bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitigation of the effect of high light on the photosynthetic apparatus ofRhodobacter alkalitoleranswhen grown in an alkaline environment
Authors: Zamal Mohammad Yusuf , Ramana Ch Venkata , Subramanyam Rajagopal 
Published: July 2023

ABSTRACTIn the phototrophic alphaproteobacteria, photosynthesis is performed by pigment-protein complexes, including the light-harvesting complexes known as LH1 and LH2. The photosystem also encompasses carotenoids to assist in well-functioning of photosynthesis. Most photosynthetic bacteria are exposed to various abiotic stresses, and here, theRhodobacter (R.) alkalitoleranswere extracted from the alkaline pond. We report the comparative study of the photosynthetic apparatus ofR. alkalitoleransin various light intensities in relation to this bacterium’s high pH tolerance ability. We found that as the light intensity increased, the stability of photosystem complexes decreased in normal pH (npH pH 6.8±0.05) conditions, whereas in high pH (hpH pH 8.6±0.05) acclimation was observed to high light. The content of bacteriochlorophylla, absorbance spectra, and circular dichroism data shows that the integrity of photosystem complexes is less affected in hpH compared to npH conditions. LP-BN of photosystem complexes also shows that LH2 is more affected in npH than hpH, whereas RC-LH1 monomer or dimer has shown interplay between monomer and dimer in hpH although the dimer and monomer both increased in npH. The sucrose density gradient of β-DM solubilized intracytoplasmic membranes, further evidences the pattern of monomer-dimer conversion. Additionally, thin layer chromatographic separation of isolated membrane lipids shows that phosphatidylcholine (PC) levels have increased in hpH conditions which further confirms the integrity of photosystem complexes in hpH conditions. Moreover, qPCR data showed that the subunit -c of ATPase levels was overexpressed in hpH. Consequently, the P515 measurement shows that more ATP production is required in hpH, which dissipates the protons from the chromatophore lumen. This could be the reason the photosystem protein complex destabilized due to more lumen acidification. To maintain homeostasis in hpH, the antiporter NhaD expressed more than in the npH condition.IMPORTANCER. alkalitoleransis an alkaline tolerant species discovered from an alkaline pond in Gujrat India. Being a photoautotrophic photosynthetic organism, it serves as a good model organism to study the photosynthetic apparatus among phototrophic alphaproteobacteria. In nature organisms not only tackle a single abiotic stress but many including temperature, light, salinity, and many other abiotic stresses. Here we investigate how two different abiotic factors light and alkaline conditions modulate the growth and photosynthetic apparatus in a phototrophic alphaproteobacterium,R. alkalitolerans. Our results of this study will give leads in developing alkali-tolerant algae and higher plants.
Efficient Formation of Single-copy Human Artificial Chromosomes
Authors: Gambogi Craig W. , Mer Elie , Brown David M. , Yankson George , Gavade Janardan N. , Logsdon Glennis A. , Heun Patrick , Glass John I. , Black Ben E. 
Published: July 2023

AbstractLarge DNA assembly methodologies underlie milestone achievements in synthetic prokaryotic and budding yeast chromosomes. While budding yeast control chromosome inheritance through ∼125 bp DNA sequence-defined centromeres, mammals and many other eukaryotes use large, epigenetic centromeres. Harnessing centromere epigenetics permits human artificial chromosome (HAC) formation but is not sufficient to avoid rampant multimerization of the initial DNA molecule upon introduction to cells. Here, we describe an approach that efficiently forms single-copy HACs. It employs a ∼750 kb construct that is sufficiently large to house the distinct chromatin types present at the inner and outer centromere, obviating the need to multimerize. Delivery to mammalian cells is streamlined by employing yeast spheroplast fusion. These developments permit faithful chromosome engineering in the context of metazoan cells.One-Sentence SummaryA quarter century after the first human artificial chromosomes, a solution to their uncontrolled multimerization is achieved.
Unconventional Activation of IRE1 Enhances TH17 Responses and Promotes Neutrophilic Airway Inflammation
Authors: Wu Dandan , Zhang Xing , Zimmerly Kourtney M. , Wang Ruoning , Livingston Amanda , Iwawaki Takao , Kumar Ashok , Wu Xiang , Mandell Michael A. , Liu Meilian , Yang Xuexian O. 
Published: July 2023

AbstractTreatment-refractory severe asthma manifests a neutrophilic phenotype associated with TH17 responses. Heightened unfolded protein responses (UPRs) are associated with the risk of asthma, including severe asthma. However, how UPRs participate in the deregulation of TH17 cells leading to this type of asthma remains elusive. In this study, we investigated the role of the UPR sensor IRE1 in TH17 cell function and neutrophilic airway inflammation. We found that IRE1 is induced in fungal asthma and is highly expressed in TH17 cells relative to naïve CD4+T cells. Cytokine (e.g. IL-23) signals induce the IRE1-XBP1s axis in a JAK2-dependent manner. This noncanonical activation of the IRE1-XBP1s pathway promotes UPRs and cytokine secretion by TH17 cells.Ern1(encoding IRE1)-deficiency decreases the expression of ER stress factors and impairs the differentiation and cytokine secretion of TH17 cells. Genetic ablation ofErn1leads to alleviated TH17 responses and airway neutrophilia in aCandida albicansasthma model. Consistently, IL-23 activates the JAK2-IRE1-XBP1s pathwayin vivoand enhances TH17 responses and neutrophilic infiltration into the airway. Taken together, our data indicate that IRE1, noncanonically activated by cytokine signals, promotes neutrophilic airway inflammation through the UPR- mediated secretory function of TH17 cells. The findings provide a novel insight into the fundamental understanding of IRE1 in TH17-biased TH2-low asthma.
Arf GAP containing dAsap regulates NMJ organization and synaptic calcium through Arf6-dependent signaling inDrosophila
Authors: Mallik Bhagaban , Kushwaha Shikha , Bisht Anjali , Harsha MJ , Frank C. Andrew , Kumar Vimlesh 
Published: July 2023

AbstractSynaptic morphogenesis involves an interplay of multiple signaling pathways and requires membrane remodeling and cytoskeleton dynamics. We identified the BAR-domain protein dAsap (Arf GAP, SH3, Ankyrin repeat, and PH domain) as one of the regulators of synaptic morphogenesis. Loss of dAsap results in decreased bouton numbers, increased inter-bouton diameter, and disrupted microtubule organization at the nerve terminals. Electrophysiological analysis of the mutants revealed a gain in neurotransmission compared to control neuromuscular junctions (NMJs).dAsapmutant NMJs have increased evoked amplitude, increased spontaneous miniature frequency, and significantly fewer synaptic failures in low calcium. Consistent with these observations,dAsapmutants have increased active zone number. Additional pharmacological and genetic manipulations that are known to impair calcium release from stores suppress the dAsap phenotypes. Finally, we show that expressing a GDP-locked form of Arf6 indAsapmutants restored the NMJ morphological defects, disrupted cytoskeleton, and aberrant neurotransmission. Thus, we propose a model in which dAsap regulates NMJ morphogenesis and synaptic calcium homeostasis through Arf6-dependent neuronal signaling.
Hypoxia blunts angiogenic signaling and upregulates the antioxidant system in elephant seal endothelial cells
Authors: Allen Kaitlin N , Torres-Velarde Julia María , Vazquez Juan Manuel , Moreno-Santillan Diana D , Sudmant Peter H , Vázquez-Medina José Pablo 
Published: July 2023

AbstractElephant seals experience extreme hypoxemia during diving bouts. Similar depletions in oxygen availability characterize pathologies including myocardial infarction and ischemic stroke in humans, but seals manage these repeated episodes without injury. However, the real-time assessment of the molecular changes underlying protection against hypoxic injury in seals remains restricted by their at-sea inaccessibility. Hence, we developed a proliferative arterial endothelial cell culture system to assess the molecular response to prolonged hypoxia. Seal and human cells exposed to 1% O2for up to 6 h demonstrated differential responses to both acute and prolonged hypoxia. Seal cells decouple stabilization of the hypoxia-sensitive transcriptional regulator HIF-1α from angiogenic signaling at both the transcriptional and cellular level. Rapid upregulation of genes involved in the glutathione (GSH) metabolism pathway supported maintenance of GSH pools and increases in intracellular succinate in seal but not human cells during hypoxia exposure. High maximal and spare respiratory capacity in seal cells after hypoxia exposure occurred in concert with increasing mitochondrial branch length and independent from major changes in extracellular acidification rate, suggesting seal cells recover oxidative metabolism without significant glycolytic dependency after hypoxia exposure. In sum, our studies show that in contrast to human cells, seal cells adapt to hypoxia exposure by dampening angiogenic signaling, increasing antioxidant protection, and maintaining mitochondrial morphological integrity and function.
Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics
Authors: Higo Junichi , Bekker Gert-Jan , Kamiya Narutoshi , Fukuda Ikuo , Fukunishi Yoshifumi 
Published: July 2023

AbstractBinding of a small and flexible molecule, ribocil A (non-binder) or B (binder), to the deep pocket of the aptamer domain of the FMN riboswitch was studied by mD-VcMD, which is a generalized-ensemble method based on molecular dynamics (MD) simulation. Ribocil A and B are structurally similar because they are optical isomers mutually. In the initial conformation of simulation, both ligands and the aptamer were completely dissociated in explicit solvent. The resultant free-energy landscape of ribocil B binding to the aptamer was funnel-like, whereas that of ribocil A was rugged, which agrees qualitatively with an experiment. When entering the gate (named “front gate”) of the pocket, the ligand interacted with the aptamer by native and non-native π-π stackings, and the stackings restrained the molecular orientation of the ligands to be advantageous to reach the binding site smoothly. The simulation showed another pathway, which also led the ligands to the binding site. Its gate (maned “rear gate”) located completely opposite to the front gate on the aptamer’s surface. However, approach from the rear gate required overcoming a free-energy barrier before reaching the binding site, and the ligands should rotate largely and sharply at the free-energy barrier. This ligand’s orientation property is discussed referring to a ligand orientation selection mechanism exserted by a membrane protein capturing its ligand.
Spatial profiling of neuro-immune interactions in gastroenteropancreatic NETs
Authors: Duan Suzann , Sawyer Travis W. , Witten Brandon L. , Song Heyu , Else Tobias , Merchant Juanita L. 
Published: July 2023

AbstractGastroenteropancreatic neuroendocrine tumors (GEP-NETs) are heterogeneous malignancies that arise from complex cellular interactions within the tissue microenvironment. Here, we sought to decipher tumor-derived signals from the surrounding microenvironment by applying Nanostring Digital Spatial Profiling (DSP) to hormone-secreting and non-functional GEP-NETs. DSP was used to evaluate the expression of 40 neural and immune-related proteins in surgically resected duodenal and pancreatic NETs (n=20) primarily comprised of gastrinomas (18/20). A total of 279 regions of interest were examined between tumors, adjacent normal and abnormal-appearing epithelium, and the surrounding stroma. The results were stratified by tissue type andMultiple Endocrine Neoplasia I (MEN1)status and protein expression was validated by immunohistochemical (IHC) staining. A tumor immune cell autonomous inflammatory signature was further evaluated by IHC and RNAscope, while functional pro-inflammatory signaling was confirmed using patient-derived duodenal organoids. Gastrin-secreting and non-functional pancreatic NETs showed a higher abundance of immune cell markers and immune infiltrate compared to duodenal gastrinomas. Tumors displayed strong intra-tissue variation in the expression of neural- and immune-related proteins. Compared to non-MEN1tumors,MEN1gastrinomas showed reduced expression of immune cell markers and upregulated expression of neuropathological proteins. Duodenal gastrinomas showed strong expression of the pro- inflammatory and pro-neural factor IL-17B. Treatment of human duodenal organoids with IL- 17B activated NF-kB and STAT3 signaling and induced the expression of neuroendocrine markers. In conclusion, multiplexed spatial protein analysis identified tissue-specific neuro- immune signatures in GEP-NETs. Moreover, duodenal gastrinomas cell autonomously express immune and pro-inflammatory factors, including tumor-derived IL-17B, that stimulate the neuroendocrine phenotype.
Distinct patterns of connectivity with motor cortex reflect component processes of sensorimotor learning
Authors: Areshenkoff Corson N. , de Brouwer Anouk J. , Gale Daniel J. , Nashed Joseph Y. , Randall Flanagan J. , Smallwood Jonathan , Gallivan Jason P. 
Published: July 2023

AbstractSensorimotor learning is supported by multiple competing processes that operate concurrently, making it a challenge to elucidate their neural underpinnings. Here, using human functional MRI, we identify three distinct axes of connectivity between the motor cortex and other brain regions during sensorimotor adaptation. These three axes uniquely correspond to subjects’ degree of implicit learning, performance errors and explicit strategy use, and involve different brain networks situated at increasing levels of the cortical hierarchy. We test the generalizability of these neural axes to a separate form of motor learning known to rely mainly on explicit processes, and show that it is only the Explicit neural axis, composed of higher-order areas in transmodal cortex, that predicts learning in this task. Together, our study uncovers multiple distinct patterns of functional connectivity with motor cortex during sensorimotor adaptation, the component processes that these patterns support, and how they generalize to other forms of motor learning.
Raman micro-spectroscopy reveals the spatial distribution of fumarate in cells and tissues
Authors: Kamp Marlous , Surmacki Jakub , Mondejar Marc Segarra , Young Tim , Chrabaszcz Karolina , Joud Fadwa , Zecchini Vincent , Speed Alyson , Frezza Christian , Bohndiek Sarah E 
Published: July 2023

AbstractAberrantly accumulated metabolites such as fumarate elicit intra– and inter-cellular pro-oncogenic cascades, yet current methods to measure them require sample perturbation or disruption and lack spatio-temporal resolution, limiting our ability to fully characterize their function and distribution in cells and within a tissue. Raman spectroscopy (RS) is a powerful bio-analytical tool that directly characterizes the chemical composition of a sample based solely on the optical fingerprint of vibrational modes. Here, we show for the first time that RS can directly detect fumarate in living cellsin vivoand animal tissuesex vivo. Using the observed linear relationship between Raman scattered intensity and fumarate concentration, we demonstrate that RS can distinguish between Fumarate hydratase (Fh1)-deficient and Fh1-proficient cells based on their fumarate concentration. Moreover, RS reveals the spatial compartmentalization of fumarate within cellular organelles: consistent with disruptive methods, in Fh1-deficient cells we observe the highest fumarate concentration (37 ± 19 mM) in the mitochondria, where the TCA cycle operates, followed by the cytoplasm (24 ± 13 mM) and then the nucleus (9 ± 6 mM). Finally, we apply RS to tissues from an inducible mouse model of FH loss in the kidney, demonstrating that RS can accurately classify FH status in these tissues. These results suggest that RS could be adopted as a valuable tool for small molecule metabolic imaging, enablingin situdynamic evaluation of fumarate compartmentalization.
Structural and Biological Evaluations of a Non-Nucleoside STING Agonist Specific for Human STINGA230Variants
Authors: Tang Zhichao , Zhao Junxing , Li Ying , Tomer Shallu , Selvaraju Manikandan , Tien Nicholas , Sun Diyun , Johnson David K. , Zhen Anjie , Li Pingwei , Wang Jingxin 
Published: July 2023

ABSTRACTPreviously we identified a non-nucleotide tricyclic agonist BDW568 that activates human STING (stimulator of interferon genes) gene variant containing A230 in a human monocyte cell line (THP-1). STINGA230alleles, including HAQ and AQ, are less common STING variants in human population. To further characterize the mechanism of BDW568, we obtained the crystal structure of the C-terminal domain of STINGA230complexed with BDW-OH (active metabolite of BDW568) at 1.95 Å resolution and found the planar tricyclic structure in BDW-OH dimerizes in the STING binding pocket and mimics the two nucleobases of the endogenous STING ligand 2’,3’-cGAMP. This binding mode also resembles a known synthetic ligand of human STING, MSA-2, but not another tricyclic mouse STING agonist DMXAA. Structure-activity-relationship (SAR) studies revealed that all three heterocycles in BDW568 and the S-acetate side chain are critical for retaining the compound’s activity. BDW568 could robustly activate the STING pathway in human primary peripheral blood mononuclear cells (PBMCs) with STINGA230genotype from healthy individuals. We also observed BDW568 could robustly activate type I interferon signaling in purified human primary macrophages that were transduced with lentivirus expressing STINGA230, suggesting its potential use to selectively activate genetically engineered macrophages in macrophage-based approaches, such as chimeric antigen receptor (CAR)-macrophage immunotherapies.
Entropy-based decoy generation methods for accurate FDR estimation in large-scale metabolomics annotations
Authors: An Shaowei , Lu Miaoshan , Wang Ruimin , Wang Jinyin , Xie Cong , Tong Junjie , Jiang Hengxuan , Yu Changbin 
Published: July 2023

AbstractLarge-scale metabolomics research faces challenges in accurate metabolite annotation and false discovery rate (FDR) estimation. Recent progress in addressing these challenges has leveraged experience from proteomics and inspiration from other sciences. Although the target-decoy strategy has been applied to metabolomics, generating reliable decoy libraries is difficult due to the complexity of metabolites. Additionally, continuous bioinformatic efforts are necessary to increase the utilization of growing spectra resources while reducing false identifications. Here we introduce the concept of ion entropy and present two entropy-based decoy generation methods. The assessment of public spectral databases using ion entropy validated it as a good metric for ion information content in massive metabolomics data. The decoy generation method developed based on this concept outperformed current representative decoy strategies in metabolomics and achieved the best FDR estimation performance. We analyzed 47 public metabolomics datasets using the constructed workflow to provide instructive suggestions. Finally, we present MetaPhoenix, a tool equipped with a well-constructed FDR estimation workflow that facilitates the development of accurate FDR-controlled analysis in the metabolomics field.
Domain-general and language-specific contributions to speech production in a second language: an fMRI study using functional localizers
Authors: Wolna Agata , Szewczyk Jakub , Diaz Michele , Domagalik Aleksandra , Szwed Marcin , Wodniecka Zofia 
Published: July 2023

AbstractFor bilinguals, speaking in a second language (L2) compared to the native language (L1) is usually more difficult. In this study we asked whether the difficulty in L2 production reflects increased demands imposed on domain-general or core language mechanisms. We compared the brain response to speech production in L1 and L2 within two functionally-defined networks in the brain: the Multiple Demand (MD) network and the language network. We found that speech production in L2 was linked to a widespread increase of brain activity in the domain-general MD network. The language network did not show a similarly robust differences in processing speech in the two languages, however, we found increased response to L2 production in the language-specific portion of the left inferior frontal gyrus (IFG). To further explore our results, we have looked at domain-general and language-specific response within the brain structures postulated to form a Bilingual Language Control (BLC) network. Within this network, we found a robust increase in response to L2 in the domain-general, but also in some language-specific voxels including in the left IFG. Our findings show that L2 production strongly engages domain-general mechanisms, but only affects language sensitive portions of the left IFG. These results put constraints on the current model of bilingual language control by precisely disentangling the domain-general and language-specific contributions to the difficulty in speech production in L2.
Multiple exposures to sevoflurane during the neonatal period impair hippocampus development and cognitive function in young mice
Authors: Yu Gaojie , Huang Xiaoting , Lin Liang , Chen Zhenyi , Zhang Jie , Jia Jia 
Published: July 2023

AbstractSevoflurane is a commonly used anesthesia for infants and young children. Sevoflurane has potential neurotoxicity in immature brains; however, its specific mechanism has not been fully elucidated. Therefore, we used an established sevoflurane anesthesia model and evaluated hippocampal synaptic function using transcriptome sequencing, biochemical analyses, and animal behavior to investigate the effect of multiple neonatal sevoflurane exposures on the hippocampus in mice. C57BL/6J mice were randomly divided into sevoflurane and control groups. All experimental conditions were identical in the two groups except for the anesthetization procedure. Mice in the sevoflurane group were anesthetized with 2.5% sevoflurane for 2 h daily for 3 consecutive days (postnatal days 6−8). Mice in the control group did not receive sevoflurane anesthesia. During anesthesia, mice were administered 50% oxygen, and the respiratory rate and skin color were monitored. On day 3 of modeling, half of the mice were randomly selected to undergo harvesting of the hippocampus. RNA sequencing (RNA-seq) of RNA extracted from the hippocampus identified 736 differentially expressed genes (DEGs), including 433 upregulated and 303 downregulated DEGs, after multiple sevoflurane exposures. Gene ontology term enrichment analysis results suggested that sevoflurane exposure altered the expression of neurodevelopment-related genes in neonatal mice. Several enriched biological processes involved in brain development (axon/forebrain development) and adenosine monophosphate-activated protein kinase signaling pathways were highlighted. Comparison with RNA-seq database information showed that DEGs of the neonatal hippocampus after multiple exposures to sevoflurane were specific to neonatal mice. Furthermore, Morris water maze testing confirmed that sevoflurane anesthesia induced learning and memory impairments in young mice. Additionally, Western blot and immunofluorescence analyses showed that sevoflurane treatment decreased synaptic protein levels, such as postsynaptic density protein 95, synaptosomal-associated protein, 25 kDa, and B-cell lymphoma 2-associated athanogene 3, in the hippocampus, which induced synaptic dysfunction, resulting in impaired nervous system development in young mice.