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1.
Brief Bioinform ; 25(3)2024 Mar 27.
Artigo em Inglês | MEDLINE | ID: mdl-38555478

RESUMO

DNA storage is one of the most promising ways for future information storage due to its high data storage density, durable storage time and low maintenance cost. However, errors are inevitable during synthesizing, storing and sequencing. Currently, many error correction algorithms have been developed to ensure accurate information retrieval, but they will decrease storage density or increase computing complexity. Here, we apply the Bloom Filter, a space-efficient probabilistic data structure, to DNA storage to achieve the anti-error, or anti-contamination function. This method only needs the original correct DNA sequences (referred to as target sequences) to produce a corresponding data structure, which will filter out almost all the incorrect sequences (referred to as non-target sequences) during sequencing data analysis. Experimental results demonstrate the universal and efficient filtering capabilities of our method. Furthermore, we employ the Counting Bloom Filter to achieve the file version control function, which significantly reduces synthesis costs when modifying DNA-form files. To achieve cost-efficient file version control function, a modified system based on yin-yang codec is developed.


Assuntos
Algoritmos , DNA , Análise de Sequência de DNA/métodos , DNA/genética , DNA/química , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Armazenamento e Recuperação da Informação
2.
Bioinformatics ; 40(3)2024 03 04.
Artigo em Inglês | MEDLINE | ID: mdl-38449297

RESUMO

MOTIVATION: The advancement of structural biology has increased the requirements for researchers to quickly and efficiently visualize molecular structures in silico. Meanwhile, it is also time-consuming for structural biologists to create publication-standard figures, as no useful tools can directly generate figures from structure data. Although manual editing can ensure that figures meet the standards required for publication, it requires a deep understanding of software operations and/or program call commands. Therefore, providing interfaces based on established software instead of manual editing becomes a significant necessity. RESULTS: We developed PyMOL-PUB, based on the original design of PyMOL, to effectively create publication-quality figures from molecular structure data. It provides functions including structural alignment methods, functional coloring schemes, conformation adjustments, and layout plotting strategies. These functions allow users to easily generate high-quality figures, demonstrate structural differences, illustrate inter-molecular interactions, and predict performances of biomacromolecules. AVAILABILITY AND IMPLEMENTATION: Our tool is publicly available at https://github.com/BGI-SynBio/PyMOL-PUB.


Assuntos
Software , Conformação Molecular
3.
Zhongguo Yi Xue Ke Xue Yuan Xue Bao ; 46(4): 513-518, 2024 Aug.
Artigo em Zh | MEDLINE | ID: mdl-39223016

RESUMO

Objective To evaluate the changes in the incidence of neural tube defects (NTDs) in Shaanxi province from 2003 to 2022,investigate the diagnosis time and outcomes of defective infants,and predict the incidence of NTDs in Shaanxi province from 2023 to 2025,thereby providing a basis for improving the birth defects surveillance system. Methods Data were collected from all the perinatal infants from 28 weeks of gestation to 7 days after birth in all the hospitals with obstetrical department in Shaanxi province during 2003-2022.The changes in the incidence of NTDs from 2003 to 2022 were analyzed based on the birth defects surveillance system. Results A total of 1 106 483 perinatal infants in Shaanxi province from 2003 to 2022 were surveyed,among which NTDs occurred in 848 perinatal infants,with an incidence of 7.66/10 000.The incidence was the highest (48.02/10 000) in 2005 and the lowest (0.57/10 000) in 2022.The NTDs in Shaanxi province were mainly spina bifida (55.90%),which was followed by anencephaly (25.71%) and encephalocele (18.40%).The incidences of the three declined with fluctuations (P<0.001).The results of the Joinpoint analysis showed that the incidence of NTDs decreased slowly with the annual percentage change of -4.04 from 2003 to 2014 and declined rapidly with the annual percentage change of -28.05 from 2014 to 2022.From 2003 to 2022,the average proportion of prenatal diagnosis of NTDs in Shaanxi province was 72.88%.Dead fetus (61.91%) was the main birth outcome,followed by live birth (26.77%),stillbirth (8.73%),and death within seven days after birth (2.59%).The incidence of NTDs in Shaanxi province from 2023 to 2025 were predicted by the GM (1,1) model as 0.49/10 000,0.41/10 000,and 0.35/10 000,respectively. Conclusion The incidence of NTDs in Shaanxi province declined significantly during 2003-2022,especially in a rapid manner after 2014.Dead fetus was the primary outcome of perinatal infants with NTDs,followed by live birth.


Assuntos
Defeitos do Tubo Neural , Humanos , Defeitos do Tubo Neural/epidemiologia , China/epidemiologia , Recém-Nascido , Incidência , Feminino , Gravidez
4.
Zhongguo Zhong Yao Za Zhi ; 49(9): 2385-2392, 2024 May.
Artigo em Zh | MEDLINE | ID: mdl-38812139

RESUMO

This study aims to investigate the mechanism of total saponins of Paridis Rhizoma in inducing the ferroptosis of MCF-7 cells and provide a theoretical basis for the clinical treatment of breast cancer with total saponins of Paridis Rhizoma. The methyl thiazolyl tetrazolium(MTT) assay was employed to examine the effects of different concentrations of total saponins of Paridis Rhizoma on the proliferation of MCF-7 cells. A phase contrast inverted microscope was used to observe the morphological changes of MCF-7 cells. The colony formation assay was employed to test the colony formation of MCF-7 cells. The lactate dehydrogenase(LDH) release test was conducted to determine the cell membrane integrity of MCF-7 cells. The cell scratch assay was employed to examine the migration of MCF-7 cells. After that, the level of reactive oxygen species(ROS) in MCF-7 cells was observed by an inverted fluorescence microscope, and the content of Fe~(2+) in MCF-7 cells was detected by the corresponding kit. Transmission electron microscopy was employed to observe the mitochondrial ultrastructure of MCF-7 cells. Western blot was employed to determine the expression of ferroptosis-related proteins, such as p53, solute carrier family 7 member 11(SLC7A11), glutathione peroxidase 4(GPX4), acyl-CoA synthetase long-chain family member 4(ACSL4), and transferrin receptor protein 1(TFR1) in MCF-7 cells. The results showed that 1.5, 3, 4.5, 6, 7.5, and 9 µg·mL~(-1) total saponins of Paridis Rhizoma significantly inhibited the proliferation of MCF-7 cells, with the IC_(50) of 4.12 µg·mL~(-1). Total saponins of Paridis Rhizoma significantly damaged the morphology of MCF-7 cells, leading to the formation of vacuoles and the gradual shrinkage and detachment of cells. Meanwhile, total saponins of Paridis Rhizoma inhibited the colony formation of MCF-7 cells, destroyed the cell membrane(leading to the release of LDH), and shortened the migration distance of MCF-7 cells. Total saponins of Paridis Rhizoma treatment significantly increased the content of ROS, induced oxidative damage, and led to the accumulation of Fe~(2+) in MCF-7 cells. Furthermore, total saponins of Paridis Rhizoma changed the mitochondrial structure, increased the mitochondrial membrane density, led to the decrease or even disappear of ridges, promoted the expression of p53 protein, down-regulated the expression of SLC7A11 and GPX4, and up-regulated the expression of ACSL4 and TFR1. In summary, total saponins of Paridis Rhizoma can significantly inhibit the proliferation and migration of MCF-7 cells and destroy the cell structure by inducing ferroptosis.


Assuntos
Neoplasias da Mama , Ferroptose , Espécies Reativas de Oxigênio , Rizoma , Saponinas , Humanos , Saponinas/farmacologia , Saponinas/química , Ferroptose/efeitos dos fármacos , Células MCF-7 , Rizoma/química , Neoplasias da Mama/tratamento farmacológico , Neoplasias da Mama/metabolismo , Neoplasias da Mama/genética , Espécies Reativas de Oxigênio/metabolismo , Feminino , Medicamentos de Ervas Chinesas/farmacologia , Medicamentos de Ervas Chinesas/química , Proliferação de Células/efeitos dos fármacos , Primulaceae/química
5.
Mol Biol Rep ; 50(5): 4375-4384, 2023 May.
Artigo em Inglês | MEDLINE | ID: mdl-36944863

RESUMO

The plant COBRA protein family plays an important role in secondary cell wall biosynthesis and the orientation of cell expansion. The COBRA gene family has been well studied in Arabidopsis thaliana, maize, rice, etc., but no systematic studies were conducted in wheat. In this study, the full-length sequence of TaCOBLs was obtained by homology cloning from wheat, and a conserved motif analysis confirmed that TaCOBLs belonged to the COBRA protein family. qRT-PCR results showed that the TaCOBL transcripts were induced by abiotic stresses, including cold, drought, salinity, and abscisic acid (ABA). Two haplotypes of TaCOBL-5B (Hap5B-a and Hap5B-b), harboring one indel (----/TATA) in the 5' flanking region (- 550 bp), were found on chromosome 5BS. A co-dominant marker, Ta5BF/Ta5BR, was developed based on the polymorphism of the two TaCOBL-5B haplotypes. Significant correlations between the two TaCOBL-5B haplotypes and cold resistance were observed under four environmental conditions. Hap5B-a, a favored haplotype acquired during wheat polyploidization, may positively contribute to enhanced cold resistance in wheat. Based on the promoter activity analysis, the Hap5B-a promoter containing a TATA-box was more active than that of Hap5B-b without the TATA-box under low temperature. Our study provides valuable information indicating that the TaCOBL genes are associated with cold response in wheat.


Assuntos
Ácido Abscísico , Proteínas de Plantas , Ácido Abscísico/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Estresse Fisiológico/genética , Regiões Promotoras Genéticas/genética , Regulação da Expressão Gênica de Plantas/genética , Plantas Geneticamente Modificadas/genética , Temperatura Baixa
6.
Zhongguo Yi Xue Ke Xue Yuan Xue Bao ; 44(5): 822-827, 2022 Oct.
Artigo em Zh | MEDLINE | ID: mdl-36325780

RESUMO

Objective To investigate the multiple correspondence of genetic and environmental risk factors with abnormal birth history and provide a scientific basis for improving the birth defects surveillance system and reducing the incidence of birth defects. Methods Data were collected from all the perinatal infants from 28-week-old fetuses to 7-day-old infants born in all the hospitals with obstetrical department in Xi'an from 2003 to 2015. Results A total of 1 236 937 perinatal infants were surveyed,including 10 619 with birth defects.The average incidence rate of birth defects was 0.86% (0.70%-1.15%).Multiple correspondence analysis showed that the women who had had 1 or 2 children with birth defects were associated with the history of spontaneous abortion,family history of birth defects,and history of exposure to toxic and harmful substances.The women who had had 3 or more children with birth defects showed stronger association with family history of birth defects.The birth defects in women with history of spontaneous abortion (257/10 619) was ranked in the order of congenital heart disease,polydactyly,neural tube defects,congenital hydrocephalus,cleft lip with cleft palate,and simple cleft lip.The birth defects in women who had given birth to children with birth defects (135/10 619) followed the order of cleft lip with cleft palate,anencephaly,hydrocephalus,neural tube defects,cleft lip,and talipes equinovarus. Conclusions Abnormal birth history is associated with family history of birth defects and history of exposure to environmental risk factors.Giving birth to three or more children with birth defects is highly correlated with the family history of birth defects.


Assuntos
Aborto Espontâneo , Fenda Labial , Fissura Palatina , Defeitos do Tubo Neural , Criança , Gravidez , Feminino , Humanos , Fenda Labial/epidemiologia , Fenda Labial/etiologia , Fissura Palatina/complicações , História Reprodutiva , Defeitos do Tubo Neural/complicações , Defeitos do Tubo Neural/epidemiologia , Fatores de Risco
7.
Biomed Environ Sci ; 30(2): 150-155, 2017 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-28292355

RESUMO

This study aimed to evaluate the sensitivity and specificity of the new clinical diagnostic and classification criteria for Kashin-Beck disease (KBD) using six clinical markers: flexion of the distal part of fingers, deformed fingers, enlarged finger joints, shortened fingers, squat down, and dwarfism. One-third of the total population in Linyou County was sampled by stratified random sampling. The survey included baseline characteristics and clinical diagnoses, and the sensitivity and specificity of the new criteria was evaluated. We identified 3,459 KBD patients, of which 69 had early stage KBD, 1,952 had stage I, 1,132 had stage II, and 306 had stage III. A screening test classified enlarged finger joints as stage I KBD, with a sensitivity and specificity of 0.978 and 0.045, respectively. Shortened fingers were classified as stage II KBD, with a sensitivity and specificity of 0.969 and 0.844, respectively, and dwarfism was classified as stage III KBD with a sensitivity and specificity of 0.951 and 0.992, respectively. Serial screening test revealed that the new clinical classification of KBD classified stages I, II, and III KBD with sensitivities of 0.949, 0.945, and 0.925 and specificities of 0.967, 0.970, and 0.993, respectively. The screening tests revealed that enlarged finger joints, shortened fingers, and dwarfism were appropriate markers for the clinical diagnosis and classification of KBD with high sensitivity and specificity.


Assuntos
Doença de Kashin-Bek/diagnóstico , Doença de Kashin-Bek/epidemiologia , Adolescente , Adulto , Criança , Pré-Escolar , China/epidemiologia , Feminino , Humanos , Doença de Kashin-Bek/classificação , Doença de Kashin-Bek/patologia , Masculino , Pessoa de Meia-Idade , Adulto Jovem
8.
Zhongguo Yi Xue Ke Xue Yuan Xue Bao ; 39(5): 629-636, 2017 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-29125104

RESUMO

Objective To investigate the polymorphisms of 23 Y-STR loci in a Han population in Jiangsu province. Methods Blood samples were collected from 4821 unrelated healthy Han males in Jiangsu province. DNA templates were amplified by PowerPlex Y23 kit,and the amplification products were detected by 3500xL genetic analyzer. Then,we calculated the allele frequencies and gene diversities respectively,as well as the haplotype frequencies and haplotype diversities. Results The gene diversity of these 23 Y-STR loci ranged 0.4099-0.9696. A total of 4781 haplotypes were detected,of which 4743 were found once. The haplotype diversity was 0.99999812. Conclusion The 23 Y-STR loci used in this study are highly polymorphic in Han individuals in Jiangsu province and therefore suitable for population genetic study and forensic individual identification.


Assuntos
Povo Asiático/genética , Cromossomos Humanos Y/genética , Genética Populacional , Polimorfismo Genético , China , Frequência do Gene , Haplótipos , Humanos , Masculino , Repetições de Microssatélites
9.
Biosens Bioelectron ; 259: 116403, 2024 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-38776802

RESUMO

Robust encapsulation and controllable release of biomolecules have wide biomedical applications ranging from biosensing, drug delivery to information storage. However, conventional biomolecule encapsulation strategies have limitations in complicated operations, optical instability, and difficulty in decapsulation. Here, we report a simple, robust, and solvent-free biomolecule encapsulation strategy based on gallium liquid metal featuring low-temperature phase transition, self-healing, high hermetic sealing, and intrinsic resistance to optical damage. We sandwiched the biomolecules with the solid gallium films followed by low-temperature welding of the films for direct sealing. The gallium can not only protect DNA and enzymes from various physical and chemical damages but also allow the on-demand release of biomolecules by applying vibration to break the liquid gallium. We demonstrated that a DNA-coded image file can be recovered with up to 99.9% sequence retention after an accelerated aging test. We also showed the practical applications of the controllable release of bioreagents in a one-pot RPA-CRISPR/Cas12a reaction for SARS-COV-2 screening with a low detection limit of 10 copies within 40 min. This work may facilitate the development of robust and stimuli-responsive biomolecule capsules by using low-melting metals for biotechnology.


Assuntos
Técnicas Biossensoriais , Transição de Fase , SARS-CoV-2 , Técnicas Biossensoriais/métodos , SARS-CoV-2/isolamento & purificação , COVID-19/virologia , Gálio/química , Humanos , DNA/química , Sistemas CRISPR-Cas , Cápsulas/química
10.
Adv Sci (Weinh) ; 10(10): e2206201, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36737843

RESUMO

DNA has been pursued as a novel biomaterial for digital data storage. While large-scale data storage and random access have been achieved in DNA oligonucleotide pools, repeated data accessing requires constant data replenishment, and these implementations are confined in professional facilities. Here, a mobile data storage system in the genome of the extremophile Halomonas bluephagenesis, which enables dual-mode storage, dynamic data maintenance, rapid readout, and robust recovery. The system relies on two key components: A versatile genetic toolbox for the integration of 10-100 kb scale synthetic DNA into H. bluephagenesis genome and an efficient error correction coding scheme targeting noisy nanopore sequencing reads. The storage and repeated retrieval of 5 KB data under non-laboratory conditions are demonstrated. The work highlights the potential of DNA data storage in domestic and field scenarios, and expands its application domain from archival data to frequently accessed data.


Assuntos
Extremófilos , Análise de Sequência de DNA , Armazenamento e Recuperação da Informação , DNA/genética , Genômica
11.
J Cancer Res Clin Oncol ; 149(12): 9927-9935, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37249648

RESUMO

PURPOSE: In cohort studies on liver cancer, there are often immortal time bias and interference of competing risk events. This study proposes to explore the role of internal and external radiotherapy for hepatocellular carcinoma using SEER data, using a competing risk model and controlling immortal time bias. METHODS: Data of SEER from 2004 till 2015 was included. To analyze whether there was a difference in survival between HCC (hepatocellular carcinoma) patients receiving external radiation and internal radiation, we used a competing risk analysis after excluding immortal time bias, and created a nomogram to assess the risk of cancer-specific death (CSD) in hepatocellular carcinoma patients receiving radiotherapy. RESULTS: Potential confounding factors adjusted, there was no significant difference in CSD between external and internal radiation therapy [HR and its 95% CI = 1.098 (0.874-1.380)]. The constructed nomogram performed better than the traditional AJCC model. The AUC and calibration curve results showed that this well-calibrated nomogram could be used to make clinical decisions regarding the prognosis and personalized treatment of hepatocellular carcinoma treated. There was no difference in the cumulative risk of death between patients with liver cancer treated with external radiation therapy and internal radiation therapy. CONCLUSION: There is no difference in the cumulative risk of death between patients with liver cancer treated with external radiation therapy and internal radiation therapy. The nomogram predicts the results more accurately. These results can be used to guide the choice of treatment options for patients with HCC and to predict their survival prognosis.


Assuntos
Carcinoma Hepatocelular , Neoplasias Hepáticas , Humanos , Carcinoma Hepatocelular/radioterapia , Carcinoma Hepatocelular/patologia , Neoplasias Hepáticas/radioterapia , Neoplasias Hepáticas/patologia , Nomogramas , Prognóstico , Medição de Risco
12.
Nat Commun ; 14(1): 6487, 2023 10 14.
Artigo em Inglês | MEDLINE | ID: mdl-37838746

RESUMO

Synthetic auxotrophy in which cell viability depends on the presence of an unnatural amino acid (unAA) provides a powerful strategy to restrict unwanted propagation of genetically modified organisms (GMOs) in open environments and potentially prevent industrial espionage. Here, we describe a generic approach for robust biocontainment of budding yeast dependent on unAA. By understanding escape mechanisms, we specifically optimize our strategies by introducing designed "immunity" to the generation of amber-suppressor tRNAs and developing the transcriptional- and translational-based biocontainment switch. We further develop a fitness-oriented screening method to easily obtain multiplex safeguard strains that exhibit robust growth and undetectable escape frequency (<~10-9) on solid media for 14 days. Finally, we show that employing our multiplex safeguard system could restrict the proliferation of strains of interest in a real fermentation scenario, highlighting the great potential of our yeast biocontainment strategy to protect the industrial proprietary strains.


Assuntos
Aminoácidos , Saccharomyces cerevisiae , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Aminoácidos/metabolismo , Organismos Geneticamente Modificados , RNA de Transferência/metabolismo
13.
Zhonghua Yi Xue Za Zhi ; 92(47): 3341-4, 2012 Dec 18.
Artigo em Zh | MEDLINE | ID: mdl-23328595

RESUMO

OBJECTIVE: To observe the expression changes of Sirt1 gene and examine the role and significance of degenerative process in human cervical endplate chondrocytes through a degeneration model of human cervical vertebral endplate chondrocyte. METHODS: Cartilage endplates of 30 patients were divided into control group (n = 16) with cervical vertebral fracture or dislocation and cervical spondylosis group (n = 14) with cervical spondylotic myelopathy. Endplate chondrocytes were isolated by enzyme digestion and cultured in vitro for 10 days. The differences of endplate chondrocytes from normal and degenerative cartilage endplates were observed by inverted phase-contrast microscope, hematoxylin and eosin staining and toluidine blue staining. Real-time reverse transcription-polymerase chain reaction (RT-PCR) and Western blot were used to detect the mRNA expressions of Sirt1, collagen II and aggrecan. RESULTS: Compared with the normal group, the cellular morphology of degenerative group showed spindle-shaped changes. The mRNA expression of Sirt1 (P = 0.034) significantly decreased. Aggrecan (P = 0.0063) and collagen II (P = 0.0072) decreased also markedly. CONCLUSION: Sirt1 gene expression is significantly down-regulated in degenerative human cervical endplate chondrocytes. Regulating the expression of Sirt1 gene may block or delay the occurrence of human cervical endplate cartilage degeneration.


Assuntos
Vértebras Cervicais/patologia , Condrócitos/patologia , Sirtuína 1/genética , Adulto , Idoso , Células Cultivadas , Vértebras Cervicais/citologia , Condrócitos/citologia , Condrócitos/metabolismo , Regulação para Baixo , Feminino , Regulação da Expressão Gênica , Humanos , Masculino , Pessoa de Meia-Idade , Doenças da Medula Espinal/patologia , Espondilose/patologia
14.
Biol Trace Elem Res ; 200(2): 543-550, 2022 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33844169

RESUMO

To evaluate the association between selenoprotein gene polymorphisms and Kashin-Beck disease (KBD) susceptibility through a systematic review and updated meta-analysis. PubMed, Google Scholar, Cochrane library, and Chinese National Knowledge Infrastructure (CNKI) were electronically searched using the terms "selenoprotein" and "Kashin-Beck disease" or "KBD" with a search time from the establishment of the database to January 2021. The Newcastle-Ottawa Scale (NOS) was used for methodological quality evaluation of the included studies. Stata 14.0 software was used to pooled odds ratio (OR) and 95% confidence interval. There were a total of eight included case-control studies covering 2025 KBD patients and 1962 controls. Meta-analysis results show that the pooled odds ratios (OR) and 95% confidence intervals (CI) for DIO2 (rs225014) were 0.69 (0.52, 0.91), 0.69 (0.50, 0.96), and 0.72 (0.52, 0.99) in the allele, heterozygote, and dominant models, respectively. The OR and 95%CI for SEPS1 (-105G>A) were 2.47 (1.85, 3.29), 9.36 (4.58, 19.12), 2.17 (1.53, 3.08), and 8.60 (4.25, 17.38) in the allele, homozygote, dominant, and recessive models, respectively. In addition, the OR and 95%CI for Sep15 (rs5859) were 2.05 (1.06, 3.96) in the allele model. These results illustrate that there was a significant association between DIO2 (rs225014), SEPS1 (-105G>A), Sep15 (rs5859), and KBD. For GPX1 (rs1050450, rs1800668, rs3811699), DIO2 (rs225014, rs1352815, rs1388382), TrxR2 (rs1139793, rs5746841), GPX4 (rs713041, rs4807542), and SEPP1 (rs7579, 25191g/a), there was no significant statistical difference between the KBD and control groups (P>0.05). We conclude that the DIO2 (rs225014), SEPS1 (-105G>A), and Sep15 (rs5859) gene polymorphism are associated with susceptibility to KBD.


Assuntos
Doença de Kashin-Bek , Povo Asiático , Estudos de Casos e Controles , Predisposição Genética para Doença , Humanos , Doença de Kashin-Bek/genética , Polimorfismo de Nucleotídeo Único/genética , Selenoproteína P , Selenoproteínas/genética
15.
Nat Comput Sci ; 2(4): 234-242, 2022 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38177542

RESUMO

DNA is a promising data storage medium due to its remarkable durability and space-efficient storage. Early bit-to-base transcoding schemes have primarily pursued information density, at the expense of introducing biocompatibility challenges or decoding failure. Here we propose a robust transcoding algorithm named the yin-yang codec, using two rules to encode two binary bits into one nucleotide, to generate DNA sequences that are highly compatible with synthesis and sequencing technologies. We encoded two representative file formats and stored them in vitro as 200 nt oligo pools and in vivo as a ~54 kbps DNA fragment in yeast cells. Sequencing results show that the yin-yang codec exhibits high robustness and reliability for a wide variety of data types, with an average recovery rate of 99.9% above 104 molecule copies and an achieved recovery rate of 87.53% at ≤102 copies. Additionally, the in vivo storage demonstration achieved an experimentally measured physical density close to the theoretical maximum.

16.
Lipids Health Dis ; 10: 108, 2011 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-21711568

RESUMO

BACKGROUND: The purpose of this study was to identify the affect on the proliferation Eca-109 cells treated with oxidized low-density lipoprotein (ox-LDL) combined with adriamycin (ADM). METHODS: Eca-109 cell were cultured in the presence of oxLDL/ADM, and cell proliferation tested by MTT and cell apoptosis was monitored by the proportion of apoptosis and cell cycle by flow cytomester. We simultaneously evaluated the level of associated- apoptosis Bcl-2, Bax, and Caspase-3 gene mRNA and protein. RESULTS: OxLDL were cytotoxic and activate apoptosis. OxLDL combined with ADM significant enhanced the proportion rate of apoptosis on a time and dose dependency. The expressions of the inhibiting apoptosis Bcl-2 gene mRNA and protein were down regulated, whereas, the expressions of the promoting apoptosis Bax, and Caspase-3 genes mRNA and protein were up regulation. CONCLUSION: These results suggested that oxLDL have cytotoxicity and activate apoptosis on the Eca-109 cells. OxLDL combined with ADM have a synergistic effect on the apoptosis induced Eca-109 cells. Furthermore, oxLDL may contribute to the improvement of clinical chemotherapy of cancer need to make further investigation.


Assuntos
Proliferação de Células/efeitos dos fármacos , Doxorrubicina/farmacologia , Lipoproteínas LDL/farmacologia , Apoptose , Carcinoma de Células Escamosas , Caspase 3/genética , Caspase 3/metabolismo , Ciclo Celular/efeitos dos fármacos , Linhagem Celular Tumoral , Forma Celular/efeitos dos fármacos , Sobrevivência Celular/efeitos dos fármacos , Sinergismo Farmacológico , Neoplasias Esofágicas , Humanos , Proteínas Proto-Oncogênicas c-bcl-2/genética , Proteínas Proto-Oncogênicas c-bcl-2/metabolismo , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Transcrição Gênica
17.
Bioengineering (Basel) ; 8(1)2021 Jan 19.
Artigo em Inglês | MEDLINE | ID: mdl-33477926

RESUMO

Synthetic biology allows the re-engineering of biological systems and promotes the development of bioengineering to a whole new level, showing great potential in biomanufacturing. Here, in order to make the heterologous lycopene biosynthesis pathway compatible with the host strain YSy 200, we evolved YSy200 using a unique Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) system that is built in the Sc2.0 synthetic yeast. By inducing SCRaMbLE, we successfully identified a host strain YSy201 that can be served as a suitable host to maintain the heterologous lycopene biosynthesis pathway. Then, we optimized the lycopene biosynthesis pathway and further integrated into the rDNA arrays of YSy201 to increase its copy number. In combination with culturing condition optimization, we successfully screened out the final yeast strain YSy222, which showed a 129.5-fold increase of lycopene yield in comparison with its parental strain. Our work shows that, the strategy of combining the engineering efforts on both the lycopene biosynthesis pathway and the host strain can improve the compatibility between the heterologous pathway and the host strain, which can further effectively increase the yield of the target product.

18.
Natl Sci Rev ; 7(6): 1092-1107, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-34692128

RESUMO

The global demand for data storage is currently outpacing the world's storage capabilities. DNA, the carrier of natural genetic information, offers a stable, resource- and energy-efficient and sustainable data storage solution. In this review, we summarize the fundamental theory, research history, and technical challenges of DNA storage. From a quantitative perspective, we evaluate the prospect of DNA, and organic polymers in general, as a novel class of data storage medium.

19.
J Phys Chem Lett ; 11(24): 10354-10361, 2020 Dec 17.
Artigo em Inglês | MEDLINE | ID: mdl-33232153

RESUMO

We report a time-domain ab initio simulation of charge carrier trapping and relaxation dynamics in pristine and defect-containing kesterite Cu2ZnSnS4 (CZTS) structures. Our simulations show that introduction of a neutral sulfur vacancy in the CZTS system leads to a decrease of the charge recombination rate by a factor of ∼4, and the doubly positively charged sulfur vacancy results in a minor decrease of carrier lifetime, as compared to the pristine CZTS system. The neutral sulfur vacancy weakens the nonadiabatic (NA) electron-phonon coupling by moderately localizing charge density and accelerates the pure dephasing process, extending charge carrier lifetime. Therefore, the neutral sulfur vacancy is electrically benign. The doubly positively charged sulfur vacancy introduces a subgap state which is hardly populated, and recombination of the electron and hole bypassing the trap state dominates. As a result, the recombination rate decreases in the doubly charged sulfur vacancy structure. The reported results identified the key role of the sulfur-related vacancy on charge carrier trapping and relaxation of CZTS materials, carrying important implications for further optimization of CZTS and other thin-film solar cell materials.

20.
Fitoterapia ; 147: 104731, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32979466

RESUMO

Two new steroidal alkaloids (1-2), together with seven known related steroidal alkaloids (3-9), were isolated from the rhizomes of Veratrum nigrum L. Their structures were elucidated by extensive spectroscopic analysis, and by comparison with literature data. Compound 1 possessed a rare 1, 3-oxazolidine unit within varazine-type alkaloids, and 2 was a 9-hydroxy-4-one derivative of 3-veratroylgermine. All isolates were evaluated inhibit tomato yellow leaf curl virus (TYLCV) activity. Compounds 5 and 7 (40 µg/mL) showed a significant anti-TYLCV activity in the host Nicotiana benthamiana with inhibition rates 74.6% and 63.4%, respectively, which are higher than that of the positive control ningnanmycin (51.4%).


Assuntos
Alcaloides/farmacologia , Begomovirus/efeitos dos fármacos , Doenças das Plantas/prevenção & controle , Esteroides/farmacologia , Veratrum/química , Alcaloides/isolamento & purificação , China , Estrutura Molecular , Compostos Fitoquímicos/isolamento & purificação , Compostos Fitoquímicos/farmacologia , Doenças das Plantas/virologia , Rizoma/química , Esteroides/isolamento & purificação , Nicotiana/virologia
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