Single-Cell RNA Sequencing of Tumor-Infiltrating NK Cells Reveals that Inhibition of Transcription Factor HIF-1α Unleashes NK Cell Activity

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Molecular epidemiology of norovirus variants detected in children under five years of age in Hyderabad,India

PurposeNoroviruses are common viral agents in acute diarrhea in all age groups worldwide. Norovirus has been classified into 10 genogroups, GI to GX with over 48 genotypes among them the GII.4 genotype has evolved over time with a clear pattern of periodic variant replacement. Immunity is strain or genotype specific with little or no protection conferred across genogroups. The present study was aimed to determine the epidemiology, prevalent genotypes of norovirus in children below five years of age in the Hyderabad region, India.MethodsThe stool samples and clinical data were collected from 458 children below 5 years of age comprising of cases with acute gastroenteritis (n ?= ?366) and a control group (n ?= ?92) admitted to the pediatric ward. All the samples were tested for Norovirus by ELISA and RT-PCR. Sequencing was done for predominant strains.Results10.3% (n ?= ?38) of cases and 3.2% (n ?= ?3) of the control group were found to be Norovirus positive. Predominant genotypes were GII-82.5% followed by GI-12.5%.ConclusionSequencing and Phylogenetic analyses of 20 GII.4 strains was done. All of the isolates are clustered away from published the GII.4 variants thus suggesting the appearance of a new variant.     

Sequence analysis of L RNA of Lassa virus

The L RNA of three Lassa virus strains originating from Nigeria, Ghana/Ivory Coast, and Sierra Leone was sequenced and the data subjected to structure predictions and phylogenetic analyses. The L gene products had 2218-2221 residues, diverged by 18% at the amino acid level, and contained several conserved regions. Only one region of 504 residues (positions 1043-1546) could be assigned a function, namely that of an RNA polymerase. Secondary structure predictions suggest that this domain is very similar to RNA-dependent RNA polymerases of known structure encoded by plus-strand RNA viruses, permitting a model to be built. Outside the polymerase region, there is little structural data, except for regions of strong alpha-helical content and probably a coiled-coil domain at the N terminus. No evidence for reassortment or recombination during Lassa virus evolution was found. The secondary structure-assisted alignment of the RNA polymerase region permitted a reliable reconstruction of the phylogeny of all negative-strand RNA viruses, indicating that Arenaviridae are most closely related to Nairoviruses. In conclusion, the data provide a basis for structural and functional characterization of the Lassa virus L protein and reveal new insights into the phylogeny of negative-strand RNA viruses.     

Turnip crinkle virus coat protein mediates suppression of RNA silencing in Nicotiana benthamiana

All of the protein products of Turnip crinkle virus (TCV; Tombusviridae, Carmovirus) were tested for their ability to suppress RNA silencing of a reporter gene after transient expression in Agrobacterium-infiltrated Nicotiana benthamiana leaves. Only the capsid protein, P38, showed suppression activity, although this was not obvious when P38 was expressed as part of a TCV infection of the same tissues. When P38 was expressed from a PVX vector, symptoms with enhanced severity that correlated with increased PVX RNA accumulation were observed. This contradiction between ectopic expression of P38 and TCV infection could be accounted for if the active determinant of suppressor activity within P38 was sequestered within the capsid protein structure. The N-terminal 25 amino acids were shown to be important for this activity. This region forms part of the unexposed R-domain that interacts with the RNA within the virus particle. This observation throws light on some of the complex biology exhibited by TCV.     

人乳腺癌MDR1基因稳定沉默细胞的筛选及其生物学特性

目的筛选MDR1沉默的人乳腺癌细胞并比较其生物学特性。方法采用BLOCK-iT Lentiviral RNAi Expres-sion System生产表达MDR1基因shRNA的慢病毒载体,转导敏感人乳腺癌细胞MCF-7和耐阿霉素人乳腺癌细胞MCF-7/ADM,杀稻瘟菌素(blasticidin)筛选获得MDR1稳定沉默细胞MCF-7/RNAi和MCF-7/ADM/RNAi。定量RT-PCR检测MDR1mRNA表达,流式细胞术检测P-GP蛋白表达和功能,MTT法检测药物敏感性。结果经10 mg/L blasticidin筛选12 d获得MCF-7/RNAi和MCF-7/ADM/RNAi细胞。MCF-7、MCF-7/RNAi、MCF-7/ADM和MCF-7/ADM/RNAi细胞的MDR1mRNA相对表达水平分别为1、0.13、17.14和2.01;P-GP表达分别为(1.5±0.3)%、(1.2±0.2)%、(89.4±3.6)%和(16.3±1.9)%;细胞内Rh123的潴留分别为(92.4±3.1)%、(90.6±4.0)%、(13.6±1.6)%、(72.4±2.8)%;IC50值分别为0.90、0.92、19.61和4.04 mg/L。结论应用慢病毒载体稳定沉默MDR1基因可有效逆转人乳腺癌细胞耐药性。     

Analysis of aberrant somatic hypermutation (SHM) in non-Hodgkin's lymphomas of patients with chronic HCV infection

Hepatitis C virus (HCV) and aberrant somatic hypermutation (SHM) have each been suggested to contribute to the development of B-cell non-Hodgkin's lymphoma (NHL). The incidence of PIM-1, PAX-5, RhoH/TTF, and c-MYC mutations in tumour biopsy specimens from 32 HCV-infected B-cell NHL patients was analysed to determine whether the extent of aberrant SHM among these patients differed from that previously reported for HCV-negative B-cell NHL patients. Mutation of PIM-1, PAX-5, RhoH/TTF, and c-MYC was detected in 4 (13%), 5 (16%), 4 (13%), and 4 (13%) of 32 samples, respectively. In HCV-positive B-cell NHL patients, the frequency of aberrant SHM was lower than that already found in HCV-negative B-cell NHL patients. This indicates that, unlike B-cell lymphomas from HCV-negative patients, aberrant SHM may not contribute significantly to malignant transformation in HCV-associated B-cell lymphomas.     

Plasma Content of Extracellular Nucleic Acids in Donors and Patients with Mammary Tumors

The concentrations of extracellular DNA and RNA were measured in the plasma of donors and patients with fibroadenoma and breast cancer. The content of extracellular DNA surpassed the normal in 80% plasma samples from patients with mammary tumors. Extracellular RNA was detected in 30% plasma samples from donors and patients with breast tumors. No correlations were found between plasma concentration of extracellular DNA and size and stage of tumor growth. Hence, measurement of extracellular DNA in the plasma of patients can be used only as an accessory test for tumor diagnosis.__________Translated from Byulleten’ Eksperimental’noi Biologii i Meditsiny, Vol. 139, No. 4, pp. 462–464, April, 2005     

Effect of tissue fixatives on telomere length determination by quantitative PCR

Telomere length is a well established marker of cellular senescence and thus biological age. Quantitative PCR allows the determination even from very low amounts of tissue by using telomere specific and single copy gene primers. Comparing a directly processed tissue sample to a 4% formaldehyde fixed one showed a significantly reduced efficiency of PCR reactions (mainly in single copy gene experiments) in a storage time-dependent manner resulting in an artificial increase in reported relative telomere length. This effect was not seen when the tissue was stored in RNA later solution. In summary, telomere length determination from formaldehyde fixed material by quantitative PCR is not a reliable method. Unfortunately therefore, many easily accessible tissue samples from pathology laboratories are unsuitable for this technique.     

一种新型的乙型肝炎病毒剪接变异体

目的 证实乙型肝炎病毒(hepatitis Bvirus，HBV)前基因组RNA在458nt～1308nt(nt，核苷酸)之间可发生剪接并产生相应的基因组剪接变异体。方法对1株分离自慢性乙型肝炎患者血清的亚基因组HBVDNA(2366bp)进行测序并以Vector NT16．0软件进行分析。将全基因组HBVDNA(3215bp)理论上可能的剪接供体及受体内的核苷酸进行定点突变并将突变株转染HepG2细胞，以位于HBVDNA458nt及1308nt两侧的特异引物检测转染后的细胞内HBV核心颗粒DNA，并以相同引物检测458nt～1308nt发生缺失的HBV DNA在不同病程的乙型肝炎患者血清中的存在情况。结果23661bp HBV DNA在458nt～1308nt之间发生缺失并符合GT-AG剪接模式。3215bp全基因组HBV DNA在459nt及1306nt分别发生G→A及A→C突变后均不能产生458nt～1308nt缺失。458nt～1308nt发生缺失的HBVDNA在慢性乙型肝炎、肝硬化及原发性肝细胞癌患者血清的检出率分别为80％、75％及70％，显著高于HBV无症状携带者10％的检出率。结论HBV前基因组RNA在458m～1308nt之间可发生剪接并产生长度为2366bp的基因组剪接变异体。该类型基因组剪接变异体基因结构特点及在HBV相关性肝病中广泛存在提示它与HBV致病性密切相关。