bluuebunny/crossref_metadata_2025 huggingface dataset:
Differentially Expressed Genes Involved in Primary Resistance to Immunotherapy in Patients with Advanced-Stage Pulmonary Cancer
Authors: Chinchilla-Tábora Luis Miguel , Montero Juan Carlos , Corchete Luis Antonio , González-Morais Idalia , del Barco Morillo Edel , Olivares-Hernández Alejandro , Rodríguez González Marta , Sayagués José María , Ludeña María Dolores
Published: February 2024

In the last few years, nivolumab has become the standard of care for advanced-stage lung cancer patients. Unfortunately, up to 60% of patients do not respond to this treatment. In our study, we identified variations in gene expression related to primary resistance to immunotherapy. Bronchoscopy biopsies were obtained from advanced non-small cell lung cancer (NSCLC) patients previously characterized as responders or non-responders after nivolumab treatment. Ten tumor biopsies (from three responders and seven non-responders) were analyzed by the differential expression of 760 genes using the NanoString nCounter platform. These genes are known to be involved in the response to anti-PD1/PD-L1 therapy. All the patients were treated with nivolumab. Examining the dysregulated expression of 24 genes made it possible to predict the response to nivolumab treatment. Supervised analysis of the gene expression profile (GEP) revealed that responder patients had significantly higher levels of expression of CXCL11, NT5E, KLRK1, CD3G, GZMA, IDO1, LCK, CXCL9, GNLY, ITGAL, HLA-DRB1, CXCR6, IFNG, CD8A, ITK, B2M, HLA-B, and HLA-A than did non-responder patients. In contrast, PNOC, CD19, TP73, ARG1, FCRL2, and PTGER1 genes had significantly lower expression levels than non-responder patients. These findings were validated as predictive biomarkers in an independent series of 201 patients treated with nivolumab (22 hepatocellular carcinomas, 14 non-squamous cell lung carcinomas, 5 head and neck squamous cell carcinomas, 1 ureter/renal pelvis carcinoma, 120 melanomas, 4 bladder carcinomas, 31 renal cell carcinomas, and 4 squamous cell lung carcinomas). ROC curve analysis showed that the expression levels of ITK, NT5E, ITGAL, and CD8A were the best predictors of response to nivolumab. Further, 13/24 genes showed an adverse impact on overall survival (OS) in an independent, large series of patients with NSCLC (2166 cases). In summary, we found a strong association between the global GEP of advanced NSCLC and the response to nivolumab. The classification of NSCLC patients based on GEP enabled us to identify those patients who genuinely benefited from treatment with immune checkpoint inhibitors (ICIs). We also demonstrated that abnormal expression of most of the markers comprising the genomic signature has an adverse influence on OS, making them significant markers for therapeutic decision-making. Additional prospective studies in larger series of patients are required to confirm the clinical utility of these biomarkers.
Novel Genetic and Phenotypic Expansion in Ameliorated PUF60-Related Disorders
Authors: Baum Emily , Huang Wenming , Vincent-Delorme Catherine , Brunelle Perrine , Antebi Adam , Dafsari Hormos Salimi
Published: February 2024

Heterozygous variants in the Poly(U) Binding Splicing Factor 60kDa gene (PUF60) have been associated with Verheij syndrome, which has the key features of coloboma, short stature, skeletal abnormalities, developmental delay, palatal abnormalities, and congenital heart and kidney defects. Here, we report five novel patients from unrelated families with PUF60-related disorders exhibiting novel genetic and clinical findings with three truncating variants, one splice-site variant with likely reduced protein expression, and one missense variant. Protein modeling of the patient’s missense variant in the PUF60 AlphaFold structure revealed a loss of polar bonds to the surrounding residues. Neurodevelopmental disorders were present in all patients, with variability in speech, motor, cognitive, social-emotional and behavioral features. Novel phenotypic expansions included movement disorders as well as immunological findings with recurrent respiratory, urinary and ear infections, atopic diseases, and skin abnormalities. We discuss the role of PUF60 in immunity with and without infection based on recent organismic and cellular studies. As our five patients showed less-severe phenotypes than classical Verheij syndrome, particularly with the absence of key features such as coloboma or palatal abnormalities, we propose a reclassification as PUF60-related neurodevelopmental disorders with multi-system involvement. These findings will aid in the genetic counseling of patients and families.
Identification and Analysis of PEPC Gene Family Reveals Functional Diversification in Orchidaceae and the Regulation of Bacterial-Type PEPC
Authors: Li Ruyi , Gao Xuyong , Wu Yuwei , Wei Chunyi , Li Ming-He , Liu Ding-Kun , Liu Zhong-Jian
Published: February 2024

Phosphoenolpyruvate carboxylase (PEPC) gene family plays a crucial role in both plant growth and response to abiotic stress. Approximately half of the Orchidaceae species are estimated to perform CAM pathway, and the availability of sequenced orchid genomes makes them ideal subjects for investigating the PEPC gene family in CAM plants. In this study, a total of 33 PEPC genes were identified across 15 orchids. Specifically, one PEPC gene was found in Cymbidium goeringii and Platanthera guangdongensis; two in Apostasia shenzhenica, Dendrobium chrysotoxum, D. huoshanense, Gastrodia elata, G. menghaiensis, Phalaenopsis aphrodite, Ph. equestris, and Pl. zijinensis; three in C. ensifolium, C. sinense, D. catenatum, D. nobile, and Vanilla planifolia. These PEPC genes were categorized into four subgroups, namely PEPC-i, PEPC-ii, and PEPC-iii (PTPC), and PEPC-iv (BTPC), supported by the comprehensive analyses of their physicochemical properties, motif, and gene structures. Remarkably, PEPC-iv contained a heretofore unreported orchid PEPC gene, identified as VpPEPC4. Differences in the number of PEPC homolog genes among these species were attributed to segmental duplication, whole-genome duplication (WGD), or gene loss events. Cis-elements identified in promoter regions were predominantly associated with light responsiveness, and circadian-related elements were observed in each PEPC-i and PEPC-ii gene. The expression levels of recruited BTPC, VpPEPC4, exhibited a lower expression level than other VpPEPCs in the tested tissues. The expression analyses and RT-qPCR results revealed diverse expression patterns in orchid PEPC genes. Duplicated genes exhibited distinct expression patterns, suggesting functional divergence. This study offered a comprehensive analysis to unveil the evolution and function of PEPC genes in Orchidaceae.
Differential Immunogenicity and Lung Disease-Inducing Potential of Mycobacterium immunogenum Genotypes and Impact of Co-Exposure with Pseudomonas: Optimizing a Mouse Model of Chronic Hypersensitivity Pneumonitis
Authors: Johansson Elisabet , Yadav Jagjit S.
Published: February 2024

Mycobacterium immunogenum (MI) colonizing metalworking fluids (MWFs) has been associated with chronic hypersensitivity pneumonitis (HP) in machinists. However, it is etiologically unclear why only certain mycobacteria-contaminated fluids induce this interstitial lung disease. We hypothesized that this may be due to differential immunogenicity and the HP-inducing potential of MI strains/genotypes as well as the confounding effect of co-inhaled endotoxin-producers. To test this hypothesis, we optimized a chronic HP mouse model in terms of MI antigen dose, timepoint of sacrifice, and form of antigen (cell lysates vs. live cells) and compared six different field-isolated MI strains. Overall, MJY10 was identified as the most immunogenic and MJY4 (or MJY13) as the least immunogenic genotype based on lung pathoimmunological changes as well as Th1 cellular response (IFN-γ release). Infection with MI live cells induced a more severe phenotype than MI cell lysate. Co-exposure with Pseudomonas fluorescens caused a greater degree of lung innate immune response and granuloma formation but a diminished adaptive (Th1) immune response (IFN-γ) in the lung and spleen. In summary, this study led to the first demonstration of differential immunogenicity and the disease-inducing potential of field strains of MI and an interfering effect of the co-contaminating Pseudomonas. The improved chronic MI-HP mouse model and the identified polar pair of MI strains will facilitate future diagnostic and therapeutic research on this poorly understood environmental lung disease.
In-Silico Identification of Novel Pharmacological Synergisms: The Trabectedin Case
Authors: Mannarino Laura , Ravasio Nicholas , D’Incalci Maurizio , Marchini Sergio , Masseroli Marco
Published: February 2024

The in-silico strategy of identifying novel uses for already existing drugs, known as drug repositioning, has enhanced drug discovery. Previous studies have shown a positive correlation between expression changes induced by the anticancer agent trabectedin and those caused by irinotecan, a topoisomerase I inhibitor. Leveraging the availability of transcriptional datasets, we developed a general in-silico drug-repositioning approach that we applied to investigate novel trabectedin synergisms. We set a workflow allowing the identification of genes selectively modulated by a drug and possible novel drug interactions. To show its effectiveness, we selected trabectedin as a case-study drug. We retrieved eight transcriptional cancer datasets including controls and samples treated with trabectedin or its analog lurbinectedin. We compared gene signature associated with each dataset to the 476,251 signatures from the Connectivity Map database. The most significant connections referred to mitomycin-c, topoisomerase II inhibitors, a PKC inhibitor, a Chk1 inhibitor, an antifungal agent, and an antagonist of the glutamate receptor. Genes coherently modulated by the drugs were involved in cell cycle, PPARalpha, and Rho GTPases pathways. Our in-silico approach for drug synergism identification showed that trabectedin modulates specific pathways that are shared with other drugs, suggesting possible synergisms.
Identification and Molecular Characterization of the CAMTA Gene Family in Solanaceae with a Focus on the Expression Analysis of Eggplant Genes under Cold Stress
Authors: Cai Peng , Lan Yanhong , Gong Fangyi , Li Chun , Xia Feng , Li Yifan , Fang Chao
Published: February 2024

Calmodulin-binding transcription activator (CAMTA) is an important calmodulin-binding protein with a conserved structure in eukaryotes which is widely involved in plant stress response, growth and development, hormone signal transduction, and other biological processes. Although CAMTA genes have been identified and characterized in many plant species, a systematic and comprehensive analysis of CAMTA genes in the Solanaceae genome is performed for the first time in this study. A total of 28 CAMTA genes were identified using bioinformatics tools, and the biochemical/physicochemical properties of these proteins were investigated. CAMTA genes were categorized into three major groups according to phylogenetic analysis. Tissue-expression profiles indicated divergent spatiotemporal expression patterns of SmCAMTAs. Furthermore, transcriptome analysis of SmCAMTA genes showed that exposure to cold induced differential expression of many eggplant CAMTA genes. Yeast two-hybrid and bimolecular fluorescent complementary assays suggested an interaction between SmCAMTA2 and SmERF1, promoting the transcription of the cold key factor SmCBF2, which may be an important mechanism for plant cold resistance. In summary, our results provide essential information for further functional research on Solanaceae family genes, and possibly other plant families, in the determination of the development of plants.
GATOR1 Mutations Impair PI3 Kinase-Dependent Growth Factor Signaling Regulation of mTORC1
Authors: Muller Maéline , Bélanger Jasmine , Hadj-Aissa Imane , Zhang Conghao , Sephton Chantelle F. , Dutchak Paul A.
Published: February 2024

GATOR1 (GAP Activity TOward Rag 1) is an evolutionarily conserved GTPase-activating protein complex that controls the activity of mTORC1 (mammalian Target Of Rapamycin Complex 1) in response to amino acid availability in cells. Genetic mutations in the GATOR1 subunits, NPRL2 (nitrogen permease regulator-like 2), NPRL3 (nitrogen permease regulator-like 3), and DEPDC5 (DEP domain containing 5), have been associated with epilepsy in humans; however, the specific effects of these mutations on GATOR1 function and mTORC1 regulation are not well understood. Herein, we report that epilepsy-linked mutations in the NPRL2 subunit of GATOR1, NPRL2-L105P, -T110S, and -D214H, increase basal mTORC1 signal transduction in cells. Notably, we show that NPRL2-L105P is a loss-of-function mutation that disrupts protein interactions with NPRL3 and DEPDC5, impairing GATOR1 complex assembly and resulting in high mTORC1 activity even under conditions of amino acid deprivation. Furthermore, our studies reveal that the GATOR1 complex is necessary for the rapid and robust inhibition of mTORC1 in response to growth factor withdrawal or pharmacological inhibition of phosphatidylinositol-3 kinase (PI3K). In the absence of the GATOR1 complex, cells are refractory to PI3K-dependent inhibition of mTORC1, permitting sustained translation and restricting the nuclear localization of TFEB, a transcription factor regulated by mTORC1. Collectively, our results show that epilepsy-linked mutations in NPRL2 can block GATOR1 complex assembly and restrict the appropriate regulation of mTORC1 by canonical PI3K-dependent growth factor signaling in the presence or absence of amino acids.
Comparative Transcriptome Analysis Reveals the Genes and Pathways Related to Wheat Root Hair Length
Authors: Zeng Jianbin , Wang Yongmei , Wu Gang , Sun Qingyi , He Xiaoyan , Zhang Xinyi , Sun Xuelian , Zhao Yan , Liu Wenxing , Xu Dengan , Dai Xuehuan , Ma Wujun
Published: February 2024

Tube-like outgrowths from root epidermal cells, known as root hairs, enhance water and nutrient absorption, facilitate microbial interactions, and contribute to plant anchorage by expanding the root surface area. Genetically regulated and strongly influenced by environmental conditions, longer root hairs generally enhance water and nutrient absorption, correlating with increased stress resistance. Wheat, a globally predominant crop pivotal for human nutrition, necessitates the identification of long root hair genotypes and their regulatory genes to enhance nutrient capture and yield potential. This study focused on 261 wheat samples of diverse genotypes during germination, revealing noticeable disparities in the length of the root hair among the genotypes. Notably, two long root hair genotypes (W106 and W136) and two short root hair genotypes (W90 and W100) were identified. Transcriptome sequencing resulted in the development of 12 root cDNA libraries, unveiling 1180 shared differentially expressed genes (DEGs). Further analyses, including GO function annotation, KEGG enrichment, MapMan metabolic pathway analysis, and protein–protein interaction (PPI) network prediction, underscored the upregulation of root hair length regulatory genes in the long root hair genotypes. These included genes are associated with GA and BA hormone signaling pathways, FRS/FRF and bHLH transcription factors, phenylpropanoid, lignin, lignan secondary metabolic pathways, the peroxidase gene for maintaining ROS steady state, and the ankyrin gene with diverse biological functions. This study contributes valuable insights into modulating the length of wheat root hair and identifies candidate genes for the genetic improvement of wheat root traits.
Hijacking 5-Fluorouracil Chemoresistance in Triple Negative Breast Cancer via microRNAs-Loaded Chitosan Nanoparticles
Authors: Fahmy Sherif Ashraf , Mahdy Noha Khalil , Mohamed Adham H. , Mokhtar Fatma A. , Youness Rana A.
Published: February 2024

Chemotherapy is still the mainstay of treatment for triple-negative breast cancer (TNBC) patients. Yet only 20% of TNBC patients show a pathologic complete response (pCR) after neoadjuvant chemotherapy. 5-Fluorouracil (5-FU) is a stable cornerstone in all recommended chemotherapeutic protocols for TNBC patients. However, TNBC patients’ innate or acquired chemoresistance rate for 5-FU is steeply escalating. This study aims to unravel the mechanism behind the chemoresistance of 5-FU in the aggressive TNBC cell line, MDA-MB-231 cells, to explore further the role of the tumor suppressor microRNAs (miRNAs), miR-1275, miR-615-5p, and Let-7i, in relieving the 5-FU chemoresistance in TNBC, and to finally provide a translational therapeutic approach to co-deliver 5-FU and the respective miRNA oligonucleotides using chitosan-based nanoparticles (CsNPs). In this regard, cellular viability and proliferation were investigated using MTT and BrdU assays, respectively. 5-FU was found to induce JAK/STAT and PI3K/Akt/mTOR pathways in MDA-MB-231 cells with contaminant repression of their upstream regulators miR-1275, miR-615-5p, and Let-7i. Moreover, CsNPs prepared using the ionic gelation method were chosen and studied as nanovectors of 5-FU and a combination of miRNA oligonucleotides targeting TNBC. The average particle sizes, surface charges, and morphologies of the different CsNPs were characterized using dynamic light scattering (DLS) and transmission electron microscopy (TEM), respectively. In addition, the encapsulation efficiency (EE%), drug loading capacity (DLC%), and release manner at two different pH values were assessed. In conclusion, the novel CsNPs co-loaded with 5-FU and the combination of the three miRNA oligonucleotides demonstrated synergistic activity and remarkable repression in cellular viability and proliferation of TNBC cells through alleviating the chemoresistance to 5-FU.
Cell Membrane-Coated Nanoparticles for Precision Medicine: A Comprehensive Review of Coating Techniques for Tissue-Specific Therapeutics
Authors: Fernández-Borbolla Andrés , García-Hevia Lorena , Fanarraga Mónica L.
Published: February 2024

Nanoencapsulation has become a recent advancement in drug delivery, enhancing stability, bioavailability, and enabling controlled, targeted substance delivery to specific cells or tissues. However, traditional nanoparticle delivery faces challenges such as a short circulation time and immune recognition. To tackle these issues, cell membrane-coated nanoparticles have been suggested as a practical alternative. The production process involves three main stages: cell lysis and membrane fragmentation, membrane isolation, and nanoparticle coating. Cell membranes are typically fragmented using hypotonic lysis with homogenization or sonication. Subsequent membrane fragments are isolated through multiple centrifugation steps. Coating nanoparticles can be achieved through extrusion, sonication, or a combination of both methods. Notably, this analysis reveals the absence of a universally applicable method for nanoparticle coating, as the three stages differ significantly in their procedures. This review explores current developments and approaches to cell membrane-coated nanoparticles, highlighting their potential as an effective alternative for targeted drug delivery and various therapeutic applications.
The Immunoregulatory and Regenerative Potential of Activated Human Stem Cell Secretome Mitigates Acute-on-Chronic Liver Failure in a Rat Model
Authors: Cuadra Barbara , Silva Veronica , Huang Ya-Lin , Diaz Yael , Rivas Claudio , Molina Cristobal , Simon Valeska , Bono Maria Rosa , Morales Bernardo , Rosemblatt Mario , Silva Sebastian , Acuña Rodrigo , Ezquer Fernando , Ezquer Marcelo
Published: February 2024

Acute-on-chronic liver failure (ACLF) is a syndrome marked by sudden liver function decline and multiorgan failure, predominantly acute kidney injury (AKY), in patients with chronic liver disease. Unregulated inflammation is a hallmark of ACLF; however, the key drivers of ACLF are not fully understood. This study explores the therapeutic properties of human mesenchymal stem cell (MSC) secretome, particularly focusing on its enhanced anti-inflammatory and pro-regenerative properties after the in vitro preconditioning of the cells. We evaluated the efficacy of the systemic administration of MSC secretome in preventing liver failure and AKI in a rat ACLF model where chronic liver disease was induced using by the administration of porcine serum, followed by D-galN/LPS administration to induce acute failure. After ACLF induction, animals were treated with saline (ACLF group) or MSC-derived secretome (ACLF-secretome group). The study revealed that MSC-secretome administration strongly reduced liver histological damage in the ACLF group, which was correlated with higher hepatocyte proliferation, increased hepatic and systemic anti-inflammatory molecule levels, and reduced neutrophil and macrophage infiltration. Additionally, renal examination revealed that MSC-secretome treatment mitigated tubular injuries, reduced apoptosis, and downregulated injury markers. These improvements were linked to increased survival rates in the ACLF-secretome group, endorsing MSC secretomes as a promising therapy for multiorgan failure in ACLF.
New Obolenskvirus Phages Brutus and Scipio: Biology, Evolution, and Phage-Host Interaction
Authors: Evseev Peter V. , Shneider Mikhail M. , Kolupaeva Lyubov V. , Kasimova Anastasia A. , Timoshina Olga Y. , Perepelov Andrey V. , Shpirt Anna M. , Shelenkov Andrey A. , Mikhailova Yulia V. , Suzina Natalia E. , Knirel Yuriy A. , Miroshnikov Konstantin A. , Popova Anastasia V.
Published: February 2024

Two novel virulent phages of the genus Obolenskvirus infecting Acinetobacter baumannii, a significant nosocomial pathogen, have been isolated and studied. Phages Brutus and Scipio were able to infect A. baumannii strains belonging to the K116 and K82 capsular types, respectively. The biological properties and genomic organization of the phages were characterized. Comparative genomic, phylogenetic, and pangenomic analyses were performed to investigate the relationship of Brutus and Scipio to other bacterial viruses and to trace the possible origin and evolutionary history of these phages and other representatives of the genus Obolenskvirus. The investigation of enzymatic activity of the tailspike depolymerase encoded in the genome of phage Scipio, the first reported virus infecting A. baumannii of the K82 capsular type, was performed. The study of new representatives of the genus Obolenskvirus and mechanisms of action of depolymerases encoded in their genomes expands knowledge about the diversity of viruses within this taxonomic group and strategies of Obolenskvirus–host bacteria interaction.
Recent Trends in Non-Invasive Methods of Diagnosis and Evaluation of Inflammatory Bowel Disease: A Short Review
Authors: Vălean Dan , Zaharie Roxana , Țaulean Roman , Usatiuc Lia , Zaharie Florin
Published: February 2024

Inflammatory bowel diseases are a conglomerate of disorders causing inflammation of the gastrointestinal tract, which have gained a significant increase in prevalence in the 21st century. As they present a challenge in the terms of diagnosis as well as treatment, IBDs can present an overwhelming impact on the individual and can take a toll on healthcare costs. Thus, a quick and precise diagnosis is required in order to prevent the high number of complications that can arise from a late diagnosis as well as a misdiagnosis. Although endoscopy remains the primary method of evaluation for IBD, recent trends have highlighted various non-invasive methods of diagnosis as well as reevaluating previous ones. This review focused on the current non-invasive methods in the diagnosis of IBD, exploring their possible implementation in the near future, with the goal of achieving earlier, feasible, and cheap methods of diagnosis as well as prognosis in IBD.
Glut-3 Gene Knockdown as a Potential Strategy to Overcome Glioblastoma Radioresistance
Authors: Pucci Gaia , Minafra Luigi , Bravatà Valentina , Calvaruso Marco , Turturici Giuseppina , Cammarata Francesco P. , Savoca Gaetano , Abbate Boris , Russo Giorgio , Cavalieri Vincenzo , Forte Giusi I.
Published: February 2024

The hypoxic pattern of glioblastoma (GBM) is known to be a primary cause of radioresistance. Our study explored the possibility of using gene knockdown of key factors involved in the molecular response to hypoxia, to overcome GBM radioresistance. We used the U87 cell line subjected to chemical hypoxia generated by CoCl2 and exposed to 2 Gy of X-rays, as single or combined treatments, and evaluated gene expression changes of biomarkers involved in the Warburg effect, cell cycle control, and survival to identify the best molecular targets to be knocked-down, among those directly activated by the HIF-1α transcription factor. By this approach, glut-3 and pdk-1 genes were chosen, and the effects of their morpholino-induced gene silencing were evaluated by exploring the proliferative rates and the molecular modifications of the above-mentioned biomarkers. We found that, after combined treatments, glut-3 gene knockdown induced a greater decrease in cell proliferation, compared to pdk-1 gene knockdown and strong upregulation of glut-1 and ldha, as a sign of cell response to restore the anaerobic glycolysis pathway. Overall, glut-3 gene knockdown offered a better chance of controlling the anaerobic use of pyruvate and a better proliferation rate reduction, suggesting it is a suitable silencing target to overcome radioresistance.
The Effects of Acid on Calcium and Phosphate Metabolism
Authors: Salcedo-Betancourt Juan D. , Moe Orson W.
Published: February 2024

A variety of changes in mineral metabolism aiming to restore acid–base balance occur in acid loading and metabolic acidosis. Phosphate plays a key role in defense against metabolic acidosis, both as an intracellular and extracellular buffer, as well as in the renal excretion of excess acid in the form of urinary titratable acid. The skeleton acts as an extracellular buffer in states of metabolic acidosis, as the bone matrix demineralizes, leading to bone apatite dissolution and the release of phosphate, calcium, carbonate, and citrate into the circulation. The renal handling of calcium, phosphate and citrate is also affected, with resultant hypercalciuria, hyperphosphaturia and hypocitraturia.
Impaired Mitochondrial Function and Marrow Failure in Patients Carrying a Variant of the SRSF4 Gene
Authors: Miano Maurizio , Bertola Nadia , Grossi Alice , Dell’Orso Gianluca , Regis Stefano , Rusmini Marta , Uva Paolo , Vozzi Diego , Fioredda Francesca , Palmisani Elena , Lupia Michela , Lanciotti Marina , Grilli Federica , Corsolini Fabio , Arcuri Luca , Giarratana Maria Carla , Ceccherini Isabella , Dufour Carlo , Cappelli Enrico , Ravera Silvia
Published: February 2024

Serine/arginine-rich splicing factors (SRSFs) are a family of proteins involved in RNA metabolism, including pre-mRNA constitutive and alternative splicing. The role of SRSF proteins in regulating mitochondrial activity has already been shown for SRSF6, but SRSF4 altered expression has never been reported as a cause of bone marrow failure. An 8-year-old patient admitted to the hematology unit because of leukopenia, lymphopenia, and neutropenia showed a missense variant of unknown significance of the SRSF4 gene (p.R235W) found via whole genome sequencing analysis and inherited from the mother who suffered from mild leuko-neutropenia. Both patients showed lower SRSF4 protein expression and altered mitochondrial function and energetic metabolism in primary lymphocytes and Epstein–Barr-virus (EBV)-immortalized lymphoblasts compared to healthy donor (HD) cells, which appeared associated with low mTOR phosphorylation and an imbalance in the proteins regulating mitochondrial biogenesis (i.e., CLUH) and dynamics (i.e., DRP1 and OPA1). Transfection with the wtSRSF4 gene restored mitochondrial function. In conclusion, this study shows that the described variant of the SRSF4 gene is pathogenetic and causes reduced SRSF4 protein expression, which leads to mitochondrial dysfunction. Since mitochondrial function is crucial for hematopoietic stem cell maintenance and some genetic bone marrow failure syndromes display mitochondrial defects, the SRSF4 mutation could have substantially contributed to the clinical phenotype of our patient.
The Effects of Fucoidan Derived from Sargassum filipendula and Fucus vesiculosus on the Survival and Mineralisation of Osteogenic Progenitors
Authors: Gupta Dhanak , Martinez Diana C. , Puertas-Mejía Miguel Angel , Hearnden Vanessa L. , Reilly Gwendolen C.
Published: February 2024

Osteosarcoma is a bone cancer primarily affecting teenagers. It has a poor prognosis and diminished quality of life after treatment due to chemotherapy side effects, surgical complications and post-surgical osteoporosis risks. The sulphated polysaccharide fucoidan, derived from brown algae, has been a subject of interest for its potential anti-cancer properties and its impact on bone regeneration. This study explores the influence of crude, low-molecular-weight (LMW, 10–50 kDa), medium-molecular-weight (MMW, 50–100 kDa) and high-molecular-weight (HMW, >100 kDa) fractions from Sargassum filipendula, harvested from the Colombian sea coast, as well as crude fucoidan from Fucus vesiculosus, on a specific human osteoprogenitor cell type, human embryonic-derived mesenchymal stem cells. Fourier transform infrared spectroscopy coupled with attenuated total reflection (FTIR-ATR) results showed the highest sulphation levels and lowest uronic acid content in crude extract from F. vesiculosus. There was a dose-dependent drop in focal adhesion formation, proliferation and osteogenic differentiation of cells for all fucoidan types, but the least toxicity was observed for LMW and MMW. Transmission electron microscopy (TEM), JC-1 (5,50,6,60-tetrachloro-1,10,3,30-tetraethylbenzimi-dazolylcarbocyanine iodide) staining and cytochrome c analyses confirmed mitochondrial damage, swollen ER and upregulated autophagy due to fucoidans, with the highest severity in the case of F. vesiculosus fucoidan. Stress-induced apoptosis-like cell death by F. vesiculosus fucoidan and stress-induced necrosis-like cell death by S. filipendula fucoidans were also confirmed. LMW and MMW doses of <200 ng/mL were the least toxic and showed potential osteoinductivity. This research underscores the multifaceted impact of fucoidans on osteoprogenitor cells and highlights the delicate balance between potential therapeutic benefits and the challenges involved in using fucoidans for post-surgery treatments in patients with osteosarcoma.
SARS-CoV-2 Infection Alters the Phenotype and Gene Expression of Adipocytes
Authors: Quaranta Paola , Scabia Gaia , Storti Barbara , Dattilo Alessia , Quintino Lara , Perrera Paola , Di Primio Cristina , Costa Mario , Pistello Mauro , Bizzarri Ranieri , Maffei Margherita
Published: February 2024

Epidemiological evidence emphasizes that excess fat mass is associated with an increased risk of severe COVID-19 disease. Nevertheless, the intricate interplay between SARS-CoV-2 and adipocytes remains poorly understood. It is crucial to decipher the progression of COVID-19 both in the acute phase and on long-term outcomes. In this study, an in vitro model using the human SGBS cell line (Simpson-Golabi-Behmel syndrome) was developed to investigate the infectivity of SARS-CoV-2 in adipocytes, and the effects of virus exposure on adipocyte function. Our results show that SGBS adipocytes expressing ACE2 are susceptible to SARS-CoV-2 infection, as evidenced by the release of the viral genome into the medium, detection of the nucleocapsid in cell lysates, and positive immunostaining for the spike protein. Infected adipocytes show remarkable changes compared to uninfected controls: increased surface area of lipid droplets, upregulated expression of genes of inflammation (Haptoglobin, MCP-1, IL-6, PAI-1), increased oxidative stress (MnSOD), and a concomitant reduction of transcripts related to adipocyte function (leptin, fatty acid synthase, perilipin). Moreover, exogenous expression of spike protein in SGBS adipocytes also led to an increase in lipid droplet size. In conclusion using the human SGBS cell line, we detected SARS-CoV-2 infectivity in adipocytes, revealing substantial morphological and functional changes in infected cells.
Strong Activity and No Resistance Induction Exerted by Cell-Free Supernatants from Lacticaseibacillus rhamnosus against Mono-Species and Dual-Species Biofilms of Wound Pathogens in In Vivo-like Conditions
Authors: Kaya Esingül , Bianchi Marta , Maisetta Giuseppantonio , Esin Semih , Batoni Giovanna
Published: February 2024

It is widely agreed that microbial biofilms play a major role in promoting infection and delaying healing of chronic wounds. In the era of microbial resistance, probiotic strains or their metabolic products are emerging as an innovative approach for the treatment of hard-to-heal (chronic) wounds due to their antimicrobial, healing, and host immune-modulatory effects. In this study, we aimed to investigate the potential of cell-free supernatants (CFS) from Lacticaseibacillus rhamnosus GG against mono- and dual-species biofilms of wound pathogens in a 3D in vitro infection model. Mature biofilms of Pseudomonas aeruginosa and Staphylococcus aureus were obtained on collagen scaffolds in the presence of a simulant wound fluid (SWF) and treated with CFS at different doses and time intervals. At 1:4 dilution in SWF, CFS caused a marked reduction in the colony forming-unit (CFU) numbers of bacteria embedded in mono-species biofilms as well as bacteria released by the biofilms in the supernatant. CFU count and electron microscopy imaging also demonstrated a marked antibiofilm effect against dual-species biofilms starting from 8 h of incubation. Furthermore, CFS exhibited acceptable levels of cytotoxicity at 24 h of incubation against HaCaT cells and, differently from ciprofloxacin, failed to induce resistance after 15 passages at sub-inhibitory concentrations. Overall, the results obtained point to L. rhamnosus GG postbiotics as a promising strategy for the treatment of wound biofilms.
Long-Term Effects of Tolvaptan in Autosomal Dominant Polycystic Kidney Disease: Predictors of Treatment Response and Safety over 6 Years of Continuous Therapy
Authors: Yamazaki Mai , Kawano Haruna , Miyoshi Miho , Kimura Tomoki , Takahashi Keiji , Muto Satoru , Horie Shigeo
Published: February 2024

Tolvaptan, an oral vasopressin V2 receptor antagonist, reduces renal volume expansion and loss of renal function in patients with autosomal dominant polycystic kidney disease (ADPKD). Data for predictive factors indicating patients more likely to benefit from long-term tolvaptan are lacking. Data were retrospectively collected from 55 patients on tolvaptan for 6 years. Changes in renal function, progression of renal dysfunction (estimated glomerular filtration rate [eGFR], 1-year change in eGFR [ΔeGFR/year]), and renal volume (total kidney volume [TKV], percentage 1-year change in TKV [ΔTKV%/year]) were evaluated at 3-years pre-tolvaptan, at baseline, and at 6 years. In 76.4% of patients, ΔeGFR/year improved at 6 years. The average 6-year ΔeGFR/year (range) minus baseline ΔeGFR/year: 3.024 (−8.77–20.58 mL/min/1.73 m2). The increase in TKV was reduced for the first 3 years. A higher BMI was associated with less of an improvement in ΔeGFR (p = 0.027), and family history was associated with more of an improvement in ΔeGFR (p = 0.044). Hypernatremia was generally mild; 3 patients had moderate-to-severe hyponatremia due to prolonged, excessive water intake in response to water diuresis—a side effect of tolvaptan. Family history of ADPKD and baseline BMI were contributing factors for ΔeGFR/year improvement on tolvaptan. Hyponatremia should be monitored with long-term tolvaptan administration.
Production of Medical Radionuclides in the Center for Radiopharmaceutical Tumor Research—A Status Report
Authors: Kreller Martin , Brühlmann Santiago Andrés , Knieß Torsten , Kopka Klaus , Walther Martin
Published: February 2024

A new Center for Radiopharmaceutical Cancer Research was established at the Helmholtz-Zentrum Dresden-Rossendorf in 2017 to centralize radionuclide and radiopharmaceutical production, as well as enable chemical and biochemical research. Routine production of several radionuclides was put into operation in recent years. We report on the production methods of radiopharmaceutical radionuclides, in particular 11C, 18F, and radio metals like 61Cu, 64Cu, 67Cu, 67Ga, 131Ba, and 133La that are used regularly. In the discussion, we report typical irradiation parameters and achieved saturation yields.
Modeling of a Process Window for Tailored Reinforcements in Overmolding Processes
Authors: Picard Philipp K. W. , Osswald Tim A. , Zaremba Swen , Drechsler Klaus
Published: February 2024

This study explores cost-effective and customized composite applications by strategically placing carbon fiber-reinforced thermoplastics in multi-material designs. The focus is on developing a model for the simultaneous processing of non-reinforced and reinforced thermoplastic layers, with the aim of identifying essential parameters to minimize insert flow and ensure desired fiber orientation and positional integrity. The analysis involves an analytical solution for two layered power-law fluids in a squeeze flow setup, aiming to model the combined flow behavior of Newtonian and pseudo-plastic fluids, highlighting the impact of the non-Newtonian nature. The behavior reveals a non-linear trend in the radial flow ratio towards the logarithmic consistency index ratio compared to a linear trend for Newtonian fluids. While a plateau regime of consistency index ratios presents challenges in flow reduction for both layers, exceeding this ratio, depending on the height ratio of the layers, enables a viable overmolding process. Therefore, attention is required when selectively placing tailored composites with long-fiber-reinforced thermoplastics or unidirectional reinforcements to avoid operating in the plateau region, which can be managed through appropriate cavity or tool designs.
Isolation and Identification of Acer truncatum Endophytic Fungus Talaromyces verruculosus and Evaluation of Its Effects on Insoluble Phosphorus Absorption Capacity and Growth of Cucumber Seedlings
Authors: Zeng Qingpan , Dong Jiawei , Lin Xiaoru , Zhou Xiaofu , Xu Hongwei
Published: February 2024

The symbiosis between endophytic fungi and plants can promote the absorption of potassium, nitrogen, phosphorus, and other nutrients by plants. Phosphorus is one of the indispensable nutrient elements for plant growth and development. However, the content of available phosphorus in soil is very low, which limits the growth of plants. Phosphorus-soluble microorganisms can improve the utilization rate of insoluble phosphorus. In this study, Talaromyces verruculosus (T. verruculosus), a potential phosphorus-soluble fungus, was isolated from Acer truncatum, a plant with strong stress resistance, and its phosphorus-soluble ability in relation to cucumber seedlings under different treatment conditions was determined. In addition, the morphological, physiological, and biochemical indexes of the cucumber seedlings were assessed. The results show that T. verruculosus could solubilize tricalcium phosphate (TCP) and lecithin, and the solubilization effect of lecithin was higher than that of TCP. After the application of T. verruclosus, the leaf photosynthetic index increased significantly. The photosynthetic system damage caused by low phosphorus stress was alleviated, and the root morphological indexes of cucumber seedlings were increased. The plant height, stem diameter, and leaf area of cucumber seedlings treated with T. verruculosus were also significantly higher than those without treatment. Therefore, it was shown that T. verruculosus is a beneficial endophytic fungus that can promote plant growth and improve plant stress resistance. This study will provide a useful reference for further research on endophytic fungi to promote growth and improve plant stress resistance.
Establishment of an Efficient Genetic Transformation System in Sanghuangporus baumii
Authors: Wang Xutong , Wang Mandi , Sun Jian , Qu Xiaolei , Wang Shixin , Sun Tingting
Published: February 2024

(1) Background: Sanghuangporus baumii, a valuable medicinal fungus, has limited studies on its gene function due to the lack of a genetic transformation system. (2) Methods: This study aimed to establish an efficient Agrobacterium tumefaciens-mediated transformation (ATMT) system for S. baumii. This study involved cloning the promoter (glyceraldehyde-3-phosphate dehydrogenase, gpd) of S. baumii, reconstructing the transformation vector, optimizing the treatment of receptor tissues, and inventing a new method for screening positive transformants. (3) Results: The established ATMT system involved replacing the CaMV35S promoter of pCAMBIA-1301 with the gpd promoter of S. baumii to construct the pCAMBIA-SH-gpd transformation vector. The vectors were then transferred to A. tumefaciens (EHA105) for infection. This study found that the transformation efficiency was higher in the infection using pCAMBIA-SH-gpd vectors than using pCAMBIA-1301 vectors. The mycelia of S. baumii were homogenized for 20 s and collected as the genetic transformation receptor. After 20 min of co-culture and 48 h of incubation in 15 mL PDL medium at 25 °C, new colonies grew. (4) Conclusions: These colonies were transferred to PDA medium (hygromycin 4 μg/mL, cefotaxime 300 μg/mL), and the transformation efficiency was determined to be 33.7% using PCR.
The Effect of Colloidal Nanoparticles on Phase Separation of Block and Heteroarm Star Copolymers Confined between Polymer Brushes
Authors: Sun Minna , Chen Wenyu , Qin Lei , Xie Xu-Ming
Published: February 2024

The effect of colloidal nanoparticles on the phase changes of the amphiphilic AB linear diblock, A1A2B, and A2B heteroarm star copolymers confined between two polymer brush substrates was investigated by using a real-space self-consistent field theory. By changing the concentrations of nanoparticles and polymer brushes, the phase structure of the amphiphilic AB copolymer transforms from lamellar to core-shell hexagonal phase to cylinder phase. The pattern of A2B heteroarm star copolymer changes from core-shell hexagonal phases to lamellar phases and the layer decreases when increasing the density of the polymer brushes. The results showed that the phase behavior of the system is strongly influenced by the polymer brush architecture and the colloidal nanoparticle numbers. The colloidal nanoparticles and the soft confined surface of polymer brushes make amphiphilic AB copolymers easier to form ordered structures. The dispersion of the nanoparticles was also investigated in detail. The soft surfaces of polymer brushes and the conformation of the block copolymers work together to force the nanoparticles to disperse evenly. It will give helpful guidance for making some new functional materials by nano etching technology, nano photoresist, and nanoprinting.
Investigation of Dynamic Behavior and Process Stability at Turning of Thin-Walled Tubular Workpieces Made of 42CrMo4 Steel Alloy
Authors: Mehdi Kamel , Monka Peter Pavol , Monkova Katarina , Sahraoui Zied , Glaa Nawel , Kascak Jakub
Published: February 2024

During machining, the surface of the machined materials is damaged and tool wear occurs, sometimes even to complete failure. Machining of thin-walled parts is generally cumbersome due to their low structural rigidity. The study deals with the effect of the feed rate and the thickness of the thin-walled part on the dynamic behavior and stability of the turning process during the roughing and finishing of thin-walled tubular workpieces made of steel alloy 42CrMo4. At the same time, the cutting forces and deformations of the workpiece were also evaluated via numerical and experimental approaches. The numerical study is based on a three-dimensional (3D) finite element model (FEM) developed using the ABAQUS/Explicit frame. In the model, the workpiece material is governed by the behavior law of Johnson–Cook. Numerical and experimental results show that the cutting forces and the quality of the machined surface depend not only on the choice of cutting parameters but also on the dynamic behavior of thin-walled parts due to their low rigidity and low structural damping during the machining operation. Cutting forces are proportional to the feed rate and inversely proportional to the thickness of the part. Their variations around the average values are low for roughing tests where the wall-part thickness is higher or equal to 3.5 mm. However, these variations intensify for finishing tests where the wall thickness is less or equal to 1.5 mm. Indeed, the recorded FFT spectra for a finishing operation show several harmonics that occurred at around 550 Hz, and the amplitude of the peaks, which describes the level of power contained in the signals, shows an increase similar to that of the amplitudes of the temporal signal. The flexibility of the part generates instability in the cutting process, but the frequencies of the vibrations are higher than the frequency of rotation of the part.
Unveiling the Black Box: A Unified XAI Framework for Signal-Based Deep Learning Models
Authors: Shojaeinasab Ardeshir , Jalayer Masoud , Baniasadi Amirali , Najjaran Homayoun
Published: February 2024

Condition monitoring (CM) is essential for maintaining operational reliability and safety in complex machinery, particularly in robotic systems. Despite the potential of deep learning (DL) in CM, its ‘black box’ nature restricts its broader adoption, especially in mission-critical applications. Addressing this challenge, our research introduces a robust, four-phase framework explicitly designed for DL-based CM in robotic systems. (1) Feature extraction utilizes advanced Fourier and wavelet transformations to enhance both the model’s accuracy and explainability. (2) Fault diagnosis employs a specialized Convolutional Long Short-Term Memory (CLSTM) model, trained on the features to classify signals effectively. (3) Model refinement uses SHAP (SHapley Additive exPlanation) values for pruning nonessential features, thereby simplifying the model and reducing data dimensionality. (4) CM interpretation develops a system offering insightful explanations of the model’s decision-making process for operators. This framework is rigorously evaluated against five existing fault diagnosis architectures, utilizing two distinct datasets: one involving torque measurements from a robotic arm for safety assessment and another capturing vibration signals from an electric motor with multiple fault types. The results affirm our framework’s superior optimization, reduced training and inference times, and effectiveness in transparently visualizing fault patterns.
An Exact Approach to the Multi-Compartment Vehicle Routing Problem: The Case of a Fuel Distribution Company
Authors: Baptista Guilherme , Vieira Miguel , Pinto Telmo
Published: February 2024

Over the years, the vehicle routing problem has been studied by several authors, creating several extensions, such as the multi-compartment vehicle routing problem. Several studies in the literature have addressed this problem, but few have solved it through exact approaches owing to model convolution. In this way, a mathematical model is proposed for the multi-compartment vehicle routing problem with time windows, in which three types of fuel products are distributed to a set of customers using a limited homogeneous fleet. The model explicitly considers time windows, as well as regulatory rest times for the drivers and time limits for each trip and for working schedules, addressing a real company’s decision support requirements, which is scarce in the literature. The optimal solution determines, for each vehicle, the distribution route and time to carry out the deliveries with the corresponding loading of products to compartments, complemented by the calculation of carbon emissions. The main objective is to minimize the total distance traveled, which corresponds to the sum of the distances traveled by each one of the allocated vehicles. The results allow the assessment of the solution optimization applied to a set of instances for a Portuguese company to evaluate the performance and compare decision support improvements with current baseline company procedures.