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1.
Nature ; 627(8005): 839-846, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38509363

RESUMO

The bone marrow adjusts blood cell production to meet physiological demands in response to insults. The spatial organization of normal and stress responses are unknown owing to the lack of methods to visualize most steps of blood production. Here we develop strategies to image multipotent haematopoiesis, erythropoiesis and lymphopoiesis in mice. We combine these with imaging of myelopoiesis1 to define the anatomy of normal and stress haematopoiesis. In the steady state, across the skeleton, single stem cells and multipotent progenitors distribute through the marrow enriched near megakaryocytes. Lineage-committed progenitors are recruited to blood vessels, where they contribute to lineage-specific microanatomical structures composed of progenitors and immature cells, which function as the production sites for each major blood lineage. This overall anatomy is resilient to insults, as it was maintained after haemorrhage, systemic bacterial infection and granulocyte colony-stimulating factor (G-CSF) treatment, and during ageing. Production sites enable haematopoietic plasticity as they differentially and selectively modulate their numbers and output in response to insults. We found that stress responses are variable across the skeleton: the tibia and the sternum respond in opposite ways to G-CSF, and the skull does not increase erythropoiesis after haemorrhage. Our studies enable in situ analyses of haematopoiesis, define the anatomy of normal and stress responses, identify discrete microanatomical production sites that confer plasticity to haematopoiesis, and uncover unprecedented heterogeneity of stress responses across the skeleton.


Assuntos
Hematopoese , Células-Tronco Hematopoéticas , Estresse Fisiológico , Animais , Feminino , Masculino , Camundongos , Envelhecimento/fisiologia , Infecções Bacterianas/patologia , Infecções Bacterianas/fisiopatologia , Vasos Sanguíneos/citologia , Linhagem da Célula , Eritropoese , Fator Estimulador de Colônias de Granulócitos/metabolismo , Hematopoese/fisiologia , Células-Tronco Hematopoéticas/citologia , Células-Tronco Hematopoéticas/metabolismo , Hemorragia/patologia , Hemorragia/fisiopatologia , Linfopoese , Megacariócitos/citologia , Células-Tronco Multipotentes/citologia , Células-Tronco Multipotentes/metabolismo , Mielopoese , Crânio/irrigação sanguínea , Crânio/patologia , Crânio/fisiopatologia , Esterno/irrigação sanguínea , Esterno/citologia , Esterno/metabolismo , Estresse Fisiológico/fisiologia , Tíbia/irrigação sanguínea , Tíbia/citologia , Tíbia/metabolismo
2.
Purinergic Signal ; 2024 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-38489005

RESUMO

Berberine (BBR) is a Chinese herb with antioxidant and anti-inflammatory properties. In a previous study, we found that BBR had a protective effect against light-induced retinal degeneration in BALB/c mice. The purinergic P2X7 receptor (P2X7R) plays a key role in retinal degeneration via inducing oxidative stress, inflammatory changes, and cell death. The aim of this study was to investigate whether BBR can induce protective effects in light damage experiments and whether P2X7R can get involved in these effects. C57BL/6 J mice and P2X7 knockout (KO) mice on the C57BL/6 J background were used. We found that BBR preserved the outer nuclear layer (ONL) thickness and retinal ganglion cells following light stimulation. Furthermore, BBR significantly suppressed photoreceptor apoptosis, pro-apoptotic c-fos expression, pro-inflammatory responses of Mϋller cells, and inflammatory factors (TNF-α, IL-1ß). In addition, protein levels of P2X7R were downregulated in BBR-treated mice. Double immunofluorescence showed that BBR reduced overexpression of P2X7R in retinal ganglion cells and Mϋller cells. Furthermore, BBR combined with the P2X7R agonist BzATP blocked the effects of BBR on retinal morphology and photoreceptor apoptosis. However, in P2X7 KO mice, BBR had an additive effect resulting in thicker ONL and more photoreceptors. The data suggest that the P2X7 receptor is involved in retinal light damage, and BBR inhibits this process by reducing histological impairment, cell death, and inflammatory responses.

3.
Genome Biol ; 25(1): 46, 2024 Feb 12.
Artigo em Inglês | MEDLINE | ID: mdl-38347618

RESUMO

Single-strand breaks are the major DNA damage in the genome and serve a crucial role in various biological processes. To reveal the significance of single-strand breaks, multiple sequencing-based single-strand break detection methods have been developed, which are costly and unfeasible for large-scale analysis. Hence, we propose SSBlazer, an explainable and scalable deep learning framework for single-strand break site prediction at the nucleotide level. SSBlazer is a lightweight model with robust generalization capabilities across various species and is capable of numerous unexplored SSB-related applications.


Assuntos
Dano ao DNA , Nucleotídeos , Reparo do DNA
4.
Int J Biol Macromol ; 261(Pt 2): 129799, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38296133

RESUMO

With the extensive use of antibiotics, resulting in increasingly serious problems of bacterial resistance, antimicrobial therapy has become a global concern. Metal-organic frameworks (MOFs) are low-density porous coordination materials composed of metal ions and organic ligands, which can form composite materials with biomacromolecules such as proteins and polysaccharides. In recent years, MOFs and their derivatives have been widely used in the antibacterial field as efficient antibacterial agents. This review offers a detailed summary of the antibacterial applications of MOFs and their composites, and the different synthesis methods and antibacterial mechanisms of MOFs and MOF-based composites are briefly introduced. Finally, the challenges and prospects of MOFs-based antibacterial materials in the rapidly developing medical field were briefly discussed. We hope this review will provide new strategies for the medical application of MOFs-based antibacterial materials.


Assuntos
Estruturas Metalorgânicas , Estruturas Metalorgânicas/farmacologia , Antibacterianos/farmacologia , Porosidade
5.
J Leukoc Biol ; 115(1): 164-176, 2024 01 05.
Artigo em Inglês | MEDLINE | ID: mdl-37170891

RESUMO

Asthma is the chronic pulmonary inflammatory response that could lead to respiratory failure when allergic reactions exacerbate. It is featured by type 2 immunity with eosinophilic inflammation, mucus, and IgE production, and Th2 cytokine secretion upon repeated challenge of allergens. The symptom severity of asthma displays an apparent circadian rhythm with aggravated airway resistance in the early morning in patients. Bmal1 is the core regulator of the circadian clock, while the regulatory role of Bmal1 in asthma remains unclear. Here, we investigate whether the myeloid Bmal1 is involved in the pathogenesis of house dust mite (HDM)-induced lung allergy. We found that knockdown of Bmal1 in macrophages suppressed the time-of-day variance of the eosinophil infiltration in the alveolar spaces in chronic asthmatic mice. This was accompanied by decreased bronchial mucus production, collagen deposition, and HDM-specific IgE production. However, the suppression effects of myeloid Bmal1 deletion did not alter the allergic responses in short-term exposure to HDM. The transcriptome profile of alveolar macrophages (AMs) showed that Bmal1-deficient AMs have enhanced phagocytosis and reduced production of allergy-mediating prostanoids thromboxane A2 and prostaglandin F2α synthesis. The attenuated thromboxane A2 and prostaglandin F2α may lead to less induction of the eosinophil chemokine Ccl11 expression in bronchial epithelial cells. In summary, our study demonstrates that Bmal1 ablation in macrophages attenuates eosinophilic inflammation in HDM-induced chronic lung allergy, which involves enhanced phagocytosis and reduced prostanoid secretion.


Assuntos
Asma , Eosinofilia , Hipersensibilidade , Humanos , Camundongos , Animais , Pyroglyphidae , Dinoprosta/metabolismo , Tromboxano A2/metabolismo , Pulmão , Alérgenos , Eosinofilia/metabolismo , Eosinofilia/patologia , Imunoglobulina E/metabolismo , Inflamação/patologia , Modelos Animais de Doenças
6.
IEEE Trans Pattern Anal Mach Intell ; 45(12): 14420-14434, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37665707

RESUMO

Label noise and class imbalance are common challenges encountered in real-world datasets. Existing approaches for robust learning often focus on addressing either label noise or class imbalance individually, resulting in suboptimal performance when both biases are present. To bridge this gap, this work introduces a novel meta-learning-based dynamic loss that adapts the objective functions during the training process to effectively learn a classifier from long-tailed noisy data. Specifically, our dynamic loss consists of two components: a label corrector and a margin generator. The label corrector is responsible for correcting noisy labels, while the margin generator generates per-class classification margins by capturing the underlying data distribution and the learning state of the classifier. In addition, we employ a hierarchical sampling strategy that enriches a small amount of unbiased metadata with diverse and challenging samples. This enables the joint optimization of the two components in the dynamic loss through meta-learning, allowing the classifier to effectively adapt to clean and balanced test data. Extensive experiments conducted on multiple real-world and synthetic datasets with various types of data biases, including CIFAR-10/100, Animal-10N, ImageNet-LT, and Webvision, demonstrate that our method achieves state-of-the-art accuracy.

7.
Appl Microbiol Biotechnol ; 107(23): 7135-7150, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37768347

RESUMO

Interleukin-18 binding protein (IL-18BP) is a natural IL-18 inhibitor in vivo, which can effectively neutralize IL-18 and inhibit the inflammatory signaling pathway induced by IL-18, thus playing an anti-inflammatory role. Traditional production methods primarily rely on eukaryotic animal cell expression systems, which often entail complex processes, lower yields, and increase production costs. In this study, we present a novel approach for expressing IL-18BP fusion protein using the Escherichia coli (E. coli) system. The N-terminal segment of IL-18BP was fused with the small ubiquitin-related modifier (SUMO) tag, enabling soluble expression, while the C-terminal segment was fused with the human IgG1 Fc fragment to prolong its in vivo lifespan. Through screening, we obtained a high-expression engineering strain from a single colony and developed optimized protocols for fermentation and purification of the recombinant SUMO-IL-18BP-Fc protein. The SUMO tag was subsequently cleaved using SUMO protease, and the purified recombinant human IL-18BP-Fc (rhIL-18BP-Fc) exhibited a purity exceeding 90% with a yield of 1 g per liter of bacterial solution. The biological activities and underlying mechanisms of rhIL-18BP-Fc were evaluated using cell lines and a mouse model. Our results demonstrated that rhIL-18BP-Fc effectively inhibited IL-18-stimulated IFN-γ production in KG-1a cells in vitro and ameliorated DSS-induced ulcerative colitis in mice. In conclusion, we successfully employed the SUMO fusion system to achieve high-level production, soluble expression, and prolonged activity of rhIL-18BP-Fc in E. coli. These findings lay the groundwork for future large-scale industrial production and pharmaceutical development of rhIL-18BP-Fc protein. KEY POINTS: • Effective expression, fermentation, and purification of bioactive rhIL-18BP-Fc protein in E. coli. • The rhIL-18BP-Fc protein has a great potential for the therapy of ulcerative colitis by inhibiting the expression of inflammatory factors.


Assuntos
Colite Ulcerativa , Interleucina-18 , Humanos , Camundongos , Animais , Interleucina-18/genética , Interleucina-18/metabolismo , Colite Ulcerativa/tratamento farmacológico , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes de Fusão/metabolismo
8.
J Nanobiotechnology ; 21(1): 300, 2023 Aug 26.
Artigo em Inglês | MEDLINE | ID: mdl-37633883

RESUMO

Bacterial infections, especially those caused by drug-resistant bacteria, have seriously threatened human life and health. There is urgent to develop new antibacterial agents to reduce the problem of antibiotics. Biomedical materials with good antimicrobial properties have been widely used in antibacterial applications. Among them, hydrogels have become the focus of research in the field of biomedical materials due to their unique three-dimensional network structure, high hydrophilicity, and good biocompatibility. In this review, the latest research progresses about hydrogels in recent years were summarized, mainly including the preparation methods of hydrogels and their antibacterial applications. According to their different antibacterial mechanisms, several representative antibacterial hydrogels were introduced, such as antibiotics loaded hydrogels, antibiotic-free hydrogels including metal-based hydrogels, antibacterial peptide and antibacterial polymers, stimuli-responsive smart hydrogels, and light-mediated hydrogels. In addition, we also discussed the applications and challenges of antibacterial hydrogels in biomedicine, which are expected to provide new directions and ideas for the application of hydrogels in clinical antibacterial therapy.


Assuntos
Antibacterianos , Materiais Biocompatíveis , Humanos , Antibacterianos/farmacologia , Materiais Biocompatíveis/farmacologia , Hidrogéis/farmacologia , Polímeros/farmacologia
9.
Neuropharmacology ; 238: 109655, 2023 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-37423482

RESUMO

Uridine 5'-diphosphoglucose (UDP-G) as a preferential agonist, but also other UDP-sugars, such as UDP galactose, function as extracellular signaling molecules under conditions of cell injury and apoptosis. Consequently, UDP-G is regarded to function as a damage-associated molecular pattern (DAMP), regulating immune responses. UDP-G promotes neutrophil recruitment, leading to the release of pro-inflammatory chemokines. As a potent endogenous agonist with the highest affinity for the P2Y14 receptor (R), it accomplishes an exclusive relationship between P2Y14Rs in regulating inflammation via cyclic adenosine monophosphate (cAMP), nod-like receptor protein 3 (NLRP3) inflammasome, mitogen-activated protein kinases (MAPKs), and signal transducer and activator of transcription 1 (STAT1) pathways. In this review, we initially present a brief introduction into the expression and function of P2Y14Rs in combination with UDP-G. Subsequently, we summarize emerging roles of UDP-G/P2Y14R signaling pathways that modulate inflammatory responses in diverse systems, and discuss the underlying mechanisms of P2Y14R activation in inflammation-related diseases. Moreover, we also refer to the applications as well as effects of novel agonists/antagonists of P2Y14Rs in inflammatory conditions. In conclusion, due to the role of the P2Y14R in the immune system and inflammatory pathways, it may represent a novel target for anti-inflammatory therapy.


Assuntos
Receptores Purinérgicos P2 , Humanos , Receptores Purinérgicos P2/metabolismo , Uridina Difosfato Glucose/metabolismo , Uridina Difosfato Glucose/farmacologia , Açúcares de Uridina Difosfato/farmacologia , Inflamação/tratamento farmacológico , Glucose
10.
Artigo em Inglês | MEDLINE | ID: mdl-37037238

RESUMO

Noisy labels, inevitably existing in pseudo-segmentation labels generated from weak object-level annotations, severely hamper model optimization for semantic segmentation. Previous works often rely on massive handcrafted losses and carefully tuned hyperparameters to resist noise, suffering poor generalization capability and high model complexity. Inspired by recent advances in meta-learning, we argue that rather than struggling to tolerate noise hidden behind clean labels passively, a more feasible solution would be to find out the noisy regions actively, so as to simply ignore them during model optimization. With this in mind, this work presents a novel meta-learning-based semantic segmentation method, MetaSeg, that comprises a primary content-aware meta-net (CAM-Net) to serve as a noise indicator for an arbitrary segmentation model counterpart. Specifically, CAM-Net learns to generate pixel-wise weights to suppress noisy regions with incorrect pseudo-labels while highlighting clean ones by exploiting hybrid strengthened features from image content, providing straightforward and reliable guidance for optimizing the segmentation model. Moreover, to break the barrier of time-consuming training when applying meta-learning to common large segmentation models, we further present a new decoupled training strategy that optimizes different model layers in a divide-and-conquer manner. Extensive experiments on object, medical, remote sensing, and human segmentation show that our method achieves superior performance, approaching that of fully supervised settings, which paves a new promising way for omni-supervised semantic segmentation.

11.
Front Pharmacol ; 14: 1152667, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37063258

RESUMO

Single-nucleotide polymorphisms are connected with the risk of epilepsy on occurrence, progress, and the individual response to drugs. Progress in genomic technology is exposing the complex genetic architecture of epilepsy. Compelling evidence has demonstrated that purines and adenosine are key mediators in the epileptic process. Our previous study found the interconnection of P2Y12 receptor single-nucleotide polymorphisms and epilepsy. However, little is known about the interaction between the purine nucleoside A2A receptor and rate-limiting enzyme ecto-5'-nucleotidase/CD73 and epilepsy from the genetic polymorphism aspect. The aim of the study is to evaluate the impact of A2AR and CD73 polymorphisms on epilepsy cases. The study group encompassed 181 patients with epilepsy and 55 healthy volunteers. A significant correlation was confirmed between CD73 rs4431401 and epilepsy (p < 0.001), with TT genotype frequency being higher and C allele being lower among epilepsy patients in comparison with healthy individuals, indicating that the presence of the TT genotype is related to an increased risk of epilepsy (OR = 2.742, p = 0.006) while carriers of the C allele demonstrated a decreased risk of epilepsy (OR = 0.304, p < 0.001). According to analysis based on gender, the allele and genotype of rs4431401 in CD73 were associated with both male and female cases (p < 0.0001, p = 0.026, respectively). Of note, we found that A2AR genetic variants rs2267076 T>C (p = 0.031), rs2298383 C>T (p = 0.045), rs4822492 T>G (p = 0.034), and rs4822489 T>G (p = 0.029) were only associated with epilepsy in female subjects instead of male. It is evident that the TT genotype and T allele of rs4431401 in CD73 were genetic risk factors for epilepsy, whereas rs2267076, rs2298383, rs4822492, and rs4822489 polymorphisms of the A2AR were mainly associated with female subjects.

12.
ACS Omega ; 8(14): 13362-13370, 2023 Apr 11.
Artigo em Inglês | MEDLINE | ID: mdl-37065036

RESUMO

The KRAS gene belongs to the RAS family and codes for 188 amino acid residues of KRAS protein, with a molecular mass of 21.6 kD. Non-synonymous single-nucleotide polymorphisms (nsSNPs) have been identified within the coding region in which some are associated with different diseases. However, structural changes are not well defined yet. In this study, we first categorized SNPs in the KRAS coding area and then used computational methods to determine their impact on the protein structure and stability. In addition, the three-dimensional model of KRAS was taken from the Protein Data Bank for structural modeling. Furthermore, genomic data were extracted from a variety of sources, including the 1000 Genome Project, dbSNPs, and ENSEMBLE, and assessed through in silico methods. Based on various tools used in this study, 10 out of 48 missense SNPs with rsIDs were found deleterious. The substitution of alanine for proline at position 146 pushed several residues toward the center of the protein. Arginine instead of leucine has a minor effect on protein structure and stability. In addition, the substitution of proline for leucine at the 34th position disrupted the structure and led to a bigger size than the wild-type protein, hence interrupting the protein interaction. Using the well-intended computational approach and applying several bioinformatic tools, we characterized and identified most damaging nsSNPs and further explored the structural dynamics and stability of KRAS protein.

13.
Int J Mol Sci ; 24(6)2023 Mar 14.
Artigo em Inglês | MEDLINE | ID: mdl-36982618

RESUMO

Ecto-5'-nucleotidase (CD73) plays a strategic role in calibrating the magnitude and chemical nature of purinergic signals that are delivered to immune cells. Its primary function is to convert extracellular ATP to adenosine in concert with ectonucleoside triphosphate diphosphohydrolase-1 (CD39) in normal tissues to limit an excessive immune response in many pathophysiological events, such as lung injury induced by a variety of contributing factors. Multiple lines of evidence suggest that the location of CD73, in proximity to adenosine receptor subtypes, indirectly determines its positive or negative effect in a variety of organs and tissues and that its action is affected by the transfer of nucleoside to subtype-specific adenosine receptors. Nonetheless, the bidirectional nature of CD73 as an emerging immune checkpoint in the pathogenesis of lung injury is still unknown. In this review, we explore the relationship between CD73 and the onset and progression of lung injury, highlighting the potential value of this molecule as a drug target for the treatment of pulmonary disease.


Assuntos
Pneumopatias , Lesão Pulmonar , Humanos , 5'-Nucleotidase , Adenosina , Trifosfato de Adenosina
14.
Purinergic Signal ; 19(1): 283-295, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-35939197

RESUMO

Extracellular ATP is a potent signaling molecule released from various cells throughout the body and is intimately involved in the pathophysiological functions of the nervous system and immune system by activating P2 purinergic receptors. Recent increasingly studies showed that extracellular ATP exhibits circadian oscillation with an approximately 24-h periodicity, which participates in regulatory pathways of central oscillator suprachiasmatic nucleus and peripheral oscillator bladder, respectively. Oscillators modulate the protein expression of ATP release channels and ectonucleotidase activity through clock genes; indeed, real-time alterations of ATP release and degradation determine outcomes of temporal character on extracellular ATP rhythm. The regulatory pathways on extracellular ATP rhythm are different in central and peripheral systems. In this review, we summarize the circadian rhythm of extracellular ATP and discuss several circadian regulatory pathways in different organs via ATP release and degradation, to provide a new understanding for purinergic signaling in the regulatory mechanism of circadian rhythm and a potential target to research the circadian regulation of extracellular ATP in other circadian oscillators.


Assuntos
Ritmo Circadiano , Núcleo Supraquiasmático , Ritmo Circadiano/genética , Núcleo Supraquiasmático/metabolismo , Trifosfato de Adenosina/metabolismo
15.
Purinergic Signal ; 19(1): 155-162, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-35175489

RESUMO

The basic research indicated that microglial P2Y12 receptors (P2Y12Rs) are involved in the pathophysiology of epilepsy through regulated microglial-neuronal interactions, aberrant neurogenesis, or immature neuronal projections. However, whether the clinic case of epilepsy would be associated with P2Y12 receptor gene polymorphisms is presented with few data. In our study, a total of 176 patients with epilepsy and 50 healthy controls were enrolled. Two single-nucleotide polymorphisms, namely rs1491974 and rs6798347, were selected for analysis. The results revealed that carriers of the G allele of rs1491974 G>A or rs6798347 G>A may be associated with an increased risk of epilepsy (OR = 0.576, 95% CI = 0.368-0.901, p = 0.015; OR = 0.603, 95% CI = 0.367-0.988, p = 0.043). Interestingly, we found that the rs1491974 G>A genotype and allele frequencies have only a significant difference in female instead of male case (p = 0.004 for genotype; p = 0.001 for allele). The subgroup analysis demonstrated that individuals with the rs1491974 G>A genotype might have more frequent seizure (OR = 0.476, 95% CI = 0.255-0.890; p = 0.019). These data implied that both rs1491974 and rs6798347 polymorphisms of P2Y12R would be able to play import roles in epilepsy susceptibility, whereas the rs1491974 polymorphism may be specifically related to seizure frequency.


Assuntos
Epilepsia , Antagonistas do Receptor Purinérgico P2Y , Humanos , Masculino , Feminino , Genótipo , Polimorfismo de Nucleotídeo Único , Frequência do Gene , Convulsões/complicações , Receptores Purinérgicos P2Y12
16.
Pediatr Radiol ; 53(2): 332-336, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-36018348

RESUMO

Chest radiography is commonly performed as a diagnostic tool of neonatal diseases. Contact-based radiation personal protective equipment (RPPE) has been widely used for radiation protection, but it does not provide full body protection and it is often shared between users, which has become a major concern during the coronavirus disease 2019 (COVID-19) pandemic. To address these issues, we developed a novel trolley to protect radiographers against X-ray radiation by reducing scatter radiation during neonatal radiographic examinations. We measured the scatter radiation doses from a standard neonatal chest radiograph to the radiosensitive organs using a phantom operator in three protection scenarios (trolley, radiation personal protective equipment [RPPE], no protection) and at three distances. The results showed that the scatter radiation surface doses were significantly reduced when using the trolley compared with RPPE and with no protection at a short distance (P<0.05 for both scenarios in all radiosensitive organs). The novel protective trolley provides a non-contact protective tool for radiographers against the hazard of scatter radiation during neonatal radiography examinations.


Assuntos
COVID-19 , Recém-Nascido , Humanos , Doses de Radiação , Radiografia , Raios X , Imagens de Fantasmas
17.
Adv Sci (Weinh) ; 10(3): e2203480, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36461702

RESUMO

Characterization of the subcellular distribution of RNA is essential for understanding the molecular basis of biological processes. Here, the subcellular nanopore direct RNA-sequencing (DRS) of four lung cancer cell lines (A549, H1975, H358, and HCC4006) is performed, coupled with a computational pipeline, Low-abundance Aware Full-length Isoform clusTEr (LAFITE), to comprehensively analyze the full-length cytoplasmic and nuclear transcriptome. Using additional DRS and orthogonal data sets, it is shown that LAFITE outperforms current methods for detecting full-length transcripts, particularly for low-abundance isoforms that are usually overlooked due to poor read coverage. Experimental validation of six novel isoforms exclusively identified by LAFITE further confirms the reliability of this pipeline. By applying LAFITE to subcellular DRS data, the complexity of the nuclear transcriptome is revealed in terms of isoform diversity, 3'-UTR usage, m6A modification patterns, and intron retention. Overall, LAFITE provides enhanced full-length isoform identification and enables a high-resolution view of the RNA landscape at the isoform level.


Assuntos
Transcriptoma , Reprodutibilidade dos Testes , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Isoformas de Proteínas/genética , Transcriptoma/genética , Frações Subcelulares/metabolismo
18.
Bioresour Technol ; 367: 128235, 2023 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36332857

RESUMO

This study explored the coupling relationships between denitrifiers and N-transformation using multi-level (DNA, RNA and enzyme) and multi-aspect (abundance, diversity, structure, key community, network pattern, and functional module) analyses during cattle-manure (CM) and biochar (CMB) composting. Amino sugar-N (ASN, 0.914) and hydrolysable unknown-N (-0.724) were main organic-N components mediating NH4+-N in CM and CMB, respectively. Biochar lowered nirK, nirS, and nosZ genes copies, up-regulated nir gene transcripts, and inhibited nitrite reductase (NIR) activity. For nirK-denitrifiers, Luteimonas was predominant taxa influencing NO2--N and amino acid-N (AAN). Unclassified_k_norank_d_Bacteria and unclassified_p_Proteobacteria regulated NO3--N and ASN, respectively. These three genera played crucial roles in mediating NIR activity and nosZ/nirK. For nirS-denitrifiers, Paracoccus and Pseudomonas mediated NH4+-N and AAN, respectively, and they were vital genera regulating NO3--N, ASN and NIR activity. Furthermore, nirK-denitrifiers was major contributor to denitrification. Overall, functional denitrifiers might simultaneously participate in multiple N-transformation processes.


Assuntos
Compostagem , Bovinos , Animais , Esterco/microbiologia , Nitrogênio , Desnitrificação/genética , Proteobactérias , Solo/química , Microbiologia do Solo
19.
Gigascience ; 112022 12 08.
Artigo em Inglês | MEDLINE | ID: mdl-36480030

RESUMO

Japanese eels (Anguilla japonica) are commercially important species, harvested extensively for food. Currently, this and related species (American and European eels) are challenging to breed on a commercial basis. As a result, the wild stock is used for aquaculture. Moreover, climate change, habitat loss, water pollution, and altered ocean currents affect eel populations negatively. Accordingly, the International Union for Conservation of Nature lists Japanese eels as endangered and on its red list. Here we presented a high-quality genome assembly for Japanese eels and demonstrated that large chromosome reorganizations occurred in the events of third-round whole-genome duplications (3R-WRDs). Several chromosomal fusions and fissions have reduced the ancestral protochromosomal number of 25 to 19 in the Anguilla lineage. A phylogenetic analysis of the expanded gene families showed that the olfactory receptors (group δ and ζ genes) and voltage-gated Ca2+ channels expanded significantly. Both gene families are crucial for olfaction and neurophysiology. Additional tandem and proximal duplications occurred following 3R-WGD to acquire immune-related genes for an adaptive advantage against various pathogens. The Japanese eel assembly presented here can be used to study other Anguilla species relating to evolution and conservation.


Assuntos
Duplicação Gênica , Cromossomos/genética , Filogenia
20.
Sci Rep ; 12(1): 20217, 2022 11 23.
Artigo em Inglês | MEDLINE | ID: mdl-36418343

RESUMO

Pseudostellaria heterophylla, also called Tai-zi-shen (TZS) in Traditional Chinese Medicine (TCM), is always used clinically to treat spleen deficiency symptoms. Polysaccharides in TZS have various pharmacological activities, including anti-diabetic, immune regulation, and myocardial protection. However, the relationship between the spleen-invigorating effects of TZS or its polysaccharides and intestinal flora are not clear. This study investigated the effects of TZS decoction (PHD) and polysaccharide (PHP) on immune function and intestinal flora in a rat model of spleen deficiency syndrome (SDS) induced by a decoction of raw rhubarb (RRD). PHD and PHP increased immune organ index, alleviated inflammatory cell filtration, and reduced the levels of pro-inflammatory cytokines in rats with spleen deficiency syndrome. In addition, the production of butyric acid was promoted in PHD and PHP groups. Moreover, 16S rRNA gene sequencing showed that PHD and PHP reduced the relative abundance of Firmicutes while increasing the one of Bacteroidetes; significantly increased the abundance of Lactobacillus and decreased the abundance of Rombutsia; and PHP significantly increased the abundance of Alloprevotella. And there was a significant positive correlation between the alleviation of SDS and short-chain fatty acids (SCFAs)-producing bacteria. These findings suggested PHD and PHP, especially PHP, has a potential to relieve spleen deficiency by reducing intestinal inflammation, modulating structure and composition of gut microbiota, and promoting the production of butyric acid.


Assuntos
Caryophyllaceae , Microbioma Gastrointestinal , Esplenopatias , Ratos , Animais , RNA Ribossômico 16S/genética , Polissacarídeos/farmacologia , Síndrome , Bacteroidetes , Esplenopatias/tratamento farmacológico , Ácido Butírico
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