BACKGROUND: The implementation of microarray analysis in prenatal diagnostics is a topic of discussion, as rare copy number variants with unknown/uncertain clinical consequences are likely to be found. The application of targeted microarrays limits such findings, but the potential disadvantage is that relevant, so far unknown, aberrations might be overlooked. Therefore, we explore the possibilities for the prenatal application of the genome-wide 250k single nucleotide polymorphism array platform. METHODS: Affymetrix 250k NspI single nucleotide polymorphism array analysis (Affymetrix, Inc., Santa Clara, California, USA) was performed on DNA from 38 prenatally karyotyped fetuses with ultrasound anomalies. Analyses were performed after termination of pregnancy, intrauterine fetal death or birth on DNA isolated from fetal or neonatal material. RESULTS: Aberrations were detected in 17 of 38 fetuses, 6 of whom with a previously identified chromosomal abnormality and 11 with previously normal or balanced karyotypes. Of the latter, the detected aberration occurred de novo and was considered of clinical relevance in five cases (16%), inherited from a healthy parent in four cases (12%), and de novo yet with unclear clinical relevance in two cases (6%). The clinically relevant abnormalities either were novel copy number variants (n=3) or concerned a uniparental disomy (n=2). CONCLUSION: In at least 16% of fetuses with ultrasound anomalies and a normal or balanced karyotype, causal (submicroscopic) aberrations were detected, illustrating the importance of the (careful) implementation of microarray analysis in prenatal diagnosis. The fact that the identified, clinically relevant, aberrations would have gone undetected with most targeted approaches underscores the added value of a genome-wide approach.
BACKGROUND: Quantitative traits, such as disease resistance, are most often controlled by a set of genes involving a complex array of regulation. The dissection of genetic basis of quantitative traits requires large numbers of genetic markers with good genome coverage. The application of next-generation sequencing technologies has allowed discovery of over eight million SNPs in catfish, but the challenge remains as to how to efficiently and economically use such SNP resources for genetic analysis. RESULTS: In this work, we developed a catfish 250K SNP array using Affymetrix Axiom genotyping technology. The SNPs were obtained from multiple sources including gene-associated SNPs, anonymous genomic SNPs, and inter-specific SNPs. A set of 640K high-quality SNPs obtained following specific requirements of array design were submitted. A panel of 250,113 SNPs was finalized for inclusion on the array. The performance evaluated by genotyping individuals from wild populations and backcross families suggested the good utility of the catfish 250K SNP array. CONCLUSIONS: This is the first high-density SNP array for catfish. The array should be a valuable resource for genome-wide association studies (GWAS), fine QTL mapping, high-density linkage map construction, haplotype analysis, and whole genome-based selection.
Saturated vapor pressures of ice at temperatures below 200K have become more important since the discovery of ice clouds in the polar stratosphere and upper mesosphere. Direct measurements of ice vapor pressures at such low temperatures are sparse and unreliable. This paper summarizes published vapor pressure data and presents new measurements at temperatures between 170 and 250K, extending the range of measured ice vapor pressures by three orders of magnitude. A simple empirical vapor pressure equation is derived which permits prediction of vapor pressures between 170K and the triple point of water, with an accuracy of about 2%: log P = A/T + B, with A = −2663.5 ± 0.8, B = 12.537 ± 0.011, P in Pa and T in kelvins. Predictions by this empirical equation agree, within experimental uncertainty, with the most reliable equation derived from thermodynamic principles.
Two types of acquired loss of heterozygosity are possible in cancer: deletions and copy-neutral uniparental disomy (UPD). Conventionally, copy number losses are identified using metaphase cytogenetics, whereas detection of UPD is accomplished by microsatellite and copy number analysis and as such, is not often used clinically. Recently, introduction of single nucleotide polymorphism (SNP) microarrays has allowed for the systematic and sensitive detection of UPD in hematologic malignancies and other cancers. In this study, we have applied 250K SNP array technology to detect previously cryptic chromosomal changes, particularly UPD, in a cohort of 301 patients with myelodysplastic syndromes (MDS), overlap MDS/myeloproliferative disorders (MPD), MPD, and acute myeloid leukemia. We show that UPD is a common chromosomal defect in myeloid malignancies, particularly in chronic myelomonocytic leukemia (CMML; 48%) and MDS/MPD-unclassifiable (38%). Furthermore, we show that mapping minimally overlapping segmental UPD regions can help target the search for both known and unknown pathogenic mutations, including newly identified missense mutations in the proto-oncogene c-Cbl in 7 of 12 patients with UPD11q. Acquired mutations of c-Cbl E3 ubiquitin ligase may explain the pathogenesis of a clonal process in a subset of MDS/MPD, including CMML.
OBJECTIVE: We evaluated both clinical and laboratory aspects of our new strategy offering quantitative fluorescence (QF)-PCR followed by non-targeted whole genome 250K single-nucleotide polymorphism array analysis instead of routine karyotyping for prenatal diagnosis of fetuses with structural anomalies. METHODS: Upon the detection of structural fetal anomalies, parents were offered a choice between QF-PCR and 250K single-nucleotide polymorphism array analysis (QF/array) or QF-PCR and routine karyotyping (QF/karyo). RESULTS: Two hundred twenty fetal samples were included. In 153/220 cases (70%), QF/array analysis was requested. In 35/153 (23%), an abnormal QF-PCR result was found. The remaining samples were analyzed by array, which revealed clinically relevant aberrations, including two known microdeletions, in 5/118 cases. Inherited copy number variants were detected in 11/118 fetuses, copy number variants with uncertain clinical relevance in 3/118 and homozygous stretches in 2/118. In 67/220 (30%) fetuses, QF/karyo was requested: 23/67 (34%) were abnormal with QF-PCR, and in 3/67, an abnormal karyotype was found. CONCLUSION: Even though QF/array does not reveal a high percentage of submicroscopic aberrations in fetuses with unselected structural anomalies, it is preferred over QF/karyo, as it provides a whole genome scan at high resolution, without additional tests needed and with a low chance on findings not related to the ultrasound anomalies.
The actin-based gel formed at 35 degrees C in the cytoplasmic extract from eggs of a sea urchin, Tripneustes gratilla, contains several high-molecular-weight proteins. Among them, the 250K-molecular-weight protein was isolated and characterized. This protein migrated slightly more slowly than filamin from chicken gizzard upon polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. It reacted only very weakly with antibodies against chicken gizzard filamin or against a high-molecular-weight actin-binding protein from Physarum plasmodia. It did not react with antibodies against chicken erythrocyte alpha-spectrin nor against the 220K protein from the same egg. A chemical crosslinking experiment revealed the presence of dimers in the purified 250K protein preparation. A rotary shadowed specimen of such a preparation showed wavy single-stranded molecules 120-170 nm long, having five to six globular domains, which may represent dimers. The appearance was different from that of spectrin or actin-binding protein from macrophage or chicken gizzard filamin. This protein increased the viscosity of F-actin solution. It bound to F-actin preferably at low KCl concentrations such as 20 mM. The binding ability was not influenced by pH between 6.0 and 7.5, although it was somewhat reduced above pH 8.0. The binding was insensitive to low Ca ion concentrations. Electron microscopy using the negative staining technique supported the idea that this protein crosslinks actin filaments. In addition, a second protein from egg gels, with a reported molecular weight of about 220K (Kane, R.E., J. Cell Biol. 66, 305-315 (1975)), comigrated with human erythrocyte alpha-spectrin on an SDS-gel and reacted with antibodies against chicken erythrocyte alpha-spectrin. This suggests that this protein is a sea urchin egg spectrin. The role of these proteins in the cytoskeleton formation in the sea urchin egg is discussed.
The hydrodynamics and mass transfer performance of 250K ripple packing were studied(experimentally) and compared with those of 250Y ripple packing. The experimental results show that 250K ripple packing can obviously eliminate effect of wall flowing,which makes the steam fluid distribution to be even.Compared with 250Y ripple packing,250K ripple packing has outstanding features in(decreasing) the pressure drop by 20%,increasing the flooding velocity by 20% and mass transfer efficiency by(about) 10%~20%.The pressure drop are correlated with the experimental data,and empirical formulas of pressure drop are obtained.
Multiple factors are involved in the variability of host's response to P. falciparum infection, like the intensity and seasonality of malaria transmission, the virulence of parasite and host characteristics like age or genetic make-up. Although admitted nowadays, the involvement of host genetic factors remains unclear. Discordant results exist, even concerning the best-known malaria resistance genes that determine the structure or function of red blood cells. Here we report on a genome-wide linkage and association study for P. falciparum infection intensity and mild malaria attack among a Senegalese population of children and young adults from 2 to 18 years old. A high density single nucleotide polymorphisms (SNP) genome scan (Affimetrix GeneChip Human Mapping 250K-nsp) was performed for 626 individuals: i.e. 249 parents and 377 children out of the 504 ones included in the follow-up. The population belongs to a unique ethnic group and was closely followed-up during 3 years. Genome-wide linkage analyses were performed on four clinical and parasitological phenotypes and association analyses using the family based association tests (FBAT) method were carried out in regions previously linked to malaria phenotypes in literature and in the regions for which we identified a linkage peak. Analyses revealed three strongly suggestive evidences for linkage: between mild malaria attack and both the 6p25.1 and the 12q22 regions (empirical p-value=5x10(-5) and 9x10(-5) respectively), and between the 20p11q11 region and the prevalence of parasite density in asymptomatic children (empirical p-value=1.5x10(-4)). Family based association analysis pointed out one significant association between the intensity of plasmodial infection and a polymorphism located in ARHGAP26 gene in the 5q31-q33 region (p-value=3.7x10(-5)). This study identified three candidate regions, two of them containing genes that could point out new pathways implicated in the response to malaria infection. Furthermore, we detected one gene associated with malaria infection in the 5q31-q33 region.
A 250K probing-resilient PUF array with measured 2GHz operation and total energy consumption of 13fJ/bit at 0.9V, 25°C is fabricated in 22nm tri-gate CMOS. Hybrid PUF circuit with integrated load modulation and run-time soft dark-bit mask generation enables identification of unstable PUF bits with 100% accuracy, eliminating the need for multiple voltage/temperature characterization while also reducing bit-error down to 1.94%. Transient behavior of the hybrid PUF cell, along with the use of balanced local clock routing improves resiliency to invasive power-up probing attacks by 75%.
Tomato black ring virus RNA-1 was translated in a rabbit reticulocyte lysate. The primary translation product of Mr 250K, which corresponds to its whole coding capacity, was synthesized within 45 min and, during further incubation in the translation medium, was proteolytically processed. Essentially, four cleavage products (P190, P120, P60 and P50) were detected and located within P250 by pulse-chase and immunoprecipitation experiments. P190 is an intermediate cleavage product which is further cleaved to form P60 and P120. P120, which contains the region that has been assigned to the virus protease and the virus polymerase, was not further cleaved in vitro.
Abstract Myelodysplastic syndromes (MDS) are characterized by the presence of clonal chromosomal abnormalities detectable by traditional cytogenetics in around 50% of patients. We demonstrated that a higher percentage of unbalanced clonal chromosomal defects and uniparental disomy (UPD) can be identified in MDS using high-density SNP arrays (50 or 250K SNP-A; Gondek et al, 2005). The higher detection rate may have important clinical consequences. However, such findings must be considered in the context of normal karyotypic variation. Before the clinical relevance of new lesions identified by SNP-A can be presumed, several issues must be addressed. The increased precision of karyotypic analysis may lead to the detection of lesions in normal bone marrow. This is especially relevant to elderly patients with MDS for whom adequate age-matched comparisons should be performed. The normal distribution of chromosomal changes across the genome must be defined as it may overlap with that in disease. The minimal clonal size detectable by SNP-A analysis is of importance, as hematopoiesis may be oligo- rather than monoclonal in many conditions. We stipulated that the clinical applicability of SNP-A-based karyotyping will depend upon the findings in healthy controls and have studied 36 normal bone marrows using SNP-A karyotype analysis. We utilized the Affymetrix 250K SNP chip and the CNAG software for copy number and LOH analysis. Using a stringent set of criteria, suspicious lesions were identified in 83% of samples. Loci altered in 2 or more samples, most likely reflecting copy number polymorphisms (CNP), were identified in 70% of individuals. With these CNP excluded, 69% of controls harbored putative lesions. 11 marrows contained 1 chromosomal change, while 2-4 were found in 14 marrows. Both loss and gain of sequences were detected. The size of the largest deletion and duplication was 1.8 Mb and 1.64 Mb, respectively. Karyotypic abnormalities identified in control samples appeared to be randomly distributed across the genome. No lesions were identified on chromosome 8 or chromosome 5q, although one deletion on chromosome 5p was found. A small deletion of 7q was detected (1.2 Mb); overall, the regions frequently affected in MDS were rarely altered in controls. Finally, we identified LOH due to UPD spanning 13q21.3 to 13q32.1 (4.95 Mb) in one healthy control. To assess the minimal detectable clonal size, we next examined the sensitivity of SNP-A analysis to the admixture of normal cells. When samples identified as abnormal (deletion of 7q, and trisomy 8) by traditional cytogenetics were serially diluted with normal genomic DNA, the previously identified lesions could still be detected when the sample contained 25% normal genomic DNA, but at 50% the copy number analysis appeared normal. Our result underscores that, only significantly expanded clones can be systematically detected by SNP-A analysis. Pathogeneic defects have to exclude regions of CNP and must be larger than changes in healthy controls. Additionally, they would preferentially occur in regions not frequently affected in normal bone marrow. Our studies reveal the physiologic level of chromosomal abnormalities present in healthy controls and allow us to design criteria for defining abnormal karyotypes as measured by SNP-A.
This paper presents a generalization methodology to derive multi‐scale GEODATA through an evaluation of ESRI ArcGIS™ software that was used as a testbed based on the principles of generalization. It focuses on integration and utilization of generalization operators in order to generalize a road network database and produce small scale maps at 1:500 000 and 1:1 000 000 from GEODATA TOPO‐250K Series 2 data. The derived maps are satisfactory when compared with the existing small‐scale road maps such as the Global Map at scale of 1:1000 000. It is suggested that a comprehensive evaluation of generalization systems and their performance is essential to marry the cartographic knowledge from experts and bring this into a generalization framework. Therefore, there is an opportunity to evaluate other generalization systems to derive a multi‐scale database from a master database in future investigations to enhance the generalization methodology.
The Hybrid Propulsion Demonstration Program (HPDP) program was formed to mature hybrid propulsion technology to a readiness level sufficient to enable commercialization for various space launch applications. The goal of the HPDP was to develop and test a 250,000 pound vacuum thrust hybrid booster in order to demonstrate hybrid propulsion technology and enable manufacturing of large hybrid boosters for current and future space launch vehicles. The HPDP has successfully conducted four tests of the 250,000 pound thrust hybrid rocket motor at NASA's Stennis Space Center. This paper documents the test series.
We have developed a 51 O(H) x 492(V) pixel IT (Interline Transfer)-CCD with 3.65 mm(H) x 2.73 mm(V) image area, corresponding to a 1/4-inch optical format. The basic characteristics of the new CCD are better than or equal to those of the conventional 113-inch 250k CCD. Simplifying the driving circuit (54% of components of the conventional CCD) and shrinking the package (70% of the size of the conventional CCD) makes possible the down-sizing of a camera system.
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The pressure dependence of the superconducting transition temperature Tc (onset) of Tl1.8Ba2.0Ca2.6Cu3.0O10+δ (Tl-2223) has been measured under quasi-hydrostatic pressure (QHP) up to 5.0 GPa. The Tc increases with increasing pressure at a relatively high rate and reaches a maximum at 255.4 K and pressure of about 4.3 GPa. This is the highest Tc yet observed for any high-Tc superconductor. The total change in Tc from ambient condition (Tc=129 K) to the high pressure applied can be greater than 126 K. The Tc above 200 K was replicated several times in our experiments. The site of the maximum of Tc and the value of dTc/dP=1.7 K/GPa (at P=0) agree with previous results obtained by D. Tristan Jover et al. (Physica C 218, 24 (1993)) and J. G. Lin et al. (Physica C 175, 627 (1991)), respectively.
Development of shear-induced crystallization precursor structure was studied by in-situ rheo-SAXS (small-angle X-ray scattering) and rheo-WAXD (wide-angle X-ray diffraction) techniques using binary polymer blends of high and low molecular weight polyethylenes near their nominal melting temperatures (120 °C). Two low molecular weight polyethylene copolymers, containing 2 mol % hexene, with weight-average molecular weights ( M w ) of 50 000 (MB-50K) and 100 000 (MB-100K), and polydispersity of about 2, were used as the noncrystallizing matrices. A high molecular weight polyethylene homopolymer with M w of 250 000 (MB-250K) and polydispersity of about 2 was used as the crystallizing minor component. Two series of model blends, MB-50K/MB-250K and MB-100K/MB-250K, each containing weight ratios of 100/0, 97/3, 95/5, and 90/10, were prepared by solution blending to ensure thorough mixing at the molecular level. At the chosen shear conditions (rate = 60 s -1, duration = 5 s, T = 120 °C), while no flow-induced structures were seen in pure MB-50K and MB-100K melts, the blends in both series showed distinct but different shear-induced structures. Results indicate that the high molecular weight component dominates the formation of crystallization precursor structures in the blend under shear, which can act as a template for further crystallization. A “shish-kebab” structure, detected by both SAXS and WAXD, was observed in the MB-100K/MB-250K (90/10) blend, while only a twisted lamellar structure (kebab) was seen in the rest of the blends under the same shear conditions. These findings suggest that the matrix viscosity plays an important role to influence the formation of crystallization precursor structure of the high molecular component under flow. In the MB-100K/MB-250K (90/10) blend, the length of the shish was estimated from the equatorial streak in SAXS, which showed a noticeable decrease with time, while the corresponding scattering intensity was found to increase. The evolution of the shish-kebab structure from SAXS is consistent with the appearance of the (110) peak in WAXD, which can be explained by the coil−stretch transition induced by flow.