Mutational analysis of the coat protein gene of tobacco mosaic virus in relation to hypersensitive response in tobacco plants with the N' gene

Tomato strain L of tobacco mosaic virus (TMV-L) induces a hypersensitive response (necrotic local lesions) on tobacco plants with the N' gene. A factor responsible for induction of the hypersensitive response has been mapped to the coat protein gene. We have constructed several mutants which have insertions or deletions in the coat protein gene. Frame-shift mutants which cause premature termination of translation of the coat protein caused no necrotic local lesions on N' plants. Mutants which result in the expression of coat protein derivatives with one amino acid inserted after residue 56, 101, or 152 caused necrotic local lesions on N' plants. Deletion mutants lacking the coding region for fewer than the C-terminal 13 amino acid residues caused necrotic local lesions, whereas mutants lacking the coding region for the C-terminal 38 residues caused no necrotic local lesions. These results show that modifications of the coat protein gene affect its ability to induce the hypersensitive response in N' plants.     

Detection of CHK1 and CCND1 gene copy number changes in breast cancer with dual-colour fluorescence in-situ hybridization

Mu K, Li L, Yang Q, Zhang T, Gao P, Meng B, Liu Z, Wang Y & Zhou G
(2011) Histopathology  58 , 601–607
Detection of CHK1 and CCND1 gene copy number changes in breast cancer with dual‐colour fluorescence in‐situ hybridization Aims: To investigate the correlation between CCND1 amplification and CHK1 deletion in breast cancer, and to explore their role in tumorigenesis and progression, a comparative study of the gene copy number changes of CCND1 and CHK1 was performed with dual‐colour fluorescence in‐situ hybridization (FISH). Methods and results: Sixty‐one infiltrating ductal breast carcinomas with foci of ductal carcinoma in situ (DCIS) components were selected for dual‐colour FISH. A strong correlation was found between CCND1 amplification and CHK1 deletion (P < 0.0001). Fourteen cases were detected that demonstrated both CCND1 amplification and CHK1 deletion. Interestingly, when comparing the infiltrating and non‐invasive areas for the same tumour, we found three cases with CCND1 amplification in the infiltrating areas but not in the DCIS areas. We did not find a CHK1 gene profile difference between infiltrating and DCIS areas in the same lesions. Conclusions: Our findings suggest that CCND1 amplification and CHK1 deletion are common events in breast cancer, and that the two genetic alterations often coexist. Our data also suggest that CHK1 deletion is an early genetic event in the development of breast cancer and can be detected at the DCIS stage, whereas CCND1 amplification is more likely to be associated with tumour progression.     

A longitudinal study of the effect of GSTT1 and GSTM1 gene copy number on survival

Deletions of the glutathione S-transferase superfamily genes GSTT1 and GSTM1 has been associated with oxidative stress related diseases and recently explored as factors implicated in longevity as well. Reported results have been conflicting, which may partially be caused by the traditional use of assays unable to discriminate between carriers of one or two functional genes. Using a quantitative realtime PCR method facilitating quantification of gene copy number, we evaluated the influence of GSTT1 and GSTM1 gene deletions on longevity in a longitudinal study of 681 elderly Danish twins. The mean follow-up time was 7.6 years and during this time a total of 294 deaths occurred. The results demonstrated a non-significant trend for carriage of two copies of the GSTM1 functional gene to be a protective factor, whereas both heterozygosity and homozygosity for the GSTT1 functional gene was associated with a moderate but significant increased mortality in women (hazard rate 2.46 (CI95: 1.43-4.23) and 2.22 (CI95: 1.25-3.94) for one and two alleles, respectively). To our knowledge, this is the first longitudinal study exploring the influence of GST gene polymorphisms on longevity and these data implies that GST gene copy numbers do affect mortality risk in the elderly.     

Detecting gene copy number fluctuations in tumor cells by microarray analysis of genomic representations

In this work, we explore the use of representations in conjunction with DNA microarray technology to measure gene copy number changes in cancer. We demonstrate that arrays of DNA probes derived from low-complexity representations can be used to detect amplifications, deletions, and polymorphic differences when hybridized to representations of genomic DNA. The method is both reproducible and verifiable, and is applicable even to microscopic amounts of primary tumors. We also present a mathematical model for array performance that is useful for designing and understanding DNA microarray hybridization protocols. The future applications and challenges of this approach are discussed.     

Lesions and virus accumulation in inoculated transgenic tobacco plants expressing the coat protein gene of tobacco mosaic virus

The objective of this work was to identify steps in virus infection which were inhibited in transgenic tobacco plants (Nicotiana tabacum cv. Xanthi) that express the coat protein (CP) gene of the U, strain of tobacco mosaic virus (TMV). These plants were shown to be protected against disease development after inoculation with U,-TMV (P. Powell Abel, R. S. Nelson, B. De, N. Hoffman, S. G. Rogers, R. T. Fraley, and R. N. Beachy, 1986, Science 232, 738-743). Experiments were also conducted to allow comparison between the protection observed for the transgenic plants and cross-protection. In addition to protection against U1-TMV, the CP-expressing transgenic plants were protected against symptom development of infection after inoculation with a severe TMV strain, PV230, a strain which is immunologically related to the U1 strain. The numbers of chlorotic lesions produced on inoculated leaves of CID-expressing transgenic Xanthi plants infected with PV230 were 30%-or-less of those on leaves of control plants. Likewise necrotic lesion numbers produced on inoculated leaves of CP-expressing transgenic Xanthi 'nc' plants infected with U1 were 5%-or-less of those on leaves of control plants. Virus accumulation in the inoculated leaves of the CP-expressing Xanthi plants was substantially lower than that in leaves of control plants and thus correlated well with the lesion numbers. These results indicate that the delay in disease development includes prevention of virus accumulation in the inoculated leaves. Furthermore, there was a substantial reduction in accumulation of virus in the first leaf above the inoculated leaves in transgenic plants compared with control plants. Inoculation with viral RNA rather than virus largely overcame the protection, leading to the conclusion that the presence of the CID on virus particles in the challenge inoculum was necessary for maximum protection. As shown by these studies, expression of the TMV-CP coding sequence in transgenic plants mimics several of the characteristics of classical cross-protection previously reported by other researchers. We therefore refer to the protection observed for the transgenic plants as "genetically engineered cross-protection."     

Detection of pathogenic gene copy number variations in patients with mental retardation by genomewide oligonucleotide array comparative genomic hybridization

Genomic imbalance is a major cause of developmental disorders. Microarray-based comparative genomic hybridization (aCGH) has revealed frequent imbalances associated with clinical syndromes, but also a large number of copy number variations (CNVs), which have complicated the interpretation of results. We studied 100 consecutive patients with unexplained mental retardation and a normal karyotype using several platforms of CGH arrays. A genomewide array with 44,290 oligonucleotide probes (OaCGH44K) detected imbalances in 15% of cases studied with sizes ranged from 459 kb to 19 Mb while revealing a small number of CNVs (0.72/individual). Another platform with approximately 240,000 oligonucleotide probes (OaCGH244K) revealed a large number of CNVs (20/individual) in selected cases and their normal parents. We used a comprehensive approach for interpreting the results of aCGH, including consideration of the size, inheritance and gene content of CNVs, and consultation with an online Database of Genomic Variants (DGV) and Online Mendelian Inheritance in Men (OMIM) for information on the genes involved. Our study suggests that genomewide oligonucleotide arrays such as the OaCGH44K platform can be used as a powerful diagnostic tool for detection of genomic imbalances associated with unexplained mental retardation or syndromic autism spectrum disorders. It is interesting to note that a small number of common variants were revealed by OaCGH244K in some study subjects but not in their parents and that some inherited CNVs had altered breakpoints. Further investigations on these alterations may provide useful information for understanding the mechanism of CNVs.     

CCL3L1 and CCL4L1: variable gene copy number in adolescents with and without human immunodeficiency virus type 1 (HIV-1) infection

As members of the chemokine family, macrophage inflammatory protein 1 alpha (MIP-1alpha) and MIP-1beta are unique in that they both consist of non-allelic isoforms encoded by different genes, namely chemokine (C-C motif) ligand 3 (CCL3), CCL4, CCL3-like 1 (CCL3L1) and CCL4L1. The products of these genes and of CCL5 (encoding RANTES, i.e., regulated on activation, normal T expressed and secreted) can block or interfere with human immunodeficiency virus type 1 (HIV-1) infection through competitive binding to chemokine (C-C motif) receptor 5 (CCR5). Our analyses of 411 adolescents confirmed that CCL3 and CCL4 genes occurred invariably as single copies (two per diploid genome), whereas the copy numbers of CCL3L1 and CCL4L1 varied extensively (0-11 and 1-6 copies, respectively). Neither CCL3L1 nor CCL4L1 gene copy number variation showed appreciable impact on susceptibility to or control of HIV-1 infection. Within individuals, linear correlation between CCL3L1 and CCL4L1 copy numbers was moderate regardless of ethnicity (Pearson correlation coefficients=0.63-0.65, P<0.0001), suggesting that the two loci are not always within the same segmental duplication unit. Persistently low serum MIP-1alpha and MIP-1beta (in the pg/ml range) compared with high CCL5 concentration (ng/ml range) implied that multi-copy genes CCL3L1 and CCL4L1 conferred little advantage in the intensity of expression among uninfected or infected adolescents.     

Correlation of DEFA1 gene copy number variation with intestinal involvement in Behcet's disease

Copy number variation has been associated with various autoimmune diseases. We investigated the copy number (CN) of the DEFA1 gene encoding α-defensin-1 in samples from Korean individuals with Behcet''s disease (BD) compared to healthy controls (HC). We recruited 55 BD patients and 35 HC. A duplex Taqman® real-time PCR assay was used to assess CN. Most samples (31.1%) had a CN of 5 with a mean CN of 5.4 ± 0.2. There was no significant difference in the CN of the DEFA1 gene between BD patients and HC. A high DEFA1 gene CN was significantly associated with intestinal involvement in BD patients. Variable DEFA1 gene CNs were observed in both BD patients and HC and a high DEFA1 gene CN may be associated with susceptibility to intestinal involvement in BD.     

Identification of osteosarcoma driver genes by integrative analysis of copy number and gene expression data

High-grade osteosarcoma is a tumor with a complex genomic profile, occurring primarily in adolescents with a second peak at middle age. The extensive genomic alterations obscure the identification of genes driving tumorigenesis during osteosarcoma development. To identify such driver genes, we integrated DNA copy number profiles (Affymetrix SNP 6.0) of 32 diagnostic biopsies with 84 expression profiles (Illumina Human-6 v2.0) of high-grade osteosarcoma as compared with its putative progenitor cells, i.e., mesenchymal stem cells (n = 12) or osteoblasts (n = 3). In addition, we performed paired analyses between copy number and expression profiles of a subset of 29 patients for which both DNA and mRNA profiles were available. Integrative analyses were performed in Nexus Copy Number software and statistical language R. Paired analyses were performed on all probes detecting significantly differentially expressed genes in corresponding LIMMA analyses. For both nonpaired and paired analyses, copy number aberration frequency was set to >35%. Nonpaired and paired integrative analyses resulted in 45 and 101 genes, respectively, which were present in both analyses using different control sets. Paired analyses detected >90% of all genes found with the corresponding nonpaired analyses. Remarkably, approximately twice as many genes as found in the corresponding nonpaired analyses were detected. Affected genes were intersected with differentially expressed genes in osteosarcoma cell lines, resulting in 31 new osteosarcoma driver genes. Cell division related genes, such as MCM4 and LATS2, were overrepresented and genomic instability was predictive for metastasis-free survival, suggesting that deregulation of the cell cycle is a driver of osteosarcomagenesis.     

Characterization of virus-induced gene silencing in tobacco plants infected with apple latent spherical virus

Summary Apple latent spherical virus (ALSV) expressing green fluorescent protein (GFP-ALSV) was used for analysis of virus-induced gene silencing (VIGS) in tobacco plants expressing GFP (GFP-tobacco). In GFP-tobacco inoculated with GFP-ALSV, small dark spots appeared on inoculated leaves at 5 days post-inoculation (dpi), then expanded, and finally covered the whole area of the leaves after 12 dpi. Most of the fluorescence of upper leaves above the 12th true leaf disappeared at 21 dpi. Thus, GFP-ALSV infection efficiently triggered VIGS of a transgene (GFP gene) in tobacco plants. Analysis of GFP-silenced leaves showed that viral RNAs and proteins accumulated in all leaves where most GFP mRNA had been degraded. The siRNAs derived from ALSV-RNAs were not detected in samples from which siRNA of GFP mRNA could be easily detected. Direct tissue blot analysis showed that the spread of GFP-ALSV always preceded the induction of VIGS in infected leaves of GFP-tobacco. GFP leaf patch tests using Nicotiana benthamiana line 16c showed that Vp20, one of the three capsid proteins, is a silencing suppressor which interferes with systemic silencing.     

A worldwide analysis of beta-defensin copy number variation suggests recent selection of a high-expressing DEFB103 gene copy in East Asia

Beta-defensins are a family of multifunctional genes with roles in defense against pathogens, reproduction, and pigmentation. In humans, six beta-defensin genes are clustered in a repeated region which is copy-number variable (CNV) as a block, with a diploid copy number between 1 and 12. The role in host defense makes the evolutionary history of this CNV particularly interesting, because morbidity due to infectious disease is likely to have been an important selective force in human evolution, and to have varied between geographical locations. Here, we show CNV of the beta-defensin region in chimpanzees, and identify a beta-defensin block in the human lineage that contains rapidly evolving noncoding regulatory sequences. We also show that variation at one of these rapidly evolving sequences affects expression levels and cytokine responsiveness of DEFB103, a key inhibitor of influenza virus fusion at the cell surface. A worldwide analysis of beta-defensin CNV in 67 populations shows an unusually high frequency of high-DEFB103-expressing copies in East Asia, the geographical origin of historical and modern influenza epidemics, possibly as a result of selection for increased resistance to influenza in this region.     

The 3'-proximal part of the Plum pox virus P1 gene determinates the symptom expression in two herbaceous host plants

Three major strains of the Plum pox virus (PPV) are the most important in Europe: PPV-D, PPV-M, and PPV-Rec. By combining the genomes of two different strains of PPV (PPV-D with PPV-Rec; PPV-D with PPV-M), 20 inter-strain chimeric infectious clones (CICPPV) were constructed. Biological properties of CICPPV were tested by inoculating them on different herbaceous host species susceptible to PPV. Four of the seven species tested, exhibited visible symptoms. In Nicotiana benthamiana all CICPPV induced systemic mosaic and leaf malformation. Pisum sativum showed a broad range of symptom severity (systemic chlorotic and necrotic lesions) but neither qualitative nor quantitative aspects of symptomatology were related to a single PPV genome locus. Nicotiana occidentalis and Nicandra physaloides proved to be suitable for symptom-based differentiation. Depending on the virus strain/chimera, N. occidentalis showed two types of symptoms: mild systemic chlorotic spots or local necrotic lesions/systemic vein necroses. N. physaloides reacted to the PPV infection either symptomless or by local necrotic lesions. Our results demonstrated that the P1/HC-pro region of the PPV genome appears to be the determinant of the symptom manifestation in these host plants. In silico analysis mapped it to the 3′-proximal part of the P1 gene.     

A whole-genome mouse BAC microarray with 1-Mb resolution for analysis of DNA copy number changes by array comparative genomic hybridization

Microarray-based comparative genomic hybridization (CGH) has become a powerful method for the genome-wide detection of chromosomal imbalances. Although BAC microarrays have been used for mouse CGH studies, the resolving power of these analyses was limited because high-density whole-genome mouse BAC microarrays were not available. We therefore developed a mouse BAC microarray containing 2803 unique BAC clones from mouse genomic libraries at 1-Mb intervals. For the general amplification of BAC clone DNA prior to spotting, we designed a set of three novel degenerate oligonucleotide-primed (DOP) PCR primers that preferentially amplify mouse genomic sequences while minimizing unwanted amplification of contaminating Escherichia coli DNA. The resulting 3K mouse BAC microarrays reproducibly identified DNA copy number alterations in cell lines and primary tumors, such as single-copy deletions, regional amplifications, and aneuploidy.     

Gene copy number regulates the production of the human chemokine CCL3-L1

Genetic variation in the chemokine system is likely to affect responses to infection, and influence the course of autoimmune and inflammatory disease. We and others have shown that the human beta-chemokine CCL3-L1, unlike its related non-allelic isoform CCL3, has high affinity for the chemokine receptors D6, CCR3 and CCR5. Moreover, CCL3-L1, but not CCL3, is susceptible to cleavage by CD26, creating a truncated -2 form with enhanced affinity for CCR1 and CCR5. Strong interaction with CCR5 means that CCL3-L1, and particularly its -2 variant, are by far the most potent natural HIV entry inhibitors described to date. Here, using real-time PCR we have shown that CCL3-L1 and a novel CCL4 isoform (termed CCL4-L1) can vary from 1-6 copies per diploid genome (pdg) in Caucasians and are occasionally completely absent. The other isoforms (CCL3 and CCL4) remain at two copies per dpg. Importantly, in a model system of pro-inflammatory chemokine production (LPS-activated monocytes)higher gene copy number correlates with an increased ratio of CCL3-L1 versus CCL3 mRNA, and enhanced chemokine production. Supernatants from samples with high copy number are able to more potently chemoattract CCR5-expressing cells, an effect blocked with anti-CCL3/CCL3-L1 antibodies. As a result of these studies, we hypothesize that genetic variation in CCL3-L1 gene copy number may affect the susceptibility to, or the progression or severity of, diseases in which this chemokine plays a role.     

Enhancement by potato virus Y of potato virus X synthesis in doubly infected tobacco depends on the timing of invasion by the viruses

The time required for movement of potato virus Y (PVY) and two strains of potato virus X (PVX) from an inoculated lower leaf of small tobacco plants to the fourth leaf above, where maximal enhancement of PVX synthesis occurs, was determined. PVY required 12 hr longer than one PVX strain and 6 hr longer than the other; timing was from the time of inoculation of lower leaves. The rates of movement of the two viruses were the same in singly or doubly inoculated plants. Lower leaves were then inoculated with PVX and PVY at times so that invasion of fourth leaves by the two viruses occurred at predicted intervals. Maximum enhancement of one PVX strain occurred when PVY invaded fourth leaves 12 hr before PVX; enhancement of the other PVX strain occurred when PVY invaded 6 hr after PVX. Enhancement was always less than maximal when invasion by either virus preceded invasion by the other by more than 24 hr. These results were interpreted as indicating that enhancement occurs only in cells invaded by the two viruses within a relatively short period of time and that maximum enhancement results when critical stages in the replication cycle of each virus coincide; in such cells replication of both viruses was probably occurring simultaneously.     

NF1基因新突变及我国首例NF1基因拷贝数目变异报道

 目的:对2例散发性1型神经纤维瘤患者进行致病基因NF1编码序列的突变筛查以及拷贝数变异(copy number variation,CNV)研究,寻找致病性突变。方法:PCR扩增NF1基因的编码区及外显子-内含子交界区,对产物进行直接测序。在50例正常对照中进行新发现突变位点的测序分析,以排除多态性。用多重连接探针扩增技术(MLPA)对患者进行NF1基因CNV的检测,并对证实有NF1拷贝缺失的患者进行长片段PCR,以找寻断裂点。结果:患者S736于NF1基因检测到一个国际上尚未报道的新突变：c.6345_6346 ins G (p.Leu2116Alafs*4),患者父母均不携带此突变,故此突变为一个de novo突变。该突变使开放阅读框移位,提前引入终止密码子,导致蛋白质分子的截断,以致部分犰狳式褶皱(ARM-type fold)结构域丢失。在另一患者S743中检测到一个包含整个NF1基因的大片段缺失,缺失区域为1.3～1.9 Mb,但断裂点尚不明,此为我国首例NF1基因拷贝数目变异的报道。结论: 患者NF1基因的de novo突变及CNV是引起这2例1型神经纤维瘤发病的分子机制,这些发现可用于临床1型神经纤维瘤的分子诊断。     

甲型肝炎病毒P1B、P2A、P3AB和P3D蛋白在原核系统中的表达和抗原活性分析

目的研究甲型肝炎病毒P1B、P2A、P3AB和P3D在原核系统中的表达,并探讨这些蛋白的抗原活性和作为诊断抗原的应用价值。方法采用PCR方法,从克隆有HAV HM175株全长cDNA基因的克隆载体pHAV16H1上扩增出目的基因,以M47作为表达载体,构建N端带硫氧还蛋白的重组表达质粒。重组质粒在大肠埃希菌BL21(DE3)中经IPTG诱导表达。采用DEAE阴离子交换和镍离子柱螯和亲和层析纯化的方法对重组蛋白进行纯化。以Western Blot和间接ELISA的方法检测重组蛋白的抗原活性。结果四个重组质粒经测序证明构建正确无误,在大肠埃希菌中表达四个蛋白的相对分子质量也正确无误。Western Blot分析和间接ELISA方法证实四个蛋白中只有p2a有抗原活性。结论原核表达的P2a蛋白,具有较好的抗原活性,在间接ELISA方法中检测出了所有的24份阳性血清和24份阴性血清,非常有希望做成诊断抗原用于诊断急性甲肝患者和区分甲型肝炎自然感染与注射疫苗所产生的不同免疫。