bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental evaluation of environmental DNA detection of a rare fish in turbid water
Authors: Holmes Ann E. , Baerwald Melinda R. , Rodzen Jeff , Schreier Brian M. , Mahardja Brian , Finger Amanda J.
Published: August 2022

Environmental DNA (eDNA) approaches enable sensitive detection of rare aquatic species. However, water conditions like turbidity can limit sensitivity, resulting in false negative detections. The dynamics of eDNA detection in turbid conditions are poorly understood, but can be better characterized through experimental work. In this study, 1-L field-collected water samples were spiked with tank-sourced eDNA from a rare, endangered estuarine fish at concentrations similar to eDNA samples collected from the natural environment. Samples using non-turbid water (5 NTU), turbid water (50 NTU), and prefiltered turbid water were filtered using four filter types (pore size range 0.45 μm-10 μm). Detection success using a species-specific Taqman qPCR assay was assessed as both eDNA copy number and detection/non-detection. Glass fiber filters (nominal pore size 1.6 μm) yielded the highest number of eDNA copies and detections in non-turbid water and the highest detection rate in turbid water when used without a prefilter. Detection was a more robust metric for evaluating species presence across turbidity conditions compared with eDNA copy number. Prefiltration improved detection rates for the other filters tested (polycarbonate and cartridge filters). Filter material and design appear to interact differently with the prefiltration step, and may be more important considerations than pore size for eDNA capture in turbid water. Interactions between eDNA particles, suspended particulate matter, and filters are important to consider for eDNA methods optimization and interpretation of rare species detections in turbid water.
Cryo-EM Structure of a Mammalian-specific Alternative Amyloid Exon
Authors: Garcia-Pardo Javier , Bartolomé-Nafría Andrea , Chaves-Sanjuan Antonio , Gil-Garcia Marcos , Visentin Cristina , Bolognesi Martino , Ricagno Stefano , Ventura Salvador
Published: August 2022

hnRNPDL is a ribonucleoprotein (RNP) involved in transcription and RNA-processing, with missense mutations causing limb-girdle muscular dystrophy-3 (LGMDD3). Mammalian-specific alternative splicing (AS) renders three natural isoforms, hnRNPDL-2 being predominant in humans. We present the cryo-electron microscopy structure of full-length hnRNPDL-2 amyloid fibrils, which are stable, non-toxic, and bind nucleic acids, with the RNA binding domains building a solenoidal coat around them. The amyloid core consists of a single Gly/Tyr-rich and highly hydrophilic filament containing internal water channels. The architecture and activity of hnRNPDL-2 fibrils are reminiscent of functional amyloids, our results suggesting that LGMDD3 might be a loss-of-function disease associated with impaired fibrillation. Strikingly, the fibril core matches exon 6, absent in the soluble hnRNPDL-3 isoform. This provides structural evidence for AS controlling hnRNPDL assembly by precisely including/skipping an amyloid exon, a mechanism that holds the potential to generate functional diversity in RNPs.
Site-1 Protease inhibits mitochondrial metabolism by controlling the TGF-β target gene MSS51
Authors: Mousa Muhammad G. , Vuppaladhadiam Lahari , Kelly Meredith O. , Pietka Terri , Ek Shelby , Shen Karen C. , Meyer Gretchen A. , Finck Brian N. , Brookheart Rita T.
Published: August 2022

The mitochondrial response to changes in cellular energy demand is necessary for cellular adaptation and organ function. Many genes are essential in orchestrating this response, including the transforming growth factor (TGF)-β1 target gene MSS51, which is an inhibitor of skeletal muscle mitochondrial metabolism. Despite the potential importance of MSS51 in the pathophysiology of obesity and musculoskeletal disease, how MSS51 is regulated is not entirely understood. Site-1 Protease (S1P) is a Golgi-resident protease that is a key activator of several transcription factors required for cellular adaptation. However, the role of S1P in muscle and mitochondrial function are unknown. Here, we identify S1P as a negative regulator of muscle mass and mitochondrial metabolism. Disruption of S1P in mouse skeletal muscle and cultured myofibers leads to a reduction in MSS51 expression, increased muscle mass, and increased mitochondrial oxygen consumption. The effects of S1P deficiency on mitochondrial activity are counteracted by overexpressing MSS51, suggesting that S1P inhibits mitochondrial metabolism by regulating the expression of MSS51. Furthermore, S1P suppression enhances TGF-β signaling via the AKT pathway, potentially explaining muscle hypertrophy in S1P deficient mice. The discovery of S1P as a regulator of mitochondrial metabolism and muscle mass expands our understanding of TGF-β signaling and suggests this protease could be a target for therapeutic intervention in muscle.
Genomic epidemiology of the cholera outbreak in Yemen reveals the spread of a multi-drug resistance plasmid between diverse lineages of Vibrio cholerae
Authors: Lassalle Florent , Al-Shalali Salah , Al-Hakimi Mukhtar , Njamkepo Elisabeth , Bashir Ismail Mahat , Dorman Matthew J. , Rauzier Jean , Blackwell Grace A. , Taylor-Brown Alyce , Beale Mathew A. , Al-Somainy Ali Abdullah , Al-Mahbashi Anas , Almoayed Khaled , Aldawla Mohammed , Al-Harazi Abdulelah , Quilici Marie-Laure , Weill François-Xavier , Dhabaan Ghulam , Thomson Nicholas R.
Published: August 2022

The humanitarian crisis in Yemen led in 2016 to the biggest cholera outbreak documented in modern history, with more than 2.5 million suspected cases to date. In late 2018, epidemiological surveillance showed that V. cholerae isolated from cholera patients had turned multi-drug resistant (MDR). We generated genomes from 260 isolates sampled in Yemen between 2018 and 2019 to identify a possible shift in circulating genotypes. 84% of V. cholerae isolates were serogroup O1 belonging to the seventh pandemic El Tor (7PET) lineage, sublineage T13 – same as in 2016 and 2017 – while the remaining 16% of strains were non-toxigenic and belonged to divergent V. cholerae lineages, likely reflecting sporadic gut colonisation by endemic strains. Phylogenomic analysis reveals a succession of T13 clones, with 2019 dominated by a clone that carried an IncC-type plasmid harbouring an MDR pseudo-compound transposon (PCT). Identical copies of these mobile elements were found independently in several unrelated lineages, suggesting exchange and recombination between endemic and epidemic strains. Treatment of severe cholera patients with macrolides in Yemen from 2016 to early 2019 coincides with the emergence of the plasmid-carrying T13 clone. The unprecedented success of this genotype where an SXT-family integrative and conjugative element (SXT/ICE) and an IncC plasmid coinhabit show the stability of this MDR plasmid in the 7PET background, which may durably reduce options for epidemic cholera case management. We advocate a heightened genomic epidemiology surveillance of cholera to help control the spread of this highly-transmissible, MDR clone.
Distinct Nrf2 Signaling Thresholds Mediate Lung Tumor Initiation and Progression
Authors: DeBlasi Janine M. , Falzone Aimee , Caldwell Samantha , Prieto-Farigua Nicolas , Prigge Justin R. , Schmidt Edward E. , Chio Iok In Christine , Karreth Florian A. , DeNicola Gina M.
Published: August 2022

Mutations in the KEAP1-NRF2 pathway occur in up to a third of non-small cell lung cancer (NSCLC) cases and often confer resistance to therapy and poor outcomes. Here, we developed murine alleles of the KEAP1 and NRF2 mutations found in human NSCLC and comprehensively interrogated their impact on tumor initiation and progression. Chronic Nrf2 stabilization by Keap1 or Nrf2 mutation was not sufficient to induce tumorigenesis, even in the absence of tumor suppressors p53 or Lkb1. When combined with KrasG12D/+, constitutive Nrf2 activation promoted lung tumor initiation and early progression of hyperplasia to low-grade tumors but impaired their progression to advanced-grade tumors, which was reversed by Nrf2 deletion. Finally, NRF2 overexpression in KEAP1 mutant NSCLC cell lines was detrimental to cell proliferation, viability, and anchorage-independent colony formation. Collectively, our results establish the context-dependence and activity threshold for NRF2 during the lung tumorigenic process.

Significance

This study reports murine lung cancer models harboring mutations in the Keap1/Nrf2 pathway and highlights the context-dependent and diverse roles of Nrf2 during lung tumor initiation and progression.
Predicting antiviral resistance mutations in SARS-CoV-2 main protease with computational and experimental screening
Authors: Sasi Vishnu M. , Ullrich Sven , Ton Jennifer , Fry Sarah E. , Johansen-Leete Jason , Payne Richard J. , Nitsche Christoph , Jackson Colin J.
Published: August 2022

The main protease (Mpro) of SARS-CoV-2 is essential for viral replication and has been the focus of many drug discovery efforts since the start of the COVID-19 pandemic. Nirmatrelvir (NTV) is an inhibitor of SARS-CoV-2 Mpro that is used in the combination drug Paxlovid for the treatment of mild to moderate COVID-19. However, with increased use of NTV across the globe, there is a possibility that future SARS-CoV-2 lineages will evolve resistance to NTV. Early prediction and monitoring of resistance mutations could allow for measures to slow the spread of resistance and for the development of new compounds with activity against resistant strains. In this work, we have used in silico mutational scanning and inhibitor docking of Mpro to identify potential resistance mutations. Subsequent in vitro experiments revealed five mutations (N142L, E166M, Q189E, Q189I, and Q192T) that reduce the potency of NTV and of a previously identified non-covalent cyclic peptide inhibitor of Mpro. The E166M mutation reduced the half-maximal inhibitory concentration (IC50) of NTV 24-fold, and 118-fold for the non-covalent peptide inhibitor. Our findings inform the ongoing genomic surveillance of emerging SARS-CoV-2 lineages.

Graphical Abstract
MND1 enables repair of two-ended DNA double-strand breaks
Authors: Koob Lisa , Friskes Anoek , van Bergen Louise , Feringa Femke M. , van den Broek Bram , Koeleman Emma S. , Schubert Michael , Blomen Vincent A. , Brummelkamp Thijn R. , Krenning Lenno , Medema René H.
Published: August 2022

Faithful and timely repair of DNA double-strand breaks (DSBs) is fundamental for the maintenance of genomic integrity. Here, we demonstrate that the meiotic recombination co-factor MND1 facilitates the repair of DSBs in somatic cells. We show that MND1 localizes to DSBs, where it stimulates DNA repair through homologous recombination (HR). Importantly, MND1 is not involved in the response to replication-associated DSBs, implying that it is dispensable for HR-mediated repair of one-ended DSBs. Instead, we find that MND1 specifically plays a role in the response to two-ended DSBs that are induced by IR or various chemotherapeutic drugs, specifically in G2. MND1 localization to DSBs is dependent on resection of the DNA ends, and seemingly occurs through direct binding of MND1 to RAD51-coated ssDNA. Importantly, the lack of MND1-driven HR repair directly potentiates the toxicity of IR-induced damage, which could open new possibilities for therapeutic intervention, specifically in HR-proficient tumors.
Energy transfer in ubiquitous rhodopsin pumps with xanthophyll antennas
Authors: Chazan Ariel , Das Ishita , Fujiwara Takayoshi , Murakoshi Shunya , Shihoya Wataru , Rozenberg Andrey , Molina-Márquez Ana , Larom Shirley , Pushkarev Alina , Malakar Partha , Ruhman Sanford , Hasegawa Masumi , Tsukamoto Yuya , Ishizuka Tomohiro , Konno Masae , Nagata Takashi , Inoue Keiichi , Mizuno Yosuke , Katayama Kota , Abe-Yoshizumi Rei , Kandori Hideki , León Rosa M. , Yoshizawa Susumu , Sheves Mordechai , Nureki Osamu , Béjà Oded
Published: August 2022

Energy transfer from light-harvesting ketocarotenoids to light-driven proton pumps xanthorhodopsins has been previously demonstrated in two unique cases: an extreme halophilic bacterium1 and a terrestrial cyanobacterium2. Attempts to find carotenoids that bind and transfer energy to rhodopsin proton pumps from the abundant marine and freshwater photoheterotrophs have thus far failed3–5. Here, using functional metagenomics combined with chromophore extraction from the environment, we detected light energy transfer from the widespread hydroxylated carotenoids zeaxanthin and lutein to the retinal moiety of xanthorhodopsins and proteorhodopsins. The light-harvesting carotenoids transfer up to 42% of the harvested energy in the violet/blue-light range to the green-light absorbing retinal chromophore. Our data suggest that these antennas have a significant impact on rhodopsin phototrophy in the world’s lakes, seas and oceans.
Dinoflagellate Proton-Pump Rhodopsin Gene in Long Island Sound: Diversity and Spatiotemporal Distribution
Authors: Zhang Huan , Nulick Kelly J. , Burris Zair , Pierce Melissa , Ma Minglei , Lin Senjie
Published: August 2022

Microbial proton-pump rhodopsin (PPR), an alternative light-harvesting mechanism to chlorophyll-based photosystems, may contribute significantly to solar energy entry into the marine ecosystem. PPR transforms solar energy to cellular energy used for various metabolic processes in the cells or flagellar movement. Although rhodopsins or their encoding genes have been documented in a wide phylogenetic range of cultured dinoflagellates, information is limited about how widespread and how spatiotemporally dynamical dinoflagellate PPR (DiPPR) are in the marine ecosystem. In this study, using the quantitative PCR method, we investigated the abundance and diversity of DiPPR genes in Long Island Sound (LIS), a temperate estuary, both spatially and temporally in 2010. DiPPR genes were found year-round and throughout LIS, with higher abundances in the eutrophic Western Sound and during April and July. The gene diversity data suggest that there are at least five distinct rhodopsin-harboring groups of dinoflagellates throughout the year. The abundance of DiPPR genes, measured as copy number per mL seawater, appeared not to be influenced by water temperature and nitrogen nutrient concentration; however, weak negative correlations with orthophosphate concentration and salinity and a positive correlation with the abundance of typical-DiPPR-harboring dinoflagellates were observed. The association of DiPPR with phosphorus nutrition warrants further studies.
Antigen presentation dynamics shape the response to emergent variants like SARS-CoV-2 Omicron strain after multiple vaccinations with wild type strain
Authors: Yang Leerang , Van Beek Matthew , Wang Zijun , Muecksch Frauke , Canis Marie , Hatziioannou Theodora , Bieniasz Paul D. , Nussenzweig Michel C. , Chakraborty Arup K.
Published: August 2022

The Omicron variant of SARS-CoV-2 evades neutralization by most serum antibodies elicited by two doses of mRNA vaccines, but a third dose of the same vaccine increases anti-Omicron neutralizing antibodies. By combining computational modeling with data from vaccinated humans we reveal mechanisms underlying this observation. After the first dose, limited antigen availability in germinal centers results in a response dominated by B cells with high germline affinities for immunodominant epitopes that are significantly mutated in an Omicron-like variant. After the second dose, expansion of these memory cells and differentiation into plasma cells shape antibody responses that are thus ineffective for such variants. However, in secondary germinal centers, pre-existing higher affinity antibodies mediate enhanced antigen presentation and they can also partially mask dominant epitopes. These effects generate memory B cells that target subdominant epitopes that are less mutated in Omicron. The third dose expands these cells and boosts anti-variant neutralizing antibodies.
Mapping the GALNT1 substrate landscape with versatile proteomics tools
Authors: Saei Amir Ata , Lundström Susanna L. , Lyu Hezheng , Gharibi Hassan , Lu Weiqi , Fang Pan , Zhang Xuepei , Meng Zhaowei , Wang Jijing , Gaetani Massimiliano , Végvári Ákos , Gygi Steven P. , Zubarev Roman A.
Published: August 2022

O-GalNAc type glycosylation is a common post-translational modification (PTM) of proteins catalyzed by polypeptide GalNAc transferases, but the substrate specificity of these transferases is poorly understood. Here we develop a strategy based on integral thermal proteome solubility profiling to identify and prioritize the protein substrates of polypeptide N-acetylgalactosaminyltransferase 1 (GALNT1). Combined with glycoprotein enrichment followed by HCD and soft EThcD gas-phase fragmentation technique, we uncover hundreds of novel GALNT1 substrates in two model human cell lines. GALNT1-mediated O-glycosylation is more common on Thr than Ser residues, with a strong preference for Pro at positions +3 and +4 in respect to O-glycosylation. These results implicate GALNT1 in potentially regulating proteins in several diverse pathways, including some unexpected processes, such as TCA cycle and DNA transcription. This study depicts a roadmap for identification of functional substrates for glycosyltransferases, facilitating fundamental insight into the role of glycosylation in homeostasis and disease.
Lessons learnt from community referral and follow up of sick young infants with Possible Severe Bacterial Infection in Turkana County, Kenya
Authors: Mbugua Samuel , Mwaura Peter , Oyiengo Laura , Liambila Wilson , Emuria Andrew , Gatungu Daniel , Gitaka Jesse
Published: August 2022

Introduction

Management of possible severe bacterial infections in young infants (0-59 days) requires timely identification of danger signs and prompt administration of efficacious antibiotic treatment. The Possible Severe Bacterial Infection guidelines underscore the importance of close follow up in an outpatient basis to ensure treatment adherence and early detection of illness-related complications. The purpose of this study was to strengthen the follow up and referral of sick young infants on day 4 and 8 by introducing community-led interventions that facilitated community health volunteers to identify sick young infants, conduct community reviews, link data with responsive facilities, and refer appropriately.

Methods

Six health facilities were included a a longitudinal, descriptive, mixed methods approach weaved around an initial formative context assessment and three-monthly assessments. Quantitative data was extracted from facility registers to identify gaps in follow up and referral feasibility. Qualitative data was through focus group discussions with community health volunteers and key informant interviews with frontline providers.

Results

Qualitative data provided insights into key barriers and facilitators of community follow up and referral. Barriers include community socio-cultural practices, competing tasks, dysfunctional community referral pathway, drivers of common infections, and unavailability of essential commodities. Key facilitators entail indication of competency in identification of danger signs in sick young infants, presence of older women, men, and community resource persons that can leveraged on in community engagement and sensitization, and mothers are the primary decision makers in care seeking. There was increased utilization of decision support tools and an increase in the number of sick young infants managed in dispensaries. The COVID-19 pandemic however negatively impacted community follow up and referral of sick young infants.

Conclusion

This study seeks to contribute evidence on strengthening PSBI community management by enhancing day 4 and day 8 follow up, review and community referral of sick young infants in Turkana, Kenya. The feasibility, adoption, and fidelity of strengthening community facility linkage through integrated communication strategies was documented, indicative of a successful community-facility linkage in dispensaries and health centers despite the effects of the COVID-19 pandemic.
Clustering schizophrenia genes by their temporal expression patterns aids functional interpretation genetics-based evidence in favor of the two-hit hypothesis
Authors: van der Meer Dennis , Cheng Weiqiu , Rokicki Jaroslav , Fernandez-Cabello Sara , Shadrin Alexey , Smeland Olav B. , Ehrhart Friederike , Gülöksüz Sinan , Steen Nils Eiel , Djurovic Srdjan , Westlye Lars T. , Andreassen Ole A. , Kaufmann Tobias
Published: August 2022

Schizophrenia is a highly heritable brain disorder with a typical symptom onset in early adulthood. The two-hit hypothesis posits that schizophrenia results from deviant early neurodevelopment, predisposing an individual, followed by a disruption of later brain maturational processes that trigger the onset of symptoms. Here, we investigate how the timing of expression of 345 putative schizophrenia risk genes may aid in understanding the interplay of neurobiological processes in the pathophysiology of schizophrenia. Clustering of brain transcriptomic data across the lifespan revealed a set of 183 genes that was significantly upregulated prenatally and downregulated postnatally and 162 genes that showed the opposite pattern. The prenatally upregulated set of genes was functionally annotated to fundamental cell cycle processes, while the postnatally upregulated set was associated with the immune system and neuronal communication. We subsequently calculated two set-specific polygenic risk scores for 743 individuals with schizophrenia and 743 sex- and age-matched healthy controls. We found an interaction between the two scores; higher prenatal polygenic risk was only significantly associated with schizophrenia diagnosis and severity, at higher levels of postnatal polygenic risk. We therefore provide genetics-based evidence in favor of the two-hit hypothesis, supporting that schizophrenia may be shaped by disruptions of separable biological processes acting at distinct phases of neurodevelopment.
Active bulging promotes biofilm formation in a bacterial swarm
Authors: Liu Siyu , Li Ye , Xu Haoran , Kearns Daniel B. , Wu Yilin
Published: August 2022

Microbial communities such as biofilms are commonly found at interfaces. However, it is unclear how the physical environment of interfaces may contribute to the development and behavior of surface-associated microbial communities. Combining multi-mode imaging, single-cell tracking and numerical simulations, here we discovered that an interfacial process denoted as “active bulging” promotes biofilm formation. During this process, an initially two-dimensional layer of swarming bacteria spontaneously develops scattered liquid bulges; the bulges have a higher propensity to transit from motile to sessile biofilm state, presumably due to the enrichment of pre-existing immotile cells in the colony. We further demonstrate that the formation of liquid bulges can be controlled reversibly by manipulating the speed and local density of cells with light. Our findings reveal a unique physical mechanism of biofilm formation and provide a new strategy for biofilm patterning in engineered living materials as well as for directed self-assembly in active fluids.
Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization
Authors: Amselem Elias , Broadwater Bo , Havermark Tora , Johansson Magnus , Elf Johan
Published: August 2022

Sub-ms 3D tracking of individual molecules in living cells is an important goal for microscopy since it will enable measurements at the scale of diffusion limited macromolecular interactions. Here, we present a 3D tracking principle based on the true excitation point spread function and cross-entropy minimization for position localization of moving fluorescent reporters that approaches the relevant regime. When tested on beads moved on a stage, we reached 67nm lateral and 109nm axial precision with a time resolution of 0.84 ms at a photon count rate of 60kHz, coming close to the theoretical and simulated predictions. A critical step in the implementation was a new method for microsecond 3D PSF positioning that combines 3D holographic beam shaping and electro-optical deflection. For the analysis of tracking data, a new point estimator for diffusion was derived and evaluated by a detailed simulation of the 3D tracking principle applied to a fictive reaction-diffusion process in an E. coli-like geometry. Finally, we successfully applied these methods to track the Trigger Factor protein in living bacterial cells. Overall our results show that it is possible to reach sub-millisecond live-cell single molecule tracking, but that it is still hard to resolve state transitions based on diffusivity at this time scale.
KLF5 governs sphingolipid metabolism and barrier function of the skin
Authors: Lyu Ying , Guan Yinglu , Deliu Lisa , Humphrey Ericka , Frontera Joanna K. , Yang Youn Joo , Zamler Daniel , Kim Kun Hee , Mohanty Vakul , Jin Kevin , Liu Virginia , Dou Jinzhuang , Veillon Lucas J. , Kumar Shwetha V. , Lorenzi Philip L. , Chen Yang , McAndrews Kathleen M. , Grivennikov Sergei , Song Xingzhi , Zhang Jianhua , Xi Yuanxin , Wang Jing , Chen Ken , Nagarajan Priyadharsini , Ge Yejing
Published: August 2022

Stem cells are fundamental units of tissue remodeling whose functions are dictated by lineage-specific transcription factors. Home to epidermal stem cells and their upward-stratifying progenies, skin relies on its secretory functions to form the outermost protective barrier, of which a transcriptional orchestrator has been elusive. KLF5 is a Krüppel-like transcription factor broadly involved in development and regeneration whose lineage specificity, if any, remains unclear. Here we report KLF5 specifically marks the epidermis, and its deletion leads to skin barrier dysfunction in vivo. Lipid envelopes and secretory lamellar bodies are defective in KLF5-deficient skin, accompanied by preferential loss of complex sphingolipids. KLF5 binds to and transcriptionally regulates genes encoding rate-limiting sphingolipid metabolism enzymes. Remarkably, skin barrier defects elicited by KLF5 ablation can be rescued by dietary interventions. Finally, we found that KLF5 is widely suppressed in human diseases with disrupted epidermal secretion, and its regulation of sphingolipid metabolism is conserved in human skin. Altogether, we established KLF5 as a disease-relevant transcription factor governing sphingolipid metabolism and barrier function in the skin, likely representing a long-sought secretory lineage-defining factor across tissue types.
Both YAP1-MAML2 and constitutively active YAP1 drive the formation of tumors that resemble NF2 mutant meningiomas in mice
Authors: Szulzewsky Frank , Arora Sonali , Arakaki Aleena K.S. , Sievers Philipp , Almiron Bonnin Damian A. , Paddison Patrick J. , Sahm Felix , Cimino Patrick J. , Gujral Taranjit S. , Holland Eric C.
Published: August 2022

YAP1 is a transcriptional coactivator regulated by the Hippo signaling pathway, including NF2. Meningiomas are the most common primary brain tumors; a large percentage exhibit heterozygous loss of chromosome 22 (harboring the NF2 gene) and functional inactivation of the remaining NF2 copy, implicating oncogenic YAP activity in these tumors. Recently, fusions between YAP1 and MAML2 have been identified in a subset of pediatric NF2 wild-type meningiomas. Here, we show that human YAP1-MAML2-positive meningiomas resemble NF2 mutant meningiomas by global and YAP-related gene expression signatures. We then show that expression of YAP1-MAML2 in mice induces tumors that resemble human YAP1 fusion-positive and NF2 mutant meningiomas by gene expression. We demonstrate that YAP1-MAML2 primarily functions by exerting TEAD-dependent YAP activity that is resistant to Hippo signaling. Treatment with YAP-TEAD inhibitors is sufficient to inhibit the viability of YAP1-MAML2-driven mouse tumors ex vivo. Finally, we show that expression of constitutively active YAP1 (S127/397A-YAP1) is sufficient to induce similar tumors, suggesting that the YAP component of the gene fusion is the critical driver of these tumors. In summary, our results implicate YAP1-MAML2 as a causal oncogenic driver and highlight TEAD-dependent YAP activity as an oncogenic driver in YAP1-MAML2 fusion meningioma as well as NF2 mutant meningioma in general.
Time-resolved serial femtosecond crystallography on fatty-acid photodecarboxylase: lessons learned
Authors: Hadjidemetriou Kyprianos , Coquelle Nicolas , Barends Thomas R. M. , De Zitter Elke , Schlichting Ilme , Colletier Jacques-Philippe , Weik Martin
Published: August 2022

Upon absorption of a blue-light photon, fatty-acid photodecarboxylase catalyzes the decarboxylation of free fatty acids to form hydrocarbons (for example alkanes or alkenes). The major components of the catalytic mechanism have recently been elucidated by combining static and time-resolved serial femtosecond crystallography (TR-SFX), time-resolved vibrational and electronic spectroscopies, quantum-chemical calculations and site-directed mutagenesis [Sorigué et al. (2021), Science, 372, eabd5687]. The TR-SFX experiments, which were carried out at four different picosecond to microsecond pump–probe delays, yielded input for the calculation of Fourier difference maps that demonstrated light-induced decarboxylation. Here, some of the difficulties encountered during the experiment as well as during data processing are highlighted, in particular regarding space-group assignment, a pump-laser power titration is described and data analysis is extended by structure-factor extrapolation of the TR-SFX data. Structure refinement against extrapolated structure factors reveals a reorientation of the generated hydrocarbon and the formation of a photoproduct close to Cys432 and Arg451. Identification of its chemical nature, CO2 or bicarbonate, was not possible because of the limited data quality, which was assigned to specificities of the crystalline system. Further TR-SFX experiments on a different crystal form are required to identify the photoproducts and their movements during the catalytic cycle.
Structural bases for the higher adherence to ACE2 conferred by the SARS-CoV-2 spike Q498Y substitution
Authors: Erausquin Elena , Glaser Fabian , Fernández-Recio Juan , López-Sagaseta Jacinto
Published: August 2022

A remarkable number of SARS-CoV-2 variants and other as yet unmonitored lineages harbor amino-acid substitutions with the potential to modulate the interface between the spike receptor-binding domain (RBD) and its receptor ACE2. The naturally occurring Q498Y substitution, which is present in currently circulating SARS-CoV-2 variants, has drawn the attention of several investigations. While computational predictions and in vitro binding studies suggest that Q498Y increases the binding affinity of the spike protein for ACE2, experimental in vivo models of infection have shown that a triple mutant carrying the Q498Y replacement is fatal in mice. To accurately characterize the binding kinetics of the RBD Q498Y–ACE2 interaction, biolayer interferometry analyses were performed. A significant enhancement of the RBD–ACE2 binding affinity relative to a reference SARS-CoV-2 variant of concern carrying three simultaneous replacements was observed. In addition, the RBD Q498Y mutant bound to ACE2 was crystallized. Compared with the structure of its wild-type counterpart, the RBD Q498Y–ACE2 complex reveals the conservation of major hydrogen-bond interactions and a more populated, nonpolar set of contacts mediated by the bulky side chain of Tyr498 that collectively lead to this increase in binding affinity. In summary, these studies contribute to a deeper understanding of the impact of a relevant mutation present in currently circulating SARS-CoV-2 variants which might lead to stronger host–pathogen interactions.
ModelCraft: an advanced automated model-building pipeline using Buccaneer
Authors: Bond Paul S. , Cowtan Kevin D.
Published: August 2022

Interactive model building can be a difficult and time-consuming step in the structure-solution process. Automated model-building programs such as Buccaneer often make it quicker and easier by completing most of the model in advance. However, they may fail to do so with low-resolution data or a poor initial model or map. The Buccaneer pipeline is a relatively simple program that iterates Buccaneer with REFMAC to refine the model and update the map. A new pipeline called ModelCraft has been developed that expands on this to include shift-field refinement, machine-learned pruning of incorrect residues, classical density modification, addition of water and dummy atoms, building of nucleic acids and final rebuilding of side chains. Testing was performed on 1180 structures solved by experimental phasing, 1338 structures solved by molecular replacement using homologues and 2030 structures solved by molecular replacement using predicted AlphaFold models. Compared with the previous Buccaneer pipeline, ModelCraft increased the mean completeness of the protein models in the experimental phasing cases from 91% to 95%, the molecular-replacement cases from 50% to 78% and the AlphaFold cases from 82% to 91%.
Eye control system based on convolutional neural network: a review
Authors: Xiong Jianbin , Nie Jinji , Li Jiehao
Published: August 2022

Purpose

This paper primarily aims to focus on a review of convolutional neural network (CNN)-based eye control systems. The performance of CNNs in big data has led to the development of eye control systems. Therefore, a review of eye control systems based on CNNs is helpful for future research.

Design/methodology/approach

In this paper, first, it covers the fundamentals of the eye control system as well as the fundamentals of CNNs. Second, the standard CNN model and the target detection model are summarized. The eye control system’s CNN gaze estimation approach and model are next described and summarized. Finally, the progress of the gaze estimation of the eye control system is discussed and anticipated.

Findings

The eye control system accomplishes the control effect using gaze estimation technology, which focuses on the features and information of the eyeball, eye movement and gaze, among other things. The traditional eye control system adopts pupil monitoring, pupil positioning, Hough algorithm and other methods. This study will focus on a CNN-based eye control system. First of all, the authors present the CNN model, which is effective in image identification, target detection and tracking. Furthermore, the CNN-based eye control system is separated into three categories: semantic information, monocular/binocular and full-face. Finally, three challenges linked to the development of an eye control system based on a CNN are discussed, along with possible solutions.

Originality/value

This research can provide theoretical and engineering basis for the eye control system platform. In addition, it also summarizes the ideas of predecessors to support the development of future research.
Systematic cross-cultural management education: a quasi-experimental analysis of guided experiential learning during intercultural simulations
Authors: Heidemann Christina , Søndergaard Mikael
Published: August 2022

Purpose

The main purpose of this paper is to test the effects of a classical intercultural simulation on participants' ability to modify their behavior in response to collectivistic and individualistic contexts. Moreover, the paper aims to examine moderating effects based on experiential learning and social identity theory.

Design/methodology/approach

The learning effects are evaluated through two separate quasi-experimental studies with 152 master students in business economics at a Danish university and 190 bachelor students in international business at a German university.

Findings

The analysis shows that intercultural simulations with artificial cultures significantly improve participants' ability to modify their behavior depending on cultural context. Participants who identify with an artificial culture that differs radically from their own take greater advantage of the simulation. The overall duration of international experience moderates participants' learning with a U-shaped effect. Culture-specific experience strengthens the positive effect of the simulation. The comparison of the two conducted studies indicates that previous cognitive teaching enhances learning.

Practical implications

The findings demonstrate the effectiveness of intercultural simulations that guide participants through all phases of the experiential learning cycle. Moreover, they underline the importance of assessing participants' cultural backgrounds before the assignment of training groups.

Originality/value

Prior research on intercultural simulations is often based on qualitative methods and mostly limited to affective outcomes, such as motivation and enjoyment of intercultural interactions. By contrast, this paper quantitatively tests to what extent intercultural simulations improve participants' ability to modify behavior depending on culture.
The impact of monetary incentives and regulatory focus on worker productivity and learning in order picking
Authors: Sgarbossa Fabio , Glock Christoph H. , Grosse Eric H. , Calzavara Martina , de Koster René
Published: August 2022

Purpose

In manual order picking systems, temporary workers are often employed to handle demand peaks. While this increases flexibility, it may hamper productivity, as they are usually unfamiliar with the processes and may have little experience. It is important for managers to understand how quickly inexperienced workers arrive at full productivity and which factors support workers in improving their productivity. This paper aims to investigate how learning improves the performance of order pickers, and how their regulatory focus (RF) and monetary incentives, as management actions, influence learning.

Design/methodology/approach

Data was collected in two case studies in controlled field-lab experiments and statistically analysed. This allowed evaluating the validity of hypotheses through an ANOVA, the calculation of correlation coefficients and the application of regression models.

Findings

A monetary incentive based on total order picking time and pick errors has a positive influence on order picking time, but not on pick quality. The incentive influences initial productivity, but not the learning rate. A dominant promotion-oriented RF increases the effect of the incentive on initial productivity, but it does not impact worker learning.

Practical implications

This study contributes to behavioral and human-focused order picking management and supports managers in setting up work plans and developing incentive systems for learning and productivity enhancement, considering worker RF.

Originality/value

This work is among the few to empirically investigate the effect of monetary incentives on learning in interaction with RF. It is the first study to investigate these concepts in an order picking scenario.
Slow fashion purchase intention drivers: an Indonesian study
Authors: Aprianingsih Atik , Fachira Ira , Setiawan Margareth , Debby Teresia , Desiana Nia , Lathifan Shafa Amira Nurryda
Published: August 2022

Purpose

This study aims to explore the relationships between particular personal values (environmental, hedonic and utilitarian) and the intention to purchase slow fashion through the mechanism of attitude toward slow fashion in Indonesia.

Design/methodology/approach

This quantitative study uses an online questionnaire to obtain survey data from 429 respondents in cities in Indonesia. The respondents were mostly aged between 18 and 45 years, with the majority between 18 and 22 years (63.40 per cent). Confirmatory factor analysis and structural equation modeling are used to test and validate the proposed model's scale validity and relationship.

Findings

Environmental, utilitarian and hedonic values are positively related to attitudes toward slow-fashion products. Further, attitudes toward slow-fashion products positively influence purchase intention.

Practical implications

The study suggests marketing strategies to stimulate the intention to purchase slow fashion through advertising that emphasizes utilitarian, environmental and hedonic values, such as the pleasure in using slow-fashion products.

Originality/value

This study is the first to investigate the relationship of environmental and motivational values (hedonic and utilitarian) to the intention to purchase slow-fashion products. The findings contribute to the theoretical and practical understandings of slow fashion by identifying pre-positioned values that trigger positive attitudes toward slow-fashion products, thereby increasing purchase intention.
Analysis of influencing factors of online community knowledge-sharing from the perspective of the platform environment
Authors: Xie Renqiang , Zhang Wende
Published: August 2022

Purpose

The number of online communities has increased rapidly with the development of the Internet. Although these communities provide users with knowledge-sharing channels, the enthusiasm of the users for participation remains low. Ecosystem theory, social cognitive theory, and some other theories emphasize the importance of environmental factors and hypothesize that the behavior of users is affected by personal factors and environmental factors. In this study, the authors investigated the impact of platform environmental factors on knowledge-sharing behavior and improved the platform environment construction of online communities.

Design/methodology/approach

First, the authors analyzed the influencing factors of online community knowledge-sharing from the perspective of the platform environment, constructed a research model, and proposed relevant hypotheses. Then, the authors designed a questionnaire and conducted a survey, and finally tested the hypotheses by using the method of structural equation model.

Findings

The results showed that community trust, community management, community incentive, community atmosphere, and community information protection had a significant positive impact on community knowledge-sharing behavior. Community trust played a significant intermediary role in the relationship between community management, community incentive, community information protection, and knowledge-sharing behavior; community information protection only affected knowledge-sharing behavior through community trust. Additionally, community atmosphere did not directly affect knowledge-sharing behavior through the intermediary of community trust.

Practical implications

This study showed that theoretical supplements and practical guidance are significant for conducting research and managing knowledge-sharing in the online community. They help community managers pay more attention to the construction of an online community platform environment.

Originality/value

In this study, the authors analyzed the influencing factors of online community knowledge-sharing from the perspective of the platform environment and introduced community trust as an intermediary variable. The research perspective and model of this study are novel to some extent.
Impact of job insecurity during COVID-19 on green entrepreneurial intention of Pakistani entrepreneurs: a moderated mediation model
Authors: Noor Uzma , Rabbani Sajeela , Dastgeer Ghulam
Published: August 2022

Purpose

The study aimed at identifying job insecurity during COVID-19 as a determinant of green entrepreneurial intentions under the mediating role of entrepreneurial passion. Further, moderated mediation model of environmental consciousness and environmental knowledge on the relationship between job insecurity during COVID-19 and green entrepreneurial intentions through entrepreneurial passion as a mediator is also measured.

Design/methodology/approach

The study employed Statistical Package for the Social Sciences (SPSS) and analysis of a moment structure (AMOS) to calculate the measurement and structure model. Data was collected from the twin cities of Pakistan (Islamabad and Rawalpindi). A total of 389 usable responses were included in the analyses.

Findings

Considering entrepreneurship as a process, the result shows a significant relationship between the study variables. Also, it is realized that entrepreneurial passion serves as an important mediator between job insecurity during COVID-19 and green entrepreneurial intention. Both entrepreneurial knowledge and environmental consciousness have an indirect conditional effect on the relationship between job insecurity during COVID-19 and green entrepreneurial intention with entrepreneurial passion as a mediator. The study tested a novel relationship between job insecurity during COVID-19 and entrepreneurial passion under the lens of contingency theory and entrepreneurial event theory.

Research limitations/implications

The extreme necessity to choose an alternative to full-time jobs is entrepreneurial endeavors that can be explored by entrepreneurs. Policymakers can capitalize on this scenario by proposing entrepreneurial opportunities which are green as well. The term Green represents an environmental friendly business, which one can start in the context of COVID-19 when everyone is oriented to cleanliness, personal hygiene and environment friendly.

Originality/value

The study tested a novel relationship between job insecurity during COVID-19 and entrepreneurial passion under the lens of contingency theory and entrepreneurial event theory. It contributes to the present stock of knowledge and understanding of the subject by contextualizing the concept of green entrepreneurial intention.
Engineering cell morphology by CRISPR interference in Acinetobacter baylyiADP1
Authors: Luo Jin , Efimova Elena , Volke Daniel Christoph , Santala Ville , Santala Suvi
Published: August 2022

Microbial production of intracellular compounds can be engineered by redirecting the carbon flux towards products and increasing the cell size. Potential engineering strategies include exploiting clustered regularly interspaced short palindromic repeats interference (CRISPRi)‐based tools for controlling gene expression. Here, we applied CRISPRi for engineering Acinetobacter baylyi ADP1, a model bacterium for synthesizing intracellular storage lipids, namely wax esters. We first established an inducible CRISPRi system for strain ADP1, which enables tightly controlled repression of target genes. We then targeted the glyoxylate shunt to redirect carbon flow towards wax esters. Second, we successfully employed CRISPRi for modifying cell morphology by repressing ftsZ, an essential gene required for cell division, in combination with targeted knock‐outs to generate significantly enlarged filamentous or spherical cells respectively. The engineered cells sustained increased wax ester production metrics, demonstrating the potential of cell morphology engineering in the production of intracellular lipids.