bluuebunny/crossref_metadata_2025 huggingface dataset:
NLRP3 inflammasome is dispensable in methicillin resistantStaphylococcus aureusurinary tract infection
Authors: Paudel Santosh , Rogers Kenneth A , Kumar Rahul , Saini Yogesh , Patial Sonika , Kulkarni Ritwij
Published: November 2022

NLRP3 inflammasome is a cytoplasmic complex that senses molecular patterns from pathogens or damaged cells to trigger an innate immune defense response marked by the production of proinflammatory cytokines IL-1β and IL-18 and an inflammatory death called pyroptosis. The NLRP3 inflammasome is activated in the urinary tract by a variety of infectious and non-infectious insults. In this study, we investigated the role of NLRP3 inflammasome by inducing methicillin resistantStaphylococcus aureus(MRSA) ascending UTI in WT andNlrp3-/-mice. At 24 and 72 hpi, compared to the WT, the MRSA-infectedNlrp3-/-showed ∼100-fold lower median CFUs, although this reduction was not statistically significant. The ablation of NLRP3 did not affect MRSA-induced urinary immune defenses as indicated by the similar levels of pro-inflammatory cytokines and chemokines and the similar numbers of granulocytes in the bladder and the kidneys of WT andNlrp3-/-mice at 24 h after MRSA infection. However, MRSA-infectedNlrp3-/-bladders, but not kidneys, showed significantly higher monocyte infiltration. The histopathological analysis of bladder and kidney sections showed similar inflammation in MRSA-infectedNlrp3-/-and WT mice. Overall, these results suggest that MRSA-induced urinary NLRP3 activity is dispensable to the host.

Importance

Indwelling urinary catheter usage increased susceptibility to methicillin-resistantStaphylococcus aureus(MRSA) urinary tract infections (UTI) which can be difficult to treat and can result in potentially fatal complications such as bacteremia, urosepsis, and shock. In this work, we examined the role of NLRP3 inflammasome in MRSA uropathogenesis. In comparison to the WT, mice deficient in NLRP3 activity showed similar MRSA burden and similar inflammation in the bladder and kidney tissues at 24 h after the experimental induction of ascending UTI. These results suggest that NLRP3 inflammasome is not involved in shaping urinary immune defenses during acute MRSA-UTI.
Regulation of multidrug efflux pumps by TetR family transcriptional repressor negatively affects secondary metabolism inStreptomyces coelicolorA3(2)
Authors: Lei Yukun , Asamizu Shumpei , Ishizuka Takumi , Onaka Hiroyasu
Published: November 2022

Streptomycesspp. are well-known producers of bioactive secondary metabolites (SMs) that serve as pharmaceutical agents. In addition to their ability to produce SMs,Streptomycesspp. have evolved diverse membrane transport systems to protect cells against antibiotics produced by itself or other microorganisms. We previously screened mutants ofStreptomyces coelicolorthat show a phenotype of reduced undecylprodigiosin (RED) production in a combined-culture withTsukamurella pulmonis. Here, we identified a point mutation, which reduced RED production, by performing genome resequencing and genetic complementation. We found that inactivation of thesco1718gene encoding the TetR family transcriptional regulator (TFR) produced a deficient phenotype for several SMs inStreptomyces coelicolorA3(2). Electrophoretic mobility shift assay and quantitative reverse transcription-PCR experiments demonstrated that SCO1718 repressed the expression of adjacent two-component ATP-binding cassette (ABC) transporter genes (sco1719-20) by binding to the operator sequence in the 5′-UTR. Notably, the Δsco1718mutant showed increased resistance to several antibiotics of other actinomycete origin. In the genome ofS. coelicolorA3(2), two other sets of TFR and two-component ABC transporter genes (sco4358-4360andsco5384-5382) were found, which had similar effects on the phenotype for both secondary metabolism and antibiotic resistance. Our results imply the switching of cell metabolism to direct offence (antibiotic production) or defense (efflux pump activation) using costly and limited quantities of cell energy sources (e.g., ATP) in the soil ecosystem.

IMPORTANCE

The bacterial metabolic potential to synthesize diverse secondary metabolites (SMs) in the environment has been revealed by recent (meta-)genomics of both unculturable and culturable bacteria. These studies imply that bacteria are continuously exposed to harmful chemical compounds in the environment.Streptomycesspp. contain antibiotic efflux pumps and SM biosynthetic gene clusters. However, the mechanism by which soil bacteria, includingStreptomyces, survive against toxic compounds in the environment remains unclear. Here, we identified three sets of TFR-ABC transporter genes inStreptomyces coelicolorA3(2). We found that each TFR controlled the expression of a respective ABC transporter, and the expression of all ABC transporters negatively impacted SM production and increased antibiotic resistance. Notably, bioinformatic analysis indicated that these TFR-ABC transporter gene sets are highly conserved and widely distributed in the genome ofStreptomycesspecies, indicating the importance of systematic regulation that directs antibiotic production and xenobiotic excretion.
NhaR, LeuO and H-NS are part of an expanded regulatory network for ectoine biosynthesis expression
Authors: Boas Lichty Katherine E. , Gregory Gwendolyn J. , Boyd E. Fidelma
Published: November 2022

Bacteria accumulate compatible solutes, to maintain cellular turgor pressure when exposed to high salinity. In the marine halophileVibrio parahaemolyticus,the compatible solute ectoine is biosynthesizedde novo, which is energetically more costly than uptake; therefore, tight regulation is required. To uncover novel regulators of the ectoine biosynthesisectABC-asp_ectoperon, a DNA affinity pulldown of proteins interacting with theectABC-asp_ectregulatory region was performed. Mass spectrometry analysis identified, amongst others, three regulators: LeuO, NhaR, and the nucleoid associated protein H-NS. In-frame non-polar deletions were made for each gene and PectA-gfppromoter reporter assays were performed in exponential and stationary phase cells. PectA-gfpexpression was significantly repressed in the ΔleuOmutant and significantly induced in the ΔnhaRmutant compared to wild type, suggesting positive and negative regulation, respectively. In the Δhnsmutant, PectA-gfpshowed increased expression in exponential phase cells, but no change compared to wild type in stationary phase cells. To examine whether H-NS interacts with LeuO or NhaR at the ectoine regulatory region, double deletion mutants were created. In a ΔleuO/Δhnsmutant, PectA-gfpshowed reduced expression, but significantly more than ΔleuOsuggesting H-NS and LeuO interact to regulate ectoine expression. Whereas ΔnhaR/Δhnshad no additional effect as compared to ΔnhaRsuggesting NhaR regulation is independent of H-NS. To examineleuOregulation further, a PleuO-gfpreporter analysis was examined that showed significantly increased expression in the ΔleuO, Δhnsand ΔleuO/Δhnsmutants as compared to wild type, indicating both are repressors. Growth pattern analysis of the mutants in M9G 6%NaCl, showed growth defects compared to wild type, indicating that these regulators play an important physiological role in salinity stress tolerance.

Importance

Ectoine is a commercially used compatible solute that acts as a biomolecule stabilizer because of its additional role as a chemical chaperone. A better understanding of how the ectoine biosynthetic pathway is regulated in natural bacterial producers can be used to increase efficient industrial production. Thede novobiosynthesis of ectoine is essential for bacteria to survive osmotic stress when exogenous compatible solutes are absent. This study identified LeuO as a positive regulator and NhaR as a negative regulator of ectoine biosynthesis and also showed that similar to enteric species, LeuO is an anti-silencer of H-NS. In addition, defects in growth in high salinity among all the mutants suggest that these regulators play a broader role in the osmotic stress response beyond ectoine biosynthesis regulation.
Early induction of cytokine release syndrome by rapidly generated CAR T cells in a preclinical mouse model
Authors: Ho Naphang , Jamali Arezoo , Braun Angela , Adabi Elham , Thalheimer Frederic B. , Buchholz Christian J.
Published: November 2022

Chimeric antigen receptor (CAR) T cells have emerged as effective strategy against B cell malignancies. Since the long manufacturing process limits patient accessability, short-term (st) CAR T cells are under investigation. Here, we evaluated CD19-CAR T cells 24 hours after exposure to lentiviral vectors. In co-culture with tumor cells and monocytes, stCAR T cells exhibited anti-tumoral activity and strong release of CRS-relevant cytokines (IL-6, IFN-γ, TNF-α, GM-CSF, IL-2, IL-10). When administered into tumor engrafted NSG-SGM3 mice, severe acute adverse events encompassing high body scoring, temperature and weight drop arised rapidly within 24 hours. Human (IFN-Y, TNF-α, IL-2, IL-10) and murine (MCP-1, IL-6, G-CSF) cytokines typical for severe cytokine release syndrome (CRS) were systemically elevated. Our data highlight potential safety risks of CAR T cells manufactured within short time and suggest simple models for their preclinical safety evaluation.
PD-1 is induced on tumor-associated macrophages in obesity to directly restrain anti-tumor immunity
Authors: Bader Jackie E. , Wolf Melissa M. , Madden Matthew Z. , Reinfeld Bradley I. , Arner Emily N. , Hathaway Emma S. , Steiner KayLee K. , Needle Gabriel A. , Landis Madelyn D. , Cottam Matthew A. , Ye Xiang , Christofides Anthos , Boussiotis Vassiliki A. , Haake Scott M. , Beckermann Kathryn E. , Rathmell W. Kimryn , Hasty Alyssa H. , Rathmell Jeffrey C.
Published: November 2022

Obesity is a leading risk factor for progression and metastasis of many cancers1,2, yet can also promote improved survival for some cancers3-5and enhance responses to some immune checkpoint blockade therapies6-8. The role of the immune system in the obesity-cancer connection and how obesity influences immunotherapy, however, remain unclear. While PD-1 expression by macrophages has been described9-12, we found that obesity selectively induced PD-1 on macrophages and that PD-1 directly impaired macrophage function. Single cell RNA sequencing of murine colorectal carcinoma tumors showed obesity remodeled myeloid and T cell populations, with fewer clonally expanded effector T cells and increased abundance of PD-1+tumor-associated macrophages (TAM). Cytokines and molecules associated with obesity, including IL-6, leptin, and insulin, and the unsaturated fatty acid palmitate, induced PD-1 expression on macrophages in a glycolysis-dependent manner. PD-1+TAMs had increased mitochondrial respiration and expression of genes regulating oxidative phosphorylation, lipid uptake and cell cycle while PD-1-TAMs showed greater signatures of phagocytosis and antigen presentation to T cells. These patterns were directly regulated by PD-1, as recombinant PD-L1 reduced macrophage glycolysis and phagocytic capacity, and this was reversed with blocking PD-1 antibody. Conversely, PD-1-deficientPdcd1-/-TAMs had high rates of glycolysis, phagocytosis, and expression of MHC-II. Myeloid-specific PD-1 deficiency correlated with slower tumor growth, enhanced TAM antigen presentation capability, and increased CD8 T cell activation together with reduced markers of exhaustion. These findings show metabolic signaling in obesity induces PD-1-mediated suppression of TAM function and reveal a unique macrophage-specific mechanism to modulate immune tumor surveillance and checkpoint blockade. This may contribute to increased cancer risk yet improved response to PD-1 blockade in TAM-enriched tumors and obesity.
Genome-scale CRISPR screening reveals host factors required for ribosome formation and viral replication
Authors: Ohlson Maikke B. , Kumar Ashwani , Eitson Jennifer L. , Jang Seoyeon , Ni Chunyang , Xing Chao , Buszczak Michael , Schoggins John W.
Published: November 2022

Viruses are known to co-opt host machinery for translation initiation, but less is known about which host factors are required for the formation of ribosomes used to synthesize viral proteins. Using a loss of function CRISPR screen, we show that synthesis of a flavivirus encoded reporter depends on multiple host factors, including several 60S ribosome biogenesis proteins. Viral phenotyping revealed that two of these factors, SBDS, a known ribosome biogenesis factor, and the relatively uncharacterized protein SPATA5, were broadly required for replication of flaviviruses, coronaviruses, alphaviruses, paramyxoviruses, an enterovirus, and a poxvirus. Mechanistic studies revealed that loss of SPATA5 caused defects in ribosomal RNA processing and ribosome assembly, suggesting that this human protein may be a functional ortholog of yeastDrg1. These studies implicate specific ribosome biogenesis proteins as viral host dependency factors that are required for synthesis of virally encoded protein and accordingly, optimal viral replication.
RUNX1 is regulated by androgen receptor to promote cancer stem markers and chemotherapy resistance in triple negative breast cancer
Authors: Fernández Natalia B , Sosa Sofía M , Roberts Justin T , Recouvreux María S , Rocha-Viegas Luciana , Christenson Jessica L , Spoelstra Nicole S , Couto Facundo L , Raimondi Ana R , Richer Jennifer K , Rubinstein Natalia
Published: November 2022

Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype for which no effective targeted therapies are available. Growing evidence suggests that chemotherapy-resistant cancer cells with stem-like properties (CSC) may repopulate the tumor. Androgen receptor (AR) is expressed in up to 50% of TNBC, and AR inhibition decreases CSC and tumor initiation. Runt-related transcription factor 1 (RUNX1) correlates with poor prognosis in TNBC and is regulated by AR in prostate cancer. Our group has shown that RUNX1 promotes TNBC cell migration and regulates tumor gene expression. We hypothesized that RUNX1 is regulated by AR and that both may work together in TNBC CSC to promote disease recurrence following chemotherapy. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) experiments in MDA-MB-453 revealed AR binding toRUNX1regulatory regions. RUNX1 expression is upregulated by dihydrotestosterone (DHT) in MDA-MB-453 and in HCI-009 patient-derived xenograft (PDX) tumors (p<0.05). RUNX1 is increased in a CSC-like experimental model in MDA-MB-453 and SUM-159PT cells (p<0.05). Inhibition of RUNX1 transcriptional activity reduced the expression of CSC markers. Interestingly, RUNX1 inhibition reduced cell viability and enhanced paclitaxel and enzalutamide sensitivity. Targeting RUNX1 may be an attractive strategy to potentiate the anti-tumor effects of AR inhibition, specifically in the slow growing CSC-like populations that resist chemotherapy leading to metastatic disease.
Functional redundancy secures resilience of chain elongation communities upon pH shifts in closed bioreactor ecosystems
Authors: Liu Bin , Sträuber Heike , Centler Florian , Harms Hauke , da Rocha Ulisses Nunes , Kleinsteuber Sabine
Published: November 2022

For anaerobic mixed cultures performing microbial chain elongation, it is unclear how pH alterations affect the abundance of key players, microbial interactions and community functioning in terms of medium-chain carboxylate yields. We explored pH effects on mixed cultures enriched in continuous anaerobic bioreactors representing closed model ecosystems. Increasing the pH from 5.5 to 6.0 caused fluctuations in community composition and yields ofn-butyrate,n-caproate andn-caprylate. Further pH increase to 6.5 restored previous yield values while the community entered a new state characterized by lower diversity and evenness but apparently higher richness, indicating the presence of species below the detection threshold in the previous state. We applied Aitchison PCA clustering, linear mixed-effects models and random forest classification on our datasets. Different pH preferences of two key chain elongation species – oneClostridiumIV species related toRuminococcaceaebacterium CPB6, and oneClostridium sensu strictospecies related toClostridium luticellarii– were determined. Based on relative abundances measured by 16S rRNA amplicon sequencing, network analysis revealed positive correlations ofClostridiumIV with lactic acid bacteria, which switched fromOlsenellatoLactobacillusalong the pH increase, illustrating the plasticity of the food web in chain elongation communities. The pH increase induced dramatic shifts in community composition whereas process performance (in terms of product range and yields) returned to the previous state. Despite long-term cultivation in closed systems over the pH shift experiment, the communities retained functional redundancy in fermentation pathways, reflected by the emergence of rare species and concomitant recovery of chain elongation functions.
MSP1encodes an essential RNA-binding PPR factor required fornad1maturation and complex I biogenesis inArabidopsismitochondria
Authors: Best Corinne , Mizrahi Ron , Edris Rana , Tang Hui , Zer Hagit , Colas des Francs-Small Catherine , Finkel Omri M. , Zhu Hongliang , Small Ian D. , Ostersetzer-Biran Oren
Published: November 2022

Mitochondria are semi-autonomous organelles that serve as hubs for aerobic energy metabolism. The biogenesis of the respiratory (OXPHOS) system relies on nuclear-encoded factors, which regulate the transcription, processing and translation of mitochondrial (mt)RNAs. These include proteins of primordial origin, as well as eukaryotic-type RNA-binding families recruited from the host genomes to function in mitogenome expression. Pentatricopeptide repeat (PPR) proteins constitute a major gene-family in angiosperms that is pivotal in many aspects of mtRNA metabolism, such as editing, splicing or stability. Here, we report the analysis ofMITOCHONDRIA STABILITY/PROCESSING PPR FACTOR1(MSP1, At4g20090), a canonical mitochondria-localized PPR protein that is necessary for mitochondrial biogenesis and embryo-development. Functional complementation confirmed that the phenotypes result from a disruption of theMSP1gene. As a loss-of-function allele ofArabidopsis MSP1leads to seed abortion, we employed an embryo-rescue method for the molecular characterization ofmsp1mutants. Our data show thatmsp1embryo-development fails to proceed beyond the heart-torpedo transition stage as a consequence of a severe nad1 pre-RNA processing-defect, resulting in the loss of respiratory complex I (CI) activity. The maturation ofnad1involves the processing of three RNA-fragments,nad1.1, nad1.2andnad1.3. Based on biochemical analyses and the mtRNA profiles in wild-type andmsp1plants, we concluded that through its association with a specific site innad1.1, MSP1 facilitates the generation of its 3’-terminus and stabilizes it -a prerequisite fornad1exons a-b splicing. Our data substantiate the importance of mtRNA metabolism for the biogenesis of the respiratory machinery during early-plant development.
Molecular characterization of microbes in the center of barnacle footprints (part I)
Authors: Zhang Zhizhou
Published: November 2022

abstract

There is a barnacle larva settlement model in which barnacle cryprid selectively locates itself only on a specific marine biofilm area that contains specific microbes. That means a local biofilm site with specific characteristics can attract barnacle larva to the maximum. If this is true, a barnacle already growing up shall still press down a chunk of biofilm area where it settles when it was a crypid. The chunk of biofilm should be at the center of barnacle footprint and may still contain most of the microbes at the attachment site. By this consideration, a group of such chunks of barnacle cement (with about 2mm diameter) was collected from the center of barnacle footprints, followed by genomic DNA extraction, PCR amplification with primers representing prokaryotes, eukaryotes, archaea and fungus, DNA sequencing and species determination. The most abundant 13 species were preliminarily determined (mainly fungi). Whether they are really wanted target microbes largely depends on future investigations on whether they possess some common features that can attract barnacle crypids.
Small proteome of the nitrogen-fixing plant symbiontSinorhizobium meliloti
Authors: Hadjeras Lydia , Heiniger Benjamin , Maaß Sandra , Scheuer Robina , Gelhausen Rick , Azarderakhsh Saina , Barth-Weber Susanne , Backofen Rolf , Becher Dörte , Ahrens Christian H. , Sharma Cynthia M. , Evguenieva-Hackenberg Elena
Published: November 2022

The soil-dwelling plant symbiontSinorhizobium melilotiis a major model organism of Alphaproteobacteria. Despite numerous detailed OMICS studies, information about small open reading frame (sORF)-encoded proteins (SEPs) is largely missing, because sORFs are poorly annotated, and SEPs are hard to detect experimentally. However, given that SEPs can fulfill important functions, cataloging the full complement of translated sORFs is critical for analyzing their roles in bacterial physiology. Ribosome profiling (Ribo-seq) can detect translated sORFs with high sensitivity, but is not yet routinely applied to bacteria because it must be adapted for each species. Here, we established a Ribo-seq procedure forS. meliloti2011 based on RNase I digestion and detected translation for 60% of the annotated coding sequences during growth in minimal medium. Using ORF prediction tools based on Ribo-seq data, subsequent filtering, and manual curation, the translation of 37 non-annotated sORFs with ≤ 70 amino acids was predicted with high confidence. The Ribo-seq data were supplemented by mass spectrometry (MS) analyses from three sample preparation approaches and two integrated proteogenomic search databases (iPtgxDBs). Searches against a standard and a 20-fold smaller Ribo-seq data-informed custom iPtgxDB confirmed many annotated SEPs and identified 11 additional novel SEPs. Epitope tagging and Western blot analysis confirmed the translation of 15 out of 20 SEPs selected from the translatome map. Overall, by applying MS and Ribo-seq as complementary approaches, the small proteome ofS. melilotiwas substantially expanded by 48 novel SEPs. Several of them are conserved fromRhizobiaceaeto Bacteria, suggesting important physiological functions.
Time-resolved cryo-EM reveals early ribosome assembly in action
Authors: Qin Bo , Lauer Simon M. , Balke Annika , Vieira-Vieira Carlos H. , Bürger Jörg , Mielke Thorsten , Selbach Matthias , Scheerer Patrick , Spahn Christian M. T. , Nikolay Rainer
Published: November 2022

Ribosome biogenesis is a fundamental multi-step cellular process in all domains of life that involves the production, processing, folding, and modification of ribosomal RNAs (rRNAs) and ribosomal proteins. To obtain insights into the still unexplored early assembly phase of the bacterial 50S subunit, we exploited a minimalin vitroreconstitution system using purified ribosomal components and scalable reaction conditions. Time-limited assembly assays combined with cryo-EM analysis visualizes the structurally complex assembly pathway starting with a particle consisting of ordered density for only ∼500 nucleotides of 23S rRNA domain I and three ribosomal proteins. In addition, our structural analysis reveals that early 50S assembly occurs in a domain-wise fashion, while late 50S assembly proceeds incrementally. Furthermore, we find that both ribosomal proteins and folded rRNA helices, occupying surface exposed regions on pre-50S particles, induce, or stabilize rRNA folds within adjacent regions, thereby creating cooperativity.
Contrasting effector profiles between bacterial colonisers of kiwifruit reveal redundant roles and interplay converging on PTI-suppression and RIN4
Authors: Jayaraman Jay , Yoon Minsoo , Hemara Lauren , Bohne Deborah , Tahir Jibran , Chen Ronan , Brendolise Cyril , Rikkerink Erik , Templeton Matt
Published: November 2022

Testing effector-knockout strains of thePseudomonas syringaepv.actinidiaebiovar 3 (Psa3) for reducedin plantagrowth in their native kiwifruit host revealed a number of non- redundant effectors that contribute to Psa3 pathogenicity. Conversely, complementation in the weak kiwifruit pathogenP. syringaepv.actinidifoliorum(Pfm) for increased growth identified redundant Psa3 effectors.

Psa3 effectors hopAZ1a and HopS2b and the entire exchangeable effector locus (ΔEEL; 10 effectors) were significant contributors to bacterial colonisation of the host and were additive in their effects on pathogenicity. Four of the EEL effectors (HopD1a, AvrB2b, HopAW1a, and HopD2a) redundantly contribute to pathogenicity through suppression of pattern-triggered immunity (PTI).

Important Psa3 effectors include several redundantly required effectors early in the infection process (HopZ5a, HopH1a, AvrPto1b, AvrRpm1a, and HopF1e). These largely target the plant immunity hub, RIN4.

This comprehensive effector profiling revealed that Psa3 carries robust effector redundancy for a large portion of its effectors, covering a few functions critical to disease.
Facing lethal temperatures: heat shock response in desert and temperate ants
Authors: de Souza Araujo Natalia , Perez Rémy , Willot Quentin , Defrance Matthieu , Aron Serge
Published: November 2022

Several genera of desert ants have adapted to endure prolonged exposure to high temperatures. The study of these ants is essential to unravel how species respond and adapt to thermal stress. We investigated the thermal tolerance and the transcriptomic heat stress response of three desert ant genera (Cataglyphis, MelophorusandOcymyrmex) and two temperate genera (FormicaandMyrmica) to explore convergent and specific adaptations. We found a variable transcriptomic response among desert species exposed to similar levels of physiological heat-stress:Cataglyphis holgerseniandMelophorus bagotidifferentially regulated very few transcripts, 0.12% (54/44,525) and 0.14% (53/38,726) respectively, whileCataglyphis bombycinaandOcymyrmex robustiorshowed greater expression alterations affecting 0.6% (253/41,912) and 1.53% (698/45,701) of their transcriptomes, respectively. These two responsive mechanisms – reactive and constitutive – were related to desert species thermal tolerance survival pattern and convergently evolved in distinct desert ant genera. By comparison, the two temperate species differentially expressed thousands of transcripts more than desert ants in response to heat stress (affecting 8% and 12,71% ofF. fuscaandMyr. sabuletitranscriptomes), suggesting that keeping restrained gene expression is an important adaptation in heat adapted species. Finally, we found a significant overlap of the molecular pathways activated in response to heat-stress in temperate and desert species, and our data revealed that larger gene expression responses also affected a greater number of taxonomically restricted genes. These results suggest that the molecular processes involved in heat-stress response are mostly evolutionary conserved in ants, but new genes may also play a role.
Glycerolipid defects in skeletal muscle contribute to rhabdomyolysis in Tango2 deficiency
Authors: Casey Jennifer G , Kim Euri S , Tao Brian S , Mansur Arian , Wallace E. Diane , Gupta Vandana A
Published: November 2022

Rhabdomyolysis is a clinical emergency characterized by severe muscle damage resulting in the release of intracellular muscle components leading to myoglobinuria and in severe cases, acute kidney failure. Rhabdomyolysis is caused by genetic factors that are linked to increased disease susceptibility in response to extrinsic triggers. Recessive mutations inTANGO2result in episodic rhabdomyolysis, metabolic crises, encephalopathy and cardiac arrhythmia, the underlying mechanism contributing to disease onset in response to specific triggers remains unclear. To address these challenges, we created a zebrafish model of Tango2 deficiency. Here we show that loss of Tango2 in zebrafish results in growth defects, early lethality and increased susceptibility of muscle defects similar toTANGO2patients. Detailed analyses of skeletal muscle revealed defects in the sarcoplasmic reticulum and mitochondria at the onset of disease development. The sarcoplasmic reticulum (SR) constitutes the primary lipid biosynthesis site and regulates calcium handling in skeletal muscle to control excitation-contraction coupling. Tango2 deficient SR exhibits increased sensitivity to calcium release that was partly restored by inhibition of Ryr1-mediated Ca2+release in skeletal muscle. Using lipidomics, we identified alterations in the glycerolipid state oftango2mutants which is critical for membrane stability and energy balance. Therefore, these studies provide insight into key disease processes in Tango2 deficiency and increased our understanding of how specific defects can predispose to environmental triggers in TANGO2-related disorders.
Trachymyrmex septentrionalisants promote fungus garden hygiene usingTrichoderma-derived metabolite cues
Authors: Kyle Kathleen E. , Puckett Sara P. , Caraballo-Rodríguez Andrés Mauricio , Rivera-Chávez José , Samples Robert M. , Earp Cody E. , Raja Huzefa A. , Pearce Cedric J. , Ernst Madeleine , van der Hooft Justin J.J. , Adams Madison E. , Oberlies Nicholas H. , Dorrestein Pieter C. , Klassen Jonathan L. , Balunas Marcy J.
Published: November 2022

Fungus-growing ants depend on a fungal mutualist that can fall prey to fungal pathogens. This mutualist is cultivated by these ants in structures called fungus gardens. Ants exhibit weeding behaviors that keep their fungus gardens healthy by physically removing compromised pieces. However, how ants detect diseases of their fungus gardens is unknown. Here, we applied the logic of Koch’s postulates using environmental fungal community gene sequencing, fungal isolation, and laboratory infection experiments to establishTrichodermaspp. as previously unrecognized pathogens ofTrachymyrmex septentrionalisfungus gardens. Our environmental data showed thatTrichodermaare the most abundant non-cultivar fungi in wildT. septentrionalisfungus gardens. We further determined that metabolites produced byTrichodermainduce an ant weeding response that mirrors their response to liveTrichoderma. Combining ant behavioral experiments with bioactivity-guided fractionation and statistical prioritization of metabolites inTrichodermaextracts demonstrated thatT. septentrionalisants weed in response to peptaibols, a specific class of secondary metabolites known to be produced byTrichodermafungi. Similar assays conducted using purified peptaibols, including the two new peptaibols trichokindins VIII and IX, suggested that weeding is likely induced by peptaibols as a class rather than by a single peptaibol metabolite. In addition to their presence in laboratory experiments, we detected peptaibols in wild fungus gardens. Our combination of environmental data and laboratory infection experiments strongly support that peptaibols act as chemical cues ofTrichodermapathogenesis inT. septentrionalisfungus gardens.

Significance Statement

An extended defense response may exist in any relationship where one partner benefits from defending a mutualistic partner. Such a response is observed in the fungus-growing ant symbiosis, where ants must identify and remove pathogens of their symbiotic fungus gardens. Here we describe the fungal pathogenTrichodermaand its associated metabolites, which induceTrachymyrmex septentrionalisant weeding behavior. Ants removed fungus garden pieces inoculated withTrichodermaspores or peptaibol-richTrichodermaextracts, and peptaibols as a class cued ant defensive behavior, allowingT. septentrionalisto differentiate healthy from diseased fungus gardens. Extended defense responses mediated by chemical cues may be underappreciated mechanisms that structure symbiotic interactions.
The NDH complex reveals a trade-off that constrains maximising photosynthesis inArabidopsis thaliana
Authors: Theeuwen Tom P.J.M. , Lawson Aaron W. , Tijink Dillian , Fornaguera Federico , Becker Frank F.M. , Caracciolo Ludovico , Fisher Nicholas , Kramer David M. , Wijnker Erik , Harbinson Jeremy , Aarts Mark G.M.
Published: November 2022

The Green Revolution has resulted in major improvements in crop productivity, but left photosynthesis largely unimproved. Despite ample variation of photosynthetic performance in crops and their wild relatives, the photosynthetic capacity of elite breeding lines remains well below its theoretical maximum. As yield is often the primary selective trait, current plant breeding approaches result in photosynthetic trade-offs that prevent positive selection for photosynthetic performance itself. Currently, genetic variation for photosynthetic performance is seldomly validated at the genetic level, and as a result these photosynthetic trade-offs remain poorly understood. Here we reveal the physiological nature of a photosynthetic trade-off caused by the NAD(P)H dehydrogenase (NDH) complex. The use of anArabidopsis thalianacybrid panel revealed how a natural allele of the chloroplastic geneNAD(P)H-QUINONE OXIDOREDUCTASE SUBUNIT 6 -a subunit of the NDH complex - results in a faster recovery of photosystem II efficiency after a transition from high to low irradiances. This improvement is due to a reduction in NDH activity. Under low-light conditions this reduction in NDH activity has a neutral effect on biomass, while under highly fluctuating light conditions, including high irradiances, more NDH activity is favoured. This shows that while allelic variation in one gene can have beneficial effects on one aspect of photosynthesis, it can, depending on environmental conditions, have negative effects on other aspects of photosynthesis. As environmental conditions are hardly ever stable in agricultural systems, understanding photosynthetic trade-offs allows us to explore shifting photosynthetic performance closer to the theoretical maximum.
Neonatal Fc receptor is a functional receptor for human astrovirus
Authors: Haga Kei , Takai-Todaka Reiko , Kato Akiko , Nakanishi Akira , Katayama Kazuhiko
Published: November 2022

Human astrovirus (HAstV) is a global cause of gastroenteritis in infants, the elderly, and immunocompromised people. However, its infection mechanism is not fully understood, with its functional receptor not yet discovered. Here, we identify neonatal Fc receptor (FcRn) as a functional receptor for HAstV (mamastrovirus 1) using genome-wide CRISPR-Cas9 library screening in Caco2 cells. Deletion ofFCGRTorB2M, which encode subunits of FcRn, rendered Caco2 cells and intestinal organoid cells unsusceptible to HAstV. We also show that human FcRn expression renders non-permissive MDCK cells susceptible and that FcRn directly binds HAstV spike protein. Thus, our findings provide insight into the entry mechanism of HAstV.
Structural basis for ubiquitylation by HOIL-1
Authors: Wu Qilong , Koliopoulos Marios G. , Rittinger Katrin , Stieglitz Benjamin
Published: November 2022

The linear ubiquitin chain assembly complex (LUBAC) synthesises linear Ub chains which constitute a binding and activation platform for components of the TNF signalling pathway. One of the components of LUBAC is the ubiquitin ligase HOIL-1 which has been shown to generate oxyester linkages on several proteins and on linear polysaccharides. Here we describe the crystal structure of a C-terminal tandem domain construct of HOIL-1 comprising the IBR and RING2 domains. The structure adopts an auto-inhibited conformation in which the catalytic cysteine of the RING2 domain is shielded by the adjacent IBR domain. Activation of HOIL-1 is triggered by linear tetra-Ub binding which enables HOIL-1 to mono-ubiquitylate linear Ub chains and polysaccharides. Interestingly, the structure reveals a unique bi-nuclear Zn-cluster which substitutes the second zinc finger of the canonical RING2 fold. We identify the C-terminal histidine of this bi-nuclear Zn-cluster as the catalytic base required for the ubiquitylation activity of HOIL-1. Our study suggests that the unique zinc-coordinating architecture of RING2 provides a binding platform for ubiquitylation targets.
Digitizing accounting education trends during COVID-19: empirical evidence from Vietnamese universities
Authors: Tran Hung Ngoc
Published: November 2022

Purpose

The study mainly aims to evaluate factors that impact online accounting education in Vietnamese universities during COVID-19.

Design/methodology/approach

The study is exploratively conducted with a quantitative sample using purposive data-collecting techniques. The sample focused on teaching staff and students at public and private universities in Vietnam during COVID-19.

Findings

The study shows that infrastructure, working/living conditions during COVID-19 and lecturing time are the top three factors impacting online digitizing accounting education.

Research limitations/implications

This research is not without limitations. The limitations are limited time and resources, which did not allow for examining other factors that impact digitizing education in accounting. The forthcoming study should examine extended factors (not mentioned in the study) such as government sponsorship, lecturers’ soft skills, national culture, qualifications and so on.

Originality/value

This study identifies and states significant factors that impact online digitizing accounting education in Vietnamese higher education during COVID-19.
Trends in scientific literature on the environmental sustainability of the artichoke (Cynara cardunculus L. spp.) supply chain
Authors: Rana Roberto Leonardo , Bux Christian , Lombardi Mariarosaria
Published: November 2022

Purpose

The research provides a systematic literature review on the environmental sustainability of the globe artichoke [Cynara cardunculus L. var. scolymus (L.) Fiori], in the cultivated cardoon [Cynara cardunculus L. var. altilis DC.] and in the wild cardoon [Cynara cardunculus L. var. sylvestris (Lamk)] supply chains, to fill in the literature data gaps and to identify new research directions.

Design/methodology/approach

In the light of the PRISMA standard guidelines, the research provides a systematic literature review according to six research strings on Scopus and Web of Science. 45 scientific articles have been selected out of 407 contributions. Data have been synthesized according to a co-word analysis through the VOSviewer software, to provide insights into the structure of the research network, to offer a multidimensional scaling and clustering into research groups and to discuss the results.

Findings

The research identifies five main research trends: (1) biomass-to-bioenergy or biomass-to-biocomposite materials; (2) waste-to-bioenergy or waste-to-bioproducts; (3) crop management to increase yield productivity; (4) environmental impacts assessment; (5) irrigation water management. Besides, the research highlights momentous challenges and adopted strategies to tackle climate change and to reduce natural resources consumption, as well as the nexus between circular economy and environmental impact assessment.

Originality/value

The novelty of this study relies on the fact that it analyses the environmental sustainability of the Cynara cardunculus L. spp. Supply chain in a systematic way, giving the opportunity to identify future research directions regarding the environmental impacts associated with agricultural production and industrial transformation.
Review of critical success factors affecting Malaysia's construction industry's sustainable health and safety practices
Authors: Oni Olatoyese Zaccheus , Olanrewaju AbdulLateef , Khor Soo Cheen
Published: November 2022

Purpose

Contrasted with some other industries, the construction industry has been linked with the most noteworthy accident occurrence rate, the majority of which has been related to poor health and safety practises. This paper therefore sets out to conduct a comprehensive review of the critical success factors that can aid sustainable health and safety practises on construction sites in Malaysia.

Design/methodology/approach

The review focussed heavily on published reports, drawn between the years 2000 and 2022. The Scopus database was used for gathering the articles reviewed for this study.

Findings

After reviewing various literature studies, a total of 106 critical success factors were identified. All these factors were then categorised under the three pillars of sustainability. A total of 48 factors were grouped under the economic factors, 37 factors were grouped under the social factors and the remaining 21 factors were grouped under the environmental factors.

Originality/value

This paper conducted a comprehensive review of the critical success factors for bridging sustainability and health and safety. This study will help in developing a sustainable health and safety model that can drastically reduce the accident rate on the construction site.
Contested logistics simulation output analysis with approximate dynamic programming: a proposed methodology
Authors: Powers Matthew , O'Flynn Brian
Published: November 2022

Purpose

Rapid sensitivity analysis and near-optimal decision-making in contested environments are valuable requirements when providing military logistics support. Port of debarkation denial motivates maneuver from strategic operational locations, further complicating logistics support. Simulations enable rapid concept design, experiment and testing that meet these complicated logistic support demands. However, simulation model analyses are time consuming as output data complexity grows with simulation input. This paper proposes a methodology that leverages the benefits of simulation-based insight and the computational speed of approximate dynamic programming (ADP).

Design/methodology/approach

This paper describes a simulated contested logistics environment and demonstrates how output data informs the parameters required for the ADP dialect of reinforcement learning (aka Q-learning). Q-learning output includes a near-optimal policy that prescribes decisions for each state modeled in the simulation. This paper's methods conform to DoD simulation modeling practices complemented with AI-enabled decision-making.

Findings

This study demonstrates simulation output data as a means of state–space reduction to mitigate the curse of dimensionality. Furthermore, massive amounts of simulation output data become unwieldy. This work demonstrates how Q-learning parameters reflect simulation inputs so that simulation model behavior can compare to near-optimal policies.

Originality/value

Fast computation is attractive for sensitivity analysis while divorcing evaluation from scenario-based limitations. The United States military is eager to embrace emerging AI analytic techniques to inform decision-making but is hesitant to abandon simulation modeling. This paper proposes Q-learning as an aid to overcome cognitive limitations in a way that satisfies the desire to wield AI-enabled decision-making combined with modeling and simulation.
Cognitive load in asynchronous discussions of an online undergraduate STEM course
Authors: Faulconer Emily K. , Bolch Charlotte , Wood Beverly
Published: November 2022

Purpose

As online course enrollments increase, it is important to understand how common course features influence students' behaviors and performance. Asynchronous online courses often include a discussion forum to promote community through interaction between students and instructors. Students interact both socially and cognitively; instructors' engagement often demonstrates social or teaching presence. Students' engagement in the discussions introduces both intrinsic and extraneous cognitive load. The purpose of this study is to validate an instrument for measuring cognitive load in asynchronous online discussions.

Design/methodology/approach

This study presents the validation of the NASA-TLX instrument for measuring cognitive load in asynchronous online discussions in an introductory physics course.

Findings

The instrument demonstrated reliability for a model with four subscales for all five discrete tasks. This study is foundational for future work that aims at testing the efficacy of interventions, and reducing extraneous cognitive load in asynchronous online discussions.

Research limitations/implications

Nonresponse error due to the unincentivized, voluntary nature of the survey introduces a sample-related limitation.

Practical implications

This study provides a strong foundation for future research focused on testing the effects of interventions aimed at reducing extraneous cognitive load in asynchronous online discussions.

Originality/value

This is a novel application of the NASA-TLX instrument for measuring cognitive load in asynchronous online discussions.
Intranasal (2R, 6R)‐hydroxynorketamine for acute pain: Behavioural and neurophysiological safety analysis in mice
Authors: Goswami Nidhi , Aleem Mohd , Manda Kailash
Published: November 2022

Ketamine is known for its antinociceptive effect and is also used for treatment‐resistant depression. However, the efficacy and safety of (2R, 6R)‐hydroxynorketamine (HNK), a ketamine metabolite has been sparingly investigated for acute pain management. The current study aims at investigating the antinociceptive effect of intranasal (2R, 6R)‐HNK using pre‐clinical models of acute pain. Additionally, the behavioural and neurophysiological safety analyses were carried out for the effective time window. Antinociceptive efficacy of (2R, 6R)‐HNK was evaluated using the hot plate test and Hargreaves' plantar test. The formalin test was carried out in both the acute and tonic phases. The neurophysiological and behavioural safety analyses were carried out separately for the haemodynamic function, cortical electroencephalography (EEG), and spontaneous behavioural functions. Analgesic effect of (2R, 6R)‐HNK was evident by a significant increase in paw‐withdrawal latency in both Hargreaves' and hot plate tests. Additionally, the (2R, 6R)‐HNK showed a significant ameliorative effect on pain‐related behaviour in the second phase of the formalin test. (2R, 6R)‐HNK exhibited an anxiolytic effect without causing any significant changes in locomotor activity and haemodynamic parameters. Power spectral density (PSD) analysis of electroencephalogram revealed no significant changes except a comparative increase in the gamma band range. Both the locomotor functions in the open field test and the PSD value of delta wave indicated no sedative effect at the given dose of (2R, 6R)‐HNK. The results demonstrated the pain‐alleviating effect of (2R, 6R)‐HNK without compromising the neurophysiological and behavioural function. Therefore, intranasal (2R, 6R)‐HNK is suggested as a safe candidate for further clinical study in the management of acute pain.