bluuebunny/crossref_metadata_2025 huggingface dataset:
Pathological C-terminal phosphomimetic substitutions alter the mechanism of liquid-liquid phase separation of TDP-43 low complexity domain
Authors: Haider Raza , Shipley Brandon , Surewicz Krystyna , Hinczewski Michael , Surewicz Witold K
Published: March 2024

C-terminally phosphorylated TAR DNA-binding protein of 43 kDa (TDP-43) marks the proteinaceous inclusions that characterize a number of age-related neurodegenerative diseases, including amyotrophic lateral sclerosis, frontotemporal lobar degeneration and Alzheimer’s disease. TDP-43 phosphorylation at S403/S404, and especially at S409/S410, is in fact accepted as a biomarker of proteinopathy. These residues are located within the low complexity domain (LCD), which also drives the protein’s liquid-liquid phase separation (LLPS). The impact of phosphorylation at these LCD sites on phase separation of the protein is a topic of great interest, as these post-translational modifications and LLPS are both implicated in proteinopathies. Here, we employed a combination of experimental and simulation-based approaches to explore this question on a phosphomimetic model of the TDP-43 LCD. Our turbidity and fluorescence microscopy data show that Ser-to-Asp substitutions at residues S403, S404, S409 and S410 alter the LLPS behavior of TDP-43 LCD. In particular, in contrast to the unmodified protein, the phosphomimetic variants display a biphasic dependence on salt concentration. Through coarse-grained modeling, we find that this biphasic salt dependence is derived from an altered mechanism of phase separation, in which LLPS-driving short-range intermolecular hydrophobic interactions are modulated by long-range attractive electrostatic interactions. Overall, thisin vitroandin silicostudy provides a physiochemical foundation for understanding the impact of pathologically-relevant C-terminal phosphorylation on the LLPS of the TDP-43 in a more complex cellular environment.

Statement of Significance

Proteinaceous inclusions composed of phosphorylated, C-terminal TDP-43 fragments have long been recognized as hallmarks of several neurodegenerative diseases, in particular amyotrophic lateral sclerosis and frontotemporal dementia. A rapidly growing number of studies indicate that these proteinopathies may be closely related to liquid-liquid phased separation (LLPS) of TDP-43, but the impact of phosphorylation on TDP-43 LLPS remains largely unexplored. In this study we used a combination of experimental methods and coarse-grained simulations to ascertain, in mechanistic terms, how phosphorylation at pathologically-critical C-terminal sites impacts liquid-liquid phase separation of the low complexity domain of TDP-43. Our results broaden our understanding of the mechanisms driving pathogenic process in these neurodegenerative diseases.
One signal activated TIL enables potent anti-tumor activity across solid tumor types
Authors: Wu Yongqiang , Ye Xueshuai , Zhu Yufeng , Liu Shengchao , Yuan Qichen , Kong Dejing , Zhao Lianmei
Published: March 2024

Adoptive T cell therapy (ACT) with autologous tumor-infiltrating lymphocytes (TIL) has shown compelling anti-tumor activity across various solid tumors. The function and status of TIL significantly influence its anti-tumor potential. In this study, we present the development of One-Signal-Activated TIL (OSAT), highlighting its robust anti-tumor activity in various syngeneic tumor models. We designed 10 unique signals by integrating CD3Zwith a secondary signaling molecule. From these, we identified a specific signal, denoted as OSAT, which efficiently induces T cell activation when paired with a sole CD3 antibody. Subsequently, we benchmarked delivery approaches for OSAT, through genome editing, lentivirus integration, and plasmid electroporation. We found that electroporation yielded the most potent expression effect among these methods. Further, we demonstrated that OSAT exhibited robust antitumor activity bothin vitroandin vivoacross diverse solid tumors. Finally, we synergized OSAT with PD-1 blockade therapy to achieve a highly effective and enduring anti-tumor impact in cancer immunotherapy, facilitating sustained enhancement of anti-tumor activity.
Enhancing tonic arousal improves voluntary but not involuntary attention in humans
Authors: Grandjean Aurélie , Mathieu Anne , Chen Sophie , Widmann Andreas , Wetzel Nicole , Bidet-Caulet Aurélie
Published: March 2024

Arousal and attention are pivotal brain functions for optimizing performance. Kahneman’s attention model (1973) theorizes a key interplay between attention and arousal, yet this relationship remains poorly understood. We investigated this interaction in 16 healthy young adults performing an auditory attention task that simultaneously assessed phasic arousal, voluntary attention and involuntary attention. Tonic arousal was modulated by low or high arousing music, as measured using skin conductance, pupil size, and heart rate. Pupil dilation responses to distracting sounds highlight an intricate interplay between tonic and phasic arousal. Importantly, increasing tonic arousal does not influence involuntary attention, whereas it does improve voluntary attention, as shown by shorter and less variable reaction times and larger electroencephalographic brain responses to task-relevant targets. This study provides experimental evidence in humans that tonic arousal can influence the attentional balance by improving voluntary attention in a transient and sustained manner, rather than by impacting involuntary attention.
Feedback and Feedforward Regulation of Interneuronal Communication
Authors: Gambrell Oliver , Vahdat Zahra , Singh Abhyudai
Published: March 2024

We formulate a mechanistic model capturing the dynamics of neurotransmitter release in a chemical synapse. The proposed modeling framework captures key aspects such as the random arrival of action potentials (AP) in the presynaptic (input) neuron, probabilistic docking and release of neurotransmitter-filled vesicles, and clearance of the released neurotransmitter from the synaptic cleft. Feedback regulation is implemented by having the released neurotransmitter impact the vesicle docking rate that occurs biologically through “autoreceptors” on the presynaptic membrane. Our analytical results show that these feedbacks can amplify or buffer fluctuations in neurotransmitter levels depending on the relative interplay of neurotransmitter clearance rate with the AP arrival rate and the vesicle replenishment rate, with faster clearance rates leading to noise amplification. We next consider a postsynaptic (output) neuron that fires an AP based on integrating upstream neurotransmitter activity. Investigating the postsynaptic AP firing times, we identify scenarios that lead to band-pass filtering, i.e., the output neuron frequency is maximized at intermediate input neuron frequencies. We extend these results to consider feedforward regulation where in addition to a direct excitatory synapse, the input neuron also impacts the output indirectly via an inhibitory interneuron, and we identify parameter regimes where feedforward neuronal networks result in band-pass filtering.
Single-cell epigenomic dysregulation of Systemic Sclerosis fibroblasts via CREB1/EGR1 axis in self-assembled human skin equivalents
Authors: Abel Tamar R. , Kosarek Noelle N. , Parvizi Rezvan , Jarnagin Helen , Torres Gretel M. , Bhandari Rajan , Huang Mengqi , Toledo Diana M. , Smith Avi , Popovich Dillon , Mariani Michael P. , Yang Heetaek , Wood Tammara , Garlick Jonathan , Pioli Patricia A. , Whitfield Michael L.
Published: March 2024

Systemic sclerosis (SSc) is an autoimmune disease characterized by skin fibrosis, internal organ involvement and vascular dropout. We previously developed and phenotypically characterized anin vitro3D skin-like tissue model of SSc, and now analyze the transcriptomic (scRNA-seq) and epigenetic (scATAC-seq) characteristics of this model at single-cell resolution. SSc 3D skin-like tissues were fabricated using autologous fibroblasts, macrophages, and plasma from SSc patients or healthy control (HC) donors. SSc tissues displayed increased dermal thickness and contractility, as well as increased α-SMA staining. Single-cell transcriptomic and epigenomic analyses identified keratinocytes, macrophages, and five populations of fibroblasts (labeled FB1 – 5). Notably, FB1 APOE-expressing fibroblasts were 12-fold enriched in SSc tissues and were characterized by high EGR1 motif accessibility. Pseudotime analysis suggests that FB1 fibroblasts differentiate from a TGF-β1-responsive fibroblast population and ligand-receptor analysis indicates that the FB1 fibroblasts are active in macrophage crosstalk via soluble ligands including FGF2 and APP. These findings provide characterization of the 3D skin-like model at single cell resolution and establish that it recapitulates subsets of fibroblasts and macrophage phenotypes observed in skin biopsies.
Thermal tolerance of mosquito eggs is associated with urban adaptation and human interactions
Authors: Chakraborty Souvik , Zigmond Emily , Shah Sher , Sylla Massamba , Akorli Jewelna , Otoo Sampson , Rose Noah H. , McBride Carolyn S. , Armbruster Peter A. , Benoit Joshua B.
Published: March 2024

Climate change is expected to profoundly affect mosquito distributions and their ability to serve as vectors for disease, specifically with the anticipated increase in heat waves. The rising temperature and frequent heat waves can accelerate mosquito life cycles, facilitating higher disease transmission. Conversely, higher temperatures could increase mosquito mortality as a negative consequence. Warmer temperatures are associated with increased human density, suggesting a need for anthropophilic mosquitoes to adapt to be more hardy to heat stress. Mosquito eggs provide an opportunity to study the biological impact of climate warming as this stage is stationary and must tolerate temperatures at the site of female oviposition. As such, egg thermotolerance is critical for survival in a specific habitat. In nature,Aedesmosquitoes exhibit different behavioral phenotypes, where specific populations prefer depositing eggs in tree holes and prefer feeding non-human vertebrates. In contrast, others, particularly human-biting specialists, favor laying eggs in artificial containers near human dwellings. This study examined the thermotolerance of eggs, along with adult stages, forAedes aegyptiandAe. albopictuslineages associated with known ancestry and shifts in their relationship with humans. Mosquitoes collected from areas with higher human population density, displaying increased human preference, and having a human-associated ancestry profile have increased egg viability following high-temperature stress. Unlike eggs, thermal tolerance among adults showed no significant correlation based on the area of collection or human-associated ancestry. This study highlights that the egg stage is likely critical to mosquito survival when associated with humans and needs to be accounted when predicting future mosquito distribution.
3D live imaging and phenotyping of the subcellular cytotoxicity in cancer immunotherapy using event-triggered Bessel oblique plane microscopy
Authors: Wang Zhaofei , Wang Jie , Zhao Yuxuan , Jin Jin , Si Wentian , Chen Longbiao , Zhang Man , Zhou Yao , Mao Shiqi , Zhang Yicheng , Zheng Chunhong , Chen Liting , Fei Peng
Published: March 2024

Clarification of the cytotoxic function of T cells is crucial for understanding human immune responses and immunotherapy procedures. Here, we report an event-triggered Bessel oblique plane microscopy (EBOPM) platform capable of smart 3D live imaging and phenotyping of chimeric antigen receptor (CAR)-modified T-cell cytotoxicity in cancer immunotherapy; the EBOPM platform has the following characteristics: an isotropic subcellular resolution of 320 nm, large-scale scouting over 400 interacting cell pairs, long-term observation across 5 hours, and quantitative analysis of the Terabyte-scale 3D, multichannel, time-lapse image datasets. Using this advanced microscopy platform, several key subcellular events in CAR-T cells were captured and comprehensively analyzed; these events included the instantaneous formation of immune synapses and the sustained changes in the microtubing morphology. Furthermore, we identified the actin retrograde flow speed, the actin depletion coefficient, the microtubule polarization and the contact area of the CAR-T/target cell conjugates as essential parameters strongly correlated with CAR-T-cell cytotoxic function. Our approach will be useful for establishing criteria for quantifying T-cell function in individual patients for all T-cell-based immunotherapies.
Cause and effect in the natural selection of the population ecological life histories of mammals
Authors: Witting Lars
Published: March 2024

The inter-specific life history and ecological variation of mammals is often explained as allometric consequences of physiological adaptations to unexplained body mass variation. But these hypotheses are unnecessary because the allometric scaling is explained already by the natural selection that explains the variation in mass. I decompose the population ecological life histories of 4,936 species of mammals to show how the selection of mass accounts for the life history and population ecological variation in mammals. This shows that 55% of the within order variance, and 91% of the between order differences, in the body mass, demography, and population ecological traits are reconciled by the response of population dynamic feedback selection to variation in net energy, mortality, and intra-specific interactive competition.
Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca
Authors: Weine Eric , Carbonetto Peter , Stephens Matthew
Published: March 2024

Motivated by theoretical and practical issues that arise when applying Principal Components Analysis (PCA) to count data, Townes et al introduced “Poisson GLM-PCA”, a variation of PCA adapted to count data, as a tool for dimensionality reduction of single-cell RNA sequencing (RNA-seq) data. However, fitting GLM-PCA is computationally challenging. Here we study this problem, and show that a simple algorithm, which we call “Alternating Poisson Regression” (APR), produces better quality fits, and in less time, than existing algorithms. APR is also memory-efficient, and lends itself to parallel implementation on multi-core processors, both of which are helpful for handling large single-cell RNA-seq data sets. We illustrate the benefits of this approach in two published single-cell RNA-seq data sets. The new algorithms are implemented in an R package, fastglmpca.

Availability and implementation

The fastglmpca R package is released on CRAN for Windows, macOS and Linux, and the source code is available at github.com/stephenslab/fastglmpca under the open source GPL-3 license. Scripts to reproduce the results in this paper are also available in the GitHub repository.

Contact

mstephens@uchicago.edu

Supplementary information

Supplementary data are available onBioRxivonline.
An Innovative Mitochondrial-targeted Gene Therapy for Cancer Treatment
Authors: Chen Kai , Ernst Patrick , Kim Seulhee , Si Yingnan , Varadkar Tanvi , Ringel Matthew D. , Liu Xiaoguang “Margaret” , Zhou Lufang
Published: March 2024

Targeting cancer cell mitochondria holds great therapeutic promise, yet current strategies to specifically and effectively destroy cancer mitochondriain vivoare limited. Here, we introduce mLumiOpto, an innovative mitochondrial-targeted luminoptogenetics gene therapy designed to directly disrupt the inner mitochondrial membrane (IMM) potential and induce cancer cell death. We synthesize a blue light-gated channelrhodopsin (CoChR) in the IMM and co-express a blue bioluminescence-emitting Nanoluciferase (NLuc) in the cytosol of the same cells. The mLumiOpto genes are selectively delivered to cancer cellsin vivoby using adeno-associated virus (AAV) carrying a cancer-specific promoter or cancer-targeted monoclonal antibody-tagged exosome-associated AAV. Induction with NLuc luciferin elicits robust endogenous bioluminescence, which activates mitochondrial CoChR, triggering cancer cell IMM permeability disruption, mitochondrial damage, and subsequent cell death. Importantly, mLumiOpto demonstrates remarkable efficacy in reducing tumor burden and killing tumor cells in glioblastoma or triple-negative breast cancer xenografted mouse models. These findings establish mLumiOpto as a novel and promising therapeutic strategy by targeting cancer cell mitochondriain vivo.
Self-quenched fluorophore-DNA labels for super-resolution fluorescence microscopy
Authors: Kessler Laurell , Balakrishnan Ashwin , Menche Tanja , Wang Dongni , Li Yunqing , Mantel Maximilian , Glogger Marius , Dietz Marina S. , Heilemann Mike
Published: March 2024

Protein labeling through transient and repetitive hybridization of short, fluorophore-labeled DNA oligonucleotides has become widely applied in various optical super-resolution microscopy methods. The main advantages are multi-target imaging and molecular quantification. A challenge is the high background signal originating from the presence of unbound fluorophore-DNA labels in solution. Here, we report self-quenching of fluorophore dimers conjugated to DNA oligonucleotides as a general concept to reduce the fluorescence background. Upon hybridization, the fluorescence signal of both fluorophores is fully restored. Here, we expand the toolbox of fluorophores suitable for self-quenching and report their spectra and hybridization equilibria. We apply self-quenched fluorophore-DNA labels to stimulated emission depletion (STED) microscopy and single-molecule localization microscopy (SMLM) and report improved imaging performances.
Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
Authors: Tarbier Marcel , Mackowiak Sebastian D. , Sekar Vaishnovi , Bonath Franziska , Yapar Etka , Fromm Bastian , Faridani Omid R. , Biryukova Inna , Friedländer Marc R.
Published: March 2024

MicroRNAs are small RNA molecules that can repress the expression of protein coding genes post-transcriptionally. Previous studies have shown that microRNAs can also have alternative functions including target noise buffering and co-expression, but these observations have been limited to a few microRNAs. Here we systematically study microRNA alternative functions in mouse embryonic stem cells, by genetically deletingDrosha- leading to global loss of microRNAs. We apply complementary single-cell RNA-seq methods to study the variation of the targets and the microRNAs themselves, and transcriptional inhibition to measure target half-lives. We find that microRNAs form four distinct co-expression groups across single cells. In particular the mir-290 and the mir-182 clusters are abundantly, variably and inversely expressed. Intriguingly, some cells have global biases towards specific miRNAs originating from either end of the hairpin precursor, suggesting the presence of unknown regulatory cofactors. We find that miRNAs generally increase variation and covariation of their targets at the RNA level, but we also find miRNAs such as miR-182 that appear to have opposite functions. In particular, miRNAs that are themselves variable in expression, such as miR-291a, are more likely to induce covariations. In summary, we apply genetic perturbation and multi-omics to give the first global picture of microRNA dynamics at the single cell level.
Clonal-aggregative multicellularity entrained by salinity in one of the closest relative of animals
Authors: Ros-Rocher Núria , Reyes-Rivera Josean , Horo Uzuki , Foroughijabbari Yeganeh , Combredet Chantal , Larson Ben T. , Coyle Maxwell C. , Houtepen Erik A. T. , Vermeij Mark J. A. , Steenwyk Jacob L. , Brunet Thibaut
Published: March 2024

Multicellularity evolved multiple times independently during eukaryotic diversification1-4. Two distinct mechanisms underpin multicellularity5: clonal development (serial cell division of a single precursor cell) and aggregation (in which independent cells assemble into a multicellular entity). Clonal and aggregative development are traditionally considered mutually exclusive1,6-9, and evolutionary hypotheses have addressed why multicellular development might diverge toward one or the other extreme3,4. Both animals and their sister group, the choanoflagellates, are currently thought to only develop clonally10,11, apparently supporting an exclusively clonal pre-history for animal multicellularity4,12. Here, we show that the choanoflagellateChoanoeca flexa, one of the closest living relatives of animals13, develops into motile and contractile monolayers of cells (or "sheets") through an unexpectedly mixed, plastic mechanism:C. flexasheets can form by purely clonal processes, purely aggregative processes, or a combination of both. We characterize the life history ofC. flexain its natural environment, ephemeral splash pools on the island of Curaçao, and show that multicellular development is controlled by salinity during natural cycles of splash pool evaporation and refilling. Different splash pools house genetically distinct strains ofC. flexabetween which aggregation is constrained by kin recognition, a hallmark of aggregative multicellularity14-17. We propose that clonal-aggregative development allows fast and reversible transitions between unicellular and multicellular lifestyles in this rapidly fluctuating environment. Our findings challenge former generalizations about the choanoflagellate-animal lineage and expand the option space for the development and evolution of multicellularity.
Multi-omics characterization of highly enriched human plasma extracellular vesicles
Authors: Su Huaqi , Fowler Christopher , Masters Colin L , Barnham Kevin J. , Reid Gavin E. , Vella Laura J.
Published: March 2024

Extracellular vesicles (EVs) in blood plasma offer a valuable reservoir of intracellular cellular cargo, making them a promising source of liquid based biomarkers. The molecular cargo of small EVs (sEVs) is of particular interest because some EV subtypes encapsulate cargo from organelles including mitochondria, endosomes, and the autophagy pathways, which are implicated in multiple diseases. However, the complexity of plasma, with its abundance of non-EV particles and plasma proteins, presents challenges for their molecular characterization using mass spectrometry based ‘omics technologies.

Here, we optimised a rigorous method to isolate sEVs from human plasma based on both density and size. Following this, we analysed the protein and lipid content of sEVs from multiple individuals. We demonstrate the advantage of obtaining highly enriched sEVs from plasma for enhancing the detection of protein networks associated with mitochondria and the endosomal network, and also tissue types including the central nervous system. Some of the EV associated proteins reported here have not been detected in plasma, nor plasma sEVs, previously. We show that sphingomyelin lipids are the most abundant lipids in plasma sEVs (33.7 mol% total lipids) and provide the first report on cholesterol ester content. We demonstrate a 16-fold decrease in cholesterol ester lipids in sEVs compared to platelet free plasma and suggest that cholesterol ester content could serve as a valuable measure for assessing the effectiveness of plasma separation protocols or kits in enriching for sEVs.

Our study highlights the benefit of reducing co-isolates from plasma sEV preparations to enable the detection of proteins and lipids with potential biomarker utility, and underscores the need for ongoing development of improved high throughput sEV isolation technologies.
Multifaceted roles of cohesin in regulating transcriptional loops
Authors: Kim Minji , Wang Ping , Clow Patricia , Chien I , Wang Xiaotao , Peng Jianhao , Chai Haoxi , Liu Xiyuan , Lee Byoungkoo , Ngan Chew Yee , Yue Feng , Milenkovic Olgica , Chuang Jeffrey H , Wei Chia-Lin , Casellas Rafael , Cheng Albert , Ruan Yijun
Published: March 2024

Cohesin is required for chromatin loop formation. However, its precise role in regulating gene transcription remains largely unknown. We investigated the relationship between cohesin and RNA Polymerase II (RNAPII) using single-molecule mapping and live-cell imaging methods in human cells. Cohesin-mediated transcriptional loops were highly correlated with those of RNAPII and followed the direction of gene transcription. Depleting RAD21, a subunit of cohesin, resulted in the loss of long-range (>100 kb) loops between distal (super-)enhancers and promoters of cell-type-specific genes. By contrast, the short-range (<50 kb) loops were insensitive to RAD21 depletion and connected genes that are mostly housekeeping. This result explains why only a small fraction of genes are affected by the loss of long-range chromatin interactions due to cohesin depletion. Remarkably, RAD21 depletion appeared to up-regulate genes located in early initiation zones (EIZ) of DNA replication, and the EIZ signals were amplified drastically without RAD21. Our results revealed new mechanistic insights of cohesin's multifaceted roles in establishing transcriptional loops, preserving long-range chromatin interactions for cell-specific genes, and maintaining timely order of DNA replication.
Heterogeneity of morphometric similarity networks in health and schizophrenia
Authors: Janssen Joost , Gallego Ana Guil , Díaz-Caneja Covadonga M. , Lois Noemi González , Janssen Niels , González-Peñas Javier , Gordaliza Pedro M. , Buimer Elizabeth E.L. , van Haren Neeltje E.M. , Arango Celso , Kahn René S. , Hulshoff Pol Hilleke E. , Schnack Hugo G.
Published: March 2024

Introduction

Morphometric similarity is a recently developed neuroimaging phenotype of inter-regional connectivity by quantifying the similarity of a region to other regions based on multiple MRI parameters. Altered average morphometric similarity has been reported in psychotic disorders at the group level, with considerable heterogeneity across individuals. We used normative modeling to address cross-sectional and longitudinal inter-individual heterogeneity of morphometric similarity in health and schizophrenia.

Methods

Morphometric similarity for 62 cortical regions was obtained from baseline and follow-up T1-weighted scans of healthy individuals and patients with chronic schizophrenia. Cortical regions were classified into seven predefined brain functional networks. Using Bayesian Linear Regression and taking into account age, sex, image quality and scanner, we trained and validated normative models in healthy controls from eleven datasets (n = 4310). Individual deviations from the norm (z-scores) in morphometric similarity were computed for each participant for each network and region at both timepoints. A z-score ≧ than 1.96 was considered supra-normal and a z-score ≦ -1.96 infra-normal. As a longitudinal metric, we calculated the change over time of the total number of infra- or supra-normal regions per participant.

Results

At baseline, patients with schizophrenia had decreased morphometric similarity of the default mode network and increased morphometric similarity of the somatomotor network when compared with healthy controls. The percentage of patients with infra- or supra-normal values for any region at baseline and follow-up was low (<6%) and did not differ from healthy controls. Mean intra-group changes over time in the total number of infra- or supra-normal regions were small in schizophrenia and healthy control groups (<1) and there were no significant between-group differences.

Conclusions

In a case-control setting, a decrease of morphometric similarity within the default mode network may be a robust finding implicated in schizophrenia. However, normative modeling suggests that significant reductions and changes over time of regional morphometric similarity are evident only in a minority of patients.
Achieving Resilience in Aging: How Mitochondrial Modulation Drives Age-associated Fluconazole Tolerance inCryptococcus neoformans
Authors: Yoo Kyungyoon , Oliveira Natalia Kronbauer , Bhattacharya Somanon , Fries Bettina C.
Published: March 2024

Cryptococcus neoformans(Cn) is an opportunistic fungal microorganism that causes life-threatening meningoencephalitis. During the infection, the microbial population is heterogeneously composed of cells with varying generational ages, with older cells accumulating during chronic infections. This is attributed to their enhanced resistance to phagocytic killing and tolerance of antifungals like fluconazole (FLC). In this study, we investigated the role of ergosterol synthesis, ATP-binding cassette (ABC) transporters, and mitochondrial metabolism in the regulation of age-dependent FLC tolerance. We find that oldCncells increase the production of ergosterol and exhibit upregulation of ABC transporters. Old cells also show transcriptional and phenotypic characteristics consistent with increased metabolic activity, leading to increased ATP production. This is accompanied by increased production of reactive oxygen species (ROS), which results in mitochondrial fragmentation. This study demonstrates that the metabolic changes occurring in the mitochondria of old cells drive the increase in ergosterol synthesis and the upregulation of ABC transporters, leading to FLC tolerance.

IMPORTANCE

Infections caused byCryptococcus neoformanscause more than 180,000 deaths annually. Estimated one-year mortality for patients receiving care ranges from 20% in developed countries to 70% in developing countries, suggesting that current treatments are inadequate. Some fungal cells can persist and replicate despite the usage of current antifungal regimens, leading to death or treatment failure. In replicative aging, older cells display a resilient phenotype, characterized by their enhanced tolerance against antifungals and resistance to killing by host cells. This study shows that age-dependent increase in mitochondrial reactive oxygen species drive changes in ABC transporters and ergosterol synthesis, ultimately leading to the heightened tolerance against fluconazole in oldC. neoformanscells. Understanding the underlying molecular mechanisms of this age-associated antifungal tolerance will enable more targeted antifungal therapies for cryptococcal infections.
Long Amplicon Nanopore Sequencing for Dual-TypingRdRpandVP1Genes of Norovirus Genogroups I and II in Wastewater
Authors: Scott G. , Ryder D. , Buckley M. , Hill R. , Treagus S. , Stapleton T. , Walker D. I. , Lowther J. , Batista F. M.
Published: March 2024

Noroviruses (NoV) are the leading cause of non-bacterial gastroenteritis across the globe with societal costs of US$60.3 billion per annum. Development of a long amplicon nanopore-based method for dual-typing theRNA-dependent RNA polymerase(RdRp) and major structural protein (VP1) regions from a single RNA fragment could improve existing norovirus typing methods. Its application to wastewater-based epidemiology (WBE) and environmental testing could enable the discovery of novel types and improve tracking throughout the population and into aquaculture and recreational water settings. Here, we develop and optimise such a method for wastewater as the sample matrix.

Reverse transcription (RT), PCR and library pooling were optimised and a consensus-based bioinformatics pipeline was developed. Inhibitor removal and LunaScript® RT gave robust amplification of the ≈1000 bpRdRP+VP1amplicon. Platinum™ Taq polymerase showed good sensitivity and reduced levels non-specific amplification (NSA) when compared to other polymerases. Optimised PCR annealing temperatures significantly reduced NSA (51.3% and 42.4% for GI and GII), increased yield (86.5% for GII) and increased taxa richness (57.7%) for GII. Analysis of three NoV positive faecal samples showed 100% nucleotide similarity with Sanger sequencing.

Eight GI genotypes, 11 polymerase types (p-types) and 13 combinations were detected in wastewater along with 4 GII genotypes, 4 p-types and 8 combinations; highlighting the diversity of norovirus taxa present in wastewater in England. The most common genotypes detected in clinical samples were all detected in wastewater while we also commonly detected several GI genotypes not reported in the clinical data. Application of this method into a WBE scheme, therefore, may allow for more accurate measurement of norovirus diversity within the population.
Telomere Length in Plants Estimated with Long Read Sequencing
Authors: Colt Kelly , Petrus Semar , Abramson Bradley W. , Mamerto Allen , Hartwick Nolan T. , Michael Todd P.
Published: March 2024

Telomeres play an important role in chromosome stability and their length is thought to be related to an organism’s lifestyle and lifespan. Telomere length is variable across plant species and between cultivars of the same species, possibly conferring adaptive advantage. However, it is not known whether telomere length is related to lifestyle or life span across a diverse array of plant species due to the lack of information on telomere length in plants. Here we leverage genomes assembled with long read sequencing data to estimate telomere length by chromosome. We find that long read assemblies based on Oxford Nanopore Technologies (ONT) accurately predict telomere length in the two model plant speciesArabidopsis thalianaandOryza sativamatching lab-based length estimates. We then estimate telomere length across an array of plant species with different lifestyles and lifespans and find that in general gymnosperms have shorter telomeres compared to eudicots and monocots. Crop species frequently have longer telomeres than their wild relatives, and species that have been maintained clonally such as hemp have long telomeres possibly reflecting that this lifestyle requires long term chromosomal stability.
Parallel scattering, saturation, and generalized Abramovskii-Gribov-Kancheli (AGK) theorem in the EPOS4 framework, with applications for heavy-ion collisions at
sNN
of 5.02 TeV and 200 GeV
Authors: Werner K.
Published: March 2024

Ultrarelativistic heavy-ion collisions will first realize many nucleon-nucleon scatterings, happening instantaneously and therefore necessarily in parallel, due to the short collision time. An appropriate quantum mechanical tool to treat that problem is S-matrix theory, and it has been known for a long time how to derive a simple geometric probabilistic picture, still widely used, and here the Abramovskii-Gribov-Kancheli (AGK) theorem plays a crucial role. All this is done in a scenario where energy conservation is not taken care of, but this is needed, in particular for Monte Carlo simulations. When introducing energy-momentum sharing properly, the AGK theorem does not apply anymore, nor do simple geometric concepts such as binary scaling. I will discuss this (very serious) problem, and how it can be solved, in the EPOS4 framework. When connecting the multiple-Pomeron approach (for parallel scatterings) and perturbative QCD, one is actually forced to implement in a very particular way saturation scales in order to get an approach free of contradictions. One recovers a generalized AGK theorem (gAGK), valid at large pt (larger than the relevant saturation scales). I discuss how gAGK is related to factorization (in proton-proton scatterings) and binary scaling (in heavy-ion collisions). I will show some applications, using this new approach as an initial condition for hydrodynamical evolutions, for heavy-ion collisions at sNN of 5.02 TeV and 200 GeV, to get some idea about the energy dependence.

Published by the American Physical Society
2024
Making things (that don’t exist) count: a study of Scope 4 emissions accounting claims
Authors: Young-Ferris Anna , Malik Arunima , Calderbank Victoria , Jacob-John Jubin
Published: March 2024

Purpose

Avoided emissions refer to greenhouse gas emission reductions that are a result of using a product or are emission removals due to a decision or an action. Although there is no uniform standard for calculating avoided emissions, market actors have started referring to avoided emissions as “Scope 4” emissions. By default, making a claim about Scope 4 emissions gives an appearance that this Scope of emissions is a natural extension of the existing and accepted Scope-based emissions accounting framework. The purpose of this study is to explore the implications of this assumed legitimacy.

Design/methodology/approach

Via a desktop review and interviews, we analyse extant Scope 4 company reporting, associated accounting methodologies and the practical implications of Scope 4 claims.

Findings

Upon examination of Scope 4 emissions and their relationship with Scopes 1, 2 and 3 emissions, we highlight a dynamic and interdependent relationship between quantification, commensuration and standardization in emissions accounting. We find that extant Scope 4 assessments do not fit the established framework for Scope-based emissions accounting. In line with literature on the territorializing nature of accounting, we call for caution about Scope 4 claims that are a distraction from the critical work of reducing absolute emissions.

Originality/value

We examine the implications of assumed alignment and borrowed legitimacy of Scope 4 with Scope-based accounting because Scope 4 is not an actual Scope, but a claim to a Scope. This is as an act of accounting territorialization.
Embedding sustainable development goals in architectural education: a case study of Menoufia University 2023 graduation projects
Authors: El-Kholei Ahmed O. , Amer Ahmed S. , Yassein Ghada A.
Published: March 2024

Purpose

Sustainable design is a new paradigm to localize sustainable development. The Union Internationale des Architectes (UIA) prepared guidelines for architectural projects to contribute to the Sustainable Development Goals (SDGs). Using the theory of change, the Department of Architecture at Menofia University set the 2023 graduation project to explore the possibility of adopting sustainable design principles and integrating SDGs into architectural education. The paper documents and evaluates the experiment to drive best practices and lessons learned.

Design/methodology/approach

The paper utilized a mixed design strategy utilizing qualitative and quantitative techniques. It gathered data from various sources, including a student questionnaire and unstructured interviews with external examiners. Data analysis included frequency distribution and sentiment, content and thematic analyses. Triangulation is applied, combining data, investigator and methodological triangulation to enhance the paper’s validity.

Findings

Integrating SDGs into the 2023 graduation project contributed to students’ understanding of sustainable urban development. Students demonstrated varying receptiveness to guidelines, focusing mainly on the SDGs (1-5, 7, 8, 10 and 11). Gender equality and economic empowerment struck a chord with the mostly female students, acknowledging that securing well-paying jobs is a way to escape the cycle of poverty. Challenges included limited resources and time constraints, a scarcity of Arabic reading materials and misunderstandings among students and staff, thus prompting collaborative efforts beyond standard studio hours. Despite challenges, the initiative contributes to sustainable urban development, providing valuable lessons learned and insights.

Originality/value

Integrating sustainable design principles into architectural education is doable but involves a complex process requiring careful preparation. The value lies in the tangible impact on sustainable urban development, emphasizing the importance of incorporating sustainable development concepts throughout the architectural curriculum. The authors advocate for increased awareness and education among stakeholders and suggest areas for future research by exploring a broader implementation and assessing the long-term effects on students’ mindsets and practices. Sustainable development is a means toward community prosperity, and the inquiry highlights the collective responsibility of scholars, practitioners and students in shaping a better future.
Adaptive innovation and ethical dilemmas: a participatory action research study amongst cyclone-impacted households in Tamil Nadu, India
Authors: Santha Sunil D. , Sasidevan Devisha , Raman Atul , Ali Khadeeja Naja , Yoosuf Soofiya , Panda Deepankar , Shenoy Gauri
Published: March 2024

Purpose

This paper showcases how the PAR embedded in posthumanist perspectives enabled us to navigate several complexities in the field through methodological situatedness and pluralism. It also attempts to critically outline the drivers and barriers that shaped our capacities to engage with the PAR.

Design/methodology/approach

The Tamil Nadu state in the Bay of Bengal along the southeast coast of India is one of the six regions in the world where severe tropical cyclones originate throughout the year. Storm surges in this region are well known for their destructive potential due to strong winds and heavy rainfall. This paper describes our participatory action research (PAR) journey towards strengthening grassroots action by providing access to safe and affordable housing for cyclone-impacted households (CIHs) in the Villupuram district of Tamil Nadu, India. The PAR was guided by an adaptive innovation model (AIM) that draws inspiration from posthumanism, action research and reflective practice traditions.

Findings

The insights from the PAR insist that we must recognise and work with diverse knowledge systems and situated practices to develop meaningful disaster risk reduction (DRR) and climate adaptation strategies. Our approach has to be rooted in the lived experiences of various vulnerable groups, their entanglements with nature and their everyday struggles of interacting with a complex social-ecological system.

Originality/value

This paper is an outcome of a PAR in a cyclone-impacted village in Tamil Nadu, India. The discussions and findings of the paper are original in nature and have not been published elsewhere.
The driving force: organizational resilience of OKKO network
Authors: Khomenko Olena
Published: March 2024

Learning outcomes

After completion of the case study, the students would be able to identify and evaluate organizational culture as a critical element of organizational resilience and assess its fit to the business context, evaluate different elements of organizational resilience and their contribution to business adaptation and develop leadership approaches that help adapt and leverage organizational culture to foster individual, team and organizational resilience.

Case overview/synopsis

This teaching case covers topics of organizational leadership, including organizational culture and organizational resilience. This case study is appropriate for the postgraduate and executive education programmes. This case study covers the approach to organizational leadership and resilience of the OKKO, a Ukrainian retail petrol station network. The dilemmas considered by top managers of the company emerged in February–April 2022 amid the unfolding Russian invasion of Ukraine. The case study protagonists solved multiple business and organizational dilemmas to continue efficient business operations while allowing the organization to adapt to a complex and fast-changing environment. They leveraged a distinct corporate culture, strong employee engagement and established business processes and management practices to ensure the viability of the business.

Complexity academic level

This case study is appropriate for postgraduate and executive education programmes. The level of difficulty is light to medium. Recommended pre-requisites are understanding human resources management terminology and reviewing preparation materials. The case study is suitable for teaching courses in leadership, people management and organizational development that cover corporate culture, leadership and organizational resilience.

Subject code

CSS 6: Human resource management

Supplementary materials

Teaching notes are available for educators only.
DealShare: Value Based Positioning in B2C Markets
Authors: Ranjani K.S. , Jha Sumi , Pandey Neeraj
Published: March 2024

Learning outcomes

After reading this case study, the students will be able to identify the various choices available in social e-commerce using network marketing, interpret data-driven decisions in social e-commerce and evaluate their role in scaling business, analyse cost and revenue management in value segments, evaluate technology adoption among the masses using appropriate communication structures and develop customer relationships and manage their sentiments in the era of social media.

Case overview/synopsis

DealShare became a unicorn in 2022 and targeted the rural and low-income groups. Based on a networking model for customer acquisition and a hyperlocal supply chain model, DealShare is increasing its customer base at a rapid pace. However, profitability was still a challenge, and converting high volume into high value continued to be a daunting task. This case study delves deep into the challenges co-founder Sourjyendu Medda and the DealShare team faced. It seeks to address key issues: how should DealShare leverage customer network for faster customer acquisition and how should they increase ticket size and profitability? As a data-driven business, what advantages does DealShare have in influencing customers’ buying behaviour using data? Dependence on social media could have a cascading effect on “word of mouth”. How can they manage customer complaints and increase engagement?

Complexity academic level

This case study has the potential to be used in different settings. In strategic cost management, this case study can demonstrate strategies for cost management in the value-conscious segment. This case study can be used in marketing management courses while teaching “positioning” in business-to-consumer markets and CRM. For second-year management students, this can be used in entrepreneurship and strategic management courses to demonstrate the network effect in social e-commerce start-up businesses. This case study is also relevant for various course modules in graduate management programmes to demonstrate the power of data-driven decision-making in business.

Supplementary materials

Teaching notes are available for educators only.

Subject code

CSS 8: Marketing
Investigating the effects of off-the-job embeddedness on turnover intentions: does affective commitment play a role?
Authors: Obeng Anthony Frank , Azinga Samuel Awuni , Bentil John , Ellis Florence Y.A. , Coffie Rosemary Boateng
Published: March 2024

Purpose

While much attention has been given to work-related factors influencing turnover intention through affective commitment, little focus has been directed to non-work factors affecting the service industry. Hence, this study aims to investigate the impact of links, fit and sacrifice, representing off-the-job embeddedness in the community, on turnover intention in the hospitality industry of Ghana: Sub-Sahara Africa using the theory of conservation of resources (COR) and social exchange. The model has been extended to include affective commitment as the mediating mechanism.

Design/methodology/approach

A multi-wave technique was used to collect data through a questionnaire from 341 full-time frontline hospitality employees in Ghana. The responses were analysed using AMOS software structural equation modelling.

Findings

The findings show that links, fit and sacrifice significantly influence employees’ turnover intentions. Moreover, it has been observed that affective commitment decreased the negative relationship and partly mediated the main relationship between the dimensions of off-the-job embeddedness and turnover intention.

Research limitations/implications

The study’s results and academic, practical implications and limitations are discussed for future research.

Originality/value

This study emphasises the theory of COR to demystify community factors employees deem as valued resources, which lighten up their commitment to their organisation and decrease their intent to leave.