bluuebunny/crossref_metadata_2025_split huggingface dataset:
The PINK1 – Parkin mitophagy signalling pathway is not functional in peripheral blood mononuclear cells
Authors: Bradshaw Aaron V. , Campbell Philip , Schapira Anthony H. V. , Morris Huw R. , Taanman Jan-Willem 
Published: February 2020

AbstractMutations in thePINK1andPRKNgenes are the most common cause of early-onset familial Parkinson disease. These genes code for the PINK1 and Parkin proteins, respectively, which are involved in the degradation of dysfunctional mitochondria through mitophagy. An early step in PINK1 – Parkin mediated mitophagy is the ubiquitination of the mitofusin proteins MFN1 and -2. The ubiquitination of MFN1 and -2 in patient samples may therefore serve as a biomarker to determine the functional effects ofPINK1andPRKNmutations, and to screen idiopathic patients for potential mitophagy defects. We aimed to characterise the expression of the PINK1 – Parkin mitophagy machinery in peripheral blood mononuclear cells (PBMCs) and assess if these cells could serve as a platform to evaluate mitophagy via analysis of MFN1 and -2 ubiquitination. Mitophagy was induced through mitochondrial depolarisation by treatment with the protonophore CCCP and ubiquitinated MFN proteins were analysed by western blotting. In addition,PINK1andPRKNmRNA and protein expression levels were characterised with reverse transcriptase quantitative PCR and western blotting, respectively. Whilst CCCP treatment led to MFN ubiquitination in primary fibroblasts, SH-SY5Y neuroblastoma cells and Jurkat leukaemic cells, treatment of PBMCs did not induce ubiquitination of MFN.PRKNmRNA and protein was readily detectable in PBMCs at comparable levels to those observed in Jurkat and fibroblast cells. In contrast, PINK1 protein was undetectable andPINK1mRNA levels remarkably low in control PBMCs. Our findings suggest that the PINK1 – Parkin mitophagy signalling pathway is not functional in PBMCs. Therefore, PBMCs are not a suitable biosample for analysis of mitophagy function in Parkinson disease patients.
Antagonistic roles of NOT1 paralogues in the timing of gene expression inPlasmodium falciparum
Authors: Liu Ying , Rai Ragini , Zhu Lei , Zhang Changqing , Rocamora Frances , Featherstone Mark , Bozdech Zbynek 
Published: February 2020

AbstractNOT1 is the scaffold of the CCR4-NOT complex, a highly conserved multi-protein complex that regulates gene expression in eukaryotes. As opposed to most eukaryotes in which NO1 is encoded by a single gene, malaria parasites,Plasmodium falciparum,carry two NOT1 paralogues, PfNOT1.1 and PfNOT1.2. Here we showed that the two PfNOT1 proteins function as mutually exclusive scaffolds within the PfCCR4-NOT protein complexes that are abundantly located in the parasite cytoplasm. Intriguingly, the two PfNOT1 paralogues appear to have directly opposing functions in regulation of mRNA abundance across theP. falciparumIDC, in which PfNTO1.1 and PfNOT1.2 induces and suppresses transcript abundance during their active transcription, respectively. Targeted disruption of either of thePfNOT1gene causes defective growth and lower invasion rates presumably due to the deregulation theP. falciparumIDC transcriptional cascade. We also demonstrate that the regulatory function of both PfNOT1.1 and PfNOT1.2 are related to another PfCCR4-NOT subunit,PfCaf1,which indicates their activity during post-transcriptional regulation. Indeed RNA decay studies suggest the active role of both PfNOT1 proteins in regulation of mRNA stability in a directly opposing manner.Author summaryCCR4-NOT complex is a highly conserved multi-protein complex that regulates gene expression in eukaryotes. NOT1 serves as the scaffold of the complex and plays important roles in gene regulation both transcriptionally and post-transcriptionally. As opposed to other eukaryotes,P. falciparumencodes two paralogues of PfNOT1, raising the question as to the significance to possess an additional copy of PfNOT1 in the parasite. Here we described antagonistic regulatory functions of two PfNOT1 paralogues in gene expression during the 48-hour intraerythrocytic developmental cycle. We also reported that their regulatory functions are predominantly post-transcriptional and proposed a model in which distinct PfCCR4-NOT complexes defined by mutually exclusive PfNOT1 scaffolds differentially regulate PfCAF1 function in mRNA decay. This study highlights the importance of post-transcriptional regulation inP. falciparumand provides novel insights into mechanisms of gene regulation in this organism. The unique presence of two PfNOT1 paralogues may also open avenues for the development of new drug targets for anti-malarial control.
PCNA activates the MutLγ endonuclease to promote meiotic crossing over
Authors: Kulkarni Dhananjaya S. , Owens Shannon , Honda Masayoshi , Ito Masaru , Yang Ye , Corrigan Mary W. , Chen Lan , Quan Aric L. , Hunter Neil 
Published: February 2020

AbstractDuring meiosis, crossover recombination connects homologous chromosomes to direct their accurate segregation1. Defects in crossing over cause infertility, miscarriage and congenital disease. Accordingly, each pair of chromosomes attains at least one crossover through processes that designate and then implement crossing over with high efficiency2. At the DNA level, crossing over is implemented through the formation and biased resolution of double-Holliday Junction intermediates3–5. A central tenet of crossover resolution is that the two Holliday junctions are resolved in opposite planes by targeting nuclease incisions to specific DNA strands6. Although the endonuclease activity of the MutLγ complex has been implicated in crossover-biased resolution7–12, the mechanisms that activate and direct strand-specific cleavage remain unknown. Here we show that the sliding clamp, PCNA, is important for crossover-biased resolution.In vitroassays with human enzymes show that hPCNA and its loader hRFC are sufficient to activate the hMutLγ endonuclease under physiological conditions. In this context, the hMutLγ endonuclease is further stimulated by a co-dependent activity of the pro-crossover factors hEXO1 and hMutSγ, the latter of which binds Holliday junctions13. hMutLγ also specifically binds a variety of branched DNAs, including Holliday junctions, but canonical resolvase activity is not observed implying that the endonuclease incises adjacent to junction branch points to effect resolution.In vivo, we show that budding yeast RFC facilitates MutLγ-dependent crossing over. Furthermore, PCNA localizes to prospective crossover sites along synapsed chromosomes. These data highlight similarities between crossover-resolution and DNA mismatch repair14–16and evoke a novel model for crossover-specific dHJ resolution during meiosis.
Regulation of the MLH1-MLH3 endonuclease in meiosis
Authors: Cannavo Elda , Sanchez Aurore , Anand Roopesh , Ranjha Lepakshi , Hugener Jannik , Adam Céline , Acharya Ananya , Weyland Nicolas , Aran-Guiu Xavier , Charbonnier Jean-Baptiste , Hoffmann Eva R. , Borde Valérie , Matos Joao , Cejka Petr 
Published: February 2020

SummaryDuring prophase of the first meiotic division, cells deliberately break their DNA. These DNA breaks are repaired by homologous recombination, which facilitates proper chromosome segregation and enables reciprocal exchange of DNA segments between homologous chromosomes, thus promoting genetic diversity in the progeny1. A successful completion of meiotic recombination requires nucleolytic processing of recombination intermediates. Genetic and cellular data implicated a pathway dependent on the putative MLH1-MLH3 (MutLγ) nuclease in generating crossovers, but mechanisms that lead to its activation were unclear2–4. Here, we have biochemically reconstituted key elements of this pro-crossover pathway. First, we show that human MSH4-MSH5 (MutSγ), which was known to support crossing over5–7, binds branched recombination intermediates and physically associates with MutLγ. This helps stabilize the ensemble at joint molecule structures and adjacent dsDNA. Second, we show that MutSγ directly stimulates DNA cleavage by the MutLγ endonuclease, which demonstrates a novel and unexpected function for MutSγ in triggering crossing-over. Third, we find that MutLγ activity is further stimulated by EXO1, but only when MutSγ is present. Fourth, we also identify the replication factor C (RFC) and the proliferating cell nuclear antigen (PCNA) as additional components of the nuclease ensemble, and show thatS. cerevisiaestrains expressing PIP box-mutated MutLγ present striking defects in forming crossovers. Finally, we show that the MutLγ-MutSγ-EXO1-RFC-PCNA nuclease ensemble preferentially cleaves DNA with Holliday junctions, but shows no canonical resolvase activity. Instead, the multilayered nuclease ensemble likely processes meiotic recombination intermediates by nicking dsDNA adjacent to junction points8. Since DNA nicking by MutLγ is dependent on its co-factors, the asymmetric distribution of MutSγ and RFC/PCNA on meiotic recombination intermediates may drive biased DNA cleavage. This unique mode of MutLγ nuclease activation might explain crossover-specific processing of Holliday junctions within the meiotic chromosomal context3, 9.
Opposing effects of an F-box protein and the HSP90 chaperone network on microtubule stability and neurite growth inCaenorhabditis elegans
Authors: Zheng Chaogu , Atlas Emily , Lee Ho Ming Terence , Jao Susan Laura Javier , Nguyen Ken C. Q. , Hall David H. , Chalfie Martin 
Published: February 2020

AbstractMolecular chaperones often work collaboratively with the ubiquitination-proteasome system (UPS) to facilitate the degradation of misfolded proteins, which typically safeguards cellular differentiation and protects cells from stress. In this study, however, we report that the Hsp70/Hsp90 chaperone machinery and an F-box protein, MEC-15, have opposing effects on neuronal differentiation and that the chaperones negatively regulate neuronal morphogenesis and functions. Using the touch receptor neurons (TRNs) ofCaenorhabditis elegans, we find thatmec-15(−)mutants display defects in microtubule formation, neurite growth, synaptic development, and neuronal functions, and these defects can be rescued by the loss of Hsp70/Hsp90 chaperones and cochaperones. MEC-15 likely functions in a SCF complex to degrade DLK-1, which is an Hsp90 client protein stabilized by the chaperones. The abundance of DLK-1, and likely other Hsp90 substrates, is fine-tuned by the antagonism between MEC-15 and chaperones; this antagonism regulates TRN development as well as synaptic functions of GABAergic motor neurons. Therefore, a balance between UPS and chaperones tightly controls neuronal differentiation.Summary statementMolecular chaperones are known to protect cells from stress. However, in this study the authors showed that the Hsp90 chaperone negatively regulates neuronal differentiation when the ubiquitination-proteasome system is compromised.
The mechanical inhibition of the isolated Vofrom V-ATPase for proton conductance
Authors: Kishikawa Jun-ichi , Nakanishi Atsuko , Furuta Aya , Kato Takayuki , Namba Keiichi , Tamakoshi Masatada , Mitsuoka Kaoru , Yokoyama Ken 
Published: February 2020

AbstractV-ATPase is an energy converting enzyme, coupling ATP hydrolysis/synthesis in the hydrophilic V1moiety, with proton flow through the Vomembrane moiety, via rotation of the central rotor complex relative to the surrounding stator apparatus. Upon dissociation from the V1domain, the Voof eukaryotic V-ATPase can adopt a physiologically relevant auto-inhibited form in which proton conductance through the Vois prevented, however the molecular mechanism of this inhibition is not fully understood. Using cryo-electron microscopy, we determined the structure of both theholoV/A-ATPase and the isolated Voat near-atomic resolution, respectively. These structures clarify how the isolated Voadopts the auto-inhibited form and how theholocomplex prevents the formation of this inhibited Voform.One Sentence SummaryCryo-EM structures of rotary V-ATPase reveal the ON-OFF switching mechanism of H+translocation in the Vomembrane domain.
Mesoscopic numerical analysis of dynamic tensile fracture of recycled concrete
Authors: Ying Liping , Peng Yijiang , Kamel Mahmoud M.A. 
Published: February 2020

Purpose
Based on the random aggregate model of recycled aggregate concrete (RAC), this paper aims to focus on the effect of loading rate on the failure pattern and the macroscopic mechanical properties.

Design/methodology/approach
RAC is regarded as a five-phase inhomogeneous composite material at the mesoscopic level. The number and position of the aggregates are modeled by the Walraven formula and Monte–Carlo stochastic method, respectively. The RAC specimen is divided by the finite-element mesh to establish the dynamic base force element model. In this model, the element mechanical parameters of each material phase satisfy Weibull distribution. To simulate and analyze the dynamic mechanical behavior of RAC under axial tension, flexural tension and shear tension, the dynamic tensile modes of the double-notched specimens, the simply supported beam and the L specimens are modeled, respectively. In addition, the different concrete samples are numerically investigated under different loading rates.

Findings
The failure strength and failure pattern of RAC have strong rate-dependent characteristics because of the inhomogeneity and the inertial effect of the material.

Originality/value
The dynamic base force element method has been successfully applied to the study of recycled concrete.
An efficient and accurate method for transient heat conduction in a periodic structure with moving heat sources
Authors: Cui Haichao , Gao Qiang , Li Xiaolan , Ouyang Huajiang 
Published: February 2020

Purpose
This paper aims to propose an efficient and accurate method to analyse the transient heat conduction in a periodic structure with moving heat sources.

Design/methodology/approach
The moving heat source is modelled as a localised Gaussian distribution in space. Based on the spatial distribution, the physical feature of transient heat conduction and the periodic property of structure, a special feature of temperature responses caused by the moving heat source is illustrated. Then, combined with the superposition principle of linear system, within a small time-step, computation of results corresponding to the whole structure excited by the Gaussian heat source is transformed into that of some small-scale structures. Lastly, the precise integration method (PIM) is used to solve the temperature responses of each small-scale structure efficiently and accurately.

Findings
Within a reasonable time-step, the heat source applied on a unit cell can only cause the temperature responses of a limited number of adjacent unit cells. According to the above feature and the periodic property of a structure, the contributions caused by the moving heat source for the most of time-steps are repeatable, and the temperature responses of the entire periodic structure can be obtained by some small-scale structures.

Originality/value
A novel numerical method is proposed for analysing moving heat source problems, and the numerical examples demonstrate that the proposed method is much more efficient than the traditional methods, even for larger-scale problems and multiple moving heat source problems.
An asymptotic-numerical comparative study for axisymmetric free surface liquid jet near and far from exit at high Reynolds number
Authors: Wang Yunpeng , Khayat Roger E. 
Published: February 2020

Purpose
The purpose of this study is to examine theoretically the axisymmetric flow of a steady free-surface jet emerging from a tube for high inertia flow and moderate surface tension effect.

Design/methodology/approach
The method of matched asymptotic expansion is used to explore the rich dynamics near the exit where a stress singularity occurs. A boundary layer approach is also proposed to capture the flow further downstream where the free surface layer has grown significantly.

Findings
The jet is found to always contract near the tube exit. In contrast to existing numerical studies, the author explores the strength of upstream influence and the flow in the wall layer, resulting from jet contraction. This influence becomes particularly evident from the nonlinear pressure dependence on the upstream distance, as well as the pressure undershoot and overshoot at the exit for weak and strong gravity levels, respectively. The approach is validated against existing experimental and numerical data for the jet profile and centerline velocity where good agreement is obtained. Far from the exit, the author shows how the solution in the diffusive region can be matched to the inviscid far solution, providing the desired appropriate initial condition for the inviscid far flow solution. The location, at which the velocity becomes uniform across the jet, depends strongly on the gravity level and exhibits a non-monotonic behavior with respect to gravity and applied pressure gradient. The author finds that under weak gravity, surface tension has little influence on the final jet radius. The work is a crucial supplement to the existing numerical literature.

Originality/value
Given the presence of the stress singularity at the exit, the work constitutes a superior alternative to a computational approach where the singularity is typically and inaccurately smoothed over. In contrast, in the present study, the singularity is entirely circumvented. Moreover, the flow details are better elucidated, and the various scales involved in different regions are better identified.
Mobile users’ information privacy concerns instrument and IoT
Authors: Foltz C. Bryan , Foltz Laura 
Published: February 2020

Purpose
Internet of Things (IoT) presents new privacy dilemmas. While IoT is becoming more common, a model to understand privacy concerns has not been established. The purpose of this paper is to examine an existing privacy model, the mobile users’ information privacy concerns (MUIPC), in the context of IoT.

Design/methodology/approach
A survey was distributed via email to 1,257 undergraduate students enrolled in a Carnegie Master’s level university in the mid-south; 192 students completed the survey, a response rate of 15.3%. SmartPLS, a structural equation modeling software, was used to evaluate the measurement model and to examine the relationships.

Findings
All relationships were significant at the 0.05 level indicating that the MUIPC model does appear to apply to IoT.

Research limitations/implications
A convenience sample was used and the response rate was low and, therefore, may not be generalizable to another population.

Originality/value
This research demonstrates the MUIPC is indeed applicable to privacy research within IoT, thus opening another avenue for future research and confirms the influence of information privacy upon intention within the IoT realm.
Managing project complexity: how to cope with multiple dimensions of complex systems
Authors: Mamédio Diórgenes Falcão , Meyer Victor 
Published: February 2020

PurposeThis study aimed to contribute to the field of project management (PM) by exploring the elements of project complexity and how individuals respond to such complexity. Multiple dimensions were examined, including technical, human and political dimensions, with a significant impact on project implementation.Design/methodology/approachAn in-depth case study was conducted, focusing on the implementation of a Brazilian hospital. Data were collected through semi-structured interviews, participant observation and document analysis. Bridging the research gap involved unraveling the project complexity elements and how to manage them, more specifically in the hospital context.FindingsThe findings revealed that project complexity challenges managers to deal with uncertainties, emergencies and unexpected situations. It implies coping with multiple factors of technical, human and political dimensions. Divergent interests contributed to the formation of coalitions, triggering relevant individual and group learning. Strategic improvisation had a potentially significant response from managers regarding project complexity to make adjustments and changes, focusing on project effectiveness and performance.Practical implicationsThe challenge of managing project complexity is to deal with the balance between structure and improvisation in response to complexity. Flexibility, adaptability, self-organisation and strategic improvisation are key elements in managerial practices that address complexity, especially in hospital projects.Originality/valueThe differentiated approach lies in the proposed model of project complexity, with elements that make up the technical, human and political dimensions, with significant results for complex projects.
Protection offered by leaf fungal endophytes to an invasive species against native herbivores depends on soil nutrients
Authors: Graff Pamela , Gundel Pedro E. , Salvat Adriana , Cristos Diego , Chaneton Enrique J. 
Published: February 2020

Abstract

Natural grassland ecosystems are increasingly threatened by excessive loadings of nutrients and by the presence of species bred for high productivity. By manipulating grazing regimes and nutrient availability, agricultural practices facilitate the establishment and spread of certain forage plant species outside managed landscapes, challenging local biodiversity. The ecological success of some species in the invaded range sometimes seems to be associated with the symbiosis with foliar fungal endophytes. Symbiotic fungi may increase the competitiveness of host species, but also the resistance to herbivory through the production of toxic secondary compounds such as alkaloids. While progress has been made in understanding how soil nutrients modulate other benefits offered by fungal endophytes to plants (e.g. stress tolerance, competitive ability, etc), the consequences for a higher trophic level (i.e. herbivores) and the potential feedbacks on plant invasion have not been explored yet.

We explored the relative and interactive importance of soil nitrogen (N) and phosphorus (P) in modulating the interaction of the invasive grass tall fescue—associated with fungal endophytes—and native herbivores in a natural grassland. We hypothesized that N and P nutrients modulate differentially leaf quality traits, namely nutritional value and fungal alkaloid contents, determining the level of damage by native insect herbivores on the exotic tall fescue.

We found that only the addition of P significantly increased native caterpillar density in the field, which corresponded to a concomitant increase in leaf damage. In contrast to expectations, the concentration of the alkaloid ergovaline in leaves was not strongly related to N. It was the level of soil P which dictated the concentration of the element (P) in the leaves and reduced the level of defence against herbivores in this endophyte‐symbiotic species. Then, herbivore performance increased, and plants were more prone to be attacked.

Synthesis. Our study indicates a strong control of soil P fertility on the triple interaction among plants, fungal endophytes and native herbivores. This highlights the potential role of increased soil nutrients on the invasion spread of endophyte‐symbiotic forage plants in natural grasslands.