bluuebunny/crossref_metadata_2025_split huggingface dataset:
Peptide:MHC dependent activation of natural killer cells through KIR2DS2 generates anti-tumor responses
Authors: Rettman Pauline , Blunt Matthew D. , Mbiribindi Berenice , Fulton Rebecca , Schittenhelm Ralf B. , Pulido Andres Vallejo , Bastidas-Legarda Leidy , Polak Marta E. , Ayala Rochelle , Purcell Anthony W. , Al-Shamkhani Aymen , Retiere Christelle , Khakoo Salim I. 
Published: April 2020

AbstractNatural killer (NK) cells are key components of the immune response to viral infections and cancer. Their functions are controlled by activating and inhibitory killer-cell immunoglobulin-like receptors (KIR) which have MHC class I ligands. KIR2DS2 is an activating KIR, that binds conserved viral peptides in the context of HLA-C and has been associated with protective responses to both cancer and viral infections. We sought to investigate whether NK cells can be specifically activated in a peptide:MHC dependent manner to generate functional immune responses as a potential immunotherapeutic strategy.We developed a peptide-based KIR targeting DNA vaccine. Immunizing KIR-Tg mice with the vaccine construct generatedin vivopeptide-specific activation of KIR2DS2-positive NK cells leading to canonical and cross-reactive peptide specific immune responsesin vitro, and alsoin vivoinhibition of tumor growth. Using immunopeptidomics we identified that the nuclear export protein XPO1, which has been associated with a poor prognosis in many different human cancers, furnishes an HLA-C restricted cancer-associated peptide ligand for KIR2DS2-positive NK cells. We thus define a novel strategy to activate KIR in a peptide-specific manner and identify a rationale for its use in cancer immunotherapy.Significance statementNatural killer (NK) cells are known to have important roles in determining the outcomes of viral infections and cancer. The killer cell immunoglobulin-like receptors (KIR), and in particular the activating receptor KIR2DS2, have been associated with the outcome of a number of different human cancers. Specific activation of NK cells through KIR2DS2 is challenging because it shares high (>98%) sequence homology with related inhibitory KIR. We have used a peptide:MHC targeting strategy to activate NK cells through KIR2DS2 and identified a novel cancer-associated ligand for this receptor. The work provides a proof-of-concept for targeting NK cells through activating KIR as a cancer immunotherapy strategy.
Autotransporters drive biofilm formation and auto-aggregation in the diderm FirmicuteVeillonella parvula
Authors: Béchon Nathalie , Jiménez-Fernández Alicia , Witwinowski Jerzy , Bierque Emilie , Taib Najwa , Cokelaer Thomas , Ma Laurence , Ghigo Jean-Marc , Gribaldo Simonetta , Beloin Christophe 
Published: April 2020

ABSTRACTThe Negativicutes are a clade of Firmicutes that have retained the ancestral diderm character and possess an outer membrane. One of the best studied Negativicute,Veillonella parvula, is an anaerobic commensal and opportunistic pathogen inhabiting complex human microbial communities, including the gut and the dental plaque microbiota. Whereas adhesion and biofilm capacity ofV. parvulais expected to be crucial for its maintenance and development in these environments, studies ofV. parvulaadhesion have been hindered by the lack of efficient genetic tools to perform functional analyses in this bacterium. Here, we took advantage of a recently described naturally transformableV. parvulaisolate, SKV38, and adapted tools developed for the closely relatedClostridia spp. to perform random transposon and targeted mutagenesis to identifyV. parvulagenes involved in biofilm formation. We show that type V secreted autotransporters -typically found in diderm bacteria-are the main determinants ofV. parvulaauto-aggregation and biofilm formation, which compete with each other for binding either to cells or to surfaces, with strong consequences onV. parvulabiofilm formation capacity. We also show that inactivation of the gene coding for a poorly characterized metal-dependent phosphohydrolase HD domain protein conserved in the Firmicutes and their closely related diderm phyla inhibits autotransporter-mediated biofilm formation. This study paves the way for further molecular characterization ofV. parvulainteractions with other bacteria and the host within complex microbiota environments.
Immunity-and-Matrix-Regulatory Cells Derived from Human Embryonic Stem Cells Safely and Effectively Treat Mouse Lung Injury and Fibrosis
Authors: Wu Jun , Song Dingyun , Li Zhongwen , Guo Baojie , Xiao Yani , Liu Wenjing , Liang Lingmin , Feng Chunjing , Gao Tingting , Chen Yanxia , Li Ying , Wang Zai , Wen Jianyan , Yang Shengnan , Liu Peipei , Wang Lei , Wang Yukai , Peng Liang , Stacey Glyn Nigel , Hu Zheng , Feng Guihai , Li Wei , Huo Yan , Jin Ronghua , Shyh-Chang Ng , Zhou Qi , Wang Liu , Hu Baoyang , Dai Huaping , Hao Jie 
Published: April 2020

AbstractLung injury and fibrosis represent the most significant outcomes of severe and acute lung disorders, including COVID-19. However, there are still no effective drugs to treat lung injury and fibrosis. In this study, we report the generation of clinical-grade human embryonic stem cells (hESCs)-derived immunity- and matrix-regulatory cells (IMRCs) produced under good manufacturing practice (GMP) requirements, that can treat lung injury and fibrosis in vivo. We generate IMRCs by sequentially differentiating hESCs with serum-free reagents. IMRCs possess a unique gene expression profile distinct from umbilical cord mesenchymal stem cells (UCMSCs), such as higher levels of proliferative, immunomodulatory and anti-fibrotic genes. Moreover, intravenous delivery of IMRCs inhibits both pulmonary inflammation and fibrosis in mouse models of lung injury, and significantly improves the survival rate of the recipient mice in a dose-dependent manner, likely through paracrine regulatory mechanisms. IMRCs are superior to both primary UCMSCs and FDA-approved pirfenidone, with an excellent efficacy and safety profile in mice and monkeys. In light of public health crises involving pneumonia, acute lung injury (ALI) and acute respiratory distress syndrome (ARDS), our findings suggest that IMRCs are ready for clinical trials on lung disorders.
Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses
Authors: Rozenberg Andrey , Oppermann Johannes , Wietek Jonas , Fernandez Lahore Rodrigo Gaston , Sandaa Ruth-Anne , Bratbak Gunnar , Hegemann Peter , Béjà Oded 
Published: April 2020

ABSTRACTChannelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity1,2. Four ChR families are currently known. Green algal3–5and cryptophyte6cation-conducting ChRs (CCRs), cryptophyte anion-conducting ChRs (ACRs)7, and the MerMAID ChRs8. Here we report the discovery of a new family of phylogenetically distinct ChRs encoded by marine giant viruses and acquired from their unicellular green algal prasinophyte hosts. These previously unknown viral and green algal ChRs act as ACRs when expressed in cultured neuroblastoma-derived cells and are likely involved in behavioral responses to light.
The deubiquitylase USP9X controls ribosomal stalling
Authors: Clancy Anne , Heride Claire , Pinto-Fernández Adán , Kallinos Andreas , Kayser-Bricker Katherine J. , Wang Weiping , Smith Victoria , Elcocks Hannah , Davis Simon , Fessler Shawn , McKinnon Crystal , Katz Marie , Hammonds Tim , Jones Neil P. , O’Connell Jonathan , Follows Bruce , Mischke Steven , Caravella Justin A. , Ioannidis Stephanos , Dinsmore Christopher , Kim Sunkyu , Behrens Axel , Komander David , Kessler Benedikt M. , Urbé Sylvie , Clague Michael J. 
Published: April 2020

AbstractWhen a ribosome stalls during translation, it runs the risk of collision with a trailing ribosome. Such an encounter leads to the formation of a stable di-ribosome complex, which needs to be resolved by a dedicated machinery. The initial stalling and the subsequent resolution of di-ribosomal complexes requires activity of Makorin and ZNF598 ubiquitin E3 ligases respectively, through ubiquitylation of the eS10 and uS10 sub-units of the ribosome. It is common for the stability of RING E3 ligases to be regulated by an interacting deubiquitylase (DUB), which often opposes auto-ubiquitylation of the E3. Here, we show that the DUB USP9X directly interacts with ZNF598 and regulates its abundance through the control of protein stability in human cells. We have developed a highly specific small molecule inhibitor of USP9X. Proteomics analysis, following inhibitor treatment of HCT116 cells, confirms previous reports linking USP9X with centrosome associated protein stability and reveals loss of ZNF598 and Makorin 2. In the absence of USP9X or following chemical inhibition of its catalytic activity, steady state levels of Makorins and ZNF598 are diminished and the ribosomal quality control pathway is impaired.
Structure of the lysosomal SCARF (L-SCARF) complex, an Arf GAP haploinsufficient in ALS and FTD
Authors: Su Ming-Yuan , Zoncu Roberto , Hurley James H. 
Published: April 2020

AbstractMutation ofC9ORF72is the most prevalent defect in amyotrophic lateral sclerosis (ALS) and frontal temporal degeneration (FTD). Together with hexanucleotide repeat expansion, haploinsufficiency ofC9ORF72contributes to neuronal dysfunction. We determined the structure of the SMCR8-C9orf72-WDR41 complex by cryo-EM. C9orf72 and SMCR8 are both longin-DENN domain proteins, while WDR41 is a beta-propeller protein that binds to SMCR8 such that the whole structure resembles an eye slip hook. Contacts between WDR41 and SMCR8DENNdrive lysosomal localization in amino acid starvation. The structure suggested that SMCR8-C9orf72 was a small GTPase activating protein (GAP). We found that SMCR8-C9orf72-WDR41 is a GAP for Arf family small GTPases, and refer to it as the Lysosomal SMCR8-C9orf72 Arf GAP (“L-SCARF”) complex. These data rationalize the function of C9orf72 both in normal physiology and in ALS/FTD.
Full three-dimensional imaging deep through multicellular thick samples with subcellular resolution by structured illumination microscopy and adaptive optics
Authors: Lin Ruizhe , Kipreos Edward T. , Zhu Jie , Khang Chang Hyun , Kner Peter 
Published: April 2020

AbstractStructured Illumination Microscopy enables live imaging with resolutions of ~120 nm. Unfortunately, optical aberrations can lead to loss of resolution and artifacts in Structured Illumination Microscopy rendering the technique unusable in samples thicker than a single cell. Here we report on the combination of Adaptive Optics and Structured Illumination Microscopy enabling imaging with 140 nm lateral and 585 nm axial resolution in tissue culture cells, C. elegans, and rice blast fungus. We demonstrate that AO improves resolution and reduces artifacts, making full 3D SIM possible in thicker samples.
RubyACRs, non-algal anion channelrhodopsins with highly red-shifted absorption
Authors: Govorunova Elena G. , Sineshchekov Oleg A. , Li Hai , Wang Yumei , Brown Leonid S. , Spudich John L. 
Published: April 2020

AbstractChannelrhodopsins are light-gated ion channels widely used to control neuronal firing with light (optogenetics). We report two previously unknown families of anion channelrhodopsins (ACRs), one from the heterotrophic protists labyrinthulomycetes and the other from haptophyte algae. Four closely related labyrinthulomycete ACRs, named RubyACRs here, exhibit a unique retinal binding pocket that creates spectral sensitivities with maxima at 590-610 nm, the most red-shifted channelrhodopsins known, long-sought for optogenetics, and more broadly the most red-shifted microbial rhodopsins so far reported. We identified three spectral tuning residues critical for the red-shifted absorption. Photocurrents recorded from the RubyACR fromAurantiochytrium limacinum(designatedAlACR1) under single-turnover excitation exhibited biphasic decay, the rate of which was only weakly voltage-dependent, in contrast to that in previously characterized cryptophyte ACRs, indicating differences in channel gating mechanisms between the two ACR families. Moreover, inA. limacinumwe identified three ACRs with absorption maxima at 485, 545, and 590 nm, indicating color-sensitive photosensing with blue, green and red spectral variation of ACRs within individual species of the labyrinthulomycete family. We also report energy transfer from a cytoplasmic fluorescent protein domain to the retinal chromophore bound within RubyACRs, not seen in similar constructs in other channelrhodopsins.Significance StatementOur identification and characterization of two ACR families, one from non-photosynthetic microorganisms, shows that light-gated anion conductance is more widely spread among eukaryotic lineages than previously thought. The uniquely far red-shifted absorption spectra of the subset we designate RubyACRs provide the long-sought inhibitory optogenetic tools producing large passive currents activated by long-wavelength light, enabling deep tissue penetration. Previously only low-efficiency ion-pumping rhodopsins were available for neural inhibition by the orange-red region of the spectrum. The unusual amino acid composition of the retinal-binding pocket in RubyACRs expands our understanding of color tuning in retinylidene proteins. Finally, energy transfer from the fluorescent protein used as a tag on RubyACRs opens a potential new dimension in molecular engineering of optogenetic tools.
Endothelial basement membrane laminins as an environmental cue in monocyte differentiation to macrophages
Authors: Li Lixia , Song Jian , Chuquisana Omar , Hannocks Melanie-Jane , Loismann Sophie , Vogl Thomas , Roth Johannes , Hallmann Rupert , Sorokin Lydia 
Published: April 2020

AbstractMonocyte differentiation to macrophages is triggered by migration across the endothelial barrier, which is constituted by both endothelial cells and their underlying basement membrane. We address here the role of the endothelial basement membrane laminins (laminins 411 and 511) in this monocyte to macrophage switch. Chimeric mice carrying CX3CR1-GFP bone marrow were employed to track CCL2-induced monocyte extravasation in a cremaster muscle model using intravital microscopy, revealing faster extravasation in mice lacking endothelial laminin 511 (Tek-cre::Lama5-/-) and slower extravasation in mice lacking laminin 411 (Lama4-/-). CX3CR1-GFPlowextravasating monocytes were found to have a higher motility at laminin 511 low sites and to preferentially exist vessels at these sites. However,in vitroexperiments reveal that this is not due to effects of laminin 511 on monocyte migration mode nor on the tightness of the endothelial barrier. Rather, using an intestinal macrophage replenishment model andin vitrodifferentiation studies we demonstrate that laminin 511 together with the attached endothelium collectively promote monocyte differentiation to macrophages. Macrophage differentiation is associated with a change in integrin profile, permitting differentiating macrophages to distinguish between laminin 511 high and low areas and to migrate preferentially across laminin 511 low sites. These studies highlight the endothelial basement membrane as a critical site for monocyte differentiation to macrophages, which may be relevant to the differentiation of other cells at vascular niches.
Inducible Depletion of Calpain-2 Mitigates Abdominal Aortic Aneurysm in Mice
Authors: Muniappan Latha , Okuyama Michihiro , Javidan Aida , Thiagarajan Devi , Jiang Weihua , Moorleghen Jessica J. , Yang Lihua , Balakrishnan Anju , Howatt Deborah A. , Uchida Haruhito A. , Saido Takaomi C. , Subramanian Venkateswaran 
Published: April 2020

ABSTRACTBACKGROUNDCytoskeletal structural proteins maintain cell structural integrity by bridging extracellular matrix (ECM) with contractile filaments. During AAA development, (i) aortic medial degeneration is associated with loss of smooth muscle cell (SMC) integrity, and (ii) fibrogenic mesenchymal cells (FMSCs) mediates ECM remodeling. Calpains cleave cytoskeletal proteins that maintain cell structural integrity. Pharmacological inhibition of calpains exert beneficial effects on Angiotensin II (AngII)-induced AAAs in low density receptor deficient (LDLR-/-) mice.OBJECTIVESTo evaluate the functional contribution of FMSCs-derived calpain-2 on (i) cytoskeletal structural protein and ECM alterations, and (ii) AAA progression.METHODSCalpain-2 protein, and cytoskeletal protein (e.g. filamin or talin) fragmentation in human and mice AAA tissues were assessed by immunohistochemical and western blot analyses. LDLR-/- mice that were either inducible-whole body or FMSC-specific calpain-2 deficient were fed a fat-enriched diet and infused with AngII for 4 weeks. The association of cytoskeletal protein to ECM was evaluated using aortic SMCs, in vitro. In addition, the effect of calpain-2 deficiency on the stability of established AAA was examined.RESULTSCalpain-2 protein, and filamin/talin fragmentation are significantly elevated in AAAs. Ubiquitous or FMSC-specific depletion of calpain-2 suppressed AngII-induced AAAs, filamin/talin fragmentation and promoted ECM protein, collagen. Calpain-2 silencing in SMCs reduced AngII-induced filamin/talin fragmentation. In addition, silencing of filamin or talin in SMCs significantly reduced collagen protein. Furthermore, calpain-2 deficiency suppressed established AAA rupture.CONCLUSIONCalpain-2 activation promotes cytoskeletal structural protein fragmentation and ECM degradation of experimental AAA aortas. Treatment with calpain-2 specific inhibitor may facilitate the clinical management of AAA.
Gap Junctions Amplify Spatial Variations in Cell Volume in Proliferating Solid Tumors
Authors: McEvoy Eoin , Han Yulong , Guo Ming , Shenoy Vivek B. 
Published: April 2020

AbstractCancer progression is driven by cell proliferation, apoptosis, and matrix invasion, which in turn depend on a myriad of factors including microenvironment stiffness, nutrient supply, and intercellular communication. Cell proliferation is regulated by volume, but in 3D clusters it remains unclear how multiple cells interact to control their size. In this study, we propose a mechano-osmotic model to investigate the evolution of volume dynamics within multicellular systems. Volume control depends on an interplay between multiple cellular constituents, including gap junctions, mechanosensitive ion channels, energy consuming ion transporters, and the actomyosin cortex, that coordinate to manipulate cellular osmolarity. In connected cells, mechanical loading is shown to significantly affect how these components cooperate to transport ions, and precise volume control is impacted by the emergence of osmotic pressure gradients between cells. Consequent increases in cellular ion concentrations drive swelling, while a loss of ions impedes the compression resistance of cells. Combining the modeling framework with novel experiments, we identify how gap junctions can amplify spatial variations in cell volume within multicellular spheroids and, further, describe how the process depends on proliferation-induced solid stress. Our model provides new insight into the role of gap junctions in cancer progression and can help guide the development of therapeutics that target inter- and extra-cellular ion transport.
Combinatorial patterns of graded RhoA activation and uniform F-actin depletion promote tissue curvature
Authors: Denk-Lobnig Marlis , Heer Natalie C , Martin Adam C 
Published: April 2020

AbstractDuring development, gene expression regulates cell mechanics and shape to sculpt tissues. Epithelial folding proceeds through distinct cell shape changes that occur in different regions of a tissue. Here, using quantitative imaging inDrosophila melanogaster, we investigate how patterned cell shape changes promote tissue bending during early embryogenesis. We find that the transcription factors Twist and Snail combinatorially regulate a unique multicellular pattern of junctional F-actin density, which corresponds to whether cells apically constrict, stretch, or maintain their shape. Part of this pattern is a gradient in junctional F-actin and apical myosin-2, and the width of this gradient regulates tissue curvature. The actomyosin gradient results from a gradient in RhoA activation that is refined by a balance between RhoGEF2 and the RhoGAP C-GAP. Thus, cell behavior in the ventral furrow is choreographed by the interplay of distinct gene expression patterns and this coordination regulates tissue shape.
Modeling of high-side active clamp forward converter with resistive parasitics
Authors: Maturi Krishnaja , Samanta Susovon 
Published: April 2020

Purpose
The purpose of this paper is to derive the small-signal/canonical model derivation of the high-side active clamp forward converter (ACFC) with diode rectification for ideal and with resistive parasitics. It also covers the analysis of ACFC small-signal model with resistive parasitics using computer-aided modeling software Personal Computer Simulation Program with Integrated Circuit Emphasis (PSPICE) 16.6. The effects of variation of system parameters on the ACFC’s state transfer functions and operations have been highlighted in this paper.

Design/methodology/approach
The large-signal model and small-signal model of the ACFC with diode rectification has been derived using AC small-signal modeling approach.

Findings
The operating point of the converter changes with the consideration of resistive parasitics compared with the ideal case. The response obtained from the hardware matches with the time domain response of the averaged model and switch model developed in PSPICE.

Research limitations/implications
This paper limits the study of ACFC small-signal behavior by using computer-aided design software PSPICE. The dead time of the converter is not considered because it is negligible when compared with the on and off time. The leakage inductance which plays a role in zero voltage switching of the ACFC switches is neglected in the analysis as it is very small compared to the magnetizing inductance. The switching losses are not considered in the modeling.

Practical implications
The mathematical computation of deriving the system transfer functions from canonical model is complex and time consuming.

Originality/value
The modeling with resistive parasitics improves the effectiveness of the equivalent model. Also, the analysis with computer-aided modeling software PSPICE gives reliable results in less time.