bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic depletion of de novo coenzyme A biosynthesis exacerbates puromycin toxicity
Authors: Khadka Sunada , Chatoff Adam , Snyder Nathaniel W. , DePinho Ronald , Muller Florian 
Published: September 2022

AbstractPuromycin is an amino nucleoside that inhibits protein synthesis by interrupting elongation of nascent peptide chains. It is a commonly used selection antibiotic in molecular biology research via engineered expression of a puromycin resistance transgene. The enzyme puromycin acetyl transferase (pac) or PuroR inactivates puromycin by N-acetylating its reactive amino group. Puromycin acetylation by pac requires the central metabolite and acetyl group donor acetyl-CoA as a substrate. We found that puromycin treatment exacerbates sensitivity of cancer cells to knockdown of pantothenate kinases, the proteins that catalyze the rate-limiting step of de novo coenzyme A production in cells. Mechanistically, we found that ablation of PANKs together with puromycin depletes acetyl-CoA levels, in a manner modulated by the dose of puromycin. Our findings provide a note of caution and context in the use of puromycin for metabolism research in that interference with the major acyl donor used for inactivating biotransformation may exacerbate toxicity under selection. Broadly, our findings also invite studies to explore how targeting CoA and acetyl-CoA synthesis may be exploited to enhance cytotoxic effects of cancer drugs that undergo acetylation.
Discovery of another mechanism for the inhibition of particulate guanylyl cyclases by the natriuretic peptide clearance receptor
Authors: Liu Dianxin , Ceddia Ryan P. , Zhang Wei , Shi Fubiao , Fang Huafeng , Collins Sheila 
Published: September 2022

AbstractThe cardiac natriuretic peptides (NPs) control pivotal physiological actions such as fluid and electrolyte balance, cardiovascular homeostasis, and adipose tissue metabolism by activating their receptor enzymes (NPRA and NPRB). These receptors are homodimers that generate intracellular cyclic guanosine monophosphate (cGMP). The NP receptor NPRC, nicknamed the clearance receptor, lacks a guanylyl cyclase domain; instead, it can bind the NPs to internalize and degrade them. The conventional paradigm is that by competing for and internalizing NPs, NPRC blunts the ability of NPs to signal through NPRA and NPRB. Here we show another previously unknown mechanism by which NPRC can interfere with the cGMP signaling function of the NP receptors. By forming a heterodimer with monomeric NPRA or NPRB, NPRC can prevent the formation of a functional guanylyl cyclase domain and thereby suppress cGMP production in a cell-autonomous manner.Significance StatementNatriuretic peptides (NP) are hormones that are established regulators of vascular and cardiac function, in part through their regulation of fluid and electrolyte balance. NPs signal through particulate guanylyl cyclases (NPRA and NPRB), which are homodimeric membrane-bound receptor enzymes that generate cGMP upon NP binding. Additionally, a ‘silent’ NP receptor (NPRC) lacks the guanylyl cyclase domain and is a negative regulator of NP signaling. It has been demonstrated that NPRC undergoes internalization and recycling and thus removes NPs, thereby blunting activation of the guanylyl cyclase-containing receptors. Here we show an additional mechanism by which NPRC inhibits NP signaling. Our results show that NPRC can directly interact with NPRA and NPRB, forming non-functional receptor heterodimers with NPRA and NPRB, thereby abrogating NP-evoked cGMP production. This finding establishes another novel mechanistic role for NPRC.
Generation of floxed alleles for cell-specific knockout in zebrafish
Authors: Shin Masahiro , Nozaki Takayuki , Toles Benjamin , Kolb Amy , Luk Kevin , Isogai Sumio , Ishida Kinji , Hanasaka Tomohito , Parsons Michael J. , Wolfe Scot A. , Lawson Nathan D. 
Published: September 2022

SUMMARYA benefit of the zebrafish as a model is its amenability to genetic approaches. However, a lack of conditional deletion alleles makes it a challenge to perform stage- or cell-specific knockout. Here, we initially applied an existing protocol to establish a floxed allele for gata2a and encountered several issues, including off-target integration and incomplete knock-in. To address these problems, we developed a protocol incorporating simultaneous co-targeting with Cas12a to insert loxP sites in cis, together with transgenic counter-screening to identify off-target insertions. We applied this protocol to establish a floxed allele of foxc1a in a single generation. We demonstrate the utility of our floxed alleles by verifying Cre-dependent deletion, which yielded expected phenotypes in each case. Finally, we used the floxed gata2a allele to demonstrate an endothelial autonomous requirement in lymphatic valve development. Together, our results provide a framework for straightforward generation and application of floxed alleles in zebrafish.
Enterococcal linear plasmids adapt to Enterococcus faecium and spread within multidrug-resistant clades
Authors: Hashimoto Yusuke , Suzuki Masato , Kobayashi Sae , Hirahara Yuki , Nomura Takahiro , Kurushima Jun , Hirakawa Hidetada , Tanimoto Koichi , Tomita Haruyoshi 
Published: September 2022

AbstractAntimicrobial resistance (AMR) of bacterial pathogens, including enterococci, is a global concern, and plasmids are crucial for spreading and maintaining AMR genes. Plasmids with linear topology were recently identified in clinical multidrug-resistant enterococci. The enterococcal linear-form plasmids, such as pELF1, confer resistance to clinically important antimicrobials, including vancomycin; however, little information exists about their epidemiological and physiological effects. In this study, we identified several lineages of enterococcal linear plasmids that are structurally conserved and occur globally. pELF1-like linear plasmids show plasticity in acquiring and maintaining AMR genes, often via transposition with the mobile genetic element IS1216E. This linear plasmid family has several characteristics enabling long-term persistence in the bacterial population, including high horizontal self-transmissibility, low-level transcription of plasmid-encoded genes, and a moderate effect on the Enterococcus faecium genome alleviating fitness cost and promoting vertical inheritance. Combined with its broad host range, the linear plasmid is an important factor in the spread and maintenance of AMR genes among enterococci.
Calcium binding and permeation in TRPV channels: insights from molecular dynamics simulations
Authors: Liu Chunhong , Song Chen 
Published: September 2022

AbstractSome calcium channels selectively permeate Ca2+, despite the high concentration of monovalent ions in the surrounding environment, which is essential for many physiological processes. Without atomistic and dynamical ion permeation details, the underlying mechanism of Ca2+ selectivity has long been an intensively studied, yet controversial, topic. This study takes advantage of the homologous Ca2+-selective TRPV6 and non-selective TRPV1 and utilizes the recently solved open-state structures and a newly developed multi-site calcium model to investigate the ion binding and permeation features in TRPV channels by molecular dynamics simulations. Our results revealed that the open-state TRPV6 and TRPV1 show distinct ion-binding patterns in the selectivity filter, which lead to different ion permeation features. Two Ca2+ ions simultaneously bind to the selectivity filter of TRPV6 compared with only one Ca2+ in case of TRPV1. Multiple Ca2+ binding at the selectivity filter of TRPV6 permeated in a concerted manner, which could efficiently block the permeation of Na+. Cations of various valences differentiate between the binding sites at the entrance of the selectivity filter in TRPV6. Ca2+ preferentially binds to the central site with a higher probability of permeation, repelling Na+ to a peripheral site. Therefore, we believe that ion binding competition at the selectivity filter of calcium channels, including the binding strength and number of binding sites, determines Ca2+ selectivity under physiological conditions. Additionally, our results showed that pore helix flexibility and the cytosolic domain of TRPV channels regulate ion permeability.
Synteny identifies reliable orthologs for phylogenomics and comparative genomics of the Brassicaceae
Authors: Walden Nora , Schranz M. Eric 
Published: September 2022

AbstractLarge genomic datasets are becoming the new normal for any facet of phylogenetic research, but identification of true orthologous genes and exclusion of problematic paralogs is still challenging when applying commonly used sequencing methods such as target enrichment. Here, we compared conventional ortholog detection using OrthoFinder with ortholog detection through genomic synteny in a dataset of eleven representative diploid Brassicaceae whole genome sequences spanning the entire phylogenetic space. We then evaluated the resulting gene sets regarding gene number, functional annotation, gene and species tree resolution. Finally, we used the syntenic gene sets for comparative genomics and ancestral genome analysis. The use of synteny resulted in considerably more orthologs and also allowed us to reliably identify paralogs. Surprisingly, we did not detect notable differences between species trees reconstructed from syntenic orthologs compared other gene sets, including the Angiosperm353 set and a Brassicaceae specific target enrichment gene set. However, the synteny dataset comprised a multitude of gene functions, strongly suggesting that this method of marker selection for phylogenomics is suitable for studies that value downstream gene function analysis, gene interaction and network studies. Finally, we present the first ancestral genome reconstruction for the Core Brassicaceae predating the Brassicaceae lineage diversification ∼25 million years ago.
Nano-scale solution of the Poisson-Nernst-Planck (PNP) equations in a fraction of two neighboring cells reveals the magnitude of intercellular electrochemical waves
Authors: Jæger Karoline Horgmo , Ivanovic Ena , Kucera Jan P. , Tveito Aslak 
Published: September 2022

AbstractThe basic building blocks of the electrophysiology of cardiomyocytes are ion channels integrated in the cell membranes. Close to the ion channels there are very strong electrical and chemical gradients. However, these gradients extend for only a few nano-meters and are therefore commonly ignored in mathematical models. The full complexity of the dynamics is modelled by the Poisson-Nernst-Planck (PNP) equations but these equations must be solved using temporal and spatial scales of nano-seconds and nano-meters. Here we report solutions of the PNP equations in a fraction of two abuttal cells separated by a tiny extracellular space. We show that when only the potassium channels of the two cells are open, a stationary solution is reached with the well-known Debye layer close to the membranes. When the sodium channels of the left cell are opened, a very strong and brief electrochemical wave emanates from the channels. If the extracellular space is sufficiently small and the number of sodium channels is sufficiently high, the wave extends all the way over to the neighboring cell and may therefore explain cardiac conduction even at very low levels of gap junctional coupling.
Online detection of bus bar plane stress based on electromagnetic loading
Authors: Guo Yufeng , Zhang Chuang , Qi Lei , Yu Haixu , Liu Suzhen , Jin Liang 
Published: September 2022

Purpose
The purpose of this study is to develop an electromagnetic loading method for online measurement of the acoustoelastic coefficients and bus bar plane stress.

Design/methodology/approach
A method based on the combination of electromagnetic loading and the acoustoelastic effect is proposed to realize online measurement of acoustoelastic coefficients and plane stress. Electromagnetic loading is performed on the bus bar specimen, and the acoustoelastic coefficients and the bus bar plane stress are obtained by the ultrasonic method. An electromagnetic loading experimental platform is designed to provide electromagnetic force to the metal plate, including an electromagnetic loading module, an ultrasonic testing module and a stress simulation module.

Findings
The feasibility of the proposed electromagnetic loading method is proved by verification experiments. The acoustoelastic coefficients and plane stress measured using the electromagnetic loading method are more accurate than those measured using the traditional method.

Originality/value
The proposed electromagnetic loading method provides a new study perspective and enables more accurate measurement of the acoustoelastic coefficients and plane stress. The study provides an important basis for evaluating the operation status of electrical equipment.
Evaluating and optimizing performance of public–private partnership projects using copula Bayesian network
Authors: Ghorbany Siavash , Yousefi Saied , Noorzai Esmatullah 
Published: September 2022

PurposeBeing an efficient mechanism for the value of money, public–private partnership (PPP) is one of the most prominent approaches for infrastructure construction. Hence, many controversies about the performance effectiveness of these delivery systems have been debated. This research aims to develop a novel performance management perspective by revealing the causal effect of key performance indicators (KPIs) on PPP infrastructures.Design/methodology/approachThe literature review was used in this study to extract the PPPs KPIs. Experts’ judgment and interviews, as well as questionnaires, were designed to obtain data. Copula Bayesian network (CBN) has been selected to achieve the research purpose. CBN is one of the most potent tools in statistics for analyzing the causal relationship of different elements and considering their quantitive impact on each other. By utilizing this technique and using Python as one of the best programming languages, this research used machine learning methods, SHAP and XGBoost, to optimize the network.FindingsThe sensitivity analysis of the KPIs verified the causation importance in PPPs performance management. This study determined the causal structure of KPIs in PPP projects, assessed each indicator’s priority to performance, and found 7 of them as a critical cluster to optimize the network. These KPIs include innovation for financing, feasibility study, macro-environment impact, appropriate financing option, risk identification, allocation, sharing, and transfer, finance infrastructure, and compliance with the legal and regulatory framework.Practical implicationsIdentifying the most scenic indicators helps the private sector to allocate the limited resources more rationally and concentrate on the most influential parts of the project. It also provides the KPIs’ critical cluster that should be controlled and monitored closely by PPP project managers. Additionally, the public sector can evaluate the performance of the private sector more accurately. Finally, this research provides a comprehensive causal insight into the PPPs’ performance management that can be used to develop management systems in future research.Originality/valueFor the first time, this research proposes a model to determine the causal structure of KPIs in PPPs and indicate the importance of this insight. The developed innovative model identifies the KPIs’ behavior and takes a non-linear approach based on CBN and machine learning methods while providing valuable information for construction and performance managers to allocate resources more efficiently.
Economic policy uncertainty, entrepreneurial risk appetite, and corporation innovation in innovative cities – empirical evidence from the Shenzhen Special Economic Zone
Authors: Zhu Mengfei , Tao Yitao 
Published: September 2022

PurposeThis study investigates the impact of economic policy uncertainty on corporation innovation in innovative cities. The study sheds light on different results from the previous literature by testing the moderator effects of entrepreneurial risk appetite on such impact.Design/methodology/approachA static panel estimator is applied to a Chinese sample of 416 firm-year observations from 2010 to 2019. This paper uses regression model to test the impact of uncertainty on enterprise innovation in innovative cities, and to test the regulatory role of entrepreneurial risk appetite. For a series of robustness analysis conducted by the author to deal with endogeneity, the results are robust.FindingsThe author finds reliable evidence that the economic policy uncertainty can promote corporations to invest more in R&D in innovative cities. In addition, the role of the entrepreneurial initiative is significant, and there is a positive moderating effect of entrepreneurial risk appetite between policy uncertainty and corporation innovation.Research limitations/implicationsFrom a practical point of view, this study examines the impact of economic policy uncertainty on corporation innovation in innovative cities for the first time. It emphasizes the role of entrepreneurial risk-taking in the development of corporation innovation in Shenzhen, an innovative city. This research is of great significance to the formulation of government policies and the innovative choice of entrepreneurs. In addition, the research shows that the entrepreneurial risk appetite in innovative cities can have a positive impact on enterprise innovation. Therefore, when formulating policies, the government should take the subjective factors of entrepreneurs into account and support enterprises with innovation potential. The evidence of this study also helps entrepreneurs make innovative decisions and enhance their confidence in enterprise development.Originality/valueBy studying the impact of economic policy uncertainty on enterprise innovation under the regulation of enterprise risk appetite, this study shows the subjective and positive role of entrepreneurs in risk grasp in innovative cities for the first time. In addition, it fills the gap of the impact of policy uncertainty on innovative urban enterprises. In fact, although it is traditionally believed that economic policy uncertainty has a negative impact on enterprise innovation, the sensitive findings of this study reveal completely different results from previous studies.
The costs of care: An ethnography of care work in residential homes for older people
Authors: Johnson Eleanor K. 
Published: September 2022

AbstractThe cost of social care, the work conditions experienced by care workers and the quality of care provided by residential homes for older people are all linked, yet we know very little about how this relationship works in practice. Drawing upon an ethnography of two differently priced residential care homes for older people in Southern England, I examine the implications of different financial regimes for care‐giving practices. I show how the scheduling and allocation of resources—conveyed, for example, in formal routines and staffing levels—structure the care workers’ time, tasks and activities in each setting. This acts to symbolically demarcate what, or who, is valued. I argue that the availability of resources facilitates and impedes the symbolic culture of care work, shapes care workers’ ability to afford dignity to the individuals in their care and affects how care workers experience, and relate to, their labour. I conclude by discussing how current practices of funding and pricing social care have effects seeping beyond the practical and measurable, and into the realm of the symbolic.
Biosynthesis of L‐5‐methyltetrahydrofolate by genetically engineered Escherichia coli
Authors: Wang Yubo , Zhang Meng , Li Lexin , Yi Jihong , Liang Jiyu , Wang Shuning , Xu Ping 
Published: September 2022

AbstractL‐5‐Methyltetrahydrofolate (L‐5‐MTHF) is the only biologically active form of folate in the human body. Production of L‐5‐MTHF by using microbes is an emerging consideration for green synthesis. However, microbes naturally produce only a small amount of L‐5‐MTHF. Here, Escherichia coli BL21(DE3) was engineered to increase the production of L‐5‐MTHF by overexpressing the intrinsic genes of dihydrofolate reductase and methylenetetrahydrofolate (methylene‐THF) reductase, introducing the genes encoding formate‐THF ligase, formyl‐THF cyclohydrolase and methylene‐THF dehydrogenase from the one‐carbon metabolic pathway of Methylobacterium extorquens or Clostridium autoethanogenum and disrupting the gene of methionine synthase involved in the consumption and synthesis inhibition of the target product. Thus, upon its native pathway, an additional pathway for L‐5‐MTHF synthesis was developed in E. coli, which was further analysed and confirmed by qRT‐PCR, enzyme assays and metabolite determination. After optimizing the conditions of induction time, temperature, cell density and concentration of IPTG and supplementing exogenous substances (folic acid, sodium formate and glucose) to the culture, the highest yield of 527.84 μg g−1 of dry cell weight for L‐5‐MTHF was obtained, which was about 11.8 folds of that of the original strain. This study paves the way for further metabolic engineering to improve the biosynthesis of L‐5‐MTHF in E. coli.
Optimal diagnostic criteria for lateral lymph node dissection using magnetic resonance imaging: a multicenter prospective study
Authors: Kawai Kazushige , Shiomi Akio , Miura Takuya , Uehara Kay , Watanabe Jun , Kazama Shinsuke , Ueno Hideki , Sakamoto Kazuhiro , Kinugasa Yusuke , Takahashi Keiichi , Hida Koya , Hamada Madoka , Ishihara Soichiro , Sugihara Kenichi 
Published: September 2022

AbstractBackgroundLLND in cases with suspected lateral lymph node (LLN) metastasis has been focused on as a novel treatment strategy in recent years. However, the optimal indication for LLND in rectal cancer patients has not been determined. This study aimed to establish the optimal indication for lateral lymph node dissection (LLND) in patients with rectal cancer using magnetic resonance imaging (MRI).MethodsA total of 209 patients with rectal adenocarcinoma who underwent total mesorectal excision and LLND in 13 hospitals were prospectively registered. By matching the sizes of the harvested LNs and those in magnetic resonance imaging (MRI), the pathological outcome of each LN was confirmed one‐by‐one. Using parameters of the LLNs in MRI, the optimal diagnostic criteria for LLND were established.ResultsOf 3241 harvested LLNs, including 83 metastatic nodes, 1010 (31.1%) were visualized on MRI. Although all parameters assessed showed strong correlations with the presence of metastasis, none of these parameters could discriminate metastatic LLNs from non‐metastatic nodes with sufficient sensitivity. However, by using the combination of long axis and short/long ratio in pretreatment MRI, we could establish optimal criteria for LLND. The sensitivity and specificity of the criteria for LLN metastasis were 94.3% and 40.2%, respectively.ConclusionsIn conclusion, we established novel criteria for LLND in rectal cancer patients using MRI. Our criteria will be of great clinical use in determining indications for LLND.