bluuebunny/crossref_metadata_2025 huggingface dataset:
Streamlining Marker-less Allelic Replacement inStreptococcus pneumoniaeThrough a Single Transformation Step Strategy: easyJanus
Authors: Chembilikandy Vipin , D’Mello Adonis , Tettelin Hervé , Martínez Eriel , Orihuela Carlos J.
Published: May 2024

The ability to genetically manipulate bacteria is a staple of modern molecular microbiology. Since the 2000’s, marker-less mutants ofStreptococcus pneumoniae(Spn) have been made by allelic-exchange predominantly using thekanR-rpsLcassette known as “Janus”. The conventional Janus protocol involves two transformation steps using multiple PCR-assembled products containing the Janus cassette and the target gene’s flanking DNA. We present an innovative strategy to achieve marker-less allelic replacement through a single transformation step. Our approach involves the integration of an additional gene downstream region upstream of the Janus cassette, resulting in a modified genetic arrangement. This single modification reduced the number of required PCR fragments from five to four, lowered the number of assembly reactions from two to one, and simplified the transformation process to a single step. To validate the efficacy of our approach, we implemented this strategy to delete inSpnserotype 4 strain TIGR4 the virulence genepspA, the entire capsular polysaccharide synthesis locuscps4, and to introduce a single nucleotide replacement into the chromosome. Notably, beyond streamlining the procedure, our method markedly reduced false positives typically encountered during negative selection with streptomycin when employing the traditional Janus protocol. Furthermore, and as consequence of reducing the amount of exogenous DNA required for construct synthesis, we show that our new method is amendable to the use of commercially available synthetic DNA for construct creation, further reducing the work needed to obtain a mutant. Our streamlined strategy, termed easyJanus, substantially expedites the genetic manipulation ofSpnfacilitating future research endeavors.

IMPORTANCE

We introduce a groundbreaking strategy aimed at streamlining the process for marker-less allelic replacement inStreptococcus pneumoniae, a Gram-positive bacterium and leading cause of pneumonia, meningitis, and ear infections. Our approach involves a modified genetic arrangement of the Janus cassette to facilitate self-excision during the segregation step. Since this new method reduces the amount of exogenous DNA required, it is highly amendable to the use of synthetic DNA for construction of the mutagenic construct. Our streamlined strategy, called easyJanus, offers significant time and cost savings, while concurrently enhancing the efficiency of obtaining marker-less allelic replacement inS. pneumoniae.
Collective responses of flocking sheep to a herding dog
Authors: Jadhav Vivek , Pasqua Roberto , Zanon Christophe , Roy Matthieu , Tredan Gilles , Bon Richard , Guttal Vishwesha , Theraulaz Guy
Published: May 2024

Across taxa, group-living organisms exhibit collective escape responses to stimuli varying from mild stress to predatory pressures. How exactly does information flow among group members leading to a collective escape remains an open question. Here we study the collective responses of a flock of sheep to a shepherd dog in a driving task between well-defined target points. We collected highresolution spatio-temporal data from 14 sheep and the dog, using Ultra Wide Band tags attached to each individual. Through the time delay analysis of velocity correlations, we identify a hierarchy among sheep in terms of directional influence. Notably, the average spatial position of a sheep along the front-back axis of the group’s velocity strongly correlates with its impact on the collective movement. Our findings demonstrate that, counter-intuitively, directional information on shorter time scales propagates from the front of the group towards the rear, and that the dog exhibits adaptive movement adjustments in response to the flock’s dynamics. Furthermore, we show that a simple shepherding model can capture key features of the collective response of the sheep flocks. In conclusion, our study reveals novel insights on how directional information propagates in escaping animal groups.
Mucin-induced surface dispersal ofStaphylococcus aureusandStaphylococcus epidermidisvia quorum sensing-dependent and independent mechanisms
Authors: Jacob Kristin M. , Hernandez-Villamizar Santiago , Hammer Neal D. , Reguera Gemma
Published: May 2024

Nasopharyngeal carriage of staphylococci spreads potentially pathogenic strains into (peri)oral regions and increases the chance of cross-infections. Some laboratory strains can also move rapidly on hydrated agar surfaces, but the biological relevance of these observations is not clear. Using soft-agar (0.3% w/v) plate assays, we demonstrate the rapid surface dispersal of (peri)oral isolates ofStaphylococcus aureusandStaphylococcus epidermidisand closely related laboratory strains in the presence of mucin glycoproteins. Mucin-induced dispersal was a stepwise process initiated by the passive spreading of the growing colonies followed by their rapid branching (dendrites) from the colony edge. Although most spreading strains used mucin as a growth substrate, dispersal was primarily dependent on the lubricating and hydrating properties of the mucins. UsingS. aureusJE2 as a genetically tractable representative, we demonstrate that mucin-induced dendritic dispersal, but not colony spreading, is facilitated by the secretion of surfactant-active Phenol-Soluble Modulins (PSMs) in a process regulated by theagrquorum sensing system. Furthermore, the dendritic dispersal ofS. aureusJE2 colonies was further stimulated in the presence of surfactant-active supernatants recovered from the most robust (peri)oral spreaders ofS. aureusandS. epidermidis. These findings suggest complementary roles for lubricating mucins and staphylococcal PSMs in the active dispersal of potentially pathogenic strains from perioral to respiratory mucosae, where gel-forming, hydrating mucins abound. They also highlight the impact that interspecies interactions have on the co-dispersal ofS. aureuswith other perioral bacteria, heightening the risk of polymicrobial infections and the severity of the clinical outcomes.

Importance

Despite lacking classical motility machinery, nasopharyngeal staphylococci spread rapidly in (peri)oral and respiratory mucosa and cause cross-infections. We describe laboratory conditions for the reproducible study of staphylococcal dispersal on mucosa-like surfaces and the identification of two dispersal stages (colony spreading and dendritic expansion) stimulated by mucin glycoproteins. The mucin type mattered, as dispersal required the surfactant activity and hydration provided by some mucin glycoproteins. While colony spreading was a passive mode of dispersal lubricated by the mucins, the more rapid and invasive form of dendritic expansion ofStaphylococcus aureusandStaphylococcus epidermidisrequired additional lubrication by surfactant-active peptides (phenol-soluble modulins) secreted at high cell densities through quorum sensing. These results highlight a hitherto unknown role for gel-forming mucins in the dispersal of staphylococcal strains associated with cross-infections and point at perioral regions as overlooked sources of carriage and infection by staphylococci.
Polyomavirus ALTOs, but not MTs, downregulate viral early gene expression by activating the NF-κB pathway
Authors: Salisbury Nicholas J. H. , Amonkar Supriya , Landazuri Vinueza Joselyn , Carter Joseph J. , Roman Ann , Galloway Denise A.
Published: May 2024

Polyomaviruses are small, circular dsDNA viruses that can cause cancer. Alternative splicing of polyomavirus early transcripts generates large and small tumor antigens (LT, ST) that play essential roles in viral replication and tumorigenesis. Some polyomaviruses also express middle tumor antigens (MTs) orAlternateLT ORFs (ALTOs), which are evolutionarily related but have distinct gene structures. MTs are a splice variant of the early transcript whereas ALTOs are overprinted on the second exon of the LT transcript in an alternate reading frame and are translated via an alternative start codon. Merkel cell polyomavirus (MCPyV), the only human polyomavirus that causes cancer, encodes an ALTO but its role in the viral lifecycle and tumorigenesis has remained elusive. Here, we show MCPyV ALTO acts as a tumor suppressor and is silenced in Merkel cell carcinoma (MCC). Rescuing ALTO in MCC cells induces growth arrest and activates NF-κB signaling. ALTO activates NF-κB by binding SQSTM1 and TRAF2&3 via twoN-TerminalActivatingRegions (NTAR1+2), resembling Epstein-Barr virus (EBV) Latent Membrane Protein 1 (LMP1).. Following activation, NF-κB dimers bind the MCPyV non-coding control region (NCCR) and downregulate early transcription. Beyond MCPyV, NTAR motifs are conserved in other polyomavirus ALTOs, which activate NF-κB signaling, but are lacking in MTs that do not. Furthermore, polyomavirus ALTOs downregulate their respective viral early transcription in an NF-κB and NTAR dependent manner. Our findings suggest that ALTOs evolved to suppress viral replication and promote viral latency and that MCPyV ALTO must be silenced for MCC to develop.
Skeletal muscle myosin heavy chain protein fragmentation as a potential marker of protein degradation in response to resistance training and disuse atrophy
Authors: Plotkin Daniel L. , Mattingly Madison L. , Anglin Derick A. , Michel J. Max , Godwin Joshua S. , McIntosh Mason C. , Bergamasco João G. A. , Scarpelli Maíra C. , Angleri Vitor , Taylor Lemuel W. , Willoughby Darryn S. , Mobley C. Brooks , Kavazis Andreas N. , Ugrinowitsch Carlos , Libardi Cleiton A. , Roberts Michael D.
Published: May 2024

We sought to examine how resistance exercise (RE), cycling exercise, and disuse atrophy affect myosin heavy chain (MyHC) protein fragmentation in humans. In the first study (1boutRE), younger adult men (n=8; 5±2 years of RE experience) performed a lower body RE bout with vastus lateralis (VL) biopsies obtained immediately before, 3-, and 6-hours post-exercise. In the second study (10weekRT), VL biopsies were obtained in untrained younger adults (n=36, 18 men and 18 women) before and 24 hours (24h) after their first/naïve RE bout. These participants also engaged in 10 weeks (24 sessions) of resistance training and donated VL biopsies before and 24h after their last RE bout. VL biopsies were also examined from a third acute cycling study (n=7) and a fourth study involving two weeks of leg immobilization (n=20, 15 men and 5 women) to determine how MyHC fragmentation was affected. In the 1boutRE study, the fragmentation of all MyHC isoforms (MyHCTotal) increased 3 hours post-RE (∼ +200%, p=0.018) and returned to pre-exercise levels by 6 hours post-RE. Immunoprecipitation of MyHCTotalrevealed ubiquitination levels remained unaffected at the 3- and 6-hour post-RE time points. Interestingly, a greater increase in magnitude for MyHC type IIa versus I isoform fragmentation occurred 3-hours post-RE (8.6±6.3-fold versus 2.1±0.7-fold, p=0.018). In all 10weekRT participants, the first/naïve and last RE bouts increased MyHCTotalfragmentation 24h post-RE (+65% and +36%, respectively; p<0.001); however, the last RE bout response was attenuated compared to the first bout (p=0.045). The first/naïve bout response was significantly elevated in females only (p<0.001), albeit females also demonstrated a last bout attenuation response (p=0.002). Although an acute cycling bout did not alter MyHCTotalfragmentation, ∼8% VL atrophy with two weeks of leg immobilization led to robust MyHCTotalfragmentation (+108%, p<0.001), and no sex-based differences were observed. In summary, RE and disuse atrophy increase MyHC protein fragmentation. A dampened response with 10 weeks of resistance training, and more refined responses in well-trained men, suggest this is an adaptive process. Given the null polyubiquitination IP findings, more research is needed to determine how MyHC fragments are processed. Moreover, further research is needed to determine how aging and disease-associated muscle atrophy affect these outcomes, and whether MyHC fragmentation is a viable surrogate for muscle protein turnover rates.
A hierarchy of processing complexity and timescales for natural sounds in human auditory cortex
Authors: Rupp Kyle M. , Hect Jasmine L. , Harford Emily E. , Holt Lori L. , Ghuman Avniel Singh , Abel Taylor J.
Published: May 2024

Efficient behavior is supported by humans’ ability to rapidly recognize acoustically distinct sounds as members of a common category. Within auditory cortex, there are critical unanswered questions regarding the organization and dynamics of sound categorization. Here, we performed intracerebral recordings in the context of epilepsy surgery as 20 patient-participants listened to natural sounds. We built encoding models to predict neural responses using features of these sounds extracted from different layers within a sound-categorization deep neural network (DNN). This approach yielded highly accurate models of neural responses throughout auditory cortex. The complexity of a cortical site’s representation (measured by the depth of the DNN layer that produced the best model) was closely related to its anatomical location, with shallow, middle, and deep layers of the DNN associated with core (primary auditory cortex), lateral belt, and parabelt regions, respectively. Smoothly varying gradients of representational complexity also existed within these regions, with complexity increasing along a posteromedial-to-anterolateral direction in core and lateral belt, and along posterior-to-anterior and dorsal-to-ventral dimensions in parabelt. When we estimated the time window over which each recording site integrates information, we found shorter integration windows in core relative to lateral belt and parabelt. Lastly, we found a relationship between the length of the integration window and the complexity of information processing within core (but not lateral belt or parabelt). These findings suggest hierarchies of timescales and processing complexity, and their interrelationship, represent a functional organizational principle of the auditory stream that underlies our perception of complex, abstract auditory information.
Single-cell transcriptomics reveal individual and synergistic effects of Trisomy 21 and GATA1s on hematopoiesis
Authors: Takasaki Kaoru , Wafula Eric K. , Kumar Sara S. , Smith David , Sit Ying Ting , Gagne Alyssa L. , French Deborah L. , Thom Christopher S. , Chou Stella T.
Published: May 2024

Trisomy 21 (T21), or Down syndrome (DS), is associated with baseline macrocytic erythrocytosis, thrombocytopenia, and neutrophilia, as well as transient abnormal myelopoiesis (TAM) and myeloid leukemia of DS (ML-DS). TAM and ML-DS blasts both arise from an aberrant megakaryocyte-erythroid progenitor and exclusively express GATA1s, the truncated isoform ofGATA1, while germlineGATA1smutations in a non-T21 context lead to congenital cytopenia(s) without a leukemic predisposition. This suggests that T21 and GATA1s both perturb hematopoiesis in multipotent progenitors, but studying their individual effects is challenging due to limited access to relevant human progenitor populations. To dissect individual developmental impacts, we used single-cell RNA-sequencing to interrogate hematopoietic progenitor cells (HPCs) from isogenic human induced pluripotent stem cells differing only by chromosome 21 and/orGATA1status. The transcriptomes of these HPCs revealed significant heterogeneity and lineage skew dictated by T21 and/or GATA1s. T21 and GATA1s each disrupted temporal regulation of lineage-specific transcriptional programs and specifically perturbed cell cycle genes. Trajectory inference revealed that GATA1s nearly eliminated erythropoiesis, slowed MK maturation, and promoted myelopoiesis in the euploid context, while in T21 cells, GATA1s competed with the enhanced erythropoiesis and impaired megakaryopoiesis driven by T21 to promote production of immature erythrocytes, MKs, and myeloid cells. The use of isogenic cells revealed distinct transcriptional programs that can be attributed specifically to T21 and GATA1s, and how they independently and synergistically result in HPC proliferation at the expense of maturation, consistent with a pro-leukemic phenotype.
SspA is a transcriptional regulator of CRISPR adaptation inE. coli
Authors: Lopez Santiago C. , Lee Yumie , Zhang Karen , Shipman Seth L.
Published: May 2024

The CRISPR integrases Cas1-Cas2 create immunological memories of viral infection by storing phage-derived DNA in CRISPR arrays, a process known as CRISPR adaptation. A number of host factors have been shown to influence adaptation, but the full pathway from infection to a fully integrated, phage-derived sequences in the array remains incomplete. Here, we deploy a new CRISPRi-based screen to identify putative host factors that participate in CRISPR adaptation in theE. coliType I-E system. Our screen uncovers a novel host factor, SspA, which transcriptionally regulates CRISPR adaptation. One target of SspA is H-NS, a known repressor of CRISPR interference proteins, but we find that the role of SspA on adaptation is not H-NS-dependent. We propose a new model of CRISPR-Cas defense that includes independent cellular control of adaptation and interference by SspA.
Effect of autonomous consumption of different sweet substances on the urinary proteome of mice
Authors: Wang Haitong , Gao Youhe
Published: May 2024

Objective

To explore the possible effects on the organism by analysing changes in the urinary proteome of mice after autonomous consumption of different sweet substances.

Methods

Urine samples were collected from C57BL/6l mice before and after active consumption of sweet substances. The sweet substances included sucrose, stevia glycosides, acesulfame, and sucralose, which are more widely used worldwide and can elicit a preference response in mice, and the concentrations of the non-nutritive sweeteners were chosen to be those that have been shown by existing studies to have the strongest preference response in mice. The analyses were performed by the non-labelled quantitative proteomics technique of high performance liquid chromatography tandem mass spectrometry (LC-MS/MS), and groups were screened for differential proteins in the urinary proteome for the analysis of protein functions and biological processes; comparisons of urinary proteomes before and after consumption of sweeteners by a single mouse were carried out; and side-by-side comparisons of different sweeteners were made.

Results and Conclusions

Urine proteome could reflect the changes in the organism of mice after voluntary consumption of sweeteners, and the effects of different sweeteners on the urine proteome were not the same. Among the four sweeteners, sucralose and sucrose induced the most similar changes in the organism, and steviol glycosides induced the furthest changes in the organism; the changes induced by sucrose, acesulfame, and sucralose were similar, and steviol glycosides induced changes different from those of the other sweeteners. Stevia glycosides induced changes that were different from the other sweeteners. The urinary proteomic proteins that differed among the four sweeteners consumed autonomously by mice included proteins that have been reported to be associated with brain reward circuits, whereas only the urinary proteomic proteins that differed among the four sweeteners consumed autonomously by mice were associated with metabolic processes in large quantities after the voluntary consumption of sucrose, acesulfame, and sucralose, and the urinary proteomic proteins that differed among the four sweeteners consumed autonomously by mice were associated with the assembly of nucleosomes, gene expression, and other processes after the voluntary consumption of stevia glycosides.
Syncytiotrophoblast extracellular vesicles contain functional kynurenine metabolising enzymes: potential implications for preeclampsia
Authors: Logenthiran Prassana , Awoyemi Toluwalase , Wilbourne Morganne , Yu Zhanru , Kessler Benedikt , Escudero Carlos , Zhang Wei , Cerdeira Sofia , Vatish Manu
Published: May 2024

Background

Placentae of women with preeclampsia (PE) exhibit reduced levels of kynurenine (Kyn), a biological compound derived from tryptophan metabolism with antioxidant, vasorelaxant, and hypotensive properties. Little is known regarding functional levels of the Kyn metabolizing enzymes (KYNME) in women with preeclampsia. Since high circulating levels of syncytiotrophoblast extracellular vesicles (STB-EVs) have been associated with preeclampsia onset, we aimed to study whether Kyn reduction in preeclampsia may be attributed to increased degradation by KYNME present in STB-EVs.

Methods

We conducted a study that included women with normal (n=9) and early-onset preeclamptic (EOPE) pregnancies (n=9). From them, STB-EVs were isolated by dual-lobe placental perfusions from normal (n=3) and EOPE (n=3). KYNME were identified using placental immunohistochemistry and western blot in placental and STB-EV extractions. Serum Kyn levels were measured using gas chromatography mass spectrometry.

Results

Cargo of STB-EVs consist of functional KYNME, which break down Kyn in a dose and time-dependent manner. No significant differences in the content of Kyn metabolizing enzymes were found in STB-EVs between normal and EOPE pregnancies. However, decreased serum levels of Kyn were found in women with EOPE relative to normal pregnancies.

Conclusion

STB-EVs carry functional KYNME and may regulate the levels of circulating Kyn during normal pregnancy and preeclampsia. Due to the dose effect of increased STB-EVs in EOPE, the functional KYNME content of said vesicles may contribute to reduced levels of Kyn. This finding opens a new avenue for investigating the potential benefits of KYNME inhibitors in conjunction with kynurenine replacement for managing preeclampsia.
Nanobodies against the myelin enzyme CNPase as tools for structural and functional studies
Authors: Markusson Sigurbjörn , Raasakka Arne , Schröder Marcel , Sograte-Idrissi Shama , Rahimi Amir Mohammad , Asadpour Ommolbanin , Körner Henrike , Lodygin Dmitri , Eichel-Vogel Maria A. , Chowdhury Risha , Sutinen Aleksi , Muruganandam Gopinath , Iyer Manasi , Cooper Madeline H. , Weigel Maya K. , Ambiel Nicholas , Werner Hauke B. , Zuchero J. Bradley , Opazo Felipe , Kursula Petri
Published: May 2024

2’,3’-cyclic nucleotide 3’-phosphodiesterase (CNPase) is an abundant constituent of central nervous system non-compact myelin, frequently used as a marker antigen for myelinating cells. The catalytic activity of CNPase, the 3’-hydrolysis of 2’,3’-cyclic nucleotides, is well characterisedin vitro, but thein vivofunction of CNPase remains unclear. CNPase interacts with the actin cytoskeleton to counteract the developmental closure of cytoplasmic channels that travel through compact myelin; its enzymatic activity may be involved in adenosine metabolism and RNA degradation. We developed a set of high-affinity nanobodies recognizing the phosphodiesterase domain of CNPase, and the crystal structures of each complex show that the five nanobodies have distinct epitopes. One of the nanobodies bound deep into the CNPase active site and acted as an inhibitor. Moreover, the nanobodies were characterised in imaging applications and as intrabodies, expressed in mammalian cells, such as primary oligodendrocytes. Fluorescently labelled nanobodies functioned in imaging of teased nerve fibers and whole brain tissue sections, as well as super-resolution microscopy. These anti-CNPase nanobodies provide new tools for structural and functional biology of myelination, including high-resolution imaging of nerve tissue.
Zika virus infection in a cell culture model reflects the transcriptomic signatures in patients
Authors: Berglund Gillian , Lennon Claudia D. , Badu Pheonah , Berglund J. Andrew , Pager Cara T.
Published: May 2024

Zika virus (ZIKV), a re-emerging flavivirus, is associated with devasting developmental and neurological disease outcomes particularly in infants infectedin utero. Towards understanding the molecular underpinnings of the unique ZIKV disease pathologies, numerous transcriptome-wide studies have been undertaken. Notably, these studies have overlooked the assimilation of RNA-seq analysis from ZIKV-infected patients with cell culture model systems. In this study we find that ZIKV-infection of human lung adenocarcinoma A549 cells, mirrored both the transcriptional and alternative splicing profiles from previously published RNA-seq data of peripheral blood mononuclear cells collected from pediatric patients during early acute, late acute, and convalescent phases of ZIKV infection. Our analyses show that ZIKV infection in cultured cells correlates with transcriptional changes in patients, while the overlap in alternative splicing profiles was not as extensive. Overall, our data indicate that cell culture model systems support dissection of select molecular changes detected in patients and establishes the groundwork for future studies elucidating the biological implications of alternative splicing during ZIKV infection.
Post-transcriptional regulation of insulin mRNA storage by G3BP1/2+condensates in beta cells
Authors: Quezada Esteban , Vasiljevic Jovana , Pal Akshaye , Münster Carla , Friedland Daniela , Schöniger Eyke , Sönmez Anke , Seiler Annika , Roch Pascal , Wegbrod Carolin , Ganß Katharina , Knoch Klaus-Peter , Kipke Nicole , Alberti Simon , Nano Rita , Piemonti Lorenzo , Aust Daniela , Weitz Jürgen , Distler Marius , Solimena Michele
Published: May 2024

Hyperglycemia upregulates insulin translation in pancreatic beta cells. Several RNA- binding proteins involved in this process have been identified, including G3BP1, a stress granule marker downregulated in islets of subjects with type 2 diabetes. We show that in mouse insulinoma MIN6-K8 cells exposed to fasting glucose levels G3BP1 and its paralog G3BP2 colocalize to cytosolic condensates with eIF3b andIns1/2mRNA. Upon glucose stimulation, the condensates dissolve and G3BP1/2, eIF3b, and insulin mRNAs redistribute throughout the cytosol. Intriguingly, G3BP1+condensates in MIN6-K8 cells differ from sodium arsenate-induced stress granules in regards to eIF2α and AMPKα phosphorylation. Knockout ofG3BP1orG3BP2prevented condensate assembly, but onlyG3BP1deletion decreased the levels ofIns1/2mRNA and proinsulin and impaired polysome formation. Like glucose, other insulin secretagogues such as Exendin-4 and palmitate, but not high KCl, prompted the dissolution of G3BP1+condensates. G3BP1+/InsmRNA+condensates were also present in mouse and human beta cells from normoglycemic donors. Hence, G3BP1+condensates represent a glucose-regulated compartment for the physiological storage and protection of insulin mRNA in resting beta cells.
The intestinal microbiome and Cetobacterium somerae inhibit viral infection through TLR2-type I IFN signaling axis in zebrafish
Authors: Liang Hui , Li Ming , Chen Jie , Zhou Wenhao , Xia Dongmei , Ding Qianwen , Yang Yalin , Zhang Zhen , Ran Chao , Zhou Zhigang
Published: May 2024

Accumulated evidences demonstrate that intestinal microbiome can inhibit viral infection. However, our knowledge of the signaling pathways and specific commensal microbes that mediate the antiviral response is limited. Here, a rhabdoviral infection model in zebrafish allows us to investigate the modes of action of microbiome-mediated antiviral effect. We observed that antibiotics-treated and germ-free zebrafish exhibited greater viral infection. Mechanistically, depletion of the intestinal microbiome alters TLR2-Myd88 signaling, and blunts neutrophil response and type I interferon (IFN) production. Moreover, a single commensal bacterium, Cetobacterium somerae, recapitulated TLR2- and type I IFN-dependent antiviral effect of the microbiome in gnotobiotic zebrafish, and C. somerae exopolysaccharides (CsEPS) was the effector molecule that engaged TLR2 to mediate antiviral function. Together, our results suggest a conserved role of intestinal microbiome in regulating type I IFN response among vertebrates, and reveal that the intestinal microbiome inhibits viral infection through a CsEPS-TLR2-type I IFN signaling axis in zebrafish.
Loss of AATF ameliorates metabolic dysfunction-associated steatohepatitis by suppressing the AKT-mTORC1 signaling pathway
Authors: Srinivas Akshatha N. , Suresh Diwakar , Anirvan Prajna , Moorthy Manju , Ramaswamy Gopalkrishna , Nataraj Suma M. , Santhekadur Prasanna Kumar , Suvarna Deepak , Singh Shivaram P. , Kumar Divya P.
Published: May 2024

Metabolic dysfunction-associated steatohepatitis (MASH) is a complex and multifaceted condition affecting over 30% of the world’s population. It is influenced by a range of molecular factors, making the identification of key disease drivers crucial for the development of targeted therapeutic strategies for MASH. Here, we demonstrate the impact of the loss of apoptosis antagonizing transcription factor (AATF) on MASH, uncovering detailed mechanisms through transcriptome and metabolome analysis. AAV8-mediated specific knockdown of AATF in hepatocytes significantly reduced body weight, liver weight, and insulin resistance in mice fed with western diet (WD). However, no such effects were observed in mice fed with chow diet (CD). Further analyses showed reduced liver injury, steatosis, and steatohepatitis in WDsiAATF mice. Transcriptomic analysis demonstrated that loss of AATF alleviated cellular stress, inflammation, and fibrosis in WD-fed mice. Moreover, AATF silencing led to alterations in lipid metabolism, notably by decreasing hepatic lipogenesis in the WD mice. Interestingly, untargeted metabolomics revealed increased biosynthesis of glycerophospholipids and beta-oxidation of fatty acids in WDsiAATF mice. Our findings reveal the molecular link between AATF and hepatic lipid metabolism, mediated by modulation of the AKT-mTORC1 signaling pathway. Based on these findings, targeting AATF may offer a promising therapeutic avenue for treating MASH.
Molecular mechanism of the flotillin complex in membrane microdomain organization
Authors: Lu Ming-Ao , Qian Yunwen , Ma Liangwen , Guo Qiang , Gao Ning
Published: May 2024

Flotillin-1 and flotillin-2, initially identified as markers of lipid rafts, assemble together as hetero-oligomers and facilitate the organization of flotillin membrane microdomains, which play a crucial role in various cellular processes, such as endocytosis, protein sorting, and vesicle trafficking. However, the molecular mechanisms underlying flotillin oligomerization and flotillin microdomain organization remain incompletely understood.

Here we present the cryo-electron microscopy structure of the human flotillin complex, at an overall resolution of 3.57 Å. It demonstrates that flotillin-1 and-2 are alternately arranged to form a 44-mer ring structure. This dome-shaped complex is hollow and sealed, attaching to the cytoplasmic leaflet of the plasma membrane and encompassing a circular domain with a diameter of approximately 30 nm. These structural features demonstrate a direct role for the flotillin complex in segregating the membrane to organize an isolated microdomain and also suggests a potential regulatory role in sequestering its interacting proteins. The cryo-electron tomography study further demonstrates the structural plasticity of the flotillin complexes in situ, indicative of dynamic conformational changes during their functional activities. In addition, aggregations of the flotillin complexes on the plasma membrane or intracellular vesicles, are frequently observed. Our data suggest that the flotillin complex constitutes the basic structural unit of membrane microdomains, and the further clustering of flotillin complexes might facilitate the formation of larger and more elaborate membrane microdomains.

These findings enhance our understanding of the architecture of the SPFH family proteins and their common role in membrane microdomain organization, and more importantly, provide models for explaining the diverse functions of flotillin proteins in different biological processes.
Co-dependent formation of theToxoplasma gondiisub-pellicular microtubules and inner membrane skeleton
Authors: Engelberg Klemens , Bauwens Ciara , Ferguson David J. P. , Gubbels Marc-Jan
Published: May 2024

One of the defining features of apicomplexan parasites is their cytoskeleton composed of alveolar vesicles, known as the inner membrane complex (IMC) undergirded by intermediate-like filament network and an array of subpellicular microtubules (SPMTs). InToxoplasma gondii, this specialized cytoskeleton is involved in all aspects of the disease-causing lytic cycle, and notably acting as a scaffold for parasite offspring in the internal budding process. Despite advances in our understanding of the architecture and molecular composition, insights pertaining to the coordinated assembly of the scaffold are still largely elusive. Here,T. gondiitachyzoites were dissected by advanced, iterative expansion microscopy (pan-ExM) revealing new insights into the very early sequential formation steps of the tubulin scaffold. A comparative study of the related parasiteSarcocystis neuronarevealed that different MT bundling organizations of the nascent SPMTs correlate with the number of central and basal alveolar vesicles.

In absence of a so far identified MT nucleation mechanism, we genetically dissectedT. gondiiγ-tubulin and γ-tubulin complex protein 4 (GCP4). While γ-tubulin depletion abolished the formation of the tubulin scaffold, a set of MTs still formed that suggests SPMTs are nucleated at the outer core of the centrosome. Depletion of GCP4 interfered with the correct assembly of SPMTs into the forming daughter buds, further indicating that the parasite utilizes the γ-tubulin complex in tubulin scaffold formation.
The meaning of the home in the realm of Korean everyday life
Authors: Lee Keunhye
Published: May 2024

Purpose

This paper investigates the relationship between home spaces and social practice to explore how social practice informs the spatial typologies of the Korean home in the realm of everyday life. It identifies everyday activities socially embedded within the culture that contribute to a phenomenological understanding of the Korean home.

Design/methodology/approach

This paper incorporates a literature review of the conceptualisation of the traditional Korean home, as well as theoretical research concerning the spatial usage of the Korean home. This paper investigates (1) architectural and social aspects of traditional Korean homes, (2) social practice in the ondol, maru and madang as living spaces, and (3) the meaning of Korean home through analysis of spatial usages.

Findings

The analysis of the relationship between everyday activity and the home suggests that the Korean home is marked by (1) flexibility (changing the role and characteristics of individual components), (2) spatial extension (combining different areas), and (3) a blurred boundary between indoors and outdoors.

Originality/value

This paper considers the social and cultural aspects of the Korean home rather than its physical and architectural components; it demonstrates that the home as an everyday space holds both social and sacredness in a manner that is responsive to Korean cultural and social identity. Therefore, this paper will contribute to an understanding and provide knowledge of particular cultural types of the Korean home.
Establishment of a smart building assessment framework in the context of smart cities
Authors: Domingos Leonor , Sousa Maria José , Resende Ricardo , Pizarro Miranda Bernardo , Rego Susana , Ferreira Rúben
Published: May 2024

Purpose

This study proposes an assessment framework for improving smart building performance in the broader context of smart city development, considering dimensions like environmental sustainability, building characteristics, intelligence, computation management and analytics. The framework is crafted to guide future research, aligning with the growing emphasis on sustainability and intelligence in evolving urban landscapes within smart cities.

Design/methodology/approach

In the initial phase, the concepts of “Smart City” and “Smart Buildings” are analyzed through a systematic literature review, considering the impact of governance on city sustainability and growth, along with the role of public policies in transforming buildings and cities. The empirical research evaluates innovation levels in small and medium-sized European cities, proposing a new framework with validated dimensions and sub-dimensions. This validation involves input from international experts through a Focus Group.

Findings

The key research findings validate the new proposed assessment framework for smart buildings within smart city development. The experts’ insights align with and support the dimensions identified in the bibliographic research, providing a comprehensive understanding of the role of smart buildings in sustainable urban development.

Originality/value

This framework not only provides insights for a new model with specific dimensions and sub-dimensions but also serves as a guide for formulating strategies and policies to enhance innovation in these settings. The value of this approach is strengthened by the validation and consolidation process involving international experts in the field.
Disasters and gender in Japanese anime films: Makoto Shinkai’sYour NameandWeathering with You
Authors: Li Zhizi
Published: May 2024

Purpose

This article focuses on the representations of natural hazards, disasters, gender roles and norms in Makoto Shinkai’s disaster-themed anime filmsYour Name(2016) andWeathering with You(2019).

Design/methodology/approach

This article commences with a literature review on disasters, disaster films, gender in disasters and gender in disaster films; then, this article thoroughly investigates the portrayal of disasters and gender in the two films, drawing data from their narratives and plots.

Findings

This article finds that the two films’ depictions of disasters and gender adhere to the traditional patterns observed in Hollywood and Japanese disaster films. The natural hazards and disasters in the two films reflect real-world disasters that occurred in Japan’s recent decades, especially the 3.11 Tohoku earthquake in 2011. Traditional gender figures and prevalent heterosexual expectations in Japanese culture and society deeply influence the two films’ portrayal of gender roles and norms.

Originality/value

Numerous academic works explored Hollywood disaster films, their representations of gender roles and norms in disaster themes. However, few focus on recent Japanese anime films such asYour NameandWeathering with You. This article aims to fill this gap.
Reasonable adjustment for inclusive development: a cautionary case study of Australian VET teachers’ experience
Authors: Nakar Sonal , Bagnall Richard G.
Published: May 2024

Purpose

Vocational education and training (VET) in Australia has for some time been driven by an agenda of “reasonable adjustment”, in which practices are modified to ensure equitable access and participation by disadvantaged students. However, the growing marketization of VET has instead encouraged the use of more flexible approaches to attract and retain students from diverse backgrounds. They have thus paralleled and confounded reasonable adjustment practices for inclusive development. This study sought to identify the moral dilemmas experienced by VET teachers arising from implementing reasonable adjustment practices.

Design/methodology/approach

This phenomenological research project used in-depth conversational interviews with 19 experienced VET teachers from a diversity of teaching fields to identify moral dilemmas experienced as arising from changes in their workplace contexts.

Findings

One of the identified dilemmas was responding flexibly to heightened student diversity, to which study participants largely responded by prioritising the economic imperative over social inclusion. Well-intended actions thus led to unintentionally damaging outcomes, raising important ethical questions about the relative value of economic and social development outcomes and the role of reasonable adjustment in their attainment. The study also highlights the lack of appropriate VET teacher training in managing ethical conflicts to minimise risks to themselves and their employing organizations.

Originality/value

As a case study of inclusive development policies in practice, this research may be seen as a cautionary tale for inclusive development policies in other countries with similarly strong VET economic and socially inclusive development policies for sustainability. The paper thus opens a dialogue for critical reflection on the current problems in a reasonable development approach in the field of comparative and international education. Those two parallel agendas have presented VET teachers and trainers with ethically challenging situations in which the economic and social development imperatives are experienced as being conflict with each other.
Explanatory and predictive analysis of smartphone security using protection motivation theory: a hybrid SEM-AI approach
Authors: Khan Naurin Farooq , Murtaza Hajra , Malik Komal , Mahmood Muzammil , Asadi Muhammad Aslam
Published: May 2024

Purpose

This research aims to understand the smartphone security behavior using protection motivation theory (PMT) and tests the current PMT model employing statistical and predictive analysis using machine learning (ML) algorithms.

Design/methodology/approach

This study employs a total of 241 questionnaire-based responses in a nonmandated security setting and uses multimethod approach. The research model includes both security intention and behavior making use of a valid smartphone security behavior scale. Structural equation modeling (SEM) – explanatory analysis was used in understanding the relationships. ML algorithms were employed to predict the accuracy of the PMT model in an experimental evaluation.

Findings

The results revealed that the threat-appraisal element of the PMT did not have any influence on the intention to secure smartphone while the response efficacy had a role in explaining the smartphone security intention and behavior. The ML predictive analysis showed that the protection motivation elements were able to predict smartphone security intention and behavior with an accuracy of 73%.

Research limitations/implications

The findings imply that the response efficacy of the individuals be improved by cybersecurity training programs in order to enhance the protection motivation. Researchers can test other PMT models, including fear appeals to improve the predictive accuracy.

Originality/value

This study is the first study that makes use of theory-driven SEM analysis and data-driven ML analysis to bridge the gap between smartphone security’s theory and practice.
Self-managing peer team as a facilitator of online teaching
Authors: Kantanen Helena , Kasanen Kati , Kohonen Susanna , Paajanen Vesa , Pirttilä Sanni , Siitonen Piia
Published: May 2024

Purpose

This qualitative study assesses the enablers of the work of a novel, self-managing digital pedagogy peer support team in a Finnish higher education institution.

Design/methodology/approach

This study employs a qualitative methodology with in-depth interviews of five digital pedagogy facilitators. The data collected are analyzed with the ATLAS.ti software. The analytical approach follows a deductive method, applying the categories derived from Magpili and Pazos (2018) who investigated the input variables of self-managing teams through their extensive literature review.

Findings

The primary findings underscore the suitability of Magpili and Pazos' variables for evaluating the performance enablers of self-managing teams. Furthermore, the findings emphasize the significance of leadership and effective communication as essential prerequisites for achieving elevated performance levels.

Research limitations/implications

This study focuses on the enablers of team performance from the perspective of the team members. To enhance comprehensiveness, subsequent phases should incorporate viewpoints from clients, namely peer instructors, and focus on the mediator and outcome aspects of the team effectiveness framework.

Practical implications

This study offers actionable recommendations for higher education institutions aiming to adopt a peer mentor model akin to the one delineated in the study.

Originality/value

This study analyzes a collaborative approach to advancing digital pedagogy within higher education institutions and discusses the enablers for successful performance within self-managing teams.
Website posts and the voice of frontline healthcare workers: a thematic analysis
Authors: Semyonov-Tal Keren
Published: May 2024

Purpose

With the soaring rise in popularity of social media platforms in recent decades, the use of website posts for the expression of work-related views has also increased. Despite websites being extensively used, there has been no examination of the views and concerns expressed by frontline workers through website posts. The present research aims to contribute to the “voice literature” first by evaluating how frontline workers utilize anonymous media platforms to express their views and work-related concerns and, second, by demonstrating how anonymous voice systems can encourage frontline health workers in providing feedback and dissatisfaction.

Design/methodology/approach

The study utilizes the thematic analysis method to analyze the content of posts by psychologists on a collaborative consultation website administrated by Israel’s Ministry of Health, discussing their perceptions of work-related concerns.

Findings

The analysis identified three work-related themes through the employees' voices. These include insufficient support from management, conflicts and excessive occupational demands. The workers expressed their apprehension with regard to organizational pressures, deficient budget allocations, excessive workloads, lack of recognition and work–life imbalances.

Originality/value

The application of thematic analysis method to anonymous open-public data should be viewed as an effective, affordable, genuine and unique research method for data analysis. Anonymous platforms can generate unique insights that may not be possible through traditional means. This can provide practitioners with a comprehensive understanding of various issues and challenges and be a useful tool for identifying shortcomings within health settings.