bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mycobacterial surface-associated ESX-1 virulence factors play a role in mycobacterial adherence and invasion into lung epithelial cells
Authors: Bao Yanqing , Zhang Qi , Wang Lin , Aguilera Javier , Reyes Salvador Vazquez , Sun Jianjun 
Published: October 2020

AbstractEsxA has long been recognized as an important virulence factor ofMycobacterium tuberculosis(Mtb) that plays an essential role in Mtb cytosolic translocation by penetrating phagosomal membranes with its acidic pH-dependent membrane permeabilizing activity (MPA). Since the reported cytolytic activity of EsxA at neutral pH is controversial, in the present study we have obtained direct evidence that it is the residual ASB-14, a detergent used in EsxA purification, but not EsxA that causes cytolysis at neutral pH. Besides, we have also found that the exogenously added EsxA was internalized into lung epithelial cells (WI-26) and inserted into the host membranes, and these processes could be blocked by cytochalasin D and bafilomycin A. This indicates that EsxA is bound by host surface receptors and internalized into acidic endosomal compartments. This observation has intrigued us to investigate the role of EsxA in mycobacterial adherence and invasion in host cells. Interestingly, compared to theMycobacterium marinum(Mm) wild type strain, the Mm strain with deletion of theesxBAoperon (MmΔEsxA:B) had a lower adherence but a higher invasion in WI-26 cells. More interestingly, either inducible knockdown of EsxAB or removal of the bacterial surface-associated EsxAB by Tween-80 exhibited opposite results compared to gene knockout. Finally, the surface-associated EsxA is correlated to mycobacterial virulence. Together, the present study has shown for the first time that EsxA is internalized into the host cells and inserts into the host membranes, and mycobacterial surface-associated EsxAB plays an important role in mycobacterial adherence and invasion in host cells, which warrants further investigation.
Sonic hedgehog signaling directs patterned cell remodeling during cranial neural tube closure
Authors: Brooks Eric R. , Islam Mohammed T. , Anderson Kathryn V. , Zallen Jennifer A. 
Published: October 2020

AbstractNeural tube closure defects are a major cause of infant mortality, with exencephaly accounting for nearly one-third of cases. However, the mechanisms of cranial neural tube closure are not well understood. Here we show that this process involves a tissue-wide pattern of apical constriction controlled by Sonic hedgehog (Shh) signaling. Midline cells in the mouse midbrain neuroepithelium are short with large apical surfaces, whereas lateral cells are taller and undergo synchronous apical constriction, driving neural fold elevation. Embryos lacking the Shh effector Gli2 fail to produce appropriate midline cell architecture, whereas embryos with expanded Shh signaling, including the IFT-A complex mutantsIft122andTtc21band embryos expressing activated Smoothened, display apical constriction defects in lateral cells. Disruption of lateral, but not midline, cell remodeling results in exencephaly. These results reveal a morphogenetic program of patterned apical constriction governed by Shh signaling that generates structural changes in the developing mammalian brain.
CRISPR-Based Transcriptional Activation Tool for Silent Genes in Filamentous Fungi
Authors: Mózsik László , Hoekzema Mirthe , de Kok Niels A.W. , Bovenberg Roel A.L. , Nygård Yvonne , Driessen Arnold J.M. 
Published: October 2020

AbstractFilamentous fungi are historically known to be a rich reservoir of bioactive compounds that are applied in a myriad of fields ranging from crop protection to medicine. The surge of genomic data available shows that fungi remain an excellent source for new pharmaceuticals. However, most of the responsible biosynthetic gene clusters are transcriptionally silent under laboratory growth conditions. Therefore, generic strategies for activation of these clusters are required. Here, we present a genome-editing-free, transcriptional regulation tool for filamentous fungi, based on the CRISPR activation (CRISPRa) methodology. Herein, a nuclease-defective mutant of Cas9 (dCas9) was fused to a highly active tripartite activator VP64-p65-Rta (VPR) to allow for sgRNA directed targeted gene regulation. dCas9-VPR was introduced, together with an easy to use sgRNA “plug-and-play” module, into an AMA1-vector, which is compatible with several filamentous fungal species. To demonstrate its potential, this vector was used to transcriptionally activate a fluorescent reporter gene under the control of thepenDEcore promoter inPenicillium rubens. Subsequently, we activated the transcriptionally silent, nativeP. rubensmacrophorin biosynthetic gene cluster by targeting dCas9-VPR to the promoter region of the transcription factormacR. This resulted in the production of antimicrobial macrophorins. This CRISPRa technology can be used for the rapid and convenient activation of silent fungal biosynthetic gene clusters, and thereby aid in the identification of novel compounds such as antimicrobials.
Integrative Analysis Reveals Histone Demethylase LSD1/KDM1A Associates with RNA Polymerase II Pausing
Authors: Kim Hani Jieun , Kim Taiyun , Oldfield Andrew J. , Yang Pengyi 
Published: October 2020

AbstractRNA polymerase II (RNAPII) pausing at gene promoters is a rate-limiting step in transcription regulation. Previous studies have elucidated the coordinated actions of pausing and releasing factors that collectively modulate RNAPII pausing. In general, the involvement of chromatin remodellers in RNAPII pausing has not been well documented. Whilst LSD1 is well-known for its role in decommissioning enhancers during ESC differentiation, its role at the promoters of genes remains poorly understood despite their widespread presence at these sites. Here, we report that LSD1 is associated with RNAPII pausing at the promoter-proximal region of genes in mouse embryonic stem cells (ESCs). We demonstrate that the knockdown of LSD1 preferentially affects genes with higher RNAPII pausing than those with lower pausing and, importantly, show that the co-localization of LSD1 and MYC, a factor known to regulate pause-release, is associated with the enrichment of other RNAPII pausing factors compared to their independent counterparts. Moreover, we found that genes co-occupied by LSD1 and MYC are significantly enriched for housekeeping genes that are involved in metabolic processes and globally depleted of transcription factors compared to those bound only by LSD1. These findings reveal a pleiotropic role of LSD1 in regulating housekeeping program besides its previously known role in regulating cell identity programs. Our integrative analysis presents evidence for a previously unanticipated role of LSD1 in RNAPII pausing through its association with pause release factors in modulating cell-type specific and cell-type invariant genes.
Mapping the substrate sequence and length of thePlasmodiumM1 and M17 aminopeptidases
Authors: Malcolm Tess R , Swiderska Karolina W. , Hayes Brooke K , Drag Marcin , Drinkwater Nyssa , McGowan Sheena 
Published: October 2020

AbstractDuring malarial infection,Plasmodiumparasites digest human hemoglobin to obtain free amino acids for protein production and maintenance of osmotic pressure. ThePlasmodiumM1 and M17 aminopeptidases are both postulated to have an essential role in the terminal stages of the hemoglobin digestion process and are validated drug targets for the design of new dualtarget anti-malarial compounds. In this study, we profiled the substrate specificity fingerprints and kinetic behaviors of M1 and M17 aminopeptidases fromPlasmodium falciparumandPlasmodium vivax,and the mouse model species,Plasmodium berghei.We found that although thePlasmodiumM1 aminopeptidases share a largely similar, broad specificity at the P1 position, theP. falciparumM1 displays the greatest diversity in specificity andP. bergheiM1 showing a preference for charged P1 residues. In contrast, thePlasmodiumM17 aminopeptidases share a highly conserved preference for hydrophobic residues at the P1 position. The aminopeptidases also demonstrated intra-peptide sequence specificity, particularly the M1 aminopeptidases, which showed a definitive preference for peptides with fewer negatively charged intrapeptide residues. When tested with a panel of peptides of increasing length, each aminopeptidase exhibited unique catalytic behavioral responses to the increase in peptide length, although all six aminopeptidases exhibited an increase in cooperativity as peptide length increased. Overall theP. vivaxandP. bergheienzymes were generally faster than theP. falciparumenzymes, which we postulate is due to subtle differences in structural dynamicity. Together, these results build a kinetic profile that allows us to better understand the catalytic nuances of the M1 and M17 aminopeptidases from differentPlasmodiumspecies.
Cas9-AAV6 Gene Correction of Beta-Globin in Autologous HSCs Improves Sickle Cell Disease Erythropoiesis in Mice
Authors: Wilkinson Adam C. , Dever Daniel P. , Baik Ron , Camarena Joab , Hsu Ian , Charlesworth Carsten T. , Morita Chika , Nakauchi Hiromitsu , Porteus Matthew H. 
Published: October 2020

AbstractCRISPR/Cas9-mediated beta-globin (HBB) gene correction of Sickle Cell Disease (SCD) patient-derived hematopoietic stem cells (HSCs) in combination with autologous transplantation represents a novel paradigm in gene therapy. Although several Cas9-basedHBB-correction approaches have been proposed, functional correction of in vivo erythropoiesis has not been investigated. Here, we used a humanized globin-cluster SCD mouse model to study Cas9-AAV6-mediatedHBB-correction in functional HSCs within the context of autologous transplantation. We discover that long-term multipotent HSCs can be gene corrected ex vivo and stable hemoglobin-A production can be achieved in vivo fromHBB-corrected HSCs following autologous transplantation. We observed a direct correlation between increasedHBB-corrected myeloid chimerism and normalized in vivo RBC features, but even low levels of chimerism resulted in robust hemoglobin-A levels. Moreover, this study offers a platform for gene editing of mouse HSCs for both basic and translational research.
Tropomyosin in mugwort cross-reacts to house dust mite, eliciting non-Th2 response in allergic rhinitis patients sensitized to house dust mite
Authors: Lan Feng , Zhao Limin , Duan Su , Zhang Nan , Zhang Haibo , Zheng Ming , Wang Qiqi , Zhang Xu , Wang Xiangdong , Ying Sun , Bachert Claus , Zhang Luo 
Published: October 2020

ABSTRACTBackgroundMugwort and house dust mite (HDM) are two of the most common inhalant allergens in Asia; however, whether or not mugwort affects polysensitized HDM+allergic rhinitis (AR) patients has not been elucidated.MethodsOverall, 15884 AR outpatients were assessed for clinical status. Amino acid sequences of mugwort were determined by mass spectrometry. Afterward, cross-reactivity between mugwort tropomyosin and Dermatophagoides pteronyssinus 10 (Der p10) was analysed by ELISA inhibition and basophils activation experiments. To compare immunologic responses eliciting by two different tropomyosins, peripheral blood mononuclear cells (PBMCs) of HDM-monosensitized patients were stimulated by mugwort, HDM, Der p10 and synthetic peptides representing mugwort tropomyosin respectively.ResultsPolysensitized HDM+AR patients were mainly sensitized to cat and mugwort, and the positive rate of monosensitized HDM+AR out-clinic patients was increased during the mugwort pollen season. Mugwort tropomyosin protein had similar structural domains to HDM tropomyosin, Der p10. ELISA inhibition experiment showed synthetic mugwort tropomyosin peptide inhibited IgE binding to Der p10; mugwort tropomyosin peptide activated basophils which were primed by HDM-specific IgE. Unlike HDM and Derp 10, mugwort and mugwort tropomyosin mainly induced IFN-γ and IL-17, release in PBMCs of monosensitized HDM+AR patients, but not IL-5.ConclusionsPan-allergen tropomyosin is a major protein accounting for the cross-reactivity between mugwort and HDM, which reminds HDM+patients to reduce mugwort exposure in mugwort pollen season in virtue of the tropomyosin induced mild inflammation.
A Multisite Model of Allosterism for the Adenosine A1 Receptor
Authors: Deganutti Giuseppe , Barkan Kerry , Ladds Graham , Reynolds Christopher A 
Published: October 2020

ABSTRACTDespite being a target for about one-third of approved drugs, G protein-coupled receptors (GPCRs) still represent a tremendous reservoir for therapeutic strategies against countless diseases. For example, several cardiovascular and central nervous systems conditions could benefit from clinical agents that activate the adenosine 1 receptor (A1R), however, the pursuit of A1R agonists for clinical use are usually impeded by both on- and off-target side effects. One of the possible strategies to overcome this issue is the development of positive allosteric modulators (PAMs) capable of selectively enhancing the effect of a specific receptor subtype and triggering functional selectivity (a phenomenon also referred to as bias). Intriguingly, besides enforcing the effect of agonists upon binding to an allosteric site, most of the A1R PAMs display intrinsic partial agonism and orthosteric competition with antagonists. To rationalize this behaviour, we simulated the binding of the prototypical PAMs PD81723 and VCP171, the antagonist 13B, and the bitopic agonist VCP746. We propose that a single PAM can bind several A1R sites rather than a unique allosteric pocket, reconciling the structure-activity relationship and the mutagenesis results.
Neuronal NOX4 knockdown alleviates pathological tau-related alterations in a humanized mouse model of tauopathy
Authors: Luengo Enrique , Trigo-Alonso Paula , Fernández-Mendívil Cristina , Nuñez Ángel , del Campo Marta , Porrero César , García-Magro Nuria , Negredo Pilar , Sánchez-Ramos Cristina , Bernal Juan A. , Rábano Alberto , Hoozemans Jeroen , Casas Ana I , Schmidt Harald H.H.W , Cuervo Ana María , López Manuela G. 
Published: October 2020

AbstractApproximately 44 million people worldwide live with Alzheimer’s disease (AD) or a related form of dementia. Aggregates of the microtubule-associated protein tau are a common marker of these neurodegenerative diseases collectively termed as tauopathies. However, all therapeutic attempts based on tau have failed, suggesting that tau may only indicate a higher-level causal mechanism. For example, increasing levels of reactive oxygen species (ROS) may trigger protein aggregation or modulate protein degradation. Here we show that type 4 NADPH oxidase (NOX), the most abundant isoform of the only dedicated reactive oxygen producing enzyme family, is upregulated in dementia and AD patients and in a humanized mouse model of tauopathy. Both global knockout and neuronal knockdown of theNox4gene in mice, diminished the accumulation of pathological tau and positively modified established tauopathy by a mechanism that implicates modulation of the autophagy-lysosomal pathway (ALP). Moreover, neuronal-targeted NOX4 knockdown was sufficient to reduce neurotoxicity and prevented cognitive decline, suggesting a direct and causal role for neuronal NOX4. Thus, NOX4 is a previously unrecognized causal, mechanism-based target in tauopathies and blood-brain barrier permeable specific NOX4 inhibitors could have therapeutic potential even in established disease.Graphical abstract
In VivoBrain Glutathione is Higher in Older Age and Correlates with Mobility
Authors: Hupfeld K. E. , Hyatt H. W. , Jerez P. Alvarez , Mikkelsen M. , Hass C. J. , Edden R. A. E. , Seidler R. D. , Porges E. C. 
Published: October 2020

AbstractBrain markers of oxidative damage increase with advancing age. In response, brain antioxidant levels may also increase with age, although this has not been well investigated. Here we used edited magnetic resonance spectroscopy to quantify endogenous levels of glutathione (GSH, one of the most abundant brain antioxidants) in 37 young (mean: 21.8 (2.5) years; 19 F) and 23 older adults (mean: 72.8 (8.9) years; 19 F). Accounting for age-related atrophy, we identified higher frontal and sensorimotor GSH levels for the older compared to the younger adults. For the older adults only, higher sensorimotor (but not frontal) GSH was correlated with poorer balance, gait, and manual dexterity. This suggests a regionally-specific relationship between higher brain oxidative stress levels and motor performance declines with age. We suggest these findings reflect a compensatory upregulation of GSH in response to increasing brain oxidative stress with normal aging. Together, these results provide insight into age differences in brain antioxidant levels and implications for motor function.
A transform of univariable time domain polynomial for extraction of temporal arcs
Authors: Thankappan Binesh 
Published: October 2020

Purpose
This paper aims to present a special transformation that is applied to univariable polynomials of an arbitrary order, resulting in the generation of the proposed offset eliminated polynomial. This transform-based approach is used in the analysis and synthesis of temporal arc functions, which are time domain polynomial functions possessing two or more values simultaneously. Using the proposed transform, the submerged values of temporal arcs can also be extracted in measurements.

Design/methodology/approach
The methodology involves a two-step mathematical procedure in which the proposed transform of the weighted modified derivative of the polynomial is generated, followed by multiplication with a linear or ramp function. The transform introduces a stretching in the temporal or spatial domain depending on the type of variable under consideration, resulting in modifications for parameters such as time derivative and relative velocity.

Findings
Detailed analysis of various parameters in this modified time domain is performed and results are presented. Additionally, using the proposed methodology, the submerged value of any temporal arc function can also be extracted in measurements, thereby unraveling the temporal arc.

Practical implications
A typical implementation study with results is also presented for an operational amplifier-based temporal arc-producing square rooting circuit for the extraction of the submerged value of the function.

Originality/value
The proposed transform-based approach has major applications in extracting the values of temporal arc functions that are submerged in conventional experimental measurements, thereby providing a novel method in unraveling that class of special functions.
Distribution of adjacent prime numbers in the Ulam spiral
Authors: Jara-Vera Vicente , Sánchez-Ávila Carmen 
Published: October 2020

Purpose
The distribution of natural numbers in the Ulam spiral manifests a series of unexpected regularities of the elusive prime numbers. Their sequencing remains a topic of research interest, with many ramifications in different branches of Mathematics, especially in number theory and the prime factorisation problem. Accordingly, the focus of the research is on the most known and widespread asymmetric cryptographic system, that is, the RSA encryption.

Design/methodology/approach
This paper presents the presence of one, two, three or four adjacencies for the diverse primes that appear in a spiral, considering the Hardy–Littlewood twin prime conjecture and the constellations of primes.

Findings
Through equations, the calculation formulas of primes inside a spiral that have one to four primes in their adjacent places is offered, with approximate expressions that facilitate the operations, showing that the adjacencies decrease very rapidly as the spiral progresses, although without disappearing.

Originality/value
A generalisation to cases in which the distances to the prime values change in an ascending way in accordance with the step of the Ulam spiral is offered.
Hybrid nanofluid flow through an exponentially stretching/shrinking sheet with mixed convection and Joule heating
Authors: Yashkun Ubaidullah , Zaimi Khairy , Ishak Anuar , Pop Ioan , Sidaoui Rabeb 
Published: October 2020

PurposeThis study aims to investigate the flow and heat transfer of a hybrid nanofluid through an exponentially stretching/shrinking sheet along with mixed convection and Joule heating. The nanoparticles alumina (Al2O3) and copper (Cu) are suspended into a base fluid (water) to form a new kind of hybrid nanofluid (Al2O3-Cu/water). Also, the effects of constant mixed convection parameter and Joule heating are considered.Design/methodology/approachThe governing partial differential equations are transformed into ordinary differential equations (ODEs) using appropriate similarity transformations. The transformed nonlinear ODEs are solves using the bvp4c solver available in MATLAB software. A comparison of the present results shows a good agreement with the published results.FindingsDual solutions for hybrid nanofluid flow obtained for a specific range of the stretching/shrinking parameter values. The values of the skin friction coefficient increases but the local Nusselt number decreases for the first solution with the increasing of the magnetic parameter. Enhancing copper volume fraction and Eckert number reduces the surface temperature, which intimates the decrement of heat transfer rate for the first and second solutions for the stretching/shrinking sheet. In detail, the first solution results show that when the Eckert number increases as 0.1, 0.4 and 0.7 at λ = 1.5, the temperature variations reduced to 10.686840, 10.671419 and 10.655996. While in the second solution, keeping the same parameters temperature variation reduced to 9.750777, 9.557349 and 9.364489, respectively. On the other hand, the results indicate that the skin friction coefficient increases with copper volume fraction. This study shows that the thermal boundary layer thickness rises due to the rise in the solid volume fraction. It is also observed that the magnetic parameter, copper volume fraction and Eckert number widen the range of the stretching/shrinking parameter for which the solution exists.Practical implicationsIn practice, the investigation on the flow and heat transfer of a hybrid nanofluid past an exponentially stretching/shrinking sheet with mixed convection and Joule heating is crucial and useful. The problems related to hybrid nanofluid have numerous real-life and industrial applications, such as microelectronics, manufacturing, naval structures, nuclear system cooling, biomedical and drug reduction.Originality/valueIn specific, this study focuses on increasing thermal conductivity using a hybrid nanofluid mathematical model. The novelty of this study is the use of natural mixed convection and Joule heating in a hybrid nanofluid. This paper can obtain dual solutions. The authors declare that this study is new, and there is no previous published work similar to the present study.