bluuebunny/crossref_metadata_2025_split huggingface dataset:
A senescence-like cellular response inhibits bovine ephemeral fever virus proliferation
Authors: Zeng Yu-Jing , Hsu Min-Kung , Tsai Chiao-An , Chu Chun-Yen , Wu Hsing-Chieh , Wang Hsian-Yu 
Published: January 2021

AbstractDuring industrial scale production of virus for vaccine manufacturing, antiviral response of host cells can dampen maximal viral antigen yield. In addition to interferon responses, many other cellular responses such as the AMPK signaling pathway or senescence-like response may inhibit or slow down virus amplification in the cell culture system. In this study, we first performed a Gene Set Enrichment Analysis of the whole-genome mRNA transcriptome and found a senescence-like cellular response in BHK-21 cells when infected with bovine ephemeral fever virus (BEFV). To demonstrate that this senescence-like state may reduce virus growth, BHK-21 subclones showing varying degrees of senescence-like state were infected with BEFV. Results showed the BHK-21 subclones showing high senescence staining could inhibit BEFV replication while low senescence-staining subclones are permissive to virus replication. Using a different approach, a senescence-like state was induced in BHK-21 using a small molecule, camptothecin (CPT), and BEFV susceptibility was examined. Results showed that indeed CPT-treated BHK-21 is more resistant to virus infection. Overall, these results indicate that a senescence-like response may be at play in BHK-21 upon virus infection. Furthermore, cell clone selection and modulating treatments using small molecules may be tools in countering anti-viral responses.
Hyperpiliation reducesPseudomonas aeruginosapathogenicity by impeding type III secretion
Authors: Kilmury Sara L.N. , Graham Katherine J. , Lamers Ryan P. , MacNeil Lesley T. , Burrows Lori L. 
Published: January 2021

ABSTRACTType IVa pili (T4aP) are important virulence factors for many bacterial pathogens. Previous studies suggested that the retraction ATPase, PilT, modulates pathogenicity due to its critical role in pilus dynamics and twitching motility. Here we use aCaenorhabditis elegansslow killing model to show that hyperpiliation, not loss of pilus retraction, reduces virulence ofPseudomonas aeruginosastrains PAK and PA14 by interfering with function of the contact-dependent type III secretion system (T3SS). Hyperactivating point mutations in theP. aeruginosaPilSR two-component system that controls transcription of the major pilin gene,pilA, increased levels of surface pili to the same extent as deletingpilT, without impairing twitching motility. These functionally hyperpiliated PilSR mutants had significant defects in pathogenicity that were rescued by deletingpilAor by increasing the length of T3SS needles via deletion of the needle-length regulator, PscP. HyperpiliatedpilTdeletion orpilOpoint mutants showed similar PilA-dependent impairments in virulence, validating the phenotype. Together, our data support a model where a surfeit of pili prevents effective engagement of contact-dependent virulence factors. These findings suggest that the role of T4aP retraction in virulence should be revised.SIGNIFICANCEPseudomonas aeruginosais a major contributor to hospital-acquired infections and particularly problematic due to its intrinsic resistance to many front-line antibiotics. Strategies to combat this and other important pathogens include development of anti-virulence therapeutics. We show that the pathogenicity ofP. aeruginosais impaired when the amount of type IVa pili (T4aP) expressed on the cell surface increases, independent of the bacteria’s ability to twitch. We propose that having excess T4aP on the cell surface can physically interfere with productive engagement of the contact-dependent type III secretion toxin delivery system. A better understanding of how T4aP modulate interaction of bacteria with target cells will improve the design of therapeutics targeting components involved in regulation of T4aP expression and function, to reduce the clinical burden ofP. aeruginosaand other T4aP-expressing bacteria.
The DEAD-box RNA helicases RhlE2 is a global regulator ofPseudomonas aeruginosalifestyle and pathogenesis
Authors: Hausmann Stéphane , Gonzalez Diego , Geiser Johan , Valentini Martina 
Published: January 2021

AbstractThe RhlE DEAD-box RNA helicase protein family is widespread among Proteobacteria, but it is the least understood due to the lack of a clear biological function. Here, we study the two RhlE homologs present in the opportunistic pathogenPseudomonas aeruginosa. RhlE1 and RhlE2 diverged duringP. aeruginosaevolution; our data indicate that this resulted in a non-redundant biological role, a distinct molecular action and an enzymatic activity differentially stimulated by RNA. Whereas RhlE1 is specifically necessary for bacteria growth in cold, we show that RhlE2 acts as global post-transcriptional regulator, affecting the level of hundreds of cellular transcripts and multiple functionalities indispensable not only forP. aeruginosaenvironmental adaptation, but also for its virulence. The global action of RhlE2 relies on a unique C-terminal extension, which establishes an RNA-dependent interaction with the RNase E endonuclease and the cellular RNA degradation machinery.
3D Visualization of the Podocyte Actin Network using Integrated Membrane Extraction, Electron Microscopy, and Deep Learning
Authors: Qu Chengqing , Roth Robyn , Loitman Charles , Hammad Dina , Genin Guy M. , Miner Jeffrey H. , Suleiman Hani Y. 
Published: January 2021

AbstractAlthough actin stress fibers are abundant in cultured cells, little is known about these structuresin vivo.In podocytes of the kidney glomerulus, much evidence suggests that mechanobiological mechanisms underlie injury, with changes to actin stress fiber structures potentially responsible for pathological changes to cell morphology. However, this hypothesis is difficult to rigorously testin vivodue to challenges with visualization. We therefore developed the first visualization technique capable of resolving the three-dimensional (3D) podocyte actin network with unprecedented detail in healthy and injured podocytes, and applied this technique to reveal the changes in the actin network that occur upon podocyte injury. Using isolated glomeruli from healthy mice as well as from three different mouse injury models (Cd2ap-/-, Lamb2-/-and theCol4a3-/-model of Alport syndrome), we applied our novel imaging technique that integrates membrane-extraction, focused ion bean scanning electron microscopy (FIB-SEM), and deep learning image segmentation. In healthy glomeruli, we observed actin cables that link the interdigitating podocyte foot processes to newly described actin structures located at the periphery of the cell body. The actin cables within the foot processes formed a continuous, mesh-like, electron dense sheet that incorporated the slit diaphragms required for kidney filtration. After injury, the actin network was markedly different, having lost its organization and presenting instead as a disorganized assemblage of actin condensates juxtaposed to the glomerular basement membrane. The new visualization method enabled us, for the first time, to observe the detailed 3D organization of actin networks in both healthy and injured podocytes. Shared features of actin condensations across all three injury models further suggested common mechanobiological pathways that govern changes to podocyte morphology after injury.
pUL36 de-ubiquitinase activity augments both the initiation and progression of lytic virus infection in IFN–primed cells
Authors: Mohnke Jonas , Stark Irmgard , Fischer Mara , Grothey Arnhild , O’Hare Peter , Sodeik Beate , Erhard Florian , Dölken Lars , Hennig Thomas 
Published: January 2021

AbstractThe conserved, structural HSV-1 tegument protein pUL36 is essential for both virus entry and assembly. While its N-terminal de-ubiquitinase (DUB) activity is dispensable for infection in cell culture, it is required for efficient virus spreadin vivoby acting as a potent viral immune evasin. Here, we show that the pUL36 DUB activity was required to overcome interferon-(IFN)-mediated suppression of both plaque initiation and progression to productive infection. Immediately upon virus entry, incoming tegument-derived pUL36-DUB activity helped the virus to escape intrinsic antiviral resistance and efficiently initiate lytic virus replication in IFN-primed cells. Subsequently,de novoexpressed pUL36-DUB augmented the efficiency of productive infection and virus yield. Interestingly, removal of IFN shortly after inoculation only resulted in a partial rescue of plaque formation, indicating that an IFN-induced defense mechanism eliminates invading virus particles unless counteracted by pUL36-DUB activity. Taken together, we demonstrated that the pUL36 DUB disarms IFN-induced antiviral responses at two levels, namely, to protect the infectivity of invading virus as well as to augment productive virus replication in IFN-primed cells.Author SummaryHSV-1 is an ubiquitous human pathogen that is responsible for common cold sores but may also cause life-threatening disease. pUL36 is an essential and conserved protein of infectious herpesvirus virions with a unique de-ubiquitinating (DUB) activity. The pUL36 DUB is dispensable for efficient virus infection in cell culture but represents an important viral immune evasinin vivo. Here, we showed that tegument-derived DUB activity delivered by the invading virus particles is required to overcome IFN-induced host resistance and to initiate efficient lytic infection.De novoexpressed pUL36 DUB subsequently augments productive infection and virus yield. These data indicate that the pUL36 DUB antagonizes the activity of yet unidentified IFN-inducible E3 ligases to facilitate productive infection at multiple levels. Our findings underscore the therapeutic potential of targeting conserved herpesvirus DUBs to prevent or treat herpesvirus disease.
Generation of a novel Nkx6-1 Venus fusion reporter mouse line
Authors: Burtscher Ingo , Tarquis-Medina Marta , Salinno Ciro , Beckenbauer Julia , Bakhti Mostafa , Lickert Heiko 
Published: January 2021

AbstractNkx6-1 is a member of the Nkx family of homeodomain transcription factors (TF) that regulates motor neuron development, neuron specification and pancreatic endocrine and β-cell differentiation. To facilitate the isolation and tracking of Nkx6-1-expressing cells, we have generated a novel Nkx6-1 Venus Fusion (Nkx6-1-VF) reporter allele. The Nkx6-1-VF knock-in reporter is regulated by endogenous cis-regulatory elements of Nkx6-1 and the fluorescent protein fusion does not interfere with the TF function, as homozygous mice are viable and fertile. In addition, the nuclear localization of Nkx6-1-VF protein reflects the endogenous Nkx6-1 protein distribution. During embryonic pancreas development, the reporter protein marks the pancreatic ductal progenitors and the endocrine lineage, but is absent in the exocrine compartment. Moreover, the levels of Nkx6-1-VF reporter is upregulated upon β-cell differentiation during the major wave of endocrinogenesis. In the adult islets of Langerhans, the reporter protein is exclusively found in insulin-secreting β-cells. Importantly, the Venus reporter activities allows successful tracking of β-cells in live-cell imaging and their specific isolation by flow sorting. In summary, the generation of Nkx6-1-VF reporter line provides a unique tool to study the spatio-temporal expression pattern of this TF during organ development and isolate and track Nkx6-1-expressing cells such as pancreatic β-cells, but also neurons and motor neurons in health and disease.
NR2F1 is a barrier to dissemination of early-evolved mammary cancer cells
Authors: Rodriguez-Tirado Carolina , Kale Nupura , Carlini Maria Jose , Shrivastava Nitisha , Khalil Bassem , Bravo-Cordero Jose Javier , Alexander Melissa , Ji Jiayi , Sosa Maria Soledad 
Published: January 2021

SummaryCancer cells disseminate during very early and sometimes asymptomatic stages of tumor progression. Granted that biological barriers to tumorigenesis exist, there must also be limiting steps to early dissemination, all of which remain largely unknown. We report that the orphan nuclear receptor NR2F1/COUP-TF1 serves as a barrier to early dissemination. High-resolution intravital imaging revealed that loss of function of NR2F1 in HER2+ early cancer cells increasedin vivodissemination without accelerating mammary tumor formation. NR2F1 expression was positively regulated by the tumor suppressive MMK3/6-p38-MAPK pathway and downregulated by HER2 and Wnt4 oncogenic signaling. NR2F1 downregulation by HER2 in early cancer cells led to decreased E-cadherin expression and β-catenin membrane localization, disorganized laminin 5 deposition, and increased expression of CK14, TWIST1, ZEB1 and PRRX1. Our findings reveal the existence of an inhibitory mechanism of dissemination regulated by NR2F1 downstream of HER2 signaling.
Emerging experience-dependent dynamics in primary somatosensory cortex reflect behavioral adaptation
Authors: Waiblinger Christian , McDonnell Megan E , Borden Peter Y , Stanley Garrett B 
Published: January 2021

ABSTRACTBehavioral experience and flexibility are crucial for survival in a constantly changing environment. Despite evolutionary pressures to develop adaptive behavioral strategies in a dynamically changing sensory landscape, the underlying neural correlates have not been well explored. Here, we use genetically encoded voltage imaging to measure signals in primary somatosensory cortex (S1) during sensory learning and behavioral adaptation in the mouse. In response to changing stimulus statistics, mice adopt a strategy that modifies their detection behavior in a context dependent manner as to maintain reward expectation. Surprisingly, neuronal activity in S1 shifts from simply representing stimulus properties to transducing signals necessary for adaptive behavior in an experience dependent manner. Our results suggest that neuronal signals in S1 are part of an adaptive framework that facilitates flexible behavior as individuals gain experience, which could be part of a general scheme that dynamically distributes the neural correlates of behavior during learning.
Speed limits of protein assembly with reversible membrane localization
Authors: Mishra Bhavya , Johnson Margaret E. 
Published: January 2021

AbstractSelf-assembly is often studied in a three-dimensional (3D) solution, but a significant fraction of binding events involve proteins that can reversibly bind and diffuse along a two-dimensional (2D) surface. In a recent study, we quantified how proteins can exploit the reduced dimension of the membrane to trigger complex formation. Here, we derive a single expression for the characteristic timescale of this multi-step assembly process, where the change in dimensionality renders rates and concentrations effectively time-dependent. We find that proteins can accelerate complex formation due to an increase in relative concentration, driving more frequent collisions which often wins out over slow-downs due to diffusion. Our model contains two protein populations that associate with one another and use a distinct site to bind membrane lipids, creating a complex reaction network. However, by identifying two major rate-limiting pathways to reach an equilibrium steady-state, we derive an accurate approximation for the mean first passage time when lipids are in abundant supply. Our theory highlights how the ‘sticking rate’, or effective adsorption coefficient of the membrane is central in controlling timescales. We also derive a corrected localization rate to quantify how the geometry of the system and diffusion can reduce rates of localization. We validate and test our results using kinetic and reaction-diffusion simulations. Our results establish how the speed of key assembly steps can shift by orders-of-magnitude when membrane localization is possible, which is critical to understanding mechanisms used in cells.
A split GFP system to enhance spatial and temporal sensitivity of translating ribosome affinity purification (TRAP)
Authors: Dinkeloo Kasia , Pelly Zoe , McDowell John M. , Pilot Guillaume 
Published: January 2021

SummaryTranslating ribosome affinity purification (TRAP) utilizes transgenic plants expressing a ribosomal protein fused to a tag for affinity purification of ribosomes and the mRNAs that they are translating. These actively translated mRNAs (translatome) can be interrogated by qPCR or RNAseq. Condition- or cell-specific promoters can be utilized to isolate the translatome of specific cell types, at different growth stages and/or in response to environmental variables. While advantageous for revealing differential expression, this approach may not provide sufficient sensitivity when activity of the condition/cell-specific promoter is weak, when ribosome turnover is low in the cells of interest, or when the targeted cells are ephemeral. In these situations, expressing tagged ribosomes under the control of these specific promoters may not yield sufficient polysomes for downstream analysis. Here, we describe a new TRAP system that employs two transgenes: one is constitutively expressed and encodes a ribosomal protein fused to one fragment of a split GFP; the second is controlled by a stimulus-specific promoter and encodes the second GFP fragment fused to an affinity purification tag. In cells where both transgenes are active, the purification tag is attached to ribosomes by bi-molecular folding and assembly of the split GFP fragments. This approach provides increased sensitivity and better temporal resolution because it labels pre-existing ribosomes and does not depend on rapid ribosome turnover. We describe the optimization and key parameters of this system, and then apply it to a plant-pathogen interaction in which spatial and temporal resolution are difficult to achieve with current technologies.SignificanceTranslating ribosome affinity purification (TRAP) has been modified to allow with increased sensitivity the isolation of RNA from sets of cells in which the activity of condition/cell-specific promoters is weak, ribosome turnover is low, or cells whose nature is ephemeral. Based on the use of a split linker constituted of the GFP driven by a pathogen-inducible promoter, this new TRAP system enabled efficient isolation of translated RNA from pathogen-infected leaf cells.
Quantitative Measurement of Rare Earth Elements in Brines: Isolation from the Charged Matrix Versus Direct LA‐ICP‐MS Measurements – A Comparative Study
Authors: Kokh Maria A. , Luais Béatrice , Truche Laurent , Boiron Marie Christine , Peiffert Chantal , Schumacher Aimeryc 
Published: January 2021

The quantification of the rare earth elements (REEs) in natural rocks and fluids is important not only for the sustainable use of geological resources but also for fundamental geological research. Due to significant improvements in experimental, modelling and analytical techniques, it was discovered that the REEs could be efficiently mobilised and transported by hydrothermal fluids. Thus, determining the REEs in fluids, especially in highly saline solutions, is a prerequisite to understand their fate in hydrothermal fluids. An analytical methodology was established to determine the trace quantities of the REEs in aqueous solutions with compositions typical to seawater and brines. The developed protocol was applied for the quantification of REEs in experimental sodium‐rich carbonate‐bearing hydrothermal solutions. For this purpose, we used two analytical approaches: (a) the REEs were chromatographically isolated from the charged matrix and introduced into a single collector quadrupole ICP‐MS and (b) direct determination of the REEs by LA‐ICP‐MS in experimental solutions loaded into glass capillaries without any additional isolation procedure. Both LA‐ICP‐MS and solution nebulisation ICP‐MS analysis after isolation of the REEs provide identical data in terms of REE concentrations in brines and are consistent within analytical uncertainties. Being an express method, LA‐ICP‐MS can be recommended for REE quantification in brines. At the same time, isolation of the REEs from the charged matrix with subsequent ICP‐MS measurement provides higher accuracy and precision, giving additional information for the REEs mass fractions that are below the detection limit of the LA‐ICP‐MS that was estimated at the ~ 10 ng g−1 level.
Low-Cycle Fatigue Life of Continuously Cyclic-Hardening Material
Authors: Zhang Zhong , Wu Xijia 
Published: January 2021

Abstract
A general fatigue life equation is derived by modifying the Tanaka-Mura-Wu dislocation pile-up model for variable strain-amplitude fatigue processes, where the fatigue crack nucleation life is expressed in terms of the root-mean-square of plastic strain range. Low-cycle fatigue tests were conducted on an austenitic stainless steel. At 400 °C and 600 °C, the material exhibits continuously cyclic-hardening behavior. The root-mean-square of plastic strain ranges is evaluated from the experimental data for each test condition at strain rates ranging from 0.0002/s to 0.02/s. The variable-amplitude Tanaka-Mura-Wu model is found to be in good agreement with the low-cycle fatigue (LCF) data, which effectively proves Miner's rule on the stored plastic strain energy basis.
Transonic Fan Blade Redesign Approach to Attenuate Nonsynchronous Vibration
Authors: Lu Yaozhi , Lad Bharat , Vahdati Mehdi 
Published: January 2021

Abstract
Due to manufacturing tolerance and deterioration during operation, different blades in a fan assembly exhibit geometric variability. This leads to asymmetry which will be amplified in the running geometry by centrifugal and aerodynamic loads. This study investigates a phenomenon known as Alternate Passage Divergence (APD), where the blade untwist creates an alternating pattern in passage geometry and stagger angle around the circumference. After the formation of alternating tip stagger pattern, APD's unsteady effect, APD-induced Non-Synchronous Vibration (APD-NSV), can cause the blades from one group to switch to the other creating a traveling wave pattern around the circumference. Thus, it can potentially lead to high cycle fatigue issues. More importantly, this phenomenon occurs close to, or at, peak efficiency conditions and can significantly reduce overall efficiency. Therefore, it is vital to attenuate the NSV behavior. In this study, a redesign approach is investigated.
Career Assistance to a Team in Crisis-Transition: An Intervention Case Study in Swedish Elite Handball
Authors: Ekengren Johan , Stambulova Natalia , Johnson Urban , Ivarsson Andreas , Schinke Robert J. 
Published: January 2021

In this paper, the authors share how a career assistance program was developed, implemented, and evaluated with a Swedish elite handball team. Within this case study, the initial version of the career assistance program’s content was created based on the career-long psychological support services in a Swedish handball framework and the first author’s applied experiences. During implementation, the head coach was terminated unexpectedly, and the team appeared in a crisis. This transitional situation led to modification of the career assistance program to help the players cope with changes. Eighteen players took part in eight workshops dealing with various aspects of their sport and nonsport life (e.g., performance, training, lifestyle, recovery, and future planning) with crisis-related issues (e.g., coping with uncertainty) incorporated. Mixed-methods evaluation revealed the players’ perceived increase in personal resources (awareness and skills) and decrease in stress and fatigue. Reflections on working in applied sport psychology from a holistic perspective in a dynamic real-life setting are provided.