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Unraveling the evolutionary origin of the P5CS gene: a story of gene fusion and horizontal transfer Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-17 João Pedro Carmo Filgueiras, Marcel Zámocký, Andreia Carina Turchetto-Zolet
The accumulation of proline in response to the most diverse types of stress is a widespread defense mechanism. In prokaryotes, fungi, and certain unicellular eukaryotes (green algae), the first two reactions of proline biosynthesis occur through two distinct enzymes, γ-glutamyl kinase (GK E.C. 2.7.2.11) and γ-glutamyl phosphate reductase (GPR E.C. 1.2.1.41), encoded by two different genes, ProB and
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Novel anti-inflammatory effects of the IL-1 receptor in kidney myeloid cells following ischemic AKI Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-17 Yanting Chen, Xiaohan Lu, Raeann L. Whitney, Yu Li, Matthew J. Robson, Randy D. Blakely, Jen-Tsan Chi, Steven D. Crowley, Jamie R. Privratsky
Introduction: Acute kidney injury (AKI) is one of the most common causes of organ failure in critically ill patients. Following AKI, the canonical pro-inflammatory cytokine interleukin-1β (IL-1β) is released predominantly from activated myeloid cells and binds to the interleukin-1 receptor R1 (IL-1R1) on leukocytes and kidney parenchymal cells. IL-1R1 on kidney tubular cells is known to amplify the
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Unraveling the prognostic significance of RGS gene family in gastric cancer and the potential implication of RGS4 in regulating tumor-infiltrating fibroblast Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-17 Yalan Yang, Siyuan Xing, Xi Luo, Lulu Guan, Yao Lu, Yiting Wang, Feng Wang
Regulator of G-protein signaling (RGS) proteins are regulators of signal transduction mediated by G protein-coupled receptors (GPCRs). Current studies have shown that some molecules in the RGS gene family are related to the occurrence, development and poor prognosis of malignant tumors. However, the RGS gene family has been rarely studied in gastric cancer. In this study, we explored the mutation and
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Gasdermin B (GSDMB) in psoriatic patients–a preliminary comprehensive study on human serum, urine and skin Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-17 Julia Nowowiejska, Anna Baran, Anna Pryczynicz, Justyna Magdalena Hermanowicz, Beata Sieklucka, Dariusz Pawlak, Iwona Flisiak
Psoriasis is one of the most common skin diseases and a crucial issue to manage in contemporary dermatology. The search for the details of its pathogenesis, markers and treatment is continuously ongoing. Our aim was to investigate the role of gasdermin B (GSDMB) in psoriasis, the second protein from the gasdermin family, involved in cell death and proliferation. GSDMB serum and urinary concentrations
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Proteomic analysis reveals a potential role for extracellular vesicles within the erythroblastic island niche Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-16 Telma Ventura, Antonella Fidanza, Marieangela C. Wilson, Daniel C. J. Ferguson, Phillip A. Lewis, Alisha May, Helen Taylor, Michael P. Rimmer, Christopher D. Gregory, Jan Frayne, Lesley M. Forrester
Introduction: Erythroblastic island (EBI) macrophages play an essential role in the production and maturation of the vast numbers of red blood cells (RBCs) that are produced throughout life. Their location within the bone marrow makes it difficult to study the cellular and molecular interactions associated with their action so we have used an in vitro model of the EBI niche using macrophages derived
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Current strategies for early epithelial ovarian cancer detection using miRNA as a potential tool Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-16 Mridula Bhadra, Manisha Sachan, Seema Nara
Ovarian cancer is one of the most aggressive and significant malignant tumor forms in the female reproductive system. It is the leading cause of death among gynecological cancers owing to its metastasis. Since its preliminary disease symptoms are lacking, it is imperative to develop early diagnostic biomarkers to aid in treatment optimization and personalization. In this vein, microRNAs, which are
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Mesenchymal stem cells in craniofacial reconstruction: a comprehensive review Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-16 Zizhuo Zheng, Hanghang Liu, Shibo Liu, En Luo, Xian Liu
Craniofacial reconstruction faces many challenges, including high complexity, strong specificity, severe injury, irregular and complex wounds, and high risk of bleeding. Traditionally, the “gold standard” for treating craniofacial bone defects has been tissue transplantation, which involves the transplantation of bone, cartilage, skin, and other tissues from other parts of the body. However, the shape
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PhbZIP2 regulates photosynthesis-related genes in an intertidal macroalgae, Pyropia haitanensis, under stress Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-15 Han Zhang, Gaoxiong Zeng, Jiajia Xie, Yichi Zhang, Dehua Ji, Yan Xu, Chaotian Xie, Wenlei Wang
Intertidal macroalgae are important research subjects in stress biology. Basic region-leucine zipper transcription factors (bZIPs) play an important regulatory role in the expression of target genes under abiotic stress. We herein identified a bZIP2 gene PhbZIP2 to regulate abiotic stress tolerance in Pyropia haitanensis, a representative intertidal macroalgal species. Cloning and sequencing of the
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Gender effect of glucose, insulin/glucagon ratio, lipids, and nitrogen-metabolites on serum HGF and EGF levels in patients with diabetes type 2 Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-15 Martha Lucinda Contreras-Zentella, Martha Gabriela Alatriste-Contreras, Juan Antonio Suárez-Cuenca, Rolando Hernández-Muñoz
Graphical AbstractInteractions and correlations between metabolites, pancreatic hormones, and growth factors. Note the gender differences, frequently opposite among metabolites, insulin and glucagon with growth factors, as well as the effect of metabolic disturbances induced by Diabetes type 2. The size of the arrows indicates the strength of the correlation and the direction whether the correlation
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Characterization of the disease-causing mechanism of KIF3B mutations from ciliopathy patients Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-11 Jessica M. Adams, Caleb Sawe, Skye Rogers, Jordyn Reid, Ronith Dasari, Martin F. Engelke
The heterodimeric kinesin-2 motor (KIF3A/KIF3B with accessory protein KAP3) drives intraflagellar transport, essential for ciliogenesis and ciliary function. Three point mutations in the KIF3B subunit have recently been linked to disease in humans (E250Q and L523P) and Bengal cats (A334T) (Cogné et al., Am. J. Hum. Genet., 2020, 106, 893–904). Patients display retinal atrophy and, in some cases, other
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A delayed and unsynchronized ovary development as revealed by transcriptome of brain and pituitary of Coilia nasus Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-11 Ziyan Yu, Zongshuai Gao, Yun Zeng, Mingyou Li, Gangchun Xu, Mingchun Ren, Yunxia Zhu, Dong Liu
Coilia nasus is an anadromous fish that has been successfully domesticated in the last decade due to its high economic value. The fish exhibits a delayed ovary development during the reproductive season, despite breeding and selection for five to six offspring. The molecular mechanism of the delayed ovary development is still unknown, so the obstacles have not been removed in the large-scale breeding
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Convergent genetic adaptation of Escherichia coli in minimal media leads to pleiotropic divergence Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-10 Pavithra Venkataraman, Prachitha Nagendra, Neetika Ahlawat, Raman G. Brajesh, Supreet Saini
Adaptation in an environment can either be beneficial, neutral or disadvantageous in another. To test the genetic basis of pleiotropic behaviour, we evolved six lines of E. coli independently in environments where glucose and galactose were the sole carbon sources, for 300 generations. All six lines in each environment exhibit convergent adaptation in the environment in which they were evolved. However
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Transcriptomic analysis identifies the shared diagnostic biomarkers and immune relationship between Atherosclerosis and abdominal aortic aneurysm based on fatty acid metabolism gene set Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-10 Xuefeng Gu, Zhongxian Yu, Tianwei Qian, Yiqi Jin, Guoxiong Xu, Jiang Li, Jianfeng Gu, Ming Li, Ke Tao
Background:Epidemiological research has demonstrated that there is a connection between lipid metabolism disorder and an increased risk of developing arteriosclerosis (AS) and abdominal aortic aneurysm (AAA). However, the precise relationship between lipid metabolism, AS, and AAA is still not fully understood. The objective of this study was to examine the pathways and potential fatty acid metabolism-related
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Implication of Stm1 in the protection of eIF5A, eEF2 and tRNA through dormant ribosomes Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-09 Mengtan Du, Xin Li, Wanlin Dong, Fuxing Zeng
Background: Dormant ribosomes are typically associated with preservation factors to protect themselves from degradation under stress conditions. Stm1/SERBP1 is one such protein that anchors the 40S and 60S subunits together. Several proteins and tRNAs bind to this complex as well, yet the molecular mechanisms remain unclear.Methods: Here, we reported the cryo-EM structures of five newly identified
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Risk factors and metabolomics of mild cognitive impairment in type 2 diabetes mellitus Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-08 Tao Luo, Xiao Jiang, Ning Xu, Xinyu Zhao, Xingjie Xie, Xiuwen Xia, XiaoLong Bian, Haixia Liu
Objective: This study aimed to explore the risk factors, metabolic characteristics, and potential biomarkers of mild cognitive impairment in type 2 diabetes mellitus (T2DM-MCI) and to provide potential evidence for the diagnosis, prevention, and treatment of mild cognitive impairment (MCI) in patients with type 2 diabetes mellitus (T2DM).Methods: A total of 103 patients with T2DM were recruited from
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Identification of mulberry leaf flavonoids and evaluating their protective effects on H2O2-induced oxidative damage in equine skeletal muscle satellite cells Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-08 Xinzhuang Zhang, Aopan Geng, Di Cao, Manglai Dugarjaviin
Introduction: Horses are susceptible to oxidative stress during strenuous endurance exercise, leading to muscle fatigue and damage. Mulberry leaf flavonoids (MLFs) possess significant antioxidant properties. However, the antioxidant efficacy of MLFs can be influenced by the extraction process, and their impact on H2O2-induced oxidative stress in equine skeletal muscle satellite cells (ESMCs) remains
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Restoring cellular copper homeostasis in Alzheimer disease: a novel peptide shuttle is internalized by an ATP-dependent endocytosis pathway involving Rab5- and Rab14-endosomes Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-05
CPPs, or Cell-Penetrating Peptides, offer invaluable utility in disease treatment due to their ability to transport various therapeutic molecules across cellular membranes. Their unique characteristics, such as biocompatibility and low immunogenicity, make them ideal candidates for delivering drugs, genes, or imaging agents directly into cells. This targeted delivery enhances treatment efficacy while
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Hsp90 inhibition leads to an increase in surface expression of multiple immunological receptors in cancer cells Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-05
Heat shock protein 90 (Hsp90) is a molecular chaperone important for maintaining protein homeostasis (proteostasis) in the cell. Hsp90 inhibitors are being explored as cancer therapeutics because of their ability to disrupt proteostasis. Inhibiting Hsp90 increases surface density of the immunological receptor Major Histocompatibility Complex 1 (MHC1). Here we show that this increase occurs across multiple
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Effects of N-glycans on the structure of human IgA2 Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-05
The transition of IgA antibodies into clinical development is crucial because they have the potential to create a new class of therapeutics with superior pathogen neutralization, cancer cell killing, and immunomodulation capacity compared to IgG. However, the biological role of IgA glycans in these processes needs to be better understood. This study provides a detailed biochemical, biophysical, and
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Effects of N-glycans on the structure of human IgA2 Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-05 Valentina Ruocco, Clemens Grünwald-Gruber, Behzad Rad, Rupert Tscheliessnig, Michal Hammel, Richard Strasser
The transition of IgA antibodies into clinical development is crucial because they have the potential to create a new class of therapeutics with superior pathogen neutralization, cancer cell killing, and immunomodulation capacity compared to IgG. However, the biological role of IgA glycans in these processes needs to be better understood. This study provides a detailed biochemical, biophysical, and
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Hsp90 inhibition leads to an increase in surface expression of multiple immunological receptors in cancer cells Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-05 Madison Wickenberg, Rebecca Mercier, Megan Yap, John Walker, Kristi Baker, Paul LaPointe
Heat shock protein 90 (Hsp90) is a molecular chaperone important for maintaining protein homeostasis (proteostasis) in the cell. Hsp90 inhibitors are being explored as cancer therapeutics because of their ability to disrupt proteostasis. Inhibiting Hsp90 increases surface density of the immunological receptor Major Histocompatibility Complex 1 (MHC1). Here we show that this increase occurs across multiple
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Restoring cellular copper homeostasis in Alzheimer disease: a novel peptide shuttle is internalized by an ATP-dependent endocytosis pathway involving Rab5- and Rab14-endosomes Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-05 Michael Okafor, Olivia Champomier, Laurent Raibaut, Sebahat Ozkan, Naima El Kholti, Stéphane Ory, Sylvette Chasserot-Golaz, Stéphane Gasman, Christelle Hureau, Peter Faller, Nicolas Vitale
CPPs, or Cell-Penetrating Peptides, offer invaluable utility in disease treatment due to their ability to transport various therapeutic molecules across cellular membranes. Their unique characteristics, such as biocompatibility and low immunogenicity, make them ideal candidates for delivering drugs, genes, or imaging agents directly into cells. This targeted delivery enhances treatment efficacy while
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Schwann cells in the normal and pathological lung microenvironment Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-04
The lungs are a key organ in the respiratory system. They are regulated by a complex network of nerves that control their development, structure, function, and response to various pathological stimuli. Accumulating evidence suggests the involvement of a neural mechanism in different pathophysiological conditions in the lungs and the development and progression of common respiratory diseases. Lung diseases
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Characterization of four peptides from milk fermented with kombucha cultures and their metal complexes—in search of new biotherapeutics Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-04
The most common skin diseases include eczema, psoriasis, acne, and fungal infections. There is often no effective cure for them. Increasing antimicrobial drug resistance prompts us to search for new, safe, and effective therapeutics. Among such interesting candidates are peptides derived from milk fermented with specific lactic acid bacteria or with kombucha cultures, which are a potential treasure
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Chemoinformatics and machine learning techniques to identify novel inhibitors of the lemur tyrosine kinase-3 receptor involved in breast cancer Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-04
Breast cancer is still the largest cause of cancer death in women, and around 70% of primary breast cancer patients are estrogen receptor (ER)-positive, which is the most frequent kind of breast cancer. The lemur tyrosine kinase-3 (LMTK3) receptor has been linked to estrogen responsiveness in breast cancer. However, the function of LMTK3 in reaction to cytotoxic chemotherapy has yet to be studied.
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An IL-17A-centric response to Epstein-Barr virus DNA mediated by dendritic Cell-T cell interactions Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-04
Introduction: The Epstein-Barr virus has been associated with a considerable number of autoimmune diseases. We have previously demonstrated that EBV DNA enhances the production of IL-17A, a pro-inflammatory cytokine, via endosomal Toll-like receptor signalling.Methods: We used RNA-seq to analyze the transcriptional profile of mouse immune cells treated with EBV DNA.Results: We observed that EBV DNA
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Chemoinformatics and machine learning techniques to identify novel inhibitors of the lemur tyrosine kinase-3 receptor involved in breast cancer Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-04 Faris Alrumaihi
Breast cancer is still the largest cause of cancer death in women, and around 70% of primary breast cancer patients are estrogen receptor (ER)-positive, which is the most frequent kind of breast cancer. The lemur tyrosine kinase-3 (LMTK3) receptor has been linked to estrogen responsiveness in breast cancer. However, the function of LMTK3 in reaction to cytotoxic chemotherapy has yet to be studied.
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Characterization of four peptides from milk fermented with kombucha cultures and their metal complexes—in search of new biotherapeutics Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-04 Justyna Kamińska, Aleksandra Hecel, Joanna Słowik, Agnieszka Rombel-Bryzek, Magdalena Rowińska-Żyrek, Danuta Witkowska
The most common skin diseases include eczema, psoriasis, acne, and fungal infections. There is often no effective cure for them. Increasing antimicrobial drug resistance prompts us to search for new, safe, and effective therapeutics. Among such interesting candidates are peptides derived from milk fermented with specific lactic acid bacteria or with kombucha cultures, which are a potential treasure
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Schwann cells in the normal and pathological lung microenvironment Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-04 Michael R. Shurin, Sarah E. Wheeler, Galina V. Shurin, Hua Zhong, Yan Zhou
The lungs are a key organ in the respiratory system. They are regulated by a complex network of nerves that control their development, structure, function, and response to various pathological stimuli. Accumulating evidence suggests the involvement of a neural mechanism in different pathophysiological conditions in the lungs and the development and progression of common respiratory diseases. Lung diseases
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An IL-17A-centric response to Epstein-Barr virus DNA mediated by dendritic Cell-T cell interactions Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-04 Marwa Shehab, Hadi Hussein, Sukayna Fadlallah, Elias A. Rahal
Introduction: The Epstein-Barr virus has been associated with a considerable number of autoimmune diseases. We have previously demonstrated that EBV DNA enhances the production of IL-17A, a pro-inflammatory cytokine, via endosomal Toll-like receptor signalling.Methods: We used RNA-seq to analyze the transcriptional profile of mouse immune cells treated with EBV DNA.Results: We observed that EBV DNA
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TGF-β mRNA levels in circulating extracellular vesicles are associated with response to anti-PD1 treatment in metastatic melanoma Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-03
Introduction: Immune checkpoint inhibitors (ICIs) represent the standard therapy for metastatic melanoma. However, a few patients do not respond to ICIs and reliable predictive biomarkers are needed.Methods: This pilot study investigates the association between mRNA levels of programmed cell death-1 (PD-1) ligand 1 (PD-L1), interferon-gamma (IFN-γ), and transforming growth factor-β (TGF-β) in circulating
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SIRT1/P53 in retinal pigment epithelial cells in diabetic retinopathy: a gene co-expression analysis and He-Ying-Qing-Re formula treatment Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-03
Objective:Diabetic retinopathy (DR) is a severe diabetic complication that leads to severe visual impairment or blindness. He-Ying-Qing-Re formula (HF), a traditional Chinese medicinal concoction, has been identified as an efficient therapy for DR with retinal vascular dysfunction for decades and has been experimentally reported to ameliorate retinal conditions in diabetic mice. This study endeavors
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Machine learning approaches to cryoEM density modification differentially affect biomacromolecule and ligand density quality Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-03 Raymond F. Berkeley, Brian D. Cook, Mark A. Jr. Herzik
The application of machine learning to cryogenic electron microscopy (cryoEM) data analysis has added a valuable set of tools to the cryoEM data processing pipeline. As these tools become more accessible and widely available, the implications of their use should be assessed. We noticed that machine learning map modification tools can have differential effects on cryoEM densities. In this perspective
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TGF-β mRNA levels in circulating extracellular vesicles are associated with response to anti-PD1 treatment in metastatic melanoma Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-03 Stefania Crucitta, Federico Cucchiara, Riccardo Marconcini, Alessandra Bulleri, Simona Manacorda, Annalisa Capuano, Dania Cioni, Amedeo Nuzzo, Evert de Jonge, Ron H. J. Mathjissen, Emanuele Neri, Ron H. N. van Schaik, Stefano Fogli, Romano Danesi, Marzia Del Re
Introduction: Immune checkpoint inhibitors (ICIs) represent the standard therapy for metastatic melanoma. However, a few patients do not respond to ICIs and reliable predictive biomarkers are needed.Methods: This pilot study investigates the association between mRNA levels of programmed cell death-1 (PD-1) ligand 1 (PD-L1), interferon-gamma (IFN-γ), and transforming growth factor-β (TGF-β) in circulating
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SIRT1/P53 in retinal pigment epithelial cells in diabetic retinopathy: a gene co-expression analysis and He-Ying-Qing-Re formula treatment Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-03 Shuyan Zhang, Jiajun Wu, Leilei Wang, Lin Mu, Xiaoyu Xu, Jiahui Li, Guoyi Tang, Guang Chen, Cheng Zhang, Yinjian Zhang, Yibin Feng
Objective:Diabetic retinopathy (DR) is a severe diabetic complication that leads to severe visual impairment or blindness. He-Ying-Qing-Re formula (HF), a traditional Chinese medicinal concoction, has been identified as an efficient therapy for DR with retinal vascular dysfunction for decades and has been experimentally reported to ameliorate retinal conditions in diabetic mice. This study endeavors
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Efficient deletion of microRNAs using CRISPR/Cas9 with dual guide RNAs Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-02
MicroRNAs (miRNAs) are short non-coding RNAs that play crucial roles in gene regulation, exerting post-transcriptional silencing, thereby influencing cellular function, development, and disease. Traditional loss-of-function methods for studying miRNA functions, such as miRNA inhibitors and sponges, present limitations in terms of specificity, transient effects, and off-target effects. Similarly, CRISPR/Cas9-based
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Efficient deletion of microRNAs using CRISPR/Cas9 with dual guide RNAs Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-04-02 Smitha Ijee, Karthik Chambayil, Anurag Dutta Chaudhury, Abhirup Bagchi, Kirti Modak, Saswati Das, Esther Sathya Bama Benjamin, Sonam Rani, Daniel Zechariah Paul, Aneesha Nath, Debanjan Roy, Dhavapriya Palani, Sweety Priyanka, Rakshini Ravichandran, Betty K. Kumary, Yazhini Sivamani, Vijayanand S., Dinesh Babu, Yukio Nakamura, Vasanth Thamodaran, Poonkuzhali Balasubramanian, Shaji R. Velayudhan
MicroRNAs (miRNAs) are short non-coding RNAs that play crucial roles in gene regulation, exerting post-transcriptional silencing, thereby influencing cellular function, development, and disease. Traditional loss-of-function methods for studying miRNA functions, such as miRNA inhibitors and sponges, present limitations in terms of specificity, transient effects, and off-target effects. Similarly, CRISPR/Cas9-based
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Effects of saponins Rb1 and Re in American ginseng combined intervention on immune system of aging model Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-28 Mao Shi, Jie Ma, Shan Jin, Tienan Wang, Yuhan Sui, Lina Chen
Aging is a major risk factor for the development of many pathological processes, such as reduced immunity, cancer, cardiovascular diseases or neurodegenerative diseases, while age-related chronic diseases are the most common causes of death. This paper studies the effects of American ginseng saponin Rb1 and Re alone and combined intervention on the immune system of aging mouse models, by using 30 mg/kg
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GEO dataset mining analysis reveals novel Staphylococcus aureus virulence gene regulatory networks and diagnostic targets in mice Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-28 Guangyu Xu, Yue Yang, Yan Lin, Yu Bai
Staphylococcus (S.) aureus infection is a serious, worldwide health concern, particularly in many communities and hospitals. Understanding the S. aureus pathogenetic regulatory network will provide significant insights into diagnostic target screening to improve clinical treatment of diseases caused by S. aureus. We screened differentially expressed genes between normal mice and S. aureus-infected
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The coordinated activities of collagen VI and XII in maintenance of tissue structure, function and repair: evidence for a physical interaction Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-28 Carl A. Gregory, Jocelyn Ma, Sebastian Lomeli
Collagen VI and collagen XII are structurally complex collagens of the extracellular matrix (ECM). Like all collagens, type VI and XII both possess triple-helical components that facilitate participation in the ECM network, but collagen VI and XII are distinct from the more abundant fibrillar collagens in that they also possess arrays of structurally globular modules with the capacity to propagate
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Benchmarking antibody clustering methods using sequence, structural, and machine learning similarity measures for antibody discovery applications Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-28 Dawid Chomicz, Jarosław Kończak, Sonia Wróbel, Tadeusz Satława, Paweł Dudzic, Bartosz Janusz, Mateusz Tarkowski, Piotr Deszyński, Tomasz Gawłowski, Anna Kostyn, Marek Orłowski, Tomasz Klaus, Lukas Schulte, Kyle Martin, Stephen R. Comeau, Konrad Krawczyk
Antibodies are proteins produced by our immune system that have been harnessed as biotherapeutics. The discovery of antibody-based therapeutics relies on analyzing large volumes of diverse sequences coming from phage display or animal immunizations. Identification of suitable therapeutic candidates is achieved by grouping the sequences by their similarity and subsequent selection of a diverse set of
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Electrophysiological properties and structural prediction of the SARS-CoV-2 viroprotein E Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-28 Salvatore Antonio Maria Cubisino, Stefan Milenkovic, Stefano Conti-Nibali, Nicolò Musso, Paolo Bonacci, Vito De Pinto, Matteo Ceccarelli, Simona Reina
COVID-19, the infectious disease caused by the most recently discovered coronavirus SARS- CoV-2, has caused millions of sick people and thousands of deaths all over the world. The viral positive-sense single-stranded RNA encodes 31 proteins among which the spike (S) is undoubtedly the best known. Recently, protein E has been reputed as a potential pharmacological target as well. It is essential for
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Modeling of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-2 considering the protein flexibility by using molecular dynamics and cross-docking Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-27 Jorge Luis Valdés-Albuernes, Erbio Díaz-Pico, Sergio Alfaro, Julio Caballero
The papain-like protease (PLpro) found in coronaviruses that can be transmitted from animals to humans is a critical target in respiratory diseases linked to Severe Acute Respiratory Syndrome (SARS-CoV). Researchers have proposed designing PLpro inhibitors. In this study, a set of 89 compounds, including recently reported 2-phenylthiophenes with nanomolar inhibitory potency, were investigated as PLpro
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Longitudinal analysis of 20 Years of external quality assurance schemes for PCR/NAAT-based bacterial genome detection in diagnostic testing Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-27 Marcel Kremser, Nathalie Weiss, Anne Kaufmann-Stoeck, Laura Vierbaum, Silke Kappler, Ingo Schellenberg, Andreas Hiergeist, Volker Fingerle, Michael Baier, Udo Reischl
Background:Quality control (QC), quality assurance, and standardization are crucial for modern diagnostic testing in the field of medical microbiology. The need for efficient QC to ensure accurate laboratory results, treatment, and infection prevention has led to significant efforts in standardizing assay reagents and workflows. External quality assessment (EQA) schemes, like those offered by INSTAND
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Evaluation of Adenanthera pavonina-derived compounds against diabetes mellitus: insight into the phytochemical analysis and in silico assays Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-27 Md. Sojiur Rahman, Md. Eram Hosen, Md. Omar Faruqe, Md. Khalekuzzaman, Md. Asadul Islam, Uzzal Kumar Acharjee, Yousef A. Bin Jardan, Hiba-Allah Nafidi, Amare Bitew Mekonnen, Mohammed Bourhia, Rashed Zaman
Adenanthera pavonina is a medicinal plant with numerous potential secondary metabolites showing a significant level of antidiabetic activity. The objective of the current study was to identify potential phytochemicals from the methanolic leaf extract of Adenanthera pavonina as therapeutic agents against diabetes mellitus using GC-MS and in silico methods. The GC-MS analysis of the leaf extract revealed
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Therapeutic potential of tyrosine-protein kinase MET in osteosarcoma Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-26 Ming Zeng, Can Liu, Haoli Gong, Zhongwen Tang, Jie Wen, Sisi Wang, Sheng Xiao
Osteosarcoma, the most prevalent primary bone tumor in children and young adults, can often be successfully treated with standard chemotherapy and surgery when diagnosed at an early stage. However, patients presenting with metastases face significant challenges in achieving a cure. Despite advancements in classical therapies over the past few decades, clinical outcomes for osteosarcoma have not substantially
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Serum proteomic profiling of precancerous gastric lesions and early gastric cancer reveals signatures associated with systemic inflammatory response and metaplastic differentiation Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-22 Yueqing Gong, Yaxin Lou, Xiurui Han, Keyan Chen, Yang Zhao, Hejun Zhang, Jing Zhang, Ying Xiong, Weiwei Fu, Shigang Ding
The noninvasive detection technique using serum for large-scale screening is useful for the early diagnosis of gastric cancer (GC). Herein, we employed liquid chromatography mass spectrometry to determine the serum proteome signatures and related pathways in individuals with gastric precancerous (pre-GC) lesions and GC and explore the effect of Helicobacter pylori (H. pylori) infection. Differentially
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The underlying mechanism and targeted therapy strategy of miRNAs cross-regulating EMT process through multiple signaling pathways in hepatocellular carcinoma Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-22 Juan Chen, Fuguo He, Hong Peng, Jinjun Guo
The consistent notion holds that hepatocellular carcinoma (HCC) initiation, progression, and clinical treatment failure treatment failure are affected by the accumulation of various genetic and epigenetic alterations. MicroRNAs (miRNAs) play an irreplaceable role in a variety of physiological and pathological states. meanwhile, epithelial-mesenchymal transition (EMT) is a crucial biological process
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Simple Scattering: Lipid nanoparticle structural data repository Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-22 Lee Joon Kim, David Shin, Wellington C. Leite, Hugh O’Neill, Oliver Ruebel, Andrew Tritt, Greg L. Hura
Lipid nanoparticles (LNPs) are being intensively researched and developed to leverage their ability to safely and effectively deliver therapeutics. To achieve optimal therapeutic delivery, a comprehensive understanding of the relationship between formulation, structure, and efficacy is critical. However, the vast chemical space involved in the production of LNPs and the resulting structural complexity
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Prostate fibroblasts and prostate cancer associated fibroblasts exhibit different metabolic, matrix degradation and PD-L1 expression responses to hypoxia Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-22 Jesus Pacheco-Torres, Raj Kumar Sharma, Yelena Mironchik, Flonne Wildes, W. Nathaniel Brennen, Dmitri Artemov, Balaji Krishnamachary, Zaver M. Bhujwalla
Fibroblasts are versatile cells that play a major role in wound healing by synthesizing and remodeling the extracellular matrix (ECM). In cancers, fibroblasts play an expanded role in tumor progression and dissemination, immunosuppression, and metabolic support of cancer cells. In prostate cancer (PCa), fibroblasts have been shown to induce growth and increase metastatic potential. To further understand
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Genetic correlation between circulating metabolites and chalazion: a two-sample Mendelian randomization study Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-21 Xin Zhang, Yuying Cai, Yaping Jiang, Wei Du, Weishu An, Qiangqiang Fu, Yihui Chen
Background: Lipid metabolism disorders were observationally associated with chalazion, but the causality of the related circulating metabolites on chalazion remained unknown. Here, we investigated the potential causal relationship between circulating metabolites and chalazion using two-sample Mendelian randomization (MR) analysis.Methods: For the primary analysis, 249 metabolic biomarkers were obtained
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An automatic diagnosis model of otitis media with high accuracy rate using transfer learning Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-21 Fangyu Qi, Zhiyu You, Jiayang Guo, Yongjun Hong, Xiaolong Wu, Dongdong Zhang, Qiyuan Li, Chengfu Cai
Introduction: Chronic Suppurative Otitis Media (CSOM) and Middle Ear Cholesteatoma are two common chronic otitis media diseases that often cause confusion among physicians due to their similar location and shape in clinical CT images of the internal auditory canal. In this study, we utilized the transfer learning method combined with CT scans of the internal auditory canal to achieve accurate lesion
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Deferiprone–resveratrol hybrid attenuates iron accumulation, oxidative stress, and antioxidant defenses in iron-loaded human Huh7 hepatic cells Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-20 Jin Li, Pimpisid Koonyosying, Woranontee Korsieporn, Narisara Paradee, Nuntouchaporn Hutachok, Honghong Xu, Yongmin Ma, Hataichanok Chuljerm, Somdet Srichairatanakool
Chronic liver diseases are complications of thalassemia with iron overload. Iron chelators are required to remove excessive iron, and antioxidants are supplemented to diminish harmful reactive oxygen species (ROS), purposing to ameliorate oxidative liver damage and dysfunctions. The deferiprone–resveratrol hybrid (DFP–RVT) is a synthetic iron chelator possessing anti-β-amyloid peptide aggregation,
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Quality assessment of glucose measurement with regard to epidemiology and clinical management of diabetes mellitus in Germany Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-20 Peter B. Luppa, Michael Zeller, Marija Pieper, Patricia Kaiser, Nathalie Weiss, Laura Vierbaum, Guido Freckmann
Background:During the last decade, Germany has seen an increased prevalence and a redistribution from undetected to diagnosed diabetes mellitus. Due to this substantial epidemiological development, the number of people with documented type 2 diabetes was 8.7 million in 2022. An estimated two million undiagnosed subjects are to be added. Beyond that, the life expectancy of diabetic subjects is increasing
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The association of TNF-alpha secretion and mtDNA copy number in CD14+ monocytes of patients with obesity and CHD Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-20 Taisiya V. Tolstik, Tatiana V. Kirichenko, Alexander M. Markin, Anastasia I. Bogatyreva, Yuliya V. Markina, Diana G. Kiseleva, Nataliya N. Shaposhnikova, Antonina V. Starodubova, Alexander N. Orekhov
IntroductionMitochondrial dysfunction may be one of the causes of inflammatory activation of monocytes and macrophages, which leads to excessive secretion of inflammatory mediators and the development of chronic inflammation.AimsThe study was aimed to evaluate the secretion of inflammatory cytokine tumor necrosis factor-α (TNF-α) in the primary culture of monocytes, and to analyze its relationship
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Regulatory role of RNA-binding proteins in microRNA biogenesis Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-19 Claire Hynes, Pavan Kumar Kakumani
MicroRNAs (miRNAs) are small non-coding RNAs that silence gene expression through their interaction with complementary sequences in the 3′ untranslated regions (UTR) of target mRNAs. miRNAs undergo a series of steps during their processing and maturation, which are tightly regulated to fine-tune their abundance and ability to function in post-transcriptional gene silencing. miRNA biogenesis typically
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Deep learning-based identification of esophageal cancer subtypes through analysis of high-resolution histopathology images Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-19 Syed Wajid Aalam, Abdul Basit Ahanger, Tariq A. Masoodi, Ajaz A. Bhat, Ammira S. Al-Shabeeb Akil, Meraj Alam Khan, Assif Assad, Muzafar A. Macha, Muzafar Rasool Bhat
Esophageal cancer (EC) remains a significant health challenge globally, with increasing incidence and high mortality rates. Despite advances in treatment, there remains a need for improved diagnostic methods and understanding of disease progression. This study addresses the significant challenges in the automatic classification of EC, particularly in distinguishing its primary subtypes: adenocarcinoma
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Roles of pyroptosis and immune infiltration in aortic dissection Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-19 Xiaogang Ge, Qiqi Cai, Yangyang Cai, Caiguo Mou, Junhui Fu, Feng Lin
Introduction: Aortic dissection (AD) is often fatal, and its pathogenesis involves immune infiltration and pyroptosis, though the molecular pathways connecting these processes remain unclear. This study aimed to investigate the role of immune infiltration and pyroptosis in AD pathogenesis using bioinformatics analysis.Methods: Two Gene Expression Omnibus datasets and a Gene Cards dataset of pyroptosis-related
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Eukaryotic yeast V1-ATPase rotary mechanism insights revealed by high-resolution single-molecule studies Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-19 Seiga Yanagisawa, Zain A. Bukhari, Karlett J. Parra, Wayne D. Frasch
Vacuolar ATP-dependent proton pumps (V-ATPases) belong to a super-family of rotary ATPases and ATP synthases. The V1 complex consumes ATP to drive rotation of a central rotor that pumps protons across membranes via the Vo complex. Eukaryotic V-ATPases are regulated by reversible disassembly of subunit C, V1 without C, and VO. ATP hydrolysis is thought to generate an unknown rotary state that initiates
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Carcinogenic effect of human tumor-derived cell-free filtrates in nude mice Front. Mol. Biosci. (IF 5.0) Pub Date : 2024-03-18 Jorge Berlanga-Acosta, Ernesto Arteaga-Hernandez, Ariana Garcia-Ojalvo, Dayanis Duvergel-Calderin, Marisol Rodriguez-Touseiro, Laura Lopez-Marin, Jose Suarez-Alba, Dasha Fuentes-Morales, Osmany Mendoza-Fuentes, Sheyla Fernández-Puentes, Yanier Nuñez-Figueredo, Gerardo Guillen-Nieto
Cancer remains a worldwide cause of morbidity and mortality. Investigational research efforts have included the administration of tumor-derived extracts to healthy animals. Having previously demonstrated that the administration of non-transmissible, human cancer-derived homogenates induced malignant tumors in mice, here, we examined the consequences of administering 50 or 100 µg of protein of crude