bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of bile-salt degradation in Sphingobium sp. strain Chol11 and P. stutzeri Chol1 reveals functional diversity of β-proteobacterial steroid degradation enzymes and suggests a novel reaction sequence for side-chain degradation involving a hydroxylation step
Authors: Feller Franziska Maria , Richtsmeier Phil , Wege Maximilian , Philipp Bodo 
Published: June 2021

AbstractThe reaction sequence for aerobic degradation of bile salts by environmental bacteria resembles degradation of other steroid compounds. Recent findings show that bacteria belonging to the Sphingomonadaceae use a pathway variant for bile-salt degradation. This study addresses this so-called Δ4,6 -variant by comparative analysis of unknown degradation steps in Sphingobium sp. strain Chol11 with known reactions found in Pseudomonas stutzeri Chol1. Investigations with strain Chol11 revealed an essential function of the acyl-CoA dehydrogenase Scd4AB for growth with bile salts. Growth of the scd4AB deletion mutant was restored with a metabolite containing a double bond within the side chain which was produced by the Δ22-acyl-CoA dehydrogenase Scd1AB from P. stutzeri Chol1. Expression of scd1AB in the scd4AB deletion mutant fully restored growth with bile salts while expression of scd4AB only enabled constricted growth in P. stutzeri Chol1 scd1A or scd1B deletion mutants. Strain Chol11 Δscd4A accumulated hydroxylated steroid metabolites which were degraded and activated with coenzyme A by the wild type. Activities of five Rieske type monooxygenases of strain Chol11 were screened by heterologous expression and compared to the B-ring cleaving KshABChol1 from P. stutzeri Chol1. Three of the Chol11 enzymes catalyzed B-ring cleavage of only Δ4,6 -steroids while KshABChol1 was more versatile. Expression of a fourth KshA homolog, Nov2c228 led to production of metabolites with hydroxylations at an unknown position. These results indicate functional diversity of β-proteobacterial enzymes for bile-salt degradation and suggest a novel side-chain degradation pathway involving an essential ACAD reaction and a steroid hydroxylation step.ImportanceThis study highlights the biochemical diversity of bacterial degradation of steroid compounds in different aspects. First, it further elucidates an unexplored variant in the degradation of bile-salt side chains by Sphingomonads, a group of environmental bacteria that is well-known for their broad metabolic capabilities. Moreover, it adds a so-far unknown hydroxylation of steroids to the reactions Rieske monooxygenases can catalyze with steroids. Additionally, it analyzes the first proteobacterial ketosteroid-9α-hydroxylase and shows that this enzyme is able to catalyze side reactions with non-native substrates.
Annealing synchronizes the 70S ribosome into a minimum-energy conformation
Authors: Chu Xiaofeng , Su Xin , Liu Mingdong , Li Li , Li Tianhao , Qin Yicheng , Lu Guoliang , Qi Lei , Liu Yunhui , Lin Jinzhong , Shen Qing-Tao 
Published: June 2021

AbstractResearchers commonly anneal metals, alloys, and semiconductors to repair defects and improve microstructures via recrystallization. Theoretical studies indicate simulated annealing on biological macromolecules helps predict the final structures with minimum free energy. Experimental validation of this homogenizing effect and further exploration of its applications are fascinating scientific questions that remain elusive. Here, we chose the apo-state 70S ribosome from Escherichia coli as a model, wherein the 30S subunit undergoes a thermally driven inter-subunit rotation and exhibits substantial structural flexibility as well as distinct free energy. We experimentally demonstrate that annealing at a fast cooling rate enhances the 70S ribosome homogeneity and improves local resolution on the 30S subunit. After annealing, the 70S ribosome is in a nonrotated state with respect to corresponding intermediate structures in unannealed or heated ribosomes, and exhibits a minimum energy in the free energy landscape. One can readily crystallize these minimum-energy ribosomes, which have great potential for synchronizing proteins on a single-molecule level. Our experimental results are consistent with theoretical analysis on the temperature-dependent Boltzmann distribution, and offer a facile yet robust approach to enhance protein stability, which is ideal for high-resolution cryogenic electron microscopy. Beyond structure determination, annealing can be extended to study protein folding and explore conformational and energy landscape.Significance statementIn metallurgy, annealing heats a metal or alloy to a predetermined temperature, holding for a certain time, and then cooling to room temperature to change the physical and sometimes also the chemical properties of the material. Researchers introduce the similar concept as simulated annealing to predict minimum-energy conformations of biological macromolecules. In this work, we experimentally verify that annealing at a fast cooling rate can synchronize the 70S ribosome into a nonrotated state with a minimum energy in the free energy landscape. Our results not only offer a facile yet robust approach to stabilize proteins for high-resolution structural analysis, but also contribute to the understanding of protein folding and temperature adaptation.
Contractile ring constriction and septation in fission yeast are integrated mutually stabilizing processes
Authors: Thiyagarajan Sathish , McDargh Zachary , Wang Shuyuan , O’Shaughnessy Ben 
Published: June 2021

AbstractIn common with other cellular machineries, the actomyosin contractile ring that divides cells during cytokinesis does not operate in isolation. Contractile rings in animal cells interact with contiguous actomyosin cortex, while ring constriction in many cell-walled organisms couples tightly to cell wall growth. In fission yeast, a septum grows in the wake of the constricting ring, ensuring cytokinesis leaves two daughter cells fully enclosed by cell wall. Here we mathematical modeled the integrated constriction-septation system in fission yeast, with a kinetic growth model evolving the 3D septum shape coupled to a molecularly explicit simulation of the contractile ring highly constrained by experimental data. Simulations revealed influences in both directions, stabilizing the ring-septum system as a whole. By providing a smooth circular anchoring surface for the ring, the inner septum leading edge stabilized ring organization and tension production; by mechanically regulating septum circularity and in-plane growth, ring tension stabilized septum growth and shape. Genetic or pharmacological perturbation of either subsystem destabilized this delicate balance, precipitating uncontrolled positive feedback with disastrous morphological and functional consequences. Thus, high curvature septum irregularities triggered bridging instabilities, in which contractile ring segments became unanchored. Bridging abolished the local tension-mediated septum shape regulation, exacerbating the irregularity in a mutually destabilizing runaway process. Our model explains a number of previously mysterious experimental observations, including unanchoring of ring segments observed in cells with mutations in the septum-growing β-glucan synthases, and irregular septa in cells with mutations in the contractile ring myosin-II Myo2. Thus, the contractile ring and cell wall growth cellular machineries operate as a single integrated system, whose stability relies on mutual regulation by the two subsystems.
Global cellular response to chemical perturbation of PLK4 activity and abnormal centrosome number
Authors: Tkach Johnny M , Philip Reuben , Sharma Amit , Strecker Jonathan , Durocher Daniel , Pelletier Laurence 
Published: June 2021

ABSTRACTCentrosomes act as the main microtubule organizing centre (MTOC) in metazoans. Centrosome number is tightly regulated by limiting centriole duplication to a single round per cell cycle. This control is achieved by multiple mechanisms, including the regulation of the protein kinase PLK4, the most upstream facilitator of centriole duplication. Altered centrosome numbers in mouse and human cells cause p53-dependent growth arrest through poorly defined mechanisms. Recent work has shown that the E3 ligase TRIM37 is required for cell cycle arrest in acentrosomal cells. To gain additional insights into this process, we undertook a series of genome-wide CRISPR/Cas9 screens to identify factors important for growth arrest triggered by treatment with centrinone B, a selective PLK4 inhibitor. We found that TRIM37 is a key mediator of growth arrest after partial or full PLK4 inhibition. Interestingly, PLK4 cellular mobility decreased in a dose-dependent manner after centrinone B treatment. In contrast to recent work, we found that growth arrest after PLK4 inhibition correlated better with PLK4 activity than with mitotic length or centrosome number. These data provide insights into the global response to changes in centrosome number and PLK4 activity and extend the role for TRIM37 in regulating the abundance, localization and function of centrosome proteins.
Hexapeptide induces M2 macrophage polarization via the JAK1/STAT6 pathway to promote angiogenesis in bone repair
Authors: Han Xinyun , Hu Junxian , Zhao Wenbo , Lu Hongwei , Dai Jingjin , He Qingyi 
Published: June 2021

AbstractAngiogenesis is essential for successful bone defect repair. In normal tissue repair, the physiological inflammatory response is the main regulator of angiogenesis through the activity of macrophages and the cytokines secreted by them. In particular, M2 macrophages which secrete high levels of PDGF-BB are typically considered to promote angiogenesis. A hexapeptide [WKYMVm, (Trp-Lys-Tyr-Met-Val-D-Met-NH2)] has been reported to modulate inflammatory activities. However, the underlying mechanisms by which WKYMVm regulates macrophages remain unclear. In this study, the possible involvement by which WKYMVm induces the polarization of macrophages and affects their behaviors was evaluated. In vitro results showed that macrophages were induced to an M2 rather than M1 phenotype and the M2 phenotype was enhanced by WKYMVm through activation of the JAK1/STAT6 signaling pathway. It was also found that WKYMVm played an important role in the PDGF-BB production increase and proangiogenic abilities in M2 macrophages. Consistent with the results in vitro, the elevated M2/M0 ratio induced by WKYMVm enhanced the formation of new blood vessels in a femoral defect mouse model. In summary, these findings suggest that WKYMVm could be a promising alternative strategy for angiogenesis in bone repair by inducing M2 macrophage polarization.
Identification of QTL hotspots affecting agronomic traits and high-throughput vegetation indices in rainfed wheat
Authors: Rufo Rubén , López Andrea , Lopes Marta S. , Bellvert Joaquim , Soriano Jose Miguel 
Published: June 2021

AbstractUnderstanding the genetic basis of agronomic traits is essential for wheat breeding programmes to develop new cultivars with enhanced grain yield under climate change conditions. The use of high-throughput phenotyping (HTP) technologies for the assessment of agronomic performance through drought-adaptive traits opens new possibilities in plant breeding. HTP together with a genome-wide association study (GWAS) mapping approach can become a useful method to dissect the genetic control of complex traits in wheat to enhance grain yield under drought stress. This study aimed to identify molecular markers associated with agronomic and remotely sensed vegetation index (VI)-related traits under rainfed conditions in bread wheat and to use anin silicocandidate gene (CG) approach to search for upregulated CGs under abiotic stress. The plant material consisted of 170 landraces and 184 modern cultivars from the Mediterranean basin that were phenotyped for agronomic and VI traits derived from multispectral images over three and two years, respectively. GWAS identified 2579 marker–trait associations (MTAs). The QTL overview index statistic detected 11 QTL hotspots involving more than one trait in at least two years. A candidate gene analysis detected 12 CGs upregulated under abiotic stress in 6 QTL hotspots. The current study highlights the utility of VI to identify chromosome regions that contribute to yield and drought tolerance under rainfed Mediterranean conditions.
Monomer model: an integrated characterization method of geometrical deviations for assembly accuracy analysis
Authors: Zhao Binbin , Wang Yunlong , Sun Qingchao , Zhang Yuanliang , Liang Xiao , Liu Xuewei 
Published: June 2021

Purpose
Assembly accuracy is the guarantee of mechanical product performance, and the characterization of the part with geometrical deviations is the basis of assembly accuracy analysis.

Design/methodology/approach
The existed small displacement torsors (SDT) model cannot fully describe the part with multiple mating surfaces, which increases the difficulty of accuracy analysis. This paper proposed an integrated characterization method for accuracy analysis. By analyzing the internal coupling relationship of the different geometrical deviations in a single part, the Monomer Model was established.

Findings
The effectiveness of the Monomer Model is verified through an analysis of a simulated rotor assembly analysis, and the corresponding accuracy analysis method based on the model reasonably predicts the assembly deviation of the rotor.

Originality/value
The Monomer Model realizes the reverse calculation of assembly deformation for the first time, which can be used to identify the weak links that affect the assembly accuracy, thus support the accuracy improvement in the re-assembly stage.
Earnings management when firms face mandatory contributions
Authors: Qin Yiyi , Cai Jun , Wei Steven 
Published: June 2021

PurposeIn this paper, we aim to answer two questions. First, whether firms manipulate reported earnings via pension assumptions when facing mandatory contributions. Second, whether firms alter their earnings management behavior when the Financial Accounting Standard Board (FASB) mandates disclosure of pension asset composition and a description of investment strategy under SFAS 132R.Design/methodology/approachOur basic approach is to run linear regressions of firm-year assumed returns on the log of pension sensitivity measures, controlling for current and lagged actual returns from pension assets, fiscal year dummies and industry dummies. The larger the pension sensitivity ratios, the stronger the effects from inflatedERRson reported earnings. We confirm the early results that the regression slopes are positive and highly significant. We construct an indicator variableDMCto capture the mandatory contributions firms face and another indicator variableD132Rto capture the effect of SFAS 132R.DMCtakes the value of one for fiscal years during which an acquisition takes place and zero otherwise.D132Rtakes the value of one for fiscal years after December 15, 2003 and zero otherwise.FindingsOur sample covers the period from June 1992 to December 2017. Our key results are as follows. The estimated coefficient (t-statistic) onDMCis 0.308 (6.87). Firms facing mandatory contributions tend to setERRsat an average 0.308% higher. The estimated coefficient (t-statistic) onD132Ris −2.190 (−13.70). The new disclosure requirement under SFAS 132R constrains all firms to setERRsat an average 2.190% lower. The estimate (t-statistic) on the interactive termDMA×D132Ris −0.237 (−3.29). When mandatory contributions happen during the post-SFAS 132R period, firms tend to setERRsat 0.237% lower than they would do otherwise in the pre-SFAS 132R period.Originality/valueWhen firms face mandatory contributions, typically firm experience negative stock market returns. We examine whether managers manage earnings to mitigate such negative impact. We find that firms inflate assumed returns on pension assets to boost their reported earnings when facing mandatory contributions. We also find that managers alter earnings management behavior, in the case of mandatory contributions, following the introduction of new pension disclosure standards under SFAS 132R that become effective on December 15, 2003. Under the new SFAS 132R requirement, firms need to disclose asset allocation and describe investment strategies. This imposes restrictions on managers' discretion in makingERRassumptions, since now the composition of pension assets is a key determinant of the assumed expected rate of return on pension assets. Firms need to justify theirERRswith their asset allocations.
Unravelling the risks of construction digitalisation in developing countries
Authors: Aghimien Douglas , Aigbavboa Clinton , Meno Tsholofelo , Ikuabe Matthew 
Published: June 2021

Purpose
This study aims to present the result of an assessment of the risk of construction digitalisation with a view to sensitising and preparing construction organisations for unforeseen issues that might arise in the course of their digital transformation.

Design/methodology/approach
The study took a post-positivist stance through a quantitative research approach. A survey of construction professionals actively involved in construction projects in South Africa was conducted using a structured questionnaire. The analysis of the data gathered was done using mean item scores, Kruskal–Wallis H test, exploratory factor analysis (EFA) and structural equation modelling (SEM).

Findings
EFA revealed five principal risk factors (human and financial, technological, legal and security, operations and socioeconomic risk factors) associated with the digitalisation of construction organisations. However, SEM revealed that four out of these risk components have significant direct relationships with some selected digitalisation outcomes. These significant risk factors are technology, legal and security issues, operations and socioeconomic issues.

Originality/value
This study provides practical insight into the risk inherent in construction digitalisation, and its result can help organisations seeking to be digitally transformed make informed decisions. Theoretically, the study reveals the risks associated with construction digitalisation – an aspect that has not gained significant attention in the current fourth industrial revolution discourse. Therefore, its findings can form a basis for future studies on the risk of digitalising construction organisations.
Cumulative degradation methodology to predict reliability of electronic systems
Authors: Thiel George , Griggio Flavio , Tiku Sanjay 
Published: June 2021

Purpose
The purpose of this paper is to describe a novel methodology for predicting reliability for consumer electronics or any other hardware systems that experience a complex lifecycle environmental profile.

Design/methodology/approach
This Physics-of-Failure–based three-step methodology can be used to predict the degradation rate of a population using a Monte Carlo approach. The three steps include: using an empirical equation describing the degradation of a performance metric, a degradation consistency condition and a technique to account for cumulative degradation across multiple life-cycle stress conditions (e.g. temperature, voltage, mechanical load, etc.).

Findings
Two case studies are provided to illustrate the methodology including one related to repeated touch-load induced artifacts for displays.

Originality/value
This novel methodology can be applied to a wide range of applications from mechanical systems to electrical circuits. The results can be fed into the several stages of engineering validation to speed up product qualification.
Effects of internal brand knowledge dissemination on the employee
Authors: Bravo Rafael , Pina José Miguel , Tirado Beatriz 
Published: June 2021

PurposeThis study aims to examine the internal brand knowledge dissemination process in the banking sector and its effects on employees. Specifically, it focuses on the key roles of employee identification with both the organization and with the customer as antecedents of behaviors supportive of the brand, i.e. employee citizenship behaviors and recommendation behaviors.Design/methodology/approachAn empirical study was carried out in a major Spanish bank. Data gathered from a survey of 315 employees were analyzed through structural equation modeling.FindingsThe results showed that employees' perceptions of brand value congruence are key in explaining their identification with both the organization and with the customer. However, the employees' perceptions of the brand's authenticity explained only their recommendations of the bank as a good place to work.Originality/valueThese findings contribute to the advance in the current knowledge of the role of variables such as brand authenticity and employee–customer identification in internal brand management. From a managerial viewpoint, the results provide insights into the importance of employees' perceptions and attitudes when it comes to brand knowledge dissemination.
Assessment of moderate wine consumption and alcohol abuse from the perspective of German and Hungarian consumers
Authors: Szolnoki Gergely , Filopoulos Stylianos , Stein-Hammer Claudia , Brazsil David 
Published: June 2021

Purpose
The health effects of alcoholic beverages and the differentiation between moderate consumption and alcohol abuse are discussed controversially in medicine, sociology and politics. Therefore, this paper aims to analyse how consumers assess the relation among health, wine consumption and alcohol abuse.

Design/methodology/approach
A representative survey in Germany and in Hungary was conducted with 2,000 and 1,500 respondents, respectively. The survey included questions regarding the assessment and definition of alcohol abuse and moderate wine consumption.

Findings
The results show that in Hungary, moderate wine consumption is defined similarly as in Germany; on the contrary, in the case of alcohol abuse, there are significant differences. Regardless of cultural background, the respondents agreed that excessive wine consumption harms health and certain consumer groups (pregnant women or people under 16 years old) should avoid drinking wine.

Practical implications
These findings can contribute to a long-term goal-oriented wine in moderation strategy for consumers and support policy advice on moderate and excessive wine consumption.

Originality/value
The results help to understand how consumers perceive moderate and excessive wine consumption in everyday life, and how they judge wine as an alcoholic beverage. To the best of authors’ knowledge, there has not been similar study published on the perceptions of wine consumers in this regard, neither in Germany nor in Hungary.