bluuebunny/crossref_metadata_2025 huggingface dataset:
An overlapped natural antisense lncRNA FCER1A-AS controls anaphylactic reaction by promoting FcεRIα expression
Authors: Tang Ruo-yu , Yin Lan , Yao Liang , Chen Xiao-Ping
Published: April 2022

Functioned as α-subunit of the high-affinity immunoglobulin E receptor (Fcε RIα), Fcε RIα plays a central role in the pathogenesis of Ig-E-mediated allergy and other IgE-related disorders. Fcε RIα is normally expressed only in limited spectrum of cells like basophils and mast cells, but the mechanism of controlling Fcε RIα expression in these cells is less well understood. In this study, we found fully overlapped natural antisense transcript (NATs) of Fcε RIα (FCER1A-AS) is co-expressed with cognate sense transcript (FCER1A-S) in IL-3 induced Fcε RIα-expressing cells or in high Fcε RIα-expressing cell line MC/9. When FCER1A-AS is selectively knocked down by CRISPR/RfxCas13d (CasRx) approach in MC/9, expression of mRNA and proteins of FCER1A-S is also markedly decreased. Furthermore, deficiency of FCER1A-AS along with lack of FCER1A-S expression is found in two different lines of gene-targeted mice in which FCER1A locus is disturbed at different sites. More importantly, the FCER1A-AS-deficient homozygous mice display similarly diminished anaphylactic reaction as FCER1A gene knockout mice. Thus, we uncovered in this investigation that the expression of FCER1A-S is positively regulated by co-expressed fully overlapped antisense transcript.
Unexpected contributions of striatal projection neurons coexpressing dopamine D1 and D2 receptors in balancing motor control
Authors: Bonnavion Patricia , Varin Christophe , Fakhfouri Ghazal , Olondo Pilar Martinez , De Groote Aurélie , Cornil Amandine , Lopez Ramiro Lorenzo , Fernandez Elisa Pozuelo , Isingrini Elsa , Rainer Quentin , Xu Kathleen , Tzavara Eleni , Vigneault Erika , Dumas Sylvie , de Kerchove d’Exaerde Alban , Giros Bruno
Published: April 2022

The central function of the striatum and its dopaminergic (DA) afferents in motor control and the integration of cognitive and emotional processes is commonly explained by the two striatal efferent pathways characterized by striatal projection neurons (SPNs) expressing DA D1 receptors and D2 receptors (D1-SPNs and D2-SPNs), without regard to SPNs coexpressing both receptors (D1/D2-SPNs). We developed an approach that enables the targeting of these hybrid SPNs and demonstrated that although these SPNs are less abundant, they play a major role in guiding the motor function of the other two main populations. D1/D2-SPNs project exclusively to the external globus pallidus (GPe) and have specific electrophysiological features with distinctive integration of DA signals. Optogenetic stimulation and loss-of-function experiments indicated that D1/D2-SPNs potentiate the prokinetic and antikinetic functions of D1-SPNs and D2-SPNs, respectively, and restrain the integrated motor response to psychostimulants. Overall, our findings demonstrate the essential role of this third unacknowledged population of D1/D2 coexpressing neurons, which orchestrates the fine-tuning of DA regulation in the thalamo-cortico-striatal loops.

One-Sentence Summary

D1/D2 SPNs modulate the motor function of both D1- and D2-SPNs
Genotypic sex shapes maternal care in the African Pygmy mouse,Mus minutoides
Authors: Heitzmann Louise D. , Challe Marie , Perez Julie , Castell Laia , Galibert Evelyne , Martin Agnes , Valjent Emmanuel , Veyrunes Frederic
Published: April 2022

Abstract

Sexually dimorphic behaviours, such as parental care, have long been thought to be driven mostly, if not exclusively, by gonadal hormones. In the past two decades, a few studies have challenged this view, highlighting the direct influence of the sex chromosome complement (XX vs XY or ZZ vs ZW). The African pygmy mouse,Mus minutoides, is a wild mouse species with naturally occurring XY sex reversal induced by a third, feminizing X* chromosome, leading to three female genotypes: XX, XX* and X*Y. Here, we show that sex reversal in X*Y females shapes a divergent maternal care strategy from both XX and XX* females, rather than altering care quality. In addition, we show that sex reversal may also impact the dopaminergic system in the anteroventral periventricular nucleus of the hypothalamus, consistent with one component of maternal care: pup retrieval. Combining behavioural ecology and neurobiology in a rodent subject to natural selection, we evaluate potential candidates for the neural basis of maternal behaviours and strengthen the underestimated role of the sex chromosomes in shaping sex differences in brain and behaviours. All things considered, we further highlight the emergence of a third sexual phenotype, challenging the binary view of phenotypic sexes.
The RNA content of extracellular vesicles fromPRPF31+/−hiPSC-RPE show potential as biomarkers of retinal degeneration
Authors: Getachew Heran , Mehrotra Sudeep , Kaur Tarandeep , Fernandez-Godino Rosario , Pierce Eric A. , Garita-Hernandez Marcela
Published: April 2022

Retinitis pigmentosa (RP), is the most common inherited retinal degeneration (IRD), leading to vision loss via dysfunction and death of photoreceptor cells and retinal pigment epithelium (RPE). Mutations in the pre-mRNA processing factor 31 (PRPF31) gene are associated with autosomal dominant RP, impairing RPE function. While adeno-associated virus (AAV)-mediated gene therapy shows promise for treating IRDs, the slow progression of these diseases often makes timely measurement of clinical efficacy challenging. Extracellular vesicles (EVs) are lipid enclosed vesicles secreted by cells and their RNA contents are being explored as circulating biomarkers of cancer and other diseases. We hypothesize that EV RNAs could serve as biomarkers of the health status of the neural retina and RPE health. To test this, we usedPRPF31+/+andPRPF31+/−human-induced pluripotent stem cell (hiPSC)-derived RPE (hi-RPE) to investigate the RNAs contained in RPE-derived EVs, and how they change in disease. We also compared the RNA contents of RPE-EVs with the RNAs contained in the hi-RPE cells themselves. We found that EVs from mutantPRPF31+/−hi-RPE cells have distinct RNA profiles compared to those from control cells, suggesting EV RNA contents change during disease and could serve as biomarkers for retinal degeneration.
Niclosamide targets macrophages to rescue the disrupted peritoneal homeostasis in endometriosis
Authors: Zhao Liang , Shi Mingxin , Winuthayanon Sarayut , MacLean James A. , Hayashi Kanako
Published: April 2022

Due to the vital roles of macrophages in the pathogenesis of endometriosis, targeting macrophages could be a new therapeutic direction. Here, we investigated the efficacy of niclosamide for the resolution of perturbed microenvironment caused by dysregulated macrophages in a mouse model of endometriosis. Single-cell transcriptomic analysis revealed the heterogeneity of macrophage subpopulations including three newly identified intermediate subtypes with sharing characteristics of traditional “small” or “large” peritoneal macrophages (SPMs and LPMs) in the peritoneal cavity. Endometriosis-like lesions (ELL) enhanced the differentiation of recruited macrophages, promoted the replenishment of resident LPMs, and increased ablation of embryo-derived LPMs, which were stepwise suppressed by niclosamide. In addition, niclosamide reversed intercellular communications between macrophages and B cells which were disrupted by ELL. Therefore, niclosamide rescued the perturbed microenvironment in endometriosis through its fine regulations on the dynamic progression of macrophages and could be a new promising therapy for endometriosis.

Niclosamide tunes the dynamic progression of peritoneal macrophages and their intercellular communications with B cells to rescue the disrupted microenvironment in the peritoneal cavity in a mouse model of endometriosis.

Graphic Abstract
Delineating antibody escape from Omicron sublineages
Authors: Gruell Henning , Vanshylla Kanika , Korenkov Michael , Tober-Lau Pinkus , Zehner Matthias , Münn Friederike , Janicki Hanna , Augustin Max , Schommers Philipp , Sander Leif Erik , Kurth Florian , Kreer Christoph , Klein Florian
Published: April 2022

SARS-CoV-2 neutralizing antibodies play a critical role in prevention and treatment of COVID-19 but are challenged by viral evolution and antibody evasion, exemplified by the highly resistant Omicron BA.1 sublineage.1–12 Importantly, the recently identified Omicron sublineages BA.2.12.1 and BA.4/5 with differing spike mutations are rapidly emerging in various countries. By determining polyclonal serum activity of 50 convalescent or vaccinated individuals against BA.1, BA.1.1, BA.2, BA.2.12.1, and BA.4/5, we reveal a further reduction of BA.4/5 susceptibility to vaccinee sera. Most notably, delineation of the sensitivity to an extended panel of 163 antibodies demonstrates pronounced antigenic differences of individual sublineages with distinct escape patterns and increased antibody resistance of BA.4/5 compared to the most prevalent BA.2 sublineage. These results suggest that the antigenic distance from BA.1 and the increased resistance compared to BA.2 may favor immune escape-mediated expansion of BA.4/5 after the first Omicron wave. Finally, while most monoclonal antibodies in clinical stages are inactive against all Omicron sublineages, we identify promising novel antibodies with high pan-Omicron neutralizing potency. Our study provides a detailed understanding of the antibody escape from the most recently emerging Omicron sublineages that can inform on effective strategies to prevent and treat COVID-19.
Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase
Authors: Pimenta-Marques Ana , Perestrelo Tania , Rodrigues Patricia , Duarte Paulo , Lince-Faria Mariana , Bettencourt-Dias Mónica
Published: April 2022

Centrioles play critical roles in our cells, being part of centrosomes and cilia, which are important microtubule organising centers (MTOC) with a variety of roles. While centrioles are very stable structures, they disappear in certain cell types upon differentiation, such as in oocytes. Little is known about the regulation of centriole structural integrity. We previously uncovered that the pericentriolar material (PCM), and its recruiter Polo kinase, are required for both the maintenance of centriole structural integrity and centrosome MTOC activity. Using an hypothesis driven RNAi screen, we show that both the cartwheel and the centriole wall play an important role in centrosome integrity. In particular, we uncovered that the centriole wall protein ANA1 is critical for the integrity of both new and mature centrioles, in Drosophila oogenesis as well as in cultured cells. Moreover, our results show that the activity of both Polo and the PCM in centriole integrity depends on ANA1. Our work suggests that the structural integrity of centrioles, once thought to be very stable organelles, depends on the turnover of key components, suggesting new perspectives for understanding the dysfunction of those structures in disease.
A novel Pyk2-derived peptide inhibits invadopodia-mediated breast cancer metastasis
Authors: Twafra Shams , Sokolik Chana G. , Sneh Tal , Srikanth Kolluru D. , Meirson Tomer , Genna Alessandro , Chill Jordan H. , Gil-Henn Hava
Published: April 2022

The non-receptor tyrosine kinase Pyk2 is highly expressed in breast cancer, where it mediates invadopodia formation and function via interaction with the actin-nucleation promoting factor cortactin. Here, we designed a cell-permeable peptide inhibitor that contains the second proline-rich region (PRR2) sequence of Pyk2, which binds to the SH3 domain of cortactin and blocks spontaneous lung metastasis in immune-competent mice by inhibiting invadopodia maturation and function. The native structure of the Pyk2-PRR2:cortactin-SH3 complex was determined using nuclear magnetic resonance (NMR), revealing an extended class II interaction surface spanning the canonical binding groove and a second hydrophobic surface which significantly contributes to ligand affinity. Using structure-guided design, we created a mutant peptide lacking critical residues involved in binding that failed to inhibit invadopodia maturation and function and consequent metastatic dissemination in mice. Our findings shed light on the specific molecular interactions between Pyk2 and cortactin and suggest that their inhibition may be used as a novel strategy for blocking breast cancer metastasis.
CyTOF-Lec: Single-cell Glycomics Analysis Reveals Glycan Features Defining Cells Differentially Susceptible to HIV
Authors: Ma Tongcui , McGregor Matthew , Giron Leila B. , Xie Guorui , George Ashley F. , Abdel-Mohsen Mohamed , Roan Nadia R.
Published: April 2022

High-parameter single-cell phenotyping has enabled in-depth classification and interrogation of immune cells, but to date has not allowed for glycan characterization. Here, we develop CyTOF-Lec as an approach to simultaneously characterize many protein and glycan features of human immune cells at the single-cell level. We implemented CyTOF-Lec to compare glycan features between different immune subsets from blood and multiple tissue compartments, and to characterize HIV-infected cell cultures. Using bioinformatics approaches to distinguish preferential infection of cellular subsets from viral-induced remodeling, we demonstrate that HIV upregulates the levels of cell surface fucose and sialic acid in a cell- intrinsic manner, and that memory CD4+ T cells co-expressing high levels of fucose and sialic acid are highly susceptible to HIV infection. Sialic acid levels were found to distinguish memory CD4+ T cell subsets expressing different amounts of viral entry receptors, pro-survival factors, homing receptors, and activation markers, and to play a direct role in memory CD4+ T cells’ susceptibility to HIV infection. The ability of sialic acid to distinguish memory CD4+ T cells with different susceptibilities to HIV infection was experimentally validated through sorting experiments. Together, these results suggest that HIV remodels not only cellular proteins but also glycans, and that glycan expression can differentiate memory CD4+ T cells with vastly different susceptibility to HIV infection.
Unexpected Complexity of the Ammonia Monooxygenase in Archaea
Authors: Hodgskiss Logan H. , Melcher Michael , Kerou Melina , Chen Weiqiang , Ponce-Toledo Rafael I. , Savvides Savvas N. , Wienkoop Stefanie , Hartl Markus , Schleper Christa
Published: April 2022

Ammonia oxidation as the first step of nitrification constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase is lacking, in particular for the environmentally abundant ammonia oxidizing archaea (AOA). Here, the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Beside the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modelling and in gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase indicating that AmoY and AmoZ serve an important structural and functional role. These data open avenues for further structure-function studies of this ecologically important key nitrification complex.
Listeria monocytogenes Co-opts Caveolin-Mediated E-cadherin Trafficking and Macropinocytosis for Epithelial Cell-to-Cell Spread
Authors: Radhakrishnan Prathima , Sathe Mugdha , Theriot Julie A.
Published: April 2022

Listeria monocytogenes is an intracellular bacterial pathogen that spreads directly between adjacent host cells without exposure to the extracellular space. Recent studies have identified several host cell factors that promote L. monocytogenes cell-to-cell spread in epithelial monolayers, but details of the mechanism remain unclear. We find that the adherens junction protein, E-cadherin, promotes L. monocytogenes cell-to-cell spread at the recipient side of cell contacts. In particular, two point mutations in E-cadherin’s cytoplasmic domain that prevent its ubiquitination hinder bacterial cell-to-cell spread efficiency without reducing the extent of contact between neighboring cells. As ubiquitination induces E-cadherin endocytosis, we hypothesize that E-cadherin promotes protrusion engulfment, where donor cell protrusions containing L. monocytogenes are taken up by the recipient cell concurrently with E-cadherin internalization. In support of this hypothesis, we show that inhibiting caveolin-mediated membrane trafficking reduces L. monocytogenes cell-to-cell spread only under conditions where E-cadherin can be ubiquitinated. Additionally, we demonstrate that macropinocytosis also contributes to dissemination of L. monocytogenes through an epithelial monolayer.
Systems modelling of TGF-β/Hippo signalling crosstalk uncovers molecular switches that coordinate YAP transcriptional complexes (submitted toiScience)
Authors: Ghomlaghi Milad , Theocharous Mandy , Shin Sung-Young , O’ Neill Eric , Nguyen Lan K.
Published: April 2022

The Hippo pathway is an evolutionarily conserved signaling network that integrates diverse cues to regulate cell fate and organ homeostasis. The central downstream pathway protein is the transcriptional co-activator Yes-associated protein (YAP). Although capable of inducing gene transcription, YAP cannot bind DNA directly. Instead, it mediates transcriptional activity through interaction with distinct DNA-binding transcriptional factors (TFs), including TEAD, SMAD, and p73, to form active and functionally opposing transcriptional complexes. Growing evidence in mammals demonstrates that YAP has a dual role and can either promote cell proliferation or apoptosis, which underpin its ability to function as both an oncogene or a tumour suppressor depending on the specific context. However, the mechanisms by which YAP coordinates its distinct transcriptional complexes and mediates context-dependent function remain poorly defined. This is in part due to the lack of systems-level studies that can decrypt the complexities of upstream signalling pathways and their crosstalk, which together dictate the transcriptional regulation at the YAP level. Here, we undertake an integrative systems-based approach combining computational network modelling and experimental studies to interrogate the dynamic formation of and transition between the YAP-SMAD and YAP-p73 transcriptional complexes, which control proliferative and apoptotic gene expression, respectively. We developed a new experimentally-validated mathematical model of the TGF-β/Hippo signalling crosstalk and used this model to elucidate dynamic network behaviour. Our integrative studies uncovered previously unknown molecular switches that control the YAP-SMAD/p73 complexes in an on/off, switch-like manner. RASSF1A and ITCH were identified as major regulators of the switches, whereby a graded increase in ITCH expression can trigger YAP to abruptly switch from binding p73 to SMAD, swiftly promoting proliferative gene expression. Further, adjusting the model to reflect cell type-specific protein expression profiles using both in-house and publicly available experimental data enabled us to study the YAP switches under diverse and varied cellular contexts. Overall, our studies provide a new quantitative and systems-level understanding of the dynamic regulation of functionally opposing YAP transcriptional complexes in mammalian cells.
The phosphatase Bph and peptidyl-prolyl isomerase PrsA are required for gelatinase expression and activity in Enterococcus faecalis
Authors: Willett Julia L. E. , Robertson Ethan B. , Dunny Gary M.
Published: April 2022

Enterococcus faecalis is a common commensal bacterium in the gastrointestinal tract as well as a frequent nosocomial pathogen. The secreted metalloprotease gelatinase (GelE) is an important E. faecalis virulence factor that contributes to numerous cellular activities such as autolysis, biofilm formation, and biofilm-associated antibiotic resistance. Expression of gelE has been extensively studied and is regulated by the Fsr quorum-sensing system. Here, we identify two additional factors regulating gelatinase expression and activity in E. faecalis OG1RF. The Bph phosphatase is required for expression of gelE in an Fsr-dependent manner. Additionally, the membrane-anchored protein foldase PrsA is required for GelE activity, but not fsr or gelE gene expression. Disrupting prsA also leads to increased antibiotic sensitivity in biofilms independent of the loss of GelE activity. Together, our results expand the model for gelatinase production in E. faecalis, which has important implications for fundamental studies of GelE function in Enterococcus and also E. faecalis pathogenesis.

Importance

In Enterococcus faecalis, gelatinase (GelE) is a virulence factor that is also important for biofilm formation and interactions with other microbes as well as the host immune system. The long-standing model for GelE production is that the Fsr quorum sensing system positively regulates expression of gelE. Here, we update that model by identifying two additional factors that contribute to gelatinase production. The biofilm-associated Bph phosphatase regulates the expression of gelE through Fsr, and the peptidyl-prolyl isomerase PrsA is required for production of active GelE through an Fsr-independent mechanism. This provides important insight into how regulatory networks outside of the fsr locus coordinate expression of gelatinase.
Collateral sensitivity as a strategy to suppress resistance emergence: the challenge of diverse evolutionary pathways
Authors: Mandt Rebecca E.K. , Luth Madeline R. , Tye Mark A. , Mazitschek Ralph , Ottilie Sabine , Winzeler Elizabeth A. , Lafuente-Monasterio Maria Jose , Gamo Francisco Javier , Wirth Dyann F. , Lukens Amanda K.
Published: April 2022

Drug resistance remains a major obstacle to malaria control and eradication efforts, necessitating the development of novel therapeutic strategies to treat this disease. Drug combinations based on collateral sensitivity, wherein resistance to one drug causes increased sensitivity to the partner drug, have been proposed as an evolutionary strategy to suppress the emergence of resistance in pathogen populations. In this study, we explore collateral sensitivity between compounds targeting the Plasmodium dihydroorotate dehydrogenase (DHODH). We profiled the cross-resistance and collateral sensitivity phenotypes of several DHODH mutant lines to a diverse panel of DHODH inhibitors. We focus on one compound, TCMDC-125334, which was active against all mutant lines tested, including the DHODH C276Y line, which arose in selections with the clinical candidate DSM265. We found that selection of the DHODH C276Y mutant with TCMDC-125334 yielded additional genetic changes in the dhodh locus. These double mutant parasites exhibited decreased sensitivity to TCMDC-125334 and were highly resistant to DSM265. Finally, we tested whether collateral sensitivity could be exploited to suppress the emergence of resistance in the context of combination treatment by exposing wildtype parasites to both DSM265 and TCMDC-125334 simultaneously. This selected for parasites with a DHODH V532A mutation which were cross-resistant to both compounds and were as fit as the wildtype parent in vitro. The emergence of these cross-resistant, evolutionarily fit parasites highlights the mutational flexibility of the DHODH enzyme.
Dissecting the conformational complexity and flipping mechanism of a prokaryotic heme transporter
Authors: Wu Di , Mehdipour Ahmad R , Finke Franziska , Goojani Hojjat G , Groh Roan R , Grund Tamara N , Reichhart Thomas MB , Zimmermann Rita , Welsch Sonja , Bald Dirk , Shepherd Mark , Hummer Gerhard , Safarian Schara
Published: April 2022

Iron-bound cyclic tetrapyrroles (hemes) are key redox-active cofactors in membrane-integrated oxygen reductases and other bioenergetic enzymes. However, the mechanisms of heme transport and insertion into respiratory chain complexes remain unclear. Here, we used a combination of cellular, biochemical, structural and computational methods to resolve ongoing controversies around the function of the heterodimeric bacterial ABC transporter CydDC. We provide multi-level evidence that CydDC is a heme transporter required for assembly and functional maturation of cytochrome bd, a pharmaceutically relevant drug target. Our systematic single-particle cryo-EM approach combined with atomistic molecular dynamics simulations provides detailed insight into the conformational landscape of CydDC during substrate binding and occlusion. Our simulations reveal that heme binds laterally from the membrane space to the transmembrane region of CydDC, enabled by a highly asymmetrical inward-facing CydDC conformation. During the binding process, heme propionates interact with positively charged residues on the surface and later in the substrate-binding pocket of the transporter, causing the heme orientation to flip 180 degrees. The membrane-accessible heme entry site of CydDC is primarily controlled by the conformational plasticity of CydD transmembrane helix 4, the extended cytoplasmic segment of which also couples heme confinement to a rotational movement of the CydC nucleotide-binding domain. Our cryo-EM data highlight that this signal transduction mechanism is necessary to drive conformational transitions toward occluded and outward-facing states.

One Sentence Summary

The heterodimeric bacterial ABC transporter CydDC is a heme flippase essential for the functional maturation of cytochrome bd.
The structure of the F420-dependent sulfite-detoxifying enzyme from Methanococcales reveals a prototypical sulfite-reductase with assimilatory traits
Authors: Jespersen Marion , Pierik Antonio J. , Wagner Tristan
Published: April 2022

The coenzyme F420-dependent sulfite reductase (Fsr group I) protects hydrogenotrophic methanogens, one of the main contributors in worldwide methane emission, from toxic sulfite. Fsr is a single peptide composed of a F420H2-oxidase and a novel class of sulfite reductase. Both catalytic domains have been proposed to be the ancestors of modern F420-oxido/reductases and dissimilatory/assimilatory sulfite reductases. Here, we describe the X-ray crystal structures of Fsr natively isolated from Methanocaldococcus jannaschii (MjFsr) and Methanothermococcus thermolithotrophicus (MtFsr), respectively refined to 2.30 Å and 1.55 Å resolution. In both organisms, Fsr oligomerizes as a 280-kDa homotetramer, where each siroheme–[4Fe–4S] is catalytically active, in contrast to dissimilatory homologues. The siroheme–[4Fe–4S], embedded in the sulfite reductase domain, is electronically connected to the flavin in the F420H2-oxidase domain by five [4Fe–4S]-clusters. EPR spectroscopy determined the redox potentials of these [4Fe–4S]2+/1+ clusters (−435 to -275 mV), through which electrons flow from FAD to the siroheme–[4Fe–4S]2+/1+ (siroheme, -114 mV; [4Fe–4S] -445 mV). The electron relay is mainly organized by two inserted ferredoxin modules, which stabilize the higher degree of oligomerization. While the F420H2-oxidase part is similar to the β-subunit of F420-reducing hydrogenases, the sulfite reductase domain is structurally analogous to dissimilatory sulfite reductases, whereas its siroheme–[4Fe–4S] cofactor is bound in the same way as in assimilatory ones. Accordingly, the reaction of MtFsr is unidirectional, reducing sulfite or nitrite with F420H2. Our results provide the first structural insights into this unique fusion, a snapshot of a primitive sulfite reductase that turns a poison into an elementary block of Life.
Comprehensive multiomic profiling of somatic mutations in malformations of cortical development
Authors: Chung Changuk , Yang Xiaoxu , Bae Taejeong , Vong Keng Ioi , Mittal Swapnil , Donkels Catharina , Phillips H. Westley , Marsh Ashley P. L. , Breuss Martin W. , Ball Laurel L. , Bernardino Garcia Camila Araújo , George Renee D. , Gu Jing , Xu Mingchu , Barrows Chelsea , James Kiely N. , Stanley Valentina , Nidhiry Anna , Khoury Sami , Howe Gabrielle , Riley Emily , Xu Xin , Copeland Brett , Wang Yifan , Kim Se Hoon , Kang Hoon-Chul , Schulze-Bonhage Andreas , Haas Carola A. , Urbach Horst , Prinz Marco , Gardner Corrine , Gurnett Christina A. , Sattar Shifteh , Nespeca Mark , Gonda David D. , Imai Katsumi , Takahashi Yukitoshi , Chen Robert , Tsai Jin-Wu , Conti Valerio , Guerrini Renzo , Devinsky Orrin , Silva Wilson A. , Machado Helio R. , Mathern Gary W. , Abyzov Alexej , Baldassari Sara , Baulac Stéphanie ,   Focal Cortical Dysplasia Neurogenetics Consortium,   Brain Somatic Mosaicism Network, Gleeson Joseph G.
Published: April 2022

Malformations of cortical development (MCD) are neurological conditions displaying focal disruption of cortical architecture and cellular organization arising during embryogenesis, largely from somatic mosaic mutations. Identifying the genetic causes of MCD has been a challenge, as mutations remain at low allelic fractions in brain tissue resected to treat epilepsy. Here, we report a genetic atlas from 317 brain resections, identifying 69 mutated genes through intensive profiling of somatic mutations, combining whole-exome and targeted-amplicon sequencing with functional validation and single-cell sequencing. Genotype-phenotype correlation analysis elucidated specific MCD gene sets associating distinct pathophysiological and clinical phenotypes. The unique spatiotemporal expression patterns identified by comparing single-nucleus transcriptional sequences of mutated genes in control and patient brains implicate critical roles in excitatory neurogenic pools during brain development, and in promoting neuronal hyperexcitability after birth.
Cancer-associated fibroblast-derived ROR2 induces WNT/PCP activation and polarized migration in receiving gastric cancer cells
Authors: Rogers Sally , Zhang Chengting , Anagnostidis Vasilis , Fishel Melissa , Gielen Fabrice , Scholpp Steffen
Published: April 2022

Bone marrow-derived mesenchymal stem cells and cancer-associated fibroblasts in the tumor-stromal environment have been linked to cancer progression in many studies. These fibroblasts provide signaling factors to the tumor cells that promote proliferation, survival, invasion, and metastasis. One signaling pathway influencing tumor cell behavior is the WNT/Planar Cell Polarity (PCP) signaling in gastric cancer. Here, we show that the gastric tumor cell line, AGS, can respond to the PCP ligand WNT5A, however, express a very low level of the bona-fide WNT/PCP receptor, ROR2. At the same time, we find that CAF display long filopodia and had significantly higher levels of ROR2 than normal gastric fibroblasts. By high-resolution imaging, we observe a direct, cytoneme-mediated transfer of a complex containing ROR2 and WNT5A from CAF to the gastric cancer cells. The amount of ROR2 transferred correlated with JNK signaling in receiving cells, showing a direct requirement for receptor transfer. Co-culture of AGS with CAF expressing a dominant-negative form of ROR2 exhibited reduced actin polarization and migration compared to wild-type CAF. Furthermore, induction of migration via paracrine ROR2 transfer was observed in a zebrafish in vivo model. These unexpected findings demonstrate a fresh role in the direct transfer of a Wnt receptor from a signal-producing cell to a receiving cell and explain the mechanism by which gastric cancer cells expressing low levels of ROR2 can respond to a WNT5A-high tumor microenvironment.
An EcR probe reveals mechanisms of the ecdysone-mediated switch from repression-to-activation on target genes in the larval wing disc
Authors: Wardwell-Ozgo Joanna , Terry Douglas , Schweibenz Colby , Tu Michael , Solimon Ola , Schofeld David , Moberg Kenneth
Published: April 2022

Fluctuating levels of steroid hormones provide both systemic and local cues to synchronize metazoan development and control germline and homeostatic processes. The main steroid hormone in Drosophila is ecdysone (Ec), which upon binding of its active form (20E) converts its receptor, EcR, from a transcriptional repressor to activator. Multiple co-repressors and co-activators are proposed to act with EcR in different tissues to control diverse targets and processes, including apoptosis, cell migration, and proliferation. Despite these diverse roles, relatively little is known regarding how EcR translates Ec temporal gradients into modulation of individual target genes. Here we use an Ec-binding fragment of EcR (EcRLBD) as a ‘sponge’ to sequester coregulators and probe the state of EcR activity as larval wing cells traverse the 3rd instar Ec gradient. This approach reveals a dramatic and rapid shift from EcR mediated repression-to-activation in late L3 cells, and that the extent of repression varies between targets. An Ala483Thr mutation that disrupts binding of the co-repressor Smr compromises the ability of EcRLBD to derepress reporters, but also limits its ability to block activation, suggesting either that a coactivator shares an EcR-interaction interface with Smr or that Smr-repression primes targets for 20E activation. Molecular and genetic data reveal that EcRLBD sequesters 20E, and that EcRLBD phenotypes can be modulated by manipulating intracellular 20E levels with Ec importer (EcI) and Cyp18a1, which inactivates 20E. Finally, we provide evidence that Smr repression of EcR activity varies spatially and by target in the wing disc. In sum these data reveal that relief of EcR-Smr repression is a major contributor to 20E induction of EcR targets in larval wing discs and highlight EcRLBD as an effective probe to define EcR-20E gene regulatory mechanisms in vivo.
Parallel cryo electron tomography on in situ lamellae
Authors: Eisenstein Fabian , Yanagisawa Haruaki , Kashihara Hiroka , Kikkawa Masahide , Tsukita Sachiko , Danev Radostin
Published: April 2022

In situ cryo electron tomography of cryo focused ion beam milled samples emerged in recent years as a powerful technique for structural studies of macromolecular complexes in their native cellular environment. The lamella-shaped samples, however, have a limited area and are created with a necessary pretilt. This severely limits the possibilities for recording tomographic tilt series in a high-throughput manner. Here, we utilise a geometrical sample model and optical image shift to record tens of tilt series in parallel, thereby saving time and gaining sample areas conventionally used for tracking of specimen movement. The parallel cryo electron tomography (PACE-tomo) method achieves a throughput faster than 5 min per tilt series and allows the collection of sample areas that were previously unreachable, thus maximising the amount of data from each lamella. Performance testing with ribosomes in vitro and in situ on state-of-the-art and general-purpose microscopes demonstrated the high-throughput and high-quality of PACE-tomo.
The BAM7 gene in Zea mays encodes a protein with similar structural and catalytic properties to Arabidopsis BAM2
Authors: Ravenburg Claire M. , Riney McKayla B. , Monroe Jonathan D. , Berndsen Christopher E.
Published: April 2022

Starch accumulates in the plastids of green plant tissues during the day to provide carbon for metabolism at night. Starch hydrolysis is catalyzed by members of the β-amylase (BAM) family, which in Arabidopsis thaliana (At) includes nine structurally and functionally diverse members. One of these enzymes, AtBAM2, is a plastid-localized enzyme that is unique among characterized β-amylases since it is tetrameric and exhibits sigmoidal kinetics. Sequence alignments show that the BAM domains of AtBAM7, a catalytically inactive, nuclear-localized transcription factor with an N-terminal DNA-binding domain, and AtBAM2 are more closely related to each other than they are to any other AtBAM. Since the BAM2 gene is found in more ancient lineages, it was hypothesized that the BAM7 gene evolved from BAM2. However, analysis of the genomes of 48 flowering plants revealed 12 species that appear to possess a BAM7 gene but lack a BAM2 gene. Upon closer inspection, these BAM7 proteins have a greater percent identity to AtBAM2 than to AtBAM7, and they share all of the AtBAM2 functional residues that BAM7 proteins normally lack. It is hypothesized that these genes may encode BAM2-like proteins although they are currently annotated as BAM7-like genes. To test this hypothesis, a cDNA for the short form of corn BAM7 (ZmBAM7-S) was designed for expression in Escherichia coli. Small-angle X-ray scattering data indicate that ZmBAM7-S has a tetrameric solution structure that is more similar to that of AtBAM2 than to that of AtBAM1. In addition, partially purified ZmBAM7-S is catalytically active and exhibits sigmoidal kinetics. Together, these data suggest that some BAM7 genes may encode a functional BAM2. Exploring and understanding the β-amylase gene structure could have an impact on the current annotation of genes.
The impact of COVID-19 on the grocery retail industry: innovative approaches for contactless store concepts in Germany
Authors: Heins Caroline
Published: April 2022

Purpose

Contactless shopping concepts meet the needs of those consumers who want to minimise social interactions, especially due to COVID-19; they also offer added value by combining the advantages of traditional shopping with digital features that stem from online shopping. The development of digitalised retail concepts has been made possible through digitisation and the use of new technologies. To date, the concepts have been created with various formats through the application of the most advanced Industry 4.0 technologies. This paper aims to provide a deepened understanding of the latest trends and draws attention to the various classes, including shopping functionalities and features.

Design/methodology/approach

This paper performs a review of current disruptive and new business retail concepts within the grocery retail industry in Germany. Therefore, a secondary research methodology and observations were performed to create an overview and a categorization. This categorization has been used to identify the related cases.

Findings

The results add to the literature as follows. First, a matching of contactless shopping to innovative business models is made. Second, a status-quo analysis of contactless shopping solutions in Germany is carried out with defined set of criteria. This study created a list of all major available contactless shopping solutions. Third, this study examines two new business models, namely, automated vending machines and walk-in stores, which meet the changes in consumer behaviour and needs in times of the COVID-19 pandemic.

Originality/value

This paper provides a deeper understanding of the latest trends within the retail industry and draws attention to disruptive business models as well as the functionalities and features of shopping solutions. New store concepts launched during the COVID-19 pandemic have resulted in unique selling propositions of 24-h everyday shopping and contactless shopping.
Digital identities of female founders and crowdfunding performance: an exploration based on the LDA topic model
Authors: Wang Yalin , Li Yaokuang , Wu Juan
Published: April 2022

Purpose

This paper aims to investigate female founders’ digital identities (i.e. the founder’s online self-representation) and explore how female founders’ digital identities affect crowdfunding performance.

Design/methodology/approach

Leveraging a data set of 3,125 Kickstarter crowdfunding campaigns launched by women between 2014 and 2019, this study uses the latent Dirichlet allocation (LDA) topic model to investigate female founders’ digital identities and explore their impacts on crowdfunding performance via logistic and Tobit regression analyses.

Findings

This study finds that on crowdfunding platforms, female founders display four main types of digital identities: educational practitioner, experienced entrepreneur, creative innovator and life dreamer. Moreover, our results reveal the differential influences of these identities on crowdfunding performance. Specifically, the experienced entrepreneur or educational practitioner portrayal may benefit fundraising; the life dreamer portrayal may hinder it; and the creative innovator portrayal may have no significant effect.

Practical implications

This study suggests how women can use their digital identities to improve their crowdfunding performance, indicating a fruitful way to overcome female entrepreneurial financing hurdles in the digital age.

Originality/value

This study highlights the digital identities of female founders engaged in crowdfunding, enriching the emerging research on digital identity in entrepreneurship and crowdfunding. Furthermore, the application of the LDA topic model in the study enlightens future research on leveraging big data analytic methods to examine female entrepreneurship in the digital economy context.
Wave propagation at the welded interface of an elastic solid and unsaturated poro-thermoelastic solid
Authors: Kumar Manjeet , Liu Xu , Kumari Manjeet , Yadav Poonam
Published: April 2022

Purpose

The purpose of this paper is to investigate propagation characteristics of seismic waves at the welded interface of an elastic solid and unsaturated poro-thermoelastic solid.

Design/methodology/approach

A theoretical formulation of partially saturated poro-thermoelastic solid is used in this study established by Zhou et al. (2019). The incidence of two primary waves (P and SV) is taken. The incident wave from the elastic solid induces two reflected waves and five refracted waves. Due to viscous pore fluids, partially saturated poro-thermoelastic solid behave dissipative, whereas elastic solid behaves non-dissipative. As a result, both reflected and incident waves are homogeneous. However, all the refracted waves are inhomogeneous. A non-singular system of linear equations is formed by the coefficients of reflection and refraction for a specified incident wave. The energy shares of various reflected and refracted waves are determined by using these reflection and refraction factors. Finally, a sensitivity analysis is performed, and the effect of critical variables on energy partitioning at the interface is observed. The numerical example shows that throughout the process of reflection/refraction, the energy of incidence is conserved at all angles of incidences.

Findings

This study demonstrated two refracted (homogeneous) and five refracted (inhomogeneous) waves due to the incident wave from elastic solid. The reflection and refraction coefficients and partitioning of incident energy are acquired as a part of diverse physical parameters of the partially saturated poro-thermoelastic media. The interference energies between unlike pairs of refracted waves have been discovered due to the dissipative behavior of unsaturated poro-thermoelastic solid.

Originality/value

The sensitivity of different energy shares to various aspects of the considered model is graphically analyzed for a specific numerical model. The energy balance is maintained by combining interaction energy and bulk wave energy shares.
Solution of a nonlinear fractional COVID-19 model
Authors: Abukhaled Marwan , Khuri Suheil , Rabah Fatima
Published: April 2022

Purpose

The purpose of this study is to obtain an analytical solution for a nonlinear system of the COVID-19 model for susceptible, exposed, infected, isolated and recovered.

Design/methodology/approach

The Laplace decomposition method and the differential transformation method are used.

Findings

The obtained analytical results are useful on two fronts: first, they would contribute to a better understanding of the dynamic spread of the COVID-19 disease and help prepare effective measures for prevention and control. Second, researchers would benefit from these results in modifying the model to study the effect of other parameters such as partial closure, awareness and vaccination of isolated groups on controlling the pandemic.

Originality/value

The approach presented is novel in its implementation of the nonlinear system of the COVID-19 model
The impact of audit characteristics, audit fees on classification shifting: evidence from Germany
Authors: Usman Muhammad , Ezeani Ernest , Salem Rami Ibrahim A. , Song Xi
Published: April 2022

Purpose

This paper aims to examine the relationship between audit characteristics (ACs) and audit fees on classification shifting (CS) among German-listed non-financial firms.

Design/methodology/approach

Using a sample of 130 German-listed (Deutscher Aktienindex, Mid Cap dax and Small caps Index) firms from 2010 until 2019, this study investigated the impact of audit committee size, audit committee meetings, audit committee financial expertise and audit fees on CS.

Findings

This study found the evidence of CS, meaning that managers misclassify recurring expenses in the income statement into non-recurring expenses to inflate core earnings. This study also found that the audit fee ratio, audit committee financial expertise and frequency of audit meetings are negatively associated with CS among German-listed firms. However, the audit committee size does not influence CS.

Research limitations/implications

This study will help the board improve its internal auditing practices and provide essential information to investors to assess how ACs affect the quality of financial reporting.

Originality/value

This study focused on a bank-oriented economy, i.e. Germany, with lower investor protection and low transparency. This paper documents new evidence on how ACs and audit fees impact CS among German firms, as most of the previous studies on CS mainly focused on market-oriented economies such as the UK and the USA.
Paragliding festival: understanding stakeholder perception of environmental attitudes and tourism performance
Authors: Gyepi-Garbrah Theophilus Francis , Preko Alexander
Published: April 2022

Purpose

Paragliding festivals have become significant events in the global tourism space, attracting tourists to local and international destinations. The purpose of this study was to assess environmental attitudes and rate the performance of the paragliding festival of the Kwahu traditional area in Ghana, from the perspectives of four stakeholder groups.

Design/methodology/approach

This study was grounded on the salient stakeholder theory. A quantitative cross-sectional study, with a convenience sampling approach, collected 372 useable questionnaires from four major stakeholders/participants (i.e. Kwahu residents, Kwahu returnees, non-Kwahu Ghanaian tourists and foreigners). Analysis of variance (ANOVA) was used to analyse the data.

Findings

The findings of the Games-Howell post-hoc test show no significant differences among the four stakeholder groups in the festival performance assessment. However, there is a significant statistical difference between the Kwahu residents and foreign tourists regarding environmental attitudes towards the paragliding festival.

Practical implications

Visitors' perceptions and experiences of the environmental performance could inform the planning and execution of festive events that have a direct impact on the natural environment. Policymakers at the community levels must enact environmental protocols that uphold the value propositions of the stakeholders and that of the community at large.

Originality/value

The study expands the application of the salience stakeholder model within festival tourism by highlighting under-represented stakeholder voices in a single study on paragliding festivals in a developing country context.