bluuebunny/crossref_metadata_2025 huggingface dataset:
Toll-like Receptor 9 Induced Dendritic Cell Activation Promotes Anti-Myeloperoxidase Autoimmunity and Glomerulonephritis
Authors: Ford Sharon L. , O’Sullivan Kim M. , Kitching A. Richard , Holdsworth Stephen R. , Gan Poh Yi , Summers Shaun A.
Published: January 2023

ANCA-associated vasculitis (AAV) is intricately linked with infections. Toll-like receptors (TLR) provide a potential link between infection and anti-myeloperoxidase (MPO) autoimmunity. TLR9 ligation has been shown to promote anti-MPO autoimmunity and glomerular vasculitis in murine MPO-AAV. This study investigates dendritic cell TLR9 ligation in murine experimental anti-MPO glomerulonephritis. We analyzed autoimmune responses to MPO following transfer of TLR9 stimulated, MPO pulsed dendritic cells and kidney injury following a sub-nephritogenic dose of sheep anti-mouse glomerular basement membrane globulin. TLR9 ligation enhanced dendritic cell activation upregulating CD40 and CD80 expression, promoting systemic anti-MPO autoimmunity and T cell recall responses and exacerbating kidney injury. CD40 upregulation by TLR9 was critical for the induction of nephritogenic autoimmunity. The presence of DEC205, which transports the TLR9 ligand to TLR9 located in the endosome, also promoted kidney injury. This confirms TLR9 mediated dendritic cell activation as a mechanism of anti-MPO autoimmunity in AAV and further defines the link between infection and the generation of MPO specific autoimmune inflammation.
Exploring the Physiological Multiplicity of Native Microalgae from the Ecuadorian Highland, Italian Lowland and Indoor Locations in Response to UV-B
Authors: Huarancca Reyes Thais , Chiellini Carolina , Barozzi Emilio , Sandoval Carla , Echeverría Cristina , Guglielminetti Lorenzo
Published: January 2023

The differential effects of UV-B on the inhibition or activation of protective mechanisms to maintain cells photosynthetically active were investigated in native microalgae. Four strains were used, including two Chlorella sorokiniana strains, F4 and LG1, isolated from a Mediterranean inland swamp and a recycled cigarette butt’s substrate, respectively, and two isolates from an Ecuadorian highland lake related to Pectinodesmus pectinatus (PEC) and Ettlia pseudoalveolaris (ETI). Monocultures were exposed to acute UV-B (1.7 W m−2) over 18 h under controlled conditions. UV-B-untreated microalgae were used as the control. Comparative physiological responses, including photosynthetic pigments, non-enzymatic antioxidants, and chlorophyll a fluorescence, were evaluated at specific time points. Results showed that UV-B significantly compromised all the physiological parameters in F4, thereby resulting in the most UV-B-sensitive strain. Contrarily, UV-B exposure did not lead to changes in the PEC physiological traits, resulting in the best UV-B-resistant strain. This could be attributed to the acclimation to high light habitat, where maintaining a constitutive phenotype (at the photosynthetic level) is strategically advantageous. Differently, LG1 and ETI at 12 h of UV-B exposure showed different UV-B responses, which is probably related to acclimation, where in LG1, the pigments were recovered, and the antioxidants were still functioning, while in ETI, the accumulation of pigments and antioxidants was increased to avoid further photodamage. Consequently, the prolonged exposure in LG1 and ETI resulted in species-specific metabolic regulation (e.g., non-enzymatic antioxidants) in order to constrain full photoinhibition under acute UV-B.
Evaluation of Two Simultaneous Metabolomic and Proteomic Extraction Protocols Assessed by Ultra-High-Performance Liquid Chromatography Tandem Mass Spectrometry
Authors: Zenati Ruba A. , Giddey Alexander D. , Al-Hroub Hamza M. , Hagyousif Yousra A. , El-Huneidi Waseem , Bustanji Yasser , Abu-Gharbieh Eman , Alqudah Mohammad A. Y. , Shara Mohd , Abuhelwa Ahmad Y. , Soares Nelson C. , Semreen Mohammad H.
Published: January 2023

Untargeted multi-omics analysis of plasma is an emerging tool for the identification of novel biomarkers for evaluating disease prognosis, and for developing a better understanding of molecular mechanisms underlying human disease. The successful application of metabolomic and proteomic approaches relies on reproducibly quantifying a wide range of metabolites and proteins. Herein, we report the results of untargeted metabolomic and proteomic analyses from blood plasma samples following analyte extraction by two frequently-used solvent systems: chloroform/methanol and methanol-only. Whole blood samples were collected from participants (n = 6) at University Hospital Sharjah (UHS) hospital, then plasma was separated and extracted by two methods: (i) methanol precipitation and (ii) 4:3 methanol:chloroform extraction. The coverage and reproducibility of the two methods were assessed by ultra-high-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS). The study revealed that metabolite extraction by methanol-only showed greater reproducibility for both metabolomic and proteomic quantifications than did methanol/chloroform, while yielding similar peptide coverage. However, coverage of extracted metabolites was higher with the methanol/chloroform precipitation.
Macrophages and Intervertebral Disc Degeneration
Authors: Koroth Jinsha , Buko Erick O. , Abbott Rebecca , Johnson Casey P. , Ogle Brenda M. , Stone Laura S. , Ellingson Arin M. , Bradley Elizabeth W.
Published: January 2023

The intervertebral disc (IVD) aids in motion and acts to absorb energy transmitted to the spine. With little inherent regenerative capacity, degeneration of the intervertebral disc results in intervertebral disc disease, which contributes to low back pain and significant disability in many individuals. Increasing evidence suggests that IVD degeneration is a disease of the whole joint that is associated with significant inflammation. Moreover, studies show elevated macrophage accumulation within the IVD with increasing levels of disease severity; however, we still need to understand the roles, be they causative or consequential, of macrophages during the degenerative process. In this narrative review, we discuss hallmarks of IVD degeneration, showcase evidence of macrophage involvement during disc degeneration, and explore burgeoning research aimed at understanding the molecular pathways regulating macrophage functions during intervertebral disc degeneration.
Advanced Glycation End Products and Activation of Toll-like Receptor-2 and -4 Induced Changes in Aquaporin-3 Expression in Mouse Keratinocytes
Authors: Luo Yonghong , Uaratanawong Rawipan , Choudhary Vivek , Hardin Mary , Zhang Catherine , Melnyk Samuel , Chen Xunsheng , Bollag Wendy B.
Published: January 2023

Prolonged inflammation and impaired re-epithelization are major contributing factors to chronic non-healing diabetic wounds; diabetes is also characterized by xerosis. Advanced glycation end products (AGEs), and the activation of toll-like receptors (TLRs), can trigger inflammatory responses. Aquaporin-3 (AQP3) plays essential roles in keratinocyte function and skin wound re-epithelialization/re-generation and hydration. Suberanilohydroxamic acid (SAHA), a histone deacetylase inhibitor, mimics the increased acetylation observed in diabetes. We investigated the effects of TLR2/TLR4 activators and AGEs on keratinocyte AQP3 expression in the presence and absence of SAHA. Primary mouse keratinocytes were treated with or without TLR2 agonist Pam3Cys-Ser-(Lys)4 (PAM), TLR4 agonist lipopolysaccharide (LPS), or AGEs, with or without SAHA. We found that (1) PAM and LPS significantly upregulated AQP3 protein basally (without SAHA) and PAM downregulated AQP3 protein with SAHA; and (2) AGEs (100 µg/mL) increased AQP3 protein expression basally and decreased AQP3 levels with SAHA. PAM and AGEs produced similar changes in AQP3 expression, suggesting a common pathway or potential crosstalk between TLR2 and AGEs signaling. Our findings suggest that TLR2 activation and AGEs may be beneficial for wound healing and skin hydration under normal conditions via AQP3 upregulation, but that these pathways are likely deleterious in diabetes chronically through decreased AQP3 expression.
Does the Composition of Gut Microbiota Affect Hypertension? Molecular Mechanisms Involved in Increasing Blood Pressure
Authors: Tokarek Julita , Budny Emilian , Saar Maciej , Kućmierz Joanna , Młynarska Ewelina , Rysz Jacek , Franczyk Beata
Published: January 2023

Arterial hypertension is a chronic disease which is very prevalent contemporarily. The aim of this review was to investigate the impact of gut microbiota on the development and potential treatment of hypertension, taking into consideration underlying molecular mechanisms. The bacteria present in the intestines have the ability to secrete different metabolites, which might play a significant role in the regulation of blood pressure. The most important include short-chain fatty acids (SCFAs), vasoactive hormones, trimethylamine (TMA) and trimethylamine N-oxide (TMAO) and uremic toxins, such as indoxyl sulfate (IS) and p-cresyl sulfate (PCS). Their action in regulating blood pressure is mainly based on their pro- or anti-inflammatory function. The use of specifically formulated probiotics to modify the composition of gut microbiota might be a beneficial way of supportive treatment of hypertension; however, further research on this topic is needed to choose the species of bacteria that could induce the hypotensive pattern.
Aggression Results in the Phosphorylation of ERK1/2 in the Nucleus Accumbens and the Dephosphorylation of mTOR in the Medial Prefrontal Cortex in Female Syrian Hamsters
Authors: Borland Johnathan M. , Dempsey Desarae A. , Peyla Anna C. , Hall Megan A. L. , Kohut-Jackson Abigail L. , Mermelstein Paul G. , Meisel Robert L.
Published: January 2023

Like many social behaviors, aggression can be rewarding, leading to behavioral plasticity. One outcome of reward-induced aggression is the long-term increase in the speed in which future aggression-based encounters is initiated. This form of aggression impacts dendritic structure and excitatory synaptic neurotransmission in the nucleus accumbens, a brain region well known to regulate motivated behaviors. Yet, little is known about the intracellular signaling mechanisms that drive these structural/functional changes and long-term changes in aggressive behavior. This study set out to further elucidate the intracellular signaling mechanisms regulating the plasticity in neurophysiology and behavior that underlie the rewarding consequences of aggressive interactions. Female Syrian hamsters experienced zero, two or five aggressive interactions and the phosphorylation of proteins in reward-associated regions was analyzed. We report that aggressive interactions result in a transient increase in the phosphorylation of extracellular-signal related kinase 1/2 (ERK1/2) in the nucleus accumbens. We also report that aggressive interactions result in a transient decrease in the phosphorylation of mammalian target of rapamycin (mTOR) in the medial prefrontal cortex, a major input structure to the nucleus accumbens. Thus, this study identifies ERK1/2 and mTOR as potential signaling pathways for regulating the long-term rewarding consequences of aggressive interactions. Furthermore, the recruitment profile of the ERK1/2 and the mTOR pathways are distinct in different brain regions.
Tricarboxylic Acid Metabolite Imbalance in Rats with Acute Thioacetamide-Induced Hepatic Encephalopathy Indicates Incomplete Recovery
Authors: Shurubor Yevgeniya I. , Rogozhin Alexander E. , Isakova Elena P. , Deryabina Yulia I. , Krasnikov Boris F.
Published: January 2023

Exposure to the toxin thioacetamide (TAA) causes acute hepatic encephalopathy (HE), changes in the functioning of systemic organs, and an imbalance in a number of energy metabolites. The deferred effects after acute HE development are poorly understood. The study considers the balance of the tricarboxylic acid (TCA) cycle metabolites in the blood plasma, liver, kidneys, and brain tissues of rats in the post-rehabilitation period. The samples of the control (n = 3) and TAA-induced groups of rats (n = 13) were collected six days after the administration of a single intraperitoneal TAA injection at doses of 200, 400, and 600 mg/kg. Despite the complete physiological recovery of rats by this date, a residual imbalance of metabolites in all the vital organs was noted. The results obtained showed a trend of stabilizing processes in the main organs of the animals and permit the use of these data both for prognostic purposes and the choice of potential therapeutic agents.
An Analytical Method for Quantifying the Yields of DNA Double-Strand Breaks Coupled with Strand Breaks by γ-H2AX Focus Formation Assay Based on Track-Structure Simulation
Authors: Yachi Yoshie , Matsuya Yusuke , Yoshii Yuji , Fukunaga Hisanori , Date Hiroyuki , Kai Takeshi
Published: January 2023

Complex DNA double-strand break (DSB), which is defined as a DSB coupled with additional strand breaks within 10 bp in this study, induced after ionizing radiation or X-rays, is recognized as fatal damage which can induce cell death with a certain probability. In general, a DSB site inside the nucleus of live cells can be experimentally detected using the γ-H2AX focus formation assay. DSB complexity is believed to be detected by analyzing the focus size using such an assay. However, the relationship between focus size and DSB complexity remains uncertain. In this study, using Monte Carlo (MC) track-structure simulation codes, i.e., an in-house WLTrack code and a Particle and Heavy Ion Transport code System (PHITS), we developed an analytical method for qualifying the DSB complexity induced by photon irradiation from the microscopic image of γ-H2AX foci. First, assuming that events (i.e., ionization and excitation) potentially induce DNA strand breaks, we scored the number of events in a water cube (5.03 × 5.03 × 5.03 nm3) along electron tracks. Second, we obtained the relationship between the number of events and the foci size experimentally measured by the γ-H2AX focus formation assay. Third, using this relationship, we evaluated the degree of DSB complexity induced after photon irradiation for various X-ray spectra using the foci size, and the experimental DSB complexity was compared to the results estimated by the well-verified DNA damage estimation model in the PHITS code. The number of events in a water cube was found to be proportional to foci size, suggesting that the number of events intrinsically related to DSB complexity at the DNA scale. The developed method was applicable to focus data measured for various X-ray spectral situations (i.e., diagnostic kV X-rays and therapeutic MV X-rays). This method would contribute to a precise understanding of the early biological impacts of photon irradiation by means of the γ-H2AX focus formation assay.
Neuronal Dot1l Activity Acts as a Mitochondrial Gene-Repressor Associated with Human Brain Aging via H3K79 Hypermethylation
Authors: Van Heesbeen Hendrikus J. , Von Oerthel Lars , De Vries Paul M. , Wagemans Cindy M. R. J. , Smidt Marten P.
Published: January 2023

Methylation of histone 3 at lysine 79 (H3K79) and its catalyst, a disrupter of telomeric silencing (DOT1l), have been coupled to multiple forms of stress, such as bioenergetic and ER challenges. However, studies on H3K79 methylation and Dot1l in the (aging) brain and neurons are limited. This, together with the increasing evidence of a dynamic neuroepigenome, made us wonder if H3K79 methylation and its activator Dot1l could play important roles in brain aging and associated disorders. In aged humans, we found strong and consistent global hypermethylation of H3K79 in neurons. Specific in dopaminergic neurons, we found a strong increase in H3K79 methylation in lipofucsin positive neurons, which are linked to pathology. In animals, where we conditionally removed Dot1l, we found a rapid loss of H3K79 methylation. As a consequence, we found some decrease in specific dopaminergic genes, and surprisingly, a clear up-regulation of almost all genes belonging to the family of the respiratory chain. These data, in relation to the observed increase in global H3K79 methylation, suggest that there is an inverse relationship between H3K79 methylation and the capacity of energy metabolism in neuronal systems.
Alteration of Lipid Metabolism in Prostate Cancer: Multifaceted Oncologic Implications
Authors: Zeković Milica , Bumbaširević Uros , Živković Marko , Pejčić Tomislav
Published: January 2023

Cancer is increasingly recognized as an extraordinarily heterogeneous disease featuring an intricate mutational landscape and vast intra- and intertumor variability on both genetic and phenotypic levels. Prostate cancer (PCa) is the second most prevalent malignant disease among men worldwide. A single metabolic program cannot epitomize the perplexing reprogramming of tumor metabolism needed to sustain the stemness of neoplastic cells and their prominent energy-consuming functional properties, such as intensive proliferation, uncontrolled growth, migration, and invasion. In cancerous tissue, lipids provide the structural integrity of biological membranes, supply energy, influence the regulation of redox homeostasis, contribute to plasticity, angiogenesis and microenvironment reshaping, mediate the modulation of the inflammatory response, and operate as signaling messengers, i.e., lipid mediators affecting myriad processes relevant for the development of the neoplasia. Comprehensive elucidation of the lipid metabolism alterations in PCa, the underlying regulatory mechanisms, and their implications in tumorigenesis and the progression of the disease are gaining growing research interest in the contemporary urologic oncology. Delineation of the unique metabolic signature of the PCa featuring major aberrant pathways including de novo lipogenesis, lipid uptake, storage and compositional reprogramming may provide novel, exciting, and promising avenues for improving diagnosis, risk stratification, and clinical management of such a complex and heterogeneous pathology.
Tailored PGE2 Immunomodulation of moDCs by Nano-Encapsulated EP2/EP4 Antagonists
Authors: Bödder Johanna , Kok Leanne M. , Fauerbach Jonathan A. , Flórez-Grau Georgina , de Vries I. Jolanda M.
Published: January 2023

Prostaglandin E2 (PGE2) is an important maturation mediator for dendritic cells (DCs). However, increased PGE2 levels in the tumor exert immunosuppressive effects on DCs by signaling through two E-Prostanoid (EP) receptors: EP2 and EP4. Blocking EP-receptor signaling of PGE2 with antagonists is currently being investigated for clinical applications to enhance anti-tumor immunity. In this study, we investigated a new delivery approach by encapsulating EP2/EP4 antagonists in polymeric nanoparticles. The nanoparticles were characterized for size, antagonist loading, and release. The efficacy of the encapsulated antagonists to block PGE2 signaling was analyzed using monocyte-derived DCs (moDCs). The obtained nanoparticles were sized between 210 and 260 nm. The encapsulation efficacy of the EP2/EP4 antagonists was 20% and 17%, respectively, and was further increased with the co-encapsulation of both antagonists. The treatment of moDCs with co-encapsulation EP2/EP4 antagonists prevented PGE2-induced co-stimulatory marker expression. Even though both antagonists showed a burst release within 15 min at 37 °C, the nanoparticles executed the immunomodulatory effects on moDCs. In summary, we demonstrate the functionality of EP2/EP4 antagonist-loaded nanoparticles to overcome PGE2 modulation of moDCs.
A Glance at Molecular Advances in Cancer Genetics: A Baffling Puzzle Still to Be Solved
Authors: Ghiorzo Paola , Bruno William
Published: January 2023

The purpose of this first Special Issue is to provide a glance at the molecular advances in cancer genetics to untangle the complexity of tumorigenesis [...]
Antiseizure Effects of Scoparone, Borneol and Their Impact on the Anticonvulsant Potency of Four Classic Antiseizure Medications in the Mouse MES Model—An Isobolographic Transformation
Authors: Łuszczki Jarogniew J. , Bojar Hubert , Góralczyk Agnieszka , Skalicka-Woźniak Krystyna
Published: January 2023

Numerous botanical drugs containing coumarins and terpenes are used in ethnomedicine all over the world for their various therapeutic properties, especially those affecting the CNS system. The treatment of epilepsy is based on antiseizure medications (ASMs), although novel strategies using naturally occurring substances with confirmed antiseizure properties are being developed nowadays. The aim of this study was to determine the anticonvulsant profiles of scoparone (a simple coumarin) and borneol (a bicyclic monoterpenoid) when administered separately and in combination, as well as their impact on the antiseizure effects of four classic ASMs (carbamazepine, phenytoin, phenobarbital and valproate) in the mouse model of maximal electroshock-induced (MES) tonic-clonic seizures. MES-induced seizures were evoked in mice receiving the respective doses of the tested natural compounds and classic ASMs (when applied alone or in combinations). Interactions for two-drug and three-drug mixtures were assessed by means of isobolographic transformation of data. Polygonograms were used to illustrate the types of interactions occurring among drugs. The total brain content of ASMs was measured in mice receiving the respective drug treatments with fluorescent polarization immunoassay. Scoparone and borneol, when administered alone, exerted anticonvulsant properties in the mouse MES model. The two-drug mixtures of scoparone with valproate, borneol with phenobarbital and borneol with valproate produced synergistic interactions in the mouse MES model, while the remaining tested two-drug mixtures produced additivity. The three-drug mixtures of scoparone + borneol with valproate and phenobarbital produced synergistic interactions in the mouse MES model. Verification of total brain concentrations of valproate and phenobarbital revealed that borneol elevated the total brain concentrations of both ASMs, while scoparone did not affect the brain content of these ASMs in mice. The synergistic interaction of scoparone with valproate observed in the mouse MES model is pharmacodynamic in nature. Borneol elevated the brain concentrations of the tested ASMs, contributing to the pharmacokinetic nature of the observed synergistic interactions with valproate and phenobarbital in the mouse MES model.
A Pathogenic Variant Reclassified to the Pseudogene PMS2P1 in a Patient with Suspected Hereditary Cancer
Authors: Fragoso-Ontiveros Veronica , De la Fuente-Hernandez Marcela Angelica , Gonzalez-Osnaya Vincent , Gamez-Rosales Mario , Perez-Montiel Maria Delia , Isla-Ortiz David , Cantu-De Leon David Francisco , Alvarez-Gomez Rosa Maria
Published: January 2023

The PMS2 gene is involved in DNA repair by the mismatch repair pathway. Deficiencies in this mechanism have been associated with Lynch Syndrome (LS), which is characterized by a high risk for colorectal, endometrial, ovarian, breast, and other cancers. Germinal pathogenic variants of PMS2 are associated with up to 5% of all cases of LS. The prevalence is overestimated for the existence of multiple homologous pseudogenes. We report the case of a 44-year-old woman diagnosed with breast cancer at 34 years without a relevant cancer family history. The presence of pathogenic variant NM_000535.7:c.1A > T, (p.Met1Leu) in PMS2 was determined by next-generation sequencing analysis with a panel of 322 cancer-associated genes and confirmed by capillary sequencing in the patient. The variant was determined in six family members (brothers, sisters, and a son) and seven non-cancerous unrelated individuals. Analysis of the amplified region showed high homology of PMS2 with five of its pseudogenes. We determined that the variant is associated with the PMS2P1 pseudogene following sequence alignment analysis. We propose considering the variant c.1A > T, (p.Met1Leu) in PMS2 for reclassification as not hereditary cancer-related, given the impact on the diagnosis and treatment of cancer patients and families carrying this variant.
Concern about the Effectiveness of mRNA Vaccination Technology and Its Long-Term Safety: Potential Interference on miRNA Machinery
Authors: Stati Gianmarco , Amerio Paolo , Nubile Mario , Sancilio Silvia , Rossi Francesco , Di Pietro Roberta
Published: January 2023

After the outbreak of the pandemic due to COVID-19 infection, several vaccines were developed on short timelines to counteract the public health crisis. To allow the administration of mRNA vaccines through a faster-paced approval process, the Emergency Use Authorization (EUA) was applied. The Ba.5 (omicron) variant of SARS-CoV-2 is the predominant one at this moment. Its highly mutable single-stranded RNA genome, along with its high transmissivity, generated concern about the effectiveness of vaccination. The interaction between the vaccine and the host cell is finely regulated by miRNA machinery, a complex network that oversees a wide range of biological processes. The dysregulation of miRNA machinery has been associated with the development of clinical complications during COVID-19 infection and, moreover, to several human pathologies, among which is cancer disease. Now that in some areas, four doses of mRNA vaccine have been administered, it is natural to wonder about its effectiveness and long-term safety.
Probiotics-Fermented Grifola frondosa Total Active Components: Better Antioxidation and Microflora Regulation for Alleviating Alcoholic Liver Damage in Mice
Authors: He Xiao-Yu , Zhu Yu-Xian , Jiang Xiao-Qin , Zhu Fu-Rong , Luo Yi-Juan , Qiu Yu-Yang , Huang Zi-Rui , Liu Bin , Zeng Feng
Published: January 2023

Alcoholic liver damage is caused by long-term drinking, and it further develops into alcoholic liver diseases. In this study, we prepared a probiotic fermentation product of Grifola frondosa total active components (PFGF) by fermentation with Lactobacillus acidophilus, Lactobacillus rhamnosus, and Pediococcus acidilactici. After fermentation, the total sugar and protein content in the PFGF significantly decreased, while the lactic acid level and antioxidant activity of the PFGF increased. Afterward, we investigated the alleviating effect of PFGF on alcoholic liver injury in alcohol-fed mice. The results showed that the PFGF intervention reduced the necrosis of the liver cells, attenuated the inflammation of the liver and intestines, restored the liver function, increased the antioxidant factors of the liver, and maintained the cecum tissue barrier. Additionally, the results of the 16S rRNA sequencing analysis indicated that the PFGF intervention increased the relative abundance of beneficial bacteria, such as Lactobacillus, Ruminococcaceae, Parabacteroids, Parasutterella, and Alistipes, to attenuate intestinal inflammation. These results demonstrate that PFGF can potentially alleviate alcoholic liver damage by restoring the intestinal barrier and regulating the intestinal microflora.
Crystal Structure of the SH3 Domain of ASAP1 in Complex with the Proline Rich Motif (PRM) of MICAL1 Reveals a Unique SH3/PRM Interaction Mode
Authors: Jia Xuanyan , Lin Leishu , Xu Shun , Li Lingxuan , Wei Zhiyi , Yu Cong , Niu Fengfeng
Published: January 2023

SH3 domains are common protein binding modules. The target sequence of SH3 domains is usually a proline-rich motif (PRM) containing a minimal “PxxP” sequence. The mechanism of how different SH3 domains specifically choose their targets from vast PxxP-containing sequences is still not very clear, as many reported SH3/PRM interactions are weak and promiscuous. Here, we identified the binding of the SH3 domain of ASAP1 to the PRM of MICAL1 with a sub-μM binding affinity, and determined the crystal structure of ASAP1-SH3 and MICAL1-PRM complex. Our structural and biochemical analyses revealed that the target-binding pocket of ASAP1-SH3 contains two negatively charged patches to recognize the “xPx + Px+” sequence in MICAL1-PRM and consequently strengthen the interaction, differing from the typical SH3/PRM interaction. This unique PRM-binding pocket is also found in the SH3 domains of GTPase Regulator associated with focal adhesion kinase (GRAF) and Src kinase associated phosphoprotein 1 (SKAP1), which we named SH3AGS. In addition, we searched the Swiss-Prot database and found ~130 proteins with the SH3AGS-binding PRM in silico. Finally, gene ontology analysis suggests that the strong interaction between the SH3AGS-containing proteins and their targets may play roles in actin cytoskeleton regulation and vesicle trafficking.
The Complex Histopathological and Immunohistochemical Spectrum of Neuroendocrine Tumors—An Overview of the Latest Classifications
Authors: Gheorghișan-Gălățeanu Ancuța-Augustina , Ilieșiu Andreea , Lambrescu Ioana Maria , Țăpoi Dana Antonia
Published: January 2023

Neuroendocrine neoplasms (NENs) originate from the neuroendocrine cell system, which may either take the shape of organoid cell aggregations or be composed of dispersed cells across various organs. Therefore, these tumors are heterogenous regarding the site of origin, functional status, degree of aggressiveness, and prognosis. When treating patients with neuroendocrine tumors, one of the most significant challenges for physicians is determining the correct tumor grade and thus classifying patients into risk categories. Over the years, the classification of these tumors has changed significantly, often causing confusion due to clinical, molecular, and immunohistochemical variability. This review aims to outline the latest NENs classifications regardless of their site of origin. Thus, an overview of the key histopathological and immunohistochemical characteristics of NENs could pave the way to validate possible predictive and prognostic markers and also guide the therapeutic conduct.
Basic Helix-Loop-Helix Transcription Factors: Regulators for Plant Growth Development and Abiotic Stress Responses
Authors: Zuo Zhi-Fang , Lee Hyo-Yeon , Kang Hong-Gyu
Published: January 2023

Plant basic helix-loop-helix (bHLH) transcription factors are involved in many physiological processes, and they play important roles in the abiotic stress responses. The literature related to genome sequences has increased, with genome-wide studies on the bHLH transcription factors in plants. Researchers have detailed the functionally characterized bHLH transcription factors from different aspects in the model plant Arabidopsis thaliana, such as iron homeostasis and abiotic stresses; however, other important economic crops, such as rice, have not been summarized and highlighted. The bHLH members in the same subfamily have similar functions; therefore, unraveling their regulatory mechanisms will help us to identify and understand the roles of some of the unknown bHLH transcription factors in the same subfamily. In this review, we summarize the available knowledge on functionally characterized bHLH transcription factors according to four categories: plant growth and development; metabolism synthesis; plant signaling, and abiotic stress responses. We also highlight the roles of the bHLH transcription factors in some economic crops, especially in rice, and discuss future research directions for possible genetic applications in crop breeding.
Human Astrocyte Spheroids as Suitable In Vitro Screening Model to Evaluate Synthetic Cannabinoid MAM2201-Induced Effects on CNS
Authors: De Simone Uliana , Pignatti Patrizia , Villani Laura , Russo Luciana Alessandra , Sargenti Azzurra , Bonetti Simone , Buscaglia Eleonora , Coccini Teresa
Published: January 2023

There is growing concern about the consumption of synthetic cannabinoids (SCs), one of the largest groups of new psychoactive substances, its consequence on human health (general population and workers), and the continuous placing of new SCs on the market. Although drug-induced alterations in neuronal function remain an essential component for theories of drug addiction, accumulating evidence indicates the important role of activated astrocytes, whose essential and pleiotropic role in brain physiology and pathology is well recognized. The study aims to clarify the mechanisms of neurotoxicity induced by one of the most potent SCs, named MAM-2201 (a naphthoyl-indole derivative), by applying a novel three-dimensional (3D) cell culture model, mimicking the physiological and biochemical properties of brain tissues better than traditional two-dimensional in vitro systems. Specifically, human astrocyte spheroids, generated from the D384 astrocyte cell line, were treated with different MAM-2201 concentrations (1–30 µM) and exposure times (24–48 h). MAM-2201 affected, in a concentration- and time-dependent manner, the cell growth and viability, size and morphological structure, E-cadherin and extracellular matrix, CB1-receptors, glial fibrillary acidic protein, and caspase-3/7 activity. The findings demonstrate MAM-2201-induced cytotoxicity to astrocyte spheroids, and support the use of this human 3D cell-based model as species-specific in vitro tool suitable for the evaluation of neurotoxicity induced by other SCs.
1,2-Dibenzoylhydrazine as a Multi-Inhibitor Compound: A Morphological and Docking Study
Authors: Patamia Vincenzo , Floresta Giuseppe , Zagni Chiara , Pistarà Venerando , Punzo Francesco , Rescifina Antonio
Published: January 2023

In the framework of the multitarget inhibitor study, we report an in silico analysis of 1,2-dibenzoylhydrazine (DBH) with respect to three essential receptors such as the ecdysone receptor (EcR), urease, and HIV-integrase. Starting from a crystallographic structural study of accidentally harvested crystals of this compound, we performed docking studies to evaluate the inhibitory capacity of DBH toward three selected targets. A crystal morphology prediction was then performed. The results of our molecular modeling calculations indicate that DBH is an excellent candidate as a ligand to inhibit the activity of EcR receptors and urease. Docking studies also revealed the activity of DBH on the HIV integrase receptor, providing an excellent starting point for developing novel inhibitors using this molecule as a starting lead compound.
Modulation of Notch Signaling at Early Stages of Differentiation of Human Induced Pluripotent Stem Cells to Dopaminergic Neurons
Authors: Katolikova Nataliia V. , Khudiakov Aleksandr A. , Shafranskaya Daria D. , Prjibelski Andrey D. , Masharskiy Alexey E. , Mor Mikael S. , Golovkin Alexey S. , Zaytseva Anastasia K. , Neganova Irina E. , Efimova Evgeniya V. , Gainetdinov Raul R. , Malashicheva Anna B.
Published: January 2023

Elaboration of protocols for differentiation of human pluripotent stem cells to dopamine neurons is an important issue for development of cell replacement therapy for Parkinson’s disease. A number of protocols have been already developed; however, their efficiency and specificity still can be improved. Investigating the role of signaling cascades, important for neurogenesis, can help to solve this problem and to provide a deeper understanding of their role in neuronal development. Notch signaling plays an essential role in development and maintenance of the central nervous system after birth. In our study, we analyzed the effect of Notch activation and inhibition at the early stages of differentiation of human induced pluripotent stem cells to dopaminergic neurons. We found that, during the first seven days of differentiation, the cells were not sensitive to the Notch inhibition. On the contrary, activation of Notch signaling during the same time period led to significant changes and was associated with an increase in expression of genes, specific for caudal parts of the brain, a decrease of expression of genes, specific for forebrain, as well as a decrease of expression of genes, important for the formation of axons and dendrites and microtubule stabilizing proteins.
Anti-HIV Potential of Beesioside I Derivatives as Maturation Inhibitors: Synthesis, 3D-QSAR, Molecular Docking and Molecular Dynamics Simulations
Authors: Zhao Zixuan , Ma Yinghong , Li Xiangyuan , Morris-Natschke Susan L. , Sun Zhaocui , Sun Zhonghao , Ma Guoxu , Dong Zhengqi , Zhao Xiaohong , Yang Meihua , Xu Xudong , Lee Kuohsiung , Wu Haifeng , Chen Chinho
Published: January 2023

HIV-1 maturation is the final step in the retroviral lifecycle that is regulated by the proteolytic cleavage of the Gag precursor protein. As a first-in-class HIV-1 maturation inhibitor (MI), bevirimat blocks virion maturation by disrupting capsid-spacer peptide 1 (CA-SP1) cleavage, which acts as the target of MIs. Previous alterations of beesioside I (1) produced (20S,24S)-15ꞵ,16ꞵ-diacetoxy-18,24; 20,24-diepoxy-9,19-cyclolanostane-3ꞵ,25-diol 3-O-3′,3′-dimethylsuccinate (3, DSC), showing similar anti-HIV potency compared to bevirimat. To ascertain the binding modes of this derivative, further modification of compound 1 was conducted. Three-dimensional quantitative structure–activity relationship (3D-QSAR) analysis combined with docking simulations and molecular dynamics (MD) were conducted. Five new derivatives were synthesized, among which compound 3b showed significant activity against HIV-1NL4-3 with an EC50 value of 0.28 µM. The developed 3D-QSAR model resulted in great predictive ability with training set (r2 = 0.99, q2 = 0.55). Molecular docking studies were complementary to the 3D-QSAR analysis, showing that DSC was differently bound to CA-SP1 with higher affinity than that of bevirimat. MD studies revealed that the complex of the ligand and the protein was stable, with root mean square deviation (RMSD) values <2.5 Å. The above results provided valuable insights into the potential of DSC as a prototype to develop new antiviral agents.
Developing a Novel Method for the Analysis of Spinal Cord–Penile Neurotransmission Mechanisms
Authors: Uta Daisuke , Kiyohara Kazuhiro , Nagaoka Yuuya , Kino Yurika , Fujita Takuya
Published: January 2023

Sexual dysfunction can be caused by impaired neurotransmission from the peripheral to the central nervous system. Therefore, it is important to evaluate the input of sensory information from the peripheral genital area and investigate the control mechanisms in the spinal cord to clarify the pathological basis of sensory abnormalities in the genital area. However, an in vivo evaluation system for the spinal cord–penile neurotransmission mechanism has not yet been developed. Here, urethane-anesthetized rats were used to evaluate neuronal firing induced by innocuous or nociceptive stimulation of the penis using extracellular recording or patch-clamp techniques in the lumbosacral spinal dorsal horn and electrophysiological evaluation in the peripheral pelvic nerves. As a result, innocuous and nociceptive stimuli-evoked neuronal firing was successfully recorded in the deep and superficial spinal dorsal horns, respectively. The innocuous stimuli-evoked nerve firing was also recorded in the pelvic nerve. These firings were suppressed by lidocaine. To the best of our knowledge, this is the first report of a successful quantitative evaluation of penile stimuli-evoked neuronal firing. This method is not only useful for analyzing the pathological basis of spinal cord–penile neurotransmission in sexual dysfunction but also provides a useful evaluation system in the search for new treatments.
A Shannon-Theoretic Approach to the Storage–Retrieval Trade-Off in PIR Systems
Authors: Tian Chao , Sun Hua , Chen Jun
Published: January 2023

We consider the storage–retrieval rate trade-off in private information retrieval (PIR) systems using a Shannon-theoretic approach. Our focus is mostly on the canonical two-message two-database case, for which a coding scheme based on random codebook generation and the binning technique is proposed. This coding scheme reveals a hidden connection between PIR and the classic multiple description source coding problem. We first show that when the retrieval rate is kept optimal, the proposed non-linear scheme can achieve better performance over any linear scheme. Moreover, a non-trivial storage-retrieval rate trade-off can be achieved beyond space-sharing between this extreme point and the other optimal extreme point, achieved by the retrieve-everything strategy. We further show that with a method akin to the expurgation technique, one can extract a zero-error PIR code from the random code. Outer bounds are also studied and compared to establish the superiority of the non-linear codes over linear codes.
Environmental Factors Drive Chalcid Body Size Increases with Altitudinal Gradients for Two Hyper-Diverse Taxa
Authors: Kang Ning , Hu Hongying , Huang Zengqian , Luo Shungang , Guo Shuhan
Published: January 2023

Body size is the most essential feature that significantly correlates with insects’ longevity, fecundity, metabolic rate, and sex ratio. Numerous biogeographical rules have been proposed to illustrate the correlation between the body sizes of different taxa and corresponding geographical or environmental factors. Whether the minute and multifarious chalcids exhibit a similar geographical pattern is still little known. In this research, we analyzed morphological data from 2953 specimens worldwide, including the two most abundant and diverse taxa (Pteromalidae and Eulophidae), which are both composed of field-collected and BOLD system specimens. We examined forewing length as a surrogate of body size and analyzed the average size separately for males and females using two methods (species and assemblage-based method). To verify Bergmann’s rule, we included temperature, precipitation, wind speed and solar radiation as explanatory variables in a generalized linear model to analyze the causes of the size variation. We found that there was an increasing trend in the body size of Pteromalidae and Eulophidae with altitude. The optimal Akaike information criterion (AIC) models showed that larger sizes are significantly negatively correlated with temperature and positively correlated with precipitation, and the possible reasons for this variation are discussed and analyzed.
Information Protection in Complexes with Unmanned Aerial Vehicles Using Moving Target Technology
Authors: Pikov Vitaly , Ryapukhin Anatoly , Veas Iniesta Daniela
Published: January 2023

This article is devoted to the problem of information security in complexes with unmanned aerial vehicles (UAV). Science knows a new promising method of information protection: moving target defense (MTD). The essence of this method is that due to periodic changes in the parameters of the infocommunication network the information about the information infrastructure collected by the attacker at the reconnaissance stage becomes irrelevant, and the attack becomes ineffective. This article also discusses the features and types of confidential information processed in complexes with UAV and provides a review of the experience of creating systems for protecting information from unauthorized access of complexes with UAV. The proposed hypothesis is tested using a model created using a tool: the GNS3 program. The model in the form of a test network in the GNS3 emulator recreates the proposed method. It was concluded that the effectiveness of the harmful impact on the complex with UAV was reduced by three times. The disadvantages of the proposed method include the problem of ensuring the availability of protected information resources for other legitimate, authorized participants in network interaction, as well as the need to solve the problem of choosing the optimal frequency of changing parameters.
Anterior and Posterior Approaches for 4-Level Degenerative Cervical Myelopathy: Low-Profile Cage Versus Cervical Pedicle Screws Fixation
Authors: Zou Peng , Zhang Rui , Yang Jun-Song , Li Er-Liang , Zhang Qian , Zhao Yuan-Ting
Published: January 2023

(1) Background: The choice of surgical access for 4-level degenerative cervical myelopathy (DCM) remains controversial, and the clinical and radiological outcomes of anterior surgery using a low-profile cage (Low-P) versus posterior surgery using cervical pedicle screw fixation (CPS) have not been compared. (2) Methods: This is a retrospective controlled study conducted between January 2019 and June 2021 of 72 patients with 4-level DCM who underwent ACDF using a low-profile cage (n = 39) or laminectomy and instrument fusion using CPS (n = 33). The minimum follow-up time was 12 months. The outcomes were C2–7Cobb angle, C2–7sagittal vertical axis (SVA) fusion rate, the Japanese Orthopedic Association (JOA) score, pain visual analog scale (VAS), neck disability index (NDI), and complications. (3) Results: Both anterior and posterior procedures significantly improved the patients’ quality-of-life parameters. Anterior cervical convexity and SVA significantly increased in both groups, but the SVA was greater in the posterior group than in the anterior group (p < 0.001). The C2–7 Cobb angle significantly improved in both groups postoperatively, and at the final follow-up, there was a slight but nonsignificant reduction in cervical lordosis in both groups (p = 0.567). There was a longer operative time, less intraoperative blood loss, and reduced mean hospital stay in the anterior group compared to the posterior group, with two cases of postoperative hematoma requiring a second operation, two cases of axial pain (AP), five cases of dysphagia, two cases of c5 palsy in the anterior group, and four cases of axial pain, and three cases of c5 palsy in the posterior group. According to Bridwell fusion grade, anterior fusion reached grade I in 28 cases (71.8%) and grade II in 10 cases (25.6%) in the anterior group, and posterior fusion reached grade I in 25 cases (75.8%) and grade II in 8 cases (24.2%) in the posterior group. (4) Conclusions: There was no difference between the anterior and posterior surgical approaches for MDCM in terms of improvement in neurological function. Posterior surgery using CPS achieved similar recovery of cervical anterior convexity as anterior surgery with a shorter operative time but was more invasive and had a greater increase in SVA. The use of Low-P in anterior surgery reduced the incidence of dysphagia and cage subsidence and was less invasive, but with a longer operative time.
Epidemiology and Risk Factors of UTIs in Children—A Single-Center Observation
Authors: Daniel Maria , Szymanik-Grzelak Hanna , Sierdziński Janusz , Podsiadły Edyta , Kowalewska-Młot Magdalena , Pańczyk-Tomaszewska Małgorzata
Published: January 2023

Urinary tract infections (UTIs) are one of childhood’s most common bacterial infections. The study aimed to determine the clinical symptoms, laboratory tests, risk factors, and etiology of different UTIs in children admitted to pediatric hospitals for three years. Methods: Patients with positive urine cultures diagnosed with acute pyelonephritis (APN) or cystitis (CYS) were analyzed for clinical symptoms, laboratory tests, risk factors, and etiology, depending on their age and sex. Results: We studied 948 children with UTIs (531 girls and 417 boys), with a median age of 12 (IQR 5–48 months). A total of 789 children had clinical symptoms; the main symptom was fever (63.4% of patients). Specific symptoms of UTIs were presented only in 16.3% of patients. Children with APN had shown significantly more frequent loss of appetite, vomiting, lethargy, seizures, and less frequent dysuria and haematuria than children with CYS. We found significantly higher median WBC, CRP, and leukocyturia in children with APN than with CYS. The risk factors of UTIs were presented in 46.6% of patients, of which 35.6% were children with APN and 61.7% with CYS. The main risk factor was CAKUT, more frequently diagnosed in children with CYS than APN, mainly in children <2 years. The most commonly isolated bacteria were Escherichia coli (74%). There was a higher percentage of urine samples with E. coli in girls than in boys. Other bacteria found were Klebsiella species, Pseudomonas aeruginosa, Proteus mirabilis, and Enterococcus species. Conclusions: Patients with APN were younger and had higher inflammatory markers. Often, fever is the only symptom of UTI in children, and other clinical signs are usually non-specific. The most common UTI etiology is E. coli, regardless of the clinical presentation and risk factors.