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1.
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
2.
Anal Chem ; 96(25): 10228-10236, 2024 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-38867346

RESUMO

Exocytosis of a single cell has been extensively researched in recent years due to its close association with numerous diseases. However, current methods only investigate exocytosis at either the single-cell or multiple-cell level, and a method for simultaneously studying exocytosis at both levels has yet to be established. In this study, a combined device incorporating ultramicroelectrode (UME) electrochemistry and surface plasmon resonance (SPR) was developed, enabling the simultaneous monitoring of single-cell and multiple-cell exocytosis. PC12 cells were cultured directly on the SPR sensing Au film, with a carboxylated carbon nanopipette (c-CNP) electrode employed for electrochemical detection in the SPR reaction cell. Upon exocytosis, the released dopamine diffuses onto the inner wall of c-CNP, undergoing an electrochemical reaction to generate a current peak. Concurrently, exocytosis can also induce changes in the refractive index of the Au film surface, leading to the SPR signal. Consequently, the device enables real-time monitoring of exocytosis from both single and multiple cells with a high spatiotemporal resolution. The c-CNP electrode exhibited excellent resistance to protein contamination, high sensitivity for dopamine detection, and the capability to continuously monitor dopamine exocytosis over an extended period. Analysis of both SPR and electrochemical signals revealed a positive correlation between changes in the SPR signal and the frequency of exocytosis. This study introduces a novel method and platform for the simultaneous investigation of single-cell and multiple-cell exocytosis.


Assuntos
Dopamina , Técnicas Eletroquímicas , Exocitose , Microeletrodos , Ressonância de Plasmônio de Superfície , Células PC12 , Animais , Ratos , Técnicas Eletroquímicas/métodos , Técnicas Eletroquímicas/instrumentação , Dopamina/análise , Dopamina/metabolismo , Ouro/química , Análise de Célula Única/instrumentação
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.
Cryobiology ; : 104937, 2024 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-38942068

RESUMO

Growing concerns over declining male semen quality and rising infertility have shifted attention to male fertility. Sperm cryopreservation emerges as a crucial tool in preserving male fertility, especially for patients who need proactive preservation, such as cancer patients before undergoing radiation or chemotherapy. Although cryopreservation does not directly address infertility, effective preservation can support future fertility. However, the process may compromise sperm DNA integrity. Despite their impairment, damaged sperm often retain vitality and may still have the potential to fertilize an egg. Nonetheless, if damaged sperm fertilize an egg, excessive DNA damage could impede embryo implantation and development, despite the egg's repair capabilities. Consequently, precise detection of sperm DNA damage is crucial and urgent. To better address the issue of sperm DNA damage detection, we have introduced a novel fluorescence biosensor technology known as the TDT/SD Probe. This technology utilizes terminal deoxynucleotidyl transferase (TdT) and strand displacement probes to accurately detect the number of sperm DNA breakage points during the cryopreservation process. Experimental results reveal that the number of sperm DNA breakpoints significantly increases after both sperm vitrification (8.17×105) and conventional slow freezing (10.80×105), compared to the DNA breakpoints of fresh semen samples (5.19×105). However, sperm vitrification has the least impact on sperm breakage points. This research provides innovative means for further optimizing sperm preservation techniques by offering a novel DNA damage detection method, enabling more precise assessment of sperm DNA damage during the freezing process.

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.
Clin Immunol ; 246: 109212, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36563946

RESUMO

Psoriasis is a chronic immune-mediated inflammatory disease. Lipids play an important role in regulating the inflammatory response. However, the alteration of lipids involved in psoriasis particular in skin lesions remain unclear. Here, we performed the lipidomics to investigate lipid profiling in the skin lesions of the imiquimod-induced psoriasis-like dermatitis and psoriasis patients. The findings showed that ceramides phosphate (CerP) and ceramides were enriched in psoriatic lesions compared with controls from both psoriasis patients and psoriasis-like mouse model. Psoriasis patients were classified into two subtypes, the CC1 and CC2, by consensus clustering of these lipid signatures. The CC1 was characterized by the higher levels of CerP, uric acid, and more severe psoriasis, compared with CC2 subtype. Interestingly, ceramide-1-phosphate (C1P), dramatically enriched in CC1 subtype, facilitated imiquimod-induced psoriasis-like inflammatory responses. Mechanistically, C1P induced the expression of inflammatory factors and activated DNA replication and cell cycle signaling pathways in the primary keratinocytes. Inhibiting the production of C1P with ceramide kinase inhibitor effectively alleviated the imiquimod-induced psoriasis-like inflammation. Taken together, we described the landscape of lipids alteration and established lipids classification based on pattern of abundance of lipids in psoriatic skin lesions. Suppression of C1P pathway is a novel potential strategy for psoriasis treatment.


Assuntos
Lipidômica , Psoríase , Animais , Camundongos , Imiquimode/farmacologia , Pele/patologia , Psoríase/tratamento farmacológico , Queratinócitos , Inflamação/patologia , Ceramidas/efeitos adversos , Lipídeos/efeitos adversos , Modelos Animais de Doenças , Camundongos Endogâmicos BALB C
7.
Anal Chem ; 95(51): 18828-18835, 2023 12 26.
Artigo em Inglês | MEDLINE | ID: mdl-38078896

RESUMO

DNA methylation is closely related to cancer. It is generally accepted that DNA methylation detection is crucial in cancer diagnosis, prognosis, and treatment monitoring. Therefore, there is an urgent demand for developing a simple, rapid, highly sensitive, and highly specific methylation detection method to detect DNA methylation at specific sites quantitatively. In this work, we introduce a DNA methylation detection method based on MutS and methylation-specific PCR, named MutS-based methylation-specific PCR (MB-MSP), which has the advantages of simplicity, speed, high specificity, sensitivity, and broad applicability. Utilizing the MutS's ability to bind mismatched base pairs, we inhibit not only the amplification of unmethylated DNA but also nonspecific primer amplification. We achieved a detection sensitivity of 0.5% for the methylated genes of ACP1, CLEC11A, and SEPT9 by MB-MSP. It has a good linear relationship and a detection time of only 1.5 h. To validate the feasibility of the MB-MSP method in clinical application, we conducted methylation detection on plasma-circulating tumor DNA samples from 10 liver cancer patients and 5 healthy people, achieving a 100% accuracy rate. In conclusion, MB-MSP, as a novel and reliable DNA methylation detection tool, holds significant application value and potential for advancing early cancer diagnosis.


Assuntos
Metilação de DNA , Neoplasias , Humanos , Proteínas MutS , DNA/genética , Reação em Cadeia da Polimerase/métodos
8.
BMC Plant Biol ; 23(1): 149, 2023 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-36935490

RESUMO

BACKGROUND: The Polygonatum cyrtonema Hua rhizomes (also known as Rhizoma Polygonati, RP) are consumed for their health benefits. The main source of the RP is wild P. cyrtonema populations in the Hunan province of China. However, the soil Cadmium (Cd) content in Huanan is increasing, thus increasing the risks of Cd accumulation in RP which may end up in the human food chain. To understand the mechanism of Cd accumulation and resistance in P. cyrtonema, we subjected P. cyrtonema plants to four levels of Cd stress [(D2) 1, (D3) 2, (D4) 4, and (D5) 8 mg/kg)] compared to (D1) 0.5 mg/kg. RESULTS: The increase in soil Cd content up to 4 mg/kg resulted in a significant increase in tissue (root hair, rhizome, stem, and leaf) Cd content. The increase in Cd concentration variably affected the antioxidant enzyme activities. We could identify 14,171 and 12,115 protein groups and peptides, respectively. There were 193, 227, 260, and 163 differentially expressed proteins (DEPs) in D2, D3, D4, and D5, respectively, compared to D1. The number of downregulated DEPs increased with an increase in Cd content up to 4 mg/kg. These downregulated proteins belonged to sugar biosynthesis, amino acid biosynthesis-related pathways, and secondary metabolism-related pathways. Our results indicate that Cd stress increases ROS generation, against which, different ROS scavenging proteins are upregulated in P. cyrtonema. Moreover, Cd stress affected the expression of lipid transport and assembly, glycolysis/gluconeogenesis, sugar biosynthesis, and ATP generation. CONCLUSION: These results suggest that an increase in soil Cd content may end up in Huangjing. Cadmium stress initiates expression changes in multiple pathways related to energy metabolism, sugar biosynthesis, and secondary metabolite biosynthesis. The proteins involved in these pathways are potential candidates for manipulation and development of Cd stress-tolerant genotypes.


Assuntos
Cádmio , Polygonatum , Humanos , Cádmio/toxicidade , Cádmio/análise , Rizoma , Proteoma , Espécies Reativas de Oxigênio , Açúcares/análise
9.
Opt Lett ; 48(1): 101-104, 2023 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-36563382

RESUMO

The topological edge state (TES) and topological corner state (TCS) in photonic crystals (PCs) provide effective ways to manipulate the propagation of light. To improve the performance and integration of topological photonic devices, the realization of multiband topological states by PCs combined with quasi-periodic structure needs to be urgently explored. In this Letter, a Penrose-triangle (P-T) PC, which arranges the basic structural unit of a 12-fold Penrose-type photonic quasi-crystal (PQC) in a triangular lattice, is proposed. The TES and TCS at low- and high-frequency bands can be generated in the same structure, accompanied by the realization of three groups of TCSs. This will provide a new structure for the generation of TESs and TCSs in PCs, and will provide a new way to improve the performance and integration of topological photonic devices.

10.
Phys Rev Lett ; 130(2): 026101, 2023 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-36706409

RESUMO

For the classification of topological phases of matter, an important consideration is whether a system is spinless or spinful, as these two classes have distinct symmetry algebra that gives rise to fundamentally different topological phases. However, only recently has it been realized theoretically that in the presence of gauge symmetry, the algebraic structure of symmetries can be projectively represented, which possibly enables the switch between spinless and spinful topological phases. Here, we report the experimental demonstration of this idea by realizing spinful topological phases in "spinless" acoustic crystals with projective space-time inversion symmetry. In particular, we realize a one-dimensional topologically gapped phase characterized by a 2Z winding number, which features double-degenerate bands in the entire Brillouin zone and two pairs of degenerate topological boundary modes. Our Letter thus overcomes a fundamental constraint on topological phases by spin classes.

11.
Cryobiology ; 113: 104591, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37804950

RESUMO

The freeze-thaw process can induce irreversible structural and functional changes in human sperm, particularly sperm DNA damage. Selecting a more accurate and sensitive detection method for evaluating sperm DNA integrity is crucial. To accurately assess sperm DNA integrity following the freeze-thaw process and significantly improve the clinical and scientific utilization of cryopreserved sperm. In this study, we utilized a novel fluorescent biosensor, assisted by terminal deoxynucleotidyl transferase (TdT) and Endonuclease IV, to detect DNA breakpoints during sperm cryopreservation. We evaluated the biosensor's performance by comparing it with the conventional DNA fragmentation index (DFI) measured using sperm chromatin structure analysis (SCSA). The cryopreserved group exhibited a significantly higher sperm DFI compared to the fresh group. No significant difference was observed between the antioxidant group and the cryopreserved group. However, the new method revealed a significant reduction in the number of DNA breakpoints in the antioxidant group compared to the cryopreserved group. The novel biosensor demonstrated superior accuracy and effectiveness in assessing sperm DNA integrity during cryopreservation compared to the conventional SCSA method. We believe that the biosensor holds significant potential for widespread use in the field of reproductive medicine.


Assuntos
Antioxidantes , Criopreservação , Masculino , Humanos , Criopreservação/métodos , Sêmen , Fragmentação do DNA , Motilidade dos Espermatozoides , Espermatozoides , Dano ao DNA , DNA/genética
12.
J Eur Acad Dermatol Venereol ; 37(7): 1344-1360, 2023 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-37013729

RESUMO

BACKGROUND: Although abnormal metabolism plays a critical role in the pathogenesis of psoriasis, the details are unclear. OBJECTIVES: Here, we identified to explore the role and mechanism of lysophosphatidylcholine (LPC) on the pathogenesis of psoriasis. METHODS: The level of LPC in plasma and skin lesions and the expression of G2A on skin lesions of psoriasis patients were detected by enzyme-linked immunosorbent assay, liquid chromatography-tandem mass spectrometry, or immunohistochemistry, respectively. The glycolysis in the skin lesions of imiquimod (IMQ)-induced psoriasis-like mouse model was detected by extracellular acidification rate. LPC was subcutaneously injected into IMQ-treated mouse ears, and the phenotype as well as the glycolysis were evaluated. Exploring the effects and mechanism of LPC on keratinocytes and CD4+ T cells by culturing primary keratinocytes and CD4+ T in vitro. RESULTS: We found that LPC was significantly increased both in the plasma and skin lesions of psoriatic patients, while G2A, exerting an essential role in LPC-inducing biological functions, was increased in psoriatic lesions. The abundance of LPC was positively correlated with glycolytic activity in the psoriasis-like mouse model. LPC treatment facilitated psoriasis-like inflammation and glycolytic activity in skin lesions. Mechanistically, the LPC/G2A axis significantly triggered glycolytic activity and produced inflammatory factors in keratinocytes, and blockade of glycolysis abrogated LPC-induced expression of inflammatory mediators in keratinocytes. LPC activated STAT1, resulting in recognition and binding to the promoters of GCK and PKLR, which are glycolytic rate-limiting enzymes. Furthermore, the LPC/G2A axis directly benefited Th1 differentiation, which was dependent on LPC-induced glycolytic activity. Notably, LPC indirectly facilitated Th17 differentiation by inducing the secretion of IL-1ß in keratinocytes-T cells coculture system. CONCLUSIONS: Taken together, our findings revealed the role of the LPC/G2A axis in the pathogenesis of psoriasis; targeting LPC/G2A is a potential strategy for psoriasis therapy.


Assuntos
Psoríase , Dermatopatias , Camundongos , Animais , Lisofosfatidilcolinas/efeitos adversos , Lisofosfatidilcolinas/metabolismo , Psoríase/patologia , Queratinócitos/metabolismo , Imiquimode/efeitos adversos , Dermatopatias/patologia , Diferenciação Celular , Modelos Animais de Doenças , Camundongos Endogâmicos BALB C , Pele/patologia
13.
Nano Lett ; 22(22): 9181-9189, 2022 11 23.
Artigo em Inglês | MEDLINE | ID: mdl-36374229

RESUMO

The balance between degradability and drug release kinetics is a major challenge for the development of drug delivery systems. Here we develop hierarchically structured nanoparticles comprising multiple noncontact silica shells using an amorphous calcium carbonate template. The system could be degraded in a sequential fashion on account of the molecularly engineered multishelled structures. The hydrolysis rate of drug-containing cores is inversely correlated with the nanoparticle concentration due to the shielding effect of the hierarchical nanostructure and could be exploited to regulate the release kinetics. Specifically, multishelled nanospheres show a low drug release rate with high doses that increases steadily as the concentration decreases due to continuous degradation, thus stabilizing the local drug concentration for effective tumor therapy. Moreover, the nanoparticles could be eventually degraded completely, which may reduce their health risks. This kind of hierarchically structured silica-based nanoparticle could serve as a sustainable drug depot and provides a new avenue for tumor treatment.


Assuntos
Nanopartículas , Nanosferas , Nanoestruturas , Neoplasias , Humanos , Liberação Controlada de Fármacos , Nanoestruturas/química , Dióxido de Silício/química , Nanosferas/química , Nanopartículas/química , Neoplasias/tratamento farmacológico , Sistemas de Liberação de Medicamentos
14.
J Cell Mol Med ; 26(9): 2579-2593, 2022 05.
Artigo em Inglês | MEDLINE | ID: mdl-35332658

RESUMO

Melanoma is a fatal cancer with a significant feature of resistance to traditional chemotherapeutic drugs and radiotherapy. A mutation in the kinase BRAF is observed in more than 66% of metastatic melanoma cases. Therefore, there is an urgent need to develop new BRAF-mutant melanoma inhibitors. High-dose chloroquine has been reported to have antitumour effects, but it often induces dose-limiting toxicity. In this study, a series of chloroquine derivatives were synthesized, and lj-2-66 had the best activity and was selected for further investigation. Furthermore, the anti-BRAF-mutant melanoma effect and mechanism of this compound were explored. CCK-8 and colony formation assays indicated that lj-2-66 significantly inhibited the proliferation of BRAF-mutant melanoma cells. Flow cytometry revealed that lj-2-66 induced G2/M arrest in melanoma cells and promoted apoptosis. Furthermore, lj-2-66 increased the level of ROS in melanoma cells and induced DNA damage. Interestingly, lj-2-66 also played a similar role in BRAF inhibitor-resistant melanoma cells. In summary, we found a novel chloroquine derivative, lj-2-66, that increased the level of ROS in melanoma cells and induced DNA damage, thus leading to G2/M arrest and apoptosis. These findings indicated that lj-2-66 may become a potential therapeutic drug for melanoma harbouring BRAF mutations.


Assuntos
Melanoma , Proteínas Proto-Oncogênicas B-raf , Apoptose , Linhagem Celular Tumoral , Proliferação de Células , Cloroquina/farmacologia , Dano ao DNA , Resistencia a Medicamentos Antineoplásicos , Pontos de Checagem da Fase G2 do Ciclo Celular , Humanos , Melanoma/tratamento farmacológico , Melanoma/genética , Melanoma/patologia , Mutação , Inibidores de Proteínas Quinases/farmacologia , Proteínas Proto-Oncogênicas B-raf/genética , Espécies Reativas de Oxigênio
15.
Clin Immunol ; 245: 109183, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36371067

RESUMO

The newly discovered subset of memory T cells, tissue resident memory T (TRM) cells, reside in peripheral tissues for a long time, contributing to a rapid immune response and constituting the first line of defense when pathogens invade cells. Tissue resident memory T cells have unique transcriptome characteristics, and their presence in peripheral tissues is regulated by many factors. TRM cells residing in different tissues often express different surface markers. In addition to CD8+ and CD4+ T cells, which are the best-characterized T cells, Treg cells and various innate T cells can reside in nonlymphoid tissues. Many recent studies have shown that tissue resident memory T cells play indispensable roles in tumor immunity and allergic diseases. This paper reviews the differentiation, regulation, variety and function of TRM cells and the roles they play in skin diseases, including cutaneous melanoma and psoriasis.


Assuntos
Melanoma , Neoplasias Cutâneas , Humanos , Memória Imunológica , Células T de Memória , Linfócitos T CD4-Positivos , Linfócitos T CD8-Positivos
16.
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
17.
Clin Chem ; 68(4): 540-549, 2022 03 31.
Artigo em Inglês | MEDLINE | ID: mdl-35050313

RESUMO

BACKGROUND: Sperm DNA integrity is crucial for normal fertilization, implantation, and embryo development. Several assays are available to assess sperm DNA fragmentation but are limited by high price, complicated processes, and low accuracy. METHODS: We developed a secondary amplification detection system based on terminal deoxynucleotidyl transferase and endonuclease IV, which could efficiently measure the number of 3'-OH (equivalent to the number of breakpoints). We applied this detection system in single stranded DNA with standard concentrations to obtain the standard curve. We then broke the double stranded genomic DNA by ultrasound and enzyme digestion and used the detection system to monitor the increase of DNA breakpoints. Finally, we used this method to measure the mean number of sperm DNA breakpoints (MDB) in 80 sperm samples. RESULTS: We successfully measured the number of 3'-OH in single stranded DNA with standard concentration and obtained the standard curve. The linear range for the number of DNA breakpoints was from 0.1 nM to 15 nM. The detection method was successfully validated on λ DNA and 80 human sperm samples. The results of real clinical samples revealed that the mean number of DNA breakpoints (MDB) had a stronger relevance with the sperm motility and clinical pregnancy outcomes than the commonly used parameter of DNA fragmentation index (DFI). CONCLUSION: We have developed a straight-forward method for direct measurement of the mean number of DNA breakpoints in sperms. The method has advantages of short time-consumption, simple operation, high analytical sensitivity, and low requirement for instrumentation, which makes it conducive to clinical application. The proposed new parameter (MDB) could be a more direct, accurate and clinically significant indicator for evaluating the sperm DNA integrity.


Assuntos
Motilidade dos Espermatozoides , Espermatozoides , DNA/genética , Quebras de DNA , Fragmentação do DNA , Feminino , Humanos , Masculino , Gravidez
18.
Opt Lett ; 47(2): 437-440, 2022 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-35030626

RESUMO

Novel phenomena found in non-Hermitian systems and robust edge states have attracted much attention. When non-Hermitian parameters (gain and loss) are above a critical value, the non-Hermitian photonic crystal (PC) bandgaps close, leading to a mixture of the topological edge state (TES) and topological corner state (TCS) with the bulk state. Meanwhile, new bandgaps also open, in which new TES and TCS can appear. Thus, with appropriate non-Hermitian parameters, TES can emerge in both the original bandgaps and the newly opened bandgaps. The results described here will further enrich understanding of the topological properties of non-Hermitian systems.

19.
Opt Lett ; 47(8): 2044-2047, 2022 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-35427332

RESUMO

The quantum spin Hall effect protected by C6 symmetry [realized in the domain wall (DW) formed by a trivial-photonic crystal (TPC) and a nontrivial-PC (NPC)] and the quantum valley Hall effect protected by C3 symmetry [realized in the DW formed by two valley PCs (VPCs)] have been widely researched due to their excellent topological properties. The topological edge states (TESs) and topological corner states (TCSs) at DWs between different symmetric structures remain to be explored, which is essential for connecting waveguides with different symmetries to construct optical communication devices. In this Letter, there is (are) one TES (two TESs) for the DW1 and DW3 (DW2 and DW4) between the TPC (NPC) and two VPCs. Through simulation calculations of the Wilson-loop of the TPC and NPC and the Berry curvature distribution of VPCs, the corresponding relationship between the topological invariant and the number of TESs is obtained. Based on the TPC, NPC, and two VPCs, the waveguides are constructed to verify the realization of TESs. The parity of the gapped TESs is analyzed, and its relationship with the TCSs is obtained. Moreover, box-shaped structures are constructed to verify the appearance of TCSs. These results have a guiding significance for the research of the interaction between topological states protected by different symmetries.

20.
Opt Lett ; 47(12): 3011-3014, 2022 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-35709038

RESUMO

In this Letter, the higher-order topological state (HOTS) and its mechanism in two-dimensional Stampfli-Triangle (2D S-T) photonic crystals (PhCs) is explored. The topological corner states (TCSs) in 2D S-T PhCs are based on two physical mechanisms: one is caused by the photonic quantum spin Hall effect (PQSHE), and the other is caused by the topological interface state. While the former leads to the spin-direction locked effect which can change the distribution of the TCSs, the latter is conducive to the emergence of multiband TCSs in the same structure due to the characteristics of plentiful photonic bandgap (PBG) and broadband in 2D S-T PhCs. These findings allow new, to the best of our knowledge, insight into the HOTS, and are significant to the future design of photonic microcavities, high-quality factor lasers, and other related integrated multiband photonic devices.

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