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1.
Bioinformatics ; 40(1)2024 01 02.
Artigo em Inglês | MEDLINE | ID: mdl-38058211

RESUMO

MOTIVATION: Pediatric kidney disease is a widespread, progressive condition that severely impacts growth and development of children. Chronic kidney disease is often more insidious in children than in adults, usually requiring a renal biopsy for diagnosis. Biopsy evaluation requires copious examination by trained pathologists, which can be tedious and prone to human error. In this study, we propose an artificial intelligence (AI) method to assist pathologists in accurate segmentation and classification of pediatric kidney structures, named as AI-based Pediatric Kidney Diagnosis (APKD). RESULTS: We collected 2935 pediatric patients diagnosed with kidney disease for the development of APKD. The dataset comprised 93 932 histological structures annotated manually by three skilled nephropathologists. APKD scored an average accuracy of 94% for each kidney structure category, including 99% in the glomerulus. We found strong correlation between the model and manual detection in detected glomeruli (Spearman correlation coefficient r = 0.98, P < .001; intraclass correlation coefficient ICC = 0.98, 95% CI = 0.96-0.98). Compared to manual detection, APKD was approximately 5.5 times faster in segmenting glomeruli. Finally, we show how the pathological features extracted by APKD can identify focal abnormalities of the glomerular capillary wall to aid in the early diagnosis of pediatric kidney disease. AVAILABILITY AND IMPLEMENTATION: https://github.com/ChunyueFeng/Kidney-DataSet.


Assuntos
Inteligência Artificial , Insuficiência Renal Crônica , Adulto , Humanos , Criança , Rim/diagnóstico por imagem , Rim/patologia , Insuficiência Renal Crônica/patologia
2.
Nucleic Acids Res ; 51(1): 29-40, 2023 01 11.
Artigo em Inglês | MEDLINE | ID: mdl-36537218

RESUMO

Toehold-mediated strand displacement and its regulatory tools are fundamental for DNA nanotechnology. However, current regulatory tools all need to change the original sequence of reactants, making the regulation inconvenient and cumbersome. More importantly, the booming development of DNA nanotechnology will soon promote the production of packaged and batched devices or circuits with specified functions. Regarding standardized, packaged DNA nanodevices, access to personalized post-modification will greatly help users, whereas none of the current regulatory tools can provide such access, which has greatly constrained DNA nanodevices from becoming more powerful and practical. Herein, we developed a novel regulation tool named Cap which has two basic functions of subtle regulation of the reaction rate and erasability. Based on these functions, we further developed three advanced functions. Through integration of all functions of Cap and its distinct advantage of working independently, we finally realized personalized tailor-made post-modification on pre-fabricated DNA circuits. A pre-fabricated dual-output DNA circuit was successfully transformed into an equal-output circuit, a signal-antagonist circuit and a covariant circuit according to our requirements. Taken together, Cap is easy to design and generalizable for all strand displacement-based DNA nanodevices. We believe the Cap tool will be widely used in regulating reaction networks and personalized tailor-made post-modification of DNA nanodevices.


Assuntos
DNA , Nanotecnologia , DNA/genética , Recombinação Genética
3.
Analyst ; 149(2): 366-375, 2024 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-38044817

RESUMO

Sperm DNA fragmentation is a sign of sperm nuclear damage. The sperm chromatin dispersion (SCD) test is a reliable and economical method for the evaluation of DNA fragmentation. However, the cut-off value for differentiation of DNA fragmented sperms is fixed at 1/3 with limited statistical justification, making the SCD test a semi-quantitative method that gives user-dependent results. We construct a collection of deep neural networks to automate the evaluation of bright-field images for SCD tests. The model can detect valid sperm nuclei and their locations from the input images captured with a 20× objective and predict the geometric parameters of the halo ring. We construct an annotated dataset consisting of N = 3120 images. The ResNet 18 based network reaches an average precision (AP50) of 91.3%, a true positive rate of 96.67%, and a true negative rate of 96.72%. The distribution of relative halo radii is fit to the multi-peak Gaussian function (p > 0.99). DNA fragmentation is regarded as those with a relative halo radius 1.6 standard deviations smaller than the mean of a normal cluster. In conclusion, we have established a deep neural network based model for the automation and quantification of the SCD test that is ready for clinical application. The DNA fragmentation index is determined using Gaussian clustering, reflecting the natural distribution of halo geometry and is more tolerable to disturbances and sample conditions, which we believe will greatly improve the clinical significance of the SCD test.


Assuntos
Cromatina , Sêmen , Masculino , Humanos , Espermatozoides , DNA/genética , Núcleo Celular , Fragmentação do DNA
4.
J Nanobiotechnology ; 22(1): 142, 2024 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-38561751

RESUMO

Seesaw circuits are essential for molecular computing and biosensing. However, a notable limitation of seesaw circuits lies in the irreversible depletion of components, precluding the attainment of system recovery and rendering nucleic acid circuits non-reusable. We developed a brand-new method for creating controllable and reusable seesaw circuits. By using the nicking endonucleases Nt.BbvCI and Nt.Alwi, we removed "functional components" while keeping the "skeletal components" for recurrent usage. T-inputs were introduced, increasing the signal-to-noise ratio of AND logic from 2.68 to 11.33 and demonstrating compatibility. We identified the logic switching feature and verified that it does not impair circuit performance. We also built intricate logic circuits, such as OR-AND gate, to demonstrate the versatility of our methodology. This controllable reusability extends the applications of nanotechnology and bioengineering, enhancing the practicality and efficiency of these circuits across various domains.


Assuntos
DNA , Ácidos Nucleicos , Endonucleases , Bioengenharia
5.
Nucleic Acids Res ; 50(22): 12674-12688, 2022 12 09.
Artigo em Inglês | MEDLINE | ID: mdl-36484104

RESUMO

Although CRISPR-Cas12a [clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 12a] combining pre-amplification technology has the advantage of high sensitivity in biosensing, its generality and specificity are insufficient, which greatly restrains its application range. Here, we discovered a new targeting substrate for LbaCas12a (Lachnospiraceae bacterium Cas12a), namely double-stranded DNA (dsDNA) with a sticky-end region (PAM-SE+ dsDNA). We discovered that CRISPR-Cas12a had special enzymatic properties for this substrate DNA, including the ability to recognize and cleave it without needing a protospacer adjacent motif (PAM) sequence and a high sensitivity to single-base mismatches in that substrate. Further mechanism studies revealed that guide RNA (gRNA) formed a triple-stranded flap structure with the substrate dsDNA. We also discovered the property of low-temperature activation of CRISPR-Cas12a and, by coupling with the unique DNA hybridization kinetics at low temperature, we constructed a complete workflow for low-abundance point mutation detection in real samples, which was fast, convenient and free of single-stranded DNA (ssDNA) transformation. The detection limits were 0.005-0.01% for synthesized strands and 0.01-0.05% for plasmid genomic DNA, and the mutation abundances provided by our system for 28 clinical samples were in accordance with next-generation sequencing results. We believe that our work not only reveals novel information about the target recognition mechanism of the CRISPR-Cas12a system, but also greatly broadens its application scenarios.


Assuntos
Proteínas Associadas a CRISPR , Sistemas CRISPR-Cas , Proteínas Associadas a CRISPR/metabolismo , Proteínas de Bactérias/metabolismo , DNA/química , DNA de Cadeia Simples/genética
6.
Anal Chem ; 95(23): 8939-8947, 2023 06 13.
Artigo em Inglês | MEDLINE | ID: mdl-37256969

RESUMO

Glutathione peroxidase 4 (GPx4) is the membrane peroxidase in mammals that is essential for protecting cells against oxidative damage and critical for ferroptosis. However, no live cell probe is currently available to specifically label GPx4. Herein, we report both inhibitory and noninhibitory fluorescent turn-on probes for specific labeling of GPx4 in live cells. With these probes, the GPx4 expression levels and degradation kinetics in live cells could be visualized, and their real-time responses to the cellular selenium availability were revealed. These probes could also potentially serve as staining reagents to predict the sensitivity of GPx4-related ferroptosis drugs. In view of these features, these GPx4-selective probes will offer opportunities for a deeper understanding of GPx4 function in natural habitats and hold great promise for biomedical applications.


Assuntos
Corantes Fluorescentes , Humanos , Células HEK293 , Sobrevivência Celular , Fosfolipídeo Hidroperóxido Glutationa Peroxidase/metabolismo , Corantes Fluorescentes/química , Selênio/metabolismo
7.
Bioinformatics ; 38(18): 4395-4402, 2022 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-35881697

RESUMO

MOTIVATION: DNA fibre assay has a potential application in genomic medicine, cancer and stem cell research at the single-molecule level. A major challenge for the clinical and research implementation of DNA fibre assays is the slow speed in which manual analysis takes place as it limits the clinical actionability. While automatic detection of DNA fibres speeds up this process considerably, current publicly available software have limited features in terms of their user interface for manual correction of results, which in turn limit their accuracy and ability to account for atypical structures that may be important in diagnosis or investigative studies. We recognize that core improvements can be made to the GUI to allow for direct interaction with automatic results to preserve accuracy as well as enhance the versatility of automatic DNA fibre detection for use in variety of situations. RESULTS: To address the unmet needs of diverse DNA fibre analysis investigations, we propose DNA Stranding, an open-source software that is able to perform accurate fibre length quantification (13.22% mean relative error) and fibre pattern recognition (R > 0.93) with up to six fibre patterns supported. With the graphical interface, we developed, user can conduct semi-automatic analyses which benefits from the advantages of both automatic and manual processes to improve workflow efficiency without compromising accuracy. AVAILABILITY AND IMPLEMENTATION: The software package is available at https://github.com/lgole/DNAStranding. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
DNA , Software , Fluxo de Trabalho , Replicação do DNA
8.
Bioinformatics ; 38(23): 5307-5314, 2022 11 30.
Artigo em Inglês | MEDLINE | ID: mdl-36264128

RESUMO

MOTIVATION: Differentiating 12 stages of the mouse seminiferous epithelial cycle is vital towards understanding the dynamic spermatogenesis process. However, it is challenging since two adjacent spermatogenic stages are morphologically similar. Distinguishing Stages I-III from Stages IV-V is important for histologists to understand sperm development in wildtype mice and spermatogenic defects in infertile mice. To achieve this, we propose a novel pipeline for computerized spermatogenesis staging (CSS). RESULTS: The CSS pipeline comprises four parts: (i) A seminiferous tubule segmentation model is developed to extract every single tubule; (ii) A multi-scale learning (MSL) model is developed to integrate local and global information of a seminiferous tubule to distinguish Stages I-V from Stages VI-XII; (iii) a multi-task learning (MTL) model is developed to segment the multiple testicular cells for Stages I-V without an exhaustive requirement for manual annotation; (iv) A set of 204D image-derived features is developed to discriminate Stages I-III from Stages IV-V by capturing cell-level and image-level representation. Experimental results suggest that the proposed MSL and MTL models outperform classic single-scale and single-task models when manual annotation is limited. In addition, the proposed image-derived features are discriminative between Stages I-III and Stages IV-V. In conclusion, the CSS pipeline can not only provide histologists with a solution to facilitate quantitative analysis for spermatogenesis stage identification but also help them to uncover novel computerized image-derived biomarkers. AVAILABILITY AND IMPLEMENTATION: https://github.com/jydada/CSS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Sêmen , Espermatogênese , Camundongos , Masculino , Animais , Túbulos Seminíferos , Testículo/anatomia & histologia
9.
Opt Lett ; 48(24): 6480-6483, 2023 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-38099778

RESUMO

Bound states in the continuum (BICs) with extremely large quality factors (Q factors) can enhance the light-matter interaction and thus achieve low-threshold lasing. Here, we theoretically propose and experimentally demonstrate the low-threshold lasing at room temperature based on BICs. A threshold of approximately 306.7 W/cm2 (peak intensity) under a 7.5 ns-pulsed optical excitation is presented in an all-dielectric metasurface system consisting of titanium dioxide (TiO2) nanopillars with a dye film. Also, the multimode lasing can be excited by the higher pumping. Our results may find exciting applications in on-chip coherent light sources, filtering, and sensing.

10.
Neurosurg Rev ; 46(1): 74, 2023 Mar 22.
Artigo em Inglês | MEDLINE | ID: mdl-36947242

RESUMO

Due to the deep location, complex anatomy, and adjacent vital neurovascular structures, skull base surgery is challenging and requires specific approaches. The emerging endoscopic transorbital approach (eTOA) technique provides a new approach to the orbital content, spheno-orbital region, lateral cavernous sinus, and Meckel's cave. In this study, the clinical utility and effectiveness of the eTOA are reported. Sixteen cases who underwent the eTOA were included in the current study. The patients were divided into 3 groups according to tumor location: Group A (intraorbital, 6 cases), group B (spheno-orbital, 7 cases), and group C (cavernous sinus, and Meckel's cave, 3 cases). The clinical data and surgical results were analyzed. Eight meningiomas, 2 hemangiomas, 1 low-grade glioma, 1 instance of inflammatory hyperplasia tissue, 1 Langerhans cell histiocytosis, 1 epidermoid cyst, 1 trigeminal schwannoma, and 1 bone fibrosis hyperplasia were observed. The mean tumor diameter was 2.4 cm. A single case in Group A and Group C underwent biopsy (12.5%), and 1 case of fibrous dysplasia in Group B underwent sufficient orbit decompression (6.25%). The remaining 13 cases underwent gross total tumor resection (81.25%). No cerebral-spinal fluid leak or infection occurred. And no cosmetic problems or significant complications were observed during the follow-up. As a minimally invasive technique, the eTOA has unique advantages for carefully selected skull base lesions because of its direct route, short working distance, and distinct attack angle.


Assuntos
Neoplasias Meníngeas , Neoplasias da Base do Crânio , Humanos , Hiperplasia/complicações , Base do Crânio/cirurgia , Endoscopia/métodos , Neoplasias da Base do Crânio/cirurgia , Neoplasias da Base do Crânio/complicações , Neoplasias Meníngeas/cirurgia , Neoplasias Meníngeas/complicações
11.
Sensors (Basel) ; 23(20)2023 Oct 19.
Artigo em Inglês | MEDLINE | ID: mdl-37896678

RESUMO

This study designs a spectrum data collection device and system based on the Internet of Things technology, aiming to solve the tedious process of chlorophyll collection and provide a more convenient and accurate method for predicting chlorophyll content. The device has the advantages of integrated design, portability, ease of operation, low power consumption, low cost, and low maintenance requirements, making it suitable for outdoor spectrum data collection and analysis in fields such as agriculture, environment, and geology. The core processor of the device uses the ESP8266-12F microcontroller to collect spectrum data by communicating with the spectrum sensor. The spectrum sensor used is the AS7341 model, but its limited number of spectral acquisition channels and low resolution may limit the exploration and analysis of spectral data. To verify the performance of the device and system, this experiment collected spectral data of Hami melon leaf samples and combined it with a chlorophyll meter for related measurements and analysis. In the experiment, twelve regression algorithms were tested, including linear regression, decision tree, and support vector regression. The results showed that in the original spectral data, the ETR method had the best prediction effect at a wavelength of 515 nm. In the training set, RMSEc was 0.3429, and Rc2 was 0.9905. In the prediction set, RMSEp was 1.5670, and Rp2 was 0.8035. In addition, eight preprocessing methods were used to denoise the original data, but the improvement in prediction accuracy was not significant. To further improve the accuracy of data analysis, principal component analysis and isolation forest algorithm were used to detect and remove outliers in the spectral data. After removing the outliers, the RFR model performed best in predicting all wavelength combinations of denoised spectral data using PBOR. In the training set, RMSEc was 0.8721, and Rc2 was 0.9429. In the prediction set, RMSEp was 1.1810, and Rp2 was 0.8683.


Assuntos
Clorofila , Espectroscopia de Luz Próxima ao Infravermelho , Espectroscopia de Luz Próxima ao Infravermelho/métodos , Análise dos Mínimos Quadrados , Clorofila/análise , Folhas de Planta/química , Agricultura
12.
Int J Mol Sci ; 24(19)2023 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-37833864

RESUMO

Engineering light-controlled K+ pumps from Na+-pumping rhodopsins (NaR) greatly expands the scope of optogenetic applications. However, the limited knowledge regarding the kinetic and selective mechanism of K+ uptake has significantly impeded the modification and design of light-controlled K+ pumps, as well as their practical applications in various fields, including neuroscience. In this study, we presented K+-dependent photocycle kinetics and photocurrent of a light-driven Na+ pump called Nonlabens dokdonensis rhodopsin 2 (NdR2). As the concentration of K+ increased, we observed the accelerated decay of M intermediate in the wild type (WT) through flash photolysis. In 100 mM KCl, the lifetime of the M decay was approximately 1.0 s, which shortened to around 0.6 s in 1 M KCl. Additionally, the K+-dependent M decay kinetics were also observed in the G263W/N61P mutant, which transports K+. In 100 mM KCl, the lifetime of the M decay was approximately 2.5 s, which shortened to around 0.2 s in 1 M KCl. According to the competitive model, in high KCl, K+ may be taken up from the cytoplasmic surface, competing with Na+ or H+ during M decay. This was further confirmed by the K+-dependent photocurrent of WT liposome. As the concentration of K+ increased to 500 mM, the amplitude of peak current significantly dropped to approximately ~60%. Titration experiments revealed that the ratio of the rate constant of H+ uptake (kH) to that of K+ uptake (kK) is >108. Compared to the WT, the G263W/N61P mutant exhibited a decrease of approximately 40-fold in kH/kK. Previous studies focused on transforming NaR into K+ pumps have primarily targeted the intracellular ion uptake region of Krokinobacter eikastus rhodopsin 2 (KR2) to enhance K+ uptake. However, our results demonstrate that the naturally occurring WT NdR2 is capable of intracellular K+ uptake without requiring structural modifications on the intracellular region. This discovery provides diverse options for future K+ pump designs. Furthermore, we propose a novel photocurrent-based approach to evaluate K+ uptake, which can serve as a reference for similar studies on other ion pumps. In conclusion, our research not only provides new insights into the mechanism of K+ uptake but also offers a valuable point of reference for the development of optogenetic tools and other applications in this field.


Assuntos
Rodopsina , ATPase Trocadora de Sódio-Potássio , ATPase Trocadora de Sódio-Potássio/metabolismo , Rodopsina/metabolismo , Transporte de Íons , Transporte Biológico
13.
Angew Chem Int Ed Engl ; 62(39): e202306691, 2023 09 25.
Artigo em Inglês | MEDLINE | ID: mdl-37455257

RESUMO

Life-like hierarchical architecture shows great potential for advancing intelligent biosensing, but modular expansion of its sensitivity and functionality remains a challenge. Drawing inspiration from intracellular liquid-liquid phase separation, we discovered that a DNA-encoded artificial cell with a liquid core (LAC) can enhance peroxidase-like activity of Hemin and its DNA G-quadruplex aptamer complex (DGAH) without substrate-selectivity, unlike its gelled core (GAC) counterpart. The LAC is easily engineered as an ultrasensitive biosensing system, benefiting from DNA's high programmability and unique signal amplification capability mediated by liquid-liquid phase separation. As proof of concept, its versatility was successfully demonstrated by coupling with two molecular recognition elements to monitor tumor-related microRNA and profile cancer cell phenotypes. This scalable design philosophy offers new insights into the design of next generation of artificial cells-based biosensors.


Assuntos
Aptâmeros de Nucleotídeos , Células Artificiais , Técnicas Biossensoriais , DNA Catalítico , Quadruplex G , MicroRNAs , Neoplasias , Humanos , DNA/genética , Hemina , DNA Catalítico/metabolismo
14.
Anal Chem ; 94(24): 8596-8604, 2022 06 21.
Artigo em Inglês | MEDLINE | ID: mdl-35670376

RESUMO

The CRISPR-Cas12a system is a new type of genome editing tool with high efficiency and targeting. However, other sequences in the genome may also be cleaved nonspecifically, resulting in unavoidable off-target effects. Therefore, it is necessary to learn more about the mechanism of CRISPR-Cas12a to recognize target sequences to avoid its off-target effects. Here, we show that insertion (DNA bubble) or deletion (RNA bubble) of the target dsDNA sequence compared with the crRNA sequence, the CRISPR-Cas12a system can still recognize and cleave the target dsDNA sequence. We conclude that the tolerance of CRISPR-Cas12a to the bubbles is closely related to the location and size of the bubble and the GC base content of crRNA. In addition, we used the unique property of CRISPR-Cas12a to invent a new method to detect mutations and successfully detect the CD41-42(-CTTT) mutation. The detection limit of this method is 0.001%. Overall, our results strongly indicate that in addition to considering off-target effects caused by base mismatches, a comprehensive off-target analysis of the insertion and deletion of the target dsDNA sequence is required, and specific guidelines for effectively reducing potential off-target cleavage are proposed, to improve the safety manual of CRISPR-Cas12a biological application.


Assuntos
Sistemas CRISPR-Cas , Edição de Genes , Sistemas CRISPR-Cas/genética , DNA/genética , Edição de Genes/métodos , Mutação , RNA/genética
15.
Opt Lett ; 47(9): 2246-2249, 2022 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-35486771

RESUMO

High-index dielectric nanostructures are of particular interest for nanoscale lasing due to their low absorption losses. However, the relatively weak near-field restricts the isolated dielectric cavities as low-threshold integrated on-chip laser sources. Here, we demonstrate lasing action in a silicon nanowire pair with 32 nm gap coated with dye-doped shell on the silicon-on-insulator platform. It is found that the quality factor Q is dominated by the coupling of the silicon nanowire pair, which depends on the gap size, the nanowire width, and the dye thickness. A lasing peak at the wavelength of 529 nm with FWHM of 0.6 nm is experimentally realized by the Si nanowire pair width, and the corresponding pumping power threshold is ∼34 µW/cm2. The proposed strategy, based on the well-established Si planar process, lays the groundwork for practical integrated nanolasers that have potential applications in photonic circuits.

16.
Neurosurg Rev ; 45(1): 491-498, 2022 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33914243

RESUMO

Pituitary adenomas (PAs) have a low incidence in pediatric and adolescent patients, and their clinical characteristics remain unclear. As a severe complication of PA, apoplexy was investigated in young patients in the present study. Eighty patients younger than 20 years with PAs who underwent surgery were included and divided into an apoplexy group and non-apoplexy group. The clinical data of these two groups were statistically analyzed and compared. The study included 33 boys and 47 girls, with a mean age of 16.9 years. There were six (7.5%) adrenocorticotropic hormone-secreting, 13 (16.3%) growth hormone-secreting, 47 (58.7%) prolactin-secreting, and 14 (17.5%) non-functioning PAs. There were 34 (42.5%) patients in the apoplexy group and 46 (57.5%) patients in the non-apoplexy group. Pre-operatively, patients in the apoplexy group were more likely to have visual impairment (hazard ratio: 2.841, 95% confidence interval: 1.073-7.519; P = 0.033) and had poorer visual impairment scores than those in the non-apoplexy group (P = 0.027). Furthermore, a longer duration of symptoms before surgery was significantly correlated with a poorer visual outcome in the apoplexy group (R = - 1.204; P = 0.035). However, apoplexy was not associated with tumor type, tumor size, resection rate, or tumor recurrence. Tumor apoplexy is common in pediatric and adolescent patients with PAs and is associated with more severe preoperative visual deficits. Hence, the appropriate timing of surgical treatment may be important for rescuing visual function in young PA patients.


Assuntos
Adenoma , Neoplasias Hipofisárias , Acidente Vascular Cerebral , Adenoma/complicações , Adenoma/cirurgia , Adolescente , Criança , Feminino , Humanos , Masculino , Recidiva Local de Neoplasia , Neoplasias Hipofisárias/complicações , Neoplasias Hipofisárias/cirurgia , Estudos Retrospectivos
17.
Anal Chem ; 93(39): 13274-13283, 2021 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-34546716

RESUMO

Gene mutations are important biomarkers for the diagnosis, classification, monitoring, and prognosis evaluation of cancers and genetic diseases. Both personalized cancer treatment and noninvasive prenatal testing require methods to accurately determine the abundance of mutation. At present, the widely adopted and convenient methods for measuring mutation abundance are mainly based on relative quantification, which requires negative samples and strict control of the analyte amounts. The development of DNA-probe-based methods that can determine the mutation abundance without negative samples nor control of analyte amount is highly preferred. The key to solving this bottleneck lies in whether the probe's response to mutation abundance can be completely independent of the number of targeted DNA strands. Herein, we propose the design of a self-internal-reference probe system. We established a theoretical model of this system and used the model to guide the design of probes. In this model, we provided quantitative corrections to the test results from the internal reference, thereby eliminating the influence of substrate amount. Therefore, the purification and quantification processes toward polymerase chain reaction (PCR) amplicons can be omitted. We applied this system to analyze unquantified PCR products aimed at cancer mutation detection and noninvasive prenatal testing.


Assuntos
Mutação
18.
Cancer Cell Int ; 21(1): 666, 2021 Dec 14.
Artigo em Inglês | MEDLINE | ID: mdl-34906149

RESUMO

BACKGROUND: C1QTNF6 (CTRP6), a member of the CTRP family, has recently been implied to play a role in the tumorigenesis of for a variety of cancer types. However, the role of C1QTNF6 in oral squamous cell carcinoma (OSCC) and its potential molecular remains unclear. METHODS: C1QTNF6 expression was detected by qRT-PCR and western blot analysis. Lentiviral vectors were constructed to knockdown C1QTNF6 in CaL27 and SCC-9 human OSCC cell lines. Cell viability, cell cycle and cell apoptosis analyses were performed by MTT assay, PI/Annexin V staining, and flow cytometry. The effect of C1QTNF6 knockdown on in vivo tumorigenicity of OSCC cells in vivo was evaluated using nude mouse xenograft tumor model. Downstream signaling mechanisms were identified by microarray and Ingenuity Pathway Analysis. RESULTS: Immunohistochemistry of OSCC tissue and data from TCGA demonstrate that C1QTNF6 was overexpressed in OSCC tissues, and that cellular proliferation was significantly decreased after C1QTNF6 was knockdown in CaL27 and SCC-9 cell lines. Knockdown of C1QTNF6 also resulted in cell cycle arrest at the G2/M phase and enhanced cell apoptosis in in CaL27 and SCC-9 cell lines. Furthermore, knockdown of C1QTNF6 in Cal-27 cells inhibited tumor growth of OSCC in vivo. Microarray analysis revealed that C1QTNF6 silencing resulted in significant alterations of gene expression, with the Acute Phase Response signaling pathway significantly activated following C1QTNF6 silencing. CONCLUSIONS: These results suggest that C1QTNF6 plays an important role in promoting OSCC tumorigenesis, which indicates that C1QTNF6 may comprise a promising therapeutic target for OSCC treatment.

19.
Macromol Rapid Commun ; 42(21): e2100441, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34431573

RESUMO

Using DNA nanostructures as templates to synthesize shape-controlled polydopamine (PDA) is a promising strategy to realize the fabrication of exquisite PDA nanomaterials. However, previous studies using small DNA tiles as templates could only afford very simple structures such as lines and crosses due to the limited space on the template and the relatively low resolution of the PDA nanopatterns. Therefore, the best resolution of the PDA nanostructures that can be achieved by this technique is carefully investigated. And by connecting several DNA tiles together, larger DNA templates are built up and achieve the synthesis of complicated digital nanopatterned PDA structures.


Assuntos
Nanoestruturas , Polímeros , DNA , Indóis
20.
Angew Chem Int Ed Engl ; 59(14): 5712-5720, 2020 03 27.
Artigo em Inglês | MEDLINE | ID: mdl-31943635

RESUMO

Amphiphilic surface groups play an important role in many biological processes. The synthesis of amphiphilic polyphenylene dendrimer branches (dendrons), providing alternating hydrophilic and lipophilic surface groups and one reactive ethynyl group at the core is reported. The amphiphilic surface groups serve as biorecognition units that bind to the surface of adenovirus 5 (Ad5), which is a common vector in gene therapy. The Ad5/dendron complexes showed high gene transduction efficiencies in coxsackie-adenovirus receptor (CAR)-negative cells. Moreover, the dendrons offer incorporation of new functions at the dendron core by in situ post-modifications, even when bound to the Ad5 surface. Surfaces coated with these dendrons were analyzed for their blood-protein binding capacity, which is essential to predict their performance in the blood stream. A new platform for introducing bioactive groups to the Ad5 surface without chemically modifying the virus particles is provided.


Assuntos
Adenoviridae/química , Dendrímeros/química , Polímeros/química , Adenoviridae/fisiologia , Animais , Proteínas Sanguíneas/química , Proteínas Sanguíneas/metabolismo , Células CHO , Sobrevivência Celular/efeitos dos fármacos , Cricetinae , Cricetulus , Reação de Cicloadição , Dendrímeros/síntese química , Dendrímeros/farmacologia , Interações Hidrofóbicas e Hidrofílicas , Lipossomos/química , Ligação Proteica , Propriedades de Superfície
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