Biomolecules

21 pages, 6484 KiB

Open AccessEditor’s ChoiceArticle

Untargeted Lipidomic Approach for Studying Different Nervous System Tissues of the Murine Model of Krabbe Disease

by Husam B. R. Alabed, Ambra Del Grosso, Valeria Bellani, Lorena Urbanelli, Sara Carpi, Miriam De Sarlo, Lorenzo Bertocci, Laura Colagiorgio, Sandra Buratta, Luca Scaccini, Dorotea Frongia Mancini, Ilaria Tonazzini, Marco Cecchini, Carla Emiliani and Roberto Maria Pellegrino

Biomolecules 2023, 13(10), 1562; https://doi.org/10.3390/biom13101562 - 23 Oct 2023

Cited by 4 | Viewed by 2070

Abstract

Krabbe disease is a rare neurodegenerative disease with an autosomal recessive character caused by a mutation in the GALC gene. The mutation leads to an accumulation of psychosine and a subsequent degeneration of oligodendrocytes and Schwann cells. Psychosine is the main biomarker of [...] Read more.

Krabbe disease is a rare neurodegenerative disease with an autosomal recessive character caused by a mutation in the GALC gene. The mutation leads to an accumulation of psychosine and a subsequent degeneration of oligodendrocytes and Schwann cells. Psychosine is the main biomarker of the disease. The Twitcher mouse is the most commonly used animal model to study Krabbe disease. Although there are many references to this model in the literature, the lipidomic study of nervous system tissues in the Twitcher model has received little attention. This study focuses on the comparison of the lipid profiles of four nervous system tissues (brain, cerebellum, spinal cord, and sciatic nerve) in the Twitcher mouse compared to the wild-type mouse. Altogether, approximately 230 molecular species belonging to 19 lipid classes were annotated and quantified. A comparison at the levels of class, molecular species, and lipid building blocks showed significant differences between the two groups, particularly in the sciatic nerve. The in-depth study of the lipid phenotype made it possible to hypothesize the genes and enzymes involved in the changes. The integration of metabolic data with genetic data may be useful from a systems biology perspective to gain a better understanding of the molecular basis of the disease. Full article

(This article belongs to the Special Issue Recent Advances in Neurological Diseases)

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11 pages, 1595 KiB

Open AccessArticle

An Introduced RNA-Only Approach for Plasmid Curing via the CRISPR-Cpf1 System in Saccharomyces cerevisiae

by Bo-Chou Chen, Yu-Zhen Chen and Huan-Yu Lin

Biomolecules 2023, 13(10), 1561; https://doi.org/10.3390/biom13101561 - 23 Oct 2023

Viewed by 2958

Abstract

The CRISPR-Cas system has been widely used for genome editing due to its convenience, simplicity and flexibility. Using a plasmid-carrying Cas protein and crRNA or sgRNA expression cassettes is an efficient strategy in the CRISPR-Cas genome editing system. However, the plasmid remains in [...] Read more.

The CRISPR-Cas system has been widely used for genome editing due to its convenience, simplicity and flexibility. Using a plasmid-carrying Cas protein and crRNA or sgRNA expression cassettes is an efficient strategy in the CRISPR-Cas genome editing system. However, the plasmid remains in the cells after genome editing. Development of general plasmid-curing strategies is necessary. Based on our previous CRISPR-Cpf1 genome-editing system in Saccharomyces cerevisiae, the crRNA, designed for the replication origin of the CRISPR-Cpf1 plasmid, and the ssDNA, as a template for homologous recombination, were introduced for plasmid curing. The efficiency of the plasmid curing was 96 ± 4%. In addition, we further simplified the plasmid curing system by transforming only one crRNA into S. cerevisiae, and the curing efficiency was about 70%. In summary, we have developed a CRISPR-mediated plasmid-curing system. The RNA-only plasmid curing system is fast and easy. This plasmid curing strategy can be applied in broad hosts by designing crRNA specific for the replication origin of the plasmid. The plasmid curing system via CRISPR-Cas editing technology can be applied to produce traceless products without foreign genes and to perform iterative processes in multiple rounds of genome editing. Full article

(This article belongs to the Special Issue Yeast Models for Gene Regulation)

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14 pages, 1820 KiB

Open AccessArticle

Historical Cohort Study of Congenital Isolated Hypoganglionosis of the Intestine: Determining the Best Surgical Interventions

by Yohei Yamada, Teizaburo Mori, Nobuhiro Takahashi, Takumi Fujimura, Motohiro Kano, Mototoshi Kato, Masataka Takahashi, Naoki Shimojima, Toshihiko Watanabe, Takako Yoshioka, Yutaka Kanamori, Tatsuo Kuroda and Akihiro Fujino

Biomolecules 2023, 13(10), 1560; https://doi.org/10.3390/biom13101560 - 23 Oct 2023

Viewed by 1899

Abstract

No standard diagnostic method or surgical treatment for congenital isolated hypoganglionosis (CIHG) has been established. This study aimed to analyze the clinical outcomes of patients with CIHG and identify the best surgical interventions provided thus far. Data on surgical interventions in 19 patients [...] Read more.

No standard diagnostic method or surgical treatment for congenital isolated hypoganglionosis (CIHG) has been established. This study aimed to analyze the clinical outcomes of patients with CIHG and identify the best surgical interventions provided thus far. Data on surgical interventions in 19 patients were collected between 1992 and 2020, including the type of enterostomy, type of revision, and length of the intestines. Ganglion cells in the myenteric plexus were enumerated using Hu C/D staining. The ratio of the length of the small intestine to its height was defined as the intestinal ratio (IR). The outcomes were assessed using the stoma output, growth parameters including the body mass index (BMI), and parenteral nutrition (PN) dependency. All patients required a diverting enterostomy. The IR ranged from 0.51 to 1.75 after multiple non-transplant surgeries. The stoma types were tube-stoma, end-stoma, Santulli-type, and Bishop–Koop (BK)-type. Patients with Santulli- or BK-type stomas had better BMIs and less PN dependency in terms of volume than those with end-stomas or tube-stomas. Two patients with BK-type stomas were off PN, and three who underwent an intestinal transplantation (Itx) achieved enteral autonomy. The management of CIHG involves a precise diagnosis using Hu C/D staining, neonatal enterostomy, and stoma revision using the adjusted IR and Itx if other treatments do not enable enteral autonomy. Full article

(This article belongs to the Special Issue Pathogenesis and Potential Treatments of Neurointestinal Diseases)

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20 pages, 4666 KiB

Open AccessArticle

Designing Nanomedicines for Breast Cancer Therapy

by Saba Abbasi Dezfouli, Amarnath P. Rajendran, Jillian Claerhout and Hasan Uludag

Biomolecules 2023, 13(10), 1559; https://doi.org/10.3390/biom13101559 - 22 Oct 2023

Cited by 1 | Viewed by 1882

Abstract

In 2020, breast cancer became the most diagnosed cancer worldwide. Conventional chemotherapies have major side effects due to their non-specific activities. Alternatively, short interfering RNA(siRNA)-carrying nanoparticles (NPs) have a high potential to overcome this non-specificity. Lipid-substituted polyethyleneimine (PEI) polymers (lipopolymers) have been reported [...] Read more.

In 2020, breast cancer became the most diagnosed cancer worldwide. Conventional chemotherapies have major side effects due to their non-specific activities. Alternatively, short interfering RNA(siRNA)-carrying nanoparticles (NPs) have a high potential to overcome this non-specificity. Lipid-substituted polyethyleneimine (PEI) polymers (lipopolymers) have been reported as efficient non-viral carriers of siRNA. This study aims to engineer novel siRNA/lipopolymer nanocomplexes by incorporating anionic additives to obtain gene silencing through siRNA activity with minimal nonspecific toxicity. We first optimized our polyplexes in GFP+ MDA-MB-231 cells to effectively silence the GFP gene. Inclusion of phosphate buffer with pH 8.0 as complex preparation media and N-Lauroylsarcosine Sodium Salt as additive, achieved ~80% silencing with the least amount of undesired cytotoxicity, which was persistent for at least 6 days. The survivin gene was then selected as a target in MDA-MB-231 cells since there is no strong drug (i.e., small organic molecule) for inhibition of its oncogenic activity. The qRT-PCR, flow cytometry analysis and MTT assay revealed >80% silencing, ~95% cell uptake and >70% cell killing by the same formulation. We conclude that our lipopolymer can be further investigated as a lead non-viral carrier for breast cancer gene therapy. Full article

(This article belongs to the Special Issue Molecular Targets for Breast Cancer Therapy)

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15 pages, 3540 KiB

Open AccessArticle

Unraveling the Metabolic Changes in Acute Pancreatitis: A Metabolomics-Based Approach for Etiological Differentiation and Acute Biomarker Discovery

by Greta Dancu, Cristi Tarta, Carmen Socaciu, Felix Bende, Mirela Danila, Roxana Sirli, Ioan Sporea, Bogdan Miutescu and Alina Popescu

Biomolecules 2023, 13(10), 1558; https://doi.org/10.3390/biom13101558 - 22 Oct 2023

Viewed by 1746

Abstract

Acute pancreatitis (AP) remains a challenging medical condition, where a deeper metabolic insight could pave the way for innovative treatments. This research harnessed serum metabolomics to discern potential diagnostic markers for AP and distinguish between its biliary (BAP) and alcohol-induced (AAP) forms. Leveraging [...] Read more.

Acute pancreatitis (AP) remains a challenging medical condition, where a deeper metabolic insight could pave the way for innovative treatments. This research harnessed serum metabolomics to discern potential diagnostic markers for AP and distinguish between its biliary (BAP) and alcohol-induced (AAP) forms. Leveraging high-performance liquid chromatography coupled with mass spectrometry, the metabolic signatures of 34 AP patients were contrasted against 26 healthy participants, and then between different etiologies of AP. The results identified metabolites primarily from glycerophospholipids, glycerolipids, fatty acyls, sterol lipids, and pteridines and derivative classes, with the Human Metabolome Database aiding in classification. Notably, these metabolites differentiated AP from healthy states with high AUROC values above 0.8. Another set of metabolites revealed differences between BAP and AAP, but these results were not as marked as the former. This lipidomic analysis provides an introduction to the metabolic landscape of acute pancreatitis, revealing changes in multiple lipid classes and metabolites and identifying these metabolites. Future research could add and discover new diagnostic biomarkers and therapeutic strategies enhancing the management of acute pancreatitis. Full article

(This article belongs to the Special Issue Biomarkers for Pancreatitis and Its Complications)

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29 pages, 712 KiB

Open AccessEditor’s ChoiceReview

TRP Channels in Cancer: Signaling Mechanisms and Translational Approaches

by Matilde Marini, Mustafa Titiz, Daniel Souza Monteiro de Araújo, Pierangelo Geppetti, Romina Nassini and Francesco De Logu

Biomolecules 2023, 13(10), 1557; https://doi.org/10.3390/biom13101557 - 22 Oct 2023

Cited by 10 | Viewed by 3491

Abstract

Ion channels play a crucial role in a wide range of biological processes, including cell cycle regulation and cancer progression. In particular, the transient receptor potential (TRP) family of channels has emerged as a promising therapeutic target due to its involvement in several [...] Read more.

Ion channels play a crucial role in a wide range of biological processes, including cell cycle regulation and cancer progression. In particular, the transient receptor potential (TRP) family of channels has emerged as a promising therapeutic target due to its involvement in several stages of cancer development and dissemination. TRP channels are expressed in a large variety of cells and tissues, and by increasing cation intracellular concentration, they monitor mechanical, thermal, and chemical stimuli under physiological and pathological conditions. Some members of the TRP superfamily, namely vanilloid (TRPV), canonical (TRPC), melastatin (TRPM), and ankyrin (TRPA), have been investigated in different types of cancer, including breast, prostate, lung, and colorectal cancer. TRP channels are involved in processes such as cell proliferation, migration, invasion, angiogenesis, and drug resistance, all related to cancer progression. Some TRP channels have been mechanistically associated with the signaling of cancer pain. Understanding the cellular and molecular mechanisms by which TRP channels influence cancer provides new opportunities for the development of targeted therapeutic strategies. Selective inhibitors of TRP channels are under initial scrutiny in experimental animals as potential anti-cancer agents. In-depth knowledge of these channels and their regulatory mechanisms may lead to new therapeutic strategies for cancer treatment, providing new perspectives for the development of effective targeted therapies. Full article

(This article belongs to the Special Issue Ion Channel Signaling in Cancer)

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12 pages, 2138 KiB

Open AccessCommunication

CETP Expression in Bone-Marrow-Derived Cells Reduces the Inflammatory Features of Atherosclerosis in Hypercholesterolemic Mice

by Thiago Rentz, Gabriel G. Dorighello, Renata R. dos Santos, Lohanna M. Barreto, Israelle N. Freitas, Carolina M. Lazaro, Daniela S. Razolli, Patricia M. Cazita and Helena C. F. Oliveira

Biomolecules 2023, 13(10), 1556; https://doi.org/10.3390/biom13101556 - 22 Oct 2023

Cited by 2 | Viewed by 1686

Abstract

CETP activity reduces plasma HDL-cholesterol concentrations, a correlate of an increased risk of atherosclerotic events. However, our recent findings suggest that CETP expression in macrophages promotes an intracellular antioxidant state, reduces free cholesterol accumulation and phagocytosis, and attenuates pro-inflammatory gene expression. To determine [...] Read more.

CETP activity reduces plasma HDL-cholesterol concentrations, a correlate of an increased risk of atherosclerotic events. However, our recent findings suggest that CETP expression in macrophages promotes an intracellular antioxidant state, reduces free cholesterol accumulation and phagocytosis, and attenuates pro-inflammatory gene expression. To determine whether CETP expression in macrophages affects atherosclerosis development, we transplanted bone marrow from transgenic mice expressing simian CETP or non-expressing littermates into hypercholesterolemic LDL-receptor-deficient mice. The CETP expression did not change the lipid-stained lesion areas but decreased the macrophage content (CD68), neutrophil accumulation (LY6G), and TNF-α aorta content of young male transplanted mice and decreased LY6G, TNF-α, iNOS, and nitrotyrosine (3-NT) in aged female transplanted mice. These findings suggest that CETP expression in bone-marrow-derived cells reduces the inflammatory features of atherosclerosis. These novel mechanistic observations may help to explain the failure of CETP inhibitors in reducing atherosclerotic events in humans. Full article

(This article belongs to the Section Molecular Medicine)

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48 pages, 2654 KiB

Open AccessReview

Navigating the ERK1/2 MAPK Cascade

by Ana Martin-Vega and Melanie H. Cobb

Biomolecules 2023, 13(10), 1555; https://doi.org/10.3390/biom13101555 - 20 Oct 2023

Cited by 26 | Viewed by 5309

Abstract

The RAS-ERK pathway is a fundamental signaling cascade crucial for many biological processes including proliferation, cell cycle control, growth, and survival; common across all cell types. Notably, ERK1/2 are implicated in specific processes in a context-dependent manner as in stem cells and pancreatic [...] Read more.

The RAS-ERK pathway is a fundamental signaling cascade crucial for many biological processes including proliferation, cell cycle control, growth, and survival; common across all cell types. Notably, ERK1/2 are implicated in specific processes in a context-dependent manner as in stem cells and pancreatic β-cells. Alterations in the different components of this cascade result in dysregulation of the effector kinases ERK1/2 which communicate with hundreds of substrates. Aberrant activation of the pathway contributes to a range of disorders, including cancer. This review provides an overview of the structure, activation, regulation, and mutational frequency of the different tiers of the cascade; with a particular focus on ERK1/2. We highlight the importance of scaffold proteins that contribute to kinase localization and coordinate interaction dynamics of the kinases with substrates, activators, and inhibitors. Additionally, we explore innovative therapeutic approaches emphasizing promising avenues in this field. Full article

(This article belongs to the Special Issue MAP Kinases: Functions in Signal Transduction and Disease)

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23 pages, 3627 KiB

Open AccessArticle

Effect of ABA Pre-Treatment on Rice Plant Transcriptome Response to Multiple Abiotic Stress

by Fatemeh Habibpourmehraban, Farhad Masoomi-Aladizgeh and Paul A. Haynes

Biomolecules 2023, 13(10), 1554; https://doi.org/10.3390/biom13101554 - 20 Oct 2023

Cited by 4 | Viewed by 1620

Abstract

Half of the world’s population depends on rice plant cultivation, yet environmental stresses continue to substantially impact the production of one of our most valuable staple foods. The aim of this study was to investigate the changes in the transcriptome of the IAC1131 [...] Read more.

Half of the world’s population depends on rice plant cultivation, yet environmental stresses continue to substantially impact the production of one of our most valuable staple foods. The aim of this study was to investigate the changes in the transcriptome of the IAC1131 rice genotype when exposed to a suite of multiple abiotic stresses, either with or without pre-treatment with the plant hormone ABA (Abscisic acid). Four groups of IAC1131 rice plants were grown including control plants incubated with ABA, non-ABA-incubated control plants, stressed plants incubated with ABA, and non-ABA-incubated stressed plants, with leaf samples harvested after 0 days (control) and 4 days (stressed). We found that high concentrations of ABA applied exogenously to the control plants under normal conditions did not alter the IAC1131 transcriptome profile significantly. The observed changes in the transcriptome of the IAC1131 plants in response to multiple abiotic stress were made even more pronounced by ABA pre-treatment, which induced the upregulation of a significant number of additional genes. Although ABA application impacted the plant transcriptome, multiple abiotic stress was the dominant factor in modifying gene expression in the IAC1131 plants. Exogenous ABA application may mitigate the effects of stress through ABA-dependent signalling pathways related to biological photosynthesis functions. Pre-treatment with ABA alters the photosynthesis function negatively by reducing stomatal conductance, therefore helping plants to conserve the energy required for survival under unfavourable environmental conditions. Full article

(This article belongs to the Special Issue Sowing the Seed to Ensure the Future of Plant Proteomics: Commemorative Issue in Honor of Dr. Dominique Job (1947–2022))

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15 pages, 4548 KiB

Open AccessEditor’s ChoiceArticle

Early Resveratrol Treatment Mitigates Joint Degeneration and Dampens Pain in a Mouse Model of Pseudoachondroplasia (PSACH)

by Jacqueline T. Hecht, Alka C. Veerisetty, Debabrata Patra, Mohammad G. Hossain, Frankie Chiu, Claire Mobed, Francis H. Gannon and Karen L. Posey

Biomolecules 2023, 13(10), 1553; https://doi.org/10.3390/biom13101553 - 20 Oct 2023

Cited by 5 | Viewed by 1840

Abstract

Pseudoachondroplasia (PSACH), a severe dwarfing condition associated with early-onset joint degeneration and lifelong joint pain, is caused by mutations in cartilage oligomeric matrix protein (COMP). The mechanisms underlying the mutant-COMP pathology have been defined using the MT-COMP mouse model of PSACH that has [...] Read more.

Pseudoachondroplasia (PSACH), a severe dwarfing condition associated with early-onset joint degeneration and lifelong joint pain, is caused by mutations in cartilage oligomeric matrix protein (COMP). The mechanisms underlying the mutant-COMP pathology have been defined using the MT-COMP mouse model of PSACH that has the common D469del mutation. Mutant-COMP protein does not fold properly, and it is retained in the rough endoplasmic reticulum (rER) of chondrocytes rather than being exported to the extracellular matrix (ECM), driving ER stress that stimulates oxidative stress and inflammation, driving a self-perpetuating cycle. CHOP (ER stress signaling protein) and TNFα inflammation drive high levels of mTORC1 signaling, shutting down autophagy and blocking ER clearance, resulting in premature loss of chondrocytes that negatively impacts linear growth and causes early joint degeneration in MT-COMP mice and PSACH. Previously, we have shown that resveratrol treatment from birth to 20 weeks prevents joint degeneration and decreases the pathological processes in articular chondrocytes. Resveratrol’s therapeutic mechanism of action in the mutant-COMP pathology was shown to act by primarily stimulating autophagy and reducing inflammation. Importantly, we demonstrated that MT-COMP mice experience pain consistent with PSACH joint pain. Here, we show, in the MT-COMP mouse, that resveratrol treatment must begin within 4 weeks to preserve joint health and reduce pain. Resveratrol treatment started at 6 or 8 weeks (to 20 weeks) was not effective in preventing joint degeneration. Collectively, our findings in MT-COMP mice show that there is a postnatal resveratrol treatment window wherein the inevitable mutant-COMP joint degeneration and pain can be prevented. Full article

(This article belongs to the Special Issue The Value of Natural Compounds as Therapeutic Agents)

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25 pages, 6486 KiB

Open AccessArticle

G Protein-Coupled Receptor Kinase 2 Selectively Enhances β-Arrestin Recruitment to the D₂ Dopamine Receptor through Mechanisms That Are Independent of Receptor Phosphorylation

by Marta Sánchez-Soto, Noelia M. Boldizsar, Kayla A. Schardien, Nora S. Madaras, Blair K. A. Willette, Laura R. Inbody, Christopher Dasaro, Amy E. Moritz, Julia Drube, Raphael S. Haider, R. Benjamin Free, Carsten Hoffman and David R. Sibley

Biomolecules 2023, 13(10), 1552; https://doi.org/10.3390/biom13101552 - 20 Oct 2023

Cited by 2 | Viewed by 3201

Abstract

The D2 dopamine receptor (D2R) signals through both G proteins and β-arrestins to regulate important physiological processes, such as movement, reward circuitry, emotion, and cognition. β-arrestins are believed to interact with G protein-coupled receptors (GPCRs) at the phosphorylated C-terminal tail or intracellular loops. [...] Read more.

The D2 dopamine receptor (D2R) signals through both G proteins and β-arrestins to regulate important physiological processes, such as movement, reward circuitry, emotion, and cognition. β-arrestins are believed to interact with G protein-coupled receptors (GPCRs) at the phosphorylated C-terminal tail or intracellular loops. GPCR kinases (GRKs) are the primary drivers of GPCR phosphorylation, and for many receptors, receptor phosphorylation is indispensable for β-arrestin recruitment. However, GRK-mediated receptor phosphorylation is not required for β-arrestin recruitment to the D2R, and the role of GRKs in D2R–β-arrestin interactions remains largely unexplored. In this study, we used GRK knockout cells engineered using CRISPR-Cas9 technology to determine the extent to which β-arrestin recruitment to the D2R is GRK-dependent. Genetic elimination of all GRK expression decreased, but did not eliminate, agonist-stimulated β-arrestin recruitment to the D2R or its subsequent internalization. However, these processes were rescued upon the re-introduction of various GRK isoforms in the cells with GRK2/3 also enhancing dopamine potency. Further, treatment with compound 101, a pharmacological inhibitor of GRK2/3 isoforms, decreased β-arrestin recruitment and receptor internalization, highlighting the importance of this GRK subfamily for D2R–β-arrestin interactions. These results were recapitulated using a phosphorylation-deficient D2R mutant, emphasizing that GRKs can enhance β-arrestin recruitment and activation independently of receptor phosphorylation. Full article

(This article belongs to the Special Issue Biogenic Amines, Their Receptors and Transporters in Health and Disease: Commemorative Issue in Honor of Professor Marc G. Caron (1946–2022))

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26 pages, 1408 KiB

Open AccessReview

The Role of the Transforming Growth Factor-β Signaling Pathway in Gastrointestinal Cancers

by Tasuku Matsuoka and Masakazu Yashiro

Biomolecules 2023, 13(10), 1551; https://doi.org/10.3390/biom13101551 - 19 Oct 2023

Cited by 5 | Viewed by 2654

Abstract

Transforming growth factor-β (TGF-β) has attracted attention as a tumor suppressor because of its potent growth-suppressive effect on epithelial cells. Dysregulation of the TGF-β signaling pathway is considered to be one of the key factors in carcinogenesis, and genetic alterations affecting TGF-β signaling [...] Read more.

Transforming growth factor-β (TGF-β) has attracted attention as a tumor suppressor because of its potent growth-suppressive effect on epithelial cells. Dysregulation of the TGF-β signaling pathway is considered to be one of the key factors in carcinogenesis, and genetic alterations affecting TGF-β signaling are extraordinarily common in cancers of the gastrointestinal system, such as hereditary nonpolyposis colon cancer and pancreatic cancer. Accumulating evidence suggests that TGF-β is produced from various types of cells in the tumor microenvironment and mediates extracellular matrix deposition, tumor angiogenesis, the formation of CAFs, and suppression of the anti-tumor immune reaction. It is also being considered as a factor that promotes the malignant transformation of cancer, particularly the invasion and metastasis of cancer cells, including epithelial-mesenchymal transition. Therefore, elucidating the role of TGF-β signaling in carcinogenesis, cancer invasion, and metastasis will provide novel basic insight for diagnosis and prognosis and the development of new molecularly targeted therapies for gastrointestinal cancers. In this review, we outline an overview of the complex mechanisms and functions of TGF-β signaling. Furthermore, we discuss the therapeutic potentials of targeting the TGF-β signaling pathway for gastrointestinal cancer treatment and discuss the remaining challenges and future perspectives on targeting this pathway. Full article

(This article belongs to the Special Issue Neurotrophic Factors and Growth Factors - Historical Perspective and New Directions for Medical Use)

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21 pages, 2761 KiB

Open AccessReview

The Genetic Background of Abnormalities in Metabolic Pathways of Phosphoinositides and Their Linkage with the Myotubular Myopathies, Neurodegenerative Disorders, and Carcinogenesis

by Maria Derkaczew, Piotr Martyniuk, Robert Hofman, Krzysztof Rutkowski, Adam Osowski and Joanna Wojtkiewicz

Biomolecules 2023, 13(10), 1550; https://doi.org/10.3390/biom13101550 - 19 Oct 2023

Cited by 1 | Viewed by 1592

Abstract

Myo-inositol belongs to one of the sugar alcohol groups known as cyclitols. Phosphatidylinositols are one of the derivatives of Myo-inositol, and constitute important mediators in many intracellular processes such as cell growth, cell differentiation, receptor recycling, cytoskeletal organization, and membrane fusion. They also [...] Read more.

Myo-inositol belongs to one of the sugar alcohol groups known as cyclitols. Phosphatidylinositols are one of the derivatives of Myo-inositol, and constitute important mediators in many intracellular processes such as cell growth, cell differentiation, receptor recycling, cytoskeletal organization, and membrane fusion. They also have even more functions that are essential for cell survival. Mutations in genes encoding phosphatidylinositols and their derivatives can lead to many disorders. This review aims to perform an in-depth analysis of these connections. Many authors emphasize the significant influence of phosphatidylinositols and phosphatidylinositols’ phosphates in the pathogenesis of myotubular myopathies, neurodegenerative disorders, carcinogenesis, and other less frequently observed diseases. In our review, we have focused on three of the most often mentioned groups of disorders. Inositols are the topic of many studies, and yet, there are no clear results of successful clinical trials. Analysis of the available literature gives promising results and shows that further research is still needed. Full article

(This article belongs to the Special Issue Potential Mechanism of Natural-Based Biomolecules for Disease Treatment)

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22 pages, 1537 KiB

Open AccessReview

Interaction of Heavy Metal Lead with Gut Microbiota: Implications for Autism Spectrum Disorder

by Yousef Tizabi, Samia Bennani, Nacer El Kouhen, Bruk Getachew and Michael Aschner

Biomolecules 2023, 13(10), 1549; https://doi.org/10.3390/biom13101549 - 19 Oct 2023

Cited by 13 | Viewed by 3221

Abstract

Autism Spectrum Disorder (ASD), a neurodevelopmental disorder characterized by persistent deficits in social interaction and communication, manifests in early childhood and is followed by restricted and stereotyped behaviors, interests, or activities in adolescence and adulthood (DSM-V). Although genetics and environmental factors have been [...] Read more.

Autism Spectrum Disorder (ASD), a neurodevelopmental disorder characterized by persistent deficits in social interaction and communication, manifests in early childhood and is followed by restricted and stereotyped behaviors, interests, or activities in adolescence and adulthood (DSM-V). Although genetics and environmental factors have been implicated, the exact causes of ASD have yet to be fully characterized. New evidence suggests that dysbiosis or perturbation in gut microbiota (GM) and exposure to lead (Pb) may play important roles in ASD etiology. Pb is a toxic heavy metal that has been linked to a wide range of negative health outcomes, including anemia, encephalopathy, gastroenteric diseases, and, more importantly, cognitive and behavioral problems inherent to ASD. Pb exposure can disrupt GM, which is essential for maintaining overall health. GM, consisting of trillions of microorganisms, has been shown to play a crucial role in the development of various physiological and psychological functions. GM interacts with the brain in a bidirectional manner referred to as the “Gut–Brain Axis (GBA)”. In this review, following a general overview of ASD and GM, the interaction of Pb with GM in the context of ASD is emphasized. The potential exploitation of this interaction for therapeutic purposes is also touched upon. Full article

(This article belongs to the Special Issue Advances in Metal Toxicology—a Honorary Special Issue Commemorating the Research of Prof. Michael Aschner in Metal Toxicity)

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16 pages, 11030 KiB

Open AccessArticle

Novel Solution for Using Neural Networks for Kidney Boundary Extraction in 2D Ultrasound Data

by Tao Peng, Yidong Gu, Shanq-Jang Ruan, Qingrong Jackie Wu and Jing Cai

Biomolecules 2023, 13(10), 1548; https://doi.org/10.3390/biom13101548 - 19 Oct 2023

Cited by 1 | Viewed by 1488

Abstract

Background and Objective: Kidney ultrasound (US) imaging is a significant imaging modality for evaluating kidney health and is essential for diagnosis, treatment, surgical intervention planning, and follow-up assessments. Kidney US image segmentation consists of extracting useful objects or regions from the total [...] Read more.

Background and Objective: Kidney ultrasound (US) imaging is a significant imaging modality for evaluating kidney health and is essential for diagnosis, treatment, surgical intervention planning, and follow-up assessments. Kidney US image segmentation consists of extracting useful objects or regions from the total image, which helps determine tissue organization and improve diagnosis. Thus, obtaining accurate kidney segmentation data is an important first step for precisely diagnosing kidney diseases. However, manual delineation of the kidney in US images is complex and tedious in clinical practice. To overcome these challenges, we developed a novel automatic method for US kidney segmentation. Methods: Our method comprises two cascaded steps for US kidney segmentation. The first step utilizes a coarse segmentation procedure based on a deep fusion learning network to roughly segment each input US kidney image. The second step utilizes a refinement procedure to fine-tune the result of the first step by combining an automatic searching polygon tracking method with a machine learning network. In the machine learning network, a suitable and explainable mathematical formula for kidney contours is denoted by basic parameters. Results: Our method is assessed using 1380 trans-abdominal US kidney images obtained from 115 patients. Based on comprehensive comparisons of different noise levels, our method achieves accurate and robust results for kidney segmentation. We use ablation experiments to assess the significance of each component of the method. Compared with state-of-the-art methods, the evaluation metrics of our method are significantly higher. The Dice similarity coefficient (DSC) of our method is 94.6 ± 3.4%, which is higher than those of recent deep learning and hybrid algorithms (89.4 ± 7.1% and 93.7 ± 3.8%, respectively). Conclusions: We develop a coarse-to-refined architecture for the accurate segmentation of US kidney images. It is important to precisely extract kidney contour features because segmentation errors can cause under-dosing of the target or over-dosing of neighboring normal tissues during US-guided brachytherapy. Hence, our method can be used to increase the rigor of kidney US segmentation. Full article

(This article belongs to the Section Synthetic Biology and Bioengineering)

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16 pages, 2178 KiB

Open AccessArticle

An Overview of Ovarian Calyx Fluid Proteins of Toxoneuron nigriceps (Viereck) (Hymenoptera: Braconidae): An Integrated Transcriptomic and Proteomic Approach

by Rosanna Salvia, Carmen Scieuzo, Andrea Boschi, Marco Pezzi, Michele Mistri, Cristina Munari, Milvia Chicca, Heiko Vogel, Flora Cozzolino, Vittoria Monaco, Maria Monti and Patrizia Falabella

Biomolecules 2023, 13(10), 1547; https://doi.org/10.3390/biom13101547 - 19 Oct 2023

Cited by 1 | Viewed by 1449

Abstract

The larval stages of the tobacco budworm, Heliothis virescens (Fabricius) (Lepidoptera: Noctuidae), are parasitized by the endophagous parasitoid wasp, Toxoneuron nigriceps (Viereck) (Hymenoptera: Braconidae). During the injections of eggs, this parasitoid wasp also injects into the host body the secretion of the venom [...] Read more.

The larval stages of the tobacco budworm, Heliothis virescens (Fabricius) (Lepidoptera: Noctuidae), are parasitized by the endophagous parasitoid wasp, Toxoneuron nigriceps (Viereck) (Hymenoptera: Braconidae). During the injections of eggs, this parasitoid wasp also injects into the host body the secretion of the venom gland and the calyx fluid, which contains a polydnavirus (T. nigriceps BracoVirus: TnBV) and the Ovarian calyx fluid Proteins (OPs). The effects of the OPs on the host immune system have recently been described. In particular, it has been demonstrated that the OPs cause hemocytes to undergo a number of changes, such as cellular oxidative stress, actin cytoskeleton modifications, vacuolization, and the inhibition of hemocyte encapsulation capacity, which results in both a loss of hemocyte functionality and cell death. In this study, by using a combined transcriptomic and proteomic analysis, the main components of T. nigriceps ovarian calyx fluid proteins were identified and their possible role in the parasitic syndrome was discussed. This study provides useful information to support the analysis of the function of ovarian calyx fluid proteins, to better understand T. nigriceps parasitization success and for a more thorough understanding of the components of ovarian calyx fluid proteins and their potential function in combination with other parasitoid factors. Full article

(This article belongs to the Section Biomacromolecules: Proteins)

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11 pages, 2105 KiB

Open AccessArticle

Optical Genome Mapping Enables Detection and Accurate Sizing of RFC1 Repeat Expansions

by Stefano Facchini, Natalia Dominik, Arianna Manini, Stephanie Efthymiou, Riccardo Currò, Bianca Rugginini, Elisa Vegezzi, Ilaria Quartesan, Benedetta Perrone, Shahedah Koya Kutty, Valentina Galassi Deforie, Ricardo P. Schnekenberg, Elena Abati, Anna Pichiecchio, Enza Maria Valente, Cristina Tassorelli, Mary M. Reilly, Henry Houlden, Enrico Bugiardini and Andrea Cortese

Biomolecules 2023, 13(10), 1546; https://doi.org/10.3390/biom13101546 - 19 Oct 2023

Cited by 6 | Viewed by 2436

Abstract

A recessive Short Tandem Repeat expansion in RFC1 has been found to be associated with cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS), and to be a frequent cause of late onset ataxia and sensory neuropathy. The usual procedure for sizing these expansions [...] Read more.

A recessive Short Tandem Repeat expansion in RFC1 has been found to be associated with cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS), and to be a frequent cause of late onset ataxia and sensory neuropathy. The usual procedure for sizing these expansions is based on Southern Blotting (SB), a time-consuming and a relatively imprecise technique. In this paper, we compare SB with Optical Genome Mapping (OGM), a method for detecting Structural Variants (SVs) based on the measurement of distances between fluorescently labelled probes, for the diagnosis of RFC1 CANVAS and disease spectrum. The two methods are applied to 17 CANVAS patients’ blood samples and resulting sizes compared, showing a good agreement. Further, long-read sequencing is used for two patients to investigate the agreement of sizes with either SB or OGM. Our study concludes that OGM represents a viable alternative to SB, allowing for a simpler technique, a more precise sizing of the expansion and ability to expand analysis of SV in the entire genome as opposed to SB which is a locus specific method. Full article

(This article belongs to the Special Issue Optical Genome Mapping in Human Neurogenetic Diagnostics: New Advances and Future Trends)

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16 pages, 2021 KiB

Open AccessArticle

NanoFIRE: A NanoLuciferase and Fluorescent Integrated Reporter Element for Robust and Sensitive Investigation of HIF and Other Signalling Pathways

by Alison E. Roennfeldt, Timothy P. Allen, Brooke N. Trowbridge, Michael R. Beard, Murray L. Whitelaw, Darryl L. Russell, David C. Bersten and Daniel J. Peet

Biomolecules 2023, 13(10), 1545; https://doi.org/10.3390/biom13101545 - 19 Oct 2023

Viewed by 2064

Abstract

The Hypoxia Inducible Factor (HIF) transcription factors are imperative for cell adaption to low oxygen conditions and development; however, they also contribute to ischaemic disease and cancer. To identify novel genetic regulators which target the HIF pathway or small molecules for therapeutic use, [...] Read more.

The Hypoxia Inducible Factor (HIF) transcription factors are imperative for cell adaption to low oxygen conditions and development; however, they also contribute to ischaemic disease and cancer. To identify novel genetic regulators which target the HIF pathway or small molecules for therapeutic use, cell-based reporter systems are commonly used. Here, we present a new, highly sensitive and versatile reporter system, NanoFIRE: a NanoLuciferase and Fluorescent Integrated Reporter Element. Under the control of a Hypoxic Response Element (HRE-NanoFIRE), this system is a robust sensor of HIF activity within cells and potently responds to both hypoxia and chemical inducers of the HIF pathway in a highly reproducible and sensitive manner, consistently achieving 20 to 150-fold induction across different cell types and a Z′ score > 0.5. We demonstrate that the NanoFIRE system is adaptable via substitution of the response element controlling NanoLuciferase and show that it can report on the activity of the transcriptional regulator Factor Inhibiting HIF, and an unrelated transcription factor, the Progesterone Receptor. Furthermore, the lentivirus-mediated stable integration of NanoFIRE highlights the versatility of this system across a wide range of cell types, including primary cells. Together, these findings demonstrate that NanoFIRE is a robust reporter system for the investigation of HIF and other transcription factor-mediated signalling pathways in cells, with applications in high throughput screening for the identification of novel small molecule and genetic regulators. Full article

(This article belongs to the Special Issue State-of-the-Art Targeting Hypoxia Signaling Pathway to Treat Human Diseases)

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16 pages, 1361 KiB

Open AccessReview

Mitochondrial Reactive Oxygen Species, Insulin Resistance, and Nrf2-Mediated Oxidative Stress Response—Toward an Actionable Strategy for Anti-Aging

by Shuya Kasai, Daichi Kokubu, Hiroki Mizukami and Ken Itoh

Biomolecules 2023, 13(10), 1544; https://doi.org/10.3390/biom13101544 - 19 Oct 2023

Cited by 10 | Viewed by 3646

Abstract

Reactive oxygen species (ROS) are produced mainly by mitochondrial respiration and function as signaling molecules in the physiological range. However, ROS production is also associated with the pathogenesis of various diseases, including insulin resistance (IR) and type 2 diabetes (T2D). This review focuses [...] Read more.

Reactive oxygen species (ROS) are produced mainly by mitochondrial respiration and function as signaling molecules in the physiological range. However, ROS production is also associated with the pathogenesis of various diseases, including insulin resistance (IR) and type 2 diabetes (T2D). This review focuses on the etiology of IR and early events, especially mitochondrial ROS (mtROS) production in insulin-sensitive tissues. Importantly, IR and/or defective adipogenesis in the white adipose tissues (WAT) is thought to increase free fatty acid and ectopic lipid deposition to develop into systemic IR. Fatty acid and ceramide accumulation mediate coenzyme Q reduction and mtROS production in IR in the skeletal muscle, while coenzyme Q synthesis downregulation is also involved in mtROS production in the WAT. Obesity-related IR is associated with the downregulation of mitochondrial catabolism of branched-chain amino acids (BCAAs) in the WAT, and the accumulation of BCAA and its metabolites as biomarkers in the blood could reliably indicate future T2D. Transcription factor NF-E2-related factor 2 (Nrf2), which regulates antioxidant enzyme expression in response to oxidative stress, is downregulated in insulin-resistant tissues. However, Nrf2 inducers, such as sulforaphane, could restore Nrf2 and target gene expression and attenuate IR in multiple tissues, including the WAT. Full article

(This article belongs to the Special Issue The Physiological and Pathological New Function of Mitochondrial ROS and Intraorganellar Cross-Talks Part II)

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14 pages, 969 KiB

Open AccessFeature PaperReview

Understanding the Immunopathology of HTLV-1-Associated Adult T-Cell Leukemia/Lymphoma: A Comprehensive Review

by Shingo Nakahata, Daniel Enriquez-Vera, M. Ishrat Jahan, Kenji Sugata and Yorifumi Satou

Biomolecules 2023, 13(10), 1543; https://doi.org/10.3390/biom13101543 - 19 Oct 2023

Cited by 3 | Viewed by 3317

Abstract

Human T-cell leukemia virus type-1 (HTLV-1) causes adult T-cell leukemia/lymphoma (ATL). HTLV-1 carriers have a lifelong asymptomatic balance between infected cells and host antiviral immunity; however, 5–10% of carriers lose this balance and develop ATL. Coinfection with Strongyloides promotes ATL development, suggesting that [...] Read more.

Human T-cell leukemia virus type-1 (HTLV-1) causes adult T-cell leukemia/lymphoma (ATL). HTLV-1 carriers have a lifelong asymptomatic balance between infected cells and host antiviral immunity; however, 5–10% of carriers lose this balance and develop ATL. Coinfection with Strongyloides promotes ATL development, suggesting that the immunological status of infected individuals is a determinant of HTLV-1 pathogenicity. As CD4+ T cells play a central role in host immunity, the deregulation of their function and differentiation via HTLV-1 promotes the immune evasion of infected T cells. During ATL development, the accumulation of genetic and epigenetic alterations in key host immunity-related genes further disturbs the immunological balance. Various approaches are available for treating these abnormalities; however, hematopoietic stem cell transplantation is currently the only treatment with the potential to cure ATL. The patient’s immune state may contribute to the treatment outcome. Additionally, the activity of the anti-CC chemokine receptor 4 antibody, mogamulizumab, depends on immune function, including antibody-dependent cytotoxicity. In this comprehensive review, we summarize the immunopathogenesis of HTLV-1 infection in ATL and discuss the clinical findings that should be considered when developing treatment strategies for ATL. Full article

(This article belongs to the Special Issue Recent Advances in Retroviruses and Endogenous Retroviruses (ERVs) in Mammalian Placenta and Beyond)

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15 pages, 1765 KiB

Open AccessArticle

MiRNA and Exosomal miRNA as New Biomarkers Useful to Phenotyping Severe Asthma

by Piera Soccio, Giorgia Moriondo, Donato Lacedonia, Pasquale Tondo, Dalila Pescatore, Carla Maria Irene Quarato, Mauro Carone, Maria Pia Foschino Barbaro and Giulia Scioscia

Biomolecules 2023, 13(10), 1542; https://doi.org/10.3390/biom13101542 - 18 Oct 2023

Cited by 7 | Viewed by 1906

Abstract

Severe asthma (SA) is a chronic inflammatory disease of the airways. Due to the extreme heterogeneity of symptoms, new biomarkers are currently needed. MiRNAs are non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. In biological fluids, miRNAs are contained within [...] Read more.

Severe asthma (SA) is a chronic inflammatory disease of the airways. Due to the extreme heterogeneity of symptoms, new biomarkers are currently needed. MiRNAs are non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. In biological fluids, miRNAs are contained within exosomes, vesicles capable of giving miRNAs considerable stability and resistance to degradation by RNAses. The main function attributed to the exosomes is intercellular communication. The goal of our study was to analyze intracellular and exosomal miRNAs in order to demonstrate their potential use as non-invasive biomarkers of asthma by showing, in particular, their role in SA. We detected miRNAs by qRT-PCR in both serum and serum-derived-exosomes of asthmatic patients and healthy controls. The levels of almost all analyzed intracellular miRNAs (miR-21, miR-223, and let-7a) were greater in asthmatic patients vs. healthy control, except for miR-223. In detail, miR-21 was greater in SA, while let-7a increased in mild-to-moderate asthma. On the other hand, in exosomes, all analyzed miRNAs were higher in SA. This study identified a series of miRNAs involved in SA, highlighting their potential role in asthma development and progression. These results need validation on a larger cohort. Full article

(This article belongs to the Special Issue Biomarkers of Severe Asthma: From Pathogenetic Mechanisms to Clinical Application)

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14 pages, 1790 KiB

Open AccessArticle

Association of Cytokine Gene Polymorphisms and Their Impact on Active and Latent Tuberculosis in Brazil’s Amazon Region

by Ednelza da Silva Graça Amoras, Thais Gouvea de Morais, Rafaella do Nascimento Ferreira, Samara Tatielle Monteiro Gomes, Francisca Dayse Martins de Sousa, Iury de Paula Souza, Ricardo Ishak, Antonio Carlos Rosário Vallinoto and Maria Alice Freitas Queiroz

Biomolecules 2023, 13(10), 1541; https://doi.org/10.3390/biom13101541 - 18 Oct 2023

Cited by 3 | Viewed by 1365

Abstract

Some genetic variations in cytokine genes can alter their expression and influence the evolution of Mycobacterium tuberculosis (Mtb) infection. This study aimed to investigate the association of polymorphisms in cytokine genes and variability in plasma levels of cytokines with the development of tuberculosis [...] Read more.

Some genetic variations in cytokine genes can alter their expression and influence the evolution of Mycobacterium tuberculosis (Mtb) infection. This study aimed to investigate the association of polymorphisms in cytokine genes and variability in plasma levels of cytokines with the development of tuberculosis (TB) and latent tuberculosis infection (LTBI). Blood samples from 245 patients with TB, 80 with LTBI, and healthy controls (n = 100) were included. Genotyping of the IFNG +874A/T, IL6 -174G/C, IL4 -590C/T, and IL10 -1082A/G polymorphisms was performed by real-time PCR, and cytokine levels were determined by flow cytometry. Higher frequencies of genotypes AA (IFNG +874A/T), GG (IL6 -174G/C), TT (IL4 -590C/T), and GG (IL10 -1082A/G) were associated with an increased risk of TB compared to that of LTBI (p = 0.0027; p = 0.0557; p = 0.0286; p = 0.0361, respectively) and the control (p = <0.0001, p = 0.0021; p = 0.01655; p = 0.0132, respectively). In combination, the A allele for IFNG +874A/T and the T allele for IL4 -590C/T were associated with a higher chance of TB (p = 0.0080; OR = 2.753 and p < 0.0001; OR = 3.273, respectively). The TB group had lower levels of IFN-γ and higher concentrations of IL-6, IL-4, and IL-10. Cytokine levels were different between the genotypes based on the polymorphisms investigated (p < 0.05). The genotype and wild-type allele for IFNG +874A/T and the genotype and polymorphic allele for IL4 -590C/T appear to be more relevant in the context of Mtb infection, which has been associated with the development of TB among individuals infected by the bacillus and with susceptibility to active infection but not with susceptibility to latent infection. Full article

(This article belongs to the Special Issue Tuberculosis: Immunopathogenesis and Therapeutic Strategies)

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13 pages, 4105 KiB

Open AccessBrief Report

Effects of Storage Temperatures on Nitrogen Assimilation and Remobilization during Post-Harvest Senescence of Pak Choi

by Savitha Dhandapani, Vidya Susan Philip, Shaik Anwar Ahamed Nabeela Nasreen, Alice Mei Xien Tan, Praveen Kumar Jayapal, Rajeev J. Ram and Bong Soo Park

Biomolecules 2023, 13(10), 1540; https://doi.org/10.3390/biom13101540 - 18 Oct 2023

Cited by 3 | Viewed by 1631

Abstract

In the agricultural industry, the post-harvest leafy vegetable quality and shelf life significantly influence market value and consumer acceptability. This study examined the effects of different storage temperatures on leaf senescence, nitrogen assimilation, and remobilization in Pak Choi (Brassica rapa subsp. chinensis [...] Read more.

In the agricultural industry, the post-harvest leafy vegetable quality and shelf life significantly influence market value and consumer acceptability. This study examined the effects of different storage temperatures on leaf senescence, nitrogen assimilation, and remobilization in Pak Choi (Brassica rapa subsp. chinensis). Mature Pak Choi plants were harvested and stored at two different temperatures, 4 °C and 25 °C. Senescence was tracked via chlorophyll content and leaf yellowing. Concurrently, alterations in the total nitrogen, nitrate, and protein content were quantified on days 0, 3, 6, and 9 in old, mid, and young leaves of Pak Choi plants. As expected, 4 °C alleviated chlorophyll degradation and delayed senescence of Pak Choi compared to 25 °C. Total nitrogen and protein contents were inversely correlated, while the nitrate content remained nearly constant across leaf groups at 25 °C. Additionally, the transcript levels of genes involved in nitrogen assimilation and remobilization revealed key candidate genes that were differentially expressed between 4 °C and 25 °C, which might be targeted to extend the shelf life of the leafy vegetables. Thus, this study provides pivotal insights into the molecular and physiological responses of Pak Choi to post-harvest storage conditions. Full article

(This article belongs to the Special Issue Nitrogen Signaling, Transport, and Function in Plants)

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28 pages, 1280 KiB

Open AccessReview

Snake Venom Components as Therapeutic Drugs in Ischemic Heart Disease

by Erij Messadi

Biomolecules 2023, 13(10), 1539; https://doi.org/10.3390/biom13101539 - 18 Oct 2023

Cited by 3 | Viewed by 4743

Abstract

Ischemic heart disease (IHD), especially myocardial infarction (MI), is a leading cause of death worldwide. Although coronary reperfusion is the most straightforward treatment for limiting the MI size, it has nevertheless been shown to exacerbate ischemic myocardial injury. Therefore, identifying and developing therapeutic [...] Read more.

Ischemic heart disease (IHD), especially myocardial infarction (MI), is a leading cause of death worldwide. Although coronary reperfusion is the most straightforward treatment for limiting the MI size, it has nevertheless been shown to exacerbate ischemic myocardial injury. Therefore, identifying and developing therapeutic strategies to treat IHD is a major medical challenge. Snake venoms contain biologically active proteins and peptides that are of major interest for pharmacological applications in the cardiovascular system (CVS). This has led to their use for the development and design of new drugs, such as the first-in-class angiotensin-converting enzyme inhibitor captopril, developed from a peptide present in Bothrops jararaca snake venom. This review discusses the potential usefulness of snake venom toxins for developing effective treatments against IHD and related diseases such as hypertension and atherosclerosis. It describes their biological effects at the molecular scale, their mechanisms of action according to their different pharmacological properties, as well as their subsequent molecular pathways and therapeutic targets. The molecules reported here have either been approved for human medical use and are currently available on the drug market or are still in the clinical or preclinical developmental stages. The information summarized here may be useful in providing insights into the development of future snake venom-derived drugs. Full article

(This article belongs to the Section Molecular Medicine)

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11 pages, 3766 KiB

Open AccessBrief Report

Treatment-Emergent Cilgavimab Resistance Was Uncommon in Vaccinated Omicron BA.4/5 Outpatients

by Cesare Ernesto Maria Gruber, Fabio Giovanni Tucci, Martina Rueca, Valentina Mazzotta, Giulia Gramigna, Alessandra Vergori, Lavinia Fabeni, Giulia Berno, Emanuela Giombini, Ornella Butera, Daniele Focosi, Ingrid Guarnetti Prandi, Giovanni Chillemi, Emanuele Nicastri, Francesco Vaia, Enrico Girardi, Andrea Antinori and Fabrizio Maggi

Biomolecules 2023, 13(10), 1538; https://doi.org/10.3390/biom13101538 - 18 Oct 2023

Cited by 1 | Viewed by 1712

Abstract

Mutations in the SARS-CoV-2 Spike glycoprotein can affect monoclonal antibody efficacy. Recent findings report the occurrence of resistant mutations in immunocompromised patients after tixagevimab/cilgavimab treatment. More recently, the Food and Drug Agency revoked the authorization for tixagevimab/cilgavimab, while this monoclonal antibody cocktail is [...] Read more.

Mutations in the SARS-CoV-2 Spike glycoprotein can affect monoclonal antibody efficacy. Recent findings report the occurrence of resistant mutations in immunocompromised patients after tixagevimab/cilgavimab treatment. More recently, the Food and Drug Agency revoked the authorization for tixagevimab/cilgavimab, while this monoclonal antibody cocktail is currently recommended by the European Medical Agency. We retrospectively reviewed 22 immunocompetent patients at high risk for disease progression who received intramuscular tixagevimab/cilgavimab as early COVID-19 treatment and presented a prolonged high viral load. Complete SARS-CoV-2 genome sequences were obtained for a deep investigation of mutation frequencies in Spike protein before and during treatment. At seven days, only one patient showed evidence of treatment-emergent cilgavimab resistance. Quasispecies analysis revealed two different deletions on the Spike protein (S:del138–144 or S:del141–145) in combination with the resistance S:K444N mutation. The structural and dynamic impact of the two quasispecies was characterized by using molecular dynamics simulations, showing the conservation of the principal functional movements in the mutated systems and their capabilities to alter the structure and dynamics of the RBD, responsible for the interaction with the ACE2 human receptor. Our study underlines the importance of prompting an early virological investigation to prevent drug resistance or clinical failures in immunocompetent patients. Full article

(This article belongs to the Special Issue Viral Drug Targets and Discovery of Antiviral Agents)

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18 pages, 4337 KiB

Open AccessArticle

Comprehensive Transcriptomic Profiling of m6A Modification in Age-Related Hearing Loss

by Menglong Feng, Xiaoqing Zhou, Yaqin Hu, Juhong Zhang, Ting Yang, Zhiji Chen and Wei Yuan

Biomolecules 2023, 13(10), 1537; https://doi.org/10.3390/biom13101537 - 18 Oct 2023

Viewed by 1851

Abstract

Age-related hearing loss (ARHL), also known as presbycusis, is one of the most common neurodegenerative disorders in elderly individuals and has a prevalence of approximately 70–80% among individuals aged 65 and older. As ARHL is an intricate and multifactorial disease, the exact pathogenesis [...] Read more.

Age-related hearing loss (ARHL), also known as presbycusis, is one of the most common neurodegenerative disorders in elderly individuals and has a prevalence of approximately 70–80% among individuals aged 65 and older. As ARHL is an intricate and multifactorial disease, the exact pathogenesis of ARHL is not fully understood. There is evidence that transcriptional dysregulation mediated by epigenetic modifications is widespread in ARHL. However, the potential role of N6-methyladenosine (m6A) modification, as a crucial component of epigenetics, in ARHL progression remains unclear. In this study, we confirmed that the downregulation of m6A modification in cochlear tissues is related to ARHL and found that the expression of the m6A methylation regulators Wilms tumour suppressor-1-associated protein (WTAP), methyltransferase-like 3 (METTL3), ALKB homologous protein 5 (ALKBH5) and fat mass and obesity-associated protein (FTO) is decreased significantly at the mRNA and protein levels in ARHL mice. Then, we used methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and RNA sequencing (RNA-Seq) to identify the differentially m6A-methylated genes in the cochlear tissues of ARHL mice. A total of 3438 genes with differential m6A methylation were identified, of which 1332 genes were m6A-hypermethylated and 2106 genes were m6A-hypomethylated in the ARHL group compared to the control group according to MeRIP-seq. Further joint analysis of RNA-Seq and MeRIP-Seq data showed that 262 genes had significant differences in both mRNA expression and m6A methylation. GO and KEGG analyses indicated that 262 unique genes were enriched mainly in the PI3K-AKT signalling pathway. In conclusion, the results of this study reveal differential m6A methylation patterns in the cochlear tissues of ARHL mice, providing a theoretical basis for further study of the pathogenesis of ARHL and potential therapeutic strategies. Full article

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31 pages, 1687 KiB

Open AccessReview

Pharmacotherapeutic Approaches to Treatment of Muscular Dystrophies

by Alan Rawls, Bridget K. Diviak, Cameron I. Smith, Grant W. Severson, Sofia A. Acosta and Jeanne Wilson-Rawls

Biomolecules 2023, 13(10), 1536; https://doi.org/10.3390/biom13101536 - 17 Oct 2023

Cited by 5 | Viewed by 4237

Abstract

Muscular dystrophies are a heterogeneous group of genetic muscle-wasting disorders that are subdivided based on the region of the body impacted by muscle weakness as well as the functional activity of the underlying genetic mutations. A common feature of the pathophysiology of muscular [...] Read more.

Muscular dystrophies are a heterogeneous group of genetic muscle-wasting disorders that are subdivided based on the region of the body impacted by muscle weakness as well as the functional activity of the underlying genetic mutations. A common feature of the pathophysiology of muscular dystrophies is chronic inflammation associated with the replacement of muscle mass with fibrotic scarring. With the progression of these disorders, many patients suffer cardiomyopathies with fibrosis of the cardiac tissue. Anti-inflammatory glucocorticoids represent the standard of care for Duchenne muscular dystrophy, the most common muscular dystrophy worldwide; however, long-term exposure to glucocorticoids results in highly adverse side effects, limiting their use. Thus, it is important to develop new pharmacotherapeutic approaches to limit inflammation and fibrosis to reduce muscle damage and promote repair. Here, we examine the pathophysiology, genetic background, and emerging therapeutic strategies for muscular dystrophies. Full article

(This article belongs to the Special Issue Muscular Dystrophy: From Molecular Basis to Therapies)

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13 pages, 707 KiB

Open AccessReview

Emerging Roles for Dendritic Cells in Heart Failure

by Danish Saleh, Rebecca T. L. Jones, Samantha L. Schroth, Edward B. Thorp and Matthew J. Feinstein

Biomolecules 2023, 13(10), 1535; https://doi.org/10.3390/biom13101535 - 17 Oct 2023

Cited by 3 | Viewed by 2346

Abstract

The field of cardio-immunology has emerged from discoveries that define roles for innate and adaptive immune responses associated with myocardial inflammation and heart failure. Dendritic cells (DCs) comprise an important cellular compartment that contributes to systemic immune surveillance at the junction of innate [...] Read more.

The field of cardio-immunology has emerged from discoveries that define roles for innate and adaptive immune responses associated with myocardial inflammation and heart failure. Dendritic cells (DCs) comprise an important cellular compartment that contributes to systemic immune surveillance at the junction of innate and adaptive immunity. Once described as a singular immune subset, we now appreciate that DCs consist of a heterogeneous pool of subpopulations, each with distinct effector functions that can uniquely regulate the acute and chronic inflammatory response. Nevertheless, the cardiovascular-specific context involving DCs in negotiating the biological response to myocardial injury is not well understood. Herein, we review our current understanding of the role of DCs in cardiac inflammation and heart failure, including gaps in knowledge and clinical relevance. Full article

(This article belongs to the Special Issue New Insights into Cardiovascular Immunology)

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26 pages, 2320 KiB

Open AccessReview

Advanced Omics Techniques for Understanding Cochlear Genome, Epigenome, and Transcriptome in Health and Disease

by Annamaria Tisi, Sakthimala Palaniappan and Mauro Maccarrone

Biomolecules 2023, 13(10), 1534; https://doi.org/10.3390/biom13101534 - 17 Oct 2023

Cited by 2 | Viewed by 2603

Abstract

Advanced genomics, transcriptomics, and epigenomics techniques are providing unprecedented insights into the understanding of the molecular underpinnings of the central nervous system, including the neuro-sensory cochlea of the inner ear. Here, we report for the first time a comprehensive and updated overview of [...] Read more.

Advanced genomics, transcriptomics, and epigenomics techniques are providing unprecedented insights into the understanding of the molecular underpinnings of the central nervous system, including the neuro-sensory cochlea of the inner ear. Here, we report for the first time a comprehensive and updated overview of the most advanced omics techniques for the study of nucleic acids and their applications in cochlear research. We describe the available in vitro and in vivo models for hearing research and the principles of genomics, transcriptomics, and epigenomics, alongside their most advanced technologies (like single-cell omics and spatial omics), which allow for the investigation of the molecular events that occur at a single-cell resolution while retaining the spatial information. Full article

(This article belongs to the Section Molecular Biology)

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16 pages, 2263 KiB

Open AccessArticle

Biological Applications of Synthetic Binders Isolated from a Conceptually New Adhiron Library

by Claudia D’Ercole, Matteo De March, Gianluca Veggiani, Sandra Oloketuyi, Rossella Svigelj and Ario de Marco

Biomolecules 2023, 13(10), 1533; https://doi.org/10.3390/biom13101533 - 17 Oct 2023

Cited by 3 | Viewed by 2095

Abstract

Background: Adhirons are small (10 kDa) synthetic ligands that might represent an alternative to antibody fragments and to alternative scaffolds such as DARPins or affibodies. Methods: We prepared a conceptionally new adhiron phage display library that allows the presence of cysteines in the [...] Read more.

Background: Adhirons are small (10 kDa) synthetic ligands that might represent an alternative to antibody fragments and to alternative scaffolds such as DARPins or affibodies. Methods: We prepared a conceptionally new adhiron phage display library that allows the presence of cysteines in the hypervariable loops and successfully panned it against antigens possessing different characteristics. Results: We recovered binders specific for membrane epitopes of plant cells by panning the library directly against pea protoplasts and against soluble C-Reactive Protein and SpyCatcher, a small protein domain for which we failed to isolate binders using pre-immune nanobody libraries. The best binders had a binding constant in the low nM range, were produced easily in bacteria (average yields of 15 mg/L of culture) in combination with different tags, were stable, and had minimal aggregation propensity, independent of the presence or absence of cysteine residues in their loops. Discussion: The isolated adhirons were significantly stronger than those isolated previously from other libraries and as good as nanobodies recovered from a naïve library of comparable theoretical diversity. Moreover, they proved to be suitable reagents for ELISA, flow cytometry, the western blot, and also as capture elements in electrochemical biosensors. Full article

(This article belongs to the Collection Feature Papers in 'Biomacromolecules: Proteins')

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