-
Journal of Chemical Information and... Mar 2024Glycosaminoglycans (GAGs) made of repeating disaccharide units intricately engage with proteins, playing a crucial role in the spatial organization of the extracellular...
Glycosaminoglycans (GAGs) made of repeating disaccharide units intricately engage with proteins, playing a crucial role in the spatial organization of the extracellular matrix (ECM) and the transduction of biological signals in cells to modulate a number of biochemical processes. Exploring protein-GAG interactions reveals several challenges for their analysis, namely, the highly charged and periodic nature of GAGs, their multipose binding, and the abundance of the interfacial water molecules in the protein-GAG complexes. Most of the studies on protein-GAG interactions are conducted using the TIP3P water model, and there are no data on the effect of various water models on the results obtained in molecular dynamics (MD) simulations of protein-GAG complexes. Hence, it is essential to perform a systematic analysis of different water models in MD simulations for these systems. In this work, we aim to evaluate the properties of the protein-GAG complexes in MD simulations using different explicit: TIP3P, SPC/E, TIP4P, TIP4PEw, OPC, and TIP5P and implicit: IGB = 1, 2, 5, 7, and 8 water models to find out which of them are best suited to study the dynamics of protein-GAG complexes. The FF14SB and GLYCAM06 force fields were used for the proteins and GAGs, respectively. The interactions of several GAG types, such as heparin, chondroitin sulfate, and hyaluronic acid with basic fibroblast growth factor, cathepsin K, and CD44 receptor, respectively, are investigated. The observed variations in different descriptors used to study the binding in these complexes emphasize the relevance of the choice of water models for the MD simulation of these complexes.
Topics: Glycosaminoglycans; Molecular Dynamics Simulation; Water; Benchmarking; Heparin; Proteins
PubMed: 38410841
DOI: 10.1021/acs.jcim.4c00030 -
The American Journal of Case Reports Feb 2024BACKGROUND Whipple disease (WD) is rare, with an incidence of only a few patients per million. It is caused by infection with the gram-positive bacterium Tropheryma...
BACKGROUND Whipple disease (WD) is rare, with an incidence of only a few patients per million. It is caused by infection with the gram-positive bacterium Tropheryma whipplei, and presents with symptoms that include joint pain, fever, diarrhea, and weight loss. This report is of a 40-year-old man with a 7-year history of polyarthritis and a late diagnosis of Whipple disease. The atypical nature of his symptoms led to misdirection and misdiagnosis for years. CASE REPORT A middle-aged white man with seronegative migratory polyarticular arthritis underwent 7 years of treatment with steroids, disease-modifying anti-rheumatic drugs (DMARDs), and a TNF (tumor necrosis factor)-alpha inhibitor, all without any clinical improvement. Throughout this period, he had persistent loose stools and iron-deficiency anemia. Extensive diagnostic investigations for various possibilities yielded negative results. However, after 7 years, he began displaying clinical signs of malabsorption. This prompted further evaluation, including an upper-gastrointestinal endoscopy and biopsy, which revealed the presence of PAS (periodic acid-Schiff)-positive Treponema whipplei, which led to the diagnosis of WD. Following initiation of appropriate treatment, the patient experienced complete resolution of symptoms. Retrospectively, all the pieces of this puzzle fell into place, providing a comprehensive understanding of the prolonged medical challenge the patient faced. CONCLUSIONS This case illuminates the diagnostic challenge faced when dealing with migratory polyarticular inflammatory arthritis and fever. This report has highlighted that Whipple disease can be associated with multiple symptoms and signs, which can result in a delay in diagnosis. However, once the diagnosis is confirmed, antibiotic treatment is effective.
Topics: Adult; Humans; Male; Anti-Bacterial Agents; Antirheumatic Agents; Arthritis; Delayed Diagnosis; Fever; Retrospective Studies; Whipple Disease
PubMed: 38402412
DOI: 10.12659/AJCR.942896 -
Indian Journal of Pathology &... Apr 2024Cryptococcosis usually occurs in immunocompromised patients and presents as meningitis and lung disease. Adrenal gland involvement may be observed, yet primary adrenal...
Cryptococcosis usually occurs in immunocompromised patients and presents as meningitis and lung disease. Adrenal gland involvement may be observed, yet primary adrenal insufficiency by cryptococcal infection is infrequent. We present a case of a middle-aged immunocompetent man with primary adrenal insufficiency and bilateral adrenal lesions, splenomegaly, and miliary mottling in the lungs on imaging. No evidence of meningitis was witnessed. The clinico-radiological findings led toward the differential diagnosis of disseminated tuberculosis or fungal infection. Detection of cryptococcus organism was done on fine-needle aspiration cytology and biopsy on periodic acid-Schiff stain and Gomori`s methenamine silver stain. Thus, it is recommended to keep the possibility of cryptococcosis in mind while dealing with instances that have a tuberculosis-like clinico-radiological presentation. The detection of the causal organism on Fine needle aspiration (FNA)/biopsy examination may be useful in confirming the diagnosis and determining the appropriate medical treatment.
Topics: Humans; Male; Cryptococcosis; Biopsy, Fine-Needle; Adrenal Insufficiency; Middle Aged; Adrenal Glands; Cryptococcus; Diagnosis, Differential; Tomography, X-Ray Computed; Lung; Microscopy; Adrenal Gland Diseases; Immunocompetence; Histocytochemistry
PubMed: 38391340
DOI: 10.4103/ijpm.ijpm_185_22 -
Human Reproduction (Oxford, England) May 2024Are there subgroups among patients with cryptozoospermia pointing to distinct etiologies?
STUDY QUESTION
Are there subgroups among patients with cryptozoospermia pointing to distinct etiologies?
SUMMARY ANSWER
We reveal two distinct subgroups of cryptozoospermic (Crypto) patients based on testicular tissue composition, testicular volume, and FSH levels.
WHAT IS KNOWN ALREADY
Cryptozoospermic patients present with a sperm concentration below 0.1 million/ml. While the etiology of the severely impaired spermatogenesis remains largely unknown, alterations of the spermatogonial compartment have been reported including a reduction of the reserve stem cells in these patients.
STUDY DESIGN, SIZE, DURATION
To assess whether there are distinct subgroups among cryptozoospermic patients, we applied the statistical method of cluster analysis. For this, we retrospectively selected 132 cryptozoospermic patients from a clinical database who underwent a testicular biopsy in the frame of fertility treatment at a university hospital. As controls (Control), we selected 160 patients with obstructive azoospermia and full spermatogenesis. All 292 patients underwent routine evaluation for endocrine, semen, and histological parameters (i.e. the percentage of tubules with elongated spermatids). Moreover, outcome of medically assisted reproduction (MAR) was assessed for cryptozoospermic (n = 73) and Control patients (n = 87), respectively. For in-depth immunohistochemical and histomorphometrical analyses, representative tissue samples from cryptozoospermic (n = 27) and Control patients (n = 12) were selected based on cluster analysis results and histological parameters.
PARTICIPANTS/MATERIALS, SETTING, METHODS
This study included two parts: firstly using clinical parameters of the entire cohort of 292 patients, we performed principal component analysis (PCA) followed by hierarchical clustering on principal components (i.e. considering hormonal values, ejaculate parameters, and histological information). Secondly, for histological analyses seminiferous tubules were categorized according to the most advanced germ cell type present in sections stained with Periodic acid Schif. On the selected cohort of 39 patients (12 Control, 27 cryptozoospermic), we performed immunohistochemistry for spermatogonial markers melanoma-associated antigen 4 (MAGEA4) and piwi like RNA-mediated gene silencing 4 (PIWIL4) followed by quantitative analyses. Moreover, the morphologically defined Adark spermatogonia, which are considered to be the reserve stem cells, were quantified.
MAIN RESULTS AND THE ROLE OF CHANCE
The PCA and hierarchical clustering revealed three different clusters, one of them containing all Control samples. The main factors driving the sorting of patients to the clusters were the percentage of tubules with elongated spermatids (Cluster 1, all Control patients and two cryptozoospermic patients), the percentage of tubules with spermatocytes (Cluster 2, cryptozoospermic patients), and tubules showing a Sertoli cells only phenotype (Cluster 3, cryptozoospermic patients). Importantly, the percentage of tubules containing elongated spermatids was comparable between Clusters 2 and 3. Additional differences were higher FSH levels (P < 0.001) and lower testicular volumes (P < 0.001) in Cluster 3 compared to Cluster 2. In the spermatogonial compartment of both cryptozoospermic Clusters, we found lower numbers of MAGEA4+ and Adark spermatogonia but higher proportions of PIWIL4+ spermatogonia, which were significantly correlated with a lower percentage of tubules containing elongated spermatids. In line with this common alteration, the outcome of MAR was comparable between Controls as well as both cryptozoospermic Clusters.
LIMITATIONS, REASONS FOR CAUTION
While we have uncovered the existence of subgroups within the cohort of cryptozoospermic patients, comprehensive genetic analyses remain to be performed to unravel potentially distinct etiologies.
WIDER IMPLICATIONS OF THE FINDINGS
The novel insight that cryptozoospermic patients can be divided into two subgroups will facilitate the strategic search for underlying genetic etiologies. Moreover, the shared alterations of the spermatogonial stem cell compartment between the two cryptozoospermic subgroups could represent a general response mechanism to the reduced output of sperm, which may be associated with a progressive phenotype. This study therefore offers novel approaches towards the understanding of the etiology underlying the reduced sperm formation in cryptozoospermic patients.
STUDY FUNDING/COMPETING INTEREST(S)
German research foundation CRU 326 (grants to: SDP, NN). Moreover, we thank the Faculty of Medicine of the University of Münster for the financial support of Lena Charlotte Schülke through the MedK-program. We acknowledge support from the Open Access Publication Fund of the University of Münster. The authors have no potential conflicts of interest.
TRIAL REGISTRATION NUMBER
N/A.
Topics: Humans; Male; Adult; Retrospective Studies; Testis; Spermatogenesis; Follicle Stimulating Hormone; Azoospermia; Sperm Count; Spermatozoa; Cluster Analysis; Oligospermia; Infertility, Male
PubMed: 38365879
DOI: 10.1093/humrep/deae013 -
The ISME Journal Jan 2024In Burkholderia-Riptortus symbiosis, the host bean bug Riptortus pedestris harbors Burkholderia symbionts in its symbiotic organ, M4 midgut, for use as a nutrient...
In Burkholderia-Riptortus symbiosis, the host bean bug Riptortus pedestris harbors Burkholderia symbionts in its symbiotic organ, M4 midgut, for use as a nutrient source. After occupying M4, excess Burkholderia symbionts are moved to the M4B region, wherein they are effectively digested and absorbed. Previous studies have shown that M4B has strong symbiont-specific antibacterial activity, which is not because of the expression of antimicrobial peptides but rather because of the expression of digestive enzymes, mainly cathepsin L protease. However, in this study, inhibition of cathepsin L activity did not reduce the bactericidal activity of M4B, indicating that there is an unknown digestive mechanism that renders specifically potent bactericidal activity against Burkholderia symbionts. Transmission electron microscopy revealed that the lumen of symbiotic M4B was filled with a fibrillar matter in contrast to the empty lumen of aposymbiotic M4B. Using chromatographic and electrophoretic analyses, we found that the bactericidal substances in M4B existed as high-molecular-weight (HMW) complexes that were resistant to protease degradation. The bactericidal HMW complexes were visualized on non-denaturing gels using protein- and polysaccharide-staining reagents, thereby indicating that the HMW complexes are composed of proteins and polysaccharides. Strongly stained M4B lumen with Periodic acid-Schiff (PAS) reagent in M4B paraffin sections confirmed HMW complexes with polysaccharide components. Furthermore, M4B smears stained with Periodic acid-Schiff revealed the presence of polysaccharide fibers. Therefore, we propose a key digestive mechanism of M4B: bacteriolytic fibers, polysaccharide fibers associated with digestive enzymes such as cathepsin L, specialized for Burkholderia symbionts in Riptortus gut symbiosis.
Topics: Animals; Cathepsin L; Symbiosis; Periodic Acid; Insecta; Heteroptera; Bacteria; Polysaccharides; Burkholderia
PubMed: 38365249
DOI: 10.1093/ismejo/wrad021 -
Cureus Jan 2024Whipple's disease (WD) is a chronic multisystemic infection caused by . It is a rare condition with a wide spectrum of clinical presentations, necessitating a high...
Whipple's disease (WD) is a chronic multisystemic infection caused by . It is a rare condition with a wide spectrum of clinical presentations, necessitating a high clinical suspicion to arrive at the diagnosis. We present the case of a 65-year-old woman who experienced chronic, intermittent, and migratory polyarthralgia, weight loss, anorexia, and pyrosis. She was admitted due to bilateral deep vein thrombosis (DVT). She exhibited lymphadenopathy without hepatosplenomegaly, and lymph node biopsy revealed reactive lymphadenitis with intrahistiocytic bacilli that reacted positively to periodic acid-Schiff staining. This led to the suspicion of WD, which was subsequently confirmed through small bowel biopsies. She initiated treatment with ceftriaxone and experienced rapid clinical improvement. WD poses a diagnostic challenge. The signs and symptoms are often nonspecific and can result in misdiagnosis as a rheumatic or neoplastic disease. The presentation with DVT, while unusual, has been reported as a manifestation of WD.
PubMed: 38344639
DOI: 10.7759/cureus.51991 -
Journal of Ethnopharmacology May 2024Wuji Wan (WJW) is a traditional Chinese medicine formula that can be found in the "Prescriptions of Taiping Benevolent Dispensary" that has been employed in treating...
The active components and potential mechanisms of Wuji Wan in the treatment of ethanol-induced gastric ulcer: An integrated metabolomics, network pharmacology and experimental validation.
ETHNOPHARMACOLOGICAL RELEVANCE
Wuji Wan (WJW) is a traditional Chinese medicine formula that can be found in the "Prescriptions of Taiping Benevolent Dispensary" that has been employed in treating gastric discomfort, burning epigastric pain, and gastric reflux for hundreds of years and has shown promise for treating gastric ulcers (GUs). However, the active components and mechanism of action against GUs remain unclear.
AIM OF THE STUDY
The aim of this study was to explore the active components of WJW and elucidate the underlying mechanism involved in treating GUs.
MATERIALS AND METHODS
Initially, cell viability was measured by a cell counting kit 8 (CCK-8) assay to evaluate the efficacy of WJW-containing serum in vitro. The gastric ulcer index, ulcer inhibition rate, hematoxylin and staining (H&E), and periodic acid-Schiff (PAS) staining were used to evaluate the therapeutic effect of WJW in vivo. Subsequently, the levels of inflammatory factors and oxidative stress factors were determined using an enzyme-linked immunosorbent assays (ELISA) on in vitro and in vivo samples. Additionally, UPLC-Q Exactive Plus Orbitrap HRMS was used to analyze the components that were absorbed into the blood of WJW and its metabolites. Network pharmacology and metabolomics were subsequently used to identify the targets and pathways. Real-time quantitative PCR (RT‒qPCR) and Western blotting were used to verify the mRNA and protein levels of the key targets and pathways. Finally, the active components were identified by molecular docking to verify the binding stability of the components and key targets.
RESULTS
WJW-containing serum ameliorated ethanol-induced damage in GES-1 cells and promoted cell healing. WJW-containing serum reduced IL-6, TNF-α, MDA, and LDH levels while increasing IL-10, SOD, and T-AOC levels in the cells. Moreover, WJW treatment resulted in decreased IL-6, TNF-α, and MDA levels and increased IL-10, SOD, PGE and NO levels in GUs rats. In addition, eight components of WJW were absorbed into the blood. The network pharmacology results revealed 192 common targets for blood entry components and GUs, and KEGG analysis revealed that apoptosis signaling pathways were the main pathways involved in WJW activity against GUs. Metabolomic screening was used to identify 13 differential metabolites. There were 23 common targets for blood entry components, GUs, and differential metabolites, with the key targets TNF (TNF-α), AKT1, PTGS2 (COX2) and MAPK1. WJW significantly inhibited the expression of Bax, Caspase-9, Caspase-3, cleaved Caspase-9, cleaved Caspase-3, TNF-α, COX2, and p-p44/42 MAPK while promoting the expression of Bcl-2 and p-AKT1. Molecular docking revealed that the active components of WJW for the treatment of GUs are berberine, palmatine, coptisine, evodiamine, rutaecarpine, evocarpine, and paeoniflorin.
CONCLUSIONS
WJW treatment reduces inflammation and oxidative stress injury and inhibits apoptosis signaling pathways. The main active components are berberine, palmatine, coptisine, evodiamine, rutaecarpine, evocarpine, and paeoniflorin. In this paper, we provide a new strategy for exploring the active components of traditional Chinese medicine formulas for the treatment of diseases based on target mechanisms.
Topics: Animals; Rats; Stomach Ulcer; Caspase 3; Caspase 9; Interleukin-10; Berberine; Cyclooxygenase 2; Interleukin-6; Molecular Docking Simulation; Network Pharmacology; Tumor Necrosis Factor-alpha; Superoxide Dismutase; Drugs, Chinese Herbal; Glucosides; Monoterpenes
PubMed: 38341112
DOI: 10.1016/j.jep.2024.117901 -
Ecotoxicology and Environmental Safety Mar 2024In order to comprehend the underlying mechanisms contributing to the development and exacerbation of asthma resulting from exposure to fine particulate matter (PM2.5),...
Oxidative stress-mediated activation of FTO exacerbates impairment of the epithelial barrier by up-regulating IKBKB via N6-methyladenosine-dependent mRNA stability in asthmatic mice exposed to PM2.5.
In order to comprehend the underlying mechanisms contributing to the development and exacerbation of asthma resulting from exposure to fine particulate matter (PM2.5), we established an asthmatic model in fat mass and obesity-associated gene knockdown mice subjected to PM2.5 exposure. Histological analyses using hematoxylin-eosin (HE) and Periodic Acid-Schiff (PAS) staining revealed that the down-regulation of the fat mass and obesity-associated gene (Fto) expression significantly ameliorated the pathophysiological alterations observed in asthmatic mice exposed to PM2.5. Furthermore, the down-regulation of Fto gene expression effectively attenuated damage to the airway epithelial barrier. Additionally, employing in vivo and in vitro models, we elucidated that PM2.5 modulated FTO expression by inducing oxidative stress. Asthmatic mice exposed to PM2.5 exhibited elevated Fto expression, which correlated with increased levels of reactive oxygen species. Similarly, when cells were exposed to PM2.5, FTO expression was up-regulated in a ROS-dependent manner. Notably, the administration of N-acetyl cysteine successfully reversed the PM2.5-induced elevation in FTO expression. Concurrently, we performed transcriptome-wide Methylated RNA immunoprecipitation Sequencing (MeRIP-seq) analysis subsequent to PM2.5 exposure. Through the implementation of Gene Set Enrichment Analysis and m6A-IP-qPCR, we successfully identified inhibitor of nuclear factor kappa B kinase subunit beta (IKBKB) as a target gene regulated by FTO. Interestingly, exposure to PM2.5 led to increased expression of IKBKB, while m6A modification on IKBKB mRNA was reduced. Furthermore, our investigation revealed that PM2.5 also regulated IKBKB through oxidative stress. Significantly, the down-regulation of IKBKB effectively mitigated epithelial barrier damage in cells exposed to PM2.5 by modulating nuclear factor-kappa B (NF-κB) signaling. Importantly, we discovered that decreased m6A modification on IKBKB mRNA facilitated by FTO enhanced its stability, consequently resulting in up-regulation of IKBKB expression. Collectively, our findings propose a novel role for FTO in the regulation of IKBKB through m6A-dependent mRNA stability in the context of PM2.5-induced oxidative stress. Therefore, it is conceivable that the utilization of antioxidants or inhibition of FTO could represent potential therapeutic strategies for the management of asthma exacerbated by PM2.5 exposure.
Topics: Animals; Mice; Alpha-Ketoglutarate-Dependent Dioxygenase FTO; Asthma; I-kappa B Kinase; Obesity; Oxidative Stress; Particulate Matter; RNA Stability; RNA, Messenger
PubMed: 38325270
DOI: 10.1016/j.ecoenv.2024.116067 -
Medical Mycology Case Reports Mar 2024We report a case of a 20-year-old young woman with a large stucco keratosis in the mons veneris, one of the clinical variants of Seborrheic keratoses (SKs). Periodic...
We report a case of a 20-year-old young woman with a large stucco keratosis in the mons veneris, one of the clinical variants of Seborrheic keratoses (SKs). Periodic acid-Schiff staining revealed a large number of spores in the stratum corneum. After oral antifungal treatment with itraconazole for 4 weeks, the benign tumor was completely cleared without residue or recurrence, which may open a new perspective for exploring the pathogenesis of SKs.
PubMed: 38323302
DOI: 10.1016/j.mmcr.2024.100630 -
Nature Communications Feb 2024Cryopyrin-associated periodic syndrome (CAPS) is an autoinflammatory condition resulting from monoallelic NLRP3 variants that facilitate IL-1β production. Although...
Cryopyrin-associated periodic syndrome (CAPS) is an autoinflammatory condition resulting from monoallelic NLRP3 variants that facilitate IL-1β production. Although these are gain-of-function variants characterized by hypersensitivity to cell priming, patients with CAPS and animal models of the disease may present inflammatory flares without identifiable external triggers. Here we find that CAPS-associated NLRP3 variants are forming constitutively active inflammasome, which induce increased basal cleavage of gasdermin D, IL-18 release and pyroptosis, with a concurrent basal pro-inflammatory gene expression signature, including the induction of nuclear receptors 4 A. The constitutively active NLRP3-inflammasome of CAPS is responsive to the selective NLRP3 inhibitor MCC950 and its activation is regulated by deubiquitination. Despite their preactivated state, the CAPS inflammasomes are responsive to activation of the NF-κB pathway. NLRP3-inflammasomes with CAPS-associated variants affect the immunometabolism of the myeloid compartment, leading to disruptions in lipids and amino acid pathways and impaired glycolysis, limiting IL-1β production. In summary, NLRP3 variants causing CAPS form a constitutively active inflammasome inducing pyroptosis and IL-18 release without cell priming, which enables the host's innate defence against pathogens while also limiting IL-1β-dependent inflammatory episodes through immunometabolism modulation.
Topics: Animals; Humans; NLR Family, Pyrin Domain-Containing 3 Protein; Inflammasomes; Interleukin-18; Cryopyrin-Associated Periodic Syndromes; Sulfonamides; Interleukin-1beta
PubMed: 38321014
DOI: 10.1038/s41467-024-44990-0