bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monoacylglycerol O-acyltransferase 1 is required for adipocyte differentiation in vitro but does not affect adiposity in mice
Authors: Singer Jason M. , Shew Trevor M. , Ferguson Daniel , Renkemeyer M. Katie , Pietka Terri A. , Hall Angela M. , Finck Brian N. , Lutkewitte Andrew J. 
Published: February 2022

ABSTRACTObjectiveMonoacylglycerol O-acyltransferase 1 (Mogat1), a lipogenic enzyme that converts monoacylglycerol to diacylglycerol, is highly expressed in adipocytes and may regulate lipolysis by re-esterifying fatty acids released during times when lipolytic rates are low. However, the role of Mogat1 in regulating adipocyte fat storage during differentiation and diet-induced obesity is relatively understudied.MethodsHere we generated adipocyte-specific Mogat1 knockout mice and subjected them to a high-fat diet to determine the effects of Mogat1 deficiency on diet-induced obesity. We also used Mogat1 floxed mice to develop preadipocyte cell lines wherein Mogat1 could be conditionally knocked out to study adipocyte differentiation in vitro.ResultsIn preadipocytes, we found that Mogat1 knockout at the onset of preadipocyte differentiation prevented the accumulation of glycerolipids and reduced the differentiation capacity of preadipocytes. However, the loss of adipocyte Mogat1 did not affect weight gain or fat mass induced by high-fat diet in mice. Furthermore, loss of Mogat1 in adipocytes did not affect plasma lipid or glucose concentrations or insulin tolerance.ConclusionsThese data suggest Mogat1 may play a role in adipocyte differentiation in vitro but not adipose tissue expansion in response to nutrient overload in mice.STUDY IMPORTANCEWhat is already known?Adipose tissue expansion through adipocyte precursor cell differentiation is critical for proper lipid storage during nutrient overload.Monoacylglycerol O-acyltransferase 1 (Mogat1), a lipogenic enzyme, is highly induced during adipocyte differentiation of human and mouse precursor cells and is reduced in patients with obesity and metabolic dysfunction.What does this study add?Mogat1 deletion during early adipocyte differentiation reduces differentiation capacity, adipogenic gene expression and lowers glycerolipid content of differentiated adipocytes.Adipocyte Mogat1 expression is dispensable for adiposity and metabolic outcomes high-fat fed mice and suggests compensation from other glycerolipid synthesis enzymes.How might these results change the direction of research?Understanding the molecular mechanisms of glycerolipid metabolism healthy adipose tissue expansion.
Comprehensive analysis of Arabidopsis thaliana DNA polymerase epsilon catalytic subunit A and B mutants – an insight into differentially expressed genes and protein-protein interactions
Authors: Wickramasuriya Anushka M. , Hewavithana Thulani M. , de Silva Kithmee K. , Ullah Ihsan , Dunwell Jim M. 
Published: February 2022

AbstractOne of the main replicative enzymes in most eukaryotes, DNA polymerase ε (POLE), is composed of four subunits, namely a single catalytic and three regulatory subunits. In Arabidopsis, the catalytic subunit of POLE is encoded by two genes: Arabidopsis thaliana DNA POLYMERASE EPSILON CATALYTIC SUBUNIT A (AtPOL2A) and B (AtPOL2B). Although studies have shown AtPOL2A to be involved in various biological processes, the role of AtPOL2B is unclear. Here, we investigated the transcriptomes of both atpol2a and atpol2b mutants, and the promoter sequences to provide a better insight into the targets of AtPOL2s at the molecular level. In the present study, leaf cDNA libraries of four AtPOL2 mutants (atpol2a-1 and atpol2b-1, -2 and - 3) were sequenced using the Illumina platform. Analysis of gene expression profiles identified a total of 198, 76, 141 and 67 differentially expressed genes in atpol2a-1, atpol2b-1, atpol2b-2 and atpol2b-3, respectively; the majority of pericentromeric transposable elements were transcriptionally active in atpol2a-1 as compared to atpol2b mutants and wild type. Protein-protein interaction network analysis and molecular docking identified three (CER1, RPA1E and AT5G60250) and two (PR1 and AT5G48490) proteins as potential interactors (cluster size > 60 and balanced score < -900) of AtPOL2A and AtPOL2B, respectively; Interestingly, these five proteins also showed a significant interaction between POLE catalytic subunit of Saccharomyces cerevisiae. Our in silico promoter analysis showed that the AtPOL2A promoter sequence is overrepresented with cis-acting regulatory elements (CREs) associate with cell cycle regulation, meristematic/reproductive tissue-specific pattern of expression and MYB protein recognition, whereas the AtPOL2B promoter sequence was mainly enriched with stress-responsive elements. The information provided here has led to the identification of targets of AtPOL2s at the molecular level and CREs putatively associated with the regulation of AtPOL2s. To our knowledge, this study provides the first comparative transcriptome profiling of single-gene mutants of AtPOL2s.
A live-attenuated SARS-CoV-2 vaccine candidate with accessory protein deletions
Authors: Liu Yang , Zhang Xianwen , Liu Jianying , Xia Hongjie , Zou Jing , Muruato Antonio E. , Periasamy Sivakumar , Plante Jessica A. , Bopp Nathen E. , Kurhade Chaitanya , Bukreyev Alexander , Ren Ping , Wang Tian , Vineet D. Menachery , Plante Kenneth S. , Xie Xuping , Weaver Scott C. , Shi Pei-Yong 
Published: February 2022

AbstractWe report a live-attenuated SARS-CoV-2 vaccine candidate with (i) re-engineered viral transcriptional regulator sequences and (ii) deleted open-reading-frames (ORF) 3, 6, 7, and 8 (Δ3678). The Δ3678 virus replicates about 7,500-fold lower than wild-type SARS-CoV-2 on primary human airway cultures, but restores its replication on interferon-deficient Vero-E6 cells that are approved for vaccine production. The Δ3678 virus is highly attenuated in both hamster and K18-hACE2 mouse models. A single-dose immunization of the Δ3678 virus protects hamsters from wild-type virus challenge and transmission. Among the deleted ORFs in the Δ3678 virus, ORF3a accounts for the most attenuation through antagonizing STAT1 phosphorylation during type-I interferon signaling. We also developed an mNeonGreen reporter Δ3678 virus for high-throughput neutralization and antiviral testing. Altogether, the results suggest that Δ3678 SARS-CoV-2 may serve as a live-attenuated vaccine candidate and a research tool for potential biosafety level-2 use.
Machine learning analysis reveals biomarkers for the detection of neurodegenerative diseases
Authors: Lam Simon , Arif Muhammad , Song Xiya , Uhlen Mathias , Mardinoglu Adil 
Published: February 2022

AbstractIt is critical to identify biomarkers for neurodegenerative diseases (NDDs) to advance disease diagnosis and accelerate drug discovery for effective treatment of patients. In this work, we retrieved genotyping and clinical data from 1223 UK Biobank participants to identify genetic and clinical biomarkers for NDDs, including Alzheimer’s disease (AD), Parkinson’s disease (PD), motor neuron disease (MND), and myasthenia gravis (MG). Using a machine learning modelling approach and Monte Carlo randomisation, we identified 16 informative clinical variables for predicting AD, PD, MND, and MG. In a multinomial model, these clinical variables could correctly predict the diagnosis of one of the four diseases with an accuracy of 88.3%. In addition to clinical biomarkers, we also explored genetic biomarkers. In a genome-wide association study of AD, PD, MND, and MG patients, we identified single nucleotide polymorphisms (SNPs) implicated in several craniofacial disorders such as apnoea and branchiootic syndrome. We found evidence for shared genetic risk loci across NDDs, including SNPs in cancer-related genes and SNPs known to be associated with non-brain cancers such as Wilms tumour, leukaemia, and pancreatic cancer. Our analysis supports current knowledge regarding the ageing-related degeneration/cancer shift.Significance statementThis study highlights the potential for hypothesis-free mathematical modelling of easily measured clinical variables to identify diagnostic biomarkers for neurodegenerative diseases (NDDs). Prior to this study, the focus in NDD research has surrounded toxic species such as amyloid beta and α-synuclein, but this approach has not enjoyed success at clinical trial. Here, we studied Alzheimer’s disease, Parkinson’s disease, motor neuron disease, and myasthenia gravis by constructing and inspecting a multinomial based on demographics and blood and urine biochemistry. Cognitive measures were important for the predictive power of the model. Model weights correctly indicated multiple trends reported in the literature. Separately, genome-wide association indicated a shared risk profile between NDD and cancer, which has also been reported in the literature.
Vascular mimicry by VE-cadherin enables trophoblast endovascular invasion and spiral artery remodeling during placental development
Authors: Sung Derek C. , Chen Xiaowen , Chen Mei , Yang Jisheng , Schultz Susan , Babu Apoorva , Xu Yitian , Gao Siqi , Keller TC Stevenson , Mericko Patricia , Lee Michelle , Yang Ying , Scallan Joshua P. , Kahn Mark L. 
Published: February 2022

AbstractDuring formation of the mammalian placenta trophoblasts invade the maternal decidua and remodel spiral arteries to bring maternal blood into the placenta. This process, known as endovascular invasion, is thought to involve the adoption of functional characteristics of vascular endothelial cells (ECs) by trophoblasts through a process termed vascular mimicry. The genetic and molecular basis of vascular mimicry remains poorly defined, however, and whether trophoblasts utilize specialized endothelial proteins in an analogous manner to create vascular channels remains untested. Vascular endothelial (VE-)cadherin is a homotypic adhesion protein that is expressed selectively by ECs in which it enables formation of tight vessels and regulation of EC junctions. VE-cadherin is also expressed in invasive trophoblasts and is a prime candidate for a molecular mechanism of vascular mimicry by those cells. Here, we show that the VE-cadherin is required for trophoblast migration and endovascular invasion into the maternal decidua in the mouse. VE-cadherin deficiency results in loss of spiral artery remodeling that leads to decreased flow of maternal blood into the placenta, fetal growth restriction, and death. These studies identify a non-endothelial role for VE-cadherin in trophoblasts during placental development and suggest that endothelial proteins may play functionally unique roles in trophoblasts that do not simply mimic those in ECs.
Neural Representations of Self-Generated Thought during Think-aloud fMRI
Authors: Li Hui-Xian , Lu Bin , Wang Yu-Wei , Li Xue-Ying , Chen Xiao , Yan Chao-Gan 
Published: February 2022

AbstractIs the brain at rest during the so-called resting-state? Ongoing experiences in the resting-state vary in unobserved and uncontrolled ways across time, individuals, and populations. However, the role of self-generated thoughts in resting-state fMRI remains largely unexplored. In this study, we collected real-time self-generated thoughts during “resting-state” fMRI scans via the think-aloud method (i.e., think-aloud fMRI), which required participants to report whatever they were currently thinking. We first investigated brain activation patterns during a think-aloud condition and found that significantly activated brain areas included all brain regions required for speech. We then calculated the relationship between divergence in thought content and brain activation during think-aloud and found that divergence in thought content was associated with many brain regions. Finally, we explored the neural representation of self-generated thoughts by performing representational similarity analysis (RSA) at three neural scales: a voxel-wise whole-brain searchlight level; a region-level whole-brain analysis using the Schaefer 400-parcels; at the systems level using the Yeo seven-networks. We found that “resting-state” self-generated thoughts were distributed across a wide range of brain regions, involving all seven Yeo networks. This study highlights the value of considering ongoing experiences during resting-state fMRI, as well as providing preliminary methodological support for think-aloud fMRI.
Prolactin-induced AMPK stabilizes alveologenesis and lactogenesis through regulation of STAT5 signaling
Authors: Jinagal Shyam Lal , Shekhar Pragati , Chandra Kailash , Mutnuru Srinivas Abhishek , Ramanan Narendrakumar , Foretz Marc , Viollet Benoit , Bhat Ramray , Rangarajan Annapoorni 
Published: February 2022

AbstractAMP-activated protein kinase (AMPK) is an evolutionarily conserved serine/threonine kinase that regulates energy homeostasis at cellular and organismal levels. It has been shown to affect several steps of breast cancer progression in a context-dependent manner. However, its role in normal mammary gland development and physiology remains ill-explored. Here, we show that AMPK expression and activity increased within murine mammary epithelia from puberty to pregnancy with highest levels during lactation, and then declined during involution. In ex vivo cultures of mammary epithelial cells (MECs) in organotypic scaffolds, treatment with lactogenic hormone prolactin (PRL) enhanced AMPK expression and activity. To understand the role of AMPK on mammary morphogenesis in vivo, we generated mice with conditional knockout of AMPKα isoforms α1 and α2 (AMPKα KO) in MECs. AMPKα KO mammary glands showed accelerated alveolar development with increased epithelial content of both luminal and myoepithelial lineages, suggestive of hyperproliferation. AMPKα KO mice also showed elevated beta-casein expression during pregnancy and lactation. These observations were phenocopied upon treatment of ex vivo cultivated wild-type MECs with a cognate AMPK inhibitor. AMPKα null MECs showed increased phosphorylated STAT5 which is known to drive alveologenesis downstream of prolactin signaling. Our study identifies a novel interplay between AMPK and PRL-STAT5 signaling that determines mammary alveologenesis and differentiation.
The BASP1 transcriptional repressor modifies chromatin through lipid-dependent and lipid-independent mechanisms
Authors: Moorhouse Alexander J. , Loats Amy E. , Medler Kathryn F , Roberts Stefan G. E. 
Published: February 2022

SummaryThe transcriptional corepressor BASP1 requires N-terminal myristoylation for its activity and functions through interactions with nuclear lipids. Here we determine the role of BASP1 lipidation in histone modification and the modulation of chromatin accessibility. We find that the removal of the active histone modifications H3K9ac and H3K4me3 by BASP1 requires the N-terminal myristoylation of BASP1. In contrast, the placement of the repressive histone modification, H3K27me3, by BASP1 does require BASP1 lipidation. RNA-seq and ATAC-seq analysis finds that BASP1 regulates the activity of multiple transcription factors and induces extensive changes in chromatin accessibility. We find that ∼50% of BASP1 target genes show lipidation-dependent chromatin compaction and transcriptional repression. Our results suggest that BASP1 elicits both lipid-dependent and lipid-independent functions in histone modification and transcriptional repression. In accordance with this, we find that the tumor suppressor activity of BASP1 is also partially dependent on its myristoylation.
Endometriotic Organoids: A Novel In Vitro Model of Endometriotic Lesion Development
Authors: Song Yong , Burns Gregory W. , Joshi Niraj R. , Arora Ripla , Kim J. Julie , Fazleabas Asgerally T. 
Published: February 2022

ABSTRACTThe development and progression of endometriotic lesions are poorly understood, but immune cell dysfunction and inflammation are closely associated with the pathophysiology of endometriosis. A lack of suitable 3D in vitro models permitting the study of interactions between cell types and the microenvironment is a contributing factor. To address this limitation, we developed endometriotic organoids (EO) to explore the role of epithelial-stromal interactions and model peritoneal cell invasion associated with lesion development. Using a non-adherent microwell culture system, spherical organoids were generated with endometriotic epithelial cells (12Z) combined with immortalized endometriotic stromal cells (iEc-ESC) or immortalized uterine stromal cells (iHUF). Organoids self-organized with stromal cells occupying the center and epithelial cells on the periphery of the organoid. Endometriotic organoids (EO), containing iEc-ESC, resulted in the development of stratified 12Z epithelial cells compared to those with iHUF where the 12Z cells developed as a single layered epithelium. Transcriptomic analysis found 4,522 differentially expressed genes (DEG) between EO and 12Z/iHUF organoids, and the top DEG included increased expression of interleukins and prostaglandin synthase enzymes. An overlap of the EO DEG with baboon endometriotic lesions was highly significant. Finally, to mimic invasion of endometrial tissue into the peritoneum, a model was developed using EO and extracellular matrix containing human peritoneal mesothelial cells (LP9). Invasion of EO into the extracellular matrix-LP9 layer was increased in presence of estrogen or THP1-derived proinflammatory macrophages. Taken together, our results strongly support the concept that EO are an appropriate model for dissecting mechanisms that contribute to endometriotic lesion development.One Sentence SummaryEndometriotic organoids are an appropriate model to study epithelial-stromal interactions and model cell invasion associated with lesion development.
SARS-CoV-2 variants show a gradual declining pathogenicity and pro-inflammatory cytokine spur, an increasing antigenic and antiinflammatory cytokine induction, and rising structural protein instability
Authors: Barh Debmalya , Tiwari Sandeep , Gomes Lucas Gabriel Rodrigues , Pinto Cecília Horta Ramalho , Andrade Bruno Silva , Ahmad Shaban , Aljabali Alaa A. A. , Alzahrani Khalid J. , Banjer Hamsa Jameel , Hassan Sk. Sarif , Tambuwala Murtaza , Redwan Elrashdy M. , Raza Khalid , Azevedo Vasco , Lundstrom Kenneth , Uversky Vladimir N. 
Published: February 2022

ABSTRACTHyper-transmissibility with decreased disease severity are typical characteristics of Omicron variant. To understand this phenomenon, we used various bioinformatics approaches to analyze randomly selected genome sequences (one each) of the Gamma, Delta, and Omicron variants submitted to NCBI from 15 to 31 December 2021. We show that: (i) Pathogenicity of SARS-CoV-2 variants decreases in the order: Wuhan > Gamma > Delta > Omicron; however, the antigenic property follows the order: Omicron > Gamma > Wuhan > Delta. (ii) Omicron Spike RBD has lower pathogenicity but higher antigenicity than other variants. (iii) Decreased disease severity by Omicron variant may be due to its decreased pro-inflammatory and IL-6 stimulation and increased IFN-γ and IL-4 induction efficacy. (iv) Mutations in N protein are associated with decreased IL-6 induction and human DDX21-mediated increased IL-4 production in Omicron. (v) Due to mutations, the stability of S, M, N, and E proteins decreases in the order: Omicron > Gamma > Delta > Wuhan. (vi) Stronger Spike RBD-hACE2 binding in Omicron is associated with increased transmissibility. However, the lowest stability of the Omicron Spike protein makes Spike RBD-hACE2 interaction weak for systemic infection and for causing severe disease. Finally (vii), the highest instability of Omicron E protein may also be associated with decreased viral maturation and low viral load leading to less severe disease and faster recovery. Our method may be used for other similar viruses, and these findings will contribute to the understanding of the dynamics of SARS-CoV-2 variants and the management of emerging variants.
Septins mediate a microtubule-actin crosstalk that enables actin growth on microtubules
Authors: Nakos Konstantinos , Radler Megan R. , Kesisova Ilona A. , Tomasso Meagan R. , Padrick Shae B. , Spiliotis Elias T. 
Published: February 2022

AbstractCellular morphogenesis and processes such as cell division and migration require the coordination of the microtubule and actin cytoskeletons (1, 2). Microtubule-actin crosstalk is poorly understood and largely regarded as the capture and regulation of microtubules by actin (1, 2). Septins are filamentous GTP-binding proteins, which comprise the fourth component of the cytoskeleton along microtubules, actin and intermediate filaments (3, 4). Here, we report that septins mediate microtubule-actin crosstalk by coupling actin polymerization to microtubule lattices. Super-resolution imaging shows that septins localize to overlapping microtubules and actin filaments in the growth cones of neurons and non-neuronal cells. We show that recombinant septin complexes directly crosslink microtubules and actin filaments into hybrid bundles. In vitro reconstitution assays reveal that microtubule-bound septins capture and align stable actin filaments with microtubules. Strikingly, septins enable the capture and polymerization of growing actin filaments on microtubule lattices. In neuronal growth cones, septins are required for the maintenance of the peripheral actin network that fans out from microtubules. These findings provide the first evidence of septins directly mediating microtubule interactions with actin filaments, and reveal a new mechanism of microtubule-templated actin growth with broader significance for the self-organization of the cytoskeleton and cellular morphogenesis.Significance StatementCellular morphogenesis and processes such as cell division and cell migration require the coordination of the actin and microtubule cytoskeletons. Despite its broader physiological significance, actin-microtubule crosstalk is molecularly and mechanistically poorly understood. Actin-microtubule crosstalk has been viewed primarily as the regulation or guidance of microtubule dynamics by actin filaments. Here, we have discovered a new mechanism by which actin filament growth is guided by microtubules. We report that septins, a poorly understood component of the cytoskeleton, can capture and link the polymerizing ends of actin filaments to microtubule polymers. We present evidence that this new septin-mediated mechanism is critical for the morphology of growth cones, which are structures that direct the growth of neuronal axons through actin-microtubule crosstalk.
Improved fluorescent proteins for dual-color post-embedding CLEM
Authors: Peng Dingming , Li Na , He Wenting , Drasbek Kim Ryun , Xu Tao , Zhang Mingshu , Xu Pingyong 
Published: February 2022

AbstractPost-embedding correlative light and electron microscopy (CLEM) has the advantage of high-precision registration and enables light and electron microscopy imaging of the same slice. However, its broad application has been hampered by the limited available fluorescent proteins (FPs) and low signal-to-background ratio (SBR). Here, we developed a green photoswitchable FP, mEosEM-E with substantially high on/off contrast in EM samples embedded in Epon resin which maximally preserves cellular structures but quenches the fluorescence of FPs. Taking advantage of the photoswitching property of mEosEM-E, the autofluorescence background from the resin was significantly reduced by a subtraction-based CLEM (sCLEM) method. Meanwhile, we identified a red fluorescent protein (RFP) mScharlet-H that exhibited higher brightness and SBR in resin than previously reported RFPs. With mEosEM-E and mScharlet-H, dual-color post-Epon-embedding CLEM images with high SBR and no cross-talk signal were successfully performed to reveal the organization of nucleolar proteins. Moreover, a dissection of the influences of different EM sample preparation steps on the fluorescence preservation for several RFPs provides useful guidance for further probe development.