Genome-Wide Characterization of Somatic Mutation Patterns in Cloned Dogs Reveals Implications for Neuronal Function, Tumorigenesis, and Aging.

Studies on somatic mutations in cloned animals have revealed slight genetic variances between clones and their originals, but have yet to identify the precise effects of these differences within the organism. Somatic mutations contribute to aging and are implicated in tumor development and other age-related diseases. Thus, we compared whole genome sequencing data from an original dog with that of cloned dogs, identifying candidate somatic mutations that were disproportionately located within genes previously implicated in aging. The substitutional signature of cloning-specific somatic mutations mirrored the uniform distribution characteristic of the signature associated with human aging. Further analysis of genes revealed significant enrichment of traits associated with body size as well as the molecular mechanisms underlying neuronal function and tumorigenesis. Overall, the somatic mutations found in cloned dogs may indicate a conserved mechanism driving aging across species and a broad spectrum of pathway alterations.

Pharmacokinetics and Biodistribution of Phages and their Current Applications in Antimicrobial Therapy.

Antimicrobial resistance remains a critical global health concern, necessitating the investigation of alternative therapeutic approaches. With the diminished efficacy of conventional small molecule drugs due to the emergence of highly resilient bacterial strains, there is growing interest in the potential for alternative therapeutic modalities. As naturally occurring viruses of bacteria, bacteriophage (or phage) are being re-envisioned as a platform to engineer properties that can be tailored to target specific bacterial strains and employ diverse antibacterial mechanisms. However, limited understanding of key pharmacological properties of phage is a major challenge to translating its use from preclinical to clinical settings. Here, we review modern advancements in phage-based antimicrobial therapy and discuss the in vivo pharmacokinetics and biodistribution of phage, addressing critical challenges in their application that must be overcome for successful clinical implementation.

Therapeutic potential of BMSC-conditioned medium in an in vitro model of renal fibrosis using the RPTEC/TERT1 cell line.

We investigated the therapeutic potential of bone marrow-derived mesenchymal stem cell-conditioned medium (BMSC-CM) on immortalized renal proximal tubule epithelial cells (RPTEC/ TERT1) in a fibrotic environment. To replicate the increased stiffness characteristic of kidneys in chronic kidney disease, we utilized polyacrylamide gel platforms. A stiff matrix was shown to increase α-smooth muscle actin (α-SMA) levels, indicating fibrogenic activation in RPTEC/TERT1 cells. Interestingly, treatment with BMSC-CM resulted in significant reductions in the levels of fibrotic markers (α-SMA and vimentin) and increases in the levels of the epithelial marker E-cadherin and aquaporin 7, particularly under stiff conditions. Furthermore, BMSC-CM modified microRNA (miRNA) expression and reduced oxidative stress levels in these cells. Our findings suggest that BMSC-CM can modulate cellular morphology, miRNA expression, and oxidative stress in RPTEC/TERT1 cells, highlighting its therapeutic potential in fibrotic kidney disease. [BMB Reports 2024; 57(2): 116-121].

Safety of COVID-19 Vaccination During Pregnancy and Lactation: A VigiBase Analysis.

BACKGROUND: There is limited evidence on the safety of coronavirus disease 2019 (COVID-19) vaccination during pregnancy and lactation. Thus, we aimed to evaluate the association between COVID-19 vaccination during pregnancy and lactation and reporting risk of adverse pregnancy or lactation outcomes. METHODS: Using VigiBase, we performed a disproportionality analysis with case/non case design. Cases were defined based on the Standardized MedDRA Queries (SMQs) of "pregnancy and neonatal topics" and non-cases were defined as all other adverse events. We included all reports with COVID-19 vaccines as the suspected cause. Using the full database as the comparators, reporting odds ratios (RORs) with 95% confidence intervals (CIs) were estimated by logistic regression while adjusting for maternal age. Infants' age and sex were additionally adjusted in analyzing the risk of COVID-19 vaccination during lactation. RESULTS: We identified 10,266 and 6,474 reports with the SMQ of "pregnancy and neonatal topics" associated with COVID-19 vaccines during pregnancy and lactation, respectively. No significant RORs of adverse pregnancy outcomes associated with COVID-19 vaccines during pregnancy were observed; however, "functional lactation disorders" showed significant disproportionality during lactation with adjusted ROR of 1.48 (95% CI, 1.21-1.79). Further analysis that analyzed "functional lactation disorders" at a preferred term level, showed higher ROR in mastitis (2.76 [95% CI, 1.45-5.27]). CONCLUSION: Overall, we did not observe a positive association between COVID-19 vaccination during pregnancy and risk of reporting adverse pregnancy outcomes. However, we found a significant disproportionate reporting association between COVID-19 vaccination during lactation and "functional lactation disorders", specifically mastitis. Continuous surveillance is warranted to confirm the safety of COVID-19 vaccine during pregnancy and lactation.

Diagnosis of Crohn's disease and ulcerative colitis using the microbiome.

BACKGROUND: Inflammatory bowel disease (IBD) is a multifactorial chronic inflammatory disease resulting from dysregulation of the mucosal immune response and gut microbiota. Crohn's disease (CD) and ulcerative colitis (UC) are difficult to distinguish, and differential diagnosis is essential for establishing a long-term treatment plan for patients. Furthermore, the abundance of mucosal bacteria is associated with the severity of the disease. This study aimed to differentiate and diagnose these two diseases using the microbiome and identify specific biomarkers associated with disease activity. RESULTS: Differences in the abundance and composition of the microbiome between IBD patients and healthy controls (HC) were observed. Compared to HC, the diversity of the gut microbiome in patients with IBD decreased; the diversity of the gut microbiome in patients with CD was significantly lower. Sixty-eight microbiota members (28 for CD and 40 for UC) associated with these diseases were identified. Additionally, as the disease progressed through different stages, the diversity of the bacteria decreased. The abundances of Alistipes shahii and Pseudodesulfovibrio aespoeensis were negatively correlated with the severity of CD, whereas the abundance of Polynucleobacter wianus was positively correlated. The severity of UC was negatively correlated with the abundance of A. shahii, Porphyromonas asaccharolytica and Akkermansia muciniphilla, while it was positively correlated with the abundance of Pantoea candidatus pantoea carbekii. A regularized logistic regression model was used for the differential diagnosis of the two diseases. The area under the curve (AUC) was used to examine the performance of the model. The model discriminated UC and CD at an AUC of 0.873 (train set), 0.778 (test set), and 0.633 (validation set) and an area under the precision-recall curve (PRAUC) of 0.888 (train set), 0.806 (test set), and 0.474 (validation set). CONCLUSIONS: Based on fecal whole-metagenome shotgun (WMS) sequencing, CD and UC were diagnosed using a machine-learning predictive model. Microbiome biomarkers associated with disease activity (UC and CD) are also proposed.

Diaphragmatic Endometriosis Presenting as Recurrent Catamenial Pneumothorax: A Case Report.

Catamenial pneumothorax is one of the most common extra-pelvic presentations of endometriosis, with the gastrointestinal tract being the most common location. Catamenial pneumothorax is defined as spontaneous recurrent pneumothorax occurring in women of reproductive age in a temporal relationship with menses. Symptoms include dyspnea, sharp chest pain, and hypoxemia. A much rarer presentation is the involvement of endometriosis with the diaphragm. In this case, we present a 31-year-old female who presented with signs of pneumothorax. She has had multiple episodes leading to suspicion of catamenial pneumothorax. However, it wasn't until her surgery that the extent of diaphragmatic involvement, characterized by numerous holes secondary to endometriosis, was discovered. She was surgically treated, which led to a drastic improvement in symptoms and a reduction in subsequent episodes. We hope that this case can add to the current limited literature on diaphragmatic endometriosis cases. Since this patient presented with mainly catamenial pneumothorax symptoms, we urge clinicians to still consider diaphragmatic involvement as a primary cause in patients with recurrent episodes of pneumothorax.

miR-96-5p targets PTEN to mediate sunitinib resistance in clear cell renal cell carcinoma.

A multiple receptor tyrosine kinase inhibitor, sunitinib, is a first-line therapy for clear cell renal cell carcinoma (CCRCC). Unfortunately, it has the major challenges of low initial response rate and resistance after about one year of treatment. Here we evaluated a microRNA (miRNA) and its target responsible for sunitinib resistance. Using miRNA profiling, we identified miR-96-5p upregulation in tumors from sunitinib-resistant CCRCC patients. By bioinformatic analysis, PTEN was selected as a potential target of miR-96-5p, which showed low levels in tumors from sunitinib-resistant CCRCC patients. Furthermore, PTEN and miR-96-5p levels were negatively correlated in a large The Cancer Genome Atlas kidney renal clear cell carcinoma cohort and high miR-96 and low PTEN represented poor prognosis in this cohort. Additionally, four-week sunitinib treatment increased miR-96-5p and decreased PTEN only in tumors from a sunitinib-resistant patient-derived xenograft model. We found a novel miR-96-5p binding site in the PTEN 3' UTR and confirmed direct repression by luciferase reporter assay. Furthermore, we demonstrated that repression of PTEN by miR-96-5p increased cell proliferation and migration in sunitinib-treated cell lines. These results highlight the direct suppression of PTEN by miR-96-5p and that high miR-96-5p and low PTEN are partially responsible for sunitinib resistance and poor prognosis in CCRCC.

Design of PD-1-decorated nanocages targeting tumor-draining lymph node for promoting T cell activation.

Targeted delivery of immunomodulatory molecules to the lymph nodes is an attractive means of improving the efficacy of anti-cancer immunotherapy. In this study, to improve the efficacy of PD-1 blockade-based therapy, nanocages were designed by surface engineering to decorate a programmed cell death protein 1 (PD-1) that is capable of binding against programmed death-ligand 1 (PD-L1) and -ligand 2 (PD-L2). This nanocage-mediated multivalent interaction remarkably increases the binding affinity and improves the antagonistic activity compared to free soluble PD-1. In addition, with the desirable nanocage size for optimal tumor-draining lymph node (TDLN) targeting (approximately 20 nm), rapid draining and increased accumulation into the TDLNs were observed. Moreover, the interference of the PD-1/PD-L axis with ultra-high affinity in the tumor microenvironment (effector phase) and the TDLNs (cognitive phase) significantly enhances the dendritic cell-mediated tumor-specific T cell activation. This characteristic successfully inhibited tumor growth and induced complete tumor eradication in some mice. Thus, the delivery of immunomodulatory molecules with nanocages can be a highly efficient strategy to achieve stronger anti-tumor immunity.

Epigenetic regulation of miR-29a/miR-30c/DNMT3A axis controls SOD2 and mitochondrial oxidative stress in human mesenchymal stem cells.

The use of human mesenchymal stem cells (hMSCs) in clinical applications requires large-scale cell expansion prior to administration. However, the prolonged culture of hMSCs results in cellular senescence, impairing their proliferation and therapeutic potentials. To understand the role of microRNAs (miRNAs) in regulating cellular senescence in hMSCs, we globally depleted miRNAs by silencing the DiGeorge syndrome critical region 8 (DGCR8) gene, an essential component of miRNA biogenesis. DGCR8 knockdown hMSCs exhibited severe proliferation defects and senescence-associated alterations, including increased levels of reactive oxygen species (ROS). Transcriptomic analysis revealed that the antioxidant gene superoxide dismutase 2 (SOD2) was significantly downregulated in DGCR8 knockdown hMSCs. Moreover, we found that DGCR8 silencing in hMSCs resulted in hypermethylation in CpG islands upstream of SOD2. 5-aza-2'-deoxycytidine treatment restored SOD2 expression and ROS levels. We also found that these effects were dependent on the epigenetic regulator DNA methyltransferase 3 alpha (DNMT3A). Using computational and experimental approaches, we demonstrated that DNMT3A expression was regulated by miR-29a-3p and miR-30c-5p. Overexpression of miR-29a-3p and/or miR-30c-5p reduced ROS levels in DGCR8 knockdown hMSCs and rescued proliferation defects, mitochondrial dysfunction, and premature senescence. Our findings provide novel insights into hMSCs senescence regulation by the miR-29a-3p/miR-30c-5p/DNMT3A/SOD2 axis.

Priming with Toll-like receptor 3 agonist or interferon-gamma enhances the therapeutic effects of human mesenchymal stem cells in a murine model of atopic dermatitis.

BACKGROUND: Atopic dermatitis (AD) is a chronic and relapsing inflammatory skin disease. Great efforts have been recently made to treat AD using mesenchymal stem cells (MSCs), which have immunomodulatory functions. However, the immunomodulatory effects of MSCs need to be enhanced for clinical application in the treatment of AD. OBJECTIVES: To evaluate and characterise the therapeutic effects of human Wharton's jelly-derived MSCs (WJ-MSCs) primed with the Toll-like receptor 3 agonist poly I:C or interferon-γ (IFN-γ) in a murine model of AD. METHODS: Mice were treated with Aspergillus fumigatus extract to induce AD and then subcutaneously injected with non-primed, poly I:C-primed or IFN-γ-primed WJ-MSCs. Clinical symptom scores, transepidermal water loss (TEWL), histological characteristics and cytokine levels were determined. Transcriptome profiling and pathway analyses of primed WJ-MSCs were conducted. RESULTS: The clinical symptom score and TEWL in skin lesions were reduced in mice administered non-primed and primed WJ-MSCs. Epidermal thickness and inflammatory cell infiltration in skin lesions were reduced more in mice administered primed WJ-MSCs than in mice administered non-primed WJ-MSCs. Secretion of interleukin-17 was significantly reduced in skin draining lymph nodes of mice administered primed WJ-MSCs. Genomics and bioinformatics analyses demonstrated the enrichment of certain pathways specifically in WJ-MSCs primed with poly I:C or IFN-γ. CONCLUSIONS: Priming with poly I:C- or IFN-γ improved the therapeutic effects of WJ-MSCs in a murine model of AD. This study suggests that priming with poly I:C or IFN-γ enhances the immunomodulatory functions of WJ-MSCs and can be used as a novel therapeutic approach for AD.

Nanofabrication of bio-self assembled monolayer and its electrochemical property for toxicant detection.

Cyclic voltammetry (CV) has been used to investigate the electrochemical behavior of a glutathione (GSH) self assembled monolayer on modified gold electrodes (Bio-SAM). The GSH monolayer exhibits an influence on electrode surface activity. Electrochemically immobilized dsDNA onto a Cyt c/GSH-SAM/Au electrode, which is useful for the fabrication of a nanobiosensing device. The immobilized Cyt c followed by dsDNA immobilized films maintained its surface activity and finally dsDNA/Cyt c/GSH-SAM/Au electrode, targeted for the detection of toxicants. The films were characterized by CV, DPV, and AFM. The differential pulse voltammetry (DPV) technique was applied to detect three kinds of common toxins, 2-aminoanthracene (2-AA), 3-bromobenzanthrone (3-BBA) and bisphenol A (BPhA). The electrochemical signals showed good inverse relationship with the increase of concentrations of toxicants. Our proposed system based on electrochemical method with nanoscale film technology can be applied at highly sensitive biosensor for detecting various toxic chemicals.

Charge retention of self-assembled ferredoxin monolayer by the reduction-oxidation control for biomemory device.

The oxidation-reduction control to store charges in self-assembled ferredoxin layer was investigated by scanning electrochemical method. Micro sized spot arrays consisting of ferredoxin proteins which used as the storage element were formed on chemically modified gold coated glass by micro contanct printing method. The formation of ferredoxin array was confirmed by the atomic force microscopy. The charge store was investigated by external applied reduction potential to ferredoxin as a write function, and the stored reducing charge was measured as a read function of storage applications. In the reduction state, the stored charge was maintained for around 90 sec. This ferredoxin layer can be used as the molecular size information storage by applying the reducing potential and measuring the current flow when achieving the current of individual ferredoxin molecule.

Signal enhancement of surface plasmon resonance based immunosensor using gold nanoparticle-antibody complex for beta-amyloid (1-40) detection.

Numerous studies have indentified that beta-amyloid (1-40) in cerebrospinal fluid as a potential biomarker for Alzheimer's disease. In order for early detection of the Alzheimer's disease, an ultrasensitive diagnostic tool is required. In this study, an ultrasensitive surface plasmon resonance (SPR) based immunosensor for beta3-amyloid (1-40) was developed and its signal enhanced (1-40) with a gold (Au) nanoparticle-antibody complex. Antibodies to beta3-amyloid (1-40) were immobilized on the Au surface leading to a highly efficient immunoreaction due to the fact the paratope of the antibody faced in the opposite direction to the solid surface. The surface morphology of the bio-surface was investigated by using scanning tunneling microscopy (STM). The binding process of antibody fragments to the Au surface, target analytes, and Au nanoparticle-antibody complexes were monitored using SPR. The plot of SPR angle difference versus beta3-amyloid (1-40) concentration shows a linear correlation over a concentration range of nine orders of magnitude, having a detetion limit up to 1 fg/ml.

Electrical detection of beta-amyloid (1-40) using scanning tunneling microscopy.

Numerous studies have shown that the presence of beta-amyloid (1-40) in cerebrospinal fluid can be used as a potential biomarker for Alzheimer's disease. Identifying biomarkers for Alzheimer's disease is highly important because these biomarkers could be used to establish the diagnosis before the disease reaches clinical severity. In this study, a vertically configured electrical detection system associated with scanning tunneling microscopy (STM) was used to characterize antigen-antibody binding interactions. The proposed technique can be easily utilized to construct a multiple measurement system in a protein chip. The immunocomplexes used in the model protein comprise beta-amyloid (1-40), corresponding antibody fragments, and gold nanoparticle-antibody conjugates. The electrical tunneling current between the STM tip and these complexes exhibited a peak-like pulse, where the frequency of these pulses was dependent on the surface density of bound complexes. Hence, a quantitative measurement of beta-amyloid concentration from a periodogram analysis of peak frequency was successfully achieved at concentrations as low as 1fg/mL.

Ultra-sensitive immunosensor for beta-amyloid (1-42) using scanning tunneling microscopy-based electrical detection.

An ultra-sensitive immunosensor for beta-amyloid is crucial because beta-amyloid is an important challenging marker to detect for early diagnosis of Alzheimer's disease. In this study, a vertically configured electrical detection system was developed based on scanning tunneling microscopy (STM) to detect antigen-antibody binding events. This technique could be used to easily construct a multiple measurement system in a biochip. We utilized immunocomplexes comprised of the model protein, beta-amyloid (1-42), corresponding antibody fragments, and gold (Au) nanoparticles-antibody conjugates for an immunosensor for Alzheimer's disease. The electrical tunneling current between the STM tip and these complexes exhibited a peak-like pulse, the frequency of which depended on the density of the bound complexes on the surface. We could therefore quantitatively measure beta-amyloid (1-42) concentrations as low as 10fg/mL using periodogram analysis of the peak frequency. Since this method accurately quantified much smaller amounts of beta-amyloid (1-42) than traditional immunosensors, this system shows promise as an ultra-sensitive immunodetection method.

Analysis of direct immobilized recombinant protein G on a gold surface.

For the immobilization of IgG, various techniques such as chemical linker, thiolated protein G methods, and fragmentation of antibodies have been reported [Y.M. Bae, B.K. Oh, W. Lee, W.H. Lee, J.W. Choi, Biosensors Bioelectron. 21 (2005) 103; W. Lee, B.K. Oh, W.H. Lee, J.W. Choi, Colloids Surf. B-Biointerfaces, 40 (2005) 143; A.A. Karyakin, G.V. Presnova, M.Y. Rubtsova, A.M. Egorov, Anal. Chem. 72 (2000) 3805]. Here, we modified the immunoglobulin Fc-binding B-domain of protein G to contain two cysteine residues at its C-terminus by a genetic engineering technique. The resulting recombinant protein, RPGcys, retained IgG-binding activity in the same manner as native protein G. RPGcys was immobilized on a gold surface by strong affinity between thiol of cysteine and gold. The orientations of both IgG layers immobilized on the base recombinant protein Gs were analyzed by fluorescence microscope, atomic force microscope (AFM), and surface plasmon resonance (SPR). Our data revealed that IgG-binding activity of RPGcys on gold surface significantly increased in comparison to wild type of protein G (RPGwild), which was physically adsorbed due to absence of cysteine residue. Immobilization of highly oriented antibodies based on cysteine-modified protein G could be useful for the fabrication of immunosensor systems.

Surface morphology and interdiffusion of LiF in Alq3-based organic light-emitting devices.

Highly efficient organic light-emitting devices (OLEDs) have been realized by insertion of a thin insulating lithium fluoride (LiF) layer between aluminum (Al) cathode and an electron transport layer, tris-(8-hydroxyquinoline) aluminum (Alq(3)). In this paper, we study the surface morphology of LiF on Alq(3) by synchrotron X-ray scattering and atomic force microscopy (AFM) as a function of thickness of LiF. We also study the interdiffusion of LiF into Al cathode as well as into Alq(3) layer as a function of temperature. Initially, LiF molecules are distributed randomly as clusters on the Alq(3) layer and then gradually form a layer as increasing LiF thickness. The interdiffusion of LiF into Al occurs more actively than into Alq(3) in annealing process. LiF on Alq(3) induces the ordering of Al to (111) direction strongly with increasing LiF thickness.