bluuebunny/crossref_metadata_2025 huggingface dataset:
Glucocorticoids suppress NF-κB-mediated neutrophil control ofAspergillus fumigatushyphal growth
Authors: Thrikawala Savini U. , Anderson Molly , Rosowski Emily E.
Published: December 2023

Glucocorticoids are a major class of therapeutic anti-inflammatory and immunosuppressive drugs prescribed to patients with inflammatory diseases, to avoid transplant rejection, and as part of cancer chemotherapy. However, exposure to these drugs increases the risk of opportunistic infections such as with the fungusAspergillus fumigatus. Prolonged glucocorticoid therapy is one of the main risks for invasive aspergillosis, which causes mortality in >50% of infected patients. The mechanisms by which glucocorticoids increase susceptibility toA. fumigatusare poorly understood. Here, we used a zebrafish larva-Aspergillusinfection model to identify innate immune mechanisms altered by glucocorticoid treatment. Infected larvae exposed to dexamethasone succumb to the infection at a significantly higher rate than control larvae. However, both macrophages and neutrophils are still recruited to the site of infection and dexamethasone treatment does not significantly affect fungal spore killing. Instead, the primary effect of dexamethasone manifests later in infection with treated larvae exhibiting increased invasive hyphal growth. In line with this, dexamethasone predominantly inhibits neutrophil function, rather than macrophage function. Dexamethasone-induced mortality also depends on the glucocorticoid receptor. One pathway that glucocorticoids can inhibit is NF-κB activation and we report that dexamethasone partially suppresses NF-κB activation at the infection site by inducing the transcription of IκB via the glucocorticoid receptor. Independent CRISPR/Cas9 targeting of IKKγ to prevent NF-κB activation also increases invasiveA. fumigatusgrowth and larval mortality. However, dexamethasone treatment of IKKγ crispant larvae further increases invasive hyphal growth, suggesting that dexamethasone may suppress other pathways in addition to NF-κB to promote host susceptibility. Collectively, we find that dexamethasone acts through the glucocorticoid receptor to suppress NF-κB-mediated neutrophil control ofA. fumigatushyphae in zebrafish larvae.

Author Summary

Glucocorticoids are drugs that stop inflammation and suppress the immune system. Glucocorticoids are effective in treating inflammatory diseases such as asthma and arthritis, preventing organ rejection after transplant surgery, and in ameliorating the side effects of cancer chemotherapy. However, as these drugs suppress the immune system, patients taking glucocorticoids are more prone to infections such as with the environmental fungusAspergillus fumigatus. The specific mechanisms that glucocorticoids inhibit to increase susceptibility to infection are largely unknown. Here, we used a larval zebrafish model ofA. fumigatusinfection to determine that glucocorticoids mainly suppress the ability of neutrophils to control the fungal hyphal growth that causes tissue damage. Our study provides insight into future strategies to treatA. fumigatusinfection in patients undergoing glucocorticoid therapy.
Normalization and gene selection for single-cell RNA-seq UMI data using sampling-adjusted sums of squares of Pearson residuals with a Poisson model
Authors: Klebanoff Victor
Published: December 2023

SCTransforminSeuratandscanpy.experimental.pp.recipe pearson residuals(scanpyhenceforth) normalize UMI counts as Pearson residuals of negative binomial models. Residual variance scores genes for downstream analysis. Although we observed that both methods usually assign the highest scores to the same genes, for many highly ranked genes (e.g. among the top 2,000) scores may be unstable – not robust to the selection of cells used to calculate residuals. As an alternative, we consider the Poisson model, for which a natural score is the mean sum of squares of Pearson residuals. We show that these scores can be unstable if a gene’s nonzero UMI counts are concentrated on a small number of cells. This explains the instability forscanpybecause of its similarity to the Poisson model. We define a metric for genes’ instability and observe that for all three methods it is negatively correlated with the number of cells on which genes’ counts are nonzero. To reduce the instability of scores based on the Poisson model, we score each gene using multiple random samples of approximately half of the cells. The minimum of these values defines a “sampling-adjusted” score. For data that we analyzed, these are more stable than scores fromSCTransformandscanpywhile generally agreeing with them on the highest ranked genes. As a second criterion to compare our proposal withSCTransform, we use differential expression analysis. For genes with high scores, the residuals’ Kruskal-Wallis H-statistics are generally greater for our method than forSCTransformand are more highly correlated with our method’s scores.
Mechanisms by which barrier-to-autointegration factor regulates dynamics of nucleocytoplasmic leakage and membrane repair following nuclear envelope rupture
Authors: Halfmann Charles T. , Scott Kelsey L. , Sears Rhiannon M. , Roux Kyle J.
Published: December 2023

The nuclear envelope (NE) creates a barrier between the cytosol and nucleus during interphase that is key for cellular compartmentalization and protecting genomic DNA. NE rupture can expose genomic DNA to the cytosol and allow admixture of the nuclear and cytosolic constituents, a proposed mechanism of cancer and NE-associated diseases. Barrier-to-autointegration factor (BAF) is a DNA-binding protein that localizes to NE ruptures where it recruits LEM-domain proteins, A-type lamins, and participates in rupture repair. To further reveal the mechanisms by which BAF responds to and aids in repairing NE ruptures, we investigated known properties of BAF including LEM domain binding, lamin binding, compartmentalization, phosphoregulation of DNA binding, and BAF dimerization. We demonstrate that it is the cytosolic population of BAF that functionally repairs NE ruptures, and phosphoregulation of BAF’s DNA-binding that enables its ability to facilitate that repair. Interestingly, BAF’s LEM or lamin binding activity appears dispensable for its role in functional repair. Furthermore, we demonstrate that BAF functions to reduce the extent of leakage though NE ruptures, suggesting that BAF effectively forms a diffusion barrier prior to NE repair. Collectively, these results enhances our knowledge of the mechanisms by which BAF responds to NE ruptures and facilitates their repair.
Presenilin-dependent regulation of tau pathology via the autophagy/proteasome pathway
Authors: del Ser-Badia Anna , Soto-Faguás Carlos M. , Vecino Rebeca , Rodríguez-Alvarez José , Vicario Carlos , Saura Carlos A.
Published: December 2023

Autosomal dominant inherited mutations in the presenilin (PS/PSEN) genes cause early-onset familial Alzheimer’s disease (AD) by enhancing cerebral accumulation of amyloid-β (Aβ) and microtubule-associated protein tau, although the precise cellular mechanisms by which PS dysfunction drives neuronal tau pathology remain still unclear. Here, we investigated the mechanisms linking PS/γ-secretase-dependent tau pathology and autophagy by using molecular, imaging and pathological approaches in brains, fibroblasts and induced pluripotent stem cells (iPSCs)-derived neurons from mutantPSEN1carriers, as well as in a novel tauopathy mouse model lackingPSin glutamatergic neurons. We found colocalization of phosphorylated tau with the autophagy marker p62 in the hippocampus of tauopathy patients withPSEN1mutations, corticobasal degeneration and Pick’s disease. Remarkably, disrupted autophagic clearance of pathological tau was evidenced by increased autophagy markers and accumulation of total and AD-associated phosphorylated tau species (pTau 181, 202, 217) in hippocampal lysates and autophagosomes of familial AD-linkedPSEN1patients andPS-deficient tau transgenic mice. Human iPSC-derived neurons harboring the familial AD-linkedPSEN1G206D mutation are less sensitive to autophagy inhibition, reduce tau release and accumulate intracellular tau oligomers. Human primary fibroblasts fromPSEN1G206D and/or L286P carriers show elevated LC3 and autolysosomes indicating that these familial AD-linkedPSEN1mutations disrupt autophagy flux. PS is required for efficient autophagy-mediated tau degradation in neurons through a dual mechanism involving autophagy induction via blockage of Akt/PRAS40-dependent mTORC1 activation and promoting autophagosome/lysosome fusion. Surprisingly, pharmacological proteasome inhibition decreases tau accumulation in neurons by promoting tau release through a mechanism that requires functionalPS.In conclusion, PS is required for autophagy/proteasome-mediated tau elimination in neurons, while familial AD-linkedPSENmutations cause progressive tau pathology by disrupting autophagy. These findings may impact on the development of new therapeutic targets for tauopathy dementias.
Infection and antibiotic-associated changes in the fecal microbiota ofC. rodentiumϕstx2dact-infected C57BL/6 mice
Authors: Mühlen Sabrina , Heroven Ann Kathrin , Elxnat Bettina , Kahl Silke , Pieper Dietmar H. , Dersch Petra
Published: December 2023

EnterohemorrhagicE. colicauses watery to bloody diarrhea, which may progress to hemorrhagic colitis and hemolytic-uremic syndrome. While early studies suggested that antibiotic treatment may worsen the pathology of an EHEC infection, recent work has shown that certain non-Shiga toxin-inducing antibiotics avert disease progression. Unfortunately, both intestinal bacterial infections and antibiotic treatment are associated with dysbiosis. This can alleviate colonization resistance, facilitate secondary infections, and potentially lead to more severe illness. To address the consequences in the context of an EHEC infection, we used the established mouse infection model organismC. rodentiumϕstx2dactand monitored changes in fecal microbiota composition during infection and antibiotic treatment.C. rodentiumϕstx2dactinfection resulted in minor changes compared to antibiotic treatment. The infection caused clear alterations in the microbial community, leading mainly to a reduction of Muribaculaceae and a transient increase in Enterobacteriaceae distinct fromCitrobacter. Antibiotic treatments of the infection resulted in marked and distinct variations in microbiota composition, diversity, and dispersion. Enrofloxacin and trimethoprim/sulfamethoxazole, which did not prevent Stx-mediated organ damage, had the least disruptive effects on the intestinal microbiota, while kanamycin and tetracycline, which rapidly cleared the infection, caused a severe reduction in diversity. Kanamycin treatment resulted in the depletion of all but Bacteroidetes genera, whereas tetracycline effects on Clostridia were less severe. Together, these data highlight the need to address the impact of individual antibiotics in the clinical care of life-threatening infections and consider microbiota-regenerating therapies.

IMPORTANCE

Understanding the impact of antibiotic treatment on enterohemorrhagicE. coli(EHEC) infections is crucial for appropriate clinical care. While discouraged by early studies, recent findings suggest certain antibiotics can impede disease progression. Here, we investigated the impact of individual antibiotics on the fecal microbiota in the context of an established EHEC mouse model usingC. rodentiumϕstx2dact. The infection caused significant variations in the microbiota, leading to a transient increase in Enterobacteriaceae distinct fromCitrobacter. However, these effects were minor compared to those observed for antibiotic treatments. Indeed, antibiotics that most efficiently cleared the infection also had the most detrimental effect on the fecal microbiota, causing a substantial reduction in microbial diversity. Conversely, antibiotics showing adverse effects or incomplete bacterial clearance had a reduced impact on microbiota composition and diversity. Taken together, our findings emphasize the delicate balance required to weigh the harmful effects of infection and antibiosis in treatment.
Benchmarking feature selection and feature extraction methods to improve the performances of machine-learning algorithms for patient classification using metabolomics biomedical data
Authors: Labory Justine , Njomgue-Fotso Evariste , Bottini Silvia
Published: December 2023

Objective

Classification tasks are an open challenge in the field of biomedicine. While several machine-learning techniques exist to accomplish this objective, several peculiarities associated with biomedical data, especially when it comes to omics measurements, prevent their use or good performance achievements. Omics approaches aim to understand a complex biological system through systematic analysis of its content at the molecular level. On the other hand, omics data are heterogeneous, sparse and affected by the classical “curse of dimensionality” problem, i.e. having much fewer observation samples (n) than omics features (p). Furthermore, a major problem with multi- omics data is the imbalance either at the class or feature level. The objective of this work is to study whether feature extraction and/or feature selection techniques can improve the performances of classification machine-learning algorithms on omics measurements.

Methods

Among all omics, metabolomics has emerged as a powerful tool in cancer research, facilitating a deeper understanding of the complex metabolic landscape associated with tumorigenesis and tumor progression. Thus, we selected three publicly available metabolomics datasets, and we applied several feature extraction techniques both linear and non-linear, coupled or not with feature selection methods, and evaluated the performances regarding patient classification in the different configurations for the three datasets.

Results

We provide general workflow and guidelines on when to use those techniques depending on the characteristics of the data available. For the three datasets, we showed that applying feature selection based on biological previous knowledge improves the performances of the classifiers. Notebook used to perform all analysis are available at:https://github.com/Plant-Net/Metabolomic_project/.
Deletion of Glyoxalase 1 exacerbates acetaminophen-induced hepatotoxicity in mice
Authors: Dobariya Prakashkumar , Xie Wei , Rao Swetha Pavani , Xie Jiashu , Seelig Davis M. , Vince Robert , Lee Michael K. , More Swati S.
Published: December 2023

Acetaminophen (APAP) overdose triggers a cascade of intracellular oxidative stress events culminating in acute liver injury. The clinically used antidote, N-acetylcysteine (NAC) has a narrow therapeutic window and early treatment is essential for satisfactory therapeutic outcome. For more versatile therapies that can be effective even at late-presentation, the intricacies of APAP-induced hepatotoxicity must be better understood. Accumulation of advanced glycation end-products (AGEs) and consequent activation of the receptor for AGEs (RAGE) are considered one of the key mechanistic features of APAP toxicity. Glyoxalase-1 (Glo-1) regulates AGE formation by limiting the levels of methylglyoxal (MEG). In this study, we studied the relevance of Glo-1 in APAP mediated activation of RAGE and downstream cell-death cascades. Constitutive Glo-1 knockout mice (GKO) and a cofactor of Glo-1, ψ-GSH, were employed as tools. Our findings show elevated oxidative stress, activation of RAGE and hepatocyte necrosis through steatosis in GKO mice treated with high-dose APAP compared to wild type controls. A unique feature of the hepatic necrosis in GKO mice is the appearance of microvesicular steatosis as a result of centrilobular necrosis, rather than inflammation seen in wild type. The GSH surrogate and general antioxidant, ψ-GSH alleviated APAP toxicity irrespective of Glo-1 status, suggesting that oxidative stress being the primary driver of APAP toxicity. Overall, exacerbation of APAP hepatotoxicity in GKO mice suggests the importance of this enzyme system in antioxidant defense against initial stages of APAP overdose.
Alternate routes to mnm5s2U synthesis in Gram-positive bacteria
Authors: Jaroch Marshall , Sun Guangxin , Tsui Ho-Ching Tiffany , Reed Colbie , Sun Jinjing , Jörg Marko , Winkler Malcolm E. , Rice Kelly C. , Stich Troy A. , Dedon Peter C. , Dos Santos Patricia C. , de Crécy-Lagard Valérie
Published: December 2023

The wobble bases of tRNAs that decode split codons are often heavily modified. In Bacteria tRNAGlu,Gln,Aspcontain a variety of xnm5s2U derivatives. The synthesis pathway for these modifications is complex and fully elucidated only in a handful of organisms, including the Gram-negativeEscherichia coliK12 model. Despite the ubiquitous presence of mnm5s2U modification, genomic analysis shows the absence ofmnmCorthologous genes, suggesting the occurrence of alternate biosynthetic schemes for the installation of this modification. Using a combination of comparative genomics and genetic studies, a member of the YtqA subgroup of the Radical Sam superfamily was found to be involved in the synthesis of mnm5s2U in bothBacillus subtilisandStreptococcus mutans. This protein, renamed MnmL, is encoded in an operon with the recently discovered MnmM methylase involved in the methylation of the pathway intermediate nm5s2U into mnm5s2U inB. subtilis. Analysis of tRNA modifications of bothS. mutansandStreptococcus pneumoniaeshows that growth conditions and genetic backgrounds influence the ratios of pathways intermediates in regulatory loops that are not yet understood. The MnmLM pathway is widespread along the bacterial tree, with some phyla, such as Bacilli, relying exclusively on these two enzymes. The occurrence of fusion proteins, alternate arrangements of biosynthetic components, and loss of biosynthetic branches provide examples of biosynthetic diversity to retain a conserved tRNA modification in nature.

Importance

The xnm5s2U modifications found in several tRNAs at the wobble base position are widespread in Bacteria where they have an important role in decoding efficiency and accuracy. This work identifies a novel enzyme (MnmL) that is a member of a subgroup of the very versatile Radical SAM superfamily and is involved in the synthesis of mnm5s2U in several Gram-positive bacteria, including human pathogens. This is another novel example of a non-orthologous displacement in the field of tRNA modification synthesis, showing how different solutions evolve to retain U34 tRNA modifications.
Spatial analysis of NOS2 and COX2 interaction with T-effector cells reveals immunosuppressive landscapes associated with poor outcome in ER- breast cancer patients
Authors: Ridnour Lisa A. , Cheng Robert Y.S. , Heinz William F. , Pore Milind , Gonzalez Ana L. , Femino Elise L. , Moffat Rebecca , Wink Adelaide L. , Imtiaz Fatima , Coutinho Leandro , Butcher Donna , Edmondson Elijah F. , Rangel M. Cristina , Wong Stephen T.C. , Lipkowitz Stanley , Glynn Sharon , Vitek Michael P. , McVicar Daniel W. , Li Xiaoxian , Anderson Stephen K. , Paolocci Nazareno , Hewitt Stephen M. , Ambs Stefan , Billiar Timothy R. , Chang Jenny C. , Lockett Stephen J. , Wink David A.
Published: December 2023

Multiple immunosuppressive mechanisms exist in the tumor microenvironment that drive poor outcomes and decrease treatment efficacy. The co-expression of NOS2 and COX2 is a strong predictor of poor prognosis in ER- breast cancer and other malignancies. Together, they generate pro-oncogenic signals that drive metastasis, drug resistance, cancer stemness, and immune suppression. Using an ER- breast cancer patient cohort, we found that the spatial expression patterns of NOS2 and COX2 with CD3+CD8+PD1- T effector (Teff) cells formed a tumor immune landscape that correlated with poor outcome. NOS2 was primarily associated with the tumor-immune interface, whereas COX2 was associated with immune desert regions of the tumor lacking Teff cells. A higher ratio of NOS2 or COX2 to Teff was highly correlated with poor outcomes. Spatial analysis revealed that regional clustering of NOS2 and COX2 was associated with stromal-restricted Teff, while only COX2 was predominant in immune deserts. Examination of other immunosuppressive elements, such as PDL1/PD1, Treg, B7H4, and IDO1, revealed that PDL1/PD1, Treg, and IDO1 were primarily associated with restricted Teff, whereas B7H4 and COX2 were found in tumor immune deserts. Regardless of the survival outcome, other leukocytes, such as CD4 T cells and macrophages, were primarily in stromal lymphoid aggregates. Finally, in a 4T1 model, COX2 inhibition led to a massive cell infiltration, thus validating the hypothesis that COX2 is an essential component of the Teff exclusion process and, thus, tumor evasion. Our study indicates that NOS2/COX2 expression plays a central role in tumor immunosuppression. Our findings indicate that new strategies combining clinically available NOS2/COX2 inhibitors with various forms of immune therapy may open a new avenue for the treatment of aggressive ER- breast cancers.
Microbial aromatic amino acid metabolism is modifiable in fermented food matrices to promote bioactivity
Authors: Kasperek Mikaela C. , Galeas Adriana Velasquez , Caetano-Silva Maria Elisa , Xie Zifan , Ulanov Alexander V. , La Frano Michael R. , Devkota Suzanne , Miller Michael , Allen Jacob M.
Published: December 2023

Ingestion of fermented foods impacts human immune function, yet the bioactive food components underlying these effects are not understood. Here, we interrogated whether fermented food bioactivity could be traced to a class of microbial metabolites derived from aromatic amino acids (ArAA), termed aryl-lactates. Using targeted metabolomics, we established that the aryl-lactates phenyllactic acid (PLA), 4-hydroxyphenyllactic acid (4-HPLA), and indole-3-lactic acid (ILA), are present in varying concentrations across a wide range of commercially available fermented foods, including many vegetable and dairy ferments. After pinpointing fermented food-associated lactic acid bacteria (LAB) that produce high levels of aryl-lactates (e.g.,Lactiplantibacillus plantarum), we utilized our knowledge of LAB metabolism to identify fermentation conditions (added cultures [e.g.,L. plantarum] and metabolic co-factors [e.g., aryl-pyruvates]) to increase aryl-lactate production in food matrices up to 5×103fold vs. standard fermentation conditions. Next, usingex vivoreporter assays, we found that a variety of food matrix conditions optimized for aryl-lactate production exhibited enhanced agonist activity for the human aryl-hydrocarbon receptor (AhR) as compared to standard fermentation conditions and/or commercial brands. Moreover, we determined that strategies to enhance aryl-lactates effectively maintained food matrix AhR bioactivity across 4 weeks of storage. Reduced microbial-induced AhR activity has emerged as a hallmark of many chronic inflammatory diseases, thus we envision strategies to enhance microbially produced aryl-lactates and thus AhR bioactivity of fermented foods can be leveraged to improve human health.
Heterogeneous distribution of kinesin-streptavidin complexes revealed by Mass Photometry
Authors: Xu Jing , Brown Nathaniel J. S. , Seol Yeonee , Neuman Keir C.
Published: December 2023

Kinesin-streptavidin complexes are widely used in microtubule-based active-matter studies. The stoichiometry of the complexes is empirically tuned but experimentally challenging to determine. Here, mass photometry measurements reveal heterogenous distributions of kinesin-streptavidin complexes. Our binding model indicates that heterogeneity arises from both the kinesin-streptavidin mixing ratio and the kinesin-biotinylation efficiency.
Role of theosaAgene inAspergillus fumigatusdevelopment, secondary metabolism and virulence
Authors: Dabholkar Apoorva , Pandit Sandesh , Devkota Ritu , Dhingra Sourabh , Lorber Sophie , Puel Olivier , Calvo Ana M.
Published: December 2023

Aspergillus fumigatusis the leading cause of aspergillosis, associated with high mortality rates, particularly in immunocompromised individuals. In search of novel genetic targets against aspergillosis, we studied the WOPR transcription factor OsaA. Deletion of theosaAgene resulted in colony growth reduction. Conidiation is also influenced byosaA; bothosaAdeletion and overexpression resulted in a decrease in spore production. Wild-type expression levels ofosaAare necessary for expression of the conidiation regulatory genesbrlA,abaAandwetA. In addition,osaAis necessary for normal cell wall integrity. Furthermore, deletion ofosaAresulted in a reduction in the ability ofA. fumigatusto adhere to surfaces, decreased thermotolerance, as well as increased sensitivity to oxidative stress. Metabolomics analysis indicated thatosaAdeletion or overexpression led to alterations in the production of multiple secondary metabolites, including gliotoxin. This was accompanied by changes in the expression of genes in the corresponding secondary metabolite gene clusters. These effects could be, at least in part, due to the observed reduction in the expression levels of theveAandlaeAglobal regulators when theosaAlocus was altered. Importantly, our study shows thatosaAis indispensable for virulence in both the neutropenic and corticosteroid-immunosuppressed mouse models.
Behavioral relevance of category selectivity revealed by human ECoG data
Authors: Hashemi Seyedamin , Ebadi Seyed Ali , Jahromy Fatemeh Zareayan , Treue Stefan , Kreiman Gabriel , Esghaei Moein
Published: December 2023

Object recognition is a crucial brain function that involves a complex interplay between various brain regions. However, the behavioral relevance of functional interactions between these regions remains largely unexplored. In this study, we examined the functional interactions between different brain regions during object recognition using intracranial electrocorticography (ECoG) recordings in subjects diagnosed with pharmacologically intractable epilepsy. We computed the phase locking value (PLV) between different brain areas and its category selectivity, and assessed its behavioral relevance by comparing correctly and incorrectly performed trials. Our results revealed that phase locking between brain regions varies across different object categories and that this variability significantly influences the perceptual behavior of subjects. Importantly, we found that the behavioral relevance of these interactions is spatially organized, with long-range (global) connections being more behaviorally relevant for the frontal lobe and local connections being more crucial for the occipital lobe. These findings underscore the unique roles of different brain areas in object recognition and pave the way for more nuanced explorations of the interplay between brain regions in object recognition and other cognitive functions.
Structure of the minor spliceosomal U11 snRNP
Authors: Zhao Jiangfeng , Peter Daniel , Brandina Irina , Liu Xiangyang , Galej Wojciech P.
Published: December 2023

The minor spliceosome catalyses the excision of U12-dependent introns from pre-mRNAs. These introns are rare, but their removal is critical for cell viability. We obtained a cryo-EM reconstruction of the 13-subunit U11 snRNP complex, revealing structures of U11 snRNA and five minor spliceosome-specific factors. U11 snRNP appears strikingly different from the equivalent major spliceosome U1 snRNP. SNRNP25 and SNRNP35 form a dimer, which specifically recognises U11 snRNA. PDCD7 forms extended helices, which bridge SNRNP25 and SNRNP48, located at the distal ends of the particle. SNRNP48 forms multiple interfaces with U11 snRNP and, together with ZMAT5, are positioned near the 5’-end of the U11 snRNA and likely stabilise the binding of the incoming 5’SS. Our structure provides mechanistic insights into U12-dependent intron recognition and the evolution of the splicing machinery.
CEP41, a ciliopathy-linked centrosomal protein, regulates microtubule assembly and cell proliferation
Authors: Prassanawar Shweta Shyam , Sarkar Tuhin , Panda Dulal
Published: December 2023

Centrosomal proteins play pivotal roles in orchestrating microtubule dynamics, and their dysregulation leads to disorders, including cancer and ciliopathies. Understanding the multifaceted roles of centrosomal proteins is vital to comprehend their involvement in disease development. Here, we report novel cellular functions of CEP41, a centrosomal and ciliary protein implicated in Joubert syndrome. We show that CEP41 is an essential microtubule-associated protein with microtubule-stabilizing activity. Purified CEP41 binds to preformed microtubules, promotes microtubule nucleation, and suppresses microtubule disassembly. When overexpressed in cultured cells, CEP41 localizes to microtubules and promotes microtubule bundling. Conversely, shRNA-mediated knockdown of CEP41 disrupts the interphase microtubule network and delays microtubule reassembly, emphasizing its role in microtubule organization. Further, we demonstrate that CEP41’s association with microtubules relies on its conserved rhodanese homology domain (RHOD) and the N-terminal region. Interestingly, a disease-causing mutation in the RHOD domain impairs CEP41-microtubule interaction. Moreover, depletion of CEP41 inhibits cell proliferation and disrupts cell cycle progression, suggesting its potential involvement in cell cycle regulation. These insights into the cellular functions of CEP41 hold promise for unraveling the impact of its mutations in ciliopathies.

A novel role of CEP41 as a microtubule-associated protein that promotes microtubule assembly and regulates cell cycle progression could offer insights into the development of ciliopathies.
Scaling of ventral hippocampal activity during anxiety
Authors: Cerquetella Carlo , Gontier Camille , Forro Thomas , Pfister Jean-Pascal , Ciocchi Stéphane
Published: December 2023

The hippocampus supports a multiplicity of functions, with the dorsal region contributing to spatial representations and memory, and the ventral hippocampus (vH) being primarily involved in emotional processing. While spatial encoding has been extensively investigated, how the vH activity is tuned to emotional states, e.g. to different anxiety levels, is not well understood. We developed an adjustable linear track maze (aLTM) for mice with which we could induce a scaling of behavioral anxiety levels within the same spatial environment. Usingin vivosingle-unit recordings, optogenetic manipulations and the application of a convolutional classifier, we examined the changes and causal effects of vH activity at different anxiety levels. We found that anxiogenic experiences activated the vH and that this activity scaled with increasing anxiety levels. We identified two processes that contributed to this scaling of anxiety-related activity: increased tuning and successive remapping of neurons to the anxiogenic compartment. Moreover, optogenetic inhibition of the vH reduced anxiety across different levels, while anxiety-related activity scaling could be decoded using a convolutional classifier. Collectively, our findings position the vH as a critical limbic region that functions as an ‘anxiometer’ by scaling its activity based on perceived anxiety levels. Our discoveries go beyond the traditional theory of cognitive maps in the hippocampus underlying spatial navigation and memory, by identifying hippocampal mechanisms selectively regulating anxiety.
A Fully-Automated Senescence Test (FAST) for the high-throughput quantification of senescence-associated markers
Authors: Neri Francesco , Takajjart Selma N. , Lerner Chad A. , Desprez Pierre-Yves , Schilling Birgit , Campisi Judith , Gerencser Akos A.
Published: December 2023

Cellular senescence is a major driver of aging and age-related diseases. Quantification of senescent cells remains challenging due to the lack of senescence-specific markers and generalist, unbiased methodology. Here, we describe the Fully-Automated Senescence Test (FAST), an image-based method for the high-throughput, single-cell assessment of senescence in cultured cells. FAST quantifies three of the most widely adopted senescence-associated markers for each cell imaged: senescence-associated β-galactosidase activity (SA-β-Gal) using X-Gal, proliferation arrest via lack of 5-ethynyl-2’-deoxyuridine (EdU) incorporation, and enlarged morphology via increased nuclear area. The presented workflow entails microplate image acquisition, image processing, data analysis, and graphing. Standardization was achieved by i) quantifying colorimetric SA-β-Gal via optical density; ii) implementing staining background controls; iii) automating image acquisition, image processing, and data analysis. In addition to the automated threshold-based scoring, a multivariate machine learning approach is provided. We show that FAST accurately quantifies senescence burden and is agnostic to cell type and microscope setup. Moreover, it effectively mitigates false-positive senescence marker staining, a common issue arising from culturing conditions. Using FAST, we compared X-Gal with fluorescent C12FDG live-cell SA-β-Gal staining on the single-cell level. We observed only a modest correlation between the two, indicating that those stains are not trivially interchangeable. Finally, we provide proof of concept that our method is suitable for screening compounds that modify senescence burden. This method will be broadly useful to the aging field by enabling rapid, unbiased, and user-friendly quantification of senescence burden in culture, as well as facilitating large-scale experiments that were previously impractical.
Computational identification of key transcription factors for embryonic and postnatalSox2+dental epithelial stem cell
Authors: Shao Fan , Van Otterloo Eric , Cao Huojun
Published: December 2023

While many reptiles can replace their tooth throughout life, human loss the tooth replacement capability after formation of the permanent teeth. It was thought that the difference in tooth regeneration capability depends on the persistence of a specialized dental epithelial structure, the dental lamina that contains dental epithelial stem cells (DESC). Currently, we know very little about DESC such as what genes are expressed or its chromatin accessibility profile. Multiple markers of DESC have been proposed such asSox2andLgr5. Few single cell RNA-seq experiments have been performed previously, but no obvious DESC cluster was identified in these scRNA-seq datasets, possible due to that the expression level of DESC markers such asSox2andLgr5is too low or the percentage of DESC is too low in whole tooth. We utilize a mouse lineSox2-GFPto enrichSox2+DESC and use Smart-Seq2 protocol and ATAC-seq protocol to generate transcriptome profile and chromatin accessibility profile of P2Sox2+DESC. Additionally, we generate transcriptome profile and chromatin accessibility profile of E11.5 Sox2+ dental lamina cells. With transcriptome profile and chromatin accessibility profile, we systematically identify potential key transcription factors for E11.5Sox2+cells and P2Sox2+cells. We identified transcription factors includingPitx2, Id3, Pitx1, Tbx1, Trp63, Nkx2-3, Grhl3, Dlx2, Runx1, Nfix, Zfp536, etc potentially formed the core transcriptional regulatory networks ofSox2+DESC in both embryonic and postnatal stages.
Optimization-Based Synthesis with Directed Cell Migration
Authors: Havenhill Eric C. , Ghosh Soham
Published: December 2023

Collective behavior of biological agents such as herds of organisms and cells is a fundamental feature in the systems biology and in the emergence of new phenomena in the biological environ-ment. Collective cell migration under a physical or chemical cue is an example of this fundamental phenomenon where individual cell migration is driven by the collective behavior of the neighboring cells and vice versa. The goal of this research is to discover the mathematical rules of collective cell migration using experimental data and testing the predictive nature of the models in independent experimental data. Such insight is made possible in this work with the hybrid use of dynamic mode decomposition (DMD) [1] and optimal control theory. Both single and multi-cellular systems are simulated, including obstacle courses, using this framework. The results of this work show how cells collectively behave during their migration and also, opens the possibility of designing robotic cells for possible therapeutic purpose where the cell trajectory can be controlled.
Neutrophil extracellular traps drive lupus flares with acute skin and kidney inflammation triggered by ultraviolet irradiation
Authors: Lyu Xing , Li Minghui , Zhang Ping L. , Wei Wei , Werth Victoria P. , Liu Ming-Lin
Published: December 2023

Sunlight triggers lupus flares causing both local skin and systemic inflammation, including lupus nephritis, through poorly understood mechanisms. To address this knowledge gap, we found that UVB irradiation of asymptomatic, young female lupus-prone mice induced skin and kidney inflammation with proteinuria, accompanied by neutrophil infiltration and neutrophil extracellular trap (NET) formation. Furthermore, UVB irradiation induced co-expression of CXCR4 and cytokines/C3 by neutrophilsin vitroandin vivo,in the skin and kidneys of lupus-prone mice, indicating their transmigratory and pro-inflammatory potentials. A causality study demonstrated that inhibiting CXCR4 attenuated renal neutrophil infiltration, accumulation of NETs, NET-associated cytokines/C3, and proteinuria in UVB-irradiated lupus-prone mice. Remarkably, inhibiting NETosis through a novel strategy targeting nuclear envelope integrity reduced deposition of NET-associated cytokines/C3 in skin and kidneys, attenuating proteinuria in UVB-irradiated MRL/lpr·lmnB1Tgmice. Our investigation unveils a new mechanism by which neutrophil NETs drive the early onset of lupus flares triggered by UVB-irradiation. Targeting neutrophil transmigration and NETosis could be promising therapeutic strategies.
The Neuroprotective Effect of Short-chain Fatty Acids Against Hypoxia-reperfusion Injury
Authors: Harijan Anjit K. , Kalaiarasan Retnamony , Ghosh Amit Kumar , Jain Ruchi P. , Bera Amal Kanti
Published: December 2023

Gut microbe-derived short-chain fatty acids (SCFAs) are known to have a profound impact on various brain functions, including cognition, mood, and overall neurological health. However, their role, if any, in protecting against hypoxic injury and ischemic stroke has not been extensively studied. In this study, we investigated the effects of two major SCFAs abundant in the gut, propionate (P) and butyrate (B), on hypoxia-reperfusion injury using a neuronal cell line and a zebrafish model. Neuro 2a (N2a) cells treated with P and B exhibited reduced levels of mitochondrial and cytosolic reactive oxygen species (ROS), diminished loss of mitochondrial membrane potential, suppressed caspase activation, and lower rates of cell death when exposed to CoCl2-induced hypoxia, compared to the control group. Furthermore, adult zebrafish fed with SCFAs-supplemented feeds showed less susceptibility to hypoxic conditions compared to the control group, as indicated by multiple behavioral measures. Histological analysis of TTC-stained brain sections revealed lesser damage in the SCFAs-fed group. We also found that FABP7 (also known as BLBP), a neuroprotective fatty acid binding protein, was upregulated in the brains of the SCFAs-fed group. Additionally, when FABP7 was overexpressed in N2a cells, it protected the cells from hypoxia-reperfusion injury. Overall, our data clearly demonstrates a neuroprotective role of P and B against hypoxic brain injury and suggests the potential of dietary supplementation with SCFAs to mitigate stroke-induced brain damage.

Highlights

Short-chain fatty acid (SCFA) Propionate (P) and Butyrate (B) protect N2a cells from hypoxia-reperfusion.

Zebrafish, when fed an SCFA-supplemented diet, are more resilient to hypoxia-reperfusion.

SCFAs in the diet boost brain expression of FABP7 (fatty acid binding protein).

FABP7 overexpression in N2a cells provides protection against hypoxia-reperfusion.

SCFAs reduce reactive oxygen species (ROS) levels and increase FABP7, contributing to neuroprotection.
Novel nitrifying symbiont lineages are vertically inherited and widespread in marine sponges
Authors: Glasl Bettina , Luter Heidi M. , Damjanovic Katarina , Kitzinger Katharina , Mueller Anna J. , Mahler Leonie , Engelberts Joan Pamela , Rix Laura , Osvatic Jay T. , Hausmann Bela , Séneca Joana , Daims Holger , Pjevac Petra , Wagner Michael
Published: December 2023

Ammonia-oxidising archaea and nitrite-oxidising bacteria are common members of marine sponge microbiomes. They derive energy for carbon fixation and growth from nitrification - the oxidation of ammonia to nitrite and further to nitrate - and are proposed to play essential roles in the carbon and nitrogen cycling of sponge holobionts. In this study, we characterise two novel nitrifying symbiont lineages, ‘Ca. Nitrosokoinonia’ and ‘Ca. Nitrosymbion’ in the marine spongeCoscinoderma matthewsiusing a combination of molecular tools, single-cell imaging techniques, and physiological rate measurements. Both represent a new genus in the ammonia-oxidising archaeal classNitrososphaeriaand the nitrite-oxidising bacterial orderNitrospirales, respectively. Furthermore, we show that larvae of this viviparous sponge are densely colonised by representatives of ‘Ca. Nitrosokoinonia’ and ‘Ca. Nitrosymbion’ indicating vertical transmission. In adults, the representatives of both symbiont genera are located extracellularly in the mesohyl. Comparative metagenome analyses and physiological data suggest that ammonia-oxidising archaeal symbionts of the genusCa. Nitrosokoinonia strongly rely on endogenously produced nitrogenous compounds (i.e., ammonium, urea, nitriles/cyanides, and creatinine) rather than on exogenous ammonium sources taken up by the sponge. Additionally, the nitrite-oxidising bacterial symbiontsCa. Nitrosymbion may reciprocally support the ammonia-oxidisers with ammonia via the utilisation of sponge-derived urea and cyanate. Interestingly, comparative analyses of published environmental 16S rRNA amplicon data revealed that ‘Ca. Nitrosokoinonia’ and ‘Ca. Nitrosymbion’ are widely distributed and predominantly associated with marine sponges and corals, suggesting a broad relevance of our findings.
Influence of different landscape configurations on insect pollinators of important horticultural crops in a western Himalayan landscape
Authors: Khan Susmita , Sinha Bitapi , Uniyal V.P.
Published: December 2023

Pollinators play critical roles in ecosystem stability and agricultural productivity, and their decline has become a global concern. One of the main reasons for pollinators decline is changing landscape configuration. We conducted this study in Kullu Valley, Himachal Pradesh, India to evaluate varied landscape configuration impacts on the diversity, richness, and abundance of insect pollinators in apple and plum orchards. Five different landscape configurations were considered for the study. The survey spanned 28 orchards across the valley during the blooming periods of 2021 and 2022. Standard sampling protocols were used to collect the pollinator specimen. We recorded a total of 107 insect species across 67 genera, 29 families and five orders (Hymenoptera, Lepidoptera, Diptera, Coleoptera, and Thysanoptera) from different orchards. Hymenoptera and Diptera were the most abundant pollinators in the study area. Pollinator richness and diversity were higher in orchards located within 1-km of natural forests and in lower elevations (>1500 meters). Orchards near large settlements, agricultural lands and complete modernised management practice showed comparative less pollinator diversity and abundance. This study demonstrates the influence of diverse land-use practices on pollinators on a landscape scale and provides insights for developing effective conservation strategies in the Himalaya.
The intracellular C-terminus confers compartment-specific targeting of voltage-gated Ca2+channels
Authors: Chin Morven , Kaeser Pascal S.
Published: December 2023

To achieve the functional polarization that underlies brain computation, neurons sort protein material into distinct compartments. Ion channel composition, for example, differs between axons and dendrites, but the molecular determinants for their polarized trafficking remain obscure. Here, we identify the mechanisms that target voltage-gated Ca2+channels (CaVs) to distinct subcellular compartments. In hippocampal neurons, CaV2s trigger neurotransmitter release at the presynaptic active zone, and CaV1s localize somatodendritically. After knockout of all three CaV2s, expression of CaV2.1, but not of CaV1.3, restores neurotransmitter release. Chimeric CaV1.3 channels with CaV2.1 intracellular C-termini localize to the active zone, mediate synaptic vesicle exocytosis, and render release fully sensitive to blockade of CaV1 channels. This dominant targeting function of the CaV2.1 C-terminus requires an EF hand in its proximal segment, and replacement of the CaV2.1 C-terminus with that of CaV1.3 abolishes CaV2.1 active zone localization. We conclude that the intracellular C-termini mediate compartment-specific CaVtargeting.
Window dressing in the banking sector of an emerging economy: evidence from aggregate data
Authors: Moosa Imad A. , Alsaad Khalid , Khatatbeh Ibrahim N.
Published: December 2023

Purpose

This study aims to investigate window dressing as practiced by commercial banks in Kuwait, using monthly aggregate balance sheet data covering the period January 1993 to December 2017.

Design/methodology/approach

This study applies the structural time series model to decompose an observed time series into unobserved components based on monthly data covering January 1993 to December 2017 on the consolidated balance sheet of commercial banks in Kuwait.

Findings

The empirical results indicate that Kuwaiti commercial banks indulge in upward window dressing to boost size and liquidity. This kind of behaviour is indicated by a statistically significant rise in assets under the control of banks in December, followed by a statistically significant decline in January. The operation is funded by borrowing, leading to a December rise and a January fall in foreign and other liabilities, which are also under the control of commercial banks.

Originality/value

This study uses a novel methodology to detect window dressing based on the seasonal behaviour of balance sheet items. This study suggests a unified framework for the motives, targets, types and consequences of window dressing and how they are related.
Developing a framework for building information modelling (BIM) adoption in New Zealand
Authors: Doan Dat Tien , Ghaffarianhoseini Ali , Naismith Nicola , Ghaffarianhoseini Amirhosein , Tookey John
Published: December 2023

Purpose

In New Zealand, building information modelling (BIM) prevalence is still in its early stages and faces many challenges. This research aims to develop a BIM adoption framework to determine the key factors affecting the success of a BIM project.

Design/methodology/approach

Both primary and secondary data were employed in this research, including 21 semi-structured interviews and industry guidelines from the three most well-known global building excellence models (BEMs). The data were analysed through content analysis due to its recognised benefits as a transparent and reliable approach.

Findings

Leadership, clients and other stakeholders, strategic planning, people, resources, process and results were identified as seven main categories along with 39 indicators in the BIM adoption framework. Based on the interviewees' perspectives, leadership is considered the most significant category, impacting all of the remaining categories.

Practical implications

Using the developed framework will enhance comprehension of BIM, offering directives for those embracing BIM. This will aid construction stakeholders in being better equipped for BIM projects. Having a skilled BIM manager can lead to the success of construction projects.

Originality/value

This research contributed to the existing body of knowledge by providing the categories with specific factors that assist BIM practitioners in assessing their BIM performance for further BIM practice improvement.