bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression Analysis of Moritella viscosa-Challenged Atlantic Salmon Identifies Disease-Responding Genes, MicroRNAs and Their Predicted Target Genes and Pathways
Authors: Ramberg Sigmund , Krasnov Aleksei , Colquhoun Duncan , Wallace Christian , Andreassen Rune
Published: September 2022

Moritella viscosa is a bacterial pathogen causing winter-ulcer disease in Atlantic salmon. The lesions on affected fish lead to increased mortality, decreased fish welfare, and inferior meat quality in farmed salmon. MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional regulation by guiding the miRNA-induced silencing complex to specific mRNA transcripts (target genes). The goal of this study was to identify miRNAs responding to Moritella viscosa in salmon by investigating miRNA expression in the head-kidney and the muscle/skin from lesion sites caused by the pathogen. Protein coding gene expression was investigated by microarray analysis in the same materials. Seventeen differentially expressed guide-miRNAs (gDE-miRNAs) were identified in the head-kidney, and thirty-nine in lesion sites, while the microarray analysis reproduced the differential expression signature of several thousand genes known as infection-responsive. In silico target prediction and enrichment analysis suggested that the gDE-miRNAs were predicted to target genes involved in immune responses, hemostasis, angiogenesis, stress responses, metabolism, cell growth, and apoptosis. The majority of the conserved gDE-miRNAs (e.g., miR-125, miR-132, miR-146, miR-152, miR-155, miR-223 and miR-2188) are known as infection-responsive in other vertebrates. Collectively, the findings indicate that gDE-miRNAs are important post-transcriptional gene regulators of the host response to bacterial infection.
Hypoxia-Inducible Factors Signaling in Osteogenesis and Skeletal Repair
Authors: Qin Qiuyue , Liu Yiping , Yang Zhen , Aimaijiang Maierhaba , Ma Rui , Yang Yixin , Zhang Yidi , Zhou Yanmin
Published: September 2022

Sufficient oxygen is required to maintain normal cellular and physiological function, such as a creature’s development, breeding, and homeostasis. Lately, some researchers have reported that both pathological hypoxia and environmental hypoxia might affect bone health. Adaptation to hypoxia is a pivotal cellular event in normal cell development and differentiation and in pathological settings such as ischemia. As central mediators of homeostasis, hypoxia-inducible transcription factors (HIFs) can allow cells to survive in a low-oxygen environment and are essential for the regulation of osteogenesis and skeletal repair. From this perspective, we summarized the role of HIF-1 and HIF-2 in signaling pathways implicated in bone development and skeletal repair and outlined the molecular mechanism of regulation of downstream growth factors and protein molecules such as VEGF, EPO, and so on. All of these present an opportunity for developing therapies for bone regeneration.
Tryptamine, a Microbial Metabolite in Fermented Rice Bran Suppressed Lipopolysaccharide-Induced Inflammation in a Murine Macrophage Model
Authors: Agista Afifah Zahra , Tanuseputero Sharon Angela , Koseki Takuya , Ardiansyah Ardiansyah , Budijanto Slamet , Sultana Halima , Ohsaki Yusuke , Yeh Chiu-Li , Yang Suh-Ching , Komai Michio , Shirakawa Hitoshi
Published: September 2022

Fermentation is thought to alter the composition and bioavailability of bioactive compounds in rice bran. However, how this process affects the anti-inflammatory effects of rice bran and the bioactive compounds that might participate in this function is yet to be elucidated. This study aimed to isolate bioactive compounds in fermented rice bran that play a key role in its anti-inflammatory function. The fermented rice bran was fractionated using a succession of solvent and solid-phase extractions. The fermented rice bran fractions were then applied to lipopolysaccharide (LPS)-activated murine macrophages to evaluate their anti-inflammatory activity. The hot water fractions (FRBA), 50% ethanol fractions (FRBB), and n-hexane fractions (FRBC) were all shown to be able to suppress the pro-inflammatory cytokine expression from LPS-stimulated RAW 264.7 cells. Subsequent fractions from the hot water fraction (FRBF and FRBE) were also able to reduce the inflammatory response of these cells to LPS. Further investigation revealed that tryptamine, a bacterial metabolite of tryptophan, was abundantly present in these extracts. These results indicate that tryptamine may play an important role in the anti-inflammatory effects of fermented rice bran. Furthermore, the anti-inflammatory effects of FRBE and tryptamine may depend on the activity of the aryl hydrocarbon receptor.
Janus Faced HMGB1 and Post-Aneurysmal Subarachnoid Hemorrhage (aSAH) Inflammation
Authors: Chaudhry Shafqat Rasul , Shafique Sumaira , Sajjad Saba , Hänggi Daniel , Muhammad Sajjad
Published: September 2022

Aneurysmal subarachnoid hemorrhage (aSAH), resulting majorly from the rupture of intracranial aneurysms, is a potentially devastating disease with high morbidity and mortality. The bleeding aneurysms can be successfully secured; however, the toxic and mechanical impact of the blood extravasation into the subarachnoid space damages the brain cells leading to the release of different damage-associated molecular pattern molecules (DAMPs). DAMPs upregulate the inflammation after binding their cognate receptors on the immune cells and underlies the early and delayed brain injury after aSAH. Moreover, these molecules are also associated with different post-aSAH complications, which lead to poor clinical outcomes. Among these DAMPs, HMGB1 represents a prototypical protein DAMP that has been well characterized for its proinflammatory role after aSAH and during different post-aSAH complications. However, recent investigations have uncovered yet another face of HMGB1, which is involved in the promotion of brain tissue remodeling, neurovascular repair, and anti-inflammatory effects after SAH. These different faces rely on different redox states of HMGB1 over the course of time after SAH. Elucidation of the dynamics of these redox states of HMGB1 has high biomarker as well as therapeutic potential. This review mainly highlights these recent findings along with the conventionally described normal role of HMGB1 as a nuclear protein and as a proinflammatory molecule during disease (aSAH).
Experimental Research Models to Assess the Cross-Reactivity between Can f 5 and Human PSA—Two Different Perspectives
Authors: Lis Kinga , Ukleja-Sokołowska Natalia , Adamczak Rafał , Bartuzi Zbigniew
Published: September 2022

The similarity in antigenic structures, including the degree of correspondence between the amino acid sequence and the spatial structure, is not always reflected in the actual cross-reactivity of allergens. Inhibition tests appear to be an invaluable tool for assessing potential cross-reactivity between allergens under natural conditions. In this publication, we present two experimental models of inhibition tests: solid phase (SP-IT) and liquid phase (LP-IT). As an exemplary research model, we used the cross-reactivity between human PSA and anti-Can f 5 IgE antibodies. We performed an SP-IT model using a microplate coated with human PSA. The LP-IT model was based on mixing anti-Can f 5 IgE positive serum with a material containing human PSA. Anti-Can f 5 IgE and PSA concentrations before and after inhibition were measured to evaluate inhibition effectiveness. The results of the performed experiments showed that both proposed models of inhibition tests are an effective tools for studying cross-reactive relationships between antigens. In the SP-IT, the concentration of anti-Can f 5 decreased by 21.6% and, in the LP-IT, it decreased by 34.51%. In turn, the PSA concentration in the SP-IT decreased by 11.25% and, in the LP-IT, it decreased by 15.49%. In conclusion, both the SP-IT and the LP-IT seem to be effective tools for assessing the actual cross-reactivity between different allergens.
Lithium Treatment Improves Cardiac Dysfunction in Rats Deprived of Rapid Eye Movement Sleep
Authors: Chen Pao-Huan , Chung Cheng-Chih , Liu Shuen-Hsin , Kao Yu-Hsun , Chen Yi-Jen
Published: September 2022

Rapid eye movement (REM) sleep deprivation triggers mania and induces cardiac fibrosis. Beyond neuroprotection, lithium has cardioprotective potential and antifibrotic activity. This study investigated whether lithium improved REM sleep deprivation-induced cardiac dysfunction and evaluated the potential mechanisms. Transthoracic echocardiography, histopathological analysis, and Western blot analysis were performed in control and REM sleep-deprived rats with or without lithium treatment (LiCl of 1 mmol/kg/day administered by oral gavage for 4 weeks) in vivo and in isolated ventricular preparations. The results revealed that REM sleep-deprived rats exhibited impaired contractility and greater fibrosis than control and lithium-treated REM sleep-deprived rats. Western blot analysis showed that REM sleep-deprived hearts had higher expression levels of transforming growth factor beta (TGF-β), phosphorylated Smad 2/3, and alpha-smooth muscle actin than lithium-treated REM sleep-deprived and control hearts. Moreover, lithium-treated REM sleep-deprived hearts had lower expression of angiotensin II type 1 receptor, phosphorylated nuclear factor kappa B p65, calcium release-activated calcium channel protein 1, transient receptor potential canonical (TRPC) 1, and TRPC3 than REM sleep-deprived hearts. The findings suggest that lithium attenuates REM sleep deprivation-induced cardiac fibrogenesis and dysfunction possibly through the downregulation of TGF-β, angiotensin II, and Ca2+ signaling.
Polyaniline-Derived Nitrogen-Containing Carbon Nanostructures with Different Morphologies as Anode Modifier in Microbial Fuel Cells
Authors: Lascu Irina , Locovei Claudiu , Bradu Corina , Gheorghiu Cristina , Tanase Ana Maria , Dumitru Anca
Published: September 2022

Anode modification with carbon nanomaterials is an important strategy for the improvement of microbial fuel cell (MFC) performance. The presence of nitrogen in the carbon network, introduced as active nitrogen functional groups, is considered beneficial for anode modification. In this aim, nitrogen-containing carbon nanostructures (NCNs) with different morphologies were obtained via carbonization of polyaniline and were further investigated as anode modifiers in MFCs. The present study investigates the influence of NCN morphology on the changes in the anodic microbial community and MFC performance. Results show that the nanofibrillar morphology of NCNs is beneficial for the improvement of MFC performance, with a maximum power density of 40.4 mW/m2, 1.25 times higher than the anode modified with carbonized polyaniline with granular morphology and 2.15 times higher than MFC using the carbon cloth-anode. The nanofibrillar morphology, due to the well-defined individual nanofibers separated by microgaps and micropores and a better organization of the carbon network, leads to a larger specific surface area and higher conductivity, which can allow more efficient substrate transport and better bacterial colonization with greater relative abundances of Geobacter and Thermoanaerobacter, justifying the improvement of MFC performance.
Italian Precision Medicine in Pediatric Oncology: Moving beyond Actionable Alterations
Authors: Pastorino Fabio , Capasso Mario , Brignole Chiara , Giglio Serena , Bensa Veronica , Cantalupo Sueva , Lasorsa Vito Alessandro , Tondo Annalisa , Mura Rossella , Sementa Angela Rita , Garaventa Alberto , Ponzoni Mirco , Amoroso Loredana
Published: September 2022

Neuroblastoma (NB) is the most common extracranial solid tumor encountered in childhood. Although there has been significant improvement in the outcomes of patients with high-risk disease, the prognosis for patients with metastatic relapse or refractory disease is poor. Hence, the clinical integration of genome sequencing into standard clinical practice is necessary in order to develop personalized therapy for children with relapsed or refractory disease. The PeRsonalizEdMEdicine (PREME) project focuses on the design of innovative therapeutic strategies for patients suffering from relapsed NB. We performed whole exome sequencing (WES) of patient-matched tumor-normal samples to identify genetic variants amenable to precision medicine. Specifically, two patients were studied (First case: a three-year-old male with early relapsed NB; Second case: a 20-year-old male who relapsed 10 years after the first diagnosis of NB). Results were reviewed by a multi-disciplinary molecular tumor board (MTB) and clinical reports were issued to the ordering physician. WES revealed the mutation c.G320C in the CUL4A gene in case 1 and the mutation c.A484G in the PSMC2 gene in case 2. Both patients were treated according to these actionable alterations, with promising results. The effective treatment of NB is one of the main challenges in pediatric oncology. In the era of precision medicine, the need to design new therapeutic strategies for NB is fundamental. Our results demonstrate the feasibility of incorporating clinical WES into pediatric oncology practice.
Structural Studies on Diverse Betacyanin Classes in Matured Pigment-Rich Fruits of Basella alba L. and Basella alba L. var. ‘Rubra’ (Malabar Spinach)
Authors: Sutor-Świeży Katarzyna , Antonik Michał , Dziedzic Ewa , Bieniasz Monika , Mielczarek Przemysław , Popenda Łukasz , Pasternak Karol , Tyszka-Czochara Małgorzata , Wybraniec Sławomir
Published: September 2022

Identification of betacyanins in Basella alba L. and Basella alba L. var. ‘Rubra’ fruits was performed by low- and high-resolution mass spectrometry (LRMS and HRMS) as well as 1H, 13C and two-dimensional NMR which revealed hitherto completely not known betacyanin classes in the plant kingdom. Especially, the presence of unique nitrogenous acyl moieties in the structures of the pigments was ascertained by the HRMS Orbitrap detection. Except for detected polar betacyanin glycosylated derivatives, presence of a series of previously not reported pigments such as malonylated betanidin 6-O-β-glusosides with their acyl migration isomers along with the evidence of the 3′′-hydroxy-butyrylated betacyanins is reported. The first complete NMR data were obtained for novel and principal acylated gomphrenins with hydroxycinnamic acids: 6′-O-E-caffeoyl-gomphrenin (malabarin), 6′-O-E-sinapoyl-gomphrenin (gandolin), 6′-O-E-4-coumaroyl-gomphrenin (globosin) and 6′-O-E-feruloyl-gomphrenin (basellin).
Pharmacokinetics of Myo-Inositol in a Wistar Rat Animal Model
Authors: Antonowski Tomasz , Osowski Adam , Szczesny Damian , Szablińska-Piernik Joanna , Juśkiewicz Jerzy , Lahuta Lesław , Rynkiewicz Andrzej , Wojtkiewicz Joanna
Published: September 2022

Myo-inositol is the most popular inositol in living organisms, where it is present as a sugar alcohol, in a free form, and can also be described as a lipid. The aim of this study was to check the concentration change of a myo-inositol solution from the time of oral administration and over a 48 h period in Wistar-type rats. All rats received 2 g/kg of inositol as a solution in distilled water by oral gavage. Estimated parameters were based on the serum concentration of myo-inositol observed in nine individual rats with regard to time. Observations were described as a one-compartment pharmacokinetic model with first-order absorption and zero-order endogenous input of checked inositol. The highest myo-inositol concentration was observed in the first hour after oral administration in the serum of all tested rats. Then, the concentration began decreasing immediately after the maximal peak. The inositol concentration continued to decrease, but after 24 h its level was still higher than before the administration. The plasma profile of the myo-inositol concentration showed a rapid decline over time, possibly due to the metabolism of this compound.
Imaging the Infection Cycle of T7 at the Single Virion Level
Authors: Kiss Bálint , Kiss Luca Annamária , Lohinai Zsombor Dávid , Mudra Dorottya , Tordai Hedvig , Herenyi Levente , Csík Gabriella , Kellermayer Miklós
Published: September 2022

T7 phages are E. coli-infecting viruses that find and invade their target with high specificity and efficiency. The exact molecular mechanisms of the T7 infection cycle are yet unclear. As the infection involves mechanical events, single-particle methods are to be employed to alleviate the problems of ensemble averaging. Here we used TIRF microscopy to uncover the spatial dynamics of the target recognition and binding by individual T7 phage particles. In the initial phase, T7 virions bound reversibly to the bacterial membrane via two-dimensional diffusive exploration. Stable bacteriophage anchoring was achieved by tail-fiber complex to receptor binding which could be observed in detail by atomic force microscopy (AFM) under aqueous buffer conditions. The six anchored fibers of a given T7 phage-displayed isotropic spatial orientation. The viral infection led to the onset of an irreversible structural program in the host which occurred in three distinct steps. First, bacterial cell surface roughness, as monitored by AFM, increased progressively. Second, membrane blebs formed on the minute time scale (average ~5 min) as observed by phase-contrast microscopy. Finally, the host cell was lysed in a violent and explosive process that was followed by the quick release and dispersion of the phage progeny. DNA ejection from T7 could be evoked in vitro by photothermal excitation, which revealed that genome release is mechanically controlled to prevent premature delivery of host-lysis genes. The single-particle approach employed here thus provided an unprecedented insight into the details of the complete viral cycle.
Proviral ALV-LTR Sequence Is Essential for Continued Proliferation of the ALV-Transformed B Cell Line
Authors: Roy Swagata , Bondada Megha Sravani , Zhang Yaoyao , Moffat Katy , Nair Venugopal , Yao Yongxiu
Published: September 2022

Avian leukosis virus (ALV) induces B-cell lymphomas and other malignancies in chickens through insertional activation of oncogenes, and c-myc activation has been commonly identified in ALV-induced tumors. Using ALV-transformed B-lymphoma-derived HP45 cell line, we applied in situ CRISPR-Cas9 editing of integrated proviral long terminal repeat (LTR) to examine the effects on gene expression and cell proliferation. Targeted deletion of LTR resulted in significant reduction in expression of a number of LTR-regulated genes including c-myc. LTR deletion also induced apoptosis of HP45 cells, affecting their proliferation, demonstrating the significance of LTR-mediated regulation of critical genes. Compared to the global effects on expression and functions of multiple genes in LTR-deleted cells, deletion of c-myc had a major effect on the HP45 cells proliferation with the phenotype similar to the LTR deletion, demonstrating the significance of c-myc expression in ALV-induced lymphomagenesis. Overall, our studies have not only shown the potential of targeted editing of the LTR for the global inhibition of retrovirus-induced transformation, but also have provided insights into the roles of LTR-regulated genes in ALV-induced neoplastic transformation.
Antibiofilm Properties of Antiseptic Agents Used on Pseudomonas aeruginosa Isolated from Diabetic Foot Ulcers
Authors: Barrigah-Benissan Koko , Ory Jerome , Dunyach-Remy Catherine , Pouget Cassandra , Lavigne Jean-Philippe , Sotto Albert
Published: September 2022

In diabetic foot ulcers (DFUs), biofilm formation is a major challenge that promotes wound chronicity and delays healing. Antiseptics have been proposed to combat biofilms in the management of DFUs. However, there is limited evidence on the activity of these agents against biofilms, and there are questions as to which agents have the best efficiency. Here, we evaluated the antibiofilm activity of sodium hypochlorite, polyvinylpyrrolidoneIodine (PVPI), polyhexamethylenebiguanide (PHMB) and octenidine against Pseudomonas aeruginosa strains using static and dynamic systems in a chronic-wound-like medium (CWM) that mimics the chronic wound environment. Using Antibiofilmogram®, a technology assessing the ability of antiseptics to reduce the initial phase of biofilm formation, we observed the significant activity of antiseptics against biofilm formation by P. aeruginosa (at 1:40 to 1:8 dilutions). Moreover, 1:100 to 1:3 dilutions of the different antiseptics reduced mature biofilms formed after 72 h by 10-log, although higher concentrations were needed in CWM (1:40 to 1:2). Finally, in the BioFlux200TM model, after biofilm debridement, sodium hypochlorite and PHMB were the most effective antiseptics. In conclusion, our study showed that among the four antiseptics tested, sodium hypochlorite demonstrated the best antibiofilm activity against P. aeruginosa biofilms and represents an alternative in the management of DFUs.
The Stimulation of Macrophages by Systematical Administration of GM-CSF Can Accelerate Adult Wound Healing Process
Authors: Zhang Jing , Jia Liyuan , Zheng Hanxue , Feng Juantao , Wei Sili , Li Juan , Cui Jihong , Chen Fulin
Published: September 2022

Skin wound repair remains a major challenge in clinical care, and various strategies have been employed to improve the repair process. Recently, it has been reported that macrophages are important for the regeneration of various tissues and organs. However, their influence on wound repair is unclear. Here, we aimed to explore whether macrophages would participate in the wound healing process and to explore new possibilities of treatment for skin defects. We firstly created a mouse full-thickness skin defect model to observe the distribution of macrophages in the regenerating tissue and then detected the influence of macrophages on skin defect repair in both macrophage-depletion and macrophage-mobilization models. We found that the number of macrophages increased significantly after skin defect and persisted during the process of wound repair. The regeneration process was significantly prolonged in macrophage-depleted animals. RT-qPCR and ELISA assays further demonstrated that the expression of growth factors was perturbed in the regenerating tissue. The activation of macrophages by granulocyte-macrophage colony-stimulating factor (GM-CSF) injection could significantly improve wound healing, accompanied with an upregulation of the expression of various growth factors. In conclusion, the current study demonstrated that macrophages are critical for skin regeneration and that GM-CSF exhibited therapeutic potential for wound healing.
Dynamical and Structural Properties of Comb Long-Chain Branched Polymer in Shear Flow
Authors: Wang Deyin , Wen Xiaohui , Zhang Dong , Tang Jiajun
Published: September 2022

Using hybrid multi-particle collision dynamics (MPCD) and a molecular dynamics (MD) method, we investigate the effect of arms and shear flow on dynamical and structural properties of the comb long-chain branched (LCB) polymer with dense arms. Firstly, we analyze dynamical properties of the LCB polymer by tracking the temporal changes on the end-to-end distance of both backbones and arms as well as the orientations of the backbone in the flow-gradient plane. Simultaneously, the rotation and tumbling behaviors with stable frequencies are observed. In other words, the LCB polymer undergoes a process of periodic stretched–folded–stretched state transition and rotation, whose period is obtained by fitting temporal changes on the orientation to a periodic function. In addition, the impact induced by random and fast motions of arms and the backbone will descend as the shear rate increases. By analyzing the period of rotation behavior of LCB polymers, we find that arms have a function in keeping the LCB polymer’s motion stable. Meanwhile, we find that the rotation period of the LCB polymer is mainly determined by the conformational distribution and the non-shrinkable state of the structure along the velocity-gradient direction. Secondly, structural properties are numerically characterized by the average gyration tensor of the LCB polymer. The changes in gyration are in accordance with the LCB polymer rolling when varying the shear rate. By analyzing the alignment of the LCB polymer and comparing with its linear and star counterparts, we find that the LCB polymer with very long arms, like the corresponding linear chain, has a high speed to reach its configuration expansion limit in the flow direction. However, the comb polymer with shorter arms has stronger resistance on configuration expansion against the imposed flow field. Moreover, with increasing arm length, the comb polymer in shear flow follows change from linear-polymer-like to capsule-like behavior.
Profiling the Influence of Gene Variants Related to Folate-Mediated One-Carbon Metabolism on the Outcome of In Vitro Fertilization (IVF) with Donor Oocytes in Recipients Receiving Folic Acid Fortification
Authors: Palomares Arturo Reyes , Ruiz-Galdon Maximiliano , Liu Kui , Reyes-Engel Armando , Rodriguez-Wallberg Kenny A.
Published: September 2022

Nutritional status and gene polymorphisms of one-carbon metabolism confer a well-known interaction that in pregnant women may affect embryo viability and the health of the newborn. Folate metabolism directly impacts nucleotide synthesis and methylation, which is of increasing interest in the reproductive medicine field. Studies assessing the genetic influence of folate metabolism on IVF treatments have currently been performed in women using their own oocytes. Most of these patients seeking to have a child or undergoing IVF treatments are advised to preventively intake folate supplies that restore known metabolic imbalances, but the treatments could lead to the promotion of specific enzymes in specific women, depending on their genetic variance. In the present study, we assess the influence of candidate gene variants related to folate metabolism, such as Serine Hydroxymethyltransferase 1 SHMT1 (rs1979276 and rs1979277), Betaine-Homocysteine S-Methyltransferase BHMT (rs3733890), Methionine synthase reductase MTRR (rs1801394), Methylenetetrahydrofolate reductase MTHFR (rs1801131 and rs1801133), methionine synthase MTR (rs12749581), ATP Binding Cassette Subfamily B Member 1 ABCB1 (rs1045642) and folate receptor alpha FOLR1 (rs2071010) on the success of IVF treatment performed in women being recipients of donated oocytes. The implication of such gene variants seems to have no direct impact on pregnancy consecution after IVF; however, several gene variants could influence pregnancy loss events or pregnancy maintenance, as consequence of folic acid fortification.
Dysregulation of miRISC Regulatory Network Promotes Hepatocellular Carcinoma by Targeting PI3K/Akt Signaling Pathway
Authors: Kannan Maheshkumar , Jayamohan Sridharan , Moorthy Rajesh Kannan , Chabattula Siva Chander , Ganeshan Mathan , Arockiam Antony Joseph Velanganni
Published: September 2022

Hepatocellular carcinoma (HCC) remains the third leading malignancy worldwide, causing high mortality in adults and children. The neuropathology-associated gene AEG-1 functions as a scaffold protein to correctly assemble the RNA-induced silencing complex (RISC) and optimize or increase its activity. The overexpression of oncogenic miRNAs periodically degrades the target tumor suppressor genes. Oncogenic miR-221 plays a seminal role in the carcinogenesis of HCC. Hence, the exact molecular and biological functions of the oncogene clusters miR-221/AEG-1 axis have not yet been examined widely in HCC. Here, we explored the expression of both miR-221 and AEG-1 and their target/associate genes by qRT-PCR and western blot. In addition, the role of the miR-221/AEG-1 axis was studied in the HCC by flow cytometry analysis. The expression level of the AEG-1 did not change in the miR-221 mimic, and miR-221-transfected HCC cells, on the other hand, decreased the miR-221 expression in AEG-1 siRNA-transfected HCC cells. The miR-221/AEG-1 axis silencing induces apoptosis and G2/M phase arrest and inhibits cellular proliferation and angiogenesis by upregulating p57, p53, RB, and PTEN and downregulating LSF, LC3A, Bcl-2, OPN, MMP9, PI3K, and Akt in HCC cells.
A Novel Strategy for Identifying NSCLC MicroRNA Biomarkers and Their Mechanism Analysis Based on a Brand-New CeRNA-Hub-FFL Network
Authors: Zhang Jin , Nie Renqing , Liu Mengxi , Zhang Xiaoyi
Published: September 2022

Finding reliable miRNA markers and revealing their potential mechanisms will play an important role in the diagnosis and treatment of NSCLC. Most existing computational methods for identifying miRNA biomarkers only consider the expression variation of miRNAs or rely heavily on training sets. These deficiencies lead to high false-positive rates. The independent regulatory model is an important complement to traditional models of co-regulation and is more impervious to the dataset. In addition, previous studies of miRNA mechanisms in the development of non-small cell lung cancer (NSCLC) have mostly focused on the post-transcriptional level and did not distinguish between NSCLC subtypes. For the above problems, we improved mainly in two areas: miRNA identification based on both the NOG network and biological functions of miRNA target genes; and the construction of a 4-node directed competitive regulatory network to illustrate the mechanisms. NSCLC was classified as lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) in this work. One miRNA biomarker of LUAD (miR-708-5p) and four of LUSC (miR-183-5p, miR-140-5p, miR-766-5p, and miR-766-3p) were obtained. They were validated using literature and external datasets. The ceRNA-hub-FFL involving transcription factors (TFs), microRNAs (miRNAs), mRNAs, and long non-coding RNAs (lncRNAs) was constructed. There were multiple interactions among these components within the net at the transcriptional, post-transcriptional, and protein levels. New regulations were revealed by the network. Meanwhile, the network revealed the reasons for the previous conflicting conclusions on the roles of CD44, ACTB, and ITGB1 in NSCLC, and demonstrated the necessity of typing studies on NSCLC. The novel miRNA markers screening method and the 4-node directed competitive ceRNA-hub-FFL network constructed in this work can provide new ideas for screening tumor markers and understanding tumor development mechanisms in depth.
Novel Strategies against Cancer: Dexibuprofen-Loaded Nanostructured Lipid Carriers
Authors: Thiruchenthooran Vaikunthavasan , Świtalska Marta , Bonilla Lorena , Espina Marta , García Maria Luisa , Wietrzyk Joanna , Sánchez-López Elena , Gliszczyńska Anna
Published: September 2022

The aim of this work was to design innovative nanostructured lipid carriers (NLCs) for the delivery of dexibuprofen (DXI) as an antiproliferative therapy against tumoral processes, and overcome its side effects. DXI-NLC samples were prepared with beeswax, Miglyol 812 and Tween 80 using high-pressure homogenization. A two-level factorial design 24 was applied to optimize the formulation, and physicochemical properties such as particle size, zeta potential, polydispersity index and entrapment efficiency were measured. Optimized parameters of DXI-NLCs exhibited a mean particle size of 152.3 nm, a polydispersity index below 0.2, and high DXI entrapment efficiency (higher than 99%). Moreover, DXI-NLCs provided a prolonged drug release, slower than the free DXI. DXI-NLCs were stable for 2 months and their morphology revealed that they possess a spherical shape. In vitro cytotoxicity and anticancer potential studies were performed towards prostate (PC-3) and breast (MDA-MB-468) cancer cell lines. The highest activity of DXI-NLCs was observed towards breast cancer cells, which were effectively inhibited at 3.4 μM. Therefore, DXI-NLCs constitute a promising antiproliferative therapy that has proven to be especially effective against breast cancer.
Segmentation Method of Magnetoelectric Brain Image Based on the Transformer and the CNN
Authors: Liu Xiaoli , Cheng Xiaorong
Published: September 2022

To address the problem of a low accuracy and blurred boundaries in segmenting multimodal brain tumor images using the TransBTS network, a 3D BCS_T model incorporating a channel space attention mechanism is proposed. Firstly, the TransBTS model hierarchy is increased to obtain more local feature information, and residual basis blocks are added to reduce feature loss. Secondly, downsampling is incorporated into the hybrid attention mechanism to enhance the critical region information extraction. Finally, weighted cross-entropy loss and generalized dice loss are employed to solve the inequality problem in the tumor sample categories. The experimental results show that the whole tumor region WT, the tumor core region TC, and the enhanced tumor region ET are improved by an average of 2.53% in the evaluation metric of the Dice similarity coefficient, compared with the TransBTS network and shortened by an average of 3.14 in the metric of Hausdorff distance 95. Therefore, the 3D BCS_T model can effectively improve the segmentation accuracy and boundary clarity of both the tumor core and the enhanced tumor categories of the small areas.
Integrative Proteomic and Phosphoproteomic Analyses Revealed Complex Mechanisms Underlying Reproductive Diapause in Bombus terrestris Queens
Authors: Liu Yan , Wang Ruijuan , Su Long , Zhao Shan , Dai Xiaoyan , Chen Hao , Wu Guang’an , Zhou Hao , Zheng Li , Zhai Yifan
Published: September 2022

Reproductive diapause is an overwintering strategy for Bombus terrestris, which is an important pollinator for agricultural production. However, the precise mechanisms underlying reproductive diapause in bumblebees remain largely unclear. Here, a combination analysis of proteomics and phosphoproteomics was used to reveal the mechanisms that occur during and after diapause in three different phases: diapause (D), postdiapause (PD), and founder postdiapause (FPD). In total, 4655 proteins and 10,600 phosphorylation sites of 3339 proteins were identified. Diapause termination and reactivation from D to the PD stage were characterized by the upregulation of proteins associated with ribosome assembly and biogenesis, transcription, and translation regulation in combination with the upregulation of phosphoproteins related to neural signal transmission, hormone biosynthesis and secretion, and energy-related metabolism. Moreover, the reproductive program was fully activated from PD to the FPD stage, as indicated by the upregulation of proteins related to fat digestion and absorption, the biosynthesis of unsaturated fatty acids, fatty acid elongation, protein processing in the endoplasmic reticulum, and the upregulation of energy-related metabolism at the phosphoproteome level. We also predicted a kinase–substrate interaction network and constructed protein–protein networks of proteomic and phosphoproteomic data. These results will help to elucidate the mechanisms underlying the regulation of diapause in B. terrestris for year-round mass breeding.
Females of Halyomorpha halys (Hemiptera: Pentatomidae) Experience a Facultative Reproductive Diapause in Northern Greece
Authors: Koutsogeorgiou Eleni I. , Kouloussis Nikos A. , Koveos Dimitrios S. , Andreadis Stefanos S.
Published: September 2022

Halyomorpha halys (Stål) (Hemiptera: Pentatomidae) is a native pest of East Asia that overwinters as an adult in natural and human-made structures. Adult emergence from overwintering sites starts in spring, whereas females produce offspring in early summer on host plants, where most feeding occurs. In this study, we investigated the reproductive physiology of overwintering females of H. halys in Northern Greece, by determining the duration of the preoviposition period and fecundity of individuals that were left to overwinter in natural conditions and were subsequently transferred to chambers with standard conditions monthly, from December 2020 to March 2021. According to our results, overwintering H. halys females do not initiate egg laying once they emerge from overwintering sites, but rather need some additional time to exit diapause and mature reproductively. The mean preoviposition period of overwintering females that were transferred from their overwintering sites to the chambers in December 2020 was 29.0 days, which was significantly longer by 8.3 days than that of females that overwintered until March 2021, and by 13.2 days than the control (26 °C, 60% RH and a 16:8 h light: dark photoperiod). No significant difference among the average number of eggs per egg mass laid by overwintering individuals brought in the chambers in different time intervals and the laboratory colony was observed. However, females that were left to overwinter until March laid a significantly higher number of eggs in total, compared to the ones whose overwintering was disrupted in February. Based on our findings, overwintering females of H. halys experience a facultative reproductive diapause in Northern Greece. Our study was the first to determine the occurrence of diapause of H. halys in N. Greece and our findings could be very valuable for assessing the damage of this pest to early-season crops and designing successful management practices.
Using Artificial Intelligence in the Reconstruction of Signals from the PADME Electromagnetic Calorimeter
Authors: Dimitrova Kalina ,   on behalf of the PADME collaboration
Published: September 2022

The PADME apparatus was built at the Frascati National Laboratory of INFN to search for a dark photon (A′) produced via the process e+e−→A′γ. The central component of the PADME detector is an electromagnetic calorimeter composed of 616 BGO crystals dedicated to the measurement of the energy and position of the final state photons. The high beam particle multiplicity over a short bunch duration requires reliable identification and measurement of overlapping signals. A regression machine-learning-based algorithm has been developed to disentangle with high efficiency close-in-time events and precisely reconstruct the amplitude of the hits and the time with sub-nanosecond resolution. The performance of the algorithm and the sequence of improvements leading to the achieved results are presented and discussed.
The SiD Digital ECal Based on Monolithic Active Pixel Sensors
Authors: Brau James E. , Breidenbach Martin , Habib Alexandre , Rota Lorenzo , Vernieri Caterina
Published: September 2022

The SiD detector concept capitalizes on high granularity in its tracker and calorimeter to achieve the momentum resolution and particle flow calorimetry physics goals in a compact design. The collaboration has had a long interest in the potential for improved granularity in both the tracker and ECal with an application of monolithic active pixel sensors (MAPS) and a study of MAPS in the SiD ECal was described in the ILC TDR. Work is progressing on the MAPS application in an upgraded SiD design with a prototyping design effort for a common SiD tracker/ECal design based on stitched reticules to achieve 10 × 10 cm2 sensors with 25 × 100 micron2 pixels. Application of large area MAPS in these systems would limit delicate and expensive bump-bonding, provide possibilities for better timing, and should be significantly cheaper than the TDR concept due to being a more conventional CMOS foundry process. The small pixels significantly improve shower separation. Recent simulation studies confirm previous performance projections, indicating electromagnetic energy resolution based on digital hit cluster counting provides better performance than the SiD TDR analog design based on 13 mm2 pixels. Furthermore, the two shower separation is excellent down to the millimeter scale. Geant4 simulation results demonstrate these expectations.
Polycaprolactone-Based 3D-Printed Scaffolds as Potential Implant Materials for Tendon-Defect Repair
Authors: Kempfert Merle , Willbold Elmar , Loewner Sebastian , Blume Cornelia , Pitts Johannes , Menzel Henning , Roger Yvonne , Hoffmann Andrea , Angrisani Nina , Reifenrath Janin
Published: September 2022

Chronic tendon ruptures are common disorders in orthopedics. The conventional surgical methods used to treat them often require the support of implants. Due to the non-availability of suitable materials, 3D-printed polycaprolactone (PCL) scaffolds were designed from two different starting materials as suitable candidates for tendon-implant applications. For the characterization, mechanical testing was performed. To increase their biocompatibility, the PCL-scaffolds were plasma-treated and coated with fibronectin and collagen I. Cytocompatibility testing was performed using L929 mouse fibroblasts and human-bone-marrow-derived mesenchymal stem cells. The mechanical testing showed that the design adaptions enhanced the mechanical stability. Cell attachment was increased in the plasma-treated specimens compared to the control specimens, although not significantly, in the viability tests. Coating with fibronectin significantly increased the cellular viability compared to the untreated controls. Collagen I treatment showed an increasing trend. The desired cell alignment and spread between the pores of the construct was most prominent on the collagen-I-coated specimens. In conclusion, 3D-printed scaffolds are possible candidates for the development of tendon implants. Enhanced cytocompatibility was achieved through surface modifications. Although adaptions in mechanical strength still require alterations in order to be applied to human-tendon ruptures, we are optimistic that a suitable implant can be designed.
Screening of Pandemic Response Box Library Reveals the High Activity of Olorofim against Pathogenic Sporothrix Species
Authors: Borba-Santos Luana Pereira , Rollin-Pinheiro Rodrigo , da Silva Fontes Yasmin , dos Santos Giulia Maria Pires , de Sousa Araújo Glauber Ribeiro , Rodrigues Anderson Messias , Guimarães Allan J. , de Souza Wanderley , Frases Susana , Ferreira-Pereira Antonio , Barreto-Bergter Eliana , Rozental Sonia
Published: September 2022

The increase in the prevalence and severity of fungal infections and the resistance to available antifungals highlights the imperative need for novel therapeutics and the search for new targets. High-content screening of libraries containing hundreds of compounds is a powerful strategy for searching for new drug candidates. In this study, we screened the Pandemic Response Box library (Medicines for Malaria Venture) of 400 diverse molecules against the Sporothrix pathogenic species. The initial screen identified twenty-four candidates that inhibited the growth of Sporothrix brasiliensis by more than 80%. Some of these compounds are known to display antifungal activity, including olorofim (MMV1782354), a new antifungal drug. Olorofim inhibited and killed the yeasts of S. brasiliensis, S. schenckii, and S. globosa at concentrations lower than itraconazole, and it also showed antibiofilm activity. According to the results obtained by fluorimetry, electron microscopy, and particle characterization analyses, we observed that olorofim induced profound alterations on the cell surface and cell cycle arrest in S. brasiliensis yeasts. We also verified that these morphophysiological alterations impaired their ability to adhere to keratinocytes in vitro. Our results indicate that olorofim is a promising new antifungal against sporotrichosis agents.
Silver Nanoparticles Prepared Using Encephalartos laurentianus De Wild Leaf Extract Have Inhibitory Activity against Candida albicans Clinical Isolates
Authors: Alherz Fatemah A. , Negm Walaa A. , Elekhnawy Engy , El-Masry Thanaa A. , Haggag Eman M. , Alqahtani Moneerah J. , Hussein Ismail A.
Published: September 2022

Candida albicans is a major human opportunistic pathogen causing infections, which range from cutaneous to invasive systemic infections. Herein, the antifungal and anti-biofilm potential of silver nanoparticles (AgNPs) green synthesized in the presence of Encephalartos laurentianus leaf extract (ELLE) were investigated. The bioactive chemicals of ELLE, including phenolics, flavonoids, and glycosides were identified and quantified for the first time. AgNPs showed minimum inhibitory concentration (MIC) values against C. albicans clinical isolates ranging from 8 to 256 µg/mL. In addition, AgNPs significantly decreased biofilm formation. The impact of AgNPs on the expression of the genes encoding biofilm formation was assessed using qRT-PCR. AgNPs had a beneficial role in the macroscopic wound healing, and they resulted in complete epithelization without any granulation tissue or inflammation. Treatment with AgNPs resulted in negative immunostaining of tumor necrosis factor-α. The levels of the inflammation markers, interleukin-6 and interleukin-1β, significantly decreased (p < 0.05) in the AgNPs-treated group. There was also a pronounced increase in the gene expression of fibronectin and platelet-derived growth factor in the wound tissues. Thus, AgNPs synthesized using ELLE may be a promising antifungal and wound healing agent.
Risk Assessment of Heavy Metals Occurrence in Two Wild Edible Oyster Mushrooms (Pleurotus spp.) Collected from Rajaji National Park
Authors: Širić Ivan , Kumar Pankaj , Adelodun Bashir , Abou Fayssal Sami , Bachheti Rakesh Kumar , Bachheti Archana , Ajibade Fidelis O. , Kumar Vinod , Taher Mostafa A. , Eid Ebrahem M.
Published: September 2022

This study aimed at assessing the concentration of six heavy metals (Cd, Cr, Cu, Fe, Mn, and Zn) in two wild edible oyster mushrooms (Pleurotus ostreatus and Pleurotus djamor) collected from Rajaji National Park in Haridwar, India. For this purpose, mushroom samples were collected from selected locations (forest, residential, tourist, industrial areas, and transportation activities) from June 2021 to July 2022 and subsequently analyzed for selected heavy metals using atomic absorption spectroscopy (AAS). Results showed that both Pleurotus spp. had significantly varying (p < 0.05) concentrations of heavy metals. However, P. ostreatus showed relatively higher concentration levels of these metals compared to P. djamor. The mean concentrations (mg/kg dry weight) of the Cd, Cr, Cu, Fe, Mn, and Zn in P. ostreatus and P. djamor were 0.10 and 0.08, 0.87 and 0.64, 16.19 and 14.77, 28.49 and 27.15, 9.93 and 8.73, and 18.15 and 15.76, respectively. As indicated by the multivariate analysis tools i.e., principal component analysis (PCA) and hierarchical cluster analysis (HCA), the locations near the residential, industrial, and transportation activities had higher concentration levels of heavy metals. Moreover, the health risk studies using the target hazard quotient (THQ < 1) showed no significant health risk as the consumption of both Pleurotus spp., except for at one location, had high-traffic activities. The findings of this study provide vital information about the occurrence of potentially toxic heavy metals in wild edible Pleurotus spp. in Rajaji National Park in Haridwar, India representing a safeguard for mushroom consumers.