bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA Polymerases in Precise and Predictable CRISPR/Cas9-mediated Chromosomal Rearrangements
Authors: Mehryar Mohammadreza M. , Shi Xin , Li Jingwei , Wu Qiang 
Published: February 2023

AbstractRecent studies have shown that Cas9-mediated CRISPR gene editing outcomes at junctions of chromosomal rearrangements are precise and predictable; however, the underlying mechanisms are poorly understood due to lack of suitable assay system and analysis tool. Here we developed a customized computer program to take account of staggered Cas9 cleavage and to rapidly process large volumes of junctional sequencing reads from chromosomal rearrangements, including DNA-fragment inversions, duplications, and deletions. We also established a sensitive assay system usingHPRT1andDCKas reporters for cell growth during DNA-fragment editing by Cas9 with dual sgRNAs and found prominent large resections at junctions of chromosomal rearrangements. In addition, we found that knockdown ofPolQ(encoding Polθ) results in increased large resections but decreased small deletions. We also found that the mechanisms for generating small deletions of 1bp and >1bp during DNA-fragment editing are different with regards to their opposite dependencies on Polθ and Polλ. Specifically, Polθ suppresses 1bp deletions but promotes >1bp deletions, whereas Polλ promotes 1bp deletions but suppresses >1bp deletions. Finally, we found that Polλ is the main DNA polymerase responsible for fill-in of the 5’ overhangs of staggered Cas9 cleavage ends. These findings contribute to our understanding of the molecular mechanisms of CRISPR/Cas9-mediated DNA-fragment editing and have important implications for controllable, precise, and predictable gene editing.
Intracellular replication ofPseudomonas aeruginosain epithelial cells requires suppression of the caspase-4 inflammasome
Authors: Kroken Abby R , Klein Keith A , Mitchell Patrick S , Nieto Vincent , Jedel Eric J , Evans David J , Fleiszig Suzanne M J 
Published: February 2023

AbstractPathogenesis ofPseudomonas aeruginosainfections can include bacterial survival inside epithelial cells. Previously, we showed this involves multiple roles played by the type three-secretion system (T3SS), and specifically the effector ExoS. This includes ExoS-dependent inhibition of a lytic host cell response that subsequently enables intracellular replication. Here, we studied the underlying cell death response to intracellularP. aeruginosa, comparing wild-type to T3SS mutants varying in capacity to induce cell death and that localize to different intracellular compartments. Results showed that corneal epithelial cell death induced by intracellularP. aeruginosalacking the T3SS, which remains in vacuoles, correlated with activation of NF-κB as measured by p65 relocalization and TNFα transcription and secretion. Deletion of caspase-4 through CRISPR-Cas9 mutagenesis delayed cell death caused by these intracellular T3SS mutants. Caspase-4 deletion also countered more rapid cell death caused by T3SS effector-null mutants still expressing the TSSS apparatus that traffic to the host cell cytoplasm, and in doing so rescued intracellular replication normally dependent on ExoS. While HeLa cells lacked a lytic death response to T3SS mutants, it was found to be enabled by interferon gamma treatment. Together, these results show that epithelial cells can activate the noncanonical inflammasome pathway to limit proliferation of intracellularP. aeruginosa, not fully dependent on bacterially-driven vacuole escape. Since ExoS inhibits the lytic response, the data implicate targeting of caspase-4, an intracellular pattern recognition receptor, as another contributor to the role of ExoS in the intracellular lifestyle ofP. aeruginosa.ImportancePseudomonas aeruginosacan exhibit an intracellular lifestyle within epithelial cells in vivo and in vitro. The type three secretion system (T3SS) effector ExoS contributes via multiple mechanisms, including extending the life of invaded host cells. Here, we aimed to understand the underlying cell death inhibited by ExoS whenP. aeruginosais intracellular. Results showed that intracellularP. aeruginosalacking T3SS effectors could elicit rapid cell lysis via the non-canonical inflammasome pathway. Caspase-4 contributed to cell lysis even when the intracellular bacteria lacked the entire T33S and were consequently unable to escape vacuoles, representing a naturally occurring subpopulation during wildtype infection. Together, the data show the caspase-4 inflammasome as an epithelial cell defense against intracellularP. aeruginosa, and implicate its targeting as another mechanism by which ExoS preserves the host cell replicative niche.
simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data
Authors: Li Chen , Chen Xiaoyang , Chen Shengquan , Jiang Rui , Zhang Xuegong 
Published: February 2023

AbstractSingle-cell chromatin accessibility sequencing (scCAS) technology provides an epigenomic perspective to characterize gene regulatory mechanisms at single-cell resolution. With an increasing number of computational methods proposed for analyzing scCAS data, a powerful simulation framework is desirable for evaluation and validation of these methods. However, existing simulators generate synthetic data by sampling reads from real data or mimicking existing cell states, which is inadequate to provide credible ground-truth labels for method evaluation. We present simCAS, an embedding-based simulator, for generating high-fidelity scCAS data from both cell-wise and peak-wise embeddings. We demonstrate simCAS outperforms existing simulators in resembling real data and show that simCAS can generate cells of different states with user-defined cell populations and differentiation trajectories. Additionally, simCAS can simulate data from different batches and encode user-specified interactions of chromatin regions in the synthetic data, which provides ground-truth labels more than cell states. We systematically demonstrate that simCAS facilitates the benchmarking of four core tasks in downstream analysis: cell clustering, trajectory inference, data integration, andcis-regulatory interaction inference. We anticipate simCAS will be a reliable and flexible simulator for evaluating the ongoing computational methods applied on scCAS data.AvailabilitysimCAS is freely available athttps://github.com/Chen-Li-17/simCAS.
Biphasic responses in cell signalling: A unified approach
Authors: Ramesh Vaidhiswaran , Krishnan J. 
Published: February 2023

AbstractBiphasic responses are encountered at all levels in biological systems. At the cellular level, biphasic dose-responses are widely encountered in cell signalling and post-translational modification systems and represent safeguards against over-activation or overexpression of species. In this paper we provide a unified theoretical synthesis of biphasic responses in cell signalling systems, by assessing signalling systems ranging from basic biochemical building blocks to canonical network structures to well-characterized exemplars on one hand, and examining different types of doses on the other. By using analytical and computational approaches applied to a range of systems across levels (described by broadly employed models) we reveal (i) design principles enabling the presence of biphasic responses, including in almost all instances, an explicit characterization of the parameter space (ii) structural factors which preclude the possibility of biphasic responses (iii) different combinations of the presence or absence of enzyme-biphasic and substrate-biphasic responses, representing safeguards against overactivation and overexpression respectively (iv) the possibility of broadly robust biphasic responses (v) the complete alteration of signalling behaviour in a network due to biphasic interactions between species (biphasic regulation) (vi) the propensity of different co-existing biphasic responses in the Erk signalling network. These results both individually and in totality have a number of important consequences for systems and synthetic biology.
Conflicts are parametrically encoded: initial evidence for a cognitive space view to reconcile the debate of domain-general and domain-specific cognitive control
Authors: Yang Guochun , Wu Haiyan , Li Qi , Liu Xun , Fu Zhongzheng , Jiang Jiefeng 
Published: February 2023

AbstractCognitive control resolves conflicts between task-relevant and -irrelevant information to enable goal-directed behavior. As conflicts can arise from different sources (e.g., sensory input, internal representations), how a limited set of cognitive control processes can effectively address diverse conflicts remains a major challenge. Based on the cognitive space theory, different conflicts can be parameterized and represented as distinct points in a (low-dimensional) cognitive space, which can then be resolved by a limited set of cognitive control processes working along the dimensions. It leads to a hypothesis that conflicts similar in their sources are also represented similarly in the cognitive space. We designed a task with five types of conflicts that could be conceptually parameterized. Both human performance and fMRI activity patterns in the right dorsolateral prefrontal (dlPFC) support that different types of conflicts are organized based on their similarity, thus suggesting cognitive space as a principle for representing conflicts.
Working memory signals in early visual cortex do not depend on visual imagery
Authors: Weber Simon , Christophel Thomas , Görgen Kai , Soch Joram , Haynes John-Dylan 
Published: February 2023

AbstractIt has been suggested that visual images are memorized across brief periods of time by vividly imagining them as if they still were there. In line with this, the contents of both working memory and visual imagery are known to be encoded already in early visual cortex. If these signals in early visual areas were indeed to reflect a combined imagery and memory code, one would predict them to be weaker for individuals with reduced visual imagery vividness. Here, we systematically investigated this question in two groups of participants. Strong and weak imagers were asked to remember images across brief delay periods. We were able to reliably reconstruct the memorized stimuli from early visual cortex during the delay. Importantly, in contrast to the prediction, the quality of reconstruction was equally accurate for both strong and weak imagers. The decodable information also closely reflected behavioral precision in both groups, suggesting it could contribute to behavioral performance, even in the extreme case of completely aphantasic individuals. Our data thus suggest that working memory signals in early visual cortex can be present even in the (near) absence of phenomenal imagery.
Mutation and selection induce correlations between selection coefficients and mutation rates
Authors: Gitschlag Bryan L. , Cano Alejandro V. , Payne Joshua L. , McCandlish David M. , Stoltzfus Arlin 
Published: February 2023

AbstractThe joint distribution of selection coefficients and mutation rates is a key determinant of the genetic architecture of molecular adaptation. Three different distributions are of immediate interest: (1) thenominaldistribution of possible changes, prior to mutation or selection, (2) thede novodistribution of realized mutations, and (3) thefixeddistribution of selectively established mutations. Here, we formally characterize the relationships between these joint distributions under the strong selection, weak mutation (SSWM) regime. Thede novodistribution is enriched relative to the nominal distribution for the highest rate mutations, and the fixed distribution is further enriched for the most highly beneficial mutations. Whereas mutation rates and selection coefficients are often assumed to be uncorrelated, we show that even with no correlation in the nominal distribution, the resultingde novoand fixed distributions can have correlations with any combination of signs. Nonetheless, we suggest that natural systems with a finite number of beneficial mutations will frequently have the kind of nominal distribution that induces negative correlations in the fixed distribution. We apply our mathematical framework, along with population simulations, to explore joint distributions of selection coefficients and mutation rates from deep mutational scanning and cancer informatics. Finally, we consider the evolutionary implications of these joint distributions together with two additional joint distributions relevant to parallelism and the rate of adaptation.
Multi-Omics Data of Perturbation Studies are Determined by Memory Effects from Subculture
Authors: Bortel Patricia , Hagn Gerhard , Skos Lukas , Bileck Andrea , Paulitschke Verena , Paulitschke Philipp , Gleiter Lion , Mohr Thomas , Gerner Christopher , Meier-Menches Samuel M. 
Published: February 2023

AbstractMass spectrometry-based omics technologies are increasingly used to map drug effects to biological pathways by identifying significant molecular events. Significance is influenced by the effect size and the variation of each molecular parameter. While the former is largely determined by the biological system, the latter can be tuned by the experimental workflow. Here, we unequivocally show that memory effects originating from subculture of colon carcinoma cells before treating with arsenic trioxide exacerbate the variation of multiple omics levels, including eicosadomics, proteomics and phosphoproteomics, without necessarily impacting on effect size. Real-time monitoring of individual samples enables control over subculture homogeneity and improves the median variation >2-fold across omics levels. This considerably facilitated mode of action deconvolution and resulted in a bilevel perturbation network of 321 causal conjectures. Controlling memory effects from subculture revealed key signaling cascades and transcriptional regulatory events that extend the molecular understanding of arsenic trioxide in solid tumors.
Hemoxygenase-1 as a key mediator of acute radiation pneumonitis revealed in a human lung alveolus-on-a-chip
Authors: Dasgupta Queeny , Jiang Amanda , Hall Sean , Mannix Robert , Wen Amy M. , Ingber Donald E. 
Published: February 2023

ABSTRACTExposure to gamma radiation either due to environmental disasters or cancer radiotherapy can result in development of acute radiation syndrome (ARS), characterized by pneumonitis and lung fibrosis. We leveraged a microfluidic organ-on-a-chip lined by human lung alveolar epithelium interfaced with pulmonary endothelium to model acute radiation-induced lung injuryin vitro. Both lung epithelium and endothelium exhibited DNA damage, cellular hypertrophy, upregulation of inflammatory cytokines, and loss of barrier function within 6 h of radiation exposure, although greater damage was observed in the endothelium. Transcriptomic analysis revealed increased expression of the cytoprotective gene, hemoxygenase-1 (HMOX-1) and gene network analysis identified it as a central mediator of radiation-induced injury. Pharmacological stimulation of HMOX-1 activity also significantly reduced acute radiation-induced lung injury, although it enhanced damage at later times. Thus, this human lung chip offers a new platform to study ARS and these results suggest that HMOX-1 may be mechanistically involved in this injury response.
Fixation Before Dissociation Using a Deep Eutectic Solvent PreservesIn VivoStates and Phospho-Signaling in Single-Cell Sequencing
Authors: Fortmann Seth D. , Frey Blake F. , Hanumanthu Vidya Sagar , Liu Shanrun , Goldsborough Andrew , Kilchrist Kameron V. , Ferrell P. Brent , Weaver Casey T. , Grant Maria B. , Welner Robert S. 
Published: February 2023

SUMMARYSingle-cell RNA-sequencing (scRNA-seq) presents an opportunity to deconstruct cellular networks but is limited by the loss of biological information, includingin vivocellular states and phospho-signaling. Herein, we present fixation before dissociation using a deep eutectic solvent (DES), which preserves multiple domains ofin vivobiological data, including morphology, RNA, proteins, and post-translational modifications. In scRNA-seq of viable versus DES bone marrow, dissociation induced global stress responses, immune and stromal cell activation, and loss of highly sensitive cell populations, which were prevented with DES. Further, we introduce a validated and flexible method for performing intracellular CITE-seq in DES-fixed cells. Leveraging this approach during Th17 T cell stimulation allowed the simultaneous quantification of transcriptomes and four phosphorylated proteins, leading to the identification of a hyperactivated state in p-ERK/p-FOS double positive cells, which we experimentally validated. We anticipate that DES-based fixatives will allow the accurate reconstruction ofin vivocellular networks and uncover cooperativity amongst intracellular pathways.
Viral attachment blocking chimera composed of DNA origami and nanobody inhibits Pseudorabies Virus infectionin vitro
Authors: Pradhan Swechchha , Swanson Carter , Leff Chloe , Tengganu Isadonna , Bergeman Melissa H. , Hogue Ian B. , Hariadi Rizal F. 
Published: February 2023

AbstractAntivirals are indispensable tools that can be targeted at viral domains directly or indirectly at cellular domains to obstruct viral infections and reduce pathogenicity. Despite their transformative use in healthcare, antivirals have been clinically approved to treat only 10 of the more than 200 known pathogenic human viruses. Additionally, many virus functions are intimately coupled with host cellular processes, which present challenges in antiviral development due to the limited number of clear targets per virus, necessitating an extensive insight into these molecular processes. Compounding this challenge, many viral pathogens have evolved to evade effective antivirals. We hypothesize that a Viral Attachment Blocking Chimera (VirABloC) composed of a viral binder and a bulky scaffold that sterically blocks interactions between a viral particle and a host cell may be suitable for the development of antivirals agnostic to the extravirion epitope that is being bound. We test this hypothesis by modifying a nanobody that specifically recognizes a non-essential epitope presented on the extra virion surface of Pseudorabies virus strain 486 with a 3-dimensional wireframe DNA origami structure ∼100 nm in diameter. The nanobody switches from having no inhibitory properties (tested up to 50 µM) to 4.2 ± 0.9 nM IC50when conjugated with the DNA origami scaffold. Mechanistic studies support that inhibition is mediated by the non-covalent attachment of the DNA origami scaffold to the virus particle, which obstructs the attachment of the viruses onto host cells. These results support the potential of VirABloC as a generalizable approach to developing antivirals.
Would consumers help achieve sustainable development in the Qinghai–Tibet Plateau with a forage–livestock balance certification label?
Authors: Zhang Yan , Jin Shaosheng , Lin Wen 
Published: February 2023

PurposeThe contradiction and conflict between grassland conservation and economic development are prominent in the Qinghai–Tibet Plateau (QTP) with its fragile environment and ecosystem. How to promote sustainable grazing in the plateau without hurting the economic welfare of local residents is a key challenge facing the Chinese government. This study explores the potential of market-based grassland conservation policies by evaluating consumer preferences and valuations for forage–livestock balance certification labeled yak products.Design/methodology/approachThis study adopts a choice experiment with four attributes of yak meat, including forage–livestock balance certification, feeding type, age at slaughter and price. A sample size of 2,999 respondents from Beijing, Shanghai, Wuhan, Guangzhou and Chengdu was collected by a professional online survey company.FindingsThe result reveals that urban Chinese consumers are willing to pay highest price premiums for forage–livestock balance certified yak meat, followed by grass-fed claim labeled meat. Consumers on average place negative valuations for grain-fed claims, meat from yak slaughtered above 2 and 4 years old. Heterogeneous analysis indicates that individuals who are female, younger, married, and better educated, and with above median income, Tibet travel or yak consumption experience, are more receptive to the forage–livestock balance certification.Originality/valueIt is the first study to explore demand-driven mechanisms for grassland conservation by focusing on consumer valuation for the forage–livestock balance certification.
Agility and digitalization: why strategic agility is a success factor for mastering digitalization – evidence from Industry 4.0 implementations across a supply chain
Authors: Pfaff Yuko Melanie 
Published: February 2023

PurposeThis paper addresses the emergence of strategic agility as adaptive capability to face the need to adapt to a constantly changing environment. Special emphasis is paid to governance mechanisms as a microfoundation of dynamic capabilities, investigating the dynamics and outcome in regards to the digitalization of supply chains and its socio-economic relations of its members.Design/methodology/approachA multiple-case study method is applied to explain the impact of a digitalization initiative in the form of an I4.0 implementation in a supply chain context. Building on qualitative in-depth interviews of experts in managerial positions, 16 cases from the manufacturing industry involving an I4.0 implementation across the supply chain were analyzed. Based on a conceptual design science approach, the CIMO logic (context, intervention, mechanisms and outcome) framework is used to investigate the interplay between agility as a dynamic capability and governance mechanisms.FindingsThe studied cases demonstrate an intensification of synergistic combinations of inter-firm resources to manage digitalization across the supply chain (SC). With the implementation of I4.0, competitive advantage along the SC takes higher priority over the competitive advantage in the individual or dyadic perspective. Strategic agility as a dynamic capability to cope with and adapt to the changing environment is hereby crucial emphasizing relational SC governance (SCG) as essential as a microfoundation to adjust the structure and management of SCs. Relationships, which allow competitive advantage as a SC balance out traditional power mechanisms within the SC hierarchy. Trust, collaboration and flexibility, aligned with common incentives in generating competitive advantages enable the SCs to mitigate uncertainty and risk while preventing opportunistic behavior.Practical implicationsThe study offers SCM managers in-depth insights into strategic agility and how to address the recent challenge of digitalization successfully. Identifying crucial dynamics within SCG mechanisms based on first-hand use cases, practical success factors for implementing I4.0 to optimize effectiveness and efficiency can be derived how to structure and manage future SCs.Originality/valueThis paper contributes to the first insights examining the implications of digitalization and the role of strategic agility as a capability to adapt. Investigating the microfoundation of governance within this capability, this research provides insights on the socio-economic level, while discussing specific mechanisms how relationships of SCs evolve proposing relevant insights for future research.