An Sp1/Sp3 site polymorphism associated with hypermethylation of the candidate tumor suppressor gene RIL in cancer

Gene silencing due to promoter methylation is an alternative to mutations and deletions, which inactivate tumor suppressor genes (TSG) in cancer. We identified RIL by Methylated CpG Island Amplification technique as a novel aberrantly methylated gene. RIL is expressed in normal tissues and maps to the 5q31 region, frequently deleted in leukemias. We found methylation of RIL in 55/80 (69%) cancer cell lines, with highest methylation in leukemia and colon. We also observed methylation in 46/80 (58%) primary tumors, whereas normal tissues showed substantially lower degrees of methylation. RIL expression was lost in 13/16 cancer cell lines and was restored by demethylating agent. Screening of 38 cell lines and 13 primary cancers by SSCP revealed no mutations in RIL, suggesting that methylation and LOH are the primary inactivation mechanisms. Stable transfection of RIL into colorectal cancer cells resulted in reduction in cell growth, clonogenicity, and increased apoptosis upon UVC treatment, suggesting that RIL is a good candidate TSG. ^ In searching for a cause of RIL hypermethylation, we identified a 12-bp polymorphic sequence around the transcription start site of the gene that creates a long allele containing 3CTC repeat. Evolutionary studies suggested that the long allele appeared late in evolution due to insertion. Using bisulfite sequencing, in cancers heterozygous for RIL, we found that the short allele is 4.4-fold more methylated than the long allele (P = 0.003). EMSA results suggested binding of factor(s) to the inserted region of the long allele, but not to the short. EMSA mutagenesis and competition studies, as well as supershifts using nuclear extracts or recombinant Sp1 strongly indicated that those DNA binding proteins are Sp1 and Sp3. Transient transfections of RIL allele-specific expression constructs showed less than 2-fold differences in luciferase activity, suggesting no major effects of the additional Sp1 site on transcription. However, stable transfection resulted in 3-fold lower levels of transcription from the short allele 60 days post-transfection, consistent with the concept that the polymorphic Sp1 site protects against time-dependent silencing. Thus, an insertional polymorphism in the RIL promoter creates an additional Sp1/Sp3 site, which appears to protect it from silencing and methylation in cancer. ^

PDZ Motifs in PTP-BL and RIL Bind to Internal Protein Segments in the LIM Domain Protein RIL

The specificity of protein–protein interactions in cellular signaling cascades is dependent on the sequence and intramolecular location of distinct amino acid motifs. We used the two-hybrid interaction trap to identify proteins that can associate with the PDZ motif-rich segment in the protein tyrosine phosphatase PTP-BL. A specific interaction was found with the Lin-11, Isl-1, Mec-3 (LIM) domain containing protein RIL. More detailed analysis demonstrated that the binding specificity resides in the second and fourth PDZ motif of PTP-BL and the LIM domain in RIL. Immunohistochemistry on various mouse tissues revealed a submembranous colocalization of PTP-BL and RIL in epithelial cells. Remarkably, there is also an N-terminal PDZ motif in RIL itself that can bind to the RIL-LIM domain. We demonstrate here that the RIL-LIM domain can be phosphorylated on tyrosine in vitro and in vivo and can be dephosphorylated in vitro by the PTPase domain of PTP-BL. Our data point to the presence of a double PDZ-binding interface on the RIL-LIM domain and suggest tyrosine phosphorylation as a regulatory mechanism for LIM-PDZ associations in the assembly of multiprotein complexes. These findings are in line with an important role of PDZ-mediated interactions in the shaping and organization of submembranous microenvironments of polarized cells.

Sustainability factors in Industrialised Building System

In Malaysia, Industrialised Building Systems (IBS) are being promoted as a potential to enhance sustainability by the building industry and government. Known elsewhere as prefabricated construction, IBS employs a combination of ready-made components in the construction of buildings that promote quality of production, enhance simplification of construction processes and minimise on-site work. The components are manufactured in a factory either on or off site. They are then positioned and assembled into building structures. The unique characteristic of IBS has the potential to respond well to the sustainability challenge facing the construction industry. Despite the promises however, IBS has yet to be effectively implemented in Malaysia. There are often misconceptions among key stakeholders about IBS applications and some of the rating schemes fail to assess IBS towards sustainability deliverables. A holistic approach to improving IBS implementation is necessary to consider sustainability perceptions on IBS among key stakeholders. As IBS design is one of the most important development phases to incorporate sustainability requirements and expectations, a framework of embedding sustainability factors into IBS design is being developed through research. This paper presents an improved IBS design process focused on sustainability, showing where and how sustainability should be assessed to improve IBS construction. The framework being developed can provide guidance and decision making assistance to not only design consultants but all relevant stakeholders by integrating sustainability concepts into IBS applications. Outcome of the research will also provide a benchmark for developing countries in adopting prefabricated construction systems.

QTL analysis of ergot resistance in sorghum

Sorghum ergot, caused predominantly by Claviceps africana Frederickson, Mantle, de Milliano, is a significant threat to the sorghum industry worldwide. The objectives of this study were firstly, to identify molecular markers linked to ergot resistance and to two pollen traits, pollen quantity (PQ) and pollen viability (PV), and secondly, to assess the relationship between the two pollen traits and ergot resistance in sorghum. A genetic linkage map of sorghum RIL population R931945-2-2 x IS 8525 (resistance source) was constructed using 303 markers including 36 SSR, 117 AFLP™, 148 DArT™ and two morphological trait loci. Composite interval mapping identified nine, five, and four QTL linked to molecular markers for percentage ergot infection (PCERGOT), PQ and PV, respectively, at a LOD >2.0. Co-location/linkage of QTL were identified on four chromosomes while other QTL for the three traits mapped independently, indicating that both pollen and non pollen-based mechanisms of ergot resistance were operating in this sorghum population. Of the nine QTL identified for PCERGOT, five were identified using the overall data set while four were specific to the group data sets defined by temperature and humidity. QTL identified on SBI-02 and SBI-06 were further validated in additional populations. This is the first report of QTL associated with ergot resistance in sorghum. The markers reported herein could be used for marker-assisted selection for this important disease of sorghum.

DArT markers: Diversity analyses and mapping in Sorghum bicolor

The sequential nature of gel-based marker systems entails low throughput and high costs per assay. Commonly used marker systems such as SSR and SNP are also dependent on sequence information. These limitations result in high cost per data point and significantly limit the capacity of breeding programs to obtain sufficient return on investment to justify the routine use of marker-assisted breeding for many traits and particularly quantitative traits. Diversity Arrays Technology (DArT™) is a cost effective hybridisation-based marker technology that offers a high multiplexing level while being independent of sequence information. This technology offers sorghum breeding programs an alternative approach to whole-genome profiling. We report on the development, application, mapping and utility of DArT™ markers for sorghum germplasm. Results: A genotyping array was developed representing approximately 12,000 genomic clones using PstI+BanII complexity with a subset of clones obtained through the suppression subtractive hybridisation (SSH) method. The genotyping array was used to analyse a diverse set of sorghum genotypes and screening a Recombinant Inbred Lines (RIL) mapping population. Over 500 markers detected variation among 90 accessions used in a diversity analysis. Cluster analysis discriminated well between all 90 genotypes. To confirm that the sorghum DArT markers behave in a Mendelian manner, we constructed a genetic linkage map for a cross between R931945-2-2 and IS 8525 integrating DArT and other marker types. In total, 596 markers could be placed on the integrated linkage map, which spanned 1431.6 cM. The genetic linkage map had an average marker density of 1/2.39 cM, with an average DArT marker density of 1/3.9 cM. Conclusion: We have successfully developed DArT markers for Sorghum bicolor and have demonstrated that DArT provides high quality markers that can be used for diversity analyses and to construct medium-density genetic linkage maps. The high number of DArT markers generated in a single assay not only provides a precise estimate of genetic relationships among genotypes, but also their even distribution over the genome offers real advantages for a range of molecular breeding and genomics applications.

Influence of suspended particles and particle cover over the density interface

The effect of the particle cover over the density interface between two layers of fluids and of the suspended solid particles in the upper turbulcnt layer on the turbulent entrainment has been studied experimentally. The entrainment distance D is a function of the time of power: D=kt, where =0.200-0.130p. For suspended particles in the upper layer and pure 2-layer fluid is equal to 0.200, but the value of k for the suspended particles is smaller than that for the pure 2-layer fluid. The non-dimensional entrainment velocity is E=KRiln, where n=1.50+0.93 p. It is shown that the particle cover over the interface changes the power of Ril in the entrainment and hinders the turbulent entrainment. The variation rule of E for the suspended particles is the same as that for the pure 2-layer fluid, but the K value of the former is smaller than that of the latter. The turbulent mixing mechanism has been discussed.

Standing wave of finite-amplitude in an circular basin with uneven bottom

The effect of the particle cover over the density interface between two layers of fluids and of the suspended solid particles in the upper turbulcnt layer on the turbulent entrainment has been studied experimentally. The entrainment distance D is a function of the time of power: D=kt, where =0.200-0.130p. For suspended particles in the upper layer and pure 2-layer fluid is equal to 0.200, but the value of k for the suspended particles is smaller than that for the pure 2-layer fluid. The non-dimensional entrainment velocity is E=KRiln, where n=1.50+0.93 p. It is shown that the particle cover over the interface changes the power of Ril in the entrainment and hinders the turbulent entrainment. The variation rule of E for the suspended particles is the same as that for the pure 2-layer fluid, but the K value of the former is smaller than that of the latter. The turbulent mixing mechanism has been discussed.

人外周血单核细胞来源的树突状细胞的体外

以人浓缩白细胞来源的CD14+单核细胞为前体,建立体外快速培养树突状细胞(dendritic cell,DC)的方法.采用密度梯度离心和MACS磁珠分选系统,收集高纯度的CD14+单核细胞;以rGM-CSF、rIL-4联合分化2天诱导不成熟DC,再将分化后的细胞以rTNF-α、IL-1β、IL-6、PGE2共同活化2天得到成熟DC.流式细胞仪检测结果表明,分化2天的不成熟DC具有吞噬能力,且表型HLA-DR、CD40、CD80表达在80%以上,CD83、CD86基本小表达,成熟后的DC能够激活T细胞增殖,HLA-DR表达增高,CD83、CD86表达占85%.

草鱼、中华鳖脾细胞培养上清液IL-2物质的检测

用刀豆蛋白A(ConA)刺激诱导草鱼和中华鳖脾细胞 ,收集细胞培养上清液 ,用小鼠胸腺细胞增殖试验和对小鼠L92 9细胞系杀伤试验检测上清液中白细胞介素 2 (简称IL 2 )活性。结果表明 :草鱼、中华鳖脾细胞培养上清液中有IL 2样活性物质 ,这种物质使小鼠的胸腺细胞3H TdR掺入量明显增加 ,在相同效靶比的条件下对小鼠L92 9细胞系杀伤率也显著增强 ,这种IL 2活性均能被抗人rIL 2血清所抑制。中华鳖脾细胞培养上清液 (含IL 2 )对中华鳖胸腺细胞也有较明显的促增殖作用并能消除兔抗中华鳖胸

The search for the IFN-gamma receptor in fish: Functional and expression analysis of putative binding and signalling chains in rainbow trout Oncorhynchus mykiss

Interferons (IFNs), consisting of three major subfamilies, type I, type II (gamma) and type III (lambda) IFN, activate vertebrate antiviral defences once bound to their receptors. The three IFN subfamilies bind to different receptors, IFNAR1 and IFNAR2 for type I IFNs, IFN gamma R1 and IFN gamma R2 for type II IFN, and IL-28R1 and IL-10R2 for type III IFNs. In fish, although many types I and II IFN genes have been cloned, little is known about their receptors. In this report, two putative IFN-gamma receptor chains were identified and sequenced in rainbow trout (Oncorhynchus mykiss), and found to have many common characteristics with mammalian type II IFN receptor family members. The presented gene synteny analysis, phylogenetic tree analysis and ligand binding analysis all suggest that these molecules are the authentic IFN gamma Rs in fish. They are widely expressed in tissues, with IFN gamma R1 typically more highly expressed than IFN gamma R2. Using the trout RTG-2 cell line it was possible to show that the individual chains could be differentially modulated, with rIFN-gamma and rIL-1 beta down regulating IFN gamma R1 expression but up regulating IFN gamma R2 expression. Overexpression of the two receptor chains in RTG-2 cells revealed that the level of IFN gamma R2 transcript was crucial for responsiveness to rIFN-gamma, in terms of inducing gamma IP expression. Transfection experiments showed that the two putative receptors specifically bound to rIFN-gamma. These findings are discussed in the context of how the IFN gamma R may bind IFN-gamma in fish and the importance of the individual receptor chains to signal transduction. (c) 2009 Elsevier Ltd. All rights reserved.

The biological effects of rainbow trout (Oncorhynchus mykiss) recombinant interleukin-8

In this report, recombinant interieukin-8 (rIL-8) was produced and its activity tested for the first time in fish. The rainbow trout rIL-8 was produced in Escherichia coli and purified using a 6xHis tag at the N-terminus. The rIL-8 induced a dose-dependent migration of head kidney leukocytes at concentrations from 0.1 to 10 ng/ml, with a peak response at 1 ng/ml. Trout rIL-8 also had a significant effect on superoxide production by head kidney cells, with maximal, activity at 0.1 and 1 ng/ml. When injected intraperitoneally into trout, rIL-8 had a clear effect on total leukocyte number in the peritoneal cavity, with increasing doses (up to 5 mu g) eliciting more cells. Of three leukocyte types distinguished, neutrophils were the dominant cell type, especially at higher rIL-8 concentrations. In contrast, the proportion of macrophages and lymphocytes decreased with rIL-8 administration, suggesting that they were not attracted at the same rate as neutrophils. (C) 2007 Elsevier Ltd. All rights reserved.

A novel inflammatory biomarker, GlycA, associates with disease activity in rheumatoid arthritis and cardio-metabolic risk in BMI-matched controls

BACKGROUND: RA and CVD both have inflammation as part of the underlying biology. Our objective was to explore the relationships of GlycA, a measure of glycosylated acute phase proteins, with inflammation and cardiometabolic risk in RA, and explore whether these relationships were similar to those for persons without RA. METHODS: Plasma GlycA was determined for 50 individuals with mild-moderate RA disease activity and 39 controls matched for age, gender, and body mass index (BMI). Regression analyses were performed to assess relationships between GlycA and important markers of traditional inflammation and cardio-metabolic health: inflammatory cytokines, disease activity, measures of adiposity and insulin resistance. RESULTS: On average, RA activity was low (DAS-28 = 3.0 ± 1.4). Traditional inflammatory markers, ESR, hsCRP, IL-1β, IL-6, IL-18 and TNF-α were greater in RA versus controls (P < 0.05 for all). GlycA concentrations were significantly elevated in RA versus controls (P = 0.036). In RA, greater GlycA associated with disease activity (DAS-28; RDAS-28 = 0.5) and inflammation (RESR = 0.7, RhsCRP = 0.7, RIL-6 = 0.3: P < 0.05 for all); in BMI-matched controls, these inflammatory associations were absent or weaker (hsCRP), but GlycA was related to IL-18 (RhsCRP = 0.3, RIL-18 = 0.4: P < 0.05). In RA, greater GlycA associated with more total abdominal adiposity and less muscle density (Rabdominal-adiposity = 0.3, Rmuscle-density = -0.3, P < 0.05 for both). In BMI-matched controls, GlycA associated with more cardio-metabolic markers: BMI, waist circumference, adiposity measures and insulin resistance (R = 0.3-0.6, P < 0.05 for all). CONCLUSIONS: GlycA provides an integrated measure of inflammation with contributions from traditional inflammatory markers and cardio-metabolic sources, dominated by inflammatory markers in persons with RA and cardio-metabolic factors in those without.

Climate Adaptation: The future of extra-care housing for the elderly in the United Kingdom.

This paper describes the result of a project to develop climate adaptation design strategies funded by the UK’s Technology Strategy Board. The aim of the project was to look at the effects of climate change in the distant future (2080) on a vulnerable group such as older people with special needs and see how architectural design strategies and technologies may be used today to help mitigate problems ahead caused by climate change.
Older people are the most vulnerable sector of society and are particularly at risk in extreme weather, either excess cold in winter or continual high temperatures in summer. In the UK it is predicted that average temperatures may rise by as much as 8 degrees in Summer by 2080 and there will be a 20% greater chance of extreme weather events. This will place extreme stress on the building stock which is designed for today’s mild maritime climate.
The project took a current proposal for an extra-care home for the elderly designed to 2010 regulations and developed a road map to 2080 using climate models developed by the UK Meteorological Office. This allowed the current design to be assessed using future climatic data, proposals for improvement of the scheme to be made within existing constraints and also a new scheme to be developed from first principals using this data, and projections of new technologies that will be available. By comparing these schemes, the approach allowed a reassessment of the initial scheme, and allowed a new design to be developed that offered a more flexible solution incorporating future retrofit which allows new renewable technologies for heating, cooling and water storage to be added at a later date.

Unexpected Role for Adaptive αβTh17 Cells in Acute Respiratory Distress Syndrome

Acute respiratory distress syndrome (ARDS) is a devastating disorder characterized by increased alveolar permeability with no effective treatment beyond supportive care. Current mechanisms underlying ARDS focus on alveolar endothelial and epithelial injury caused by products of innate immune cells and platelets. However, the role of adaptive immune cells in ARDS remains largely unknown. In this study, we report that expansion of Ag-specific αβTh17 cells contributes to ARDS by local secretion of IL-17A, which in turn directly increases alveolar epithelial permeability. Mice with a highly restrictive defect in Ag-specific αβTh17 cells were protected from experimental ARDS induced by a single dose of endotracheal LPS. Loss of IL-17 receptor C or Ab blockade of IL-17A was similarly protective, further suggesting that IL-17A released by these cells was responsible for this effect. LPS induced a rapid and specific clonal expansion of αβTh17 cells in the lung, as determined by deep sequencing of the hypervariable CD3RβVJ region of the TCR. Our findings could be relevant to ARDS in humans, because we found significant elevation of IL-17A in bronchoalveolar lavage fluid from patients with ARDS, and rIL-17A directly increased permeability across cultured human alveolar epithelial monolayers. These results reveal a previously unexpected role for adaptive immune responses that increase alveolar permeability in ARDS and suggest that αβTh17 cells and IL-17A could be novel therapeutic targets for this currently untreatable disease.