bluuebunny/crossref_metadata_2025 huggingface dataset:
Inner Amino Acid Contacts Are Key Factors of Multistage Structural Rearrangements of DNA and Affect Substrate Specificity of Apurinic/Apyrimidinic Endonuclease APE1
Authors: Bulygin Anatoly A. , Syryamina Victoria N. , Kuznetsova Aleksandra A. , Novopashina Darya S. , Dzuba Sergei A. , Kuznetsov Nikita A.
Published: July 2023

Apurinic/apyrimidinic endonuclease 1 (APE1) is one of the most important enzymes in base excision repair. Studies on this enzyme have been conducted for a long time, but some aspects of its activity remain poorly understood. One such question concerns the mechanism of damaged-nucleotide recognition by the enzyme, and the answer could shed light on substrate specificity control in all enzymes of this class. In the present study, by pulsed electron–electron double resonance (DEER, also known as PELDOR) spectroscopy and pre–steady-state kinetic analysis along with wild-type (WT) APE1 from Danio rerio (zAPE1) or three mutants (carrying substitution N253G, A254G, or E260A), we aimed to elucidate the molecular events in the process of damage recognition. The data revealed that the zAPE1 mutant E260A has much higher activity toward DNA substrates containing 5,6-dihydro-2′-deoxyuridine (DHU), 2′-deoxyuridine (dU), alpha-2′-deoxyadenosine (αA), or 1,N6-ethenoadenosine (εA). Examination of conformational changes in DNA clearly revealed multistep DNA rearrangements during the formation of the catalytic complex. These structural rearrangements of DNA are directly associated with the capacity of damaged DNA for enzyme-induced bending and unwinding, which are required for eversion of the damaged nucleotide from the DNA duplex and for its placement into the active site of the enzyme. Taken together, the results experimentally prove the factors that control substrate specificity of the AP endonuclease zAPE1.
Transglutaminase 2 Facilitates Murine Wound Healing in a Strain-Dependent Manner
Authors: Yiu Ting W. , Holman Sara R. , Kaidonis Xenia , Graham Robert M. , Iismaa Siiri E.
Published: July 2023

Transglutaminase 2 (TG2) plays a role in cellular processes that are relevant to wound healing, but to date no studies of wound healing in TG2 knockout mice have been reported. Here, using 129T2/SvEmsJ (129)- or C57BL/6 (B6)-backcrossed TG2 knockout mice, we show that TG2 facilitates murine wound healing in a strain-dependent manner. Early healing of in vivo cutaneous wounds and closure of in vitro scratch wounds in murine embryonic fibroblast (MEF) monolayers were delayed in 129, but not B6, TG2 knockouts, relative to their wild-type counterparts, with wound closure in 129 being faster than in B6 wild-types. A single dose of exogenous recombinant wild-type TG2 to 129 TG2−/− mice or MEFs immediately post-wounding accelerated wound closure. Neutrophil and monocyte recruitment to 129 cutaneous wounds was not affected by Tgm2 deletion up to 5 days post-wounding. Tgm2 mRNA and TG2 protein abundance were higher in 129 than in B6 wild-types and increased in abundance following cutaneous and scratch wounding. Tgm1 and factor XIIA (F13A) mRNA abundance increased post-wounding, but there was no compensation by TG family members in TG2−/− relative to TG2+/+ mice in either strain before or after wounding. 129 TG2+/+ MEF adhesion was greater and spreading was faster than that of B6 TG2+/+ MEFs, and was dependent on syndecan binding in the presence, but not absence, of RGD inhibition of integrin binding. Adhesion and spreading of 129, but not B6, TG2−/− MEFs was impaired relative to their wild-type counterparts and was accelerated by exogenous addition or transfection of TG2 protein or cDNA, respectively, and was independent of the transamidase or GTP-binding activity of TG2. Rho-family GTPase activation, central to cytoskeletal organization, was altered in 129 TG2−/− MEFs, with delayed RhoA and earlier Rac1 activation than in TG2+/+ MEFs. These findings indicate that the rate of wound healing is different between 129 and B6 mouse strains, correlating with TG2 abundance, and although not essential for wound healing, TG2 facilitates integrin- and syndecan-mediated RhoA- and Rac1-activation in fibroblasts to promote efficient wound contraction.
Inflammation, Dopaminergic Brain and Bilirubin
Authors: Jayanti Sri , Dalla Verde Camilla , Tiribelli Claudio , Gazzin Silvia
Published: July 2023

Dopamine is a well-known neurotransmitter due to its involvement in Parkinson’s disease (PD). Dopamine is not only involved in PD but also controls multiple mental and physical activities, such as the pleasure of food, friends and loved ones, music, art, mood, cognition, motivation, fear, affective disorders, addiction, attention deficit disorder, depression, and schizophrenia. Dopaminergic neurons (DOPAn) are susceptible to stressors, and inflammation is a recognized risk for neuronal malfunctioning and cell death in major neurodegenerative diseases. Less is known for non-neurodegenerative conditions. Among the endogenous defenses, bilirubin, a heme metabolite, has been shown to possess important anti-inflammatory activity and, most importantly, to prevent DOPAn demise in an ex vivo model of PD by acting on the tumor necrosis factor-alpha (TNFα). This review summarizes the evidence linking DOPAn, inflammation (when possible, specifically TNFα), and bilirubin as an anti-inflammatory in order to understand what is known, the gaps that need filling, and the hypotheses of anti-inflammatory strategies to preserve dopamine homeostasis with bilirubin included.
Hydration and Structural Adaptations of the Human CYP1A1, CYP1A2, and CYP1B1 Active Sites by Molecular Dynamics Simulations
Authors: Dutkiewicz Zbigniew , Mikstacka Renata
Published: July 2023

Cytochromes CYP1A1, CYP1A2, and CYP1B1, the members of the cytochrome P450 family 1, catalyze the metabolism of endogenous compounds, drugs, and non-drug xenobiotics which include substances involved in the process of carcinogenesis, cancer chemoprevention, and therapy. In the present study, the interactions of three selected polymethoxy-trans-stilbenes, analogs of a bioactive polyphenol trans-resveratrol (3,5,4′-trihydroxy-trans-stilbene) with the binding sites of CYP1 isozymes were investigated with molecular dynamics (MD) simulations. The most pronounced structural changes in the CYP1 binding sites were observed in two substrate recognition sites (SRS): SRS2 (helix F) and SRS3 (helix G). MD simulations show that the number and position of water molecules occurring in CYP1 APO and in the structures complexed with ligands are diverse. The presence of water in binding sites results in the formation of water–protein, water–ligand, and bridging ligand–water–protein hydrogen bonds. Analysis of the solvent and substrate channels opening during the MD simulation showed significant differences between cytochromes in relation to the solvent channel and the substrate channels 2c, 2ac, and 2f. The results of this investigation lead to a deeper understanding of the molecular processes that occur in the CYP1 binding sites and may be useful for further molecular studies of CYP1 functions.
Physico-Chemical Approaches to Investigate Surface Hydroxyls as Determinants of Molecular Initiating Events in Oxide Particle Toxicity
Authors: Pavan Cristina , Santalucia Rosangela , Escolano-Casado Guillermo , Ugliengo Piero , Mino Lorenzo , Turci Francesco
Published: July 2023

The study of molecular recognition patterns is crucial for understanding the interactions between inorganic (nano)particles and biomolecules. In this review we focus on hydroxyls (OH) exposed at the surface of oxide particles (OxPs) which can play a key role in molecular initiating events leading to OxPs toxicity. We discuss here the main analytical methods available to characterize surface OH from a quantitative and qualitative point of view, covering thermogravimetry, titration, ζ potential measurements, and spectroscopic approaches (NMR, XPS). The importance of modelling techniques (MD, DFT) for an atomistic description of the interactions between membranes/proteins and OxPs surfaces is also discussed. From this background, we distilled a new approach methodology (NAM) based on the combination of IR spectroscopy and bioanalytical assays to investigate the molecular interactions of OxPs with biomolecules and membranes. This NAM has been already successfully applied to SiO2 particles to identify the OH patterns responsible for the OxPs’ toxicity and can be conceivably extended to other surface-hydroxylated oxides.
Recent Advances in Machine-Learning-Based Chemoinformatics: A Comprehensive Review
Authors: Niazi Sarfaraz K. , Mariam Zamara
Published: July 2023

In modern drug discovery, the combination of chemoinformatics and quantitative structure–activity relationship (QSAR) modeling has emerged as a formidable alliance, enabling researchers to harness the vast potential of machine learning (ML) techniques for predictive molecular design and analysis. This review delves into the fundamental aspects of chemoinformatics, elucidating the intricate nature of chemical data and the crucial role of molecular descriptors in unveiling the underlying molecular properties. Molecular descriptors, including 2D fingerprints and topological indices, in conjunction with the structure–activity relationships (SARs), are pivotal in unlocking the pathway to small-molecule drug discovery. Technical intricacies of developing robust ML-QSAR models, including feature selection, model validation, and performance evaluation, are discussed herewith. Various ML algorithms, such as regression analysis and support vector machines, are showcased in the text for their ability to predict and comprehend the relationships between molecular structures and biological activities. This review serves as a comprehensive guide for researchers, providing an understanding of the synergy between chemoinformatics, QSAR, and ML. Due to embracing these cutting-edge technologies, predictive molecular analysis holds promise for expediting the discovery of novel therapeutic agents in the pharmaceutical sciences.
Xylose Isomerase Depletion Enhances Virulence of Xanthomonas citri subsp. citri in Citrus aurantifolia
Authors: Alexandrino André Vessoni , Prieto Evandro Luis , Nicolela Nicole Castro Silva , da Silva Marin Tamiris Garcia , dos Santos Talita Alves , de Oliveira da Silva João Pedro Maia , da Cunha Anderson Ferreira , Behlau Franklin , Novo-Mansur Maria Teresa Marques
Published: July 2023

Citrus canker, caused by the bacterium Xanthomonas citri (Xcc), is one of the most devastating diseases for the citrus industry. Xylose is a constituent of the cell wall of plants, and the ability of Xcc to use this carbohydrate may play a role in virulence. Xcc has two genes codifying for xylose isomerase (XI), a bifunctional enzyme that interconverts D-xylose into D-xylulose and D-glucose into D-fructose. The aim of this work was to investigate the functional role of the two putative XI ORFs, XAC1776 (xylA1) and XAC4225 (xylA2), in Xcc pathogenicity. XI-coding genes of Xcc were deleted, and the single mutants (XccΔxylA1 or XccΔxylA2) or the double mutant (XccΔxylA1ΔxylA2) remained viable. The deletion of one or both XI genes (xylA1 and/or xylA2) increased the aggressiveness of the mutants, causing disease symptoms. RT-qPCR analysis of wild strain and xylA deletion mutants grown in vivo and in vitro revealed that the highest expression level of hrpX and xylR was observed in vivo for the double mutant. The results indicate that XI depletion increases the expression of the hrp regulatory genes in Xcc. We concluded that the intracellular accumulation of xylose enhances Xcc virulence.
Albizia julibrissin Exerts Anti-Obesity Effects by Inducing the Browning of 3T3L1 White Adipocytes
Authors: Kim Yuna , Ji Hyanggi , Ryu Dehun , Cho Eunae , Park Deokhoon , Jung Eunsun
Published: July 2023

This study investigated the effects of the Albizia julibrissin Leaf extracts (AJLE) on adipocytes using 3T3-L1 cells. AJLE inhibited adipogenesis by reducing the expression of peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT/enhancer binding proteins (C/EBPs) that regulate enzymes involved in fat synthesis and storage, and subsequently reduced intracellular lipid droplets, glycerol-3-phosphate dehydrogenase (GPDH), and triglyceride (TG). AJLE also increased the expression of brown adipocyte markers, such as uncoupling protein-1 (UCP-1), PR/SET domain 16 (PRDM16), and bone morphogenetic protein 7 (BMP7) by inducing the differentiation of brown adipocytes, as shown by a decrease in the lipid droplet sizes and increasing mitochondrial mass. AJLE increased the expression of transcription factor A, mitochondrial (TFAM), mitochondrial DNA (mtDNA) copy number, and UCP-1 protein expression, all of which are key factors in regulating mitochondrial biogenesis. AJLE-induced browning was shown to be regulated by the coordination of AMPK, p38, and SIRT1 signaling pathways. The ability of AJLE to inhibit adipogenesis and induce brown adipocyte differentiation may help treat obesity and related diseases.
Synthesis and Properties of (1R(S),5R(S),7R(S),8R(S))-1,8-Bis(hydroxymethyl)-6-azadispiro[4.1.4.2]tridecane-6-oxyl: Reduction-Resistant Spin Labels with High Spin Relaxation Times
Authors: Khoroshunova Yulia V. , Morozov Denis A. , Kuznetsov Danil A. , Rybalova Tatyana V. , Glazachev Yurii I. , Bagryanskaya Elena G. , Kirilyuk Igor A.
Published: July 2023

Site-directed spin labeling followed by investigation using Electron Paramagnetic Resonance spectroscopy is a rapidly expanding powerful biophysical technique to study structure, local dynamics and functions of biomolecules using pulsed EPR techniques and nitroxides are the most widely used spin labels. Modern trends of this method include measurements directly inside a living cell, as well as measurements without deep freezing (below 70 K), which provide information that is more consistent with the behavior of the molecules under study in natural conditions. Such studies require nitroxides, which are resistant to the action of biogenic reductants and have high spin relaxation (dephasing) times, Tm. (1R(S),5R(S),7R(S),8R(S))-1,8-bis(hydroxymethyl)-6-azadispiro[4.1.4.2]tridecane-6-oxyl is a unique nitroxide that combines these features. We have developed a convenient method for the synthesis of this radical and studied the ways of its functionalization. Promising spin labels have been obtained, the parameters of their spin relaxation T1 and Tm have been measured, and the kinetics of reduction with ascorbate have been studied.
COVID-19 Infection May Drive EC-like Myofibroblasts towards Myofibroblasts to Contribute to Pulmonary Fibrosis
Authors: Wu Xiuju , Zhang Daoqin , Boström Kristina I. , Yao Yucheng
Published: July 2023

COVID-19 has an extensive impact on Homo sapiens globally. Patients with COVID-19 are at an increased risk of developing pulmonary fibrosis. A previous study identified that myofibroblasts could be derived from pulmonary endothelial lineage cells as an important cell source that contributes to pulmonary fibrosis. Here, we analyzed publicly available data and showed that COVID-19 infection drove endothelial lineage cells towards myofibroblasts in pulmonary fibrosis of patients with COVID-19. We also discovered a similar differentiation trajectory in mouse lungs after viral infection. The results suggest that COVID-19 infection leads to the development of pulmonary fibrosis partly through the activation of endothelial cell (EC)-like myofibroblasts.
Transcriptome and Metabolome Analyses Reveal Perfluorooctanoic Acid-Induced Kidney Injury by Interfering with PPAR Signaling Pathway
Authors: Zhang Yan , Li Yang , Gao Nana , Gong Yinglan , Shi Wanyu , Wang Xiaodan
Published: July 2023

Perfluorooctanoic acid (PFOA) is widely used in aviation science and technology, transportation, electronics, kitchenware, and other household products. It is stable in the environment and has potential nephrotoxicity. To investigate the effect of PFOA exposure during pregnancy on the kidneys of offspring mice, a total of 20 mice at day 0 of gestation were randomly divided into two groups (10 mice in each group), and each group was administered 0.2 mL of PFOA at a dose of 3.5 mg/kg or deionized water by gavage during gestation. The kidney weight, kidney index, histopathological observation, serum biochemistry, transcriptomics, and metabolomics of the kidneys of the 35-day offspring mice were analyzed. In addition, malondialdehyde (MDA), superoxide dismutase (SOD), and catalase (CAT) levels in the kidney were measured. Transcriptome analysis results showed that 387 genes were up-regulated and 283 genes were down-regulated compared with the control group. These differentially expressed genes (DEGs) were mainly concentrated in the peroxisome-proliferator-activated receptor (PPAR) signaling pathway and circadian rhythm. Compared with the control group, 64 and 73 metabolites were up- and down-regulated, respectively, in the PFOA group. The altered metabolites were mainly enriched in the biosynthesis of unsaturated fatty acids. PFOA can affect the expression levels of circadian rhythm-related genes in the kidneys of offspring mice, and this change is influenced by the PPAR signaling pathway. PFOA causes oxidative stress in the kidneys, which is responsible for significant changes in metabolites associated with the biosynthesis of unsaturated fatty acids.
Checkpoint Inhibitor-Induced Colitis: From Pathogenesis to Management
Authors: Terrin Maria , Migliorisi Giulia , Dal Buono Arianna , Gabbiadini Roberto , Mastrorocco Elisabetta , Quadarella Alessandro , Repici Alessandro , Santoro Armando , Armuzzi Alessandro
Published: July 2023

The advent of immunotherapy, specifically of immune checkpoint inhibitors (ICIs), for the treatment of solid tumors has deeply transformed therapeutic algorithms in medical oncology. Approximately one-third of patients treated with ICIs may de velop immune-related adverse events, and the gastrointestinal tract is often affected by different grades of mucosal inflammation. Checkpoint inhibitors colitis (CIC) presents with watery or bloody diarrhea and, in the case of severe symptoms, requires ICIs discontinuation. The pathogenesis of CIC is multifactorial and still partially unknown: anti-tumor activity that collaterally effects the colonic tissue and the upregulation of specific systemic inflammatory pathways (i.e., CD8+ cytotoxic and CD4+ T lymphocytes) are mainly involved. Many questions remain regarding treatment timing and options, and biological treatment, especially with anti-TNF alpha, can be offered to these patients with the aim of rapidly resuming oncological therapies. CIC shares similar pathogenesis and aspects with inflammatory bowel disease (IBD) and the use of ICI in IBD patients is under evaluation. This review aims to summarize the pathogenetic mechanism underlying CIC and to discuss the current evidenced-based management options, including the role of biological therapy, emphasizing the relevant clinical impact on CIC and the need for prompt recognition and treatment.
Loss of ANCO1 Expression Regulates Chromatin Accessibility and Drives Progression of Early-Stage Triple-Negative Breast Cancer
Authors: Yuan Meng , Barefoot Megan E. , Peterson Kendell , Campbell Moray J. , Blancato Jan K. , Chen Manjing , Schmidt Marcel O. , Kiliti Amber J. , Fang Hong-Bin , Wellstein Anton , Riegel Anna T. , Sharif Ghada M.
Published: July 2023

Mutations in the gene ankyrin repeat domain containing 11 (ANKRD11/ANCO1) play a role in neurodegenerative disorders, and its loss of heterozygosity and low expression are seen in some cancers. Here, we show that low ANCO1 mRNA and protein expression levels are prognostic markers for poor clinical outcomes in breast cancer and that loss of nuclear ANCO1 protein expression predicts lower overall survival of patients with triple-negative breast cancer (TNBC). Knockdown of ANCO1 in early-stage TNBC cells led to aneuploidy, cellular senescence, and enhanced invasion in a 3D matrix. The presence of a subpopulation of ANCO1-depleted cells enabled invasion of the overall cell population in vitro and they converted more rapidly to invasive lesions in a xenograft mouse model. In ANCO1-depleted cells, ChIP-seq analysis showed a global increase in H3K27Ac signals that were enriched for AP-1, TEAD, STAT3, and NFκB motifs. ANCO1-regulated H3K27Ac peaks had a significantly higher overlap with known breast cancer enhancers compared to ANCO1-independent ones. H3K27Ac engagement was associated with transcriptional activation of genes in the PI3K-AKT, epithelial–mesenchymal transition (EMT), and senescence pathways. In conclusion, ANCO1 has hallmarks of a tumor suppressor whose loss of expression activates breast-cancer-specific enhancers and oncogenic pathways that can accelerate the early-stage progression of breast cancer.
Cell-Based Measurement of Mitochondrial Function in Human Airway Smooth Muscle Cells
Authors: Mahadev Bhat Sanjana , Yap Jane Q. , Ramirez-Ramirez Oscar A. , Delmotte Philippe , Sieck Gary C.
Published: July 2023

Cellular mitochondrial function can be assessed using high-resolution respirometry that measures the O2 consumption rate (OCR) across a number of cells. However, a direct measurement of cellular mitochondrial function provides valuable information and physiological insight. In the present study, we used a quantitative histochemical technique to measure the activity of succinate dehydrogenase (SDH), a key enzyme located in the inner mitochondrial membrane, which participates in both the tricarboxylic acid (TCA) cycle and electron transport chain (ETC) as Complex II. In this study, we determine the maximum velocity of the SDH reaction (SDHmax) in individual human airway smooth muscle (hASM) cells. To measure SDHmax, hASM cells were exposed to a solution containing 80 mM succinate and 1.5 mM nitroblue tetrazolium (NBT, reaction indicator). As the reaction proceeded, the change in optical density (OD) due to the reduction of NBT to its diformazan (peak absorbance wavelength of 570 nm) was measured using a confocal microscope with the pathlength for light absorbance tightly controlled. SDHmax was determined during the linear period of the SDH reaction and expressed as mmol fumarate/liter of cell/min. We determine that this technique is rigorous and reproducible, and reliable for the measurement of mitochondrial function in individual cells.
Chromatin Configuration in Diplotene Mouse and Human Oocytes during the Period of Transcriptional Activity Extinction
Authors: Bogolyubova Irina , Salimov Daniil , Bogolyubov Dmitry
Published: July 2023

In the oocyte nucleus, called the germinal vesicle (GV) at the prolonged diplotene stage of the meiotic prophase, chromatin undergoes a global rearrangement, which is often accompanied by the cessation of its transcriptional activity. In many mammals, including mice and humans, chromatin condenses around a special nuclear organelle called the atypical nucleolus or formerly nucleolus-like body. Chromatin configuration is an important indicator of the quality of GV oocytes and largely predicts their ability to resume meiosis and successful embryonic development. In mice, GV oocytes are traditionally divided into the NSN (non-surrounded nucleolus) and SN (surrounded nucleolus) based on the specific chromatin configuration. The NSN–SN transition is a key event in mouse oogenesis and the main prerequisite for the normal development of the embryo. As for humans, there is no single nomenclature for the chromatin configuration at the GV stage. This often leads to discrepancies and misunderstandings, the overcoming of which should expand the scope of the application of mouse oocytes as a model for developing new methods for assessing and improving the quality of human oocytes. As a first approximation and with a certain proviso, the mouse NSN/SN classification can be used for the primary characterization of human GV oocytes. The task of this review is to analyze and discuss the existing classifications of chromatin configuration in mouse and human GV oocytes with an emphasis on transcriptional activity extinction at the end of oocyte growth.
Induced Pluripotent Stem Cells for Tissue-Engineered Skeletal Muscles
Authors: Zhao Shudong , Chen Jishizhan , Wu Lei , Tao Xin , Yaqub Naheem , Chang Jinke
Published: July 2023

Skeletal muscle, which comprises a significant portion of the body, is responsible for vital functions such as movement, metabolism, and overall health. However, severe injuries often result in volumetric muscle loss (VML) and compromise the regenerative capacity of the muscle. Tissue-engineered muscles offer a potential solution to address lost or damaged muscle tissue, thereby restoring muscle function and improving patients’ quality of life. Induced pluripotent stem cells (iPSCs) have emerged as a valuable cell source for muscle tissue engineering due to their pluripotency and self-renewal capacity, enabling the construction of tissue-engineered artificial skeletal muscles with applications in transplantation, disease modelling, and bio-hybrid robots. Next-generation iPSC-based models have the potential to revolutionize drug discovery by offering personalized muscle cells for testing, reducing reliance on animal models. This review provides a comprehensive overview of iPSCs in tissue-engineered artificial skeletal muscles, highlighting the advancements, applications, advantages, and challenges for clinical translation. We also discussed overcoming limitations and considerations in differentiation protocols, characterization methods, large-scale production, and translational regulations. By tackling these challenges, iPSCs can unlock transformative advancements in muscle tissue engineering and therapeutic interventions for the future.
Lipids in Neurodegenerative Diseases
Authors: Chiurchiù Valerio
Published: July 2023

Lipids are undoubtedly the major constituents of the cell membranes of all living organisms, and the most efficient source of energy [...]
Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak
Authors: Zhou Jianglin , Wang Xuejun , Zhou Zhe , Wang Shengqi
Published: July 2023

The exceptionally widespread outbreak of human monkeypox, an emerging zoonosis caused by the monkeypox virus (MPXV), with more than 69,000 confirmed cases in 100 non-endemic countries since 2022, is a major public health concern. Codon usage patterns reflect genetic variation and adaptation to new hosts and ecological niches. However, detailed analyses of codon usage bias in MPXV based on large-scale genomic data, especially for strains responsible for the 2022 outbreak, are lacking. In this study, we analyzed codon usage in MPXV and its relationship with host adaptation. We confirmed the ongoing outbreak of MPXVs belonging to the West Africa (WA) lineage by principal component analysis based on their codon usage patterns. The 2022 outbreak strains had a relatively low codon usage bias. Codon usage of MPXVs was shaped by mutation and natural selection; however, different from past strains, codon usage in the 2022 outbreak strains was predominantly determined by mutation pressure. Additionally, as revealed by the codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses, the codon usage patterns of MPXVs were also affected by their hosts. In particular, the 2022 outbreak strains showed slightly but significantly greater adaptation to many primates, including humans, and were subjected to stronger selection pressure induced by hosts. Our results suggest that MPXVs contributing to the 2022 outbreak have unique evolutionary features, emphasizing the importance of sustained monitoring of their transmission and evolution.
Quetiapine Moderates Doxorubicin-Induced Cognitive Deficits: Influence of Oxidative Stress, Neuroinflammation, and Cellular Apoptosis
Authors: Mani Vasudevan , Alshammeri Bander Shehail
Published: July 2023

Chemotherapy is considered a major choice in cancer treatment. Unfortunately, several cognitive deficiencies and psychiatric complications have been reported in patients with cancer during treatment and for the rest of their lives. Doxorubicin (DOX) plays an important role in chemotherapy regimens but affects both the central and peripheral nervous systems. Antipsychotic drugs alleviate the behavioral symptoms of aging-related dementia, and the atypical class, quetiapine (QUET), has been shown to have beneficial effects on various cognitive impairments. The present investigation aimed to determine the possible mechanism underlying the effect of thirty-day administrations of QUET (10 or 20 mg/kg, p.o.) on DOX-induced cognitive deficits (DICDs). DICDs were achieved through four doses of DOX (2 mg/kg, i.p.) at an interval of seven days during drug treatment. Elevated plus maze (EPM), novel object recognition (NOR), and Y-maze tasks were performed to confirm the DICDs and find the impact of QUET on them. The ELISA tests were executed with oxidative [malondialdehyde (MDA), catalase, and reduced glutathione (GSH)], inflammatory [cyclooxygenase-2 (COX-2), nuclear factor kappa B (NF-κB), and tumor necrosis factor-alpha (TNF-α)], and apoptosis [B-cell lymphoma 2 (Bcl2), Bcl2 associated X protein (Bax), and Caspase-3] markers were assessed in the brain homogenate to explore the related mechanisms. DICD lengthened the transfer latency time in EPM, shortened the exploration time of the novel object, reduced the discrimination ability of the objects in NOR, and lowered the number of arm entries and time spent in the novel arm. QUET alleviated DICD-related symptoms. In addition, QUET reduced neuronal oxidative stress by reducing MDA and elevating GSH levels in the rat brain. Moreover, it reduced neuronal inflammation by controlling the levels of COX-2, NF-κB, and TNF-α. By improving the Bcl-2 level and reducing both Bax and Caspase-3 levels, it protected against neuronal apoptosis. Collectively, our results supported that QUET may protect against DICD, which could be explained by the inhibition of neuronal inflammation and the attenuation of cellular apoptosis protecting against oxidative stress.
Target Discovery of Matrine against PRRSV in Marc-145 Cells via Activity-Based Protein Profiling
Authors: Ling Xiaoya , Cao Zhigang , Sun Panpan , Zhang Hua , Sun Yaogui , Zhong Jia , Yin Wei , Fan Kuohai , Zheng Xiaozhong , Li Hongquan , Sun Na
Published: July 2023

Porcine reproductive and respiratory syndrome (PRRS) seriously endangers the sustainable development of the pig industry. Our previous studies have shown that matrine can resist porcine reproductive and respiratory syndrome virus (PRRSV) infection. This study aimed to explore the anti-PRRSV targets of matrine in Marc-145 cells. Biotin-labeled matrine 1 and 2 were used as probes. MTT assay was used to determine the maximum non-cytotoxic concentration (MNTC) of each probe in Marc-145 cells. The anti-PRRSV activity of each probe was evaluated via MTT, qPCR and Western blot, and its anti-inflammatory activity was evaluated via qPCR and Western blot. The targets of matrine in Marc-145 cells were searched using activity-based protein profiling (ABPP), and compared with the targets predicted via network pharmacology for screening the potential targets of matrine against PRRSV. The protein–protein interaction networks (PPI) of potential targets were constructed using a network database and GO/KEGG enrichment analysis was performed. ACAT1, ALB, HMOX1, HSPA8, HSP90AB1, PARP1 and STAT1 were identified as potential targets of matrine, and their functions were related to antiviral capacity and immunity. Matrine may play an anti-PRRSV role by directly acting on ACAT1, ALB, HMOX1, HSPA8, HSP90AB1, PARP1 and STAT1.
Plant Genomics—Advancing Our Understanding of Plants
Authors: You Frank M.
Published: July 2023

Plant genomics has made significant progress in recent years, enabling researchers to identify genes and genomic regions responsible for plant growth, development, and stress response [...]
The Extracellular Vesicle Citrullinome and Signature in a Piglet Model of Neonatal Seizures
Authors: Mitra Subhabrata , Harvey-Jones Kelly , Kraev Igor , Verma Vinita , Meehan Christopher , Mintoft Alison , Norris Georgina , Campbell Ellie , Tucker Katie , Robertson Nicola J. , Hristova Mariya , Lange Sigrun
Published: July 2023

Neonatal seizures are commonly associated with acute perinatal brain injury, while understanding regarding the downstream molecular pathways related to seizures remains unclear. Furthermore, effective treatment and reliable biomarkers are still lacking. Post-translational modifications can contribute to changes in protein function, and post-translational citrullination, which is caused by modification of arginine to citrulline via the calcium-mediated activation of the peptidylarginine deiminase (PAD) enzyme family, is being increasingly linked to neurological injury. Extracellular vesicles (EVs) are lipid-bilayer structures released from cells; they can be isolated from most body fluids and act as potential liquid biomarkers for disease conditions and response to treatment. As EVs carry a range of genetic and protein cargo that can be characteristic of pathological processes, the current study assessed modified citrullinated protein cargo in EVs isolated from plasma and CSF in a piglet neonatal seizure model, also following phenobarbitone treatment. Our findings provide novel insights into roles for PAD-mediated changes on EV signatures in neonatal seizures and highlight the potential of plasma- and CSF-EVs to monitor responses to treatment.
Impaired Insulin Signaling Mediated by the Small GTPase Rac1 in Skeletal Muscle of the Leptin-Deficient Obese Mouse
Authors: Chan Man Piu , Takenaka Nobuyuki , Satoh Takaya
Published: July 2023

Insulin-stimulated glucose uptake in skeletal muscle is mediated by the glucose transporter GLUT4. The small GTPase Rac1 acts as a switch of signal transduction that regulates GLUT4 translocation to the plasma membrane following insulin stimulation. However, it remains obscure whether signaling cascades upstream and downstream of Rac1 in skeletal muscle are impaired by obesity that causes insulin resistance and type 2 diabetes. In an attempt to clarify this point, we investigated Rac1 signaling in the leptin-deficient (Lepob/ob) mouse model. Here, we show that insulin-stimulated GLUT4 translocation and Rac1 activation are almost completely abolished in Lepob/ob mouse skeletal muscle. Phosphorylation of the protein kinase Akt2 and plasma membrane translocation of the guanine nucleotide exchange factor FLJ00068 following insulin stimulation were also diminished in Lepob/ob mice. On the other hand, the activation of another small GTPase RalA, which acts downstream of Rac1, by the constitutively activated form of Akt2, FLJ00068, or Rac1, was partially abrogated in Lepob/ob mice. Taken together, we conclude that insulin-stimulated glucose uptake is impaired by two mechanisms in Lepob/ob mouse skeletal muscle: one is the complete inhibition of Akt2-mediated activation of Rac1, and the other is the partial inhibition of RalA activation downstream of Rac1.
Molecular Characterization of Galectin-3 in Large Yellow Croaker Larimichthys crocea Functioning in Antibacterial Activity
Authors: Yang Yao , Wu Baolan , Li Wanbo , Han Fang
Published: July 2023

Galectins are proteins that play a crucial role in the innate immune response against pathogenic microorganisms. Previous studies have suggested that Galectin-3 could be a candidate gene for antibacterial immunity in the large yellow croaker Larimichthys crocea. In this study, we cloned the Galectin-3 gene in the large yellow croaker, and named it LcGal-3. The deduced amino acid sequence of LcGal-3 contains a carbohydrate recognition domain with two conserved β-galactoside binding motifs. Quantitative reverse transcription PCR (qRT-PCR) analysis revealed that LcGal-3 was expressed in all the organs/tissues that were tested, with the highest expression level in the gill. In Larimichthys crocea kidney cell lines, LcGal-3 protein was distributed in both the cytoplasm and nucleus. Moreover, we found that the expression of LcGal-3 was significantly upregulated upon infection with Pseudomonas plecoglossicida, as demonstrated by qRT-PCR analyses. We also purified the LcGal-3 protein that was expressed in prokaryotes, and found that it has the ability to agglutinate large yellow croaker red blood cells in a Ca2+-independent manner. The agglutination activity of LcGal-3 was inhibited by lipopolysaccharides (LPS) in a concentration-dependent manner, as shown in the sugar inhibition test. Additionally, LcGal-3 exhibited agglutination and antibacterial activities against three Gram-negative bacteria, including P. plecoglossicida, Vibrio parahaemolyticus, and Vibrio harveyi. Furthermore, we studied the agglutination mechanism of the LcGal-3 protein using blood coagulation tests with LcGal-3 deletion and point mutation proteins. Our results indicate that LcGal-3 protein plays a critical role in the innate immunity of the large yellow croaker, providing a basis for further studies on the immune mechanism and disease-resistant breeding in L. crocea and other marine fish.
Assessment of the Biocontrol Potential of Bacillus velezensis WL–23 against Kiwifruit Canker Caused by Pseudomonas syringae pv. actinidiae
Authors: Wang Bingce , Guo Yushan , Chen Xuetang , Ma Jiling , Lei Xia , Wang Weizhen , Long Youhua
Published: July 2023

Kiwifruit canker disease, caused by Pseudomonas syringae pv. actinidiae (Psa), is the main threat to kiwifruit production worldwide. Currently, there is no safe and effective disease prevention method; therefore, biological control technologies are being explored for Psa. In this study, Bacillus velezensis WL–23 was isolated from the leaf microbial community of kiwifruit and used to control kiwifruit cankers. Indoor confrontation experiments showed that both WL–23 and its aseptic filtrate had excellent inhibitory activity against the main fungal and bacterial pathogens of kiwifruit. Changes in OD600, relative conductivity, alkaline proteinase, and nucleic acid content were recorded during Psa growth after treatment with the aseptic filtrate, showing that Psa proliferation was inhibited and the integrity of the cell membrane was destroyed; this was further verified using scanning electron microscopy and transmission electron microscopy. In vivo, WL–23 promoted plant growth, increased plant antioxidant enzyme activity, and reduced canker incidence. Therefore, WL–23 is expected to become a biological control agent due to its great potential to contribute to sustainable agriculture.
The UPR Maintains Proteostasis and the Viability and Function of Hippocampal Neurons in Adult Mice
Authors: Liu Pingting , Karim Md Razaul , Covelo Ana , Yue Yuan , Lee Michael K. , Lin Wensheng
Published: July 2023

The unfolded protein response (UPR), which comprises three branches: PERK, ATF6α, and IRE1, is a major mechanism for maintaining cellular proteostasis. Many studies show that the UPR is a major player in regulating neuron viability and function in various neurodegenerative diseases; however, its role in neurodegeneration is highly controversial. Moreover, while evidence suggests activation of the UPR in neurons under normal conditions, deficiency of individual branches of the UPR has no major effect on brain neurons in animals. It remains unclear whether or how the UPR participates in regulating neuronal proteostasis under normal and disease conditions. To determine the physiological role of the UPR in neurons, we generated mice with double deletion of PERK and ATF6α in neurons. We found that inactivation of PERK and ATF6α in neurons caused lysosomal dysfunction (as evidenced by decreased expression of the V0a1 subunit of v-ATPase and decreased activation of cathepsin D), impairment of autophagic flux (as evidenced by increased ratio of LC3-II/LC3-I and increased p62 level), and accumulation of p-tau and Aβ42 in the hippocampus, and led to impairment of spatial memory, impairment of hippocampal LTP, and hippocampal degeneration in adult mice. These results suggest that the UPR is required for maintaining neuronal proteostasis (particularly tau and Aβ homeostasis) and the viability and function of neurons in the hippocampus of adult mice.
Gender Differences and miRNAs Expression in Cancer: Implications on Prognosis and Susceptibility
Authors: Caserta Santino , Gangemi Sebastiano , Murdaca Giuseppe , Allegra Alessandro
Published: July 2023

MicroRNAs are small, noncoding molecules of about twenty-two nucleotides with crucial roles in both healthy and pathological cells. Their expression depends not only on genetic factors, but also on epigenetic mechanisms like genomic imprinting and inactivation of X chromosome in females that influence in a sex-dependent manner onset, progression, and response to therapy of different diseases like cancer. There is evidence of a correlation between miRNAs, sex, and cancer both in solid tumors and in hematological malignancies; as an example, in lymphomas, with a prevalence rate higher in men than women, miR-142 is “silenced” because of its hypermethylation by DNA methyltransferase-1 and it is blocked in its normal activity of regulating the migration of the cell. This condition corresponds in clinical practice with a more aggressive tumor. In addition, cancer treatment can have advantages from the evaluation of miRNAs expression; in fact, therapy with estrogens in hepatocellular carcinoma determines an upregulation of the oncosuppressors miR-26a, miR-92, and miR-122 and, consequently, apoptosis. The aim of this review is to present an exhaustive collection of scientific data about the possible role of sex differences on the expression of miRNAs and the mechanisms through which miRNAs influence cancerogenesis, autophagy, and apoptosis of cells from diverse types of tumors.
Designing Ex Situ Conservation Strategies for Butia capitata [Mart. (Becc.) Arecaceae], a Threatened Palm Tree from Brazilian Savannah Biome, through Zygotic Embryo Cryopreservation
Authors: Frugeri Giuliano Carvalho , Nogueira Gabriela Ferreira , Souza André Luís Xavier de , Scherwinski-Pereira Jonny Everson
Published: July 2023

Jelly palm (Butia capitata) is a species of palm tree endemic to the Brazilian Savannah (Cerrado) Biome, which stands out for its use as food, which has resulted in a predatory exploitation of its natural populations. This study aimed to characterize fruits and diaspores of natural populations of jelly palm (‘Arinos’, ‘Mirabela’ and ‘Serranópolis’), in addition to developing ex situ conservation strategies of the species, through the storage of zygotic embryos at ultra-low temperatures of liquid nitrogen (LN). Initially, fruits, seeds and embryos were evaluated for their morphological characteristics. For conservation, hydrated zygotic embryos were desiccated for up to 12 h in a laminar-flow chamber and immersed directly in LN with different moisture contents. As a result, we observed morphological differences among the studied populations. The population ‘Arinos’ showed more expressive results for most of the evaluated characteristics, such as length, width of fruits and seeds. The cryopreservation of zygotic embryos proved to be efficient for the conservation of the species reaching germination rates between 70 and 86%, when the moisture content of the embryos immersed in LN were between 10 and 14%. The plants that reached the stage of the greenhouse had a rate of more than 80% survival. The variability in the characteristics of fruits and diaspores of the analyzed populations allow for establishing divergent groups for the definition of conservation strategies or genetic improvement. The developed cryopreservation protocol can be considered simple and efficient for the conservation of the genetic variability of the species.
Linguistic Communication Channels Reveal Connections between Texts: The New Testament and Greek Literature
Authors: Matricciani Emilio
Published: July 2023

We studied two fundamental linguistic channels—the sentences and the interpunctions channels—and showed they can reveal deeper connections between texts. The applied theory does not follow the actual paradigm of linguistic studies. As a study case, we considered the Greek New Testament, with the purpose of determining mathematical connections between its texts and possible differences in the writing style (mathematically defined) of the writers and in the reading skill required of their readers. The analysis was based on deep-language parameters and communication/information theory. To set the New Testament texts in the larger Greek classical literature, we considered texts written by Aesop, Polybius, Flavius Josephus, and Plutarch. The results largely confirmed what scholars have found about the New Testament texts, therefore giving credibility to the theory. The Gospel according to John is very similar to the fables written by Aesop. Surprisingly, the Epistle to the Hebrews and Apocalypse are each other’s “photocopies” in the two linguistic channels and not linked to all other texts. These two texts deserve further study by historians of the early Christian church literature at the level of meaning, readers, and possible Old Testament texts that might have influenced them. The theory can guide scholars to study any literary corpus.
Improved Spacecraft Authentication Method for Satellite Internet System Using Residue Codes
Authors: Olenev Alexandr Anatolyevich , Kalmykov Igor Anatolyevich , Pashintsev Vladimir Petrovich , Chistousov Nikita Konstantinovich , Dukhovnyj Daniil Vyacheslavovich , Kalmykova Natalya Igorevna
Published: July 2023

Low-orbit satellite internet (LOSI) expands the scope of the Industrial Internet of Things (IIoT) in the oil and gas industry (OGI) to include areas of the Far North. However, due to the large length of the communication channel, the number of threats and attacks increases. A special place among them is occupied by relay spoofing interference. In this case, an intruder satellite intercepts the control signal coming from the satellite (SC), delays it, and then imposes it on the receiver located on the unattended OGI object. This can lead to a disruption of the facility and even cause an environmental disaster. To prevent a spoofing attack, a satellite authentication method has been developed that uses a zero-knowledge authentication protocol (ZKAP). These protocols have high cryptographic strength without the use of encryption. However, they have a significant drawback. This is their low authentication speed, which is caused by calculations over a large module Q (128 bits or more). It is possible to reduce the time of determining the status of an SC by switching to parallel computing. To solve this problem, the paper proposes to use residue codes (RC). Addition, subtraction, and multiplication operations are performed in parallel in RC. Thus, a correct choice of a set of modules of RC allows for providing an operating range of calculations not less than the number Q. Therefore, the development of a spacecraft authentication method for the satellite internet system using RC that allows for reducing the authentication time is an urgent task.
Artificial Intelligence Generative Tools and Conceptual Knowledge in Problem Solving in Chemistry
Authors: Daher Wajeeh , Diab Hussam , Rayan Anwar
Published: July 2023

In recent years, artificial intelligence (AI) has emerged as a valuable resource for teaching and learning, and it has also shown promise as a tool to help solve problems. A tool that has gained attention in education is ChatGPT, which supports teaching and learning through AI. This research investigates the difficulties faced by ChatGPT in comprehending and responding to chemistry problems pertaining to the topic of Introduction to Material Science. By employing the theoretical framework proposed by Holme et al., encompassing categories such as transfer, depth, predict/explain, problem solving, and translate, we evaluate ChatGPT’s conceptual understanding difficulties. We presented ChatGPT with a set of thirty chemistry problems within the Introduction to Material Science domain and tasked it with generating solutions. Our findings indicated that ChatGPT encountered significant conceptual knowledge difficulties across various categories, with a notable emphasis on representations and depth, where difficulties in representations hindered effective knowledge transfer.