bluuebunny/crossref_metadata_2025 huggingface dataset:
Nigella sativa: A Comprehensive Review of Its Therapeutic Potential, Pharmacological Properties, and Clinical Applications
Authors: Alberts Adina , Moldoveanu Elena-Theodora , Niculescu Adelina-Gabriela , Grumezescu Alexandru Mihai
Published: December 2024

Nigella sativa (NS) is an annual herb belonging to the Ranunculaceae family, also known as black cumin or black seed. This plant has been used since ancient times due to its therapeutic properties and has proven effective in gastrointestinal, respiratory, cardiovascular, infectious, and inflammatory conditions. In this review, the aim is to highlight the therapeutic effects of the plant known in Arab countries as “the plant that cures any disease”, which are provided by the phytochemical compounds in its composition, such as thymoquinone, p-cymene, α-thujene, longifolene, β-pinene, α-pinene, and carvacrol. These compounds confer an antioxidant effect to the seeds, leading to a significant decrease in ROS and a potent anti-inflammatory effect. Also, in this review, the aim is to highlight that NS seeds may have a synergistic effect with other drugs, such as chemotherapeutic agents or antibiotics, which may lead to a reduction in the therapeutic dose, may have an improved effect, and could lead to overcoming obstacles such as drug resistance. The studies provided in this review showed that NS has the potential to be a therapeutic agent both as a monotherapy and as an adjuvant. Although there are studies demonstrating the therapeutic properties of NS, there is a need for much more extensive research and more clinical trials with clearly established objectives so that the mechanism of action of the active substances in NS is much better understood. With the data provided so far, NS can be used in food and drug production in small quantities and can be administered for short periods. Further investigations may lead to an understanding of the therapeutic profile and the most effective mode of administration, as well as a clearer perspective on the toxicological profile of NS.
Defects in the Mitochondrial Genome of Dogs with Recurrent Tumours
Authors: Kowal Krzysztof , Ziółkowska-Twarowska Kaja , Tkaczyk-Wlizło Angelika , Grzybowska-Szatkowska Ludmiła , Ślaska Brygida
Published: December 2024

This study presents a comprehensive analysis of mitochondrial DNA (mtDNA) variations in dogs diagnosed with primary and recurrent tumours, employing Oxford Nanopore Technologies (ONT) for sequencing. Our investigation focused on mtDNA extracted from blood and tumour tissues of three dogs, aiming to pinpoint polymorphisms, mutations, and heteroplasmy levels that could influence mitochondrial function in cancer pathogenesis. Notably, we observed the presence of mutations in the D-loop region, especially in the VNTR region, which may be crucial for mitochondrial replication, transcription, and genome stability, suggesting its potential role in cancer progression. The study is pioneering in its use of long-read sequencing to explore the mutational landscape of mtDNA in canine tumours, revealing that while the overall mutational load did not differ between primary and recurrent tumours, specific changes in m.16168A/G, m.16188G/A, and m.16298A/G are linked with tumour tissues. Interestingly, the heteroplasmy outside the D-loop region was not specific to tumour tissues and did not provoke any malignant damage in protein-coding sequences, which in turn may be a tolerant effect of the reactive oxygen species (ROS) cellular stress mechanism.
The Astragalus Membranaceus Herb Attenuates Leukemia by Inhibiting the FLI1 Oncogene and Enhancing Anti-Tumor Immunity
Authors: Yu Kunlin , Tang Yao , Wang Chunlin , Liu Wuling , Hu Maoting , Hu Anling , Kuang Yi , Zacksenhaus Eldad , Yu Xue-Zhong , Xiao Xiao , Ben-David Yaacov
Published: December 2024

Astragalus membranaceus (AM) herb is a component of traditional Chinese medicine used to treat various cancers. Herein, we demonstrate a strong anti-leukemic effect of AM injected (Ai) into the mouse model of erythroleukemia induced by Friend virus. Chemical analysis combined with mass spectrometry of AM/Ai identified the compounds Betulinic acid, Kaempferol, Hederagenin, and formononetin, all major mediators of leukemia inhibition in culture and in vivo. Docking analysis demonstrated binding of these four compounds to FLI1, resulting in downregulation of its targets, induction of apoptosis, differentiation, and suppression of cell proliferation. Chemical composition analysis identified other compounds previously known having anti-tumor activity independent of the FLI1 blockade. Among these, Astragaloside-A (As-A) has marginal effect on cells in culture, but strongly inhibits leukemogenesis in vivo, likely through improvement of anti-tumor immunity. Indeed, both IDO1 and TDO2 were identified as targets of As-A, leading to suppression of tryptophane-mediated Kyn production and leukemia suppression. Moreover, As-A interacts with histamine decarboxylase (HDC), leading to suppression of anti-inflammatory genes TNF, IL1B/IL1A, TNFAIP3, and CXCR2, but not IL6. These results implicate HDC as a novel immune checkpoint mediator, induced in the tumor microenvironment to promote leukemia. Functional analysis of AM components may allow development of combination therapy with optimal anti-leukemia effect.
Association of Computed Tomography Scan-Assessed Body Composition with Immune and PI3K/AKT Pathway Proteins in Distinct Breast Cancer Tumor Components
Authors: Cheng Ting-Yuan David , Fu Dongtao Ann , Falzarano Sara M. , Zhang Runzhi , Datta Susmita , Zhang Weizhou , Omilian Angela R. , Aduse-Poku Livingstone , Bian Jiang , Irianto Jerome , Asirvatham Jaya Ruth , Campbell-Thompson Martha
Published: December 2024

This hypothesis-generating study aims to examine the extent to which computed tomography-assessed body composition phenotypes are associated with immune and phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) signaling pathways in breast tumors. A total of 52 patients with newly diagnosed breast cancer were classified into four body composition types: adequate (lowest two tertiles of total adipose tissue [TAT]) and highest two tertiles of total skeletal muscle [TSM] areas); high adiposity (highest tertile of TAT and highest two tertiles of TSM); low muscle (lowest tertile of TSM and lowest two tertiles of TAT); and high adiposity with low muscle (highest tertile of TAT and lowest tertile of TSM). Immune and PI3K/AKT pathway proteins were profiled in tumor epithelium and the leukocyte-enriched stromal microenvironment using GeoMx (NanoString). Linear mixed models were used to compare log2-transformed protein levels. Compared with the normal type, the low muscle type was associated with higher expression of INPP4B (log2-fold change = 1.14, p = 0.0003, false discovery rate = 0.028). Other significant associations included low muscle type with increased CTLA4 and decreased pan-AKT expression in tumor epithelium, and high adiposity with increased CD3, CD8, CD20, and CD45RO expression in stroma (p < 0.05; false discovery rate > 0.2). With confirmation, body composition can be associated with signaling pathways in distinct components of breast tumors, highlighting the potential utility of body composition in informing tumor biology and therapy efficacies.
The Combination of Resveratrol and Conjugated Linoleic Acid Dienes Enhances the Individual Effects of These Molecules on De Novo Fatty Acid Biosynthesis in 3T3-L1 Adipocytes
Authors: Oczkowicz Jarosław , Piasna-Słupecka Ewelina , Drozdowska Mariola , Koronowicz Aneta , Kopeć Aneta
Published: December 2024

Consuming food containing ingredients with a documented impact on lipid metabolism can help fight overweight and obesity. The simplest way to reduce the level of fatty acids is to block their synthesis or increase the rate of their degradation. This study aimed to determine the effect of resveratrol, cis-9, trans-11 conjugated linoleic acid (CLA), trans-10, cis-12 CLA, and various variants of their combinations on de novo fatty acid biosynthesis in 3T3-L1 adipocytes. The influence of the above-mentioned bioactive substances on cells grown under standard conditions and after induction of oxidative stress was measured. The effect of the tested compounds on the expression of selected genes related to the de novo fatty acid biosynthesis process (Fasn, Acc1, Acly, Prkaa1, Prkaa2, Prkaca, Srebp1) was evaluated. As part of the conducted experiments, how the level of the corresponding mRNA translates into the content of selected proteins (acetyl-CoA carboxylase 1 (ACC) and fatty acid synthase (FASN) was studied. It was found that the inhibition of fatty acid biosynthesis processes was stronger in the case of the combination of the tested CLA isomers (cis-9, trans-11 CLA, trans-10, cis-12 CLA) with resveratrol than in cases of their individual action.
Integrating Single-Cell RNA-Seq and ATAC-Seq Analysis Reveals Uterine Cell Heterogeneity and Regulatory Networks Linked to Pimpled Eggs in Chickens
Authors: Li Wenqiang , Ma Xueying , Li Xiaomin , Zhang Xuguang , Sun Yifei , Ning Chao , Zhang Qin , Wang Dan , Tang Hui
Published: December 2024

Pimpled eggs have defective shells, which severely impacts hatching rates and transportation safety. In this study, we constructed single-cell resolution transcriptomic and chromatin accessibility maps from uterine tissues of chickens using single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq). We identified 11 major cell types and characterized their marker genes, along with specific transcription factors (TFs) that determine cell fate. CellChat analysis showed that fibroblasts had the most extensive intercellular communication network and that the chickens laying pimpled eggs had amplified immune-related signaling pathways. Differential expression and enrichment analyses indicated that inflammation in pimpled egg-laying chickens may lead to disruptions in their circadian rhythm and changes in the expression of ion transport-related genes, which negatively impacts eggshell quality. We then integrated TF analysis to construct a regulatory network involving TF–target gene–Gene Ontology associations related to pimpled eggs. We found that the transcription factors ATF3, ATF4, JUN, and FOS regulate uterine activities upstream, while the downregulation of ion pumps and genes associated with metal ion binding directly promotes the formation of pimpled eggs. Finally, by integrating the results of scRNA-seq and scATAC-seq, we identified a rare cell type—ionocytes. Our study constructed single-cell resolution transcriptomic and chromatin accessibility maps of chicken uterine tissue and explored the molecular regulatory mechanisms underlying pimpled egg formation. Our findings provide deeper insights into the structure and function of the chicken uterus, as well as the molecular mechanisms of eggshell formation.
Apoptosis-Inducing and Proliferation-Inhibiting Effects of Doramectin on Mz-ChA-1 Human Cholangiocarcinoma Cells
Authors: Zhang Yunfang , Wu Wei , Shi Yan , Huang Yuehong , Dai Ting , Ke Lina , Chen Lizhu , Chen Mingliang , Wang Qin
Published: December 2024

Cholangiocarcinoma is a malignant tumor that emerges in the intrahepatic or extrahepatic bile ducts. Doramectin (DOR), a third-generation derivative of avermectins (AVMs), is renowned for its low toxicity and high efficiency. However, no research has hitherto focused on the anti-cholangiocarcinoma effects of these drugs. In this study, we undertook a preliminary exploration of the mechanism through which DOR inhibits the viability of human cholangiocarcinoma cells (Mz-ChA-1) via transcriptome analysis and molecular validation at the cellular level. The results indicated that DOR could suppress the growth and proliferation of Mz-ChA-1 cells in a dose-dependent manner. Moreover, it significantly diminished their migration and invasion abilities. Cell cycle analysis disclosed arrest in the G1 phase, accompanied by an increase in p21 expression and a decrease in the levels of the cyclin E1 and CDK2 proteins. Additionally, DOR induced apoptosis via the ROS-triggered mitochondrial pathway. This was attested by an elevation in the BAX/BCL-2 ratio, the activation of caspase 3/7 and the cleavage of PARP1. These mechanistic insights underscore DOR’s potential as a therapeutic agent against cholangiocarcinoma
The Role of Scavenger Receptor BI in Sepsis
Authors: Hao Dan , Xue Jian-Yao , Wang Qian , Guo Ling , Li Xiang-An
Published: December 2024

Sepsis is a life-threatening condition resulting from a dysregulated host response to infection. Currently, there is no effective therapy for sepsis due to an incomplete understanding of its pathogenesis. Scavenger receptor BI (SR-BI) is a high-density lipoprotein (HDL) receptor that plays a key role in HDL metabolism by modulating the selective uptake of cholesteryl ester from HDL. Recent studies, including those from our laboratory, indicate that SR-BI protects against sepsis through multiple mechanisms: (1) preventing nitric oxide-induced cytotoxicity; (2) promoting hepatic lipopolysaccharide (LPS) clearance and regulating cholesterol metabolism in the liver; (3) inhibiting LPS-induced inflammatory signaling in macrophages; and (4) mediating the uptake of cholesterol from HDL for inducible glucocorticoid (iGC) synthesis in the adrenal gland, which controls systemic inflammatory response. In this article, we review the roles of SR-BI in sepsis.
MHTAPred-SS: A Highly Targeted Autoencoder-Driven Deep Multi-Task Learning Framework for Accurate Protein Secondary Structure Prediction
Authors: Feng Runqiu , Wang Xun , Xia Zhijun , Han Tongyu , Wang Hanyu , Yu Wenqian
Published: December 2024

Accurate protein secondary structure prediction (PSSP) plays a crucial role in biopharmaceutics and disease diagnosis. Current prediction methods are mainly based on multiple sequence alignment (MSA) encoding and collaborative operations of diverse networks. However, existing encoding approaches lead to poor feature space utilization, and encoding quality decreases with fewer homologous proteins. Moreover, the performance of simple stacked networks is greatly limited by feature extraction capabilities and learning strategies. To this end, we propose MHTAPred-SS, a novel PSSP framework based on the fusion of six features, including the embedding feature derived from a pre-trained protein language model. First, we propose a highly targeted autoencoder (HTA) as the driver to encode sequences in a homologous protein-independent manner. Second, under the guidance of biological knowledge, we design a protein secondary structure prediction model based on the multi-task learning strategy (PSSP-MTL). Experimental results on six independent test sets show that MHTAPred-SS achieves state-of-the-art performance, with values of 88.14%, 84.89%, 78.74% and 77.15% for Q3, SOV3, Q8 and SOV8 metrics on the TEST2016 dataset, respectively. Additionally, we demonstrate that MHTAPred-SS has significant advantages in single-category and boundary secondary structure prediction, and can finely capture the distribution of secondary structure segments, thereby contributing to subsequent tasks.
The Role of Gene Expression Dysregulation in the Pathogenesis of Mucopolysaccharidosis: A Comparative Analysis of Shared and Specific Molecular Markers in Neuronopathic and Non-Neuronopathic Types of the Disease
Authors: Wiśniewska Karolina , Żabińska Magdalena , Szulc Aneta , Gaffke Lidia , Węgrzyn Grzegorz , Pierzynowska Karolina
Published: December 2024

Mucopolysaccharidosis (MPS) comprises a group of inherited metabolic diseases. Each MPS type is caused by a deficiency in the activity of one kind of enzymes involved in glycosaminoglycan (GAG) degradation, resulting from the presence of pathogenic variant(s) of the corresponding gene. All types/subtypes of MPS, which are classified on the basis of all kinds of defective enzymes and accumulated GAG(s), are severe diseases. However, neuronopathy only occurs in some MPS types/subtypes (specifically severe forms of MPS I and MPS II, all subtypes of MPS III, and MPS VII), while in others, the symptoms related to central nervous system dysfunctions are either mild or absent. The early diagnosis of neuronopathy is important for the proper treatment and/or management of the disease; however, there are no specific markers that could be easily used for this in a clinical practice. Therefore, in this work, a comparative analysis of shared and specific gene expression alterations in neuronopathic and non-neuronopathic MPS types was performed using cultures of cells derived from patients. Using transcriptomic analyses (based on the RNA-seq method, confirmed by measuring the levels of a selected gene product), we identified genes (including PFN1, ADAMTSL1, and ABHD5) with dysregulated expression that are common for all, or almost all, types of MPS, suggesting their roles in MPS pathogenesis. Moreover, a distinct set of genes (including ARL6IP6 and PDIA3) exhibited expression changes only in neuronopathic MPS types/subtypes, but not in non-neuronopathic ones, suggesting their possible applications as biomarkers for neurodegeneration in MPS. These findings provide new insights into both the molecular mechanisms of MPS pathogenesis and the development of differentiation method(s) between neuronopathic and non-neuronopathic courses of the disease.
Artificial Intelligence-Assisted Comparative Analysis of the Overlapping Molecular Pathophysiology of Alzheimer’s Disease, Amyotrophic Lateral Sclerosis, and Frontotemporal Dementia
Authors: Wei Zihan , Iyer Meghna R. , Zhao Benjamin , Deng Jennifer , Mitchell Cassie S.
Published: December 2024

The overlapping molecular pathophysiology of Alzheimer’s Disease (AD), Amyotrophic Lateral Sclerosis (ALS), and Frontotemporal Dementia (FTD) was analyzed using relationships from a knowledge graph of 33+ million biomedical journal articles. The unsupervised learning rank aggregation algorithm from SemNet 2.0 compared the most important amino acid, peptide, and protein (AAPP) nodes connected to AD, ALS, or FTD. FTD shared 99.9% of its nodes with ALS and AD; AD shared 64.2% of its nodes with FTD and ALS; and ALS shared 68.3% of its nodes with AD and FTD. The results were validated and mapped to functional biological processes using supervised human supervision and an external large language model. The overall percentages of mapped intersecting biological processes were as follows: inflammation and immune response, 19%; synapse and neurotransmission, 19%; cell cycle, 15%; protein aggregation, 12%; membrane regulation, 11%; stress response and regulation, 9%; and gene regulation, 4%. Once normalized for node count, biological mappings for cell cycle regulation and stress response were more prominent in the intersection of AD and FTD. Protein aggregation, gene regulation, and energetics were more prominent in the intersection of ALS and FTD. Synapse and neurotransmission, membrane regulation, and inflammation and immune response were greater at the intersection of AD and ALS. Given the extensive molecular pathophysiology overlap, small differences in regulation, genetic, or environmental factors likely shape the underlying expressed disease phenotype. The results help prioritize testable hypotheses for future clinical or experimental research.
Treatment with Ascorbyl Glucoside–Arginine Complex Ameliorates Solar Lentigos
Authors: Takada Mariko , Numano Kayoko , Nakano Masahiko , Yamamoto Akio , Imokawa Genji
Published: December 2024

Little is known about the anti-pigmenting effects of skin-whitening agents on solar lentigos (SLs). To characterize the anti-pigmenting effects of a newly designed derivative ascorbyl glucoside–arginine complex (AGAC) on SLs, lotions with or without 28% AGAC were applied twice daily for 24 weeks in a double-blind half-face study of 27 Japanese females with SLs. The pigmentation scores and skin colors of previously selected SLs on the right and left sides of the faces of the subjects were evaluated using a photo-scale, a color difference meter and a Mexameter. Treatment with the test lotion elicited a significant decrease in pigmentation scores at 24 weeks compared to week 0, with a significant decrease in pigmentation scores at 24 weeks compared to the placebo lotion. In the test lotion-treated SLs, the lightness (L) and melanin index (MI) values that reflect the pigmentation level significantly increased and decreased, respectively, at 12 and 24 weeks of treatment compared to week 0. Comparisons of increased L values or decreased MI values between the test and placebo lotion-treated SLs demonstrated that the test lotion-treated SLs had significantly higher increased L or decreased MI values than the placebo lotion-treated SLs both at 12 and 24 weeks of treatment. The sum of our results strongly indicates that AGAC is distinctly effective in ameliorating the hyperpigmentation levels of SLs at a level visibly recognizable by the subjects, without any hypo-pigmenting effects or skin problems.
Mechanisms of Aluminum Toxicity Impacting Root Growth in Shatian Pomelo
Authors: Yan Jingfu , Zhu Wenbo , Wu Dongshen , Chen Xinya , Yang Shaoxia , Xue Yingbin , Liu Ying , Liu Ying
Published: December 2024

Aluminum (Al) toxicity in acidic soils poses significant challenges to crop growth and development. However, the response mechanism of Shatian pomelo (Citrus maxima ‘Shatian Yu’) roots to Al toxicity remains poorly understood. This study employed root phenotype analysis, physiological response index measurement, root transcriptome analysis, and quantitative PCR (qPCR) validation to investigate the effects of Al toxicity on Shatian pomelo roots. The findings revealed that Al toxicity inhibited root growth and development, resulting in reduced root biomass, total root length, total root surface area, root volume, average root diameter, and root tip count. Antioxidant enzyme activities (peroxidase, superoxide dismutase, ascorbate peroxidase, and catalase activity) and soluble protein content increased with rising Al toxicity, whereas malondialdehyde content initially increased and then declined. Additionally, Al toxicity stress increased Al (1439.25%) content and decreased boron (B, 50.64%), magnesium (Mg, 42.04%), calcium (Ca, 46.02%), manganese (Mn, 86.75%), and iron (Fe, 69.92%) levels in the roots. RNA sequencing (RNA-seq) analysis identified 3855 differentially expressed genes (DEGs) between 0 mmol/L Al (control) and 4 mmol/L Al (Al toxicity) concentrations, with 1457 genes up-regulated and 2398 down-regulated, indicating a complex molecular regulatory response. The qPCR results further validated these findings. This study elucidates the response mechanisms of Shatian pomelo roots to Al toxicity stress, providing insights into the regulatory pathways involved. The findings offer valuable reference points for breeding Al-resistant Shatian pomelo varieties. The results of this study provide important genetic tools and technical support for the screening and breeding of highly resistant varieties of Shatian pomelo. On the one hand, by detecting the key indexes (such as antioxidant enzyme activity and nutrient absorption capacity) of Shatian pomelo, varieties with excellent anti-Al toxicity characteristics can be selected. On the other hand, the Al-resistant genes identified in this study, such as TFM1 and ALERTFA0, can be used to develop molecular markers, assisted marker breeding, or transgenic breeding to accelerate the breeding process of Al-resistant strains.
Lymphocyte Involvement in the Pathology of Pulmonary Arterial Hypertension
Authors: Tomaszewski Michał , Styczeń Agnieszka , Krysa Martyna , Michalski Adam , Morawska-Michalska Izabela , Hymos Anna , Wawer Joanna , Rolińska Agnieszka , Rahnama Mansur , Urbanowicz Tomasz , Grywalska Ewelina
Published: December 2024

Pulmonary arterial hypertension (PAH) is a disease characterized by increased pulmonary vascular resistance and right heart failure, with emerging evidence suggesting a key role for immune dysregulation in its pathogenesis. This study aimed to assess the involvement of lymphocytes, particularly regulatory T cells (Tregs), and the expression of immune checkpoint molecules PD-1 and PD-L1 on peripheral blood subpopulations in patients diagnosed with PAH. The study involved 25 patients; peripheral blood mononuclear cells were isolated and subsequently analyzed using flow cytometry to quantify the Treg cell percentage and evaluate PD-1 and PD-L1 expression across the T and B cells. We observed a significantly higher percentage of Tregs in idiopathic PAH (iPAH) patients compared to healthy controls and those with congenital heart disease-associated PAH (CHD-PAH), connective tissue disease-associated PAH (CTD-PAH), and chronic thromboembolic pulmonary hypertension (CTEPH). An overexpression of PD-1 and PD-L1 was found on CD4+ and CD8+ lymphocytes in all PAH groups, particularly in iPAH and CHD-PAH patients. These findings align with previous research highlighting Treg dysfunction and PD-1/PD-L1 overexpression as contributors to PAH pathogenesis. Our results suggest that targeting immune checkpoints and modulating Treg function could represent novel therapeutic strategies for PAH. Future research should focus on validating these biomarkers in larger, independent cohorts and exploring their clinical utility in diagnosing and managing PAH.
Host–Parasite Interactions in Toxoplasma gondii-Infected Cells: Roles of Mitochondria, Microtubules, and the Parasitophorous Vacuole
Authors: Barik Sailen , Andrews Joel
Published: December 2024

An intracellular protozoan, the Apicomplexan parasite Toxoplasma gondii (T. gondii) infects nucleated cells, in which it triggers the formation of a specialized membrane-confined cytoplasmic vacuole, named the parasitophorous vacuole (PV). One of the most prominent events in the parasite’s intracellular life is the congregation of the host cell mitochondria around the PV. However, the significance of this event has remained largely unsolved since the parasite itself possesses a functional mitochondrion, which is essential for its replication. Here, we explore several fundamental aspects of the interaction between the PV and the host cell mitochondria. They include the detailed features of the congregation, the nature and mechanism of the mitochondrial travel to the PV, and the potential significance of the migration and congregation. Using a combination of biochemical assays, high-resolution imaging, and RNAi-mediated knockdown, we show that: (i) mitochondrial travel to the PV starts very early in parasite infection, as soon as the smallest PV takes shape; (ii) the travel utilizes the contractile microtubular network of the host cell; and (iii) near the end of the parasitic life cycle, when most PVs have reached their largest sustainable size and are about to lyse in order to release the progeny parasites, the associated mitochondria change their usual elongated shape to small spheres, apparently resulting from increased fission. Intriguingly, despite the well-known mitochondrial role as a major producer of cellular ATP, the parasite does not seem to use cellular mitochondrial ATP. Together, these findings may serve as foundations for future research in host–parasite interaction, particularly in the elucidation of its mechanisms, and the possible development of novel antiparasitic drug regimens.
Sestrin2 Suppression Promotes Endothelial–Mesenchymal Transition and Exacerbates Methylglyoxal-Induced Endothelial Dysfunction
Authors: Abdelsalam Shahenda Salah , Zahid Muhammad Ammar , Ghanem Sarah Khalaf , Khan Abbas , Parray Aijaz , Agouni Abdelali
Published: December 2024

Sestrin2 (SESN2) is a stress-inducible protein known for its cytoprotective functions, but its role in diabetic vascular complications remains unclear. This study investigated the impact of SESN2 on methylglyoxal (MGO)-induced endothelial–mesenchymal transition (EndMT). Human endothelial cells were transfected with SESN2 siRNA duplexes to silence SESN2 expression, followed by MGO treatment. SESN2 knockdown significantly exacerbated MGO-induced oxidative stress, as evidenced by the reduced expression of antioxidant markers. Furthermore, SESN2 silencing enhanced the inflammatory response to MGO, demonstrated by the increased levels of pro-inflammatory cytokines. Notably, SESN2 deficiency promoted EndMT, a key process in diabetes-induced cardiovascular complications, as shown by the increased expression of mesenchymal markers and the decreased expression of endothelial markers. These findings suggest that SESN2 plays a critical protective role in endothelial cells against MGO-induced damage. The study provides novel insights into the molecular mechanisms underlying diabetic cardiovascular complications and identifies SESN2 as a potential therapeutic target for preventing endothelial dysfunction in diabetes. Our results indicate that SESN2 downregulation may contribute to the pathogenesis of diabetic vascular complications by promoting EndMT, increased oxidative stress, and inflammation.
Characterisation of the Plasma and Faecal Metabolomes in Participants with Functional Gastrointestinal Disorders
Authors: Fraser Karl , James Shanalee C. , Young Wayne , Gearry Richard B. , Heenan Phoebe E. , Keenan Jacqueline I. , Talley Nicholas J. , McNabb Warren C. , Roy Nicole C.
Published: December 2024

There is evidence of perturbed microbial and host processes in the gastrointestinal tract of individuals with functional gastrointestinal disorders (FGID) compared to healthy controls. The faecal metabolome provides insight into the metabolic processes localised to the intestinal tract, while the plasma metabolome highlights the overall perturbances of host and/or microbial responses. This study profiled the faecal (n = 221) and plasma (n = 206) metabolomes of individuals with functional constipation (FC), constipation-predominant irritable bowel syndrome (IBS-C), functional diarrhoea (FD), diarrhoea-predominant IBS (IBS-D) and healthy controls (identified using the Rome Criteria IV) using multimodal LC-MS technologies. Discriminant analysis separated patients with the ‘all constipation’ group (FC and IBS-C) from the healthy control group and ‘all diarrhoea’ group (FD and IBS-D) from the healthy control group in both sample types. In plasma, almost all multimodal metabolite analyses separated the ‘all constipation’ or ‘all diarrhoea’ group from the healthy controls, and the IBS-C or IBS-D group from the healthy control group. Plasma phospholipids and metabolites linked to several amino acid and nucleoside pathways differed (p < 0.05) between healthy controls and IBS-C. In contrast, metabolites involved in bile acid and amino acid metabolism were the key differentiating classes in the plasma of subjects with IBS-D from healthy controls. Faecal lipids, particularly ceramides, diglycerides, and triglycerides, varied (p < 0.05) between healthy controls and the ‘all constipation’ group and between healthy controls and ‘all diarrhoea’ group. The faecal and plasma metabolomes showed perturbations between constipation, diarrhoea and healthy control groups that may reflect processes and mechanisms linked to FGIDs.
Improved Genetic Characterization of Hypercholesterolemia in Latvian Patients with Familial Hypercholesterolemia: A Combined Monogenic and Polygenic Approach Using Whole-Genome Sequencing
Authors: Atava Ivanna , Briviba Monta , Nesterovics Georgijs , Saripo Vita , Gilis Dainus , Meiere Ruta , Terauda Elizabete , Skudrina Gunda , Klovins Janis , Latkovskis Gustavs
Published: December 2024

Despite the implementation of next-generation sequencing-based genetic testing on patients with clinical familial hypercholesterolemia (FH), most cases lack complete genetic characterization. We aim to investigate the utility of the polygenic risk score (PRS) in specifying the genetic background of patients from the Latvian Registry of FH (LRFH). We analyzed the whole-genome sequencing (WGS) data of the clinically diagnosed FH patients (n = 339) and controls selected from the Latvian reference population (n = 515). Variant pathogenicity in FH patients was classified according to the ACMG/AMP guidelines. The low-density lipoprotein cholesterol (LDL-C) and lipoprotein (a) (LPA) PRS were calculated based on the WGS data. We identified unique causative variants in 80 (23.6%) of the tested individuals (39 variants in FH genes and 4 variants in phenocopy genes, with 6 variants being novel). The LDL-C PRS was highly discriminative compared to the LPA PRS. Nevertheless, both PRS were able to explain the genetic cause of hypercholesterolemia in 26.3% of the remaining non-monogenic patients. The combined genetic analysis of monogenic and polygenic hypercholesterolemia resulted in 43.7% genetically explained hypercholesterolemia cases. Even though the application of PRS alone does not exclude monogenic testing in clinical FH patients, it is a valuable tool for diagnosis specification.
A Critical Review on microRNAs as Prognostic Biomarkers in Laryngeal Carcinoma
Authors: Komitova Kristina S. , Dimitrov Lyuben D. , Stancheva Gergana S. , Kyurkchiyan Silva G. , Petkova Veronika , Dimitrov Stoyan I. , Skelina Silviya P. , Kaneva Radka P. , Popov Todor M.
Published: December 2024

During the past decade, a vast number of studies were dedicated to unravelling the obscurities of non-coding RNAs in all fields of the medical sciences. A great amount of data has been accumulated, and consequently a natural need for organization and classification in all subfields arises. The aim of this review is to summarize all reports on microRNAs that were delineated as prognostic biomarkers in laryngeal carcinoma. Additionally, we attempt to allocate and organize these molecules according to their association with key pathways and oncogenes affected in laryngeal carcinoma. Finally, we critically analyze the common shortcomings and biases of the methodologies in some of the published papers in this area of research. A literature search was performed using the PubMed and MEDLINE databases with the keywords “laryngeal carcinoma” OR “laryngeal cancer” AND “microRNA” OR “miRNA” AND “prognostic marker” OR “prognosis”. Only research articles written in English were included, without any specific restrictions on study type. We have found 43 articles that report 39 microRNAs with prognostic value associated with laryngeal carcinoma, and all of them are summarized along with the major characteristics and methodology of the respective studies. A second layer of the review is structural analysis of the outlined microRNAs and their association with oncogenes and pathways connected with the cell cycle (p53, CCND1, CDKN2A/p16, E2F1), RTK/RAS/PI3K cascades (EGFR, PI3K, PTEN), cell differentiation (NOTCH, p63, FAT1), and cell death (FADD, TRAF3). Finally, we critically review common shortcomings in the methodology of the papers and their possible effect on their results.
Unveiling Secondary Mutations in Blended Phenotypes: Dual ERCC4 and OTOA Pathogenic Variants Through WES Analysis
Authors: Failla Pinella , Saccuzzo Lucia , Galesi Ornella , Greco Donatella , Barresi Vincenza , Amata Silvestra , Romano Corrado , Fichera Marco
Published: December 2024

This study describes two siblings from consanguineous parents who exhibit intellectual disability, microcephaly, photosensitivity, bilateral sensorineural hearing loss, numerous freckles, and other clinical features that suggest a potential disruption of the nucleotide excision repair (NER) pathway. Whole exome sequencing (WES) identified a novel homozygous missense variant in the ERCC4 gene, which was predicted to be pathogenic. However, a subsequent peculiar audiometric finding prompted further investigation, revealing a homozygous deletion in the OTOA gene linked to neurosensorial hearing loss. Both variants were located within a run of homozygosity (ROH) on chromosome 16p13.12-p12.2, implicating a complex genetic basis for the observed phenotype. While this study reports a potentially novel ERCC4 variant, it underscores the importance of comprehensive analysis and deep phenotyping in WES data to improve diagnostic accuracy. Our findings advocate for an expanded approach in WES analysis, ensuring more precise diagnoses and improved genetic counseling, particularly when specialized tests for structural variant analysis are unavailable.
Interferon-α Inhibits NET Formation in Neutrophils Derived from Patients with Myeloproliferative Neoplasms in a Neutrophil Sub-Population-Specific Manner
Authors: Partouche Shirly , Goldberg Idan , Halperin Erez , Atamna Bahaa , Shacham-Abulafia Adi , Shapira Saar , Samara Aladin , Gover-Proaktor Ayala , Leader Avi , Spectre Galia , Raanani Pia , Granot Galit , Wolach Ofir
Published: December 2024

Neutrophils and neutrophil extracellular traps (NETs) contribute to thrombosis and hyperinflammation in myeloproliferative neoplasms (MPN). High-density neutrophils (HDNs) and low-density neutrophils (LDNs) have recently been characterized as distinct neutrophil sub-populations with distinct morphological and functional properties. We aim to study the kinetics of NET formation and inhibition with interferon-α (IFNα) in neutrophils derived from patients with MPN as compared to matched healthy controls. Ex vivo NET formation was assessed by neutrophil-elastase activity, neutrophil-associated nucleosomes, myeloperoxidase (MPO), and citrullinated histone H3 content. IFNα significantly inhibited NET formation in neutrophils derived from MPN patients. Neutrophil sub-population analysis demonstrated that HDNs drive the increase in NET formation as compared to LDNs in patients and in healthy controls and are effectively inhibited by IFNα, an effect that is lost in LDNs. In conclusion, we demonstrate that in MPN, HDNs drive excess NET formation and are more sensitive to IFNα inhibition. These observations uncover unique neutrophil sub-population biology and dynamics in MPN.
Non-Invasive Nanometer Resolution Assessment of Cell–Soft Hydrogel System Mechanical Properties by Scanning Ion Conductance Microscopy
Authors: Tikhonova Tatiana N. , Barkovaya Anastasia V. , Efremov Yuri M. , Mamed-Nabizade Vugara V. , Kolmogorov Vasilii S. , Timashev Peter S. , Sysoev Nikolay N. , Fadeev Victor V. , Gorelkin Petr V. , Adler-Abramovich Lihi , Erofeev Alexander S. , Shirshin Evgeny A.
Published: December 2024

Biomimetic hydrogels have garnered increased interest due to their considerable potential for use in various fields, such as tissue engineering, 3D cell cultivation, and drug delivery. The primary challenge for applying hydrogels in tissue engineering is accurately evaluating their mechanical characteristics. In this context, we propose a method using scanning ion conductance microscopy (SICM) to determine the rigidity of living human breast cancer cells MCF-7 cells grown on a soft, self-assembled Fmoc-FF peptide hydrogel. Moreover, it is demonstrated that the map of Young’s modulus distribution obtained by the SICM method allows for determining the core location. The Young’s modules for MCF-7 cells decrease with the substrate stiffening, with values of 1050 Pa, 835 Pa, and 600 Pa measured on a Petri dish, Fmoc-FF hydrogel, and Fmoc-FF/chitosan hydrogel, respectively. A comparative analysis of the SICM results and the data obtained by atomic force microscopy was in good agreement, allowing for the use of a composite cell–substrate model (CoCS) to evaluate the ‘soft substrate effect’. Using the CoCS model allowed us to conclude that the MCF-7 softening was due to the cells’ mechanical properties variations due to cytoskeletal changes. This research provides immediate insights into changes in cell mechanical properties resulting from different soft scaffold substrates.
Comparative Physiological, Proteomic, and Metabolomic Insights into a Promising Low-Pruning Mulberry Cultivar for Silkworm Rearing
Authors: Liu Yan , Lv Zhiqiang , Wei Jia , Liu Peigang , Pan Meiliang , Ma Huanyan , Lin Tianbao
Published: December 2024

Mulberry (Morus spp.) is an economically significant plant in the production of silk through feeding leaves to silkworm larvae. Traditional silkworm rearing is heavily labor-intensive, particularly in leaf collection, which leads to low efficiency and impedes the development of sericulture. Here, to assess the feasibility and effectiveness of a novel low-pruning mulberry cultivar, ZJ1, in the silkworm rearing industry, a comprehensive investigation integrating physiological, proteomic, and metabolomic analyses was conducted in comparison with the traditionally high-pruning cultivar, N14. The low-pruning mulberry variety ZJ1 exhibited a notable increase in annual leaf yield of 43.94%, along with a significant enrichment of serine and isoleucine contents, in contrast to those of the high-pruning variety N14. Through iTRAQ proteomics and LC-MS/MS metabolomics analyses, a total of 561 reduced and 803 increased differentially expressed proteins (DEPs), as well as 332 differential expressed metabolites (DEMs) in positive ions and 192 DEMs in negative ions, were identified in the ZJ1 group relative to the N14 group, respectively. The observed features in amino acid profiles and the enrichment of the sucrose-related metabolic pathway provided interesting insights for future endeavors in mulberry variety improvement and the optimization of silkworm diet formulations. Collectively, the low-pruning cultivar ZJ1, characterized by its rapid growth, high leaf productivity, and suitability for mechanized operations, is expected to be an efficient substitute in improving the future sericultural industry, especially in urbanized and industrialized regions.
The Study of Ropivacaine Pharmacokinetics in a Clinical Setting: A Critical Scoping Review from the Perspective of Analytical Methodologies
Authors: Butiulca Mihaela , Farczadi Lenard , Vari Camil Eugen , Imre Silvia , Azamfirei Leonard , Lazar Alexandra
Published: December 2024

Ropivacaine, a widely used regional anesthetic also used for pain management, has been increasingly used in recent years due to its increased efficacy and improved safety compared to similar anesthetics. Biomonitoring of ropivacaine and its metabolites during and after anesthesia is an essential process for ensuring therapeutic efficacy and safe usage for patients. The most useful biomonitoring tool in recent years has been liquid chromatography coupled with mass spectrometry (LC-MS/MS), which offers selectivity, sensitivity, as well as accuracy of measurements. The current manuscript summarizes and discusses the existing liquid chromatographic methods described in the literature, as well as the personal experience with developing bioanalytical and analytical methods for the quantification of ropivacaine in biological samples for clinical applications. It is focused on methodological aspects, recent advancements, challenges, and future perspectives, highlighting the importance of LC-MS/MS techniques in ropivacaine analysis.
Driving Automation Systems Penetration and Traffic Safety: Implications for Infrastructure Design and Policy
Authors: Antonakaki Antonia , Oikonomou Maria G. , Garefalakis Thodoris , Yannis George
Published: December 2024

The increasing penetration of autonomous vehicles (AVs) presents new challenges and opportunities for road safety. This study aims to evaluate the impact of AV penetration rates on traffic safety through the use of microscopic simulation scenarios based on the Villaverde network in Madrid. Eleven scenarios were simulated with SAE Level 5 AV market penetration rates (MPRs) ranging from 0% to 100% in 10% increments. Vehicle conflicts, defined as instances where the time to collision was less than 1.5 s, were analyzed along with traffic composition and roadway characteristics. Multiple linear and multinomial logistic regression models were applied to examine the relationships between time-to-collision (TTC), conflict numbers, maximum conflict speed, and critical influencing factors such as vehicle type and road capacity. The results indicate that higher AV penetration rates generally improve traffic safety, although the coexistence of conventional vehicles and vehicles equipped with driving automation systems introduces traffic heterogeneity, potentially influencing safety outcomes. These findings suggest that while AVs have a positive effect on road safety, further analysis is needed to address the complexities introduced by mixed-traffic conditions.
Results of an Online Survey on Intensive Care Management of Patients with Aneurysmal Subarachnoid Hemorrhage in German-Speaking Countries
Authors: Myftiu Anisa , Mäder Lisa , Aroyo Ilia , Kollmar Rainer ,   on behalf of the IGNITE Study Group & DIVI Section Studies & Standards
Published: December 2024

Background: The clinical course of patients with aneurysmal SAH (aSAH) is often dynamic and highly unpredictable. Since its management varies between hospitals despite guidelines, this survey aimed to assess the current state of intensive care treatment for aSAH in the German-speaking region and provide insights that could aid standardization of care for aSAH patients in the intensive care setting. Methods: From February 2023 to April 2023, medical professionals of the German Interdisciplinary Association for Intensive Care and Emergency Medicine (DIVI), the Initiative of German Neuro-Intensive Trial Engagement (IGNITE) network and manually recorded clinics with intensive care units were invited to participate in a standardized anonymous online questionnaire including 44 questions. The questionnaire was validated in multiple steps by experts of different specialties including those from the DIVI. A descriptive data analysis was carried out. Results: A total of 135 out of 220 participants answered the survey completely. The results showed that most patients were treated in anesthesia-led intensive care units at university and maximum care hospitals. Aneurysms were usually treated within 24 h after bleeding. If vasospasm was detected, induced hypertension was usually implemented as the first treatment option. In refractory vasospasm, interventional spasmolysis with calcium antagonists was usually carried out (81%), despite unclear evidence. There were significant discrepancies in blood pressure target values, particularly after aneurysm repair or after delayed cerebral ischemia (DCI), as well as in hemoglobin limit values for erythrocyte substitution. Despite the limited level of evidence, most institutions used temperature management (68%), including hypothermia (56%), for severe cases. Conclusions: While we anticipated variations between individual intensive care facilities, our survey identified numerous similarities in the treatment of aSAH patients. Methods such as interventional spasmolysis and temperature management were used frequently despite limited evidence. Our results can serve as a fundamental framework for formulating recommendations for intensive care treatment and planning of multicenter studies.