165 THE EFFECT OF shRNA TARGETING CLUSTER OF DIFFERENTIATION ANTIGEN 14 ON GENE EXPRESSION OF TNF-α, TLR4, AND IL-6 IN LIPOPOLYSACCHARIDE-INDUCED BUFFALO PERIPHERAL BLOOD MONOCYTE/MACROPHAGE

Cluster of differentiation antigen 14 (CD14) plays a crucial role in the inflammatory response to lipopolysaccharide (LPS), which interacts with TLR4 and MD-2 to enable cell activation, leading to inflammation. Several studies have proved that upstream inhibition of bacterial LPS/toll-like receptor 4 (TLR4)/CD14-mediated inflammation pathway is an effective therapeutic approach for attenuating damaging immune activation. In this study, to explore the effect of CD14 down-regulation on TLR4 signal conductive-related genes expression after stimulation by LPS, five CD14 shRNA (319/421/755/970/1041) sequences and a negative control sequence (NC-1864) were synthesised and used to construct lentiviral recombinant plasmid pSicoR-GFP-shRNA. Lentiviral recombinant plasmids of pSicoR-GFP-shRNA and fusion expression vector of pDsRed-N1-buffalo CD14 were co-transfected into HEK293 using liposome. At 72 h after transfection, the expression of exogenous buffalo CD14 mRNA was reduced at different level for all shRNA plasmids, in which shRNA-1041 had the highest interfering efficiency by RT-qPCR and fluorescence-activated cell sorting analysis. Then, buffalo peripheral blood monocyte/macrophage was purified and infected by the CD14 shRNA lentivirus. After 7 days of infection, the cells were stimulated by 1 µg mL–1 LPS for 3 h, then the mRNA expression level of CD14, TLR4, IL-6, and TNF-α transcripts in the cells were detected by the RT-qPCR method. After stimulation by LPS, the expression of endogenous CD14 was significantly reduced by CD14 shRNA-1041, the mRNA expression level of TLR4, IL-6, and TNF-α genes was also significantly down-regulated in comparison with control group (P ≤ 0.01). In conclusion, the selected CD14 shRNA-1041 cannot only inhibit the expression of endogenous CD14 mRNA in buffalo peripheral blood monocyte/macrophage, but also downregulate the mRNA expression of CD14, TLR4, IL-6, and TNF-α. The above results demonstrate that knockdown of endogenous CD14 has obvious coordination effects on the signal conductive function of TLR4 after stimulating by LPS, and shRNA technology will provide a new way to prevent endotoxin-related diseases in livestock. This work was supported by the National Transgenic Project (2009ZX08007-009B), Guangxi natural science funding (2012GXNSFCB053002), and funding of State Key Laboratory of Subtropical Bioresource Conservation and Utilisation (KSL-CUSAb-2012-02).

The histidine-805 in motif-C of the phage SP6 RNA polymerase is essential for its activity as revealed by random mutagenesis

In order to identify functional residues of the bacteriophage SP6 RNA polymerase, its C-terminal one-twelfth region was randomly mutagenized using polymerase chain reactions of its gene under the conditions for reduced fidelity of Taq DNA polymerase. Using a two-vector system that permits phenotypic isolation of mutants with reduced in vivo transcription activity, 3 single and 1 multiple mutants were isolated. A single substitution of Gln for His805 resulted in complete inactivation of the enzyme. A multiple mutant carrying substitutions at 808, 820, 835, 843 and 848 also abolished the activity. However, changes of Pro856-->Ser and Asp862-->Glu individually reduced the activity only slightly. It is noteworthy that His805 is one of the two motif-C residues that are absolutely conserved among all the DNA polymerases and monomeric RNA polymerases.

Significance and relationship between DJ-1 gene and surviving gene expression in laryngeal carcinoma

This study aimed at exploring the correlation between DJ-1 gene and survivin gene in laryngeal squamous cell carcinoma by analyzing their gene expression levels and their relationship with clinicopathologic parameters. The expression of DJ-1 gene and survivin gene in 82 laryngeal carcinoma tissues from patients and 82 negative surgical margin tissue samples were detected by immunohistochemistry, respectively. The correlation of their expression levels and patients' clinical parameters were then analyzed by Pearson correlation analysis. The positive detection rates of DJ-1 and survivin in laryngeal carcinoma tissues were 71.95% and 60.98%, which were higher than those of the normal control that were 29.27% and 0.00%, respectively (P<0.01). The positive detection rates of DJ-1 and survivin were found associated with tumor stages (P<0.05), but not with lymph node metastasis. The DJ-1 gene expression level was related to cell differentiation (P<0.05). Finally, a positive correlation between DJ-1 and survivin gene expression in laryngeal carcinoma was found. The overall survival rate of patients was 51.2%, and disease-free survival (DFS) was 39.0%. DFS in DJ-1 negative-expression group was 87.0%, and 20.3% in DJ-1 positive-expression group. The negative expression of DJ-1 was associated with a shorter mean patient DFS time (44.643±1.417 months), whereas positive expression of DJ-1 was associated with a longer mean DSF time (25.943±;1.297 months). DJ-1 and survivin play a vital role in the occurrence and development of laryngeal carcinoma. DJ-1 may promote the carcinogenesis of laryngeal cells by up-regulating the survivin gene expression.

Nanostructure Evolution During Processing of Thin-Film Gels: A High-Resolution Electron Microscopic Study. 2. The Thin-Film Gel Derived From Pb(Zr0.45Ti0.55)O2(OR)2

High-resolution electron microscopic examination of alkoxide thin-film gels has been employed to study the drying and aging of thin-film Pb(Zr0.45Ti0.55)O2(OR)2as it evolves from the gel to the ferroelectric perovskite product. The initially amorphous film is observed to aggregate to form ordered islands with inter-metal distances close to that of the final structure embedded in a highly disordered matrix. When these aggregates are at the surface they grow and decompose more rapidly to the perovskite product. The progress to a polycrystalline final state is followed and recorded in real time and in time-lapse at high resolution.

Establishing a surveillance network for severe lower respiratory tract infections in Korean infants and young children

To reduce morbidity and mortality through integrated case management, a pilot study to detect respiratory viruses in patients with acute lower respiratory infections (ALRIs) was designed as part of a nationwide surveillance for this disease in Korea. The study population consisted of hospitalized patients under the age of 5 years with bronchiolitis, pneumonia, croup, or acute respiratory distress syndrome. A prospective 6-month study was performed. Two hundred and ninety-seven nasopharyngeal secretions were collected and multiplex reverse transcriptase polymerase chain reactions (RT-PCR)/polymerase chain reactions (PCR) were performed to detect respiratory viruses. If there were any positive RT-PCR/PCR results, viral cultures were proceeded for confirmation. Respiratory viruses were identified in 49.6% of 296 patients. The detection rates were as follows: respiratory syncytial virus (RSV) was the most commonly detected in 52.7% (87/165), human metapneumovirus (hMPV) in 15.8%, human corona virus (hCoV) in 5.5%, adenovirus in 9.7%, human bocavirus (hBoV) in 5.5%, parainfluenza virus (PIV) in 3.6%, rhinovirus (RV) in 4.2%, and the influenza virus in 3% of the patients with ALRIs. The consistent rate of positive results between RT-PCR and viral culture was 92% (105/114). Using our methods to detect viral causes seemed to be acceptable for the national surveillance of severe acute respiratory infections in infants and children.

Pathologic Analysis of the Brain from Streptococcus suis Type 2 Experimentally Infected Pigs

Streptococcus suis type 2 ( S. suis 2) is known as a major porcine pathogen worldwide and causes meningitis, septicemia, endocarditis, arthritis, and septic shock in pigs. Suilysin, a secreted protein of S. suis 2, is considered to be an important S. suis 2 virulence-associated factor. In this paper, the cerebellar lesions following experimental infection of pigs with S. suis 2 were studied. An immunohistochemical technique was applied to compare the distribution of bacteria and secreted suilysin protein in brain. The infected pigs developed histologic lesions of meningoencephalitis. Immunohistochemistry identified bacteria within the cytoplasm of neutrophils and macrophages localized in meningeal lesions. The secreted suilysin protein showed a similar localization within the cytoplasm of inflammatory cells, indicating that suilysin had high expression in vivo and may contribute to the pathogenesis of streptococcal meningoencephalitis.

Downregulation of Wnt2 and beta-catenin by siRNA suppresses malignant glioma cell growth

Increasing evidence suggests that aberrant activation of Wnt signaling is involved in tumor development and progression. Our earlier study on gene expression profile in human gliomas by microarray found that some members of Wnt family were overexpressed. To further investigate the involvement of Wnt signaling in gliomas, the expression of core components of Wnt signaling cascade in 45 astrocytic glioma specimens with different tumor grades was examined by reverse transcription-PCR and immunohistochemistry. Wnt2, Wnt5a, frizzled2 and beta-catenin were overexpressed in gliomas. Knockdown of Wnt2 and its key mediator beta-catenin in the canonical Wnt pathway by siRNA in human U251 glioma cells inhibited cell proliferation and invasive ability, and induced apoptotic cell death. Furthermore, treating the nude mice carrying established subcutaneous U251 gliomas with siRNA targeting Wnt2 and beta-catenin intratumorally also delayed the tumor growth. In both in vitro and in vivo studies, downregulation of Wnt2 and beta-catenin was associated with the decrease of PI3K/p-AKT expression, indicating the interplay between Wnt/beta-catenin and PI3K/AKT signaling cascades. In conclusion, the canonical Wnt pathway is of critical importance in the gliomagenesis and intervention of this pathway may provide a new therapeutic approach for malignant gliomas.

RBF multiuser detector with channel estimation capability in a synchronous MC-CDMA system

The authors propose a multiuser detector with channel estimation capability using a radial basis function (RBF) network in a synchronous multicarrier-code division multiple access (MC-CDMA) system. The authors propose to connect an RBF network to the frequency domain to effectively utilize the frequency diversity. Simulations were performed over frequency-selective and multi-path fading channels. These simulations confirmed that the proposed receiver can be used both for the channel estimation and as a multi-user receiver, thus permitting an increase in the number of active users.

Early postnatal development of corpus callosum and corticospinal white matter assessed with quantitative tractography

BACKGROUND AND PURPOSE

The early postnatal period is perhaps the most dynamic phase of white matter development. We hypothesized that the early postnatal development of the corpus callosum and corticospinal tracts could be studied in unsedated healthy neonates by using novel approaches to diffusion tensor imaging (DTI) and quantitative tractography.

MATERIALS AND METHODS

Isotropic 2 x 2 x 2 mm(3) DTI and structural images were acquired from 47 healthy neonates. DTI and structural images were coregistered and fractional anisotropy (FA), mean diffusivity (MD), and normalized T1-weighted (T1W) and T2-weighted (T2W) signal intensities were determined in central midline and peripheral cortical regions of the white matter tracts of the genu and splenium of the corpus callosum and the central midbrain and peripheral cortical regions of the corticospinal tracts by using quantitative tractography.

RESULTS

We observed that central regions exhibited lower MD, higher FA values, higher T1W intensity, and lower T2W intensity than peripheral cortical regions. As expected, MD decreased, FA increased, and T2W signal intensity decreased with increasing age in the genu and corticospinal tract, whereas there was no significant change in T1W signal intensity. The central midline region of the splenium fiber tract has a unique pattern, with no change in MD, FA, or T2W signal intensity with age, suggesting different growth trajectory compared with the other tracts. FA seems to be more dependent on tract organization, whereas MD seems to be more sensitive to myelination.

CONCLUSIONS

Our novel approach may detect small regional differences and age-related changes in the corpus callosum and corticospinal white matter tracts in unsedated healthy neonates and may be used for future studies of pediatric brain disorders that affect developing white matter.

High isolation rate of adenovirus serotype 7 from South Korean military recruits with mild acute respiratory disease

Adenovirus is a major cause of acute respiratory disease (ARD) in military recruits. When South Korean military recruits with ARD were surveyed, adenovirus was identified in 122 (61.0%) of the 200 recruits studied. Moreover, all cases of ARD involving adenovirus were caused by serotype 7.

Silencing E1A mRNA by RNA interference inhibits adenovirus replication

The adenovirus family contains 51 human serotypes, and most human adenoviruses cause widespread respiratory tract infections. Adenovirus infections can result in severe complications in some cases, such as in adenovirus type 11 infection in immunocompromised patients. However, effective treatment methods for adenovirus infections are currently unavailable. This prompted the search for antiviral agents effective against adenovirus infections. In the present study, adenovirus E1A was targeted by RNA interference (RNAi) using synthetic small interfering RNAs (siRNAs) in an attempt to inhibit viral replication, since adenovirus E1A proteins are known to be involved in the transcriptional activation of the viral and cellular genes necessary for controlling the cell cycle and viral replication. The results indicated that the siRNAs effectively reduced the amount of adenovirus E1A mRNA and the levels of replicative intermediates. Additionally, siRNA-mediated gene silencing inhibited adenovirus replication by suppressing the E1A mRNA. These results suggest that the RNAi-mediated targeting of adenovirus E1A may have a potentially therapeutic effect in controlling adenovirus infections.

Thiopurine S-methyltransferase polymorphisms and the relationship between the mutant alleles and the adverse effects in systemic lupus erythematosus patients taking azathioprine

OBJECTIVE

The present study sought to elucidate the genetic basis of thiopurine methyltransferase (TPMT) polymorphism and subsequently to investigate the relationship between mutant TPMT and an adverse response observed in Korean patients with systemic lupus erythematosus (SLE) taking azathioprine (AZA).

METHODS

The TPMT genotype of 342 patients with SLE was determined by MALDI-TOF mass spectrometry and correlated with the effects of clinical exposure to AZA.

RESULTS

TPMT polymorphism was detected in 17 of the 342 study subjects (5.0%), 12 heterozygous for the TPMT*3C allele and 5 heterozygous for the TPMT*6 allele. Numerous patients taking AZA demonstrated adverse drug responses. Severe nausea occurred in 4 patients with the TPMT*3C allele, while 1 patient with the TPMT*6 allele suffered severe bone marrow toxicity. Leucopenia (n = 17), nausea (n = 4), and abnormal liver function (n = 1) were suspected in 23 of the 94 lupus patients taking AZA. AZA was relatively well tolerated by the remainder of the patients. The heterozygous genotype for the TPMT*3C and *6 alleles was frequently detected in Korean SLE patients.

CONCLUSION

Contrary to previous hypotheses, this study identified no statistical correlation between TPMT genotype and AZA toxicity. We thus conclude that TMPT genotyping cannot replace regular blood monitoring in SLE patients receiving AZA treatment.

Genetic polymorphisms of OPG, RANK, and ESR1 and bone mineral density in Korean postmenopausal women

To evaluate the effects of genetic polymorphisms of OPG, RANK, and ESR1, which regulate osteoclastogenesis, on bone mineral density (BMD), a cross-sectional study was conducted in 650 Korean postmenopausal women. BMDs of the distal radius and the calcaneus were measured by dual energy X-ray absorptiometry (DXA). Genetic polymorphisms of OPG 163 A > G, 1181 G > C; RANK 421 C > T, 575 T > C; and ESR1 1335 C > T, 2142 G > A were determined by matrix-assisted laser desorption/ionization-time of flight (MALDI-ToF) mass spectrometry. The differences between the BMDs of the genotypes of OPG, RANK, and ESR1 were analyzed by multiple linear regression model adjusted for age and body mass index. Women with the OPG 1181 CC genotype had higher BMDs at the distal radius (7%) and calcaneus (10%) than those with the GG genotype; and these differences were statistically significant (P = 0.001 and P = 0.007, respectively). A significant association was also observed between RANK 575 T > C and calcaneus BMD (P for trend = 0.017). No significant association was observed between BMDs and the polymorphisms of ESR1. The association between OPG 1181 G > C and BMD was profound in subjects with the RANK 575 TT or ESR1 2142 GG genotypes; women with OPG 1181 CC had higher BMDs at the distal radius (11%) and calcaneus (11%) than those with OPG 1181 GG only in women with RANK 575 TT genotype (P = 0.002 and P = 0.021, respectively). These results suggest that OPG genetic polymorphisms, especially with the RANK 575 TT or ESR1 2142 GG genotypes, are related to low BMD in postmenopausal Korean women.

Feeding practices in 105 counties of rural China

BACKGROUND

China has the largest population in the world with more than 70% of the people living in rural areas. Over 34% of children under the age of 5 years are responded to show moderate or severe growth stunting, so United Nations International Children's Emergency Fund and Chinese Ministry of Health conducted this large-scale survey in China. This study aimed to learn the feeding practice, to find the problems in child-feeding practice and to provide evidence for the government to develop an approach to child malnutrition in rural China.

METHODS

A structured questionnaire was used to survey 21,036 mothers of children with age of 0-24 months.

RESULTS

Of the 20,915 children, 98.22% were breastfeeding and 24.36% were exclusively breastfeeding. The proportion of children with weekly protein intake was 78.47%. Among the infants under 4 months, the risk of pneumonia in the group of exclusive breastfeeding was 1.69%, while in the group of non-exclusive breastfeeding was 3.63%, showing a statistically significant difference between the two groups. The risk of diarrhoea in the group of exclusive breastfeeding and in the group of non-exclusive breastfeeding among the infants under 4 months was 24.37% and 40.86%, respectively, also showing a statistically significant difference between the two groups. For children with age 4-6 months, the complementary feeding contributed to a higher prevalence of diarrhoea, but not pneumonia.

CONCLUSIONS

The breastfeeding was very common, but the exclusive breastfeeding was quite low and the exclusive breastfeeding for children under the age of 4 months decreased the risks of pneumonia and diarrhoea. For children with age 4-6 months, the exclusive breastfeeding could decrease the risk of diarrhoea, too. Protein intake was insufficient for children in rural China. The rural people lacked health knowledge and were greatly influenced by traditional feeding practices.

Proposal for genetic characterisation of wild-type mumps strains: Preliminary standardisation of the nomenclature

Though mumps virus (MuV) is a monotypic virus, genetic variation between strains has been described. Viruses have been placed into genotypes designated A-L based on the nucleotide sequence of the small hydrophobic (SH) gene, which is the most variable gene in the mumps genome. Molecular characterisation of MuV is an important component of mumps surveillance because it can help identify the transmission pathways of the virus as well as distinguish between wild-type and vaccine strains. Here, we propose a standardized nomenclature and an analysis protocol for the genetic characterisation of mumps strains to facilitate expansion of molecular epidemiological studies. In addition to assigning standard reference strains for the recognized genotypes of MuV, a convention is proposed for naming for strains and criteria to designate a new genotype.

The influence of a polymorphism at position -857 of the tumour necrosis factor gene on clinical response to etanercept therapy in rheumatoid arthritis

OBJECTIVES

We aimed to test whether polymorphisms in the etanercept target genes TNFA and LTA are associated with clinical responses to etanercept therapy in RA patients.

METHODS

Clinical responses of 70 patients treated with etanercept were determined according to the ACR criteria. We genotyped 13 single-nucleotide polymorphisms (SNPs) within TNFA and LTA and tested whether they influenced the responses to 12 weeks of etanercept therapy. Univariate and multivariate analyses were performed to compare allele, genotype and haplotype distributions between responders and non-responders.

RESULTS

Association of the -857C/T SNP at the TNFA promoter was marginally significant when patients were divided into responders and non-responders according to improvement criteria ACR20 or ACR70. When ACR70 responders (the best responders) were compared with ACR20 non-responders (the worst responders), however, the association was prominent [odds ratio (OR) = 12, 95% confidence interval (CI) = 1.4-105, P = 0.0077, P(corrected) = 0.054], as the frequency of the T allele was 5% in the ACR20 non-responders but 39% in the ACR70 responders. Moreover, the ratio of ACR70 responder number to ACR20 non-responder number among T-allele carriers was >10-fold higher than in the C-allele homozygotes (OR = 12, 95% CI = 1.2-120, P = 0.033).

CONCLUSIONS

RA patients with the T allele of TNFA -857C/T SNP respond better to etanercept therapy than homozygotes for the C allele, indicating that, when the results have been confirmed, this SNP could become a useful genetic marker for predicting responses.

Activity of a synthetic hexadecasaccharide (SanOrg123781A) in a pig model of arterial thrombosis

The activity of SanOrg123781A, a new synthetic antithrombotic drug inhibiting both factor Xa and thrombin through antithrombin (AT), was compared to that of unfractionated heparin (UFH) and of the synthetic pentasaccharide (fondaparinux, SP) in an ex vivo arterial thrombosis model in the pig. Six groups of four pigs were administered intravenously with SanOrg123781A (1, 3, 10 and 30 nmol kg(-1)), UFH (30 nmol kg(-1)) or SP (30 nmol kg(-1)). In this arterial model in which platelet thrombus was formed on a thrombogenic surface under a constant high shear rate, UFH and SP had moderate antithrombotic effects while SanOrg123781A exhibited a strong, dose-dependent inhibitory activity on platelet adhesion and platelet thrombus formation. In contrast to UFH, SanOrg123781A did not modify the activated partial thromboplastin time (aPTT) even at 30 nmol kg(-1), but strongly inhibited thrombin generation. At the same dose, despite a lower antithrombotic activity than SanOrg123781A, UFH significantly affected all the coagulation parameters. Taken together, these results show that SanOrg123781A, due to its potent and selective antifactor Xa and antifactor IIa activities is a promising new antithrombotic agent even in arterial setting.

Pathogenesis of and immunity to a new influenza A (H5N1) virus isolated from duck meat

The outbreak of avian influenza H5N1 in Hong Kong in 1997 raised concerns about the potential for the H5 subtype to cause a human pandemic. In 2001 a new H5N1 virus, A/Duck Meat/Anyang/AVL-1/2001 (A/Dkmt), was isolated from imported duck meat in Korea. The pathogenesis of this virus was investigated in mice. A/Dkmt virus had low infectivity but was lethal for mice at high doses, and at lethal doses, the virus replicated in the brains of infected mice. A/Dkmt virus cross-reacted poorly with ferret antisera raised against human H5N1 viruses, but prior infection with A/Dkmt virus protected mice from death after secondary infection with human H5N1 virus.

Pathogenicity and antigenicity of a new influenza A (H5N1) virus isolated from duck meat

Avian influenza A viruses are the ancestral origin of all human influenza viruses. The outbreak of highly pathogenic (HP) avian H5N1 in Hong Kong in 1997 highlighted the potential of these viruses to infect and cause severe disease in humans. Since 1999, HP H5N1 viruses were isolated several times from domestic poultry in Asia. In 2001, a HP H5N1 virus, A/Duck/Anyang/AVL-1/2001 (Dk/Anyang), was isolated from imported frozen duck meat in Korea. Because of this novel source of HP H5N1 virus isolation, concerns were raised about the potential for human exposure and infection; we therefore compared the Dk/Anyang virus with HP H5N1 viruses isolated from humans in 1997 in terms of antigenicity and pathogenicity for mammals. At high doses, Dk/Anyang virus caused up to 50% mortality in BALB/c mice, was isolated from the brains and lymphoid organs of mice, and caused lymphopenia. Overall Dk/Anyang virus was substantially less pathogenic for mice than the H5N1 virus isolated from a fatal human case in 1997. Likewise, Dk/Anyang virus was apathogenic for ferrets. Dk/Anyang virus was antigenically distinguishable by hemagglutination-inhibition (HI) assay from human H5N1 viruses isolated in 1997 and avian H5N1 viruses isolated in 2001 in Hong Kong. Nevertheless, prior infection with Dk/Anyang virus protected mice from death after secondary infection with HP human H5N1 viruses. These results indicate that compared with HP human H5N1 viruses, Dk/Anyang virus is substantially less pathogenic for mammalian species. Nevertheless, the novel source of isolation of this avian H5N1 virus must be considered when evaluating the potential risk to public health.

Intrinsically disordered protein

Proteins can exist in a trinity of structures: the ordered state, the molten globule, and the random coil. The five following examples suggest that native protein structure can correspond to any of the three states (not just the ordered state) and that protein function can arise from any of the three states and their transitions. (1) In a process that likely mimics infection, fd phage converts from the ordered into the disordered molten globular state. (2) Nucleosome hyperacetylation is crucial to DNA replication and transcription; this chemical modification greatly increases the net negative charge of the nucleosome core particle. We propose that the increased charge imbalance promotes its conversion to a much less rigid form. (3) Clusterin contains an ordered domain and also a native molten globular region. The molten globular domain likely functions as a proteinaceous detergent for cell remodeling and removal of apoptotic debris. (4) In a critical signaling event, a helix in calcineurin becomes bound and surrounded by calmodulin, thereby turning on calcineurin's serine/threonine phosphatase activity. Locating the calcineurin helix within a region of disorder is essential for enabling calmodulin to surround its target upon binding. (5) Calsequestrin regulates calcium levels in the sarcoplasmic reticulum by binding approximately 50 ions/molecule. Disordered polyanion tails at the carboxy terminus bind many of these calcium ions, perhaps without adopting a unique structure. In addition to these examples, we will discuss 16 more proteins with native disorder. These disordered regions include molecular recognition domains, protein folding inhibitors, flexible linkers, entropic springs, entropic clocks, and entropic bristles. Motivated by such examples of intrinsic disorder, we are studying the relationships between amino acid sequence and order/disorder, and from this information we are predicting intrinsic order/disorder from amino acid sequence. The sequence-structure relationships indicate that disorder is an encoded property, and the predictions strongly suggest that proteins in nature are much richer in intrinsic disorder than are those in the Protein Data Bank. Recent predictions on 29 genomes indicate that proteins from eucaryotes apparently have more intrinsic disorder than those from either bacteria or archaea, with typically > 30% of eucaryotic proteins having disordered regions of length > or = 50 consecutive residues.

Sequence analysis of hemagglutinin and nucleoprotein genes of measles viruses isolated in Korea during the 2000 epidemic

To characterize the genetic properties of currently circulating measles viruses in Korea, the complete nucleotide sequences of hemagglutinin (H) protein and nucleoprotein (N) genes of Korean viruses were analyzed. The entire genes of H and N were directly amplified by RT-PCR from each clinical specimen and sequenced. Sequence analyses of H and N genes indicated that all Korean viruses had a high degree of homology (>99.8%) when compared with each other. The Korean viruses differed from other wild-type viruses by as much as 6.8% in the H gene and 6.5% in the N gene at the nucleotide level. The deduced amino acid variability was up to 6.4% for the H protein and up to 6.5% for the N protein. Phylogenetic analyses of nucleotide sequences and deduced amino acid sequences of the H and N genes revealed that all Korean viruses were grouped into the clade H1.

FADD-deficient T cells exhibit a disaccord in regulation of the cell cycle machinery

FADD is an adapter protein that was originally isolated as a transducer of apoptotic signals for death domain-containing receptors. However, FADD-deficient mice are embryonic lethal and FADD(-/-) T cells developed from FADD(-/-) embryonic stem cells in the RAG-1(-/-) hosts lack the full potential to proliferate when stimulated through their T-cell receptor complex, suggesting that FADD protein might play a dualistic role in mediating not only cell death signaling but other non-apoptotic cellular pathways as well. Here we show that a substantial number of freshly isolated FADD(-/-) peripheral T cells are cycling but are defective in their co-stimulatory response when stimulated. Analysis of several cell cycle proteins shows normal down-regulation of p27 inhibitor but increased levels of p21, decreased levels of cyclin D2, and constitutive activation of several cyclin-dependent kinases in activated T cells. These data suggest that FADD is involved in the regulation of cell cycle machinery in T lymphocytes.

Drosophila Med6 is required for elevated expression of a large but distinct set of developmentally regulated genes

Mediator is the evolutionarily conserved coactivator required for the integration and recruitment of diverse regulatory signals to basal transcription machinery. To elucidate the functions of metazoan Mediator, we isolated Drosophila melanogaster Med6 mutants. dMed6 is essential for viability and/or proliferation of most cells. dMed6 mutants failed to pupate and died in the third larval instar with severe proliferation defects in imaginal discs and other larval mitotic cells. cDNA microarray, quantitative reverse transcription-PCR, and in situ expression analyses of developmentally regulated genes in dMed6 mutants showed that transcriptional activation of many, but not all, genes was affected. Among the genes found to be affected were some that play a role in cell proliferation and metabolism. Therefore, dMed6 is required in most cells for transcriptional regulation of many genes important for diverse aspects of Drosophila development.

T cell-specific FADD-deficient mice: FADD is required for early T cell development

FADD/Mort1, initially identified as a Fas-associated death-domain containing protein, functions as an adapter molecule in apoptosis initiated by Fas, tumor necrosis factor receptor-I, DR3, and TRAIL-receptors. However, FADD likely participates in additional signaling cascades. FADD-null mutations in mice are embryonic-lethal, and analysis of FADD(-)/- T cells from RAG-1(-)/- reconstituted chimeras has suggested a role for FADD in proliferation of mature T cells. Here, we report the generation of T cell-specific FADD-deficient mice via a conditional genomic rescue approach. We find that FADD-deficiency leads to inhibition of T cell development at the CD4(-)CD8(-) stage and a reduction in the number of mature T cells. The FADD mutation does not affect apoptosis or the proximal signaling events of the pre-T cell receptor; introduction of a T cell receptor transgene fails to rescue the mutant phenotype. These data suggest that FADD, through either a death-domain containing receptor or a novel receptor-independent mechanism, is required for the proliferative phase of early T cell development.

Sequence-specific termination by T7 RNA polymerase requires formation of paused conformation prior to the point of RNA release

BACKGROUND

The sequence-specific, hairpin-independent termination signal for the bacteriophage RNA polymerases in Escherichia coli rrnB t1 terminator consists of two modules. The upstream module includes the conserved sequence and the downstream one is U-rich.

RESULTS

Elongation complexes of T7 RNA polymerase paused 2 bp before reaching the termination site at a 500 microM concentration of NTP. At 5-50 microM NTP, however, they paused and terminated there or resumed elongation beyond the termination site. Only at higher concentrations of NTP (500 microM), the pause complex proceeded slowly to and became incompetent at the termination site. At 4 bp or more before the termination site, the unprotected single-stranded region of transcription bubble shrank at the trailing edge to 4-5 bp from approximately 10 bp, resulting from duplex formation of the conserved sequence. The pause and bubble collapse were not observed with an inactive mutant of the termination signal.

CONCLUSION

Sequence-specific termination requires the slow elongation mode of paused conformation, working only at high concentrations of NTP for a few bp prior to the RNA release site. The collapse of bubble that was observed several base pairs before the termination site and/or the resulting duplex might subsequently lead to the paused conformation of T7 elongation complexes.

Expression of cloned cDNA for the human mitochondrial RNA polymerase in Escherichia coli and purification

A full-length cDNA for the mature, mitochondrial form of human mitochondrial RNA polymerase was cloned and expressed under the control of T5 or tac promoter in Escherichia coli. The cDNA was efficiently expressed at 37 degrees C, but virtually all the polymerase produced was insoluble, and renaturation of the inclusion bodies was unsuccessful. When the cells were grown at 25 degrees C, however, a portion of approximately 10% was soluble and active. The protein was purified 100-fold from the soluble lysates to homogeneity by two-step chromatography using Ni-nitrilotriacetic acid-Sepharose and heparin-agarose columns, as an N-terminal histidine tag attached and as the tag cleaved away. The purified polymerases with and without the histidine tag were both active in RNA polymerization in vitro as measured with poly(dA-dT) template, and specific activity was 140,000 units/mg. The purified enzyme has the same biochemical properties as the polymerase fraction partially purified from the human mitochondria, except for the promoter-specific activity that was not observed with the purified polymerase in the presence of mitochondrial transcription factor A. Additional factor(s) and/or mammalian-specific or regulatory modification(s) of the polymerase should be necessary for promoter-specific transcription.

Effects of ipt gene expression on the physiological and chemical characteristics of Artemisia annua L

An isopentenyl transferase gene (ipt) from T-DNA was transferred into Artemisia annua L. via Agrobacterium tumefaciens. The ipt gene was placed in a binary vector under the control of the CaMV 35S promoter. Leaf explants were infected with A. tumefaciens LBA4404 containing pBIipt to induce the buds. Nineteen shoot lines were selected, which were resistant to kanamycin. Polymerase chain reactions and Southern blotting confirmed that at least five shoot lines contained the foreign gene. The results of RT-PCR and Northern blotting analyses suggested that the foreign ipt gene of the transgenic shoot was expressed. Cytokinins, chlorophyll and artemisinin contents were found increased at different degree. Content of cytokinins (iPA and iP) was elevated 2- to 3-fold, chlorophyll increased 20-60% and artemisinin increased 30-70% compared with the control plants, respectively. A direct correlation was found between the contents of cytokinins, chlorophyll and artemisinin. This may be the first report on the relationship between endogenous cytokinin content and the production of secondary metabolites in plants.

Leucine 41 is a gate for water entry in the reduction of Clostridium pasteurianum rubredoxin

Biological electron transfer is an efficient process even though the distances between the redox moieties are often quite large. It is therefore of great interest to gain an understanding of the physical basis of the rates and driving forces of these reactions. The structural relaxation of the protein that occurs upon change in redox state gives rise to the reorganizational energy, which is important in the rates and the driving forces of the proteins involved. To determine the structural relaxation in a redox protein, we have developed methods to hold a redox protein in its final oxidation state during crystallization while maintaining the same pH and salt conditions of the crystallization of the protein in its initial oxidation state. Based on 1.5 A resolution crystal structures and molecular dynamics simulations of oxidized and reduced rubredoxins (Rd) from Clostridium pasteurianum (Cp), the structural rearrangements upon reduction suggest specific mechanisms by which electron transfer reactions of rubredoxin should be facilitated. First, expansion of the [Fe-S] cluster and concomitant contraction of the NH...S hydrogen bonds lead to greater electrostatic stabilization of the extra negative charge. Second, a gating mechanism caused by the conformational change of Leucine 41, a nonpolar side chain, allows transient penetration of water molecules, which greatly increases the polarity of the redox site environment and also provides a source of protons. Our method of producing crystals of Cp Rd from a reducing solution leads to a distribution of water molecules not observed in the crystal structure of the reduced Rd from Pyrococcus furiosus. How general this correlation is among redox proteins must be determined in future work. The combination of our high-resolution crystal structures and molecular dynamics simulations provides a molecular picture of the structural rearrangement that occurs upon reduction in Cp rubredoxin.

Two site contact of elongating transcripts to phage T7 RNA polymerase at C-terminal regions

A series of active elongation complexes of the phage T7 RNA polymerase were obtained through stepwise walking of the polymerase along an immobilized DNA template. Transcripts were radiolabeled at the 16th to 18th residues, and a photocross-linkable 4-thio-UMP was separately incorporated at the 22nd, 24th, 32nd, and 38th residues. Such complexes (up to 51 nucleotides) produced by the incorporation of one nucleotide at a time were isolated and individually subjected to long wave UV cross-linking. Only when the cross-linker was positioned at the 3'-end (-1) of the elongating RNA and 8 nucleotides upstream (-9), was the RNA substantially cross-linked to the polymerase, regardless of how far it was from the 5'-end of the transcripts. Linkage of the 3'-end residue was mapped to the Thr(636)-Met(666) region, which contains nucleotide-binding sites. The -9 residue was cross-linked to the Ala(724)-Met(750) region rather than to the N-terminal region. These two contacts were maintained throughout the elongation complexes and reveal a route of nascent RNA through the T7 RNA polymerase in elongation complexes.