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1.
Yi Chuan ; 45(4): 354-363, 2023 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-37077168

RESUMEN

Drosophila is a crucial biological experimental teaching material extensively utilized in experimental teaching. In this experimental teaching, each student typically needs to manually identify hundreds of fruit flies and record multiple of each fly. This task involves substantial workload, and the classification standards can be inconsistent. To address this issue, we introduce a deep convolutional neural network that classifies the traits of every fruit fly, using a two-stage consisting of an object detector and a trait classifier. We propose a keypoint-assisted classification model with tailored training session for the trait classification task and significantly enhanced the model interpretability. Additionally, we've enhanced the RandAugment method to better fit the features of our task. The model is trained with progressive learning and adaptive regularization under limited computational resources. The final classification model, which utilizes MobileNetV3 as backbone, achieves an accuracy of 97.5%, 97.5% and 98% for the eyes, wings, gender tasks, respectively. After optimization, the model is highly lightweight, classifying 600 fruit fly traits from raw images in 10 seconds and having a size less than 5 MB. It can be easily deployed on any android device. The development of this system is conducive to promoting the experimental teaching, such as verifying genetic laws with Drosophila as the research object. It can also be used for scientific research involving a large number of Drosophila classifications, statistics and analyses.


Asunto(s)
Drosophila , Redes Neurales de la Computación , Animales , Drosophila/genética , Computadores , Tecnología
2.
Am J Hematol ; 98(1): 66-78, 2023 01.
Artículo en Inglés | MEDLINE | ID: mdl-36219502

RESUMEN

Mixed phenotype acute leukemia (MPAL) is a subtype of leukemia in which lymphoid and myeloid markers are co-expressed. Knowledge regarding the genetic features of MPAL is lacking due to its rarity and heterogeneity. Here, we applied an integrated genomic and transcriptomic approach to explore the molecular characteristics of 176 adult patients with MPAL, including 86 patients with T-lymphoid/myeloid MPAL (T/My MPAL-NOS), 42 with Ph+ MPAL, 36 with B-lymphoid/myeloid MPAL (B/My MPAL-NOS), 4 with t(v;11q23), and 8 with MPAL, NOS, rare types. Genetically, T/My MPAL-NOS was similar to B/T MPAL-NOS but differed from Ph+ MPAL and B/My MPAL-NOS. T/My MPAL-NOS exhibited higher CEBPA, DNMT3A, and NOTCH1 mutations. Ph+ MPAL demonstrated higher RUNX1 mutations. B/T MPAL-NOS showed higher NOTCH1 mutations. By integrating next-generation sequencing and RNA sequencing data of 89 MPAL patients, we defined eight molecular subgroups (G1-G8) with distinct mutational and gene expression characteristics. G1 was associated with CEBPA mutations, G2 and G3 with NOTCH1 mutations, G4 with BCL11B rearrangement and FLT3 mutations, G5 and G8 with BCR::ABL1 fusion, G6 with KMT2A rearrangement/KMT2A rearrangement-like features, and G7 with ZNF384 rearrangement/ZNF384 rearrangement-like characteristics. Subsequently, we analyzed single-cell RNA sequencing data from five patients. Groups G1, G2, G3, and G4 exhibited overexpression of hematopoietic stem cell disease-like and common myeloid progenitor disease-like signatures, G5 and G6 had high expression of granulocyte-monocyte progenitor disease-like and monocyte disease-like signatures, and G7 and G8 had common lymphoid progenitor disease-like signatures. Collectively, our findings indicate that integrative genomic and transcriptomic profiling may facilitate more precise diagnosis and develop better treatment options for MPAL.


Asunto(s)
Leucemia Mieloide Aguda , Transcriptoma , Humanos , Enfermedad Aguda , Fenotipo , Genómica
3.
Gene ; 820: 146289, 2022 Apr 30.
Artículo en Inglés | MEDLINE | ID: mdl-35143940

RESUMEN

Reactivation of fetal hemoglobin by editing the B-cell lymphoma/leukemia 11A (BCL11A) erythroid enhancer is an effective gene therapy for ß-thalassemia. Using the CRISPR/Cas9 system, fetal γ-globin expression can be robustly reactivated to mitigate the clinical course of ß-thalassemia. In our study, we found that the transfection efficiencies of CD34+ hematopoietic stem/progenitor cells (HSPCs) were significantly and negatively correlated with the length of plasmids and greatly affected by the linearization of plasmids. Furthermore, the transgene expression of minicircles (MC) without plasmid backbone sequences was better both in vitro and in vivo compared with conventional plasmids. Thus, MC DNA was used to deliver the cassette of Staphylococcus aureus Cas9 (SaCas9) into HSPCs, and a single-guide RNA targeting the erythroid enhancer region of BCL11A was selected. After electroporation with MC DNA, an evident efficiency of gene editing and reactivation of γ-globin expression in erythroblasts derived from unsorted HSPCs was acquired. No significant off-target effects were found by deep sequencing. Furthermore, fragments derived from lentiviral vectors, but not MC DNA, were highly enriched in promoter, exon, intron, distal-intergenic, and cancer-associated genes, indicating that MC DNA provided a relatively safe and efficient vector for delivering transgenes. The developed MC DNA vector provided a potential approach for the delivery of SaCas9 cassette and the reactivation of γ-globin expression for ameliorating syndromes of ß-thalassemia.


Asunto(s)
ADN Circular/uso terapéutico , Hemoglobina Fetal/metabolismo , Proteínas Represoras/metabolismo , Talasemia beta/genética , Talasemia beta/terapia , gamma-Globinas/genética , gamma-Globinas/metabolismo , Animales , Proteínas Bacterianas/metabolismo , Proteína 9 Asociada a CRISPR/metabolismo , Sistemas CRISPR-Cas , ADN Circular/metabolismo , Edición Génica , Terapia Genética/métodos , Vectores Genéticos , Células Madre Hematopoyéticas/metabolismo , Humanos , Masculino , Ratones , Ratones Endogámicos C57BL , Plásmidos , Regiones Promotoras Genéticas , ARN Guía de Kinetoplastida/metabolismo , ARN Guía de Kinetoplastida/uso terapéutico
4.
Yi Chuan ; 43(4): 362-374, 2021 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-33972210

RESUMEN

The emerging cleavage under target and tagment (CUT&Tag) technology uses Tn5 transposase to cleavage near the DNA binding site of target protein and study the generated DNA fragments by the next-generation sequencing. It can quickly identify protein-DNA interactions, which greatly simplifies the experimental process of ChIP-Seq. After CUT&Tag tagment reaction, DNA recovery or other post-processing is required to perform library construction PCR. Different recovery methods have significant impact respectively. By establishing Streptavidin beads recovery CUT&Tag(srCUT&Tag), we can quickly and conveniently complete the product recovery of CUT&Tag. We carried out CUT&Tag assay of H3K4me3, RNA Polymerase II (RNA polymerase II, RNAPII), transcription factor CTCF and HMGA1 in K562 cells with different recovery methods, including ethanol precipitation, fragment separation magnetic beads (SPRI) Magnetic bead recovery, direct PCR method, as well as our srCUT&Tag recovery method. The results show that among the CUT&Tag results of four different targets, the SPRI magnetic bead recovery and our srCUT&Tag methods have higher recovery efficiency than the direct PCR method and ethanol precipitation method. All CUT&Tag results showed that the recovery of SPRI magnetic beads would lose most of the product fragments less than 150 bp. In the recovery of CTCF and HMGA1, direct PCR lost most of the fragments larger than 300 bp and has significant difference from result of other recovery method. This enables srCUT&Tag to provide more real and higher-resolution information than other recovery method. In summary, the newly established srCUT&Tag recovery method can improve the efficiency of CUT&Tag library construction and obtain better data quality compared with the existing CUT&Tag product recovery method, providing a better technical choice for epigenetics research.


Asunto(s)
ADN , Secuenciación de Nucleótidos de Alto Rendimiento , Sitios de Unión , Epigenómica , Biblioteca de Genes , Análisis de Secuencia de ADN
5.
Biochem Biophys Res Commun ; 552: 157-163, 2021 05 07.
Artículo en Inglés | MEDLINE | ID: mdl-33744764

RESUMEN

ß-Thalassemia is an autosomal recessive genetic disease caused by defects in the production of adult hemoglobin (HbA, α2ß2), which leads to an imbalance between α- and non-α-globin chains. Reactivation of γ-globin expression is an effective strategy to treat ß-thalassemia patients. Previously, it was demonstrated that hemoglobin subunit beta pseudogene 1 (HBBP1) is associated with elevated fetal hemoglobin (HbF, α2γ2) in ß-thalassemia patients. However, the mechanism underlying HBBP1-mediated HbF production is unknown. In this study, using bioinformatics analysis, we found that HBBP1 is involved in γ-globin production, and then preliminarily confirmed this finding in K562 cells. When HBBP1 was overexpressed, γ-globin expression was increased at the transcript and protein levels in HUDEP-2 cells. Next, we found that ETS transcription factor ELK1 (ELK1) binds to the HBBP1 proximal promoter and significantly promotes its activity. Moreover, the synthesis of γ-globin was enhanced when ELK1 was overexpressed in HUDEP-2 cells. Surprisingly, ELK1 also directly bound to and activated the γ-globin proximal promoter. Furthermore, we found that HBBP1 and ELK1 can interact with each other in HUDEP-2 cells. Collectively, these findings suggest that HBBP1 can induce γ-globin by enhancing ELK1 expression, providing some clues for γ-globin reactivation in ß-thalassemia.


Asunto(s)
Regulación de la Expresión Génica , ARN Largo no Codificante/genética , Talasemia beta/genética , Proteína Elk-1 con Dominio ets/genética , gamma-Globinas/genética , Diferenciación Celular/genética , Línea Celular , Células Precursoras Eritroides/metabolismo , Perfilación de la Expresión Génica/métodos , Humanos , Células K562 , Interferencia de ARN , Talasemia beta/metabolismo , Proteína Elk-1 con Dominio ets/metabolismo , gamma-Globinas/metabolismo
6.
J Hum Genet ; 65(10): 823-829, 2020 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-32427951

RESUMEN

Human Y-chromosome haplogroup C2b-F1067 is one of the dominant paternal lineages of populations in Eastern Eurasia. In order to explore the origin, diversification, and expansion of this haplogroup, we generated 206 new Y-chromosome sequences from C2b-F1067 males and coanalyzed 220 Y-chromosome sequences of this haplogroup. BEAST software was used to reconstruct a revised phylogenetic tree of haplogroup C2b-F1067 with age estimates. The revised phylogeny of C2b-F1067 included 155 sublineages, 1986 non-private variants, and >6000 private variants. The age estimation suggested that the initial splitting of C2b-F1067 happened at about 32.8 thousand years ago (kya) and the major sublineages of this haplgroup experienced continuous expansion in the most recent 10,000 years. We identified numerous sublineages that were nearly specific for Korean, Mongolian, Chinese, and other ethnic minorities in China. In particular, we evaluated the candidate-specific lineage for the Dayan Khan family and the Confucius family, the descendants of the ruling family of the Chinese Shang dynasty. These findings suggest that ancient populations with varied C2b-F1067 sublineages played an important role during the formation of most modern populations in Eastern Eurasia, and thus eventually became the founding paternal lineages of these populations.


Asunto(s)
Pueblo Asiatico/genética , Cromosomas Humanos Y/genética , Etnicidad/genética , Haplotipos/genética , Migración Humana , Filogenia , Pueblo Asiatico/clasificación , Pueblo Asiatico/historia , Etnicidad/historia , Asia Oriental , Historia Antigua , Humanos , Masculino , Paternidad , Polimorfismo de Nucleótido Simple
7.
Yi Chuan ; 41(5): 439-446, 2019 May 20.
Artículo en Chino | MEDLINE | ID: mdl-31106780

RESUMEN

Genetics is a branch of biology that studies the laws of inheritance and variation from the level of genes (genomes). Genetics teaching should be compatible with the evolving genetic disciplines and social needs. In view of the continuous development of the genetics knowledge system and the requirements for the training of biological students, our teaching team carried out the curriculum design and implementation of genetics blended course under the principle of constructive alignment. The reform actions include: (1) constructing genetics online resources with genetic analysis as the main line; (2) optimizing the learning objectives according to bloom's educational goals classification; (3) designing learning activities and learning assessments under the principle of constructive alignment; (4) enrich the forms of learning activities, highlighting learning-centered course design and learner interaction, promoting active learning, and improving learning outcomes. The results of the questionnaire survey and exam result analysis suggest that the blended course reform has achieved initial results. The course is fully affirmed by the students and helps to improve learning outcomes, which is worthy of further consolidation and promotion. This paper generally introduces the curriculum design and preliminary practice of genetics blended course, providing new insights and approaches for the continued development of genetics teaching in the new era.


Asunto(s)
Curriculum , Genética/educación , Humanos , Investigación , Estudiantes , Enseñanza
8.
Yi Chuan ; 41(4): 318-326, 2019 Apr 20.
Artículo en Chino | MEDLINE | ID: mdl-30992253

RESUMEN

Breast cancer is one of the most common malignant tumors endangering women. It has been found that the subunits of the COP9 complex are closely related to the occurrence and development of malignant tumors, and the CSN4 subunit plays an important role in regulating the whole complex. In the breast cancer cell line MDA-MB-231, we successfully established a lentivirus-mediated CSN4-knockdown cell line. CCK8 cell proliferation assays and colony formation experiments confirmed that CSN4 knockdown significantly decreased the cellular proliferation rate. Cell cycle analysis showed that CSN4 knockdown increased sub-G1 population and induced apoptosis. In addition, Western blotting assays confirmed that CSN4 regulates the expression of CDK6 and Caspase3, suggesting that CSN4 modulates the proliferation and apoptosis of breast cancer cells by regulating the expression of CDK6 and Caspase3 genes and thereby tumorigenesis. This study has deepened our understanding of the molecular mechanism of apoptosis and cell growth in breast cancers, and further revealed the role and mechanism of CSN4 in cancer biology.


Asunto(s)
Proteínas Adaptadoras Transductoras de Señales/genética , Apoptosis , Neoplasias de la Mama/genética , Neoplasias de la Mama/patología , Complejo del Señalosoma COP9/genética , Proliferación Celular , Caspasa 3/metabolismo , Línea Celular Tumoral , Quinasa 6 Dependiente de la Ciclina/metabolismo , Femenino , Regulación Neoplásica de la Expresión Génica , Técnicas de Silenciamiento del Gen , Humanos
9.
Cancer Med ; 8(4): 1633-1640, 2019 04.
Artículo en Inglés | MEDLINE | ID: mdl-30864275

RESUMEN

The goal of this study was to evaluate the feasibility of detecting Helicobacter pylori clarithromycin resistance in gastric mucosa using the amplification refractory mutation system combined with quantitative real-time PCR (ARMS-PCR). Gastric mucosal specimens (150) were collected from patients who were unsuccessfully treated for H. pylori eradication. Each specimen was divided into 2 samples. One sample was used to extract genomic DNA and detect any gene mutations of H. pylori produced by ARMS- PCR. Sequencing was used to assess the accuracy of this method. The other sample was used to culture H. pylori. The E-test minimum inhibitory concentration (MIC) was used to assess clarithromycin resistance. The results were compared with a paired chi-square test to validate the coincidence rate among the 3 methods. The coincidence rate between the sequencing and ARMS-PCR results was 98.7%, thus verifying the accuracy of ARMS-PCR. E-tests detected 144 clarithromycin resistance cases, including 45 sensitivity cases; the resistance rate was 70%. The coincidence rate between the results of the E-test and ARMS-PCR was 97.1%, and no significant difference between the 2 methods was observed. ARMS-PCR is a simple and fast method that has high sensitivity and specificity and can be used to detect the clarithromycin resistance of H. pylori in gastric mucosa. ARMS-PCR is expected to be used to study drug resistance mechanisms and use in assays of individual therapies for H. pylori eradication.


Asunto(s)
Antibacterianos/farmacología , Claritromicina/farmacología , Mucosa Gástrica/microbiología , Infecciones por Helicobacter/microbiología , Helicobacter pylori/efectos de los fármacos , Helicobacter pylori/genética , Mutación , Farmacorresistencia Bacteriana , Amplificación de Genes , Humanos , Pruebas de Sensibilidad Microbiana , Reacción en Cadena en Tiempo Real de la Polimerasa
10.
Yi Chuan ; 40(10): 916-923, 2018 Oct 20.
Artículo en Chino | MEDLINE | ID: mdl-30369473

RESUMEN

Chinese genetics educators have carried out a comprehensive and systematic exploration and reform since 1978. With the guidance and help of the Genetics Society of China, they have made significant strides in the fields of genetics teaching system, publication of genetics textbooks, content of genetics teaching, workshop on genetics teaching, experimental teaching, application of advanced techniques, etc. These efforts have made remarkable achievements and promoted the vitality of genetics. The comprehensive development of education and teaching has trained a large number of excellent genetic talents for the development of China's economy and society. Here, we sum up the overall achievements of the teaching reform and propose some suggestions on the future development of genetics teaching in China, hoping that the quality of genetics teaching in China will take a new step in the new era.


Asunto(s)
Genética/educación , Enseñanza/historia , China , Genética/historia , Genética/normas , Historia del Siglo XX , Historia del Siglo XXI , Humanos , Enseñanza/educación , Enseñanza/normas
11.
Oncol Rep ; 39(3): 1011-1022, 2018 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-29399702

RESUMEN

Glioma is the most aggressive and malignant primary brain tumor in adults. In the present study, we identified a vital oncoprotein, capping actin protein, gelsolin-like (CapG), and investigated its roles in the prognosis, proliferation and metastasis in glioma. The mRNA and protein levels of CapG were significantly increased in human glioma, and higher CapG expression was an independent prognostic factor for predicting unfavorable prognosis. The expression level of CapG was found to be associated with several common molecular features of glioblastoma (GBM; WHO grade IV glioma) in The Cancer Genome Atlas (TCGA) cohort. When analyzing the prognosis of GBM patients according to these molecular features, we observed that the prognostic value of CapG was affected by amplification of CDK6 or EGFR. However, overexpression of CapG markedly promoted cell growth in vitro, while depletion of CapG significantly inhibited cell proliferation by blocking the cell cycle in G1/S transition. Moreover, CapG manipulation in glioma cell lines U87 and U251 showed CapG-dependent cellular migration and invasiveness. These data suggest that CapG may serve as a prognostic biomarker with potentially important therapeutic implications for glioma.


Asunto(s)
Neoplasias Encefálicas/metabolismo , Glioma/metabolismo , Proteínas de Microfilamentos/metabolismo , Proteínas Nucleares/metabolismo , Biomarcadores de Tumor/genética , Biomarcadores de Tumor/metabolismo , Neoplasias Encefálicas/mortalidad , Neoplasias Encefálicas/patología , Neoplasias Encefálicas/secundario , Línea Celular Tumoral , Movimiento Celular , Proliferación Celular , Puntos de Control de la Fase G1 del Ciclo Celular , Expresión Génica , Glioma/mortalidad , Glioma/patología , Glioma/secundario , Humanos , Proteínas de Microfilamentos/biosíntesis , Proteínas de Microfilamentos/genética , Invasividad Neoplásica , Proteínas Nucleares/biosíntesis , Proteínas Nucleares/genética , Pronóstico
12.
Am J Cancer Res ; 7(6): 1384-1388, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28670498

RESUMEN

Hepatocellular carcinoma (HCC) is a big problem in China where the Hepatitis B (HBV) infection patients are near to 120 million. Early screening and diagnosis is the key to reduce the incidence and mortality of HCC. Serum AFP detection is the main methods for diagnosis, recurrent monitoring and therapeutic evaluation of primary HCC. Hepatitis patients should detect the AFP at least once every six months to help early diagnosis of HCC. Unfortunately, most hepatitis and other liver disease patients do not test their AFP regularly. Therefore, a rapid, convenient detect kit for AFP is necessary for the hepatitis patients to test AFP at home by themselves. It will be very helpful to the HCC early screening and early diagnosis. We screened 859 individuals who were HBsAg positive and had high risk of HCC in Qidong by using two different kits, AFP one-step rapid detection kit (Shanghai Outdo Biotech) and AFP Diagnostics ELISA kit (Zhengzhou Autobio Diagnostics), and compared the results. As a result, the positive accordance rate and the negative accordance rate of AFP one-step rapid detection kit and the Autobio ELISA kit were 95.65% (22/23) and 99.40% (831/836), respectively. The total diagnose accordance rate reached up to 99.30% (853/859). The screening results showed a high accordance rate of two methods. It is so meaningful to achieve home-test and improve HCC early screening and diagnosis by using AFP one-step rapid detection kit.

13.
Yi Chuan ; 39(3): 250-262, 2017 03 20.
Artículo en Inglés | MEDLINE | ID: mdl-28420621

RESUMEN

Platinum-based chemotherapy is an important treatment for non-small cell lung cancer. However, the effectiveness of the treatment varies among the patients. We investigated the association between DNA polymorphisms of the autophagy pathway and responses of such treatment among 1004 Chinese patients. Ninety-nine SNPs located on 13 genes of the autophagy pathway were genotyped and assessed for their association with clinical benefit, progression-free survival (PFS) and overall survival (OS). The results showed that rs7953348 (G>A) (P=0.017, OR: 0.67, 95%CI: 0.49-0.93) and rs12303764 (A>C) (P=0.009, OR: 0.63, 95%CI: 0.45-0.89) at the ULK1 gene, and rs17742719 (C>A) (P=0.002, OR: 1.83, 95%CI: 1.26-2.66), rs8003279 (A>G) (P=0.006, OR: 1.65, 95%CI: 1.16~2.35) and rs1009647 (G>A) (P=0.002, OR: 1.70, 95%CI: 1.22-2.37) at the ATG14 gene were associated with clinical benefit. Polymorphisms at rs7955890 (G>A) (P=0.004, HR: 0.63; 95%CI: 0.46-0.86) and rs17032060 (G>A) (P=0.006, HR: 0.65, 95%CI: 0.48-0.88) at the DRAM gene, and rs13082005 (G>A) (P=0.012, HR: 1.27, 95%CI: 1.05-1.53) at the ATG3 gene were significantly associated with PFS. We also found that rs7953348 (G>A) (P=0.011, HR: 0.74, 95%CI: 0.58-0.93) at the ULK1 gene and rs1864183 (G>A) (P=0.016, HR: 0.42, 95%CI: 0.21-0.85) at the ATG10 gene were associated with OS. Thus, the study demonstrated that the autophagy pathway might play important role(s) in platinum-based chemotherapy. DNA polymorphisms in its component genes can potentially be predictors for clinical responses of platinum-based chemotherapy among the patients with non-small lung cancer.


Asunto(s)
Autofagia/genética , Carcinoma de Pulmón de Células no Pequeñas/genética , Platino (Metal)/uso terapéutico , Polimorfismo Genético/genética , Adulto , Anciano , Homólogo de la Proteína 1 Relacionada con la Autofagia/genética , Proteínas Relacionadas con la Autofagia/genética , Carcinoma de Pulmón de Células no Pequeñas/tratamiento farmacológico , Femenino , Genotipo , Humanos , Péptidos y Proteínas de Señalización Intracelular/genética , Masculino , Proteínas de la Membrana/genética , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple/genética , Enzimas Ubiquitina-Conjugadoras/genética , Proteínas de Transporte Vesicular/genética
14.
World J Gastroenterol ; 22(44): 9813-9821, 2016 Nov 28.
Artículo en Inglés | MEDLINE | ID: mdl-27956805

RESUMEN

AIM: To investigate the association between interferon-induced protein with tetratricopeptide repeats 1 (IFIT1) polymorphisms and interferon-α (IFNα) treatment efficiency among Chinese hepatitis B virus (HBV) infection patients. METHODS: Two hundred and twenty five newly diagnosed chronic hepatitis B (CHB) patients were enrolled in the study. All of these patients received IFNα treatment for a course of 48 wk, and were followed up for 24 wk after the treatment was end. Clinical information about virological response, hepatitis B e antigen (HBeAg) seroconversion rate and combined response at the end of the treatment, as well as the sustained response by the time of following up 24 wk after the treatment, was collected. Four tag-single nucleotide polymorphisms (SNPs) of IFIT1 were selected and assessed for their association with these clinical outcomes. RESULTS: At the end of the treatment, HBeAg seroconversion was observed in 27.1% patients. Thirty-six point nine percent patients achieved virological response, and 15.6% patients exhibited combined response. Sustained response was obtained in 26.2% patients. The main HBV genotype of the study was genotype B. Patients who infected with HBV genotype B or C showed better treatment efficiency, no matter which clinical outcome was considered. Among the four SNPs assessed, rs303218 (A > G) was found to be significantly associated with the end point virological response when assuming additive model [OR = 0.64 (95%CI: 0.42-0.96), P = 0.032]. Patients who carried rs303218 GG genotype had a rather higher rate of achieving virological response (response rate: 52%, OR = 0.40, 95%CI: 0.18-0.91; P = 0.028) when compared to those had AA genotype (response rate: 27%). The most significant interaction was observed in patients who had relative lower baseline aspartate transaminase. No association between SNPs and HBeAg seroconversion, combined response or sustained response was observed. CONCLUSION: IFIT1 involves in the regulation of IFNα treatment for CHB and its polymorphism rs303218 can predict the end point virological response. The finding requires further validation.


Asunto(s)
Antivirales/uso terapéutico , Proteínas Portadoras/genética , Virus de la Hepatitis B/efectos de los fármacos , Hepatitis B Crónica/tratamiento farmacológico , Interferón-alfa/uso terapéutico , Variantes Farmacogenómicas , Polimorfismo de Nucleótido Simple , Proteínas Adaptadoras Transductoras de Señales , Adolescente , Adulto , Biomarcadores/sangre , Distribución de Chi-Cuadrado , China , ADN Viral/sangre , Femenino , Genotipo , Antígenos e de la Hepatitis B/sangre , Virus de la Hepatitis B/genética , Virus de la Hepatitis B/inmunología , Hepatitis B Crónica/diagnóstico , Hepatitis B Crónica/genética , Humanos , Modelos Logísticos , Masculino , Persona de Mediana Edad , Oportunidad Relativa , Proteínas de Unión al ARN , Estudios Retrospectivos , Respuesta Virológica Sostenida , Factores de Tiempo , Resultado del Tratamiento , Adulto Joven
15.
Yi Chuan ; 38(4): 350-9, 2016 04.
Artículo en Inglés | MEDLINE | ID: mdl-27103458

RESUMEN

Hepatitis B virus (HBV) is a dented double-stranded DNA virus. After infecting human hepatic cells, it forms cccDNA that replicates persistently and integrates randomly into the host's genome during the process of reserve transcription. On average, in each cell with chronic HBV infection, there are about 33 copies of cccDNA with a half of 35-57 days, which can be difficult to eradicate. A new strategy is to inhibit HBV transcription by using locked nucleic acid (LNA). Besides, cleaving HBV genome by targeted genome editing technologies could potentially cure patients. In this study, we explored new genome editing tools for HBV treatment. Based on LNA's ability to form triple helix by binding to duplex DNA, its stability towards nuclease and polymerase, and its sensitivity to single base mismatches, we designed LNA-modified oligonucleotides as DNA binding domain to effectively increase the specificity of target gene recognition. Meanwhile, by utilizing the small molecular weight and dimerization dependent activity of nuclease Fok I, we used Fok I recombinant dimer protein as DNA cleavage domain. Here, we established a method by chemical coupling of LNA-oligonucleotide with Fok I cleavage domain, and also validated the targeted cleavage of HBV genes with our new tools in vitro. These results provide new possibilities for future in vivo anti-virus gene therapy with high specificity and no integration risk.


Asunto(s)
Desoxirribonucleasas de Localización Especificada Tipo II/química , Virus de la Hepatitis B/genética , Oligonucleótidos/química , Secuencia de Bases , Datos de Secuencia Molecular
16.
Yi Chuan ; 38(2): 163-9, 2016 02.
Artículo en Chino | MEDLINE | ID: mdl-26907780

RESUMEN

The traditional Type Ⅱ restriction enzyme-based method is restricted by the purification steps, and therefore, cannot be applied to specific DNA assembly in chaotic system. To solve this problem, Thermostable Ligase Chain Reaction (TLCR) was introduced in the process of DNA assembly and capture. This technique combines the feature of thermostable DNA ligase and sequence specific oligo ligation template, "Helper", to achieve specific assembly of target fragments and exponential increase of products in multiple thermocyclings. Two plasmid construction experiments were carried out in order to test the feasibility and practical performance of TLCR. One was that, TLCR was used to specifically capture a 1.5 kb fragment into vector from an unpurified chaotic system which contained 7 different sizes of fragments. The results showed that the capturing accuracy was around 80%, which proved the feasibility and accuracy of using TLCR to specific assembly of DNA fragments in a complicated mixed system. In the other experiment, TLCR was used to capture two fragments (total length was 27 kb) from Hind Ⅲ digestion of Lambda genome into vector by order. The results also showed an accuracy of around 80%. As demonstrated in the results, TLCR can simplify the process of DNA recombination experiments and is suitable for the assembly of multiple and large DNA fragments. This technique can provide convenience to biological experiments.


Asunto(s)
ADN Ligasas/metabolismo , ADN/genética , ADN/metabolismo , Reacción en Cadena de la Ligasa/métodos , Recombinación Genética , ADN Ligasa (ATP) , Estabilidad de Enzimas , Calor , Modelos Genéticos , Reacción en Cadena de la Polimerasa/métodos , Reproducibilidad de los Resultados
17.
Yi Chuan ; 37(11): 1143-8, 2015 11.
Artículo en Chino | MEDLINE | ID: mdl-26582528

RESUMEN

Hemophilia B, or the Christmas disease, is a common human disease caused by coagulation factor Ⅸ (FⅨ) deficiency. It is an X-linked recessive hereditary disease. Here we obtained FⅨ-knockout mouse strains with phenotype of hemophilia B with the CRISPR/Cas system efficiently. We chose the 8th exon as the target locus, and co-injected codon-optimized Cas9 mRNA with sgRNA of FⅨ into C57BL/6 mice zygotes. We obtained 60 mice in total and genotyped them by high resolution melting (HRM) and sequencing. The results showed the mutation rate was 85.0% in total, and 79.5% and 95.2% in males and females, respectively. No off-targets were detected in the similar locus by HRM. We future measured the FⅨ activity of each mice. The FⅨ: C of mutant mice were significantly below the normal level and reduced to 6.82% of wild-type mice. The activity assay demonstrated that all the mutant mice were lack of FⅨ. In summary, we have generated hemophilia B model mice with extreme efficiency, using the RNA-guided Cas9 nuclease gene editing system.


Asunto(s)
Sistemas CRISPR-Cas/genética , Modelos Animales de Enfermedad , Hemofilia B/genética , Animales , Secuencia de Bases , Femenino , Genotipo , Masculino , Ratones , Ratones Endogámicos C57BL , Datos de Secuencia Molecular , ARN Guía de Kinetoplastida/genética
19.
Fa Yi Xue Za Zhi ; 30(1): 50-1, 54, 2014 Feb.
Artículo en Chino | MEDLINE | ID: mdl-24804386

RESUMEN

OBJECTIVE: To extract sperm DNA from mixed stain by the modified differential lysis method combined with silicon bead method and to evaluate its application value. METHODS: Fifty-two mixed stains containing female STR genotypes detected by differential lysis method were collected. The sperm DNA was extracted by the modified method combined with silicon bead method, then genotyped with the Identifiler Kit, and compared with the results of genotyping by the conventional differential lysis method as control. RESULTS: Of the 52 samples, 38 samples with sole male STR genotypes in all loci were detected. The detection rate of male STR genotypes was 98.08% through the modified method combined with silicon bead method. CONCLUSION: The modified differential lysis method combined with silicon bead method can be used in extraction of sperm DNA from mixed stain.


Asunto(s)
Dermatoglifia del ADN , ADN/aislamiento & purificación , Espermatozoides , Femenino , Genotipo , Humanos , Masculino , Reacción en Cadena de la Polimerasa , Silicio
20.
Yi Chuan ; 35(8): 1040-4, 2013 Aug.
Artículo en Chino | MEDLINE | ID: mdl-23956093

RESUMEN

Blood type, which harbors abundant genetics meaning, is one of the most common phenotypes in human life. With the development of science and technology, its significance is unceasingly updated and new finding is increasingly emerging, which constantly attracts people to decipher the heredity mechanism of blood type. In addition to four main associated contents, i.e., Mendelian inheritance, genetic linkage, gene mutations, and chromosome abnormalities, the blood type case also covers many other aspects of the genetics knowledge. Based on the genetic knowledge context, we can interest the students and improve the teaching output in genetic teaching practice by combining with explaining ABO blood type case and heredity mechanism, expanding leucocyte groups, and introducing infrequent blood type such as Bombay blood, Rh and MN. By carrying out the related experimental teaching, we could drive the student to integrate theory with practice. In genetic experimental teaching, 80% of the students chose this optional experiment, molecular identification of ABO blood type, and it greatly interested them. Using appropriate blood type case in teaching related knowledge, organizing PPT exhi-bition and the debating discussion activities, it could provide opportunities for student to propose their own opinions, guide the student to thinking deeply, and develop their abilities to analyze and solve problem. Afterwards, students will gain in-depth comprehension about the fundamental knowledge of genetics.


Asunto(s)
Conocimiento , Estudiantes , Comprensión , Genética/educación , Humanos , Enseñanza , Tecnología
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