bluuebunny/crossref_metadata_2025 huggingface dataset:
Prenatal exposure to valproic acid induces sex-specific alterations in cortical and hippocampal neuronal structure and function in rats
Authors: Williams Olivia O. F. , Coppolino Madeleine , Micelli Cecilia B. , McCallum Ryan T. , Henry-Duru Paula T. , Manduca Joshua D. , Lalonde Jasmin , Perreault Melissa L.
Published: September 2024

Background

There are substantial differences in the characteristics of males and females with an autism spectrum disorder (ASD), yet there is little knowledge surrounding the mechanistic underpinnings of these differences. The valproic acid (VPA) rodent model is the most widely used model for the study of idiopathic ASD, but almost all of the studies have used male rodents.

Method

To fill this knowledge gap, we evaluated sex differences for neuronal activity, morphology, and glycogen synthase kinase-3 (GSK-3) signaling in primary cortical (CTX) and hippocampal (HIP) neurons prepared from rats exposed to VPAin utero.In vivo, sex-specific VPA-induced alterations in the frontal CTX transcriptome at birth were also determined.

Results

Overall, VPA induced more robust changes in neuronal function and structure in the CTX than in the HIP. Male- and female-derived primary CTX neurons from rats exposed to prenatal VPA had elevated activity and showed more disorganized firing. In the HIP, only the female VPA neurons showed elevated firing, while the male VPA neurons exhibited disorganized activity. Dendritic arborization of CTX neurons from VPA rats was less complex in both sexes, though this was more pronounced in the females. Conversely, both female and male HIP neurons from VPA rats showed elevated complexity distal to the soma. Female VPA CTX neurons also had an elevated number of dendritic spines. The relative activity of the α and β isoforms of GSK-3 were suppressed in both female and male VPA CTX neurons, with no changes in the HIP neurons. On postnatal day 0, alterations in CTX genes associated with neuropeptides (e.g.,penk,pdyn) and receptors (e.g.,drd1,adora2a) were seen in both sexes, though they were downregulated in females and upregulated in males.

Limitations

Primary neuron studies may not recapitulate findings performedin vivoor at later stages of development.

Conclusion

Together these findings suggest that substantial sex differences in neuronal structure and function in the VPA model may have relevance to the reported sex differences in idiopathic ASD.
A conserved cell-type gradient across the human mediodorsal and paraventricular thalamus
Authors: Schulmann Anton , Feng Ningping , Auluck Pavan K , Mukherjee Arghya , Komal Ruchi , Leng Yan , Gao Claire , Williams Avram Sarah K , Roy Snehashis , Usdin Ted B , Xu Qing , Imamovic Vesna , Patel Yash , Akula Nirmala , Raznahan Armin , Menon Vilas , Roussos Panos , Duncan Laramie , Elkahloun Abdel , Singh Jatinder , Kelly Michael C , Halassa Michael M , Hattar Samer , Penzo Mario A , Marenco Stefano , McMahon Francis J
Published: September 2024

The mediodorsal thalamus (MD) and adjacent midline nuclei are important for cognition and mental illness, but their cellular composition is not well defined. Using single-nucleus and spatial transcriptomics, we identified a conserved excitatory neuron gradient, with distinct spatial mapping of individual clusters. One end of the gradient was expanded in human MD compared to mice, which may be related to the expansion of granular prefrontal cortex in hominids. Moreover, neurons preferentially mapping onto the parvocellular division MD were associated with genetic risk for schizophrenia and bipolar disorder. Midbrain-derived inhibitory interneurons were enriched in human MD and implicated in genetic risk for major depressive disorder.
The alternative polyadenylation regulator CFIm25 promotes macrophage differentiation and activates the NF-κβ pathway
Authors: Mukherjee Srimoyee , Barua Atish , Wang Luyang , Tian Bin , Moore Claire L.
Published: September 2024

Macrophages are required for our body’s development and tissue repair and protect against microbial attacks. We previously reported a crucial role for regulation of mRNA 3’-end cleavage and polyadenylation (C/P) in monocyte to macrophage differentiation. The CFIm25 subunit of the C/P complex showed a striking increase upon differentiation of monocytes with Phorbol Myristate Acetate, suggesting that it promotes this process. To test this hypothesis, CFIm25 was overexpressed in two different monocytic cell lines, followed by differentiation. Both cell lines showed a significant increase in macrophage characteristics and an earlier slowing of the cell cycle. In contrast, depletion of CFIm25 hindered differentiation. Cell cycle slowing upon CFIm25 overexpression was consistent with a greater decrease in the proliferation markers PCNA and cyclin D1, coupled with increased 3’UTR lengthening of cyclin D1 mRNA. Since choice of other poly(A) sites could be affected by manipulating CFIm25, we identified additional genes with altered use of poly(A) sites during differentiation and examined how this changed upon CFIm25 overexpression. The mRNAs of positive regulators of NF-κB signaling, TAB2 and TBL1XR1, and NFKB1, which encodes the NF-κB p50 precursor, underwent 3’UTR shortening that was associated with increased protein expression compared to the control. Cells overexpressing CFIm25 also showed elevated levels of phosphorylated NF-κB-p65 and the NF-κB targets p21, Bcl-XL, ICAM1 and TNF-α at an earlier time and greater resistance to NF-κB chemical inhibition. In conclusion, our study supports a model in which CFIm25 accelerates the monocyte to macrophage transition by promoting alternative polyadenylation events which lead to activation of the NF-κB pathway.
Analysis of C-reactive protein omics-measures associates methylation risk score with sleep health and related health outcomes
Authors: Wang Ziqing , Wallace Danielle A , Spitzer Brian W , Huang Tianyi , Taylor Kent , Rotter Jerome I , Rich Stephen S , Liu Peter Y , Daviglus Martha L. , Hou Lifang , Ramos Alberto R , Kaur Sonya , Durda J Peter , González Hector M , Fornage Myriam , Redline Susan , Isasi Carmen R , Sofer Tamar
Published: September 2024

Introduction

DNA methylation (DNAm) predictors of high sensitivity C-reactive protein (CRP) offer a stable and accurate means of assessing chronic inflammation, bypassing the CRP protein fluctuations secondary to acute illness. Poor sleep health is associated with elevated inflammation (including elevated blood CRP levels) which may explain associations of sleep insufficiency with metabolic, cardiovascular and neurological diseases. Our study aims to characterize the relationships among sleep health phenotypes and CRP markers —blood, genetic, and epigenetic indicators— within the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).

Methods

In HCHS/SOL, methylation risk scores (MRS)-CRP and polygenetic risk score (PRS)-CRP were constructed separately as weighted sums of methylation beta values or allele counts, respectively, for each individual. Sleep health phenotypes were measured using self-reported questionnaires and objective measurements. Survey-weighted linear regression established the association between the multiple sleep phenotypes (obstructive sleep apnea (OSA), sleep duration, insomnia and excessive sleepiness symptom), cognitive assessments, diabetes and hypertension with CRP markers while adjusting for age, sex, BMI, study center, and the first five principal components of genetic ancestry in HCHS/SOL.

Results

We included 2221 HCHS/SOL participants (age range 37-76 yrs, 65.7% female) in the analysis. Both the MRS-CRP (95% confidence interval (CI): 0.32-0.42, p = 3.3 x 10-38) and the PRS-CRP (95% CI: 0.15-0.25, p = 1 x 10-14) were associated with blood CRP level. Moreover, MRS-CRP was associated with sleep health phenotypes (OSA, long sleep duration) and related conditions (diabetes and hypertension), while PRS-CRP markers were not associated with these traits. Circulating CRP level was associated with sleep duration and diabetes. Associations between OSA traits and metabolic comorbidities weakened after adjusting for MRS-CRP, most strongly for diabetes, and least for hypertension.

Conclusions

MRS-CRP is a promising estimate for systemic and chronic inflammation as reflected by circulating CRP levels, which either mediates or serves as a common cause of the association between sleep phenotypes and related comorbidities, especially in the presence of diabetes.
Reproducible comparison and interpretation of machine learning classifiers to predict autism on the ABIDE multimodal dataset
Authors: Dong Yilan , Batalle Dafnis , Deprez Maria
Published: September 2024

Autism is a neurodevelopmental condition affecting ∼1% of the population. Recently, machine learning models have been trained to classify participants with autism using their neuroimaging features, though the performance of these models varies in the literature. Differences in experimental setup hamper the direct comparison of different machine-learning approaches. In this paper, five of the most widely used and best-performing machine learning models in the field were trained to classify participants with autism and typically developing (TD) participants, using functional connectivity matrices, structural volumetric measures and phenotypic information from the Autism Brain Imaging Data Exchange (ABIDE) dataset. Their performance was compared under the same evaluation standard. The models implemented included: graph convolutional networks (GCN), edge-variational graph convolutional networks (EV-GCN), fully connected networks (FCN), auto-encoder followed by a fully connected network (AE-FCN) and support vector machine (SVM). Our results show that all models performed similarly, achieving a classification accuracy around 70%. Our results suggest that different inclusion criteria, data modalities and evaluation pipelines rather than different machine learning models may explain variations in accuracy in published literature. The highest accuracy in our framework was obtained by an ensemble of GCN models trained on combination of functional MRI and structural MRI features, reaching classification accuracy of 72.2% and AUC = 0.78 on the test set. The combined structural and functional modalities exhibited higher predictive ability compared to using single modality features alone. Ensemble methods were found to be helpful to improve the performance of the models. Furthermore, we also investigated the stability of features identified by the different machine learning models using the SmoothGrad interpretation method. The FCN model demonstrated the highest stability selecting relevant features contributing to model decision making. Code available at:https://github.com/YilanDong19/Machine-learning-with-ABIDE.
Meta-analysis study of the therapeutic impact of Mesenchymal stem cells derived exosomes for chronic kidney diseases
Authors: Himanshu k , Gunjan k , Pandey Ramendera Pati , Mukherjee Riya , Chang Chung-Ming
Published: September 2024

Mesenchymal stem cell-derived exosomes (EXOs) represent a promising avenue for treating chronic kidney diseases (CKD), though their precise impact remains somewhat elusive. To address this gap, we conducted a systematic analysis, scouring databases and clinical trial repositories for relevant studies from 2019 to 2023. Seventeen papers were meticulously selected for their focus on mesenchymal stem cell-derived exosomes (MSC-EXOs) and their potential in CKD treatment. Our comprehensive meta-analysis, incorporating 15 preclinical and 6 clinical studies, underscores the efficacy of MSC-EXOs in improving renal function while attenuating tubular injury, inflammation, apoptosis, collagen deposition, and renal fibrosis. Notably, post-treatment with MSC-EXOs exhibited significant associations with various CKD markers, with pooled proportions indicating a considerable impact on blood urea nitrogen (BUN) and serum creatinine (SCR) levels. Subgroup analyses based on animal models further elucidated heterogeneity within the studies. In conclusion, MSC-EXOs demonstrate promise in enhancing renal function and reducing CKD risk, as evidenced by both preclinical and clinical data. Their efficacy in lowering SCR and BUN levels while enhancing filtration rate suggests MSC-EXOs as a viable and secure alternative to cell-based therapies, thereby providing valuable insights for personalized CKD treatments despite inherent limitations.

Graphical abstract

Graphical highlight:

MSC-EXOs show promise in improving renal function and reducing CKD risk, as evidenced by comprehensive meta-analysis findings.

Pooled proportions indicate significant associations between MSC-EXO treatment and reduced BUN and SCR levels and increased GFR rate, highlighting their potential therapeutic efficacy.

Exosomes show a significant effect on renal function, as indicated by the study findings.
Mitochondrial transplantation: A novel therapy for liver ischemia/reperfusion injury
Authors: Mukkala Avinash Naraiah , David Bruna Araujo , Ailenberg Menachem , Liang Jady , Vaswani Chirag Manoj , Karakas Danielle , Goldfarb Rachel , Barbour William , Gasner Avishai , Wu Ruoxian Scarlet , Petrut Raluca , Jerkic Mirjana , Andreazza Ana C. , Santos Claudia dos , Ni Heyu , Zhang Haibo , Kapus Andras , Kubes Paul , Rotstein Ori David
Published: September 2024

MINI-ABSTRACT

Mitochondrial transplantation prevented liver ischemia/reperfusion-induced hepatocellular injury and inflammation.In vivointravital microscopy demonstrated that liver resident macrophages, namely Kupffer cells, rapidly sequestered, internalized and acidified transplanted mitochondria through the CRIg immunoreceptor. Mechanistically, both Kupffer cells and CRIg were necessary for the hepatoprotective and anti-inflammatory effects of mitochondrial transplantation.

STRUCTURED ABSTRACT

Objective

To investigate the hepatoprotective effects of mitochondrial transplantation in a murine liver ischemia/reperfusion (I/R) model.

Summary background data

Sequential liver ischemia followed by reperfusion (I/R) is a pathophysiological process underlying hepatocellular injury in a number of clinical contexts, such as hemorrhagic shock/resuscitation, major elective liver surgery and organ transplantation. A unifying pathogenic consequence of I/R is mitochondrial dysfunction. Restoration of mitochondria via transplantation (MTx) has emerged as potential therapeutic in I/R. However, its role in liver I/R and its mechanisms of action remain poorly defined.

Methods

We investigated the hepatoprotective effects of MTx in anin vivomouse model of liver I/R and usedin vivoimaging and various knockout and transgenic mouse models to determine the mechanism of protection.

Results

We found that I/R-induced hepatocellular injury was prevented by MTx, as measured by plasma ALT, AST and liver histology. Additionally, I/R-induced pro-inflammatory cytokine release (IL-6, TNFα) was dampened by MTx, and anti-inflammatory IL-10 was enhanced. Moreover, MTx lowered neutrophil infiltration into both the liver sinusoids and lung BALF, suggesting a local and distant reduction in inflammation. Usingin vivointravital imaging, we found that I/R-subjected Kupffer cells (KCs), rapidly sequestered transplanted mitochondria, and acidified mitochondria within lysosomal compartments. To specifically interrogate the role of KCs, we depleted KCs using the diphtheria toxin-inducible Clec4f/iDTR transgenic mouse, then induced I/R, and discovered that KCs are necessary for the beneficial effects of MTx. Finally, we induced I/R in complement receptor of the immunoglobulin superfamily (CRIg) knockout mice and found that CRIg was required for mitochondria capture by KCs and mitochondrial-mediated hepatoprotection.

Conclusions

In this study, we demonstrated that CRIg-dependent capture of mitochondria by I/R-subjected Kupffer cells is a hepatoprotective mechanismin vivo. These data progress knowledge on the mechanisms of MTx and opens new avenues for clinical translation.
Arc/Arg3.1 binds the nuclear polyadenylate-binding protein RRM and regulates neuronal activity-dependent formation of nuclear speckles
Authors: Kanhema Tambudzai , Parobczak Kamil , Patil Sudarshan , Holm-Kaczmarek Dagmara , Hallin Erik , Ludwiczak Jan , Szczepankiewicz Andrzej A. , Pauzin Francois P. , Szum Adrian , Ishizuka Yuta , Dunin-Horkawicz Stanisław , Kursula Petri , Wilczynski Grzegorz , Magalska Adriana , Bramham Clive R.
Published: September 2024

Arc is a neuronal activity-induced protein interaction hub with critical roles in synaptic plasticity and memory. Arc localizes to synapses and the nucleus, but its nuclear functions are little known. We show that Arc accumulates in the interchromatin space of dentate granule cell nuclei and the nucleosol subcellular fraction following seizure activity and in vivo dentate gyrus LTP. Proteomic analysis of affinity-purified Arc complexes identified proteins with functions in post-transcriptional mRNA processing. During LTP, Arc undergoes enhanced complex formation with polyadenylate binding protein nuclear 1 (PABPN1) and paraspeckle splicing factor (PSF) in the nucleosol. In vitro peptide binding arrays show selective binding of Arc to the PABPN1 polyA RNA recognition motif. In hippocampal neuronal cultures, Arc knockdown increases formation of PABPN1 nuclear speckles and blocks chemical-LTP associated increases in small PABPN1 foci. These results implicate Arc in basal and neuronal activity-dependent regulation of PABPN1 speckles involved in mRNA processing and polyadenylation.
Characterization of the genome editing with miniature nucleases TnpB, IscB and enIscB inEscherichia colistrains
Authors: Tang Hongjie , Gao Jie , Sun Mingjun , Zhang Suyi , Li Qi
Published: September 2024

DNA nucleases TnpB and IscB were regarded as new antibacterial strategy to combat the drug-resistant bacteria represented byEscherichia colidue to its specificity in targeting DNA and smallest size, but the genome-editing of TnpB/IscB inE. coliremains unclear. This study characterized the genome-editing of TnpB/IscB inE. colistrains. First, the toxicity and cleavage results showed TnpB only worked inE. coliMG1655, while IscB and enIscB could perform in ATCC9637 and BL21(DE3). Next, TnpB-based genome-editing tool was established in MG1655, while IscB/enIscB achieved in ATCC9637/BL21(DE3). The copy number of TnpB/IscB/enIscB were changed to explore the impact of editing efficiency. Moreover, the editing plasmids were successfully cured. Finally, the escaping mechanism ofE. coliunder editing of TnpB/IscB was revealed. Overall, this study successfully applied TnpB/IscB/enIscB to genome-editing inE. coli, which will broaden genetic manipulation toolbox inE. coliand facilitate the development of new antimicrobial drugs.
A 3D endometrium-on-a-chip reveals the role of conceptus-derived factors CAPG and PDI in conceptus-endometrial communication
Authors: Tinning Haidee , Wang Dapeng , Forde Niamh
Published: September 2024

Early embryo loss affects all mammalian species, including humans and agriculturally important food-producing mammals such as cattle. The developing conceptus (embryo and extra-embryonic membranes) secretes factors which modify the endometrium and can be critical for early pregnancy processes such maternal recognition of pregnancy (MRP) and enhancing uterine receptivity to implantation. For example, a competent bovine conceptus secretes IFNT to initiate MRP. The bovine conceptus also secretes other proteins at the time of MRP, including CAPG and PDI, which are highly conserved among placental mammals. We have previously shown that these proteins act upon the endometrium to modulate receptivity, embryo development, and implantation in species with different implantation strategies (humans and cattle). We hypothesise that developing a novel 3D bovine endometrium on a chip system will enhance our understanding of the role of conceptus-derived factors in altering the endometrium and/or ULF secretion. Here we have developed a 3D bovine endometrium on a chip system, comprising both stromal and epithelial cell culture combined with culture medium flow better mimics thein vivoendometrium and exposure to conceptus-derived factors than conventional 2D endometrial cell culture. We have demonstrated that the conceptus-derived proteins CAPG and PDI modulate the endometrial transcriptome and secretory response to promote pathways associated with early pregnancy and alter ULF composition. This work highlights the critical need for more robust andin vivo-like culture systems to study endometrial-conceptus interactionsin vitroto further investigate the role of conceptus derived factors for pregnancy success.

SIGNIFICANCE STATEMENT

We have developed anin vitro3D bovine endometrium-on-a-chip system comprising both primary stromal cells under static conditions and epithelial cells under flow conditions to mimic thein vivoendometrial environment from the conceptuses perspective. The secretome of the 3D endometrium-on-a-chip was characterised, was found to contain proteins associated with cell adhesion and tissue development, and contained proteins previously identified inin vivouterine luminal fluid. PDI and CAPG (previously identified conceptus-derived factors) altered the transcriptome and secretome of cells within the system. Exposure to CAPG or PDI altered the secretome of proteins previously identified in pregnant uterine luminal fluid or associated with early pregnancy, and exposure to CAPG or PDI also altered the transcriptome to support processes such as immune response, secretion, proliferation, and adhesion related pathways. This data supports previously published works and highlights the need for the use of morein vivo-likein vitromodels to study conceptus-endometrial interactions.
A robustly rooted tree of eukaryotes reveals their excavate ancestry
Authors: Williamson Kelsey , Eme Laura , Baños Hector , McCarthy Charley , Susko Edward , Kamikawa Ryoma , Orr Russell J. S. , Muñoz-Gómez Sergio A. , Simpson Alastair G. B. , Roger Andrew J.
Published: September 2024

The eukaryote Tree of Life (eToL) depicts the relationships among all eukaryotic organisms; its root represents the last eukaryotic common ancestor (LECA) from which all extant complex lifeforms are descended. Locating this root is crucial for reconstructing the features of LECA, both as the endpoint of eukaryogenesis and the start-point for the evolution of the myriad complex traits underpinning the diversification of living eukaryotes. However, the position of the root remains contentious due to pervasive phylogenetic artefacts stemming from inadequate evolutionary models, poor taxon sampling, and limited phylogenetic signal. Here, we estimate the root of the eToL with unprecedented resolution based on a new, much larger, dataset of mitochondrial proteins which includes all known eukaryotic supergroups. Our comprehensive analyses with state-of-the-art phylogenetic models reveal that the eukaryotic root lies between two multi-supergroup assemblages: ‘Opimoda+’ and ‘Diphoda+’. Compellingly, this position is consistently supported across different models and robustness analyses. Notably, groups containing ‘typical excavates’ are placed on both sides of the root, suggesting the complex features of the ‘excavate’ cell architecture trace back to LECA. This study is the most comprehensive phylogenetic investigation of the eukaryote root to date, shedding light on the ancestral cells from which extant eukaryotes arose and providing a crucial framework for investigating the origin and evolution of canonical eukaryotic features.
Culture Conditions Differentially Regulate the Inflammatory Niche and Cellular Phenotype of Tracheo-Bronchial Basal Stem Cells
Authors: Murthy Shubha , Seabold Denise A. , Gautam Lalit K. , Caceres Adrian M. , Sease Rosemary , Calvert Ben A. , Busch Shana , Neely Aaron , Marconett Crystal N. , Ryan Amy L.
Published: September 2024

Human bronchial epithelial cells (HBECs) derived from the tracheo-bronchial regions of human airways provide an excellentin vitromodel for studying pathological mechanisms and evaluating therapeutics in human airway cells. This cell population comprises a mixed population of basal cells (BCs), the predominant stem cell in airways capable of both self-renewal and functional differentiation. Despite their potential for regenerative medicine, BCs exhibit significant phenotypic variability in culture. To investigate how culture conditions influence BC phenotype and function, we expanded three independent BC isolates in three media, airway epithelial cell growth medium (AECGM), dual-SMAD inhibitor (DSI)-enriched AECGM, and Pneumacult Ex plus (PEx+). Extensive RNA sequencing, immune assays and electrical measurements revealed that PEx+ media significantly drove cell proliferation and a broad pro-inflammatory phenotype in BCs. In contrast, BCs expanded in AECGM, displayed increased expression of structural and extracellular matrix components at high passage. Whereas culture in AECGM increased expression of some cytokines at high passage, DSI suppressed inflammation altogether thus implicating TGF-β in BC inflammatory processes. Differentiation capacity declined with time in culture irrespective of expansion media except for PLUNC expressing secretory cells that were elevated at high passage in AECGM and PEx+ suggestive of an immune modulatory role of PLUNC in BCs. These findings underscore the profound impact of media conditions on inflammatory niche and function ofin vitroexpanded BCs. The broad pro-inflammatory phenotype driven by PEx+ media, in particular, should be considered in the development of cell-based models for airway diseases and therapeutic application.

NEW & NOTEWORTHY

Airway basal cells, vital for airway regeneration and potential therapies, show significant changes based on culture conditions. Our study reveals that media composition and culture duration greatly affect basal cell properties with profound changes in the pro-inflammatory phenotype and extracellular matrix deposition driven by changes in growth conditions. These results underscore the critical impact of culture conditions on BC phenotype, influencing cell-based models for airway disease research and therapy.
Correlative Imaging for Comprehensive Molecular Mapping of Individual Cell Types in Biological Tissues
Authors: Yang Manxi , Iqfath Mushfeqa , Meke Frederick Nguele , Qu Zihan , Hernly Emerson L. , Su Pei , Zhang Zhong-Yin , Laskin Julia
Published: September 2024

Mass spectrometry imaging (MSI) is a powerful technique for label-free spatial mapping of multiple classes of biomolecules in tissue sections. However, differences in desorption and ionization efficiency of different classes of molecules make it challenging to simultaneously map biomolecules at each omics layer in the same tissue sample. Herein, we present a correlative imaging method using nanospray desorption electrospray ionization (nano-DESI) MSI, which enables the spatial mapping of lipids, metabolites, peptides, and proteins with cellular-level spatial resolution in a single tissue section. We demonstrate the molecular profiling of specific cell types and identify truncated peptides in mouse pancreatic tissue. Distinct chemical gradients of peptides and lipids extending from endocrine cells to exocrine cells indicate their different roles in endocrine-exocrine crosstalk and intracellular signaling. The results underscore the power of the developed imaging approach for spatial multi-omics analysis that provides deep insights into cellular diversity and the intricate molecular interactions that occur within heterogenous biological tissues.
Proteomic Investigation of Neurotrophictrans-Banglene Reveals Potential Link to Iron Homeostasis
Authors: Gunawardana Piyumi B. Wijesiri , Gohil Khyati , Moon Kyung-Mee , Foster Leonard J. , Williams Florence J.
Published: September 2024

In an effort to gain insight into cellular systems impacted by neurotrophictrans-banglene (t-BG), global proteomic profiling and Western blot analyses were employed. Expression level changes in response tot-BG treatment were compared to those observed with nerve growth factor (NGF), a natural neurotrophic protein and functional analog tot-BG. Findings from these studies did not point to direct interception of NGF/TrkA signaling byt-BG. Instead, significant alterations in iron-binding and iron-regulating proteins were observed. Intracellular iron measurements by FerroOrange indicate lower ferrous (Fe2+) iron levels int-BG treated cells but not in NGF treated cells. These results highlight a potential connection between iron regulation and neurotrophic activity.
Microbial Metabolic Enzymes, Pathways and Microbial Hosts for Co-Metabolic Degradation of Organic Micropollutants in Wastewater
Authors: Lyu Boyu , Manna Bharat , Zhou Xueyang , Leung Ivanhoe K. H. , Singhal Naresh
Published: September 2024

Organic micropollutants (OMPs) in wastewater present significant environmental challenges, but effective removal strategies are hindered by our limited understanding of their co-metabolic biodegradation. We aim to elucidate the microbial enzymes, metabolic pathways, and community members involved in OMP co-metabolic degradation, thereby paving the way for more effective wastewater treatment strategies. We integrated multi-omics (metagenomics, metaproteomics, and metabolomics) and functional group analysis to investigate 24 OMPs under three aeration conditions. Our findings reveal that oxidoreductases, particularly cytochrome P450s and peroxidases, are crucial for recalcitrant OMPs containing halogen groups (-Cl, -F) like fluoxetine and diuron. Hydrolases, including amidases, are instrumental in targeting amide-containing (-CONH₂) OMPs such as bezafibrate and carbamazepine. Regarding microbial metabolism involved in OMP co-metabolic degradation, we found that amino acid metabolism is crucial for degrading amine-containing (-NH₂) OMPs like metoprolol and citalopram. Lipid metabolism, particularly for fatty acids, contributes to the degradation of carboxylic acid (-COOH) containing OMPs such as bezafibrate and naproxen. Finally, withActinobacteria,Bacteroidetes, andProteobacteriaemerging as primary contributors to these functionalities, we established connections between OMP functional groups, degradation enzymes, metabolic pathways, and microbial phyla. Our findings provide generalized insights into structure-function relationships in OMP co-metabolic degradation, offering the potential for improved wastewater treatment strategies.

Graphical abstract
Zbtb38 inhibits apoptosis by transcriptionally regulatingXIAPexpression
Authors: Matsuda Eishou , Shigeoka Toshiaki , Nagaoka Hiroyuki , Nurulita Nunuk Aries , Tada Shogo , Ishida Yasumasa , Bessho Yasumasa
Published: September 2024

X-linked inhibitor of apoptosis protein (XIAP) is a key suppressor of apoptosis, a major form of programmed cell death critical for cellular differentiation, embryogenesis, and cancer development. Despite its importance, the upstream regulators and regulatory elements ofXIAPare not well understood. This study provides evidence that the zinc finger transcription factor Zbtb38, a negative regulator of apoptosis, regulatesXIAPexpression in Zbtb38 loss- and gain-of-function experiments. Notably, XIAP overexpression rescued the apoptosis induced byZbtb38knockdown, indicating that Zbtb38-mediated apoptosis is at least partially dependent on XIAP. Chromatin immunoprecipitation and luciferase assays revealed that Zbtb38 binds to and activates E-boxes within theXIAPenhancer, underscoring the critical role of these E-boxes inXIAPexpression. Additionally, Zbtb38 loss during embryonic stem (ES) cell differentiation and embryogenesis resulted in increased apoptosis and decreased expression of XIAP and Bcl-2, highlighting their importance in these processes. Furthermore, Zbtb38 downregulation induced apoptosis in cancer cells lacking p53 expression, suggesting that Zbtb38 could be a potential therapeutic target in cancer.
Four Strategies for Whole-Genome Annotation of Transposable Elements and Repeats in Maize
Authors: Benson Christopher W. , Heringer Pedro , Ou Shujun
Published: September 2024

Transposable elements (TEs) and tandem repeat arrays are ubiquitous components of genomes across all domains of life. Many types of repetitive DNA do not appear to encode for functional proteins, and those that do, typically only code for enzymes involved in their own replication. Nevertheless, repetitive DNA sequences can significantly alter genome structure, and can have a profound impact on an organism's biology at both the molecular and organismal levels. Advances in long-read sequencing technology have enabled the resolution of previously collapsed contigs and scaffolds that are rich in repeats, which has made the accurate annotation of TEs and other repetitive sequences a crucial early step in genome analysis. Here, we provide a detailed tutorial for streamlined annotation of TEs and repeats in the genome of the model plantZea mays(maize). Maize is ideally suited to illustrate these procedures due to its repeat-rich genome and the volume of publicly available and high-quality genomic resources. We outline four possible approaches for TE and repeat annotation, each aimed at accommodating a different set of scientific interests. Additionally, we demonstrate how to evaluate annotation quality, and provide scripts to help graphically depict TE and repeat landscapes. Although the protocol is tailored for maize, we also offer pointers for researchers working on other systems throughout and expect that these procedures will be broadly applicable to any eukaryotic genome.
Sampling and Analysis of the Maize Microbiome
Authors: Wallace Jason G. , Favela Alonso , Raglin Sierra
Published: September 2024

Maize is an important plant for both global food security and genetics research. As the importance of microorganisms to plant health is becoming clearer, there is a growing interest in understanding the relationship between maize and its associated microbiome; i.e., the collection of microorganisms living on, around, and inside the plant. The ultimate goal of this research is to use these microbial communities to support more robust and sustainable maize production. Here, we provide an overview of recent progress in the field of maize microbiome research. We discuss the major microbiome compartments (rhizosphere, phyllosphere, and endosphere) and known functions of the microbiome. We also review the methods currently available to study the maize microbiome and its functions, and discuss how to carry out maize microbiome experiments, including both a general workflow (suitable for most microbiome analyses) and maize-specific experimental considerations.
Electric Field of DNA in Solution: Who Is in Charge?
Authors: Hedley Jonathan G. , Coshic Kush , Aksimentiev Aleksei , Kornyshev Alexei A.
Published: September 2024

In solution, DNA, the “most important molecule of life,” is a highly charged macromolecule that bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions (cations of the solution) adsorbed at or condensed near it, DNA still produces a substantial electric field in its vicinity, which is screened by buffer electrolytes at longer distances from the DNA. This electric field is experienced by any charged or dipolar species approaching and interacting with the DNA. So far, such a field has been explored predominantly within the scope of a primitive model of the electrolytic solution, not considering more complicated structural effects of the water solvent. In this paper, we investigate the distribution of electric field around DNA using linear response nonlocal electrostatic theory, applied here for helix-specific charge distributions, and compare the predictions of such a theory with specially performed, fully atomistic, large-scale, molecular dynamics simulations. Both approaches are applied to unravel the role of the structure of water at close distances to and within the grooves of a DNA molecule in the formation of the electric field. As predicted by the theory and reported by the simulations, the main finding of this study is that oscillations in the electrostatic potential distribution are present around DNA, caused by the overscreening effect of structured water. Surprisingly, electrolyte ions at physiological concentrations do not strongly disrupt these oscillations and are rather distributed according to these oscillating patterns, indicating that water structural effects dominate the short-range electrostatics. We also show that (i) structured water adsorbed in the grooves of DNA leads to a positive electrostatic potential core relative to the bulk, (ii) the Debye length some 10 Å away from the DNA surface is reduced, effectively renormalized by the helical pitch of the DNA molecule, and (iii) Lorentzian contributions to the nonlocal dielectric function of water, effectively reducing the dielectric constant close to the DNA surface, enhance the overall electric field. The impressive agreement between the atomistic simulations and the developed theory substantiates the use of nonlocal electrostatics when considering solvent effects in molecular processes in biology.

Published by the American Physical Society
2024
Psychometric evaluation of technology adoption propensity (TAP) index within independent samples of Turkish individuals
Authors: Celik Hakan , Aybas Meryem
Published: September 2024

Purpose

The technology adoption propensity (TAP) index is a parsimonious yet robust tool for measuring an individual’s willingness to accept new technologies. However, further investigation is still needed to evaluate its merits in non-Western countries. With this task in mind, this study assesses the psychometric properties and predictive capabilities of TAP in Turkey.

Design/methodology/approach

The researchers utilized an iterative process of forward-backward translation and three rounds of piloting to ensure the cross-cultural, conceptual and linguistic equivalence for the chosen tool. The final survey was conducted online on a convenience sample of 352 academics and in person for 2 other convenience samples that comprised a total of 259 municipal officers and 300 individuals.

Findings

TAP’s four-subscale structure was confirmed by a principal component analysis (PCA), and A confirmatory factor analysis (CFA) showed an acceptable fit across all samples. The total composition of the optimism, proficiency, dependence and vulnerability subscales was found to have adequate internal consistency and discriminant validity. Measurement invariance testing further demonstrated that TAP’s factorial organization was invariant across gender, age and income at configural, metric, scalar and strict levels. Finally, logistic and ordinary leas squares (OLS) regression analyses revealed that the TAP scores were predictive of prior technology adoption and use frequency.

Originality/value

Although these results are still preliminary, the confirmation and replication of TAP in Turkey clearly suggest that TAP is a dependable tool for assessing technology readiness that can be utilized well across different cultures.
Development and validation of social entrepreneurship career decisions scale among higher education students
Authors: Viswanath Parvathy , Kumar Aneesh
Published: September 2024

Purpose

The importance of sustainable development has become increasingly significant in today’s fast-paced world. The 17 sustainable development goals (SDGs) aim to solve a range of environmental, economic and social challenges, which requires global collaboration among governments and private organisations. In light of this, social entrepreneurship has garnered significant attention as it combines the social purpose of non-profits with the market-driven approach of for-profits to address SDG goals. Yet the cognitive processes underpinning the career decisions of social entrepreneurs remain underexplored. This study aims to develop and validate a scale to measure social entrepreneurial career decisions based on the appraisal of perceived challenges.

Design/methodology/approach

The study followed the steps of tool development and was carried out in three phases: item analysis, exploratory factor analysis (EFA) and confirmatory factor analysis (CFA).

Findings

The final 20-item scale focuses on the appraisal components in pre-entry social entrepreneurial career decision-making and has four factors, which are relevance, coping potential, knowledge and resources and normative significance.

Research limitations/implications

The study contributes to the literature on entrepreneurial cognition, specifically focusing on social entrepreneurship. The scale could guide model testing and quantitative research in social entrepreneurial cognition. The four-dimensional structure identified in the study may also have implications for researchers interested in the antecedents and effects of social entrepreneurial decision-making.

Practical implications

Accurate measurement of cognitive appraisal is necessary to understand the perceived challenges and thought processes of potential social entrepreneurs. The scale could be used to examine the cognitive appraisal patterns among students. Social entrepreneurship educators and policymakers can use the scale to design and assess educational programs.

Originality/value

Distinct from existing studies, this scale offers a multidimensional approach that captures the stages of career decision-making, providing a robust tool to enhance our understanding of the decision-making dynamics in social entrepreneurship.
Factors influencing consumers’ loyalty in the use of mobile telecommunication services: the case study in Vietnam
Authors: Nguyen Van Khoa , Pham Thi Huyen , Phan Thuy Anh
Published: September 2024

Purpose

The research aimed to identify factors influencing customer loyalty in the use of mobile telecommunication services in Vietnam, focusing on two dimensions “attitudinal loyalty” and “behavioral loyalty.”

Design/methodology/approach

Based on survey data collected from 820 in two of Vietnam’s major cities users, Hanoi and Ho Chi Minh City, the data were processed using SPSS and AMOS software.

Findings

The study identified four factors affecting customer loyalty to mobile telecommunication services, with perceived service quality directly impacting both attitudinal and behavioral loyalty. Corporate image and perceived switching costs influenced attitudinal loyalty, while trust affected behavioral loyalty. Moreover, perceived service quality indirectly influenced attitudinal loyalty through corporate image and perceived switching costs.

Research limitations/implications

The study only focuses on a limited number of factors influencing mobile telecommunications service user loyalty, its restricted geographical sample from only Hanoi and Ho Chi Minh City, and the simplification of perceived switching costs without considering their various components, such as psychological, financial and procedural costs, which could provide more comprehensive experimental and theoretical insights.

Practical implications

The study reveals that customer loyalty in Vietnam’s mobile telecommunications sector is linked to the relationship between attitude toward the service provider and continued usage behavior, categorizing customer groups into genuine loyalty, latent loyalty, feigned loyalty and disloyalty. It suggests that service providers should focus on improving service quality and cultivating a positive, transparent corporate image to bolster customer trust, foster stable relationships and remain competitive in the market.

Originality/value

The research model combines Oliver’s (1999) theory of loyalty with Aydin and Özer’s (2005) research model, focusing on perceived service quality, corporate image, trust and perceived switching costs, examining their relationships with both behavioral and attitudinal loyalty simultaneously.
Dominance needs, gender, and leader emergence in self-managed work teams
Authors: Yong Kwan Lim Yong-Kwan JoAnne
Published: September 2024

Purpose

Examining dominance in influencing leadership perceptions for men and women has received significant scholarly attention. The studies typically show that dominance is beneficial for men in attaining leadership positions but not for women. However, the studies were predominantly conducted more than two decades ago. Given the developments in gender research, this study extends the dominance line of inquiry by probing the impact of dominance need on leader emergence for men versus women in self-managed work teams. Furthermore, this study aims to examine if team dominance needs dispersion posits as a boundary condition for the combined impact of dominance needs and gender on leader emergence.

Design/methodology/approach

The authors conducted a longitudinal study that lasted one semester and involved 44 ad hoc self-managed work teams.

Findings

This study found that dominance needs facilitated leader emergence regardless of gender, and team dominance needs dispersion. Furthermore, men with high dominance needs were likelier to emerge as leaders than women with high dominance needs in high dominance needs dispersion teams. By contrast, women low in dominance needs received a harsher penalty in their leadership emergence than men low in dominance needs in low dominance needs dispersion teams

Originality/value

These results depart from the usual findings regarding the backlash effects that dominant women face and paint a rosy picture regarding the use of dominance in shaping leader emergence. However, the findings support the notion in gender stereotypes research that women are judged more critically than men in ascending to leadership positions.
Cognitive–analytical and emotional–social tasks achievement of service robots through human–robot interaction
Authors: Sun Sunny , Ye Huiyue , Law Rob
Published: September 2024

Purpose

Along with the development of the robotics industry, service robots have been gradually used in the hospitality industry. Nevertheless, service robot categorization and the fulfillment of the cognitive and emotional needs of consumers by hotel service robots have yet to be fully explored. Hence, the purpose of this study are to categorize hotel service robots, to explore consumers’ robot hotel experience, to identify the consumers’ preference of hotel service robot in general, to reveal consumers’ preference for hotel service robots based on their fulfillment of emotional needs and to examine the completion of cognitive–analytical and emotional–social tasks.

Design/methodology/approach

Through in-depth interviews with technology managers and questionnaire survey among consumers who have and have not had robot hotel stay experience to achieve the aforementioned research objectives.

Findings

Findings of in-depth interviews show that service robots can be categorized as check-in/out robots, artificial intelligence (AI) robots and service delivery robots. Results of questionnaire survey indicate that consumers prefer non-humanoid robots (n = 213, p = 47.87%) among check-in/out robots, the Xiaodu Smart Display (n = 163, p = 36. 63%) among the AI robots and the machine-shaped robot porter (I) (n = 178, p = 40.00%) among the service delivery robots.

Practical implications

This study provides implications, such as the adoption of robot-shaped AI with a screen display, to hotel managers to meet the needs of consumers regarding the completion of cognitive–analytical and emotional–social tasks of robots.

Originality/value

This study extends uncanny valley theory by identifying preference for the shape and functions of different categories of service robots and contributes to the limited literature on hotel robots.