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1.
Genes (Basel) ; 14(1)2023 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-36672868

RESUMO

Boron neutron capture therapy (BNCT) is an approach to the radiotherapy of solid tumors that was first outlined in the 1930s but has attracted considerable attention recently with the advent of a new generation of neutron sources. In BNCT, tumor cells accumulate 10B atoms that react with epithermal neutrons, producing energetic α particles and 7Li atoms that damage the cell's genome. The damage inflicted by BNCT appears not to be easily repairable and is thus lethal for the cell; however, the molecular events underlying the action of BNCT remain largely unaddressed. In this review, the chemistry of DNA damage during BNCT is outlined, the major mechanisms of DNA break sensing and repair are summarized, and the specifics of the repair of BNCT-induced DNA lesions are discussed.


Assuntos
Fenômenos Biológicos , Terapia por Captura de Nêutron de Boro , Neoplasias Encefálicas , Humanos , Dano ao DNA , Neoplasias Encefálicas/radioterapia
2.
BMC Plant Biol ; 23(1): 54, 2023 Jan 24.
Artigo em Inglês | MEDLINE | ID: mdl-36694111

RESUMO

BACKGROUND: Sugarcane growth and yield are complex biological processes influenced by endophytic nitrogen-fixing bacteria, for which the molecular mechanisms involved are largely unknown. In this study, integrated metabolomic and RNA-seq were conducted to investigate the interaction between an endophytic bacterial strain, Burkholderia GXS16, and sugarcane tissue culture seedlings. RESULTS: During treatment, the colonization of GXS16 in sugarcane roots were determined, along with the enhanced activities of various antioxidant enzymes. Accordingly, 161, 113, and 37 differentially accumulated metabolites (DAMs) were found in the pairwise comparisons of adjacent stages. In addition, transcriptomic analyses obtained 1,371 (IN-vs-CN), 1,457 (KN-vs-IN), and 365 (LN-vs-KN) differentially expressed genes (DEGs), which were mainly involved in the pathways of glutathione metabolism and carbon metabolism. We then assessed the pattern of metabolite accumulation and gene expression in sugarcane during GXS16 colonization. The results showed that both DAMs and DGEs in the upregulated expression profiles were involved in the flavonoid biosynthesis pathway. Overall, p-coumaroyl-CoA in sugarcane roots transferred into homoeriodictyol chalcone and 5-deoxyleucopelargonidin due to the upregulation of the expression of genes shikimate O-hydroxycinnamoyltransferase (HCT), chalcone synthase (CHS), and phlorizin synthase (PGT1). CONCLUSIONS: This study provides insights into the gene regulatory mechanisms involved in the interaction between GXS16 and sugarcane roots, which will facilitate future applications of endophytic nitrogen-fixing bacteria to promote crop growth.


Assuntos
Fenômenos Biológicos , Bactérias Fixadoras de Nitrogênio , Saccharum , Transcriptoma , Regulação da Expressão Gênica de Plantas
3.
Sci Rep ; 13(1): 1617, 2023 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-36709392

RESUMO

Segmentation of white matter tracts in diffusion magnetic resonance images is an important first step in many imaging studies of the brain in health and disease. Similar to medical image segmentation in general, a popular approach to white matter tract segmentation is to use U-Net based artificial neural network architectures. Despite many suggested improvements to the U-Net architecture in recent years, there is a lack of systematic comparison of architectural variants for white matter tract segmentation. In this paper, we evaluate multiple U-Net based architectures specifically for this purpose. We compare the results of these networks to those achieved by our own various architecture changes, as well as to new U-Net architectures designed automatically via neural architecture search (NAS). To the best of our knowledge, this is the first study to systematically compare multiple U-Net based architectures for white matter tract segmentation, and the first to use NAS. We find that the recently proposed medical imaging segmentation network UNet3+ slightly outperforms the current state of the art for white matter tract segmentation, and achieves a notably better mean Dice score for segmentation of the fornix (+ 0.01 and + 0.006 mean Dice increase for left and right fornix respectively), a tract that the current state of the art model struggles to segment. UNet3+ also outperforms the current state of the art when little training data is available. Additionally, manual architecture search found that a minor segmentation improvement is observed when an additional, deeper layer is added to the U-shape of UNet3+. However, all networks, including those designed via NAS, achieve similar results, suggesting that there may be benefit in exploring networks that deviate from the general U-Net paradigm.


Assuntos
Fenômenos Biológicos , Substância Branca , Substância Branca/diagnóstico por imagem , Redes Neurais de Computação , Encéfalo/diagnóstico por imagem , Imageamento por Ressonância Magnética/métodos , Processamento de Imagem Assistida por Computador/métodos
4.
Reproduction ; 165(1): R1-R8, 2023 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-36194446

RESUMO

In brief: RNA modifications play key roles in regulating various biological processes. This article discusses and summarizes the recent advances of RNA m6A modifications related to mammalian gametogenesis, early embryonic development, and miscarriage. Abstract: The epitranscriptome is defined as the collection of post-transcriptional chemical modifications of RNA in a cell. RNA methylation refers to the chemical post-transcriptional modification of RNA by selectively adding methyl groups under the catalysis of a methyltransferase. The N6 methyladenosine (m6A) is one of the most common of the more than 100 known RNA modifications. Recent research has revealed that RNA m6A modifications are reversible. Additionally, m6A containing RNA can be selectively identified by immunoprecipitation followed by high-throughput sequencing (MeRIP-SEQ). These two developments have inspired a tremendous effort to unravel the biological role of m6A. The role of RNA m6A modifications in immune regulation, cell division, stem cell renewal, gametogenesis, embryonic development, and placental function has gradually emerged, which is of great significance for the study of post-transcriptional regulation of gene expression in reproductive biology. This review summarizes the current knowledge about RNA m6A modification in a variety of mammalian reproductive events.


Assuntos
Fenômenos Biológicos , Placenta , Gravidez , Animais , Feminino , Placenta/metabolismo , Metilação , RNA , Mamíferos/genética , Mamíferos/metabolismo , Gametogênese
5.
BMC Biol ; 20(1): 270, 2022 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-36464676

RESUMO

BACKGROUND: Recently, bacterial extracellular vesicles (EVs) have been considered to play crucial roles in various biological processes and have great potential for developing cancer therapeutics and biomedicine. However, studies on bacterial EVs have mainly focused on outer membrane vesicles released from gram-negative bacteria since the outermost peptidoglycan layer in gram-positive bacteria is thought to preclude the release of EVs as a physical barrier. RESULTS: Here, we examined the ultrastructural organization of the EV produced by gram-positive bacteria using super-resolution stochastic optical reconstruction microscopy (STORM) at the nanoscale, which has not been resolved using conventional microscopy. Based on the super-resolution images of EVs, we propose three major mechanisms of EV biogenesis, i.e., membrane blebbing (mechanisms 1 and 2) or explosive cell lysis (mechanism 3), which are different from the mechanisms in gram-negative bacteria, despite some similarities. CONCLUSIONS: These findings highlight the significant role of cell wall degradation in regulating various mechanisms of EV biogenesis and call for a reassessment of previously unresolved EV biogenesis in gram-positive bacteria.


Assuntos
Fenômenos Biológicos , Vesículas Extracelulares , Microscopia , Bactérias Gram-Positivas , Morte Celular
6.
Int J Mol Sci ; 23(23)2022 Dec 04.
Artigo em Inglês | MEDLINE | ID: mdl-36499626

RESUMO

Ovarian cancer is currently the most lethal gynecological cancer. At present, primary debulking surgery combined with platinum-based chemotherapy is the standard treatment strategy for ovarian cancer. Although cisplatin-based chemotherapy has greatly improved the prognosis of patients, the subsequent primary or acquired drug resistance of cancer cells has become an obstacle to a favorable prognosis. Mortalin is a chaperone that plays an important role in multiple cellular and biological processes. Our previous studies have found that mortalin is associated with the proliferation and migration of ovarian cancer cells and their resistance to cisplatin-based chemotherapy. In this study, microRNA (miR)-200b/c downregulated mortalin expression and inhibited the proliferation and migration of the paired cisplatin-sensitive (A2780S) and cisplatin-resistant (A2780CP) epithelial ovarian cancer cell lines. Moreover, miR-200c increased the sensitivity of ovarian cancer cells to cisplatin treatment by regulating mortalin levels. Nuclear factor (NF)-κB directly regulated mortalin and miR-200b/c expression levels, while NF-κB and miR-200b/c jointly regulated the expression of mortalin. The combination of cisplatin and miR-200c significantly enhanced the therapeutic effects on ovarian cancer in vivo, suggesting that miR-200c may serve as a potential therapeutic agent for ovarian cancer.


Assuntos
Antineoplásicos , Fenômenos Biológicos , MicroRNAs , Neoplasias Ovarianas , Humanos , Feminino , Cisplatino/farmacologia , Cisplatino/metabolismo , NF-kappa B/genética , NF-kappa B/metabolismo , MicroRNAs/genética , MicroRNAs/metabolismo , Linhagem Celular Tumoral , Neoplasias Ovarianas/tratamento farmacológico , Neoplasias Ovarianas/genética , Neoplasias Ovarianas/metabolismo , Proliferação de Células , Resistencia a Medicamentos Antineoplásicos/genética , Regulação Neoplásica da Expressão Gênica , Antineoplásicos/farmacologia
10.
Int J Biol Sci ; 18(16): 6129-6144, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36439870

RESUMO

The circadian clock confers daily rhythmicity to many crucial biological processes and behaviors and its disruption is closely associated with carcinogenesis in several types of cancer. Brain and muscle arnt-like protein 1 (BMAL1) is a core circadian rhythm component in mammals and its dysregulation has been shown to contribute to aberrant metabolism in human diseases. However, the biological functions of BMAL1, especially its involvement in aberrant lipid metabolism in hepatocellular carcinoma (HCC), remain elusive. In the present study, we found that BMAL1 was frequently down-regulated in HCC cells mainly due to the up-regulation of miR-494-3p. Down-regulation of BMAL1 was significantly associated with poor survival in HCC patients. BMAL1 down-regulation promoted HCC cell growth and metastasis both in vitro and in vivo. Mechanistically, through cooperating with EZH2, BMAL1 transcriptionally suppressed the expression of glycerol-3-phosphate acyltransferase mitochondrial (GPAM), a key enzyme involved in the regulation of lipid biosynthesis, leading to reduced levels lysophosphatidic acid (LPA), which have long been known as mediator of oncogenesis. Particularly, treatment with SR8278, an activator of BMAL1, exhibited a therapeutic effect on HCC in vitro and in vivo. In conclusion, BMAL1 plays a critical anti-oncogenic role in HCC, providing strong research evidence for BMAL1 as a prospective target for HCC therapy.


Assuntos
Fenômenos Biológicos , Carcinoma Hepatocelular , Neoplasias Hepáticas , MicroRNAs , Animais , Humanos , Carcinoma Hepatocelular/genética , Regulação para Baixo/genética , Fatores de Transcrição ARNTL/genética , Neoplasias Hepáticas/genética , Carcinogênese , MicroRNAs/genética , Mamíferos
11.
Sci Rep ; 12(1): 20061, 2022 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-36414633

RESUMO

Compelling evidence from human and non-human studies suggests that responses to multisensory events are fastened when stimuli occur within the space surrounding the bodily self (i.e., peripersonal space; PPS). However, some human studies did not find such effect. We propose that these dissonant voices might actually uncover a specific mechanism, modulating PPS boundaries according to sensory regularities. We exploited a visuo-tactile paradigm, wherein participants provided speeded responses to tactile stimuli and rated their perceived intensity while ignoring simultaneous visual stimuli, appearing near the stimulated hand (VTNear) or far from it (VTFar; near the non-stimulated hand). Tactile stimuli could be delivered only to one hand (unilateral task) or to both hands randomly (bilateral task). Results revealed that a space-dependent multisensory enhancement (i.e., faster responses and higher perceived intensity in VTNear than VTFar) was present when highly predictable tactile stimulation induced PPS to be circumscribed around the stimulated hand (unilateral task). Conversely, when stimulus location was unpredictable (bilateral task), participants showed a comparable multisensory enhancement in both bimodal conditions, suggesting a PPS widening to include both hands. We propose that the detection of environmental regularities actively shapes PPS boundaries, thus optimizing the detection and reaction to incoming sensory stimuli.


Assuntos
Fenômenos Biológicos , Percepção do Tato , Humanos , Espaço Pessoal , Motivação , Tato/fisiologia , Percepção do Tato/fisiologia
12.
Int J Mol Sci ; 23(22)2022 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-36430318

RESUMO

The role of membrane lipids is increasingly claimed to explain biological activities of natural amphiphile molecules. To decipher this role, biophysical studies with biomimetic membrane models are often helpful to obtain insights at the molecular and atomic levels. In this review, the added value of biophysics to study lipid-driven biological processes is illustrated using the case of surfactins, a class of natural lipopeptides produced by Bacillus sp. showing a broad range of biological activities. The mechanism of interaction of surfactins with biomimetic models showed to be dependent on the surfactins-to-lipid ratio with action as membrane disturber without membrane lysis at low and intermediate ratios and a membrane permeabilizing effect at higher ratios. These two mechanisms are relevant to explain surfactins' biological activities occurring without membrane lysis, such as their antiviral and plant immunity-eliciting activities, and the one involving cell lysis, such as their antibacterial and hemolytic activities. In both biological and biophysical studies, influence of surfactin structure and membrane lipids on the mechanisms was observed with a similar trend. Hence, biomimetic models represent interesting tools to elucidate the biological mechanisms targeting membrane lipids and can contribute to the development of new molecules for pharmaceutical or agronomic applications.


Assuntos
Bacillus , Fenômenos Biológicos , Lipopeptídeos/farmacologia , Lipopeptídeos/química , Biofísica , Lipídeos de Membrana
14.
Front Immunol ; 13: 1037739, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36389847

RESUMO

Molting is one of the most important biological processes of crustacean species, and a number of molecular mechanisms facilitate this complex procedure. However, the understanding of the immune mechanisms underlying crustacean molting cycle remains very limited. This study performed transcriptome sequencing in hemolymph and hepatopancreas of the swimming crab (Portunus trituberculatus) during the four molting stages: post-molt (AB), inter-molt (C), pre-molt (D), and ecdysis (E). The results showed that there were 78,572 unigenes that were obtained in the hemolymph and hepatopancreas of P. trituberculatus. Further analysis showed that 98 DEGs were involved in immunity response of hemolymph and hepatopancreas, and most of the DEGs participated in the process of signal transduction, pattern recognition proteins/receptors, and antioxidative enzymes system. Specifically, the key genes and pathway involved in signal transduction including the GPCR126, beta-integrin, integrin, three genes in mitogen-activated protein kinase (MAPK) signaling cascade (MAPKKK10, MAPKK4, and p38 MAPK), and four genes in Toll pathway (Toll-like receptor, cactus, pelle-like kinase, and NFIL3). For the pattern recognition proteins/receptors, the lowest expression level of 11 genes was found in the E stage, including C-type lectin receptor, C-type lectin domain family 6 member A and SRB3/C in the hemolymph, and hepatopancreatic lectin 4, C-type lectin, SRB, Down syndrome cell adhesion molecule homolog, Down syndrome cell adhesion molecule isoform, and A2M. Moreover, the expression level of copper/zinc superoxide dismutase isoform 4, glutathione peroxidase, glutathione S-transferase, peroxiredoxin, peroxiredoxin 6, and dual oxidase 2 in stage C or stage D significantly higher than that of stage E or stage AB. These results fill in the gap of the continuous transcriptional changes that are evident during the molting cycle of crab and further provided valuable information for elucidating the molecular mechanisms of immune regulation during the molting cycle of crab.


Assuntos
Fenômenos Biológicos , Braquiúros , Síndrome de Down , Animais , Braquiúros/genética , Braquiúros/metabolismo , Transcriptoma , Muda/genética , Natação , Lectinas Tipo C/metabolismo , Integrinas/metabolismo , Moléculas de Adesão Celular/metabolismo
15.
PLoS Biol ; 20(11): e3001875, 2022 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-36395079

RESUMO

Well-designed animations can help students to focus on the underlying principles and processes in biology rather than relying on rote memorization. We present question-driven, terminology-free, "candymation" videos for teaching the concepts behind mitosis and meiosis as an example.


Assuntos
Fenômenos Biológicos , Estudantes , Humanos
16.
Biomed Res Int ; 2022: 4740686, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36349315

RESUMO

Background: Biological processes serve crucial functions in the initiation and development of cancer. Therefore, we constructed and validated a model for bladder cancer (BLCA) with good predictive power for immunity, prognosis, and therapy. Methods: Using the expression of the gene sets based on biological processes, BLCA patients were divided into three clusters by consensus cluster analysis. By performing LASSO regression analysis twice, key genes were selected, and the biological processes-related genes' (BPRG) score was calculated. Differences in immune infiltration, tumor microenvironment, tumor mutation burden, immunotherapy, and sensitivity towards chemotherapy were analyzed between two groups divided by BPRG score. Results: Good accuracy was observed for the three clusters. They showed different prognoses and levels of immune cell infiltration. The selected key genes were mainly enriched in immune-related pathways. The high-BPRG score group was related to poor prognosis, higher immune cell infiltration, interstitial scores, and increased tumor mutation. Moreover, the effects of immunotherapy were good, and those of chemotherapy were poor. Conclusion: Overall, key genes may be involved in various complex immune regulation processes. Therefore, the quantification and verification of the BPRG score are expected to facilitate the understanding of the immunosuppressive microenvironment in BLCA and guide the choice of chemotherapeutic drugs and immunotherapeutic regimens and help predict the prognoses of patients with BLCA.


Assuntos
Fenômenos Biológicos , Neoplasias da Bexiga Urinária , Humanos , Neoplasias da Bexiga Urinária/tratamento farmacológico , Neoplasias da Bexiga Urinária/genética , Neoplasias da Bexiga Urinária/metabolismo , Perfilação da Expressão Gênica , Prognóstico , Imunidade , Microambiente Tumoral/genética
17.
Int J Mol Med ; 50(6)2022 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-36367164

RESUMO

The synthesis and release of glucocorticoids in living organisms are related to their response to unfavorable stressful conditions in order to maintain homeostatic functions and survive. One such hormone in humans is cortisol, which is produced by the hypothalamic­pituitary­adrenal cortex axis and binds with the glucocorticoid receptor (GR) following its secretion. GR controls a number of distinct gene networks. Non­coding RNAs (ncRNAs), such as microRNAs (miRNAs) and long non­coding RNAs (lncRNAs), regulate the expression and function of GR, having a considerable impact on various biological processes and treatment approaches for numerous disorders. In the present review, the GR pathways and signaling as part of the stress response system are discussed. A detailed report on the role of miRNAs and lncRNAs in glucocorticoid signaling is also presented.


Assuntos
Fenômenos Biológicos , MicroRNAs , RNA Longo não Codificante , Humanos , RNA Longo não Codificante/genética , MicroRNAs/genética , MicroRNAs/metabolismo , Glucocorticoides , Redes Reguladoras de Genes , Receptores de Glucocorticoides/genética
18.
Nat Commun ; 13(1): 6643, 2022 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-36333308

RESUMO

High spatial resolution, low background, and deep tissue penetration have made near-infrared II (NIR-II) fluorescence imaging one of the most critical tools for in vivo observation and measurement. However, the relatively short retention time and potential toxicity of synthetic NIR-II fluorophores limit their long-term application. Here, we report the use of infrared fluorescent proteins (iRFPs) as in vitro and in vivo NIR-II probes permitting prolonged continuous imaging (up to 15 months). As a representative example, iRFP713 is knocked into the mouse genome to generate a transgenic model to allow temporal and/or spatial expression control of the probe. To demonstrate its feasibility in a genuine diagnostic context, we adopt two liver regeneration models and successfully track the process for a week. The performance and monitoring efficacy are comparable to those of µCT and superior to those of indocyanine green dye. We are also able to effectively observe the pancreas, despite its deep location, under both physiological and pathological conditions. These results indicate that the iRFP-assisted NIR-II fluorescence system is suitable for monitoring various tissues and in vivo biological processes, providing a powerful noninvasive long-term imaging platform.


Assuntos
Fenômenos Biológicos , Imagem Óptica , Animais , Camundongos , Corantes Fluorescentes , Verde de Indocianina
19.
Dis Markers ; 2022: 9119423, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36438896

RESUMO

Triptolide (TP) has demonstrated innumerous biological effects and pharmacological potential against different cancer types. Hepatocellular carcinoma has a high incidence in men, and its incidence is increasing year by year. Studies have shown that angiogenesis plays an important role in the formation of tumors and that angiogenesis is closely related to tumor growth and metastasis. Deregulation of sphingolipids signaling has been associated with several pathological conditions, including cancer. In the present study, we aimed at exploring the potential molecular mechanism of TP's antivascular and antitumor effects in vitro from the perspective of sphinolipids. Human umbilical vein endothelial cells (HUVECs) and HepG2 cells were, respectively, treated with different concentrations of TP and transfected. Then, the effect of HUVECs on HepG2 cells was investigated using a three-dimensional coculture model system. CCK-8 assay was performed for cell proliferation. Cell migration and invasion abilities were assessed using the transwell assay. Cell adhesion and tube formation were detected by Matrigel. RT-PCR and western blotting were used to detect the mRNA and protein expression. The S1P production was measured via ELISA assay. Our results showed that TP inhibited HUVECs and HepG2 cells proliferation, migration, invasion, adhesion, angiogenesis, and serine palmitoyltransferase long chain base subunit 2 (SPTLC2) expression; upregulating SPTLC2 facilitated the proliferation, migration, invasion, adhesion, angiogenesis, and sphingosine-1-phosphate (S1P) production of HUVECs and HepG2 cells, while interfering with SPTLC2 expression inhibited them; HUVECs facilitated the proliferation, migration, invasion, S1P production, S1PR1, and S1PR2 expression of HepG2 cells, while S1PR3 expression was decreased. In conclusion, SPTLC2 may be associated with the antivascular and antitumor effects of TP, and SPTLC2 is expected to become a new marker for tumor therapy. HUVECs can promote the proliferation, migration, and invasion of HepG2 cells, which may be related to the S1P/sphingosine-1-phosphate receptor (S1PR) signaling pathway.


Assuntos
Fenômenos Biológicos , Serina C-Palmitoiltransferase , Masculino , Humanos , Células Endoteliais da Veia Umbilical Humana , Células Hep G2 , Transdução de Sinais
20.
Sci Rep ; 12(1): 17963, 2022 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-36289281

RESUMO

According to databases such as OMIM, Humsavar, Clinvar and Monarch, 1494 human enzymes are presently associated to 2539 genetic diseases, 75% of which are rare (with an Orphanet code). The Mondo ontology initiative allows a standardization of the disease name into specific codes, making it possible a computational association between genes, variants, diseases, and their effects on biological processes. Here, we tackle the problem of which biological processes enzymes can affect when the protein variant is disease-associated. We adopt Reactome to describe human biological processes, and by mapping disease-associated enzymes in the Reactome pathways, we establish a Reactome-disease association. This allows a novel categorization of human monogenic and polygenic diseases based on Reactome pathways and reactions. Our analysis aims at dissecting the complexity of the human genetic disease universe, highlighting all the possible links within diseases and Reactome pathways. The novel mapping helps understanding the biochemical/molecular biology of the disease and allows a direct glimpse on the present knowledge of other molecules involved. This is useful for a complete overview of the disease molecular mechanism/s and for planning future investigations. Data are collected in DAR, a database that is free for search and available at https://dar.biocomp.unibo.it .


Assuntos
Fenômenos Biológicos , Humanos , Bases de Dados Factuais , Biologia Computacional
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