bluuebunny/crossref_metadata_2025 huggingface dataset:
Heterologous expression and characterization of mutant cellulase from indigenous strain of Aspergillus niger
Authors: Ahmad Waqas , Zafar Muddassar , Anwar Zahid , Mehmood Ashraf Naeem , Ahmad Saira
Published: February 2024

The current study highlights the effect of mutagenesis on endoglucanase B activity of indigenous strain ofAspergillus nigerand its heterologous expression studies in thepET28a+vector. The physical and chemical mutagens were employed to incorporate mutations inA. niger. For determination of mutations, mRNA was isolated followed by cDNA synthesis and cellulase gene was amplified, purified and sequenced both from native and mutantA. niger.On comparison of gene sequences, it was observed that 5 nucleotide base pairs have been replaced in the mutant cellulase. The mutant recombinant enzyme showed 4.5 times higher activity (428.5 µmol/mL/min) as compared to activity of native enzyme (94 µmol/mL/min). The mutant gene was further investigated using Phyre2 and I-Tesser tools which exhibited 71% structural homology with Endoglucanase B ofThermoascus aurantiacus. The root mean square deviation (RMSD), root mean square fluctuation (RMSF), solvent accessible surface area (SASA), radius of gyration (Rg) and hydrogen bonds analysis were carried at 35 °C and 50 °C to explore the integrity of structure of recombinant mutant endoglucanase B which corresponded to its optimal temperature. Hydrogen bonds analysis showed more stability of recombinant mutant endoglucanase B as compared to native enzyme. Both native and mutant endoglucanase B genes were expressed inpET 28a+and purified with nickel affinity chromatography. Theoretical masses determined through ExPaSy Protparam were found 38.7 and 38.5 kDa for native and mutant enzymes, respectively. The optimal pH and temperature values for the mutant were 5.0 and 50 °C while for native these were found 4.0 and 35 °C, respectively. On reacting with carboxy methyl cellulose (CMC) as substrate, the mutant enzyme exhibited less Km(0.452 mg/mL) and more Vmax(50.25 µmol/ml/min) as compared to native having 0.534 mg/mL as Kmand 38.76 µmol/ml/min as Vmax. Among metal ions, Mg2+showed maximum inducing effect (200 %) on cellulase activity at 50 mM concentration followed by Ca2+(140%) at 100 mM concentration. Hence, expression of a recombinant mutant cellulase fromA. nigersignificantly enhanced its cellulytic potential which could be employed for further industrial applications at pilot scale.
SPRITE: improving spatial gene expression imputation with gene and cell networks
Authors: Sun Eric D. , Ma Rong , Zou James
Published: February 2024

Spatially resolved single-cell transcriptomics have provided unprecedented insights into gene expressionin situ, particularly in the context of cell interactions or organization of tissues. However, current technologies for profiling spatial gene expression at single-cell resolution are generally limited to the measurement of a small number of genes. To address this limitation, several algorithms have been developed to impute or predict the expression of additional genes that were not present in the measured gene panel. Current algorithms do not leverage the rich spatial and gene relational information in spatial transcriptomics. To improve spatial gene expression predictions, we introduce SPRITE (Spatial Propagation and Reinforcement of Imputed Transcript Expression) as a meta-algorithm that processes predictions obtained from existing methods by propagating information across gene correlation networks and spatial neighborhood graphs. SPRITE improves spatial gene expression predictions across multiple spatial transcriptomics datasets. Furthermore, SPRITE predicted spatial gene expression leads to improved clustering, visualization, and classification of cells. SPRITE is available as a software package and can be used in spatial transcriptomics data analysis to improve inferences based on predicted gene expression.
The lncRNAMalat1is trafficked to the cytoplasm as a localized mRNA encoding a small peptide in neurons
Authors: Xiao Wen , Halabi Reem , Lin Chia-Ho , Nazim Mohammad , Yeom Kyu-Hyeon , Black Douglas L
Published: February 2024

Synaptic function is modulated by local translation of mRNAs that are transported to distal portions of axons and dendrites. The Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is broadly expressed across cell types, almost exclusively as a nuclear non-coding RNA. We found that in differentiating neurons, a portion ofMalat1RNA redistributes to the cytoplasm. Depletion ofMalat1from neurons stimulated expression of particular pre- and post-synaptic proteins, implicatingMalat1in their regulation. NeuronalMalat1is localized to both axons and dendrites in puncta that co-stain with Staufen1 protein, similar to neuronal granules formed by locally translated mRNAs. Ribosome profiling of mouse cortical neurons identified ribosome footprints within a region ofMalat1containing short open reading frames. The upstream-most reading frame (M1) of theMalat1locus was linked to the GFP coding sequence in mouse ES cells. When these gene-edited cells were differentiated into glutamatergic neurons, the M1-GFP fusion protein was expressed. Antibody staining for the M1 peptide confirmed its presence in wildtype neurons, and showed enhancement of M1 expression after synaptic stimulation with KCL. Our results indicate thatMalat1serves as a cytoplasmic coding RNA in the brain that is both modulated by and modulates synaptic function.
IL-3-driven T cell-basophil crosstalk enhances anti-tumor immunity
Authors: Wei Jian , Mayberry Colleen L. , Lv Xiaoting , Hu Fangyan , Sears John D. , Khan Taushif , Logan Natalie A. , Wilson John J. , Chaussabel Damien , Chang Chih-Hao
Published: February 2024

Cytotoxic T lymphocytes (CTLs) are pivotal in combating cancer, yet their efficacy is often hindered by the immunosuppressive tumor microenvironment, resulting in exhaustion. This study investigates the role of interleukin (IL)-3 in orchestrating anti-tumor immunity through CTL modulation. Intratumoral CTLs undergo a progressive decline in IL-3 production, which is correlated with impaired cytotoxic function. Augmenting IL-3, through intraperitoneal administration, IL-3-expressing melanoma cells, or IL-3-engineered CD8+T cells, confers protection against tumor progression, concomitant with increased CTL activity. CTLs are critical in this therapeutic efficacy as IL-3 demonstrates no impact on tumor growth in RAG1 knockout mice or following CD8+T cell-depletion. Rather than acting directly, CTL-derived IL-3 exerts its influence on basophils, synergistically amplifying anti-tumor immunity within CTLs. Introducing IL-3-activated basophils retards tumor progression, whereas basophil depletion diminishes the effectiveness of IL-3 supplementation. Furthermore, IL-3 prompts basophils to produce IL-4, which subsequently elevates IFN-γ production and viability of CTLs. Notably, the importance of basophil-derived IL-4 is evident from the absent benefits in IL-3-supplementated, IL-4 knockout tumor-bearing mice. Overall, this research unveils IL-3-mediated CTL-basophil crosstalk in regulating anti-tumor immunity and offers the prospect of harnessing IL-3 sustenance as a promising approach for optimizing and enhancing cancer immunotherapy.

Significance Statement

This study elucidates the critical role of IL-3 in orchestrating anti-tumor immunity, particularly within the context of CTLs and melanoma growth. It reveals a progressive decline in CTL-derived IL-3 during tumor progression, correlated with CTL exhaustion—a formidable barrier in cancer immunotherapy. Intriguingly, augmentation of IL-3, achieved through diverse means, effectively impedes tumor progression by enhancing CTL activity. This research unveils a novel mechanism: IL-3-mediated crosstalk between CTLs and IL-4-producing basophils, resulting in the rejuvenation of CTLs and amplifying their anti-tumor ability. These insights hold promise for the advancement and optimization of cancer immunotherapeutic strategies, deepening our comprehension of CTL dynamics within the tumor microenvironment, and advancing our ability to combat cancer effectively.
Bilateral regulation of EGFR activity and local PI dynamics observed with superresolution microscopy
Authors: Abe Mitsuhiro , Yanagawa Masataka , Hiroshima Michio , Kobayashi Toshihide , Sako Yasushi
Published: February 2024

Anionic lipid molecules, including phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2), are implicated in the regulation of epidermal growth factor receptor (EGFR). However, the role of the spatiotemporal dynamics of PI(4,5)P2in the regulation of EGFR activity in living cells is not fully understood, as it is difficult to visualize the local lipid domains around EGFR. In this study, both EGFR and PI(4,5)P2nanodomains in the plasma membrane were visualized using super-resolution single-molecule microscopy. The EGFR and PI(4,5)P2nanodomains aggregated before stimulation with epidermal growth factor (EGF) through transient visits of EGFR to the PI(4,5)P2nanodomains. The degree of coaggregation decreased after EGF stimulation and depended on phospholipase Cγ, the EGFR effector hydrolyzing PI(4,5)P2. Artificial reduction in the PI(4,5)P2content of the plasma membrane reduced both the dimerization and autophosphorylation of EGFR after stimulation with EGF. Inhibition of PI(4,5)P2hydrolysis after EGF stimulation decreased phosphorylation of EGFR-Thr654. Thus, EGFR kinase activity and the density of PI(4,5)P2around EGFR molecules were found to be mutually regulated.
Reconstructing microvascular network skeletons from 3D images: what is the ground truth?
Authors: Walsh Claire , Berg Maxime , West Hannah , Holroyd Natalie A. , Walker-Samuel Simon , Shipley Rebecca J.
Published: February 2024

Structural changes to microvascular networks are increasingly highlighted as markers of pathogenesis in a wide range of disease, e.g. Alzheimer’s disease, vascular dementia and tumour growth. This has motivated the development of dedicated 3D imaging techniques, alongside the creation of computational modelling frameworks capable of using 3D reconstructed networks to simulate functional behaviours such as blood flow or transport processes. Extraction of 3D networks from imaging data broadly consists of two image processing steps: segmentation followed by skeletonisation. Much research effort has been devoted to segmentation field, and there are standard and widely-applied methodologies for creating and assessing gold standards or ground truths produced by manual annotation or automated algorithms.

The Skeletonisation field, however, lacks widely applied, simple to compute metrics for the validation or optimisation of the numerous algorithms that exist to extract skeletons from binary images. This is particularly problematic as 3D imaging datasets increase in size and visual inspection becomes an insufficient validation approach. In this work, we first demonstrate the extent of the problem by applying 4 widely-used skeletonisation algorithms to 3 different imaging datasets. In doing so we show significant variability between reconstructed skeletons of the same segmented imaging dataset. Moreover, we show that such a structural variability propagates to simulated metrics such as blood flow. To mitigate this variability we introduce a new, fast and easy to compute super-metric that compares the volume, connectivity, medialness, correct bifurcation point identification and homology of the reconstructed skeletons to the original segmented data. We then show that such a metric can be used to select the best performing skeletonisation algorithm for a given dataset, as well as to optimize its parameters. Finally, we demonstrate that the super-metric can also be used to quickly identify how a particular skeletonisation algorithm could be improved, becoming a powerful tool in understanding the complex implication of small structural changes in a network.
Memory’s gatekeeper: the role of PFC in the encoding of familiar events
Authors: Guerreiro Inês C. , Clopath Claudia
Published: February 2024

Theoretical models conventionally portray the consolidation of memories as a slow process that unfolds during sleep. According to the classical Complementary Learning Systems (CLS) theory (as presented in J. McClelland et al., 1995), the hippocampus (HPC) rapidly changes its connectivity during wakefulness to encode ongoing events and create memory ensembles that are later transferred to the prefrontal cortex (PFC) during sleep. However, recent experimental studies challenge this notion by showing that new information consistent with prior knowledge can be rapidly consolidated in PFC during wakefulness, and that PFC lesions disrupt the encoding of familiar events in the HPC. These results challenge the widely accepted view that consolidation is a slow process that unfolds during sleep and highlight the role of PFC during the initial stages of memory encoding. The contributions of the PFC to memory encoding have therefore largely been overlooked. Moreover, most theoretical frameworks assume random and uncorrelated patterns representing memories, disregarding the correlations between our experiences. To address this shortcomings, we developed a HPC-PFC network model that simulates interactions between the HPC and PFC during the encoding of a memory (awake stage), and subsequent consolidation (sleeping stage) to examine the contributions of each region to the consolidation of novel and familiar memories. Our results show that the PFC network uses stored memory “schemas” consolidated during previous experiences to identify inputs that evoke familiar patterns of activity, quickly integrated it in its network, and gate which components are encoded in the HPC. More specifically, the PFC uses GABAergic long-range projections to inhibit HPC neurons representing input components correlated with a previously stored memory “schema”, eliciting sparse hippocampal activity during exposure to familiar events, as it has been experimentally observed.
MicroRNAs and mRNA Regulatory Network of Parenchymal Hematoma after Endovascular Mechanical Reperfusion for Acute Ischemic Stroke in Rat
Authors: Zhuang Jin-Kun , Huang Zhong-Run , Qin Wang , Li Chang-Luo , Li Qi , Xiang Chun , Tuo Yong-Hua , Liu Zhong , Chen Qian-Yu , Shi Zhong-Song
Published: February 2024

Hemorrhagic transformation after endovascular thrombectomy predicts poor outcomes in acute ischemic stroke with large vessel occlusion. The roles of microRNAs in the pathogenesis of parenchymal hematoma (PH) are still unclear. This study aims to investigate the microRNA and mRNA regulatory network associated with PH after mechanical reperfusion in the animal stroke model and oxygen-glucose deprivation/reoxygenation (OGD/R) model. Twenty-five microRNAs were assessed in the reperfusion-induced hemorrhage model in rats with hyperglycemic conditions receiving 5-hour middle cerebral artery occlusion. Thirteen down-regulated microRNAs (miRNA-29a-5p, miRNA-29c-3p, miRNA-126a-5p, miRNA-132-3p, miRNA-136-3p, miRNA-142-3p, miRNA-153-5p, miRNA-218a-5p, miRNA-219a-2-3p, miRNA-369-5p, miRNA-376a-5p, miRNA-376b-5p, miRNA-383-5p) and one up-regulated microRNA (miRNA-195-3p) were found in rat peri-infarct with PH. Ten of these 14 PH-related microRNAs were significantly differentially expressed in at least two of five models of neuron, astrocyte, microglia, BMEC, and pericyte after OGD/R, consistent with the animal model results. Thirty-one predicted hub target genes were significantly differentially expressed in rat peri-infarct with PH. Forty-nine microRNA-mRNA regulatory axes of PH were revealed, which were related to the mechanisms of oxidative stress, apoptosis, immune, and inflammation. Simultaneously differentially expressed microRNAs and related genes in several cells of the neurovascular unit may serve as valuable targets for PH after endovascular thrombectomy in acute ischemic stroke.
Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria
Authors: Beauchemin Eve T. , Hunter Claire , Maurice Corinne F.
Published: February 2024

The bacteria living in the human gut are essential for host health. Though the composition and metabolism of these bacteria is well described in both healthy hosts and those with intestinal disease, less is known about the activity of the gut bacteria prior to, and during, disease development – especially regarding gut bacterial replication. Here, we use a recently developed single-cell technique alongside existing metagenomics-based tools to identify, track, and quantify the replicating gut bacteria and their replication dynamics in the dextran sodium sulfate mouse model of colitis. We show that the proportion of replicating gut bacteria decreases when mice have the highest levels of inflammation and returns to baseline levels as mice begin recovering. We additionally report significant alterations in the composition of the total replicating gut bacterial community during colitis development. On the taxa level, we observe significant changes in the abundance of taxa such as the mucus-degradingAkkermansia muciniphilaand the poorly describedErysipelatoclostridiumgenus. We further demonstrate that many taxa exhibit variable replication rates during colitis, includingA. muciniphila. Lastly, we show that colitis development is positively correlated with increases in the presence and abundance of bacteria predicted to be fast replicators, suggesting that taxa with the potential to replicate quickly may have an advantage during intestinal inflammation. These data support the need for additional research using activity-based approaches to further characterize the gut bacterial response to intestinal inflammation and its consequences for both the host and the gut microbial community at large.

Importance

It is well known that the bacteria living inside the gut are important for human health. Indeed, the type of bacteria which are present and their metabolism is different in healthy people versus those with intestinal disease. However, less is known about how these gut bacteria are replicating, especially as someone begins to develop intestinal disease. This is especially important as it is thought that the active gut bacteria may be more relevant to health. Here, we begin addressing this gap by using several complementary approaches to characterize the replicating gut bacteria in a mouse model of intestinal inflammation. We reveal which gut bacteria are replicating, and how quickly, as mice develop and recover from inflammation. This work can serve as a model for future research to identify how the active gut bacteria may be impacting health, or why these particular bacteria tend to thrive during intestinal inflammation.
Expression of the locus of enterocyte effacement genes during the invasion process of the atypical enteropathogenicEscherichia coli1711-4 strain of serotype O51:H40
Authors: Romão Fabiano T. , Santos Ana C. M. , Sperandio Vanessa , Hernandes Rodrigo T. , Gomes Tânia A. T.
Published: February 2024

Atypical enteropathogenicEscherichia coli(aEPEC) is a significant cause of diarrhea in developing countries. Some aEPEC strains, including the Brazilian representative strain of serotype O51:H40 called aEPEC 1711-4, can use flagella to attach to, invade, and persist in T84 and Caco-2 intestinal cells. They can even translocate from the gut to extraintestinal sites in a rat model. Although various aspects of the virulence of this strain were studied and the requirement of the T3SS for the efficiency of the invasion process was demonstrated, the expression of the LEE genes during the invasion and intracellular persistence remains unclear. To address this, the expression of flagella and the different LEE operons was evaluated during kinetic experiments of the interaction of aEPEC 1711-4 with enterocytesin vitro. The genome of the strain was also sequenced. The results showed that flagella expression remained unchanged, but the expression ofeaeandescJincreased during the early interaction and invasion of aEPEC 1711-4 into Caco-2 cells, and there was no change 24 hours post-infection during the persistence period. The number of pedestal-like structures formed on HeLa cells also increased during the 24-hour analysis. No known gene related to the invasion process was identified in the genome of aEPEC 1711-4, which was shown to belong to the global EPEC lineage 10. These findings suggest that LEE components and the intimate adherence promoted by intimin are necessary for the invasion and persistence of aEPEC 1711-4, but the detailed mechanism needs further study.

Importance

Atypical enteropathogenicEscherichia coli(aEPEC) is a major cause of diarrhea, especially in developing countries, like Brazil. However, due to the genome heterogeneity of each clonal group, it is difficult to comprehend the pathogenicity of this strain fully. Among the aEPEC strains, 1711-4 can invade eukaryotic cellsin vitro, cross the gut barrier, and reach extraintestinal sites in animal models. By studying how different known aEPEC virulence factors are expressed during the invasion process, we can gain insight into the commonality of this phenotype among other aEPEC strains. This will help us develop preventive measures to control infections caused by invasive strains. No known virulence-encoding genes linked to the invasion process were found. Nevertheless, additional studies are still necessary to evaluate the role of other factors in this phenotype.
Bacterial community structure analysis onListeria monocytogenesinoculated spinach leaves is affected by PCR based methods to exclude chloroplast co-amplification
Authors: Culliney Paul , Schmalenberger Achim
Published: February 2024

Consumption of ready-to-eat leafy vegetables has increased in popularity due to their anticipated health benefits, but their consumption also poses a potential health risk in the form of foodborne pathogens.Listeria monocytogenesis a ubiquitous pathogen that has been regularly found on leafy vegetables including spinach. Growth determining factors go beyond plant species and cultivation practice and may include the phyllosphere bacteriome to affect the growth potential ofL. monocytogenes. This study investigated the bacteriome of spinach leaves, stored under EURL challenge conditions for 9 days after inoculation withL. monocytogenesusing two methods of excluding chloroplast co-amplification (COMPETE, BLOCK) at the PCR step as well as a post-PCR chloroplast sequence filter option (CONTROL). While all three approaches have demonstrated a change of bacterial communities over time, the pPNA based BLOCK approach resulted in greater diversity similarities to the CONTROL option. The COMPETE solution with a specifically designed primer to prevent chloroplast amplification had a strong underrepresentation of the Planctomycetota phylum and to a lesser extend underrepresentation of Chloroflexi and Verrucomicrobiota due to the inheritance of the selected primer region that allowed to deselect chloroplast co-amplification. However, the COMPETE approach had the lowest level of chloroplast co-amplification. Higher growth potential ofL. monocytogenesfrom day 7 to 9 co-occurred with higher relative abundances of Pseudomonadaceae and lower numbers of Lactobacillales, suggesting that particular phylogenetic groups may support growth ofL. monocytogenes. While chloroplast co-amplification with spinach in the present study was relatively modest and a purely filter based chloroplast removal was sufficient, other leafy vegetables may require one of the tested co-amplification prevention solutions. While the COMPETE solution in the present study was linked to some amplification bias, the approach may be useful when otherwise co-amplification is very high and the demonstrated BLOCK approach with pPNA is insufficient.
DiffTopo: Fold exploration using coarse grained protein topology representations
Authors: Miao Yangyang , Correia Bruno
Published: February 2024

Abstract

A major challenge in the field of computational de novo protein design is the exploration of uncharted areas within protein structural space, i.e., generating “designable” protein structures that nature has not explored. However, the large degrees of freedom of protein structural backbones complicate the sampling process during protein design. In this work, we propose a new coarse grained protein structure representation method DiffTopo - an E(3) Equivariant 3D conditional diffusion model, which greatly increases the sampling efficiency. Combined with the RFdiffusion framework, novel protein folds can be generated rapidly, allowing for efficient exploration of the designable topology space. This opens up possibilities to solve the problem of generating new folds as well to functionalize de novo proteins through motif scaffolding, where functional or enzymatic sites can be introduced into novel protein frameworks.
Pediatric human nose organoids demonstrate greater susceptibility, epithelial responses, and cytotoxicity than adults during RSV infection
Authors: Aloisio Gina M. , Nagaraj Divya , Murray Ashley M. , Schultz Emily M. , McBride Trevor , Aideyan Letisha , Nicholson Erin G. , Henke David , Ferlic-Stark Laura , Rajan Anubama , Kambal Amal , Johnson Hannah L. , Mosa Elina , Stossi Fabio , Blutt Sarah E. , Piedra Pedro A. , Avadhanula Vasanthi
Published: February 2024

Respiratory syncytial virus (RSV) is a common cause of respiratory infections, causing significant morbidity and mortality, especially in young children. Why RSV infection in children is more severe as compared to healthy adults is not fully understood. In the present study, we infect both pediatric and adult human nose organoid-air liquid interface (HNO-ALIs) cell lines with two contemporary RSV isolates and demonstrate how they differ in virus replication, induction of the epithelial cytokine response, cell injury, and remodeling. Pediatric HNO-ALIs were more susceptible to early RSV replication, elicited a greater overall cytokine response, demonstrated enhanced mucous production, and manifested greater cellular damage compared to their adult counterparts. Adult HNO-ALIs displayed enhanced mucus production and robust cytokine response that was well controlled by superior regulatory cytokine response and possibly resulted in lower cellular damage than in pediatric lines. Taken together, our data suggest substantial differences in how pediatric and adult upper respiratory tract epithelium responds to RSV infection. These differences in epithelial cellular response can lead to poor mucociliary clearance and predispose infants to a worse respiratory outcome of RSV infection.
Influenza A Virus Disruption of Dendritic Cell-Natural Killer Cell Crosstalk Impacts Activation of Helper and Cytotoxic T cell Subsets
Authors: Morson Connor A. , Uppalapati Chandana K. , Lopez Brina S. , Kronstad Lisa M.
Published: February 2024

Dendritic cells (DC) and Natural killer (NK) cells engage in reciprocal interactions to trigger an efficient innate immune response while governing the adaptive immune response. Here we used anex vivoautologous human primary immune cell co-culture of DCs and NK cells to investigate the impact of DC-NK cell crosstalk on activation of CD4+and CD8+naïve T cell responses to influenza A viral (IAV) infection. Using multiparameter flow cytometry, we observed that culturing T cells with DC and NK cells led to enhanced expression of CD69 and CD25 activation markers and increased proliferative ability of both CD4+and CD8+T cell subsets. Exposure of DCs to the pandemic A/California/07/2009 (H1N1) strain in NK cell co-culture led to a reduced frequency of CD4+CD69+, CD8+CD69+, CD4+CD25+, CD8+CD25+T cell subsets and a reduced expansion of CD4+T cells. The IAV-mediated curtailment of T cell activation was dependent on the ability of A/California/07/2009 (H1N1) to replicate as inactivation of the virus rescued expression of CD69, CD25 on both CD4+and CD8+T cell subsets and triggered expansion of CD4+T cells. Further, we discovered exposure of DCs to the A/Victoria/361/2011 (H3N2) IAV strain also significantly impaired expression of CD69 on CD4+and CD8+T cells and CD25 on CD8+T cells. In contrast with the A/California/07/2009 (H1N1 strain), inactivation of A/Victoria/361/2011 (H3N2) failed to fully restore T cell expression of CD69 and CD25 and proliferation. Collectively, these data demonstrate that IAV partially usurps the ability of DC-NK cell crosstalk to activate naïve CD4+and CD8+T cells in a strain-dependent manner. These data may inform the immunological signals required to trigger a potent cellular immune response to IAV, which may elicit broader and more durable protection than current inactivated vaccine platforms.
Optogenetic mapping of rhythmic phase-dependent excitability in the mouse striatum
Authors: Mohapatra Manish , Carmichael J. Eric , Smith Kyle S. , van der Meer Matthijs A. A.
Published: February 2024

The striatum is thought to switch flexibly between multiple converging inputs to support adaptive behavior. The “communication through coherence” (CTC) hypothesis is a potential mechanism to implement such a flexible switching. For CTC to work in the striatum, striatal excitability must show rhythmic fluctuations, such as those related to the phase of the striatal local field potential (LFP). To test this fundamental requirement, we delivered a constant input stimulus to ChR2-expressing striatal fast-spiking PV+ interneurons (FSIs) in head-fixed awake mice (PV-Cre:Ai-32, n = 18, 9 female), and determined whether the response to this stimulus varied with LFP phase. We found that approximately one-third (41.2%) of FSIs exhibited significant phase-dependent excitability in at least one LFP frequency band. Phase-dependent excitability was most prominent in the delta (2–5 Hz) frequency band, both in terms of prevalence (23.5% of FSIs sampled) and magnitude (phase modulation strength: 22% of average response). The most excitable phase tended to align with endogenous phase-locking, again most clearly in the delta band. These results bolster the functional relevance of the striatal field potential and spike-field relationships, and provide proof-of-principle support for the possibility of CTC in the striatum.

Significance Statement

The striatum is thought to switch dynamically between multiple converging inputs. A leading idea for how this is accomplished is through communication through coherence (CTC). A fundamental, but previously untested, requirement for CTC to work is that striatum must show changes in excitability that depend on local field potential phase. We find that about one-third of striatal neurons show phase-dependent excitability, providing proof of principle for CTC-like switching in striatum.
Thehomieinsulator has sub-elements with different insulating and long-range pairing properties
Authors: Fujioka Miki , Ke Wenfan , Schedl Paul , Jaynes James B
Published: February 2024

Chromatin insulators are major determinants of chromosome architecture. Specific architectures induced by insulators profoundly influence nuclear processes, including how enhancers and promoters interact over long distances and between homologous chromosomes. Insulators can pair with copies of themselves in trans to facilitate homolog pairing. They can also pair with other insulators, sometimes with great specificity, inducing long-range chromosomal loops. Contrary to their canonical function of enhancer blocking, these loops can bring distant enhancers and promoters together to activate gene expression, while at the same time blocking other interactions incis. The details of these effects depend on the choice of pairing partner, and on the orientation specificity of pairing, implicating the 3-dimensional architecture as a major functional determinant. Here we dissect the homie insulator from the Drosophilaeven skipped(eve) locus, to understand its substructure. We test pairing function incisbased onhomie-carrying transgenes interacting with endogenouseve. The assay is sensitive to both pairing strength and orientation. Using this assay, we found that a Su(Hw) binding site inhomieis required for efficient long-range interaction, although some activity remains without it. This binding site also contributes to the canonical insulator activities of enhancer blocking and barrier function. Based on this and other results from our functional dissection, each of the canonical insulator activities, chromosomal loop formation, enhancer blocking, and barrier activity, are partially separable. Our results show the complexity inherent in insulator functions, which can be provided by an array of different proteins with both shared and distinct properties.
Quantitative omnigenic model discovers interpretable genome-wide associations
Authors: Ružičková Natália , Hledík Michal , Tkačik Gašper
Published: February 2024

As their statistical power grows, genome-wide association studies (GWAS) have identified an increasing number of loci underlying quantitative traits of interest. These loci are scattered throughout the genome and are individually responsible only for small fractions of the total heritable trait variance. The recently proposed omnigenic model provides a conceptual framework to explain these observations by postulating that numerous distant loci contribute to each complex trait via effect propagation through intracellular regulatory networks. We formalize this conceptual framework by proposing the “quantitative omnigenic model” (QOM), a statistical model that combines prior knowledge of the regulatory network topology with genomic data. By applying our model to gene expression traits in yeast, we demonstrate that QOM achieves similar gene expression prediction performance to traditional GWAS with hundreds of times less parameters, while simultaneously extracting candidate causal and quantitative chains of effect propagation through the regulatory network for every individual gene. We estimate the fraction of heritable trait variance incis-and intrans-, break the latter down by effect propagation order, assess thetrans-variance not attributable to transcriptional regulation, and show that QOM correctly accounts for the low-dimensional structure of gene expression covariance. We furthermore demonstrate the relevance of QOM for systems biology, by employing it as a statistical test for the quality of regulatory network reconstructions, and linking it to the propagation of non-transcriptional (including environmental) effects.

Significance statement

Genetic variation leads to differences in traits implicated in health and disease. Identifying genetic variants associated with these traits is spearheaded by “genome-wide association studies” (GWAS) – statistically rigorous procedures whose power has grown with the number of genotyped samples. Nevertheless, GWAS have a substantial shortcoming: they are ill-equipped to detect the causal basis and reveal the complex systemic mechanisms of polygenic traits. Even a single genetic change can propagate throughout the entire genetic regulatory network causing a myriad of spurious detections, thereby significantly limiting GWAS usefulness. To this end, we propose a novel statistical approach that incorporates known regulatory network information with the potential to boost interpretability of state-of-the-art genomic analyses while simultaneously extracting systems biology insights.
First report and characterization of a plasmid-encodedblaSFO-1in a multi-drug resistantAeromonas hydrophilaclinical isolate
Authors: Skwor Troy , Jones Dan , Cahak Caitlin , Newton Ryan J
Published: February 2024

Antibiotic resistance remains one of the most pressing public health issues facing the world today. At the forefront of this battle lies the ever-increasing identification of extended spectrum beta-lactamases and carbapenemases within human pathogens, conferring resistance towards broad-spectrum and last-resort anti-microbials. This study was prompted due to the identification of a pathogenicAeromonas hydrophilaisolate (strain MAH-4) collected from abdominal fluid, which presented a robust resistance pattern against second, third, and fourth generation cephalosporins, ertapenem, ciprofloxacin, gentamicin, levofloxacin and moxifloxacin, and beta lactam/beta-lactamase inhibitor combinations. Whole genome sequencing was performed and identified a 328 kb plasmid (pMAH4) encoding 10 antibiotic resistance genes, includingblaSFO-1,blaTEM-1,andblaOXA-1ofA. hydrophiaMAH-4. This is the first report of beta-lactamase SFO-1 within a clinical strain ofAeromonas. Due to the remarkable sequence identity of pMAH4 to plasmids associated withEnterobacteralesgenera likeKlebsiella, and the extensive capabilities ofAeromonasfor horizontal gene transfer, our identification of a clinical isolate encoding SFO-1 on a plasmid suggests ARG mobility betweenEnterobacteralesand non-Enterobacteralesspecies.
A detailed dissection of the expression, localization, structure, and diagnostic potential of cyst wall proteins of the eye pathogenAcanthamoeba
Authors: Kanakapura Sundararaj Bharath , Goyal Manish , Samuelson John
Published: February 2024

The cyst wall of the eye pathogenAcanthamoeba castellaniicontains cellulose and chitin and has ectocyst and endocyst layers connected by conical ostioles. Previously, we used mass spectrometry of purified walls to identify an abundant laccase and three families of lectins (Jonah, Luke, and Leo). Here we show that frameshifts in the protein prediction in AmoebaDB, which incorrectly add 12 transmembrane helices, cause Jonah to mislocalize to a ring around ostioles rather than to the ectocyst layer. RT-PCR, double labels with GFP and RFP or mCherry, and promoter swaps show that ectocyst localization does not just correlate with but is caused by earlier expression, while localization in the endocyst layer and ostioles is caused by later expression. A chitin-binding domain from anEntamoebachitinase shows chitin forms thick fibrils in the ectocyst layer and a honeycomb in the endocyst layer. AlphaFold shows Ac wall proteins originate from bacteria by horizontal gene transfer (β-helical folds of Jonah and three cupredoxin-like domains of the laccase), share common ancestry with wall proteins of slime molds (β-jelly-roll folds of Luke), or are unique toAcanthamoeba(four disulfide knots of Leo). Ala mutations show linear arrays of aromatic amino acids in β-jelly-roll folds of Luke and disulfide knots of Leo are necessary for binding cellulose and proper localization of proteins in the cyst wall. Finally, rabbit antibodies to recombinant Jonah, Luke, Leo, and laccase efficiently detect calcoflour white-labeled cysts of 10 of 11Acanthamoebaisolates tested, suggesting all four proteins are excellent diagnostic targets.

IMPORTANCE

Acanthamoebaeare free-living amoeba in the soil and water that causeAcanthamoebakeratitis in under-resourced countries, where water for washing hands may be scarce.Acanthamoebais an emerging pathogen in the United States, because of its association with contact lens use. Here we show early expression during encystation causes a Jonah lectin and a laccase to localize to the outer layer of the cyst wall, while later expression cause Luke and Leo lectins to localize to the inner layer and the conical ostioles that connect the layers. We used structural predictions to identify the aromatic amino acids of Luke and Leo necessary for binding cellulose in the wall and to identify domains of Jonah and laccase useful for making recombinant proteins to immunize rabbits. Rabbit antibodies to Jonah, Luke, Leo, and laccase all efficiently detected cysts of tenAcanthamoebaisolates, including five T4 genotypes that cause most keratitis cases.
Chemogenetic silencing reveals presynaptic Gi/o protein-mediated inhibition of synchronized activity in the developing hippocampusin vivo
Authors: Graf Jürgen , Samiee Arash , Flossmann Tom , Holthoff Knut , Kirmse Knut
Published: February 2024

The development of neuronal circuits is an activity-dependent process. Research aimed at deciphering the learning rules governing these developmental refinements is increasingly utilizing a class of chemogenetic tools that employ Gi/oprotein signaling (Gi-DREADDs) for neuronal silencing. However, their mechanisms of action and inhibitory efficacy in immature neurons with incompletely developed Gi/osignaling are poorly understood. Here, we analyze the impact of Gi/osignaling on cellular and network excitability in the neonatal hippocampus by expressing the Gi-DREADD hM4Di in telencephalic glutamatergic neurons of neonatal mice of both sexes. Using acousto-optic two-photon Ca2+imaging, we report that activation of hM4Di leads to a complete arrest of spontaneous synchronized activity in CA1in vitro. Electrophysiological analyses demonstrate that hM4Di-mediated silencing is not accounted for by changes in intrinsic excitability of CA1 pyramidal cells (PCs). Instead, activation of hM4Di robustly restrains synaptic glutamate release by the first postnatal week, effectively reducing recurrent excitation in CA1.In vivo, inhibition through hM4Di potently suppresses early sharp waves (eSPWs) and discontinuous oscillatory network activity in CA1 of head-fixed mice before eye opening. In summary, hM4Di dampens glutamatergic neurotransmission through a presynaptic mechanism sufficient to terminate spontaneous synchronized activity in the neonatal CA1. Our findings have implications for designing and interpreting experiments utilizing Gi-DREADDs in immature neurons and further point to a potential role of Gi/o-dependent endogenous neuromodulators in activity-dependent hippocampal development.

Significance Statement

Recent advances in understanding how early activity shapes developing brain circuits increasingly rely on Gi/o-dependent inhibitory chemogenetic tools (Gi-DREADDs). However, their single-cellular mechanisms and efficacy in neurons with immature Gi/osignaling are elusive. To close this gap, we analyzed the impact of the Gi-DREADD hM4Di in the neonatal murine hippocampus. We report that hM4Di does not mediate hyperpolarization or shunting but rather acts as a potent presynaptic silencer of glutamatergic neurotransmission in CA1 pyramidal cells. Presynaptic inhibition of excitation suffices to arrest spontaneous synchronized network activityin vitroandin vivo. Our findings provide novel insights into the generative mechanisms of spontaneous synchronized activity and bear relevance for applying chemogenetic silencing at early stages of brain development.
Distinct representational roles of distributed cortical regions for working memory storage
Authors: Chopurian Vivien , Weber Simon , Christophel Thomas
Published: February 2024

While distributed cortical areas represent working memory contents, their necessity for memory maintenance has been questioned. To understand whether these regions serve separable roles when multiple items are maintained, we examined the effect of visual working memory load on neural information across cortical regions. In each trial of the fMRI experiment, participants (N=81) had to memorize two items, each either an orientation or a pure pitch, for 13.8s and continuously recalled the target after the delay. We kept the overall working memory load constant, but varied the sensory modality of each item to vary the effective visual load. We show that increasing visual load decreased behavioural recall performance for orientations and continuous orientation-specific decodable information in visual cortex but not in frontoparietal areas. Simulations show that this selective drop in decodable information is best interpreted as a drop in mnemonic information represented by patterns of visual cortex activity. Our results provide evidence for distinct roles of visual cortices, where single orientations can be stored with high fidelity, and anterior cortices, where multiple orientations could be represented in distinct cortical patterns.

Significance statement

This study investigated the role of these distributed regions for maintaining multiple items in work- ing memory. We find that orientation information could be decoded in visual and frontoparietal areas for low and high visual load. However, a visual-load-dependent decline in decoding accu- racy during the maintenance period was only observed in visual but not frontoparietal areas. Our results highlight the interplay between different cortical regions for the maintenance of multiple working memory items.
3-Fermion Topological Quantum Computation
Authors: Roberts Sam , Williamson Dominic J.
Published: February 2024

We present a scheme for universal topological quantum computation based on Clifford-complete braiding and fusion of symmetry defects in the 3-fermion anyon theory, supplemented with magic state injection. We formulate a fault-tolerant measurement-based realization of this computational scheme on the lattice using ground states of the Walker-Wang model for the 3-fermion anyon theory with symmetry defects. The Walker-Wang measurement-based topological quantum computation paradigm that we introduce provides a general construction of computational resource states with thermally stable symmetry-protected topological order. We also demonstrate how symmetry defects of the 3-fermion anyon theory can be realized in a two-dimensional subsystem code due to Bombín—making contact with an alternative implementation of the 3-fermion defect-computation scheme via code deformations.

Published by the American Physical Society
2024
Navigating the change: a case study of the textile industry on digital leadership, digital transformation and innovative business models
Authors: Malik Mehreen , Raziq Muhammad Mustafa , Sarwar Naukhez , Gohar Madiha
Published: February 2024

Purpose

We explore the skills required for digital leadership for reshaping existing business models toward digital models. Digital leadership is pivotal in gaining a competitive advantage and achieving successful digital transformation. However, little is known with regard to the underlying mechanisms related to digital leadership and transformation.

Design/methodology/approach

Data are collected through semi-structured interviews involving 20 participants from five Pakistani textile companies. Thematic analysis was employed as a data analysis tool.

Findings

Findings show that certain skills such as technological know-how, innovativeness, adaptability, ability to lead and steer, honesty, integrity, transformative vision, communication and collaboration are conducive to successful digital transformation in textile manufacturing firms. Similarly, digital leaders can significantly enhance business model innovation, create value for the firm, help develop new products (value proposition) and create Ecosystem partnerships (value network).

Originality/value

This article bridges gaps between existing literature on digital transformation and leadership. Digital leadership skills for digital transformation and the role of digital leaders in business model innovation have not been explored before. The conceptual framework is put forth, propositions are proposed and the findings offer some future research directions.