detection of CMY-2 produced by resistant bacteria.IMPORTANCEThe still increasing antimicrobial resistance in human clinic or veterinary medicine is a major threat for modern chemotherapy. Beside the major caution in the use of current antibiotics, it is important to develop new classes of antibiotics. This work was focused on β-lactamases that are the enzymes involved in the hydrolysis of the major class of antibiotics, the β-lactam compounds. We selected camelid antibodies that inhibit CMY-2, a class C β-lactamase produced by bacteria isolated from the veterinary and human settings. We characterized the conformational epitope present in CMY-2 in order to create a new family of inhibitors based on the paratope of the antibody. Finally, we designed a primary version of a detection system based on an ELISA using VHH and polyclonal antibodies.
A modular platform for bioluminescent RNA tracking
Authors: Ng Kevin K. , Cole Kyle H. , Halbers Lila P. , Chan Christelle E.T. , Fuller Erin B. , Callicoatte Chelsea , Metcalfe Mariajose , Chen Claire C. , Barhoosh Ahfnan A. , Reid-McLaughlin Edison , Kent Alexandra D. , Steward Oswald , Lupták Andrej , Prescher Jennifer A. 
Published: July 2022

AbstractA complete understanding of RNA biology requires methods for tracking transcriptsin vivo. Common strategies rely on fluorogenic probes that are limited in sensitivity, dynamic range, and depth of interrogation, owing to their need for excitation light and tissue autofluorescence. To overcome these challenges, we developed a bioluminescent platform for serial imaging of RNAs. Small RNA tags were engineered to recruit light-emitting luciferase fragments (termed RNA lanterns) upon transcription. Robust photon production was observed for RNA targets both in cells and in live animals. Importantly, only a single copy of the tag was necessary for sensitive detection, in sharp contrast to fluorescent platforms requiring multiple repeats. Overall, this work provides a foundational platform for visualizing RNA dynamics from the micro to the macro scale.
Synergizing exchangeable fluorophore labels for multi-target STED microscopy
Authors: Glogger M. , Wang D. , Kompa J. , Balakrishnan A. , Hiblot J. , Barth H.D. , Johnsson K. , Heilemann M. 
Published: July 2022

AbstractInvestigating the interplay of cellular proteins with optical microscopy requires multi-target labeling. Spectral multiplexing using high-affinity or covalent labels is limited in the number of fluorophores that can be discriminated in a single imaging experiment. Advanced microscopy methods such as STED microscopy additionally demand balanced excitation, depletion and emission wavelengths for all fluorophores, further reducing multiplexing capabilities. Non-covalent, weak-affinity labels bypass this “spectral barrier” through label exchange and sequential imaging of different targets. Here, we combine exchangeable HaloTag ligands, weak-affinity DNA hybridization and hydrophophic and protein-peptide interactions to increase labeling flexibility and demonstrate 6-target STED microscopy in single cells. We further show that exchangeable labels reduce photobleaching, facilitate long acquisition times and multi-color live-cell and high-fidelity 3D STED microscopy. The synergy of different types of exchangeable labels increase the multiplexing capabilities in fluorescence microscopy, and by that, the information content of microscopy images.
Host pathways associated with human bacterial infections extend to commensal Wolbachia-Drosophila endosymbiosis
Authors: Sharmin Zinat , Samarah Hani , Aldaya Bourricaudy Rafael , Serbus Laura Renee 
Published: July 2022

ABSTRACTWolbachia bacteria are among the most successful endosymbionts in nature, carried by half of all insect species. Unlike human bacterial pathogens that kill host cells and tissues, Wolbachia endosymbionts are generally carried by insects with little adverse effect. The striking difference in outcome raises a basic question of what aspects of infection mechanisms are conserved across systems. In this study, 37 small molecule inhibitors were used to test whether 14 candidate host processes that affect the abundance of other intracellular bacteria also affect Wolbachia. Compounds that significantly affected the absolute abundance of the Wolbachia surface protein (wsp) gene in D. melanogaster were retested in D. simulans flies. 5 compounds that consistently increased wsp abundance in both systems were associated with the Imd pathway, Calcium signaling, Ras/mTOR signaling, and the Wnt pathway. By contrast, the only compound to suppress wsp abundance was a Ubiquitin-proteasome pathway inhibitor. The implicated host processes were retested for impact on Wolbachia using constitutive and inducible RNAi expression systems in D. melanogaster. These tests corroborated a function for the host target of rapamycin (tor) and armadillo (arm) genes in affecting bodywide wsp abundance. Prior studies have reported that Ras/mTOR and Wnt pathways interact with ATG6 (Beclin-1), representing a possible convergence point for signaling impacts on Wolbachia. ATG6 disruption tests, driven by inducible RNAi expression, also elevated wsp abundance. This work suggests that combined effects of the Wnt pathway, Ras/mTOR signaling, and autophagy normally support Wolbachia containment, moderating the Wolbachia-host endosymbiosis.IMPORTANCEDisease-related microbes have been intensively studied as a model for infection. An intrinsic complication of such studies is bacterial induction of cell stress and cell death. To expand our understanding of cellular infection mechanisms, we studied a bacterial endosymbiont of insects, called Wolbachia, that does not kill the cells it infects. We asked whether cellular processes involved in pathogen infection are also associated with Wolbachia infections. Chemical and genetic tests were used to investigate cellular effects on Wolbachia abundance within fruit flies. We identified a subset of cellular processes with robust, repeatable effects on Wolbachia infection: the Wnt pathway and the Ras/mTor pathway. The results also suggest that multiple cellular pathways act together, which collectively suppresses Wolbachia abundance in vivo. Active host containment may explain in part why Wolbachia is mostly regarded as a neutral endosymbiont, and not as a pathogen.
A New Software Tool for Computer Assisted In Vivo High-Content Analysis of Transplanted Fluorescent Cells in intact Zebrafish Larvae
Authors: Førde Jan-Lukas , Nerbø Reiten Ingeborg , Fladmark Kari Espolin , Kittang Astrid Olsnes , Herfindal Lars 
Published: July 2022

AbstractAcute myeloid leukaemia and myelodysplastic syndromes are cancers of the bone marrow with poor prognosis in frail and older patients. To investigate cancer pathophysiology and therapies, confocal imaging of fluorescent cancer cells, and their response to treatments in zebrafish larvae, yields valuable information. While zebrafish larvae are well suited for confocal imaging, the lack of efficient processing of large datasets remains a severe bottleneck. To alleviate this problem, we present a software-tool to segment cells from confocal images and track characteristics such as volume, location in the larva and fluorescent intensity on a single-cell basis. Using this software-tool, we were able to characterize the responses of the cancer cell lines Molm-13 and MDS-L to established treatments. By utilizing the computer-assisted processing of confocal images as presented here, more information can be obtained while being less time-consuming and reducing the demand of manual data handling, when compared to a manual approach, thereby accelerating the pursuit of novel anti-cancer treatments.Summary statementWe present a software tool for automatic cell segmentation of fluorescent cancer cells in zebrafish larvae to determine characteristics of the cancer cell population on a single-cell basis.
Mean-field approximations with adaptive coupling for networks with spike-timing-dependent plasticity
Authors: Duchet Benoit , Bick Christian , Byrne Áine 
Published: July 2022

AbstractUnderstanding the effect of spike-timing-dependent plasticity (STDP) is key to elucidate how neural networks change over long timescales and to design interventions aimed at modulating such networks in neurological disorders. However, progress is restricted by the significant computational cost associated with simulating neural network models with STDP, and by the lack of low-dimensional description that could provide analytical insights. Phase-difference-dependent plasticity (PDDP) rules approximate STDP in phase oscillator networks, which prescribe synaptic changes based on phase differences of neuron pairs rather than differences in spike timing. Here we construct mean-field approximations for phase oscillator networks with STDP to describe part of the phase space for this very high dimensional system. We first show that single-harmonic PDDP rules can approximate a simple form of symmetric STDP, while multi-harmonic rules are required to accurately approximate causal STDP. We then derive exact expressions for the evolution of the average PDDP coupling weight in terms of network synchrony. For adaptive networks of Kuramoto oscillators that form clusters, we formulate a family of low-dimensional descriptions based on the mean field dynamics of each cluster and average coupling weights between and within clusters. Finally, we show that such a two-cluster mean-field model can be fitted to synthetic data to provide a low-dimensional approximation of a full adaptive network with symmetric STDP. Our framework represents a step towards a low-dimensional description of adaptive networks with STDP, and could for example inform the development of new therapies aimed at maximizing the long-lasting effects of brain stimulation.
Optimizing multifunctional fluorescent ligands for intracellular labeling
Authors: Kumar Pratik , Vevea Jason D. , Tkachuk Ariana N. , Campbell Kirby , Watson Emma T. , Ayala Anthony X. , Grimm Jonathan B. , Chapman Edwin R. , Solecki David J. , Lavis Luke D. 
Published: July 2022

AbstractEnzyme-based self-labeling tags enable covalent attachment of synthetic molecules to proteins inside living cells. A frontier of this field is designing multifunctional ligands that contain both fluorophores and affinity tags or pharmacological agents and can still efficiently enter cells. Self-labeling tag ligands with short linkers can enter cells readily but often show less activity due to steric issues; ligands with long linkers can be more potent but show lower cell permeability. Here, we overcome this tug-of-war between efficacy and cell-permeability by devising a rational strategy for making cell permeable multifunctional ligands for labeling HaloTag fusions. We found that the lactone–zwitterion equilibrium sconstant (KL–Z) of rhodamines inversely correlates with their distribution coefficients (logD7.4), suggesting that ligands based on dyes exhibiting lowKL–Zand high logD7.4values, such as Si-rhodamines, would efficiently enter cells. We designed cell-permeable multifunctional HaloTag ligands with a biotin moiety to purify mitochondria or a JQ1 appendage to translocate BRD4 from euchromatin to the nucleolus or heterochromatin. We discovered that translocation of BRD4 to constitutive heterochromatin in cells expressing HaloTag–HP1a fusion proteins can lead to apparent increases in transcriptional activity. These new reagents enable affinity capture and translocation of intracellular proteins in living cells and the use of Si-rhodamines and other lowKL–Z/high logD7.4dye scaffolds will facilitate the design of new multifunctional chemical tools for biology.SIGNIFICANCE STATEMENTUnderstanding cellular processes requires tools to measure and manipulate proteins in living cells. Self- labeling tags, such as the HaloTag and SNAP-tag, enable modification of cellular proteins with synthetic molecules. Creating ligands for these systems that have more than one chemical motif remains challenging, however, due to competing demands between cell permeability and functionality. We discovered that multifunctional ligands based on Si-rhodamines efficiently entered cells and enabled affinity purification of mitochondria or translocation of nuclear proteins; the performance of these molecules could be verified by fluorescence microscopy. These compounds should be useful for a variety of biological experiments and our general framework will allow the design of other multifunctional ligands to study living systems.
Molecular glue CELMoD compounds are allosteric regulators of cereblon conformation
Authors: Watson Edmond R. , Novick Scott J. , Matyskiela Mary E. , Chamberlain Philip P. , de la Peña Andres Hernandez , Zhu Jin-Yi , Tran Eileen , Griffin Patrick R. , Wertz Ingrid E. , Lander Gabriel C. 
Published: July 2022

AbstractCereblon (CRBN) is an ubiquitin ligase (E3) adaptor protein co-opted by CRBN E3 Ligase Modulatory Drugs (CELMoD) agents that target therapeutically-relevant proteins for degradation. Prior crystallographic studies defined the drug-binding site within CRBN’s Thalidomide Binding Domain (TBD), but the allostery of drug-induced neosubstrate binding remains unclear. We therefore performed cryo-EM analyses of the DDB1∼CRBN apo-complex, and compared these structures with DDB1∼CRBN in the presence of CELMoD compounds alone and complexed with neosubstrates. Association of CELMoD compounds to the TBD is necessary and sufficient for triggering CRBN allosteric rearrangement from an “open” conformation to the canonical “closed” conformation. Importantly, the neosubstrate Ikaros only stably associates with the closed CRBN conformation, illustrating the importance of allostery for CELMoD compound efficacy, and informing structure-guided design strategies to improve therapeutic efficacy.
Emergence of multiple set-points of cellular homeostatic tension
Authors: Ueda Yuika , Deguchi Shinji 
Published: July 2022

AbstractStress fibers (SFs), a contractile actin bundle in nonmuscle mesenchymal cells, are known to intrinsically sustain a constant level of tension or tensional stress, a process called cellular tensional homeostasis. Malfunction in this homeostatic process has been implicated in many diseases such atherosclerosis, but its mechanisms remain incompletely understood. Interestingly, the homeostatic stress in individual SFs is altered upon recruitment of α-smooth muscle actin in particular cellular contexts to reinforce the preexisting SFs. While this transition of the set-point stress is somewhat a universal process observed across different cell types, no clear explanation has been provided as to why cells end up possessing different stable stresses. To address the underlying physics, here we describe that imposing a realistic assumption on the nature of SFs yields the presence of multiple set-points of the homeostatic stress, which transition among them depending on the magnitude of the cellular tension. We derive non-dimensional parameters that characterize the extent of the transition and predict that SFs tend to acquire secondary stable stresses if they are subject to as large a change in stiffness as possible or to as immediate a transition as possible upon increasing the tension. This is a minimal and simple explanation, but given the frequent emergence of force-dependent transformation of various subcellular structures in addition to that of SFs, the theoretical concept presented here would offer an essential guide to addressing potential common mechanisms governing complicated cellular mechanobiological responses.
Teaching the concept of decision-usefulness, and accounting as a technical, social and moral practice: the case of COVID-19 “case number” reporting
Authors: Sidaway Shannon I.L. , Juric Daniela , Deegan Craig 
Published: July 2022

Purpose
The purpose of this paper is to demonstrate how teaching broader accounting concepts through real life non-financial case study information (such as COVID-19 case reporting) can assist students understanding accounting’s technical, social and moral perspectives. Accounting education and practice has traditionally focussed on the technical aspects of accounting and has situated accounting within a financial context.

Design/methodology/approach
This exploratory study uses content analysis of COVID-19 case and death numbers reported by several international health reporting agencies. This study does not set out to provide a detailed technical or comparative jurisdictional analysis of the decision-usefulness of COVID-19 information. Rather, this study looks at the “decision-usefulness” of the COVID-19 case and death number information, and provides examples that educators can draw upon for inspiration when showing how the qualitative characteristics of decision-useful information can be applied to non-financial information. This study also highlights, by use of a “novel data set”, the technical, social and moral aspects of accounting.

Findings
This study finds that the COVID-19 pandemic provides an opportunity for accounting education by positioning the qualitative characteristics of decision-useful information beyond a financial context. The exploration of accounting within this setting effectively demonstrates that accounting has “technical”, “social” and “moral” dimensions.

Originality/value
This paper fulfils an identified need to include teaching of decision-usefulness of non-financial information in the accounting curriculum to ensure that future professional accountants possess technical and professional competency skills.
Finite element modeling of reinforced concrete short columns subjected to shear in two perpendicular directions
Authors: Alraqad Marya , Allouzi Rabab , Alkloub Amer 
Published: July 2022

PurposeShort columns can cause serious damage when subjected to an earthquake due to their high stiffness with low ductility. These columns can be exposed to multidirectional shear forces, which encouraged this study to investigate the behavior of structural short columns under bi-directional shear.Design/methodology/approachFinite element analysis (FEA) using ABAQUS is conducted and calibrated based on experimental data tested by previous researchers who studied the uni-directional behavior of short columns subjected to cyclic shear displacements. Then, the calibrated column models are further investigated to study the influence of bidirectional cyclic shear. Two scenarios are investigated, namely “simultaneous” and “sequential,” to compare the performance in terms of shear strength reduction.FindingsThe results show that the shear strength reduction significantly appears when 1:1 simultaneous bi-directional cyclic shear is applied. However, the shear reduction is more significant when the sequential scenario is applied. The seismic forces or deformations applied in orthogonal directions should be combined to achieve the maximum seismic response of structures as specified in Federal Emergency Management Agency (FEMA) 356 Standard. Finally, the combinations presented in literature to consider bi-directional shear are investigated. Based on FE results, the effect of applied 1:0.30 bi-directional cyclic shear simultaneously does not result in significant effect on the considered columns properly design for seismic forces.Originality/valueTo investigate the effect of multidirectional shear forces on the shear strength capacity of short columns, the presented effect of multidirectional shear forces in literature to consider bi-directional shear are investigated.