Science/Society Case Study - Ozone

ERIC Educational Resources Information Center

Moore, John W., Ed.; Moore, Elizabeth A., Ed.

1975-01-01

Describes various threats to the stability of the ozone layer of the atmosphere, including freons emitted from aerosol cans, combustion products from jet aircraft engines, and nuclear explosions in the atmosphere. (MLH)

mlh3 mutations in baker’s yeast alter meiotic recombination outcomes by increasing noncrossover events genome-wide

PubMed Central

Al-Sweel, Najla; Raghavan, Vandana; Khondakar, Nabila; Manhart, Carol M.; Surtees, Jennifer A.

2017-01-01

Mlh1-Mlh3 is an endonuclease hypothesized to act in meiosis to resolve double Holliday junctions into crossovers. It also plays a minor role in eukaryotic DNA mismatch repair (MMR). To understand how Mlh1-Mlh3 functions in both meiosis and MMR, we analyzed in baker’s yeast 60 new mlh3 alleles. Five alleles specifically disrupted MMR, whereas one (mlh3-32) specifically disrupted meiotic crossing over. Mlh1-mlh3 representatives for each class were purified and characterized. Both Mlh1-mlh3-32 (MMR+, crossover-) and Mlh1-mlh3-45 (MMR-, crossover+) displayed wild-type endonuclease activities in vitro. Msh2-Msh3, an MSH complex that acts with Mlh1-Mlh3 in MMR, stimulated the endonuclease activity of Mlh1-mlh3-32 but not Mlh1-mlh3-45, suggesting that Mlh1-mlh3-45 is defective in MSH interactions. Whole genome recombination maps were constructed for wild-type and MMR+ crossover-, MMR- crossover+, endonuclease defective and null mlh3 mutants in an S288c/YJM789 hybrid background. Compared to wild-type, all of the mlh3 mutants showed increases in the number of noncrossover events, consistent with recombination intermediates being resolved through alternative recombination pathways. Our observations provide a structure-function map for Mlh3 that reveals the importance of protein-protein interactions in regulating Mlh1-Mlh3’s enzymatic activity. They also illustrate how defective meiotic components can alter the fate of meiotic recombination intermediates, providing new insights for how meiotic recombination pathways are regulated. PMID:28827832

Reduced migration of MLH1 deficient colon cancer cells depends on SPTAN1.

PubMed

Hinrichsen, Inga; Ernst, Benjamin Philipp; Nuber, Franziska; Passmann, Sandra; Schäfer, Dieter; Steinke, Verena; Friedrichs, Nicolaus; Plotz, Guido; Zeuzem, Stefan; Brieger, Angela

2014-01-24

Defects in the DNA mismatch repair (MMR) protein MLH1 are frequently observed in sporadic and hereditary colorectal cancers (CRC). Affected tumors generate much less metastatic potential than the MLH1 proficient forms. Although MLH1 has been shown to be not only involved in postreplicative MMR but also in several MMR independent processes like cytoskeletal organization, the connection between MLH1 and metastasis remains unclear. We recently identified non-erythroid spectrin αII (SPTAN1), a scaffolding protein involved in cell adhesion and motility, to interact with MLH1. In the current study, the interaction of MLH1 and SPTAN1 and its potential consequences for CRC metastasis was evaluated. Nine cancer cell lines as well as fresh and paraffin embedded colon cancer tissue from 12 patients were used in gene expression studies of SPTAN1 and MLH1. Co-expression of SPTAN1 and MLH1 was analyzed by siRNA knock down of MLH1 in HeLa, HEK293, MLH1 positive HCT116, SW480 and LoVo cells. Effects on cellular motility were determined in MLH1 deficient HCT116 and MLH1 deficient HEK293T compared to their MLH1 proficient sister cells, respectively. MLH1 deficiency is clearly associated with SPTAN1 reduction. Moreover, siRNA knock down of MLH1 decreased the mRNA level of SPTAN1 in HeLa, HEK293 as well as in MLH1 positive HCT116 cells, which indicates a co-expression of SPTAN1 by MLH1. In addition, cellular motility of MLH1 deficient HCT116 and MLH1 deficient HEK293T cells was impaired compared to the MLH1 proficient sister clones. Consequently, overexpression of SPTAN1 increased migration of MLH1 deficient cells while knock down of SPTAN1 decreased cellular mobility of MLH1 proficient cells, indicating SPTAN1-dependent migration ability. These data suggest that SPTAN1 levels decreased in concordance with MLH1 reduction and impaired cellular mobility in MLH1 deficient colon cancer cells. Therefore, aggressiveness of MLH1-positive CRC might be related to SPTAN1.

Reduced migration of MLH1 deficient colon cancer cells depends on SPTAN1

PubMed Central

2014-01-01

Introduction Defects in the DNA mismatch repair (MMR) protein MLH1 are frequently observed in sporadic and hereditary colorectal cancers (CRC). Affected tumors generate much less metastatic potential than the MLH1 proficient forms. Although MLH1 has been shown to be not only involved in postreplicative MMR but also in several MMR independent processes like cytoskeletal organization, the connection between MLH1 and metastasis remains unclear. We recently identified non-erythroid spectrin αII (SPTAN1), a scaffolding protein involved in cell adhesion and motility, to interact with MLH1. In the current study, the interaction of MLH1 and SPTAN1 and its potential consequences for CRC metastasis was evaluated. Methods Nine cancer cell lines as well as fresh and paraffin embedded colon cancer tissue from 12 patients were used in gene expression studies of SPTAN1 and MLH1. Co-expression of SPTAN1 and MLH1 was analyzed by siRNA knock down of MLH1 in HeLa, HEK293, MLH1 positive HCT116, SW480 and LoVo cells. Effects on cellular motility were determined in MLH1 deficient HCT116 and MLH1 deficient HEK293T compared to their MLH1 proficient sister cells, respectively. Results MLH1 deficiency is clearly associated with SPTAN1 reduction. Moreover, siRNA knock down of MLH1 decreased the mRNA level of SPTAN1 in HeLa, HEK293 as well as in MLH1 positive HCT116 cells, which indicates a co-expression of SPTAN1 by MLH1. In addition, cellular motility of MLH1 deficient HCT116 and MLH1 deficient HEK293T cells was impaired compared to the MLH1 proficient sister clones. Consequently, overexpression of SPTAN1 increased migration of MLH1 deficient cells while knock down of SPTAN1 decreased cellular mobility of MLH1 proficient cells, indicating SPTAN1-dependent migration ability. Conclusions These data suggest that SPTAN1 levels decreased in concordance with MLH1 reduction and impaired cellular mobility in MLH1 deficient colon cancer cells. Therefore, aggressiveness of MLH1-positive CRC might be related to SPTAN1. PMID:24456667

Mlh2 Is an Accessory Factor for DNA Mismatch Repair in Saccharomyces cerevisiae

PubMed Central

Srivatsan, Anjana; Bowen, Nikki; Gries, Kerstin; Desai, Arshad; Putnam, Christopher D.; Kolodner, Richard D.

2014-01-01

In Saccharomyces cerevisiae, the essential mismatch repair (MMR) endonuclease Mlh1-Pms1 forms foci promoted by Msh2-Msh6 or Msh2-Msh3 in response to mispaired bases. Here we analyzed the Mlh1-Mlh2 complex, whose role in MMR has been unclear. Mlh1-Mlh2 formed foci that often colocalized with and had a longer lifetime than Mlh1-Pms1 foci. Mlh1-Mlh2 foci were similar to Mlh1-Pms1 foci: they required mispair recognition by Msh2-Msh6, increased in response to increased mispairs or downstream defects in MMR, and formed after induction of DNA damage by phleomycin but not double-stranded breaks by I-SceI. Mlh1-Mlh2 could be recruited to mispair-containing DNA in vitro by either Msh2-Msh6 or Msh2-Msh3. Deletion of MLH2 caused a synergistic increase in mutation rate in combination with deletion of MSH6 or reduced expression of Pms1. Phylogenetic analysis demonstrated that the S. cerevisiae Mlh2 protein and the mammalian PMS1 protein are homologs. These results support a hypothesis that Mlh1-Mlh2 is a non-essential accessory factor that acts to enhance the activity of Mlh1-Pms1. PMID:24811092

Drag-reducing polymers diminish near-wall concentration of platelets in microchannel blood flow

PubMed Central

Zhao, R.; Marhefka, J.N.; Antaki, J.F.; Kameneva, M.V.

2011-01-01

The accumulation of platelets near the blood vessel wall or artificial surface is an important factor in the cascade of events responsible for coagulation and/or thrombosis. In small blood vessels and flow channels this phenomenon has been attributed to the blood phase separation that creates a red blood cell (RBC)-poor layer near the wall. We hypothesized that blood soluble drag-reducing polymers (DRP), which were previously shown to lessen the near-wall RBC depletion layer in small channels, may consequently reduce the near-wall platelet excess. This study investigated the effects of DRP on the lateral distribution of platelet-sized fluorescent particles (diam. = 2 µm, 2.5 × 108/ml) in a glass square microchannel (width and depth = 100 µm). RBC suspensions in PBS were mixed with particles and driven through the microchannel at flow rates of 6–18 ml/h with and without added DRP (10 ppm of PEO, MW = 4500 kDa). Microscopic flow visualization revealed an elevated concentration of particles in the near-wall region for the control samples at all tested flow rates (between 2.4 ± 0.8 times at 6 ml/h and 3.3 ± 0.3 times at 18 ml/h). The addition of a minute concentration of DRP virtually eliminated the near-wall particle excess, effectively resulting in their even distribution across the channel, suggesting a potentially significant role of DRP in managing and mitigating thrombosis. PMID:21084744

Subsets of microsatellite-unstable colorectal cancers exhibit discordance between the CpG island methylator phenotype and MLH1 methylation status.

PubMed

Kim, Jung H; Rhee, Ye-Y; Bae, Jeong-M; Kwon, Hyeong-J; Cho, Nam-Y; Kim, Mi J; Kang, Gyeong H

2013-07-01

Although the presence of MLH1 methylation in microsatellite-unstable colorectal cancer generally indicates involvement of the CpG island methylator phenotype (CIMP) in the development of the tumor, these two conditions do not always correlate. A minority of microsatellite-unstable colorectal cancers exhibit discordance between CIMP and MLH1 methylation statuses. However, the clinicopathological features of such microsatellite-unstable colorectal cancers with discrepant MLH1 methylation and CIMP statuses remain poorly studied. Microsatellite-unstable colorectal cancers (n=220) were analyzed for CIMP and MLH1 methylation statuses using the MethyLight assay. Based on the combinatorial CIMP and MLH1 methylation statuses, the microsatellite-unstable colorectal cancers were grouped into four subtypes (CIMP-high (CIMP-H) MLH1 methylation-positive (MLH1m+), CIMP-H MLH1 methylation-negative, CIMP-low/0 (CIMP-L/0) MLH1m+, and CIMP-L/0 MLH1 methylation-negative), which were compared in terms of their associations with clinicopathological and molecular features. The CIMP-L/0 MLH1 methylation-negative and CIMP-H MLH1m+ subtypes were predominant, comprising 63.6 and 24.1% of total microsatellite-unstable colorectal cancers, respectively. The discordant subtypes, CIMP-H MLH1 methylation-negative and CIMP-L/0 MLH1m+, were found in 5 and 7% of microsatellite-unstable colorectal cancers, respectively. The CIMP-H MLH1 methylation-negative subtype exhibited elevated incidence rates in male patients and was associated with larger tumor size, more frequent loss of MSH2 expression, increased frequency of KRAS mutation, and advanced cancer stage. The CIMP-L/0 MLH1m+ subtype was associated with onset at an earlier age, a predominance of MLH1 loss, and earlier cancer stage. None of the CIMP-L/0 MLH1m+ subtype patients succumbed to death during the follow-up. Our findings suggest that the discordant subtypes of colorectal cancers exhibit distinct clinicopathological and molecular features, although the proportion of discordant subtypes is low. The microsatellite-unstable colorectal cancers of the same CIMP status tended to exhibit different clinicopathological features depending on MLH1 methylation status.

Haplotype defined by the MLH1-93G/A polymorphism is associated with MLH1 promoter hypermethylation in sporadic colorectal cancers.

PubMed

Miyakura, Yasuyuki; Tahara, Makiko; Lefor, Alan T; Yasuda, Yoshikazu; Sugano, Kokichi

2014-11-24

Methylation of the MLH1 promoter region has been suggested to be a major mechanism of gene inactivation in sporadic microsatellite instability-positive (MSI-H) colorectal cancers (CRCs). Recently, single-nucleotide polymorphism (SNP) in the MLH1 promoter region (MLH1-93G/A; rs1800734) has been proposed to be associated with MLH1 promoter methylation, loss of MLH1 protein expression and MSI-H tumors. We examined the association of MLH1-93G/A and six other SNPs surrounding MLH1-93G/A with the methylation status in 210 consecutive sporadic CRCs in Japanese patients. Methylation of the MLH1 promoter region was evaluated by Na-bisulfite polymerase chain reaction (PCR)/single-strand conformation polymorphism (SSCP) analysis. The genotype frequencies of SNPs located in the 54-kb region surrounding the MLH1-93G/A SNP were examined by SSCP analysis. Methylation of the MLH1 promoter region was observed in 28.6% (60/210) of sporadic CRCs. The proportions of MLH1-93G/A genotypes A/A, A/G and G/G were 26% (n=54), 51% (n=108) and 23% (n=48), respectively, and they were significantly associated with the methylation status (p=0.01). There were no significant associations between genotype frequency of the six other SNPs and methylation status. The A-allele of MLH1-93G/A was more common in cases with methylation than the G-allele (p=0.0094), especially in females (p=0.0067). In logistic regression, the A/A genotype of the MLH1-93G/A SNP was shown to be the most significant risk factor for methylation of the MLH1 promoter region (odds ratio 2.82, p=0.003). Furthermore, a haplotype of the A-allele of rs2276807 located -47 kb upstream from the MLH1-93G/A SNP and the A-allele of MLH1-93G/A SNP was significantly associated with MLH1 promoter methylation. These results indicate that individuals, and particularly females, carrying the A-allele at the MLH1-93G/A SNP, especially in association with the A-allele of rs2276807, may harbor an increased risk of methylation of the MLH1 promoter region.

Bone-97 Alcohol and Skeletal Adaptation to Mechanical Usage

DTIC Science & Technology

2002-10-01

nucleotide mismatches and recruit heterodimers of the MutL homologues (MLH1- PMS2 , MLH1-PMS1, or MLH1-MLH3) to base mismatches (32, 34). These MLH1...generate modified base pairs) (44, 46, 66). Indeed, cells deficient in MLH1 or its interacting protein PMS2 are resistant to apoptosis induced by cisplatin

The mismatch repair and meiotic recombination endonuclease Mlh1-Mlh3 is activated by polymer formation and can cleave DNA substrates in trans

PubMed Central

Manhart, Carol M.; Ni, Xiaodan; White, Martin A.; Ortega, Joaquin; Surtees, Jennifer A.

2017-01-01

Crossing over between homologs is initiated in meiotic prophase by the formation of DNA double-strand breaks that occur throughout the genome. In the major interference-responsive crossover pathway in baker’s yeast, these breaks are resected to form 3' single-strand tails that participate in a homology search, ultimately forming double Holliday junctions (dHJs) that primarily include both homologs. These dHJs are resolved by endonuclease activity to form exclusively crossovers, which are critical for proper homolog segregation in Meiosis I. Recent genetic, biochemical, and molecular studies in yeast are consistent with the hypothesis of Mlh1-Mlh3 DNA mismatch repair complex acting as the major endonuclease activity that resolves dHJs into crossovers. However, the mechanism by which the Mlh1-Mlh3 endonuclease is activated is unknown. Here, we provide evidence that Mlh1-Mlh3 does not behave like a structure-specific endonuclease but forms polymers required to generate nicks in DNA. This conclusion is supported by DNA binding studies performed with different-sized substrates that contain or lack polymerization barriers and endonuclease assays performed with varying ratios of endonuclease-deficient and endonuclease-proficient Mlh1-Mlh3. In addition, Mlh1-Mlh3 can generate religatable double-strand breaks and form an active nucleoprotein complex that can nick DNA substrates in trans. Together these observations argue that Mlh1-Mlh3 may not act like a canonical, RuvC-like Holliday junction resolvase and support a novel model in which Mlh1-Mlh3 is loaded onto DNA to form an activated polymer that cleaves DNA. PMID:28453523

The mismatch repair and meiotic recombination endonuclease Mlh1-Mlh3 is activated by polymer formation and can cleave DNA substrates in trans.

PubMed

Manhart, Carol M; Ni, Xiaodan; White, Martin A; Ortega, Joaquin; Surtees, Jennifer A; Alani, Eric

2017-04-01

Crossing over between homologs is initiated in meiotic prophase by the formation of DNA double-strand breaks that occur throughout the genome. In the major interference-responsive crossover pathway in baker's yeast, these breaks are resected to form 3' single-strand tails that participate in a homology search, ultimately forming double Holliday junctions (dHJs) that primarily include both homologs. These dHJs are resolved by endonuclease activity to form exclusively crossovers, which are critical for proper homolog segregation in Meiosis I. Recent genetic, biochemical, and molecular studies in yeast are consistent with the hypothesis of Mlh1-Mlh3 DNA mismatch repair complex acting as the major endonuclease activity that resolves dHJs into crossovers. However, the mechanism by which the Mlh1-Mlh3 endonuclease is activated is unknown. Here, we provide evidence that Mlh1-Mlh3 does not behave like a structure-specific endonuclease but forms polymers required to generate nicks in DNA. This conclusion is supported by DNA binding studies performed with different-sized substrates that contain or lack polymerization barriers and endonuclease assays performed with varying ratios of endonuclease-deficient and endonuclease-proficient Mlh1-Mlh3. In addition, Mlh1-Mlh3 can generate religatable double-strand breaks and form an active nucleoprotein complex that can nick DNA substrates in trans. Together these observations argue that Mlh1-Mlh3 may not act like a canonical, RuvC-like Holliday junction resolvase and support a novel model in which Mlh1-Mlh3 is loaded onto DNA to form an activated polymer that cleaves DNA.

Tumors with unmethylated MLH1 and the CpG island methylator phenotype are associated with a poor prognosis in stage II colorectal cancer patients

PubMed Central

Fu, Tao; Liu, Yanliang; Li, Kai; Wan, Weiwei; Pappou, Emmanouil P.; Iacobuzio-Donahue, Christine A.; Kerner, Zachary; Baylin, Stephen B.; Wolfgang, Christopher L.; Ahuja, Nita

2016-01-01

We previously developed a novel tumor subtype classification model for duodenal adenocarcinomas based on a combination of the CpG island methylator phenotype (CIMP) and MLH1 methylation status. Here, we tested the prognostic value of this model in stage II colorectal cancer (CRC) patients. Tumors were assigned to CIMP+/MLH1-unmethylated (MLH1-U), CIMP+/MLH1-methylated (MLH1-M), CIMP−/MLH1-U, or CIMP−/MLH1-M groups. Age, tumor location, lymphovascular invasion, and mucin production differed among the four patient subgroups, and CIMP+/MLH1-U tumors were more likely to have lymphovascular invasion and mucin production. Kaplan-Meier analyses revealed differences in both disease-free survival (DFS) and overall survival (OS) among the four groups. In a multivariate analysis, CIMP/MLH1 methylation status was predictive of both DFS and OS, and DFS and OS were shortest in CIMP+/MLH1-U stage II CRC patients. These results suggest that tumor subtype classification based on the combination of CIMP and MLH1 methylation status is informative in stage II CRC patients, and that CIMP+/MLH1-U tumors exhibit aggressive features and are associated with poor clinical outcomes. PMID:27880934

Tumors with unmethylated MLH1 and the CpG island methylator phenotype are associated with a poor prognosis in stage II colorectal cancer patients.

PubMed

Fu, Tao; Liu, Yanliang; Li, Kai; Wan, Weiwei; Pappou, Emmanouil P; Iacobuzio-Donahue, Christine A; Kerner, Zachary; Baylin, Stephen B; Wolfgang, Christopher L; Ahuja, Nita

2016-12-27

We previously developed a novel tumor subtype classification model for duodenal adenocarcinomas based on a combination of the CpG island methylator phenotype (CIMP) and MLH1 methylation status. Here, we tested the prognostic value of this model in stage II colorectal cancer (CRC) patients. Tumors were assigned to CIMP+/MLH1-unmethylated (MLH1-U), CIMP+/MLH1-methylated (MLH1-M), CIMP-/MLH1-U, or CIMP-/MLH1-M groups. Age, tumor location, lymphovascular invasion, and mucin production differed among the four patient subgroups, and CIMP+/MLH1-U tumors were more likely to have lymphovascular invasion and mucin production. Kaplan-Meier analyses revealed differences in both disease-free survival (DFS) and overall survival (OS) among the four groups. In a multivariate analysis, CIMP/MLH1 methylation status was predictive of both DFS and OS, and DFS and OS were shortest in CIMP+/MLH1-U stage II CRC patients. These results suggest that tumor subtype classification based on the combination of CIMP and MLH1 methylation status is informative in stage II CRC patients, and that CIMP+/MLH1-U tumors exhibit aggressive features and are associated with poor clinical outcomes.

The Saccharomyces cerevisiae Mlh1-Mlh3 Heterodimer Is an Endonuclease That Preferentially Binds to Holliday Junctions*

PubMed Central

Ranjha, Lepakshi; Anand, Roopesh; Cejka, Petr

2014-01-01

MutLγ, a heterodimer of the MutL homologues Mlh1 and Mlh3, plays a critical role during meiotic homologous recombination. The meiotic function of Mlh3 is fully dependent on the integrity of a putative nuclease motif DQHAX2EX4E, inferring that the anticipated nuclease activity of Mlh1-Mlh3 is involved in the processing of joint molecules to generate crossover recombination products. Although a vast body of genetic and cell biological data regarding Mlh1-Mlh3 is available, mechanistic insights into its function have been lacking due to the unavailability of the recombinant protein complex. Here we expressed the yeast Mlh1-Mlh3 heterodimer and purified it into near homogeneity. We show that recombinant MutLγ is a nuclease that nicks double-stranded DNA. We demonstrate that MutLγ binds DNA with a high affinity and shows a marked preference for Holliday junctions. We also expressed the human MLH1-MLH3 complex and show that preferential binding to Holliday junctions is a conserved capacity of eukaryotic MutLγ complexes. Specific DNA recognition has never been observed with any other eukaryotic MutL homologue. MutLγ thus represents a new paradigm for the function of the eukaryotic MutL protein family. We provide insights into the mode of Holliday junction recognition and show that Mlh1-Mlh3 prefers to bind the open unstacked Holliday junction form. This further supports the model where MutLγ is part of a complex acting on joint molecules to generate crossovers in meiosis. PMID:24443562

The Saccharomyces cerevisiae Mlh1-Mlh3 heterodimer is an endonuclease that preferentially binds to Holliday junctions.

PubMed

Ranjha, Lepakshi; Anand, Roopesh; Cejka, Petr

2014-02-28

MutLγ, a heterodimer of the MutL homologues Mlh1 and Mlh3, plays a critical role during meiotic homologous recombination. The meiotic function of Mlh3 is fully dependent on the integrity of a putative nuclease motif DQHAX2EX4E, inferring that the anticipated nuclease activity of Mlh1-Mlh3 is involved in the processing of joint molecules to generate crossover recombination products. Although a vast body of genetic and cell biological data regarding Mlh1-Mlh3 is available, mechanistic insights into its function have been lacking due to the unavailability of the recombinant protein complex. Here we expressed the yeast Mlh1-Mlh3 heterodimer and purified it into near homogeneity. We show that recombinant MutLγ is a nuclease that nicks double-stranded DNA. We demonstrate that MutLγ binds DNA with a high affinity and shows a marked preference for Holliday junctions. We also expressed the human MLH1-MLH3 complex and show that preferential binding to Holliday junctions is a conserved capacity of eukaryotic MutLγ complexes. Specific DNA recognition has never been observed with any other eukaryotic MutL homologue. MutLγ thus represents a new paradigm for the function of the eukaryotic MutL protein family. We provide insights into the mode of Holliday junction recognition and show that Mlh1-Mlh3 prefers to bind the open unstacked Holliday junction form. This further supports the model where MutLγ is part of a complex acting on joint molecules to generate crossovers in meiosis.

Genetic Analysis of mlh3 Mutations Reveals Interactions Between Crossover Promoting Factors During Meiosis in Baker’s Yeast

PubMed Central

Brown, Megan Sonntag; Lim, Elisha; Chen, Cheng; Nishant, K. T.; Alani, Eric

2013-01-01

Crossing over between homologous chromosomes occurs during the prophase of meiosis I and is critical for chromosome segregation. In baker’s yeast, two heterodimeric complexes, Msh4-Msh5 and Mlh1-Mlh3, act in meiosis to promote interference-dependent crossing over. Mlh1-Mlh3 also plays a role in DNA mismatch repair (MMR) by interacting with Msh2-Msh3 to repair insertion and deletion mutations. Mlh3 contains an ATP-binding domain that is highly conserved among MLH proteins. To explore roles for Mlh3 in meiosis and MMR, we performed a structure−function analysis of eight mlh3 ATPase mutants. In contrast to previous work, our data suggest that ATP hydrolysis by both Mlh1 and Mlh3 is important for both meiotic and MMR functions. In meiotic assays, these mutants showed a roughly linear relationship between spore viability and genetic map distance. To further understand the relationship between crossing over and meiotic viability, we analyzed crossing over on four chromosomes of varying lengths in mlh3Δ mms4Δ strains and observed strong decreases (6- to 17-fold) in crossing over in all intervals. Curiously, mlh3Δ mms4Δ double mutants displayed spore viability levels that were greater than observed in mms4Δ strains that show modest defects in crossing over. The viability in double mutants also appeared greater than would be expected for strains that show such severe defects in crossing over. Together, these observations provide insights for how Mlh1-Mlh3 acts in crossover resolution and MMR and for how chromosome segregation in Meiosis I can occur in the absence of crossing over. PMID:23316435

Mismatch repair genes Mlh1 and Mlh3 modify CAG instability in Huntington's disease mice: genome-wide and candidate approaches.

PubMed

Pinto, Ricardo Mouro; Dragileva, Ella; Kirby, Andrew; Lloret, Alejandro; Lopez, Edith; St Claire, Jason; Panigrahi, Gagan B; Hou, Caixia; Holloway, Kim; Gillis, Tammy; Guide, Jolene R; Cohen, Paula E; Li, Guo-Min; Pearson, Christopher E; Daly, Mark J; Wheeler, Vanessa C

2013-10-01

The Huntington's disease gene (HTT) CAG repeat mutation undergoes somatic expansion that correlates with pathogenesis. Modifiers of somatic expansion may therefore provide routes for therapies targeting the underlying mutation, an approach that is likely applicable to other trinucleotide repeat diseases. Huntington's disease Hdh(Q111) mice exhibit higher levels of somatic HTT CAG expansion on a C57BL/6 genetic background (B6.Hdh(Q111) ) than on a 129 background (129.Hdh(Q111) ). Linkage mapping in (B6x129).Hdh(Q111) F2 intercross animals identified a single quantitative trait locus underlying the strain-specific difference in expansion in the striatum, implicating mismatch repair (MMR) gene Mlh1 as the most likely candidate modifier. Crossing B6.Hdh(Q111) mice onto an Mlh1 null background demonstrated that Mlh1 is essential for somatic CAG expansions and that it is an enhancer of nuclear huntingtin accumulation in striatal neurons. Hdh(Q111) somatic expansion was also abolished in mice deficient in the Mlh3 gene, implicating MutLγ (MLH1-MLH3) complex as a key driver of somatic expansion. Strikingly, Mlh1 and Mlh3 genes encoding MMR effector proteins were as critical to somatic expansion as Msh2 and Msh3 genes encoding DNA mismatch recognition complex MutSβ (MSH2-MSH3). The Mlh1 locus is highly polymorphic between B6 and 129 strains. While we were unable to detect any difference in base-base mismatch or short slipped-repeat repair activity between B6 and 129 MLH1 variants, repair efficiency was MLH1 dose-dependent. MLH1 mRNA and protein levels were significantly decreased in 129 mice compared to B6 mice, consistent with a dose-sensitive MLH1-dependent DNA repair mechanism underlying the somatic expansion difference between these strains. Together, these data identify Mlh1 and Mlh3 as novel critical genetic modifiers of HTT CAG instability, point to Mlh1 genetic variation as the likely source of the instability difference in B6 and 129 strains and suggest that MLH1 protein levels play an important role in driving of the efficiency of somatic expansions.

Mismatch Repair Genes Mlh1 and Mlh3 Modify CAG Instability in Huntington's Disease Mice: Genome-Wide and Candidate Approaches

PubMed Central

Pinto, Ricardo Mouro; Dragileva, Ella; Kirby, Andrew; Lloret, Alejandro; Lopez, Edith; St. Claire, Jason; Panigrahi, Gagan B.; Hou, Caixia; Holloway, Kim; Gillis, Tammy; Guide, Jolene R.; Cohen, Paula E.; Li, Guo-Min; Pearson, Christopher E.; Daly, Mark J.; Wheeler, Vanessa C.

2013-01-01

The Huntington's disease gene (HTT) CAG repeat mutation undergoes somatic expansion that correlates with pathogenesis. Modifiers of somatic expansion may therefore provide routes for therapies targeting the underlying mutation, an approach that is likely applicable to other trinucleotide repeat diseases. Huntington's disease HdhQ111 mice exhibit higher levels of somatic HTT CAG expansion on a C57BL/6 genetic background (B6.HdhQ111) than on a 129 background (129.HdhQ111). Linkage mapping in (B6x129).HdhQ111 F2 intercross animals identified a single quantitative trait locus underlying the strain-specific difference in expansion in the striatum, implicating mismatch repair (MMR) gene Mlh1 as the most likely candidate modifier. Crossing B6.HdhQ111 mice onto an Mlh1 null background demonstrated that Mlh1 is essential for somatic CAG expansions and that it is an enhancer of nuclear huntingtin accumulation in striatal neurons. HdhQ111 somatic expansion was also abolished in mice deficient in the Mlh3 gene, implicating MutLγ (MLH1–MLH3) complex as a key driver of somatic expansion. Strikingly, Mlh1 and Mlh3 genes encoding MMR effector proteins were as critical to somatic expansion as Msh2 and Msh3 genes encoding DNA mismatch recognition complex MutSβ (MSH2–MSH3). The Mlh1 locus is highly polymorphic between B6 and 129 strains. While we were unable to detect any difference in base-base mismatch or short slipped-repeat repair activity between B6 and 129 MLH1 variants, repair efficiency was MLH1 dose-dependent. MLH1 mRNA and protein levels were significantly decreased in 129 mice compared to B6 mice, consistent with a dose-sensitive MLH1-dependent DNA repair mechanism underlying the somatic expansion difference between these strains. Together, these data identify Mlh1 and Mlh3 as novel critical genetic modifiers of HTT CAG instability, point to Mlh1 genetic variation as the likely source of the instability difference in B6 and 129 strains and suggest that MLH1 protein levels play an important role in driving of the efficiency of somatic expansions. PMID:24204323

The Saccharomyces cerevisiae MLH3 gene functions in MSH3-dependent suppression of frameshift mutations.

PubMed

Flores-Rozas, H; Kolodner, R D

1998-10-13

The Saccharomyces cerevisiae genome encodes four MutL homologs. Of these, MLH1 and PMS1 are known to act in the MSH2-dependent pathway that repairs DNA mismatches. We have investigated the role of MLH3 in mismatch repair. Mutations in MLH3 increased the rate of reversion of the hom3-10 allele by increasing the rate of deletion of a single T in a run of 7 Ts. Combination of mutations in MLH3 and MSH6 caused a synergistic increase in the hom3-10 reversion rate, whereas the hom3-10 reversion rate in an mlh3 msh3 double mutant was the same as in the respective single mutants. Similar results were observed when the accumulation of mutations at frameshift hot spots in the LYS2 gene was analyzed, although mutation of MLH3 did not cause the same extent of affect at every LYS2 frameshift hot spot. MLH3 interacted with MLH1 in a two-hybrid system. These data are consistent with the idea that a proportion of the repair of specific insertion/deletion mispairs by the MSH3-dependent mismatch repair pathway uses a heterodimeric MLH1-MLH3 complex in place of the MLH1-PMS1 complex.

Expression and promoter DNA methylation of MLH1 in colorectal cancer and lung cancer.

PubMed

Ma, Yunxia; Chen, Yuan; Petersen, Iver

2017-04-01

Aberrant DNA methylation is a common molecular feature in human cancer. The aims of this study were to analyze the methylation status of MLH1, one of the DNA mismatch repair (MMR) genes, in human colorectal and lung cancer and to evaluate its clinical relevance. The expression of MLH1 was analyzed in 8 colorectal cancer (CRC) and 8 lung cancer cell lines by real-time RT-PCR and western blotting. The MLH1 protein expression was evaluated by immunohistochemistry on tissue microarrays including 121 primary CRC and 90 lung cancer patient samples. In cancer cell lines, the methylation status of MLH1 promoter and exon 2 was investigated by bisulfite sequencing (BS). Methylation-specific-PCR (MSP) was used to evaluate methylation status of MLH1. The expression of MLH1 mRNA was detected in 8 CRC cell lines as well as normal colonic fibroblast cells CCD-33Co. At protein levels, MLH1 was lost in one CRC cell line HCT-116 and normal cells CCD-33Co. No methylation was found in the promoter and exon 2 of MLH1 in CRC cell lines. MLH1 was expressed in 8 lung cancer cell lines at both mRNA and protein levels. Compared to cancer cells, normal bronchial epithelial cells (HBEC) had lower expression of MLH1 protein. In primary CRC, 54.5% of cases exhibited positive staining, while 47.8% of lung tumors were positive for MLH1 protein. MSP analysis showed that 58 out of 92 (63.0%) CRC and 41 out of 73 (56.2%) lung cancer exhibited MLH1 methylation. In CRC, the MLH1 methylation was significantly associated with tumor invasion in veins (P=0.012). However, no significant links were found between MLH1 expression and promoter methylation in both tumor entities. MLH1 methylation is a frequent molecular event in CRC and lung cancer patients. In CRC, methylation of MLH1 could be linked to vascular invasiveness. Copyright © 2017 Elsevier GmbH. All rights reserved.

Finding the needle in a haystack: identification of cases of Lynch syndrome with MLH1 epimutation.

PubMed

Hitchins, Megan P

2016-07-01

Constitutional epimutation of the DNA mismatch repair gene, MLH1, represents a minor cause of Lynch syndrome. MLH1 epimutations are characterized by the soma-wide distribution of methylation of a single allele of the MLH1 promoter accompanied by constitutive allelic loss of transcription. 'Primary' MLH1 epimutations, considered pure epigenetic defects, tend to arise de novo in patients without a family history or any apparent genetic mutation. These demonstrate non-Mendelian inheritance. 'Secondary' MLH1 epimutations have a genetic basis and have been linked to non-coding genetic alterations in the vicinity of MLH1. These demonstrate autosomal dominant inheritance. Despite convincing evidence of their role in causing Lynch-type cancers, routine screening for MLH1 epimutations has not been widely adopted. Complicating factors may include: the need to perform additional methylation-based testing beyond the standard genetic screening for a germline mutation; the lack of a consensus algorithm for the selection of patients warranting MLH1 epimutation testing; overlapping molecular pathology features of MLH1 methylation and loss of MLH1 expression with more prevalent sporadic MSI cancers; the rarity of MLH1 epimutation; the variable inter-generational inheritance patterns; and the cost-effectiveness of screening. Nevertheless, a positive molecular diagnosis of MLH1 epimutation is clinically important because carriers have a high personal risk of developing metachronous Lynch-type cancers, and their relatives may also be at risk of carriage. Extending existing universal and clinic-based screening algorithms for Lynch syndrome to include an additional arm of selection criteria for cases warranting MLH1 epimutation testing could provide a cost-effective means of diagnosing these cases.

Loss of MLH1 sensitizes colon cancer cells to DNA-PKcs inhibitor KU60648.

PubMed

Hinrichsen, Inga; Ackermann, Anne; Düding, Tonja; Graband, Annika; Filmann, Natalie; Plotz, Guido; Zeuzem, Stefan; Brieger, Angela

2017-07-01

Germline mutations of MLH1 are responsible for tumor generation in nearly 50% of patients with Lynch Syndrome, and around 15% of sporadic colorectal cancers show MLH1-deficiency due to promotor hypermethylation. Although these tumors are of lower aggressiveness the benefit for these patients from standard chemotherapy is still under discussion. Recently, it was shown that the sensitivity to the DNA-PKcs inhibitor KU60648 is linked to loss of the MMR protein MSH3. However, loss of MSH3 is rather secondary, as a consequence of MMR-deficiency, and frequently detectable in MLH1-deficient tumors. Therefore, we examined the expression of MLH1, MSH2, MSH6, and MSH3 in different MMR-deficient and proficient cell lines and determined their sensitivity to KU60648 by analyzing cell viability and survival. MLH1-dependent ability of double strand break (DSB) repair was monitored after irradiation via γH2AX detection. A panel of 12 colon cancer cell lines, two pairs of cells, where MLH1 knock down was compared to controls with the same genetic background, and one MLH1-deficient cell line where MLH1 was overexpressed, were included. In summary, we found that MLH1 and/or MSH3-deficient cells exhibited a significantly higher sensitivity to KU60648 than MMR-proficient cells and that overexpression of MLH1 in MLH1-deficient cells resulted in a decrease of cell sensitivity. KU60648 efficiency seems to be associated with reduced DSB repair capacity. Since the molecular testing of colon tumors for MLH1 expression is a clinical standard we believe that MLH1 is a much better marker and a greater number of patients would benefit from KU60648 treatment. © 2017 Wiley Periodicals, Inc.

Disruption of a -35kb enhancer impairs CTCF binding and MLH1 expression in colorectal cells.

PubMed

Liu, Qing; Thoms, Julie A; Nunez, Andrea C; Huang, Yizhou; Knezevic, Kathy; Packham, Deborah; Poulos, Rebecca C; Williams, Rachel; Beck, Dominik; Hawkins, Nicholas J; Ward, Robyn L; Wong, Jason W H; Hesson, Luke B; Sloane, Mathew A; Pimanda, John

2018-06-13

MLH1 is a major tumour suppressor gene involved in the pathogenesis of Lynch syndrome and various sporadic cancers. Despite their potential pathogenic importance, genomic regions capable of regulating MLH1 expression over long distances have yet to be identified. Here we use chromosome conformation capture (3C) to screen a 650-kb region flanking the MLH1 locus to identify interactions between the MLH1 promoter and distal regions in MLH1 expressing and non-expressing cells. Putative enhancers were functionally validated using luciferase reporter assays, chromatin immunoprecipitation and CRISPR-Cas9 mediated deletion of endogenous regions. To evaluate whether germline variants in the enhancer might contribute to impaired MLH1 expression in patients with suspected Lynch syndrome, we also screened germline DNA from a cohort of 74 patients with no known coding mutations or epimutations at the MLH1 promoter. A 1.8kb DNA fragment, 35kb upstream of the MLH1 transcription start site enhances MLH1 gene expression in colorectal cells. The enhancer was bound by CTCF and CRISPR-Cas9 mediated deletion of a core binding region impairs endogenous MLH1 expression. 5.4% of suspected Lynch syndrome patients have a rare single nucleotide variant (G>A; rs143969848; 2.5% in gnomAD European, non-Finnish) within a highly conserved CTCF binding motif, which disrupts enhancer activity in SW620 colorectal carcinoma cells. A CTCF bound region within the MLH1 -35 enhancer regulates MLH1 expression in colorectal cells and is worthy of scrutiny in future genetic screening strategies for suspected Lynch syndrome associated with loss of MLH1 expression. Copyright ©2018, American Association for Cancer Research.

DNA mismatch repair gene MLH1 induces apoptosis in prostate cancer cells.

PubMed

Fukuhara, Shinichiro; Chang, Inik; Mitsui, Yozo; Chiyomaru, Takeshi; Yamamura, Soichiro; Majid, Shahana; Saini, Sharanjot; Hirata, Hiroshi; Deng, Guoren; Gill, Ankurpreet; Wong, Darryn K; Shiina, Hiroaki; Nonomura, Norio; Dahiya, Rajvir; Tanaka, Yuichiro

2014-11-30

Mismatch repair (MMR) enzymes have been shown to be deficient in prostate cancer (PCa). MMR can influence the regulation of tumor development in various cancers but their role on PCa has not been investigated. The aim of the present study was to determine the functional effects of the mutL-homolog 1 (MLH1) gene on growth of PCa cells. The DU145 cell line has been established as MLH1-deficient and thus, this cell line was utilized to determine effects of MLH1 by gene expression. Lack of MLH1 protein expression was confirmed by Western blotting in DU145 cells whereas levels were high in normal PWR-1E and RWPE-1 prostatic cells. MLH1-expressing stable transfectant DU145 cells were then created to characterize the effects this MMR gene has on various growth properties. Expression of MLH1 resulted in decreased cell proliferation, migration and invasion properties. Lack of cell growth in vivo also indicated a tumor suppressive effect by MLH1. Interestingly, MLH1 caused an increase in apoptosis along with phosphorylated c-Abl, and treatment with MLH1 siRNAs countered this effect. Furthermore, inhibition of c-Abl with STI571 also abrogated the effect on apoptosis caused by MLH1. These results demonstrate MLH1 protects against PCa development by inducing c-Abl-mediated apoptosis.

DNA mismatch repair gene MLH1 induces apoptosis in prostate cancer cells

PubMed Central

Mitsui, Yozo; Chiyomaru, Takeshi; Yamamura, Soichiro; Majid, Shahana; Saini, Sharanjot; Hirata, Hiroshi; Deng, Guoren; Gill, Ankurpreet; Wong, Darryn K.; Shiina, Hiroaki; Nonomura, Norio; Dahiya, Rajvir; Tanaka, Yuichiro

2014-01-01

Mismatch repair (MMR) enzymes have been shown to be deficient in prostate cancer (PCa). MMR can influence the regulation of tumor development in various cancers but their role on PCa has not been investigated. The aim of the present study was to determine the functional effects of the mutL-homolog 1 (MLH1) gene on growth of PCa cells. The DU145 cell line has been established as MLH1-deficient and thus, this cell line was utilized to determine effects of MLH1 by gene expression. Lack of MLH1 protein expression was confirmed by Western blotting in DU145 cells whereas levels were high in normal PWR-1E and RWPE-1 prostatic cells. MLH1-expressing stable transfectant DU145 cells were then created to characterize the effects this MMR gene has on various growth properties. Expression of MLH1 resulted in decreased cell proliferation, migration and invasion properties. Lack of cell growth in vivo also indicated a tumor suppressive effect by MLH1. Interestingly, MLH1 caused an increase in apoptosis along with phosphorylated c-Abl, and treatment with MLH1 siRNAs countered this effect. Furthermore, inhibition of c-Abl with STI571 also abrogated the effect on apoptosis caused by MLH1. These results demonstrate MLH1 protects against PCa development by inducing c-Abl-mediated apoptosis. PMID:25526032

MLH1-deficient Colorectal Carcinoma With Wild-type BRAF and MLH1 Promoter Hypermethylation Harbor KRAS Mutations and Arise From Conventional Adenomas.

PubMed

Farchoukh, Lama; Kuan, Shih-Fan; Dudley, Beth; Brand, Randall; Nikiforova, Marina; Pai, Reetesh K

2016-10-01

Between 10% and 15% of colorectal carcinomas demonstrate sporadic DNA mismatch-repair protein deficiency as a result of MLH1 promoter methylation and are thought to arise from sessile serrated adenomas, termed the serrated neoplasia pathway. Although the presence of the BRAF V600E mutation is indicative of a sporadic cancer, up to 30% to 50% of colorectal carcinomas with MLH1 promoter hypermethylation will lack a BRAF mutation. We report the clinicopathologic and molecular features of MLH1-deficient colorectal carcinoma with wild-type BRAF and MLH1 promoter hypermethylation (referred to as MLH1-hypermethylated BRAF wild-type colorectal carcinoma, n=36) in comparison with MLH1-deficient BRAF-mutated colorectal carcinoma (n=113) and Lynch syndrome-associated colorectal carcinoma (n=36). KRAS mutations were identified in 31% of MLH1-hypermethylated BRAF wild-type colorectal carcinomas compared with 0% of MLH1-deficient BRAF-mutated colorectal carcinomas and 37% of Lynch syndrome-associated colorectal carcinomas. When a precursor polyp was identified, MLH1-hypermethylated BRAF wild-type colorectal carcinomas arose from precursor polyps resembling conventional tubular/tubulovillous adenomas in contrast to MLH1-deficient BRAF-mutated colorectal carcinomas, which arose from precursor sessile serrated adenomas (P<0.001). Both MLH1-hypermethylated BRAF wild-type colorectal carcinoma and MLH1-deficient BRAF-mutated colorectal carcinoma had a predilection for the right colon compared with Lynch syndrome-associated colorectal carcinoma (86% vs. 92% vs. 49%, P<0.001). There was no significant difference in mucinous differentiation, tumor-infiltrating lymphocytes, Crohn-like reaction, and medullary differentiation between the 3 tumor groups. Using Kaplan-Meier survival functions, there was no significant difference in disease-specific survival between the 3 patient groups (P>0.05). In conclusion, our results indicate that MLH1-hypermethylated BRAF wild-type colorectal carcinomas can harbor KRAS mutations and arise from precursor polyps resembling conventional tubular/tubulovillous adenomas.

Prevalence of MLH1 constitutional epimutations as a cause of Lynch syndrome in unselected versus selected consecutive series of patients with colorectal cancer.

PubMed

Castillejo, Adela; Hernández-Illán, Eva; Rodriguez-Soler, María; Pérez-Carbonell, Lucía; Egoavil, Cecilia; Barberá, Victor M; Castillejo, María-Isabel; Guarinos, Carla; Martínez-de-Dueñas, Eduardo; Juan, María-Jose; Sánchez-Heras, Ana-Beatriz; García-Casado, Zaida; Ruiz-Ponte, Clara; Brea-Fernández, Alejandro; Juárez, Miriam; Bujanda, Luis; Clofent, Juan; Llor, Xavier; Andreu, Montserrat; Castells, Antoni; Carracedo, Angel; Alenda, Cristina; Payá, Artemio; Jover, Rodrigo; Soto, José-Luis

2015-07-01

The prevalence of MLH1 constitutional epimutations in the general population is unknown. We sought to analyse the prevalence of MLH1 constitutional epimutations in unselected and selected series of patients with colorectal cancer (CRC). Patients with diagnoses of CRC (n=2123) were included in the unselected group. For comparison, a group of 847 selected patients with CRC who fulfilled the revised Bethesda guidelines (rBG) were also included. Somatic and constitutional MLH1 methylation was assayed via methylation-specific multiplex ligation-dependent probe amplification of cases lacking MLH1 expression. Germline alterations in mismatch-repair (MMR) genes were assessed via Sanger sequencing and methylation-specific multiplex ligation-dependent probe amplification. Loss of MLH1 expression occurred in 5.5% of the unselected series and 12.5% of the selected series (p<0.0001). No constitutional epimutations in MLH1 were detected in the unselected population (0/62); five cases from the selected series were positive for MLH1 epimutations (15.6%, 5/32; p=0.004). Our results suggest a negligible prevalence of MLH1 constitutional epimutations in unselected cases of CRC. Therefore, MLH1 constitutional epimutation analysis should be conducted only for patients who fulfil the rBG and who lack MLH1 expression with methylated MLH1. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

MLH1 function is context dependent in colorectal cancers.

PubMed

Jackson, Thomas; Ahmed, Mohamed A H; Seth, Rashmi; Jackson, Darryl; Ilyas, Mohammad

2011-02-01

Loss of mismatch repair (MMR) function in sporadic colorectal cancer occurs most commonly because of inactivation of MLH1, and it causes an increase in mutation rate. However, it is uncertain whether loss of MMR alters any other cellular function. The aim of this study was to investigate the role of MMR in regulating cell numbers and apoptosis. MLH1 protein levels were manipulated by (a) cloning and forcibly expressing MLH1 in HCT116 (a cell line with MLH1 mutation) and RKO (a cell line with MLH1 silencing), and (b) knockdown of MLH1 in SW480 (a cell line with normal MMR function). Cell number and apoptotic bodies were measured in standard and 'high stress' (ie, after staurosporine exposure) conditions. Restoration of MLH1 function in HCT116 and RKO resulted in increased cell number (p<0.001 for both cell lines) and decreased numbers of floating apoptotic bodies (p<0.01 in HCT116) in standard culture conditions. However, on induction of apoptotic stress, restoration of MLH1 resulted in reduced cell numbers (p<0.005). Knockdown of MLH1 in SW480 had no effect on cell numbers or apoptosis. MLH1 function may be context dependent: in 'low stress' conditions it may act to inhibit apoptosis, while in 'high stress' conditions it may induce apoptosis. However, within the context of chromosomal instability, the effect of MLH1 on cell numbers is limited.

Structure and growth of Bi(110) islands on Si(111)√{3 }×√{3 }-B substrates

NASA Astrophysics Data System (ADS)

Nagase, Kentaro; Kokubo, Ikuya; Yamazaki, Shiro; Nakatsuji, Kan; Hirayama, Hiroyuki

2018-05-01

The structure and growth of ultrathin Bi(110) islands were investigated on a Si(111)√{3 }×√{3 }-B substrate by scanning tunneling microscopy and scanning tunneling spectroscopy (STS). Both even- and odd-layer-height islands nucleated on a one-monolayer-thick wetting layer. The islands preferred the even layer heights over the odd layer heights with an area ratio of 3:1. A weak, long-range corrugation was observed to overlap on the atomic arrangement at the top of the islands. The average distance between the peaks of the corrugation oscillated in accordance with the alternation of even and odd layer heights. Nucleation of single- and double-layer terraces occurred on the islands with even layer heights but not on those with odd layer heights. The unit cell of the single-layer terrace was aligned with that of the underlying even-layer-height island. The inequality in the height preference and the height-dependent oscillation of the corrugation suggested that the even- and odd-layer-height islands possessed different structures. The dominance and stability against terrace nucleation of the even-layer-height islands were consistent with the theoretically predicted stability of the paired layer-stacked black-phosphorus (BP)-like structure for ultrathin Bi(110) films. The alignment of the unit cell at the terrace on the island and STS spectra suggested a BP-like/bulklike/BP-like sandwich structure for the odd-layer-height Bi(110) islands.

Micronucleus-specific histone H1 is required for micronuclear chromosome integrity in Tetrahymena thermophila

PubMed Central

Qiao, Juxia; Xu, Jing; Bo, Tao

2017-01-01

Histone H1 molecules play a key role in establishing and maintaining higher order chromatin structures. They can bind to linker DNA entering and exiting the nucleosome and regulate transcriptional activity. Tetrahymena thermophila has two histone H1, namely, macronuclear histone H1 and micronuclear histone H1 (Mlh1). Mlh1 is specifically localized at micronuclei during growth and starvation stages. Moreover, Mlh1 is localized around micronuclei and forms a specific structure during the conjugation stage. It co-localizes partially with spindle apparatus during micronuclear meiosis. Analysis of MLH1 knock-out revealed that Mlh1 was required for the micronuclear integrity and development during conjugation stage. Overexpression of Mlh1 led to abnormal conjugation progression. RT-PCR analysis indicated that the expression level of HMGB3 increased in ΔMLH1 strains, while the expression level of MLH1 increased in ΔHMGB3 cells during conjugation. These results indicate that micronuclear integrity and sexual development require normal expression level of Mlh1 and that HmgB3 and Mlh1 may functionally compensate each other in regulating micronuclear structure in T. thermophila. PMID:29095884

Clinicopathologic Risk Factor Distributions for MLH1 Promoter Region Methylation in CIMP-Positive Tumors.

PubMed

Levine, A Joan; Phipps, Amanda I; Baron, John A; Buchanan, Daniel D; Ahnen, Dennis J; Cohen, Stacey A; Lindor, Noralane M; Newcomb, Polly A; Rosty, Christophe; Haile, Robert W; Laird, Peter W; Weisenberger, Daniel J

2016-01-01

The CpG island methylator phenotype (CIMP) is a major molecular pathway in colorectal cancer. Approximately 25% to 60% of CIMP tumors are microsatellite unstable (MSI-H) due to DNA hypermethylation of the MLH1 gene promoter. Our aim was to determine if the distributions of clinicopathologic factors in CIMP-positive tumors with MLH1 DNA methylation differed from those in CIMP-positive tumors without DNA methylation of MLH1. We assessed the associations between age, sex, tumor-site, MSI status BRAF and KRAS mutations, and family colorectal cancer history with MLH1 methylation status in a large population-based sample of CIMP-positive colorectal cancers defined by a 5-marker panel using unconditional logistic regression to assess the odds of MLH1 methylation by study variables. Subjects with CIMP-positive tumors without MLH1 methylation were significantly younger, more likely to be male, and more likely to have distal colon or rectal primaries and the MSI-L phenotype. CIMP-positive MLH1-unmethylated tumors were significantly less likely than CIMP-positive MLH1-methylated tumors to harbor a BRAF V600E mutation and significantly more likely to harbor a KRAS mutation. MLH1 methylation was associated with significantly better overall survival (HR, 0.50; 95% confidence interval, 0.31-0.82). These data suggest that MLH1 methylation in CIMP-positive tumors is not a completely random event and implies that there are environmental or genetic determinants that modify the probability that MLH1 will become methylated during CIMP pathogenesis. MLH1 DNA methylation status should be taken into account in etiologic studies. ©2015 American Association for Cancer Research.

MLH1-93 G/a polymorphism is associated with MLH1 promoter methylation and protein loss in dysplastic sessile serrated adenomas with BRAFV600E mutation.

PubMed

Fennell, Lochlan J; Jamieson, Saara; McKeone, Diane; Corish, Tracie; Rohdmann, Megan; Furner, Tori; Bettington, Mark; Liu, Cheng; Kawamata, Futoshi; Bond, Catherine; Van De Pols, Jolieke; Leggett, Barbara; Whitehall, Vicki

2018-01-05

Sessile serrated adenomas with BRAF mutation progress rapidly to cancer following the development of dysplasia (SSAD). Approximately 75% of SSADs methylate the mismatch repair gene MLH1, develop mismatch repair deficiency and the resultant cancers have a good prognosis. The remaining SSADs and BRAF mutant traditional serrated adenomas (TSA) develop into microsatellite stable cancers with a poor prognosis. The reason for this dichotomy is unknown. In this study, we assessed the genotypic frequency of the MLH1-93 polymorphism rs1800734 in SSADs and TSAs to determine if the uncommon variant A allele predisposes to MLH1 promoter hypermethylation. We performed genotyping for the MLH1-93 polymorphism, quantitative methylation specific PCR, and MLH1 immunohistochemistry on 124 SSAD, 128 TSA, 203 BRAF mutant CRCs and 147 control subjects with normal colonoscopy. The minor A allele was significantly associated with a dose dependent increase in methylation at the MLH1 promoter in SSADs (p = 0.022). The AA genotype was only observed in SSADs with MLH1 loss. The A allele was also overrepresented in BRAF mutant cancers with MLH1 loss. Only one of the TSAs showed loss of MLH1 and the overall genotype distribution in TSAs did not differ from controls. The MLH1-93 AA genotype is significantly associated with promoter hypermethylation and MLH1 loss in the context of SSADs. BRAF mutant microsatellite stable colorectal cancers with the AA genotype most likely arise in TSAs since the A allele does not predispose to methylation in this context.

The unstructured linker arms of Mlh1-Pms1 are important for interactions with DNA during mismatch repair

PubMed Central

Plys, Aaron J.; Rogacheva, Maria V.; Greene, Eric C.; Alani, Eric

2012-01-01

DNA mismatch repair (MMR) models have proposed that MSH proteins identify DNA polymerase errors while interacting with the DNA replication fork. MLH proteins (primarily Mlh1-Pms1 in baker’s yeast) then survey the genome for lesion-bound MSH proteins. The resulting MSH-MLH complex formed at a DNA lesion initiates downstream steps in repair. MLH proteins act as dimers and contain long (20 – 30 nanometers) unstructured arms that connect two terminal globular domains. These arms can vary between 100 to 300 amino acids in length, are highly divergent between organisms, and are resistant to amino acid substitutions. To test the roles of the linker arms in MMR, we engineered a protease cleavage site into the Mlh1 linker arm domain of baker’s yeast Mlh1-Pms1. Cleavage of the Mlh1 linker arm in vitro resulted in a defect in Mlh1-Pms1 DNA binding activity, and in vivo proteolytic cleavage resulted in a complete defect in MMR. We then generated a series of truncation mutants bearing Mlh1 and Pms1 linker arms of varying lengths. This work revealed that MMR is greatly compromised when portions of the Mlh1 linker are removed, whereas repair is less sensitive to truncation of the Pms1 linker arm. Purified complexes containing truncations in Mlh1 and Pms1 linker arms were analyzed and found to have differential defects in DNA binding that also correlated with the ability to form a ternary complex with Msh2-Msh6 and mismatch DNA. These observations are consistent with the unstructured linker domains of MLH proteins providing distinct interactions with DNA during MMR. PMID:22659005

Clinicopathological risk factor distributions for MLH1 promoter region methylation in CIMP positive tumors

PubMed Central

Levine, A. Joan; Phipps, Amanda I.; Baron, John A.; Buchanan, Daniel D.; Ahnen, Dennis J.; Cohen, Stacey A.; Lindor, Noralane M.; Newcomb, Polly A.; Rosty, Christophe; Haile, Robert W.; Laird, Peter W.; Weisenberger, Daniel J.

2015-01-01

Background The CpG Island Methylator Phenotype (CIMP) is a major molecular pathway in colorectal cancer (CRC). Approximately 25% to 60% of CIMP tumors are microsatellite unstable (MSI-H) due to DNA hypermethylation of the MLH1 gene promoter. Our aim was to determine if the distributions of clinicopathologic factors in CIMP-positive tumors with MLH1 DNA methylation differed from those in CIMP-positive tumors without DNA methylation of MLH1. Methods We assessed the associations between age, sex, tumor-site, MSI status BRAF and KRAS mutations and family CRC history with MLH1 methylation status in a large population-based sample of CIMP-positive CRCs defined by a 5-marker panel using unconditional logistic regression to assess the odds of MLH1 methylation by study variables. Results Subjects with CIMP-positive tumors without MLH1 methylation were significantly younger, more likely to be male, more likely to have distal colon or rectal primaries and the MSI-L phenotype. CIMP-positive MLH1-unmethylated tumors were significantly less likely than CIMP-positive MLH1-methylated tumors to harbor a BRAF V600E mutation and significantly more likely to harbor a KRAS mutation. MLH1 methylation was associated with significantly better overall survival (HR=0.50; 95% Confidence Interval (0.31, 0.82)). Conclusions These data suggest that MLH1 methylation in CIMP-positive tumors is not a completely random event and implies that there are environmental or genetic determinants that modify the probability that MLH1 will become methylated during CIMP pathogenesis. Impact MLH1 DNA methylation status should be taken into account in etiologic studies. PMID:26512054

Isolated Loss of PMS2 Immunohistochemical Expression is Frequently Caused by Heterogenous MLH1 Promoter Hypermethylation in Lynch Syndrome Screening for Endometrial Cancer Patients

PubMed Central

Sato, Naoki; Sugawara, Tae; Takahashi, Kazue; Kito, Masahiko; Makino, Kenichi; Sato, Toshiharu; Shimizu, Dai; Shirasawa, Hiromistu; Miura, Hiroshi; Sato, Wataru; Kumazawa, Yukiyo; Sato, Akira; Kumagai, Jin; Terada, Yukihiro

2016-01-01

Lynch syndrome (LS) is an autosomal-dominant inherited disorder mainly caused by a germline mutation in the DNA mismatch repair (MMR) genes (MLH1, MSH2, MSH6, and PMS2) and is associated with increased risk for various cancers, particularly colorectal cancer and endometrial cancer (EC). Women with LS account for 2% to 6% of EC patients; it is clinically important to identify LS in such individuals for predicting and/or preventing additional LS-associated cancers. PMS2 germline mutation (PMS2-LS) is the rarest contribution to LS etiology among the 4 LS-associated MMR germline mutations, and its detection is complicated. Therefore, prudent screening for PMS2-LS is important as it leads to an efficient LS identification strategy. Immunohistochemistry is recommended as a screening method for LS in EC. Isolated loss of PMS2 (IL-PMS2) expression is caused not only by PMS2-LS but also by MLH1 germline mutation or MLH1 promoter hypermethylation (MLH-PHM). This study aimed to determine the association between MLH1-PHM and IL-PMS2 to avoid inappropriate genetic analysis. We performed MLH1 methylation analysis and MLH1/PMS2 germline mutation testing on the IL-PMS2 cases. By performing MMR-immunohistochemistry on 360 unselected ECs, we could select 8 (2.2%) cases as IL-PMS2. Heterogenous MLH1 staining and MLH1-PHM were detected in 4 of 8 (50%) IL-PMS2 tumors. Of the 5 IL-PMS2 patients who underwent genetic analysis, 1 had PMS2 germline mutation with normal MLH1 expression (without MLH1-PHM), and no MLH1 germline mutation was detected. We suggest that MLH1 promoter methylation analysis for IL-PMS2 EC should be performed to exclude sporadic cases before further PMS2 genetic testing. PMID:26848797

Isolated Loss of PMS2 Immunohistochemical Expression is Frequently Caused by Heterogenous MLH1 Promoter Hypermethylation in Lynch Syndrome Screening for Endometrial Cancer Patients.

PubMed

Kato, Aya; Sato, Naoki; Sugawara, Tae; Takahashi, Kazue; Kito, Masahiko; Makino, Kenichi; Sato, Toshiharu; Shimizu, Dai; Shirasawa, Hiromistu; Miura, Hiroshi; Sato, Wataru; Kumazawa, Yukiyo; Sato, Akira; Kumagai, Jin; Terada, Yukihiro

2016-06-01

Lynch syndrome (LS) is an autosomal-dominant inherited disorder mainly caused by a germline mutation in the DNA mismatch repair (MMR) genes (MLH1, MSH2, MSH6, and PMS2) and is associated with increased risk for various cancers, particularly colorectal cancer and endometrial cancer (EC). Women with LS account for 2% to 6% of EC patients; it is clinically important to identify LS in such individuals for predicting and/or preventing additional LS-associated cancers. PMS2 germline mutation (PMS2-LS) is the rarest contribution to LS etiology among the 4 LS-associated MMR germline mutations, and its detection is complicated. Therefore, prudent screening for PMS2-LS is important as it leads to an efficient LS identification strategy. Immunohistochemistry is recommended as a screening method for LS in EC. Isolated loss of PMS2 (IL-PMS2) expression is caused not only by PMS2-LS but also by MLH1 germline mutation or MLH1 promoter hypermethylation (MLH-PHM). This study aimed to determine the association between MLH1-PHM and IL-PMS2 to avoid inappropriate genetic analysis. We performed MLH1 methylation analysis and MLH1/PMS2 germline mutation testing on the IL-PMS2 cases. By performing MMR-immunohistochemistry on 360 unselected ECs, we could select 8 (2.2%) cases as IL-PMS2. Heterogenous MLH1 staining and MLH1-PHM were detected in 4 of 8 (50%) IL-PMS2 tumors. Of the 5 IL-PMS2 patients who underwent genetic analysis, 1 had PMS2 germline mutation with normal MLH1 expression (without MLH1-PHM), and no MLH1 germline mutation was detected. We suggest that MLH1 promoter methylation analysis for IL-PMS2 EC should be performed to exclude sporadic cases before further PMS2 genetic testing.

Autophagy influences the low-dose hyper-radiosensitivity of human lung adenocarcinoma cells by regulating MLH1.

PubMed

Wang, Qiong; Xiao, Zhuya; Lin, Zhenyu; Zhou, Jie; Chen, Weihong; Jie, Wuyun; Cao, Xing; Yin, Zhongyuan; Cheng, Jing

2017-06-01

To investigate the impact of autophagy on the low-dose hyper-radiosensitivity (HRS) of human lung adenocarcinoma cells via MLH1 regulation. Immunofluorescent staining, Western blotting, and electron microscopy were utilized to detect autophagy in A549 and H460 cells. shRNA was used to silence MLH1 expression. The levels of MLH1, mTOR, p-mTOR, BNIP3, and Beclin-1 were measured by real-time polymerase chain reaction (PCR) and Western blotting. A549 cells, which have low levels of MLH1 expression, displayed HRS/induced radioresistance (IRR). Conversely, the radiosensitivity of H460 cells, which express high levels of MLH1, conformed to the linear-quadratic (LQ) model. After down-regulating MLH1 expression, A549 cells showed increased HRS and inhibition of autophagy, whereas H460 cells exhibited HRS/IRR. The levels of mTOR, p-mTOR, and BNIP3 were reduced in cells harboring MLH1 shRNA, and the changes in the mTOR/p-mTOR ratio mirrored those in MLH1 expression. Low MLH1-expressing A549 cells may exhibit HRS. Both the mTOR/p-mTOR and BNIP3/Beclin-1 signaling pathways were found to be related to HRS, but only mTOR/p-mTOR is involved in the regulation of HRS via MLH1 and autophagy.

MLH1 expression predicts the response to preoperative therapy and is associated with PD-L1 expression in esophageal cancer.

PubMed

Momose, Kota; Yamasaki, Makoto; Tanaka, Koji; Miyazaki, Yasuhiro; Makino, Tomoki; Takahashi, Tsuyoshi; Kurokawa, Yukinori; Nakajima, Kiyokazu; Takiguchi, Shuji; Mori, Masaki; Doki, Yuichiro

2017-07-01

Programmed death-ligand 1 (PD-1/PD-L1) inhibition therapy demonstrates potential as a future treatment for esophageal cancer. Mismatch repair status and tumor PD-L1 expression are the candidate predictive biomarkers for response to this therapy. In colorectal cancer, mismatch repair-deficient tumors are associated with improved survival, although they are not sensitive to 5-fluorouracil-based chemotherapy. The purpose of the present study was to investigate the association between MutL homolog 1 (MLH1) expression and prognosis, response to therapy and PD-L1 expression in esophageal cancer. Immunohistochemistry was used to evaluate MLH1 and PD-L1 expression in 251 resected specimens. Of the specimens, 30.3% exhibited low MLH1 expression and 15.5% exhibited high PD-L1 expression. The 5-year overall survival rates for the high MLH1 expression group and the low MLH1 expression group were 51.3 and 55.6%, respectively (P=0.5260). The responder ratio was 45.7% in the high MLH1 expression group and 15.4% in the low MLH1 expression group (P<0.0001). The frequency of high PD-L1 expression was 11.4% in the high MLH1 expression group (P=0.0064) and 25.0% in the low MLH1 expression group. MLH1 expression may be a predictive factor for the response to preoperative therapy in esophageal cancer, and esophageal cancer with low MLH1 expression may have a mechanism that assists in promoting tumor PD-L1 expression.

Impact of MLH1 expression on tumor evolution after curative surgical tumor resection in a murine orthotopic xenograft model for human MSI colon cancer.

PubMed

Meunier, Katy; Ferron, Marianne; Calmel, Claire; Fléjou, Jean-François; Pocard, Marc; Praz, Françoise

2017-09-01

Colorectal cancers (CRCs) displaying microsatellite instability (MSI) most often result from MLH1 deficiency. The aim of this study was to assess the impact of MLH1 expression per se on tumor evolution after curative surgical resection using a xenograft tumor model. Transplantable tumors established with the human MLH1-deficient HCT116 cell line and its MLH1-complemented isogenic clone, mlh1-3, were implanted onto the caecum of NOD/SCID mice. Curative surgical resection was performed at day 10 in half of the animals. The HCT116-derived tumors were more voluminous compared to the mlh1-3 ones (P = .001). Lymph node metastases and peritoneal carcinomatosis occurred significantly more often in the group of mice grafted with HCT116 (P = .007 and P = .035, respectively). Mlh1-3-grafted mice did not develop peritoneal carcinomatosis or liver metastasis. After surgical resection, lymph node metastases only arose in the group of mice implanted with HCT116 and the rate of cure was significantly lower than in the mlh1-3 group (P = .047). The murine orthotopic xenograft model based on isogenic human CRC cell lines allowed us to reveal the impact of MLH1 expression on tumor evolution in mice who underwent curative surgical resection and in mice whose tumor was left in situ. Our data indicate that the behavior of MLH1-deficient CRC is not only governed by mutations arising in genes harboring microsatellite repeated sequences but also from their defect in MLH1 as such. © 2017 Wiley Periodicals, Inc.

Utility of MLH1 Methylation Analysis in the Clinical Evaluation of Lynch Syndrome in Women with Endometrial Cancer

PubMed Central

Bruegl, Amanda S.; Djordjevic, Bojana; Urbauer, Diana L.; Westin, Shannon N.; Soliman, Pamela T.; Lu, Karen H.; Luthra, Rajyalakshmi; Broaddus, Russell R.

2013-01-01

Clinical screening criteria, such as young age of endometrial cancer diagnosis and family history of signature cancers, have traditionally been used to identify women with Lynch Syndrome, which is caused by mutation of a DNA mismatch repair gene. Immunohistochemistry and microsatellite instability analysis have evolved as important screening tools to evaluate endometrial cancer patients for Lynch Syndrome. A complicating factor is that 15-20% of sporadic endometrial cancers have immunohistochemical loss of the DNA mismatch repair protein MLH1 and high levels of microsatellite instability due to methylation of MLH1. The PCR-based MLH1 methylation assay potentially resolves this issue, yet many clinical laboratories do not perform this assay. The objective of this study was to determine if clinical and pathologic features help to distinguish sporadic endometrial carcinomas with MLH1 loss secondary to MLH1 methylation from Lynch Syndrome-associated endometrial carcinomas with MLH1 loss and absence of MLH1 methylation. Of 337 endometrial carcinomas examined, 54 had immunohistochemical loss of MLH1. 40/54 had MLH1 methylation and were designated as sporadic, while 14/54 lacked MLH1 methylation and were designated as Lynch Syndrome. Diabetes and deep myometrial invasion were associated with Lynch Syndrome; no other clinical or pathological variable distinguished the 2 groups. Combining Society of Gynecologic Oncology screening criteria with these 2 features accurately captured all Lynch Syndrome cases, but with low specificity. In summary, no single clinical/pathologic feature or screening criteria tool accurately identified all Lynch Syndrome-associated endometrial carcinomas, highlighting the importance of the MLH1 methylation assay in the clinical evaluation of these patients. PMID:23888949

Utility of MLH1 methylation analysis in the clinical evaluation of Lynch Syndrome in women with endometrial cancer.

PubMed

Bruegl, Amanda S; Djordjevic, Bojana; Urbauer, Diana L; Westin, Shannon N; Soliman, Pamela T; Lu, Karen H; Luthra, Rajyalakshmi; Broaddus, Russell R

2014-01-01

Clinical screening criteria, such as young age of endometrial cancer diagnosis and family history of signature cancers, have traditionally been used to identify women with Lynch Syndrome, which is caused by mutation of a DNA mismatch repair gene. Immunohistochemistry and microsatellite instability analysis have evolved as important screening tools to evaluate endometrial cancer patients for Lynch Syndrome. A complicating factor is that 15-20% of sporadic endometrial cancers have immunohistochemical loss of the DNA mismatch repair protein MLH1 and high levels of microsatellite instability due to methylation of MLH1. The PCR-based MLH1 methylation assay potentially resolves this issue, yet many clinical laboratories do not perform this assay. The objective of this study was to determine if clinical and pathologic features help to distinguish sporadic endometrial carcinomas with MLH1 loss secondary to MLH1 methylation from Lynch Syndrome-associated endometrial carcinomas with MLH1 loss and absence of MLH1 methylation. Of 337 endometrial carcinomas examined, 54 had immunohistochemical loss of MLH1. 40/54 had MLH1 methylation and were designated as sporadic, while 14/54 lacked MLH1 methylation and were designated as Lynch Syndrome. Diabetes and deep myometrial invasion were associated with Lynch Syndrome; no other clinical or pathological variable distinguished the 2 groups. Combining Society of Gynecologic Oncology screening criteria with these 2 features accurately captured all Lynch Syndrome cases, but with low specificity. In summary, no single clinical/pathologic feature or screening criteria tool accurately identified all Lynch Syndrome-associated endometrial carcinomas, highlighting the importance of the MLH1 methylation assay in the clinical evaluation of these patients.

Promoter hypermethylation of mismatch repair gene hMLH1 predicts the clinical response of malignant astrocytomas to nitrosourea.

PubMed

Fukushima, Takao; Katayama, Yoichi; Watanabe, Takao; Yoshino, Atsuo; Ogino, Akiyoshi; Ohta, Takashi; Komine, Chiaki

2005-02-15

In certain types of human cancers, transcriptional inactivation of hMLH1 by promoter hypermethylation plays a causal role in the loss of mismatch repair functions that modulate cytotoxic pathways in response to DNA-damaging agents. The aim of the present study was to investigate the role of promoter methylation of the hMLH1 gene in malignant astrocytomas. We examined the hMLH1 promoter methylation in a homogeneous cohort of patients with 41 malignant astrocytomas treated by 1-(4-amino-2-methyl-5-pyrimidinyl)methyl-3-2(2-chloroethyl)-3-nitrosourea chemotherapy in combination with radiation and interferon therapy, and assessed the correlation of such methylation with clinical outcome. hMLH1 promoter methylation was found in 6 (15%) of the 41 newly diagnosed malignant astrocytomas. Hypermethylation of the hMLH1 promoter corresponded closely with a loss of immunohistochemical staining for hMLH1 protein (P = 0.0013). Patients with hMLH1-methylated tumors displayed a greater chance of responding to adjuvant therapy as compared with those with hMLH1-unmethylated tumors (P = 0.0150). The presence of hMLH1 hypermethylation was significantly associated with a longer progression-free survival on both univariate analysis (P = 0.0340) and multivariate analysis (P = 0.0161). The present study identified hMLH1 methylation status as a predictor of the clinical response of malignant astrocytomas to chloroethylnitrosourea-based adjuvant therapy. The findings obtained suggest that determination of the methylation status of hMLH1 could provide a potential basis for designing rational chemotherapeutic strategies, as well as for predicting prognosis.

Differential cellular responses to prolonged LDR-IR in MLH1-proficient and MLH1-deficient colorectal cancer HCT116 cells.

PubMed

Yan, Tao; Seo, Yuji; Kinsella, Timothy J

2009-11-15

MLH1 is a key DNA mismatch repair (MMR) protein involved in maintaining genomic stability by participating in the repair of endogenous and exogenous mispairs in the daughter strands during S phase. Exogenous mispairs can result following treatment with several classes of chemotherapeutic drugs, as well as with ionizing radiation. In this study, we investigated the role of the MLH1 protein in determining the cellular and molecular responses to prolonged low-dose rate ionizing radiation (LDR-IR), which is similar to the clinical use of cancer brachytherapy. An isogenic pair of MMR(+) (MLH1(+)) and MMR(-) (MLH1(-)) human colorectal cancer HCT116 cells was exposed to prolonged LDR-IR (1.3-17 cGy/h x 24-96 h). The clonogenic survival and gene mutation rates were examined. Cell cycle distribution was analyzed with flow cytometry. Changes in selected DNA damage repair proteins, DNA damage response proteins, and cell death marker proteins were examined with Western blotting. MLH1(+) HCT116 cells showed greater radiosensitivity with enhanced expression of apoptotic and autophagic markers, a reduced HPRT gene mutation rate, and more pronounced cell cycle alterations (increased late-S population and a G(2)/M arrest) following LDR-IR compared with MLH1(-) HCT116 cells. Importantly, a progressive increase in MLH1 protein levels was found in MLH1(+) cells during prolonged LDR-IR, which was temporally correlated with a progressive decrease in Rad51 protein (involved in homologous recombination) levels. MLH1 status significantly affects cellular responses to prolonged LDR-IR. MLH1 may enhance cell radiosensitivity to prolonged LDR-IR through inhibition of homologous recombination (through inhibition of Rad51).

Lynch syndrome-associated endometrial carcinoma with MLH1 germline mutation and MLH1 promoter hypermethylation: a case report and literature review.

PubMed

Yokoyama, Takanori; Takehara, Kazuhiro; Sugimoto, Nao; Kaneko, Keika; Fujimoto, Etsuko; Okazawa-Sakai, Mika; Okame, Shinichi; Shiroyama, Yuko; Yokoyama, Takashi; Teramoto, Norihiro; Ohsumi, Shozo; Saito, Shinya; Imai, Kazuho; Sugano, Kokichi

2018-05-21

Lynch syndrome is an autosomal dominant inherited disease caused by germline mutations in mismatch repair genes. Analysis for microsatellite instability (MSI) and immunohistochemistry (IHC) of protein expressions of disease-associated genes is used to screen for Lynch syndrome in endometrial cancer patients. When losses of both MLH1 and PMS2 proteins are observed by IHC, MLH1 promoter methylation analysis is conducted to distinguish Lynch syndrome-associated endometrial cancer from sporadic cancer. Here we report a woman who developed endometrial cancer at the age of 49 years. She had a family history of colorectal cancer (first-degree relative aged 52 years) and stomach cancer (second-degree relative with the age of onset unknown). No other family history was present, and she failed to meet the Amsterdam II criteria for the diagnosis of Lynch syndrome. Losses of MLH1 and PMS2, but not MSH2 and MSH6, proteins were observed by IHC in endometrial cancer tissues. Because MLH1 promoter hypermethylation was detected in endometrial cancer tissue samples, the epigenetic silencing of MLH1 was suspected as the cause of the protein loss. However, because of the early onset of endometrial cancer and the positive family history, a diagnosis of Lynch syndrome was also suspected. Therefore, we provided her with genetic counseling. After obtaining her consent, MLH1 promoter methylation testing and genetic testing of peripheral blood were performed. MLH1 promoter methylation was not observed in peripheral blood. However, genetic testing revealed a large deletion of exon 5 in MLH1; thus, we diagnosed the presence of Lynch syndrome. Both MLH1 germline mutation and MLH1 promoter hypermethylation may be observed in endometrial cancer. Therefore, even if MLH1 promoter hypermethylation is detected, a diagnosis of Lynch syndrome cannot be excluded.

Human MutL homolog 1 immunoexpression in oral leukoplakia and oral squamous cell carcinoma: A prospective study in Indian population

PubMed Central

Chaudhari, Narendra T; Tupkari, Jagdish V; Joy, Tabita; Ahire, Manisha S

2016-01-01

Background: Mammalian mismatch repair system is responsible for maintaining genomic stability during repeated duplications, and human MutL homolog 1 (hMLH1) protein constitutes an important part of it. Various isolated studies have reported the altered expression of hMLH1 in oral leukoplakia (OL) and oral squamous cell carcinoma (OSCC). Research is lacking in the quantitative estimation and comparison of hMLH1 expression in OL and OSCC. Aims: To evaluate, quantify and compare hMLH1 immunoexpression in normal oral mucosa, OL and OSCC. Settings and Design: Thirty patients of OL and thirty patients of OSCC formed the study group and thirty patients were included in the control group (normal oral mucosa). Formalin-fixed paraffin wax blocks were prepared from the tissue samples. Materials and Methods: Immunohistochemistry for hMLH1 was performed, and the total number of positive cells was counted in high-power fields, and based on that percentage positivity of hMLH1 was calculated in all the cases. Statistical Analysis: Kruskal–Wallis and t-test were used. P < 0.05 was considered to be statistically significant. Results: The mean hMLH1 value in control group, leukoplakia and OSCC was 78.26, 54.33 and 40.97 respectively. hMLH1 immunoexpression showed decreasing indexes from control group to leukoplakia and then further to OSCC. hMLH1 expression was significantly lower in OSCC as compared to leukoplakia. There was no significant correlation of mean hMLH1 expression between different clinical and histopathological stages of leukoplakia and OSCC. Conclusions: hMLH1 immunoexpression was inversely related to the degree of dysplasia. These findings suggest that there is a progressive decrease in hMLH1 expression from control to leukoplakia and further to OSCC. Thus, it can be concluded that hMLH1 can be used as a reliable biomarker for malignant transformation. PMID:27721611

The MLH1 ATPase domain is needed for suppressing aberrant formation of interstitial telomeric sequences.

PubMed

Jia, Pingping; Chai, Weihang

2018-05-01

Genome instability gives rise to cancer. MLH1, commonly known for its important role in mismatch repair (MMR), DNA damage signaling and double-strand break (DSB) repair, safeguards genome stability. Recently we have reported a novel role of MLH1 in preventing aberrant formation of interstitial telomeric sequences (ITSs) at intra-chromosomal regions. Deficiency in MLH1, in particular its N-terminus, leads to an increase of ITSs. Here, we identify that the ATPase activity in the MLH1 N-terminal domain is important for suppressing the formation of ITSs. The ATPase activity is also needed for recruiting MLH1 to DSBs. Moreover, defective ATPase activity of MLH1 causes an increase in micronuclei formation. Our results highlight the crucial role of MLH1's ATPase domain in preventing the aberrant formation of telomeric sequences at the intra-chromosomal regions and preserving genome stability. Copyright © 2018 Elsevier B.V. All rights reserved.

Biallelic MLH1 SNP cDNA expression or constitutional promoter methylation can hide genomic rearrangements causing Lynch syndrome.

PubMed

Morak, Monika; Koehler, Udo; Schackert, Hans Konrad; Steinke, Verena; Royer-Pokora, Brigitte; Schulmann, Karsten; Kloor, Matthias; Höchter, Wilhelm; Weingart, Josef; Keiling, Cortina; Massdorf, Trisari; Holinski-Feder, Elke

2011-08-01

A positive family history, germline mutations in DNA mismatch repair genes, tumours with high microsatellite instability, and loss of mismatch repair protein expression are the hallmarks of hereditary non-polyposis colorectal cancer (Lynch syndrome). However, in ~10-15% of cases of suspected Lynch syndrome, no disease-causing mechanism can be detected. Oligo array analysis was performed to search for genomic imbalances in patients with suspected mutation-negative Lynch syndrome with MLH1 deficiency in their colorectal tumours. A deletion in the LRRFIP2 (leucine-rich repeat flightless-interacting protein 2) gene flanking the MLH1 gene was detected, which turned out to be a paracentric inversion on chromosome 3p22.2 creating two new stable fusion transcripts between MLH1 and LRRFIP2. A single-nucleotide polymorphism in MLH1 exon 8 was expressed from both alleles, initially pointing to appropriate MLH1 function at least in peripheral cells. In a second case, an inherited duplication of the MLH1 gene region resulted in constitutional MLH1 promoter methylation. Constitutional MLH1 promoter methylation may therefore in rare cases be a heritable disease mechanism and should not be overlooked in seemingly sporadic patients.

Epigenetic Loss of MLH1 Expression in Normal Human Hematopoietic Stem Cell Clones is Defined by the Promoter CpG Methylation Pattern Observed by High-Throughput Methylation Specific Sequencing

PubMed Central

Kenyon, Jonathan; Nickel-Meester, Gabrielle; Qing, Yulan; Santos-Guasch, Gabriela; Drake, Ellen; PingfuFu; Sun, Shuying; Bai, Xiaodong; Wald, David; Arts, Eric; Gerson, Stanton L.

2016-01-01

Normal human hematopoietic stem and progenitor cells (HPC) lose expression of MLH1, an important mismatch repair (MMR) pathway gene, with age. Loss of MMR leads to replication dependent mutational events and microsatellite instability observed in secondary acute myelogenous leukemia and other hematologic malignancies. Epigenetic CpG methylation upstream of the MLH1 promoter is a contributing factor to acquired loss of MLH1 expression in tumors of the epithelia and proximal mucosa. Using single molecule high-throughput bisulfite sequencing we have characterized the CpG methylation landscape from −938 to −337 bp upstream of the MLH1 transcriptional start site (position +0), from 30 hematopoietic colony forming cell clones (CFC) either expressing or not expressing MLH1. We identify a correlation between MLH1 promoter methylation and loss of MLH1 expression. Additionally, using the CpG site methylation frequencies obtained in this study we were able to generate a classification algorithm capable of sorting the expressing and non-expressing CFC. Thus, as has been previously described for many tumor cell types, we report for the first time a correlation between the loss of MLH1 expression and increased MLH1 promoter methylation in CFC derived from CD34+ selected hematopoietic stem and progenitor cells. PMID:27570841

Epigenetic Loss of MLH1 Expression in Normal Human Hematopoietic Stem Cell Clones is Defined by the Promoter CpG Methylation Pattern Observed by High-Throughput Methylation Specific Sequencing.

PubMed

Kenyon, Jonathan; Nickel-Meester, Gabrielle; Qing, Yulan; Santos-Guasch, Gabriela; Drake, Ellen; PingfuFu; Sun, Shuying; Bai, Xiaodong; Wald, David; Arts, Eric; Gerson, Stanton L

Normal human hematopoietic stem and progenitor cells (HPC) lose expression of MLH1 , an important mismatch repair (MMR) pathway gene, with age. Loss of MMR leads to replication dependent mutational events and microsatellite instability observed in secondary acute myelogenous leukemia and other hematologic malignancies. Epigenetic CpG methylation upstream of the MLH1 promoter is a contributing factor to acquired loss of MLH1 expression in tumors of the epithelia and proximal mucosa. Using single molecule high-throughput bisulfite sequencing we have characterized the CpG methylation landscape from -938 to -337 bp upstream of the MLH1 transcriptional start site (position +0), from 30 hematopoietic colony forming cell clones (CFC) either expressing or not expressing MLH1 . We identify a correlation between MLH1 promoter methylation and loss of MLH1 expression. Additionally, using the CpG site methylation frequencies obtained in this study we were able to generate a classification algorithm capable of sorting the expressing and non-expressing CFC. Thus, as has been previously described for many tumor cell types, we report for the first time a correlation between the loss of MLH1 expression and increased MLH1 promoter methylation in CFC derived from CD34 + selected hematopoietic stem and progenitor cells.

Prognostic value of MLH1 promoter methylation in male patients with esophageal squamous cell carcinoma.

PubMed

Wu, Dongping; Chen, Xiaoying; Xu, Yan; Wang, Haiyong; Yu, Guangmao; Jiang, Luping; Hong, Qingxiao; Duan, Shiwei

2017-04-01

The DNA mismatch repair (MMR) gene MutL homolog 1 ( MLH1 ) is critical for the maintenance of genomic integrity. Methylation of the MLH1 gene promoter was identified as a prognostic marker for numerous types of cancer including glioblastoma, colorectal, ovarian and gastric cancer. The present study aimed to determine whether MLH1 promoter methylation was associated with survival in male patients with esophageal squamous cell carcinoma (ESCC). Formalin-fixed, paraffin-embedded ESCC tissues were collected from 87 male patients. MLH1 promoter methylation was assessed using the methylation-specific polymerase chain reaction approach. Kaplan-Meier survival curves and log-rank tests were used to evaluate the association between MLH1 promoter methylation and overall survival (OS) in patients with ESCC. Cox regression analysis was used to obtain crude and multivariate hazard ratios (HR), and 95% confidence intervals (CI). The present study revealed that MLH1 promoter methylation was observed in 53/87 (60.9%) of male patients with ESCC. Kaplan-Meier survival analysis demonstrated that MLH1 promoter hypermethylation was significantly associated with poorer prognosis in patients with ESCC (P=0.048). Multivariate survival analysis revealed that MLH1 promoter hypermethylation was an independent predictor of poor OS in male patients with ESCC (HR=1.716; 95% CI=1.008-2.921). Therefore, MLH1 promoter hypermethylation may be a predictor of prognosis in male patients with ESCC.

Distinct features between MLH1-methylated and unmethylated colorectal carcinomas with the CpG island methylator phenotype: implications in the serrated neoplasia pathway

PubMed Central

Cho, Nam-Yun; Kang, Gyeong Hoon

2016-01-01

The presence or absence of MLH1 methylation may critically affect the heterogeneity of colorectal carcinoma (CRC) with the CpG island methylator phenotype (CIMP). Here, we investigated the differential characteristics of CIMP-high (CIMP-H) CRCs according to MLH1 methylation status. To further confirm the MLH1-dependent features in CIMP-H CRC, an independent analysis was performed using data from The Cancer Genome Atlas (TCGA). In our CIMP-H CRC samples, MLH1-methylated tumors were characterized by older patient age, proximal colonic location, mucinous histology, intense lymphoid reactions, RUNX3/SOCS1 promoter methylation, BRAF mutations, and microsatellite instability-high (MSI-H) status. By contrast, MLH1-unmethylated tumors were associated with earlier age of onset, increased distal colorectal localization, adverse pathologic features, and KRAS mutations. In the TCGA dataset, the MLH1-silenced CIMP-H CRC demonstrated proximal location, MSI-H status, hypermutated phenotype, and frequent BRAF mutations, but the MLH1-non-silenced CIMP-H CRC was significantly associated with high frequencies of KRAS and APC mutations. In conclusion, the differential nature of CIMP-H CRCs depends primarily on the MLH1 methylation status. Based on the current knowledge, the sessile serrated adenoma/polyp may be the major precursor of MLH1-methylated CIMP-H CRCs, whereas MLH1-unmethylated CIMP-H CRCs may develop predominantly from KRAS-mutated traditional serrated adenomas and less commonly from BRAF-mutated traditional serrated adenomas and/or sessile serrated adenomas/polyps. PMID:26883113

Distinct features between MLH1-methylated and unmethylated colorectal carcinomas with the CpG island methylator phenotype: implications in the serrated neoplasia pathway.

PubMed

Kim, Jung Ho; Bae, Jeong Mo; Cho, Nam-Yun; Kang, Gyeong Hoon

2016-03-22

The presence or absence of MLH1 methylation may critically affect the heterogeneity of colorectal carcinoma (CRC) with the CpG island methylator phenotype (CIMP). Here, we investigated the differential characteristics of CIMP-high (CIMP-H) CRCs according to MLH1 methylation status. To further confirm the MLH1-dependent features in CIMP-H CRC, an independent analysis was performed using data from The Cancer Genome Atlas (TCGA). In our CIMP-H CRC samples, MLH1-methylated tumors were characterized by older patient age, proximal colonic location, mucinous histology, intense lymphoid reactions, RUNX3/SOCS1 promoter methylation, BRAF mutations, and microsatellite instability-high (MSI-H) status. By contrast, MLH1-unmethylated tumors were associated with earlier age of onset, increased distal colorectal localization, adverse pathologic features, and KRAS mutations. In the TCGA dataset, the MLH1-silenced CIMP-H CRC demonstrated proximal location, MSI-H status, hypermutated phenotype, and frequent BRAF mutations, but the MLH1-non-silenced CIMP-H CRC was significantly associated with high frequencies of KRAS and APC mutations. In conclusion, the differential nature of CIMP-H CRCs depends primarily on the MLH1 methylation status. Based on the current knowledge, the sessile serrated adenoma/polyp may be the major precursor of MLH1-methylated CIMP-H CRCs, whereas MLH1-unmethylated CIMP-H CRCs may develop predominantly from KRAS-mutated traditional serrated adenomas and less commonly from BRAF-mutated traditional serrated adenomas and/or sessile serrated adenomas/polyps.

Intervention outcomes among HIV-affected families over 18 months.

PubMed

Rotheram-Borus, Mary Jane; Rice, Eric; Comulada, W Scott; Best, Karin; Elia, Carla; Peters, Katherine; Li, Li; Green, Sara; Valladares, Ena

2012-07-01

We evaluate the efficacy of a family-based intervention over time among HIV-affected families. Mothers living with HIV (MLH; n = 339) in Los Angeles and their school-aged children were randomized to either an intervention or control condition and followed for 18 months. MLH and their children in the intervention received 16 cognitive-behavioral, small-group sessions designed to help them maintain physical and mental health, parent while ill, address HIV-related stressors, and reduce HIV-transmission behaviors. At recruitment, MLH reported few problem behaviors related to physical health, mental health, or sexual or drug transmission acts. Compared to MLH in the control condition, intervention MLH were significantly more likely to monitor their own CD4 cell counts and their children were more likely to decrease alcohol and drug use. Most MLH and their children had relatively healthy family relationships. Family-based HIV interventions should be limited to MLH who are experiencing substantial problems.

High Mutation Levels are Compatible with Normal Embryonic Development in Mlh1-Deficient Mice.

PubMed

Fan, Xiaoyan; Li, Yan; Zhang, Yulong; Sang, Meixiang; Cai, Jianhui; Li, Qiaoxia; Ozaki, Toshinori; Ono, Tetsuya; He, Dongwei

2016-10-01

To elucidate the role of the mismatch repair gene Mlh1 in genome instability during the fetal stage, spontaneous mutations were studied in Mlh1-deficient lacZ-transgenic mouse fetuses. Mutation levels were high at 9.5 days post coitum (dpc) and gradually increased during the embryonic stage, after which they remained unchanged. In addition, mutations that were found in brain, liver, spleen, small intestine and thymus showed similar levels and no statistically significant difference was found. The molecular nature of mutations at 12.5 dpc in fetuses of Mlh1 +/+ and Mlh1 -/- mice showed their own unique spectra, suggesting that deletion mutations were the main causes in the deficiency of the Mlh1 gene. Of note, fetuses of irradiated mice exhibited marked differences such as post-implantation loss and Mendelian distribution. Collectively, these results strongly suggest that high mutation ofMlh1 -/- -deficient fetuses has little effect on the fetuses during their early developmental stages, whereas Mlh1 -/- -deficient fetuses from X-ray irradiated mothers are clearly effected.

Mlh1-Mlh3, a Meiotic Crossover and DNA Mismatch Repair Factor, Is a Msh2-Msh3-stimulated Endonuclease*

PubMed Central

Rogacheva, Maria V.; Manhart, Carol M.; Chen, Cheng; Guarne, Alba; Surtees, Jennifer; Alani, Eric

2014-01-01

Crossing over between homologous chromosomes is initiated in meiotic prophase in most sexually reproducing organisms by the appearance of programmed double strand breaks throughout the genome. In Saccharomyces cerevisiae the double-strand breaks are resected to form three prime single-strand tails that primarily invade complementary sequences in unbroken homologs. These invasion intermediates are converted into double Holliday junctions and then resolved into crossovers that facilitate homolog segregation during Meiosis I. Work in yeast suggests that Msh4-Msh5 stabilizes invasion intermediates and double Holliday junctions, which are resolved into crossovers in steps requiring Sgs1 helicase, Exo1, and a putative endonuclease activity encoded by the DNA mismatch repair factor Mlh1-Mlh3. We purified Mlh1-Mlh3 and showed that it is a metal-dependent and Msh2-Msh3-stimulated endonuclease that makes single-strand breaks in supercoiled DNA. These observations support a direct role for an Mlh1-Mlh3 endonuclease activity in resolving recombination intermediates and in DNA mismatch repair. PMID:24403070

Mlh1-Mlh3, a meiotic crossover and DNA mismatch repair factor, is a Msh2-Msh3-stimulated endonuclease.

PubMed

Rogacheva, Maria V; Manhart, Carol M; Chen, Cheng; Guarne, Alba; Surtees, Jennifer; Alani, Eric

2014-02-28

Crossing over between homologous chromosomes is initiated in meiotic prophase in most sexually reproducing organisms by the appearance of programmed double strand breaks throughout the genome. In Saccharomyces cerevisiae the double-strand breaks are resected to form three prime single-strand tails that primarily invade complementary sequences in unbroken homologs. These invasion intermediates are converted into double Holliday junctions and then resolved into crossovers that facilitate homolog segregation during Meiosis I. Work in yeast suggests that Msh4-Msh5 stabilizes invasion intermediates and double Holliday junctions, which are resolved into crossovers in steps requiring Sgs1 helicase, Exo1, and a putative endonuclease activity encoded by the DNA mismatch repair factor Mlh1-Mlh3. We purified Mlh1-Mlh3 and showed that it is a metal-dependent and Msh2-Msh3-stimulated endonuclease that makes single-strand breaks in supercoiled DNA. These observations support a direct role for an Mlh1-Mlh3 endonuclease activity in resolving recombination intermediates and in DNA mismatch repair.

Modulation of transcription factor binding and epigenetic regulation of the MLH1 CpG island and shore by polymorphism rs1800734 in colorectal cancer

PubMed Central

Savio, Andrea J.; Bapat, Bharati

2017-01-01

ABSTRACT The MLH1 promoter polymorphism rs1800734 is associated with MLH1 CpG island hypermethylation and expression loss in colorectal cancer (CRC). Conversely, variant rs1800734 is associated with MLH1 shore, but not island, hypomethylation in peripheral blood mononuclear cell DNA. To explore these distinct patterns, MLH1 CpG island and shore methylation was assessed in CRC cell lines stratified by rs1800734 genotype. Cell lines containing the variant A allele demonstrated MLH1 shore hypomethylation compared to wild type (GG). There was significant enrichment of transcription factor AP4 at the MLH1 promoter in GG and GA cell lines, but not the AA cell line, by chromatin immunoprecipitation studies. Preferential binding to the G allele was confirmed by sequencing in the GA cell line. The enhancer-associated histone modification H3K4me1 was enriched at the MLH1 shore; however, H3K27ac was not, indicating the shore is an inactive enhancer. These results demonstrate the role of variant rs1800734 in altering transcription factor binding as well as epigenetics at regions beyond the MLH1 CpG island in which it is located. PMID:28304185

Modulation of transcription factor binding and epigenetic regulation of the MLH1 CpG island and shore by polymorphism rs1800734 in colorectal cancer.

PubMed

Savio, Andrea J; Bapat, Bharati

2017-06-03

The MLH1 promoter polymorphism rs1800734 is associated with MLH1 CpG island hypermethylation and expression loss in colorectal cancer (CRC). Conversely, variant rs1800734 is associated with MLH1 shore, but not island, hypomethylation in peripheral blood mononuclear cell DNA. To explore these distinct patterns, MLH1 CpG island and shore methylation was assessed in CRC cell lines stratified by rs1800734 genotype. Cell lines containing the variant A allele demonstrated MLH1 shore hypomethylation compared to wild type (GG). There was significant enrichment of transcription factor AP4 at the MLH1 promoter in GG and GA cell lines, but not the AA cell line, by chromatin immunoprecipitation studies. Preferential binding to the G allele was confirmed by sequencing in the GA cell line. The enhancer-associated histone modification H3K4me1 was enriched at the MLH1 shore; however, H3K27ac was not, indicating the shore is an inactive enhancer. These results demonstrate the role of variant rs1800734 in altering transcription factor binding as well as epigenetics at regions beyond the MLH1 CpG island in which it is located.

Evaluation of promoter methylation status of MLH1 gene in Iranian patients with colorectal tumors and adenoma polyps.

PubMed

Zarandi, Ashkan; Irani, Shiva; Savabkar, Sanaz; Chaleshi, Vahid; Ghavideldarestani, Maryam; Mirfakhraie, Reza; Khodadoostan, Mahsa; Nazemalhosseini-Mojarad, Ehsan; Asadzadeh Aghdaei, Hamid

2017-01-01

The aim of this study was to evaluate the methylation status of the promoter region of MLH1 gene in colorectal cancer (CRC) and its precursor lesions as well as elucidate its association with various clinicopathological characteristics among Iranian population. Epigenetic silencing of mismatch repair genes, such as MLH1 , by methylation of CpG islands of their promoter region has been proved to be an important mechanism in colorectal carcinogenesis. Fifty colorectal cancer and polyp tissue samples including 13 Primary colorectal tumor and 37 Adenoma polyp samples were enrolled in this study. Methylation-specific polymerase chain reaction (MSP) was performed to find the frequency of MLH1 Promoter Methylation. Promoter methylation of MLH1 gene was detected in 5 out of 13 tumor tissues and 4 out of 37 adenoma polyp. The frequency of MLH1 methylation in tumor samples was significantly higher compared to that in polyp tissues (P= 0.026). No significant association was observed between MLH1 promoter methylation and clinicopathological characteristics of the patients. The frequency of  MLH1  promoter methylation in CRC and colon polyp was 18%. Our findings indicated that methylation of MLH1 promoter region alone cannot be considered as a biomarker for early detection of CRC.

Effect of MLH1 -93G>A on gene expression in patients with colorectal cancer.

PubMed

Funck, Alexandre; Santos, Juliana C; Silva-Fernandes, Isabelle J L; Rabenhorst, Silvia H B; Martinez, Carlos A R; Ribeiro, Marcelo L

2014-09-01

The DNA repair machinery plays a key role in maintaining genomic stability by preventing the emergence of mutations. Furthermore, the -93G>A polymorphism in the MLH1 gene has been associated with an increased risk of developing colorectal cancer. Therefore, the aim of this study was to examine the expression pattern and effect of this polymorphism in normal and tumour samples from patients with colorectal cancer. The MLH1 -93G>A (rs1800734) polymorphism was detected by PCR-RFLP in 49 cases of colorectal cancer. MLH1 expression was investigated using real-time quantitative PCR. The results indicate a significant decrease in MLH1 expression in tumour samples compared to their normal counterparts. The MLH1 gene was also significantly repressed in samples from patients who had some degree of tumour invasion into other organs. Similarly, those patients who were in a more advanced tumour stage (TNM III and IV) exhibited a significant reduction in MLH1 gene expression. Finally, the mutant genotype AA of MLH1 was associated with a significant decrease in the expression of this gene. This finding suggests that this polymorphism could increase the risk of developing colorectal cancer by a defective mismatch repair system, particularly through the loss of MLH1 expression in an allele-specific manner.

Association between promoter methylation of MLH1 and MSH2 and reactive oxygen species in oligozoospermic men-A pilot study.

PubMed

Gunes, S; Agarwal, A; Henkel, R; Mahmutoglu, A M; Sharma, R; Esteves, S C; Aljowair, A; Emirzeoglu, D; Alkhani, A; Pelegrini, L; Joumah, A; Sabanegh, E

2018-04-01

MLH1 and MSH2 are important genes for DNA mismatch repair and crossing over during meiosis and are implicated in male infertility. Therefore, the methylation patterns of the DNA mismatch repair genes MLH1 and MSH2 in oligozoospermic males were investigated. Ten oligozoospermic patients and 29 normozoospermic donors were analysed. Methylation profiles of the MLH1 and MSH2 promotors were analysed. In addition, sperm motility and seminal reactive oxygen species (ROS) were recorded. Receiver operating characteristic (ROC) analysis was conducted to determine the accuracy of the DNA methylation status of MLH1 and MSH2 to distinguish between oligozoospermic and normozoospermic men. In oligozoospermic men, MLH1 was significantly (p = .0013) more methylated compared to normozoospermic men. Additionally, there was a significant positive association (r = .384; p = .0159) between seminal ROS levels and MLH1 methylation. Contrary, no association between MSH2 methylation and oligozoospermia was found. ROC curve analysis for methylation status of MLH1 was significant (p = .0275) with an area under the curve of 61.1%, a sensitivity of 22.2% and a specificity of 100.0%. This pilot study indicates oligozoospermic patients have more methylation of MLH1 than normozoospermic patients. Whether hypermethylation of the MLH1 promoter plays a role in repairing relevant mismatches of sperm DNA strands in idiopathic oligozoospermia warrants further investigation. © 2017 Blackwell Verlag GmbH.

MLH1 as a direct target of MiR-155 and a potential predictor of favorable prognosis in pancreatic cancer.

PubMed

Liu, Wen-Jing; Zhao, Yu-Pei; Zhang, Tai-Ping; Zhou, Li; Cui, Quan-Cai; Zhou, Wei-Xun; You, Lei; Chen, Ge; Shu, Hong

2013-08-01

The regulation of Mut L homologue 1 (MLH1) expression by microRNA (miR)-155 and its prognostic significance in pancreatic cancer (PC) remain to be elucidated. This study aimed to address the issues. MiR-155 mimics and inhibitor were transfected to PC cell lines, Panc-1 and Capan-1. Expression of MLH1 was subsequently evaluated. Then, luciferase activity was detected after miR-155 mimics and pRL-TK plasmids containing wild-type and mutant 3'UTRs of MLH1 mRNA were co-transfected. Finally, immunohistochemical staining for MLH1 was performed in PC samples. Transfection of miR-155 mimics and inhibitor led to reversely altered protein expressions of miR-155 and MLH1, whereas the corresponding mRNA expressions were similar. A significant decrease in luciferase activity in the cells transfected with the wild-type pRL-TK plasmid was shown in contrast to those transfected with the mutant one. In addition, MLH1 was less expressed in tumor than in para-tumor tissues of PC. Extensive MLH1 expression was significantly associated with favorable differentiation and less lymph node metastasis. MLH1 expression was found to be a prognosticator in univariate analysis, and being of marginally significant impact in multivariate test. MLH1 might serve as a direct target of miR-155 and a potential prognosis predictor in PC.

Identification of constitutional MLH1 epimutations and promoter variants in colorectal cancer patients from the Colon Cancer Family Registry

PubMed Central

Ward, Robyn L.; Dobbins, Timothy; Lindor, Noralane M.; Rapkins, Robert W.; Hitchins, Megan P.

2013-01-01

Purpose: Constitutional MLH1 epimutations manifest as promoter methylation and silencing of the affected allele in normal tissues, predisposing to Lynch syndrome–associated cancers. This study investigated their frequency and inheritance. Methods: A total of 416 individuals with a colorectal cancer showing loss of MLH1 expression and without deleterious germline mutations in MLH1 were ascertained from the Colon Cancer Family Registry (C-CFR). Constitutive DNA samples were screened for MLH1 methylation in all 416 subjects and for promoter sequence changes in 357 individuals. Results: Constitutional MLH1 epimutations were identified in 16 subjects. Of these, seven (1.7%) had mono- or hemi-allelic methylation and eight had low-level methylation (2%). In one subject the epimutation was linked to the c.-27C>A promoter variant. Testing of 37 relatives from nine probands revealed paternal transmission of low-level methylation segregating with a c.+27G>A variant in one case. Five additional probands had a promoter variant without an MLH1 epimutation, with three showing diminished promoter activity in functional assays. Conclusion: Although rare, sequence changes in the regulatory region of MLH1 and aberrant methylation may alone or together predispose to the development of cancer. Screening for these changes is warranted in individuals who have a negative germline sequence screen of MLH1 and loss of MLH1 expression in their tumor. PMID:22878509

Tumor mismatch repair immunohistochemistry and DNA MLH1 methylation testing of patients with endometrial cancer diagnosed at age younger than 60 years optimizes triage for population-level germline mismatch repair gene mutation testing.

PubMed

Buchanan, Daniel D; Tan, Yen Y; Walsh, Michael D; Clendenning, Mark; Metcalf, Alexander M; Ferguson, Kaltin; Arnold, Sven T; Thompson, Bryony A; Lose, Felicity A; Parsons, Michael T; Walters, Rhiannon J; Pearson, Sally-Ann; Cummings, Margaret; Oehler, Martin K; Blomfield, Penelope B; Quinn, Michael A; Kirk, Judy A; Stewart, Colin J; Obermair, Andreas; Young, Joanne P; Webb, Penelope M; Spurdle, Amanda B

2014-01-10

Clinicopathologic data from a population-based endometrial cancer cohort, unselected for age or family history, were analyzed to determine the optimal scheme for identification of patients with germline mismatch repair (MMR) gene mutations. Endometrial cancers from 702 patients recruited into the Australian National Endometrial Cancer Study (ANECS) were tested for MMR protein expression using immunohistochemistry (IHC) and for MLH1 gene promoter methylation in MLH1-deficient cases. MMR mutation testing was performed on germline DNA of patients with MMR-protein deficient tumors. Prediction of germline mutation status was compared for combinations of tumor characteristics, age at diagnosis, and various clinical criteria (Amsterdam, Bethesda, Society of Gynecologic Oncology, ANECS). Tumor MMR-protein deficiency was detected in 170 (24%) of 702 cases. Germline testing of 158 MMR-deficient cases identified 22 truncating mutations (3% of all cases) and four unclassified variants. Tumor MLH1 methylation was detected in 99 (89%) of 111 cases demonstrating MLH1/PMS2 IHC loss; all were germline MLH1 mutation negative. A combination of MMR IHC plus MLH1 methylation testing in women younger than 60 years of age at diagnosis provided the highest positive predictive value for the identification of mutation carriers at 46% versus ≤ 41% for any other criteria considered. Population-level identification of patients with MMR mutation-positive endometrial cancer is optimized by stepwise testing for tumor MMR IHC loss in patients younger than 60 years, tumor MLH1 methylation in individuals with MLH1 IHC loss, and germline mutations in patients exhibiting loss of MSH6, MSH2, or PMS2 or loss of MLH1/PMS2 with absence of MLH1 methylation.

Influence of MLH1 on colon cancer sensitivity to poly(ADP-ribose) polymerase inhibitor combined with irinotecan.

PubMed

Tentori, Lucio; Leonetti, Carlo; Muzi, Alessia; Dorio, Annalisa Susanna; Porru, Manuela; Dolci, Susanna; Campolo, Federica; Vernole, Patrizia; Lacal, Pedro Miguel; Praz, Françoise; Graziani, Grazia

2013-07-01

Poly(ADP-ribose) polymerase inhibitors (PARPi) are currently evaluated in clinical trials in combination with topoisomerase I (Top1) inhibitors against a variety of cancers, including colon carcinoma. Since the mismatch repair component MLH1 is defective in 10-15% of colorectal cancers we have investigated whether MLH1 affects response to the Top1 inhibitor irinotecan, alone or in combination with PARPi. To this end, the colon cancer cell lines HCT116, carrying MLH1 mutations on chromosome 3 and HCT116 in which the wild-type MLH1 gene was replaced via chromosomal transfer (HCT116+3) or by transfection of the corresponding MLH1 cDNA (HCT116 1-2) were used. HCT116 cells or HCT116+3 cells stably silenced for PARP-1 expression were also analysed. The results of in vitro and in vivo experiments indicated that MLH1, together with low levels of Top1, contributed to colon cancer resistance to irinotecan. In the MLH1-proficient cells SN-38, the active metabolite of irinotecan, induced lower levels of DNA damage than in MLH1-deficient cells, as shown by the weaker induction of γ-H2AX and p53 phosphorylation. The presence of MLH1 contributed to induce of prompt Chk1 phosphorylation, restoring G2/M cell cycle checkpoint and repair of DNA damage. On the contrary, in the absence of MLH1, HCT116 cells showed minor Chk1 phosphorylation and underwent apoptosis. Remarkably, inhibition of PARP function by PARPi or by PARP-1 gene silencing always increased the antitumor activity of irinotecan, even in the presence of low PARP-1 expression.

Functional examination of MLH1, MSH2, and MSH6 intronic mutations identified in Danish colorectal cancer patients.

PubMed

Petersen, Sanne M; Dandanell, Mette; Rasmussen, Lene J; Gerdes, Anne-Marie; Krogh, Lotte N; Bernstein, Inge; Okkels, Henrik; Wikman, Friedrik; Nielsen, Finn C; Hansen, Thomas V O

2013-10-03

Germ-line mutations in the DNA mismatch repair genes MLH1, MSH2, and MSH6 predispose to the development of colorectal cancer (Lynch syndrome or hereditary nonpolyposis colorectal cancer). These mutations include disease-causing frame-shift, nonsense, and splicing mutations as well as large genomic rearrangements. However, a large number of mutations, including missense, silent, and intronic variants, are classified as variants of unknown clinical significance. Intronic MLH1, MSH2, or MSH6 variants were investigated using in silico prediction tools and mini-gene assay to asses the effect on splicing. We describe in silico and in vitro characterization of nine intronic MLH1, MSH2, or MSH6 mutations identified in Danish colorectal cancer patients, of which four mutations are novel. The analysis revealed aberrant splicing of five mutations (MLH1 c.588 + 5G > A, MLH1 c.677 + 3A > T, MLH1 c.1732-2A > T, MSH2 c.1276 + 1G > T, and MSH2 c.1662-2A > C), while four mutations had no effect on splicing compared to wild type (MLH1 c.117-34A > T, MLH1 c.1039-8 T > A, MSH2 c.2459-18delT, and MSH6 c.3439-16C > T). In conclusion, we classify five MLH1/MSH2 mutations as pathogenic, whereas four MLH1/MSH2/MSH6 mutations are classified as neutral. This study supports the notion that in silico prediction tools and mini-gene assays are important for the classification of intronic variants, and thereby crucial for the genetic counseling of patients and their family members.

A tailored approach to BRAF and MLH1 methylation testing in a universal screening program for Lynch syndrome.

PubMed

Adar, Tomer; Rodgers, Linda H; Shannon, Kristen M; Yoshida, Makoto; Ma, Tianle; Mattia, Anthony; Lauwers, Gregory Y; Iafrate, Anthony J; Chung, Daniel C

2017-03-01

To determine the correlation between BRAF genotype and MLH1 promoter methylation in a screening program for Lynch syndrome (LS), a universal screening program for LS was established in two medical centers. Tumors with abnormal MLH1 staining were evaluated for both BRAF V600E genotype and MLH1 promoter methylation. Tumors positive for both were considered sporadic, and genetic testing was recommended for all others. A total 1011 colorectal cancer cases were screened for Lynch syndrome, and 148 (14.6%) exhibited absent MLH1 immunostaining. Both BRAF and MLH1 methylation testing were completed in 126 cases. Concordant results (both positive or both negative) were obtained in 86 (68.3%) and 16 (12.7%) cases, respectively, with 81% concordance overall. The positive and negative predictive values for a BRAF mutation in predicting MLH1 promoter methylation were 98.9% and 41%, respectively, and the negative predictive value fell to 15% in patients ≥70 years old. Using BRAF genotyping as a sole test to evaluate cases with absent MLH1 staining would have increased referral rates for genetic testing by 2.3-fold compared with MLH1 methylation testing alone (31% vs 13.5%, respectively, P<0.01). However, a hybrid approach that reserves MLH1 methylation testing for BRAF wild-type cases only would significantly decrease the number of methylation assays performed and reduce the referral rate for genetic testing to 12.7%. A BRAF mutation has an excellent positive predictive value but poor negative predictive value in predicting MLH1 promoter methylation. A hybrid use of these tests may reduce the number of low-risk patients referred to genetic counseling and facilitate wider implementation of Lynch syndrome screening programs.

Reduced microRNA-188-3p expression contributes to apoptosis of spermatogenic cells in patients with azoospermia.

PubMed

Song, Wen-Yan; Meng, Hui; Wang, Xue-Gai; Jin, Hai-Xia; Yao, Gui-Dong; Shi, Sen-Lin; Wu, Liang; Zhang, Xiang-Yang; Sun, Ying-Pu

2017-02-01

Human mutL homologl (MLH1) works coordinately in sequential steps to initiate repair of DNA mismatches, and aberrant MLH1 expression is related to spermatogenetic malfunction. In the present study, MLH1 expression in patients with azoospermia was investigated, and moderating effects of miR-188-3p on MLH1 expression and spermatogenesis were identified. Testicular tissues from 16 patients with obstructive azoospermia (OA) and non-obstructive azoospermia (NOA), and tissues of eight healthy patients were collected. Real-time PCR, Western blotting and immunohistochemical staining were used to detect MLH1 expression. Chromatin immunoprecipitation assay and luciferase reporter assay were performed to evaluate histone acetylation level of miR-188-3p and relationships between miR-188-3p and MLH1. Testicular MLH1 expression at mRNA and protein levels was significantly increased, while miR-188-3p expression was lower in patients with OA and NOA than that in controls. Reduced histone acetylation level of miR-188-3p promoter was observed in patients with azoospermia. Overexpression/inhibition of HDAC1, but not HDAC2, contributed to the significant reduction/increase of miR-188-3p expression. miR-188-3p targeted 3' UTR of MLH1 and regulated MLH1 expression. miR-188-3p inhibitor led to elevation of apoptotic level of spermatogenic cells in mice, while this effect was reversed by si-MLH1. Down-regulation of miR-188-3p by reducing histone acetylation up-regulated MLH1 expression and contributed to promotion of apoptosis in spermatogenic cells, in patients with azoospermia. © 2016 John Wiley & Sons Ltd.

An intact Pms2 ATPase domain is not essential for male fertility

PubMed Central

Fischer, Jared M; Dudley, Sandra; Miller, Ashleigh J; Liskay, R Michael

2016-01-01

The DNA mismatch repair (MMR) machinery in mammals plays critical roles in both mutation avoidance and spermatogenesis. Meiotic analysis of knockout mice of two different MMR genes, Mlh1 and Mlh3, revealed both male and female infertility associated with a defect in meiotic crossing over. In contrast, another MMR gene knockout, Pms2 (Pms2ko/ko), which contained a deletion of a portion of the ATPase domain, produced animals that were male sterile but female fertile. However, the meiotic phenotype of Pms2ko/ko males was less clear-cut than for Mlh1- or Mlh3-deficient meiosis. More recently, we generated a different Pms2 mutant allele (Pms2cre), which results in deletion of the same portion of the ATPase domain. Surprisingly, Pms2cre/cre male mice were completely fertile, suggesting that the ATPase domain of Pms2 is not required for male fertility. To explore the difference in male fertility, we examined the Pms2 RNA and found that alternative splicing of the Pms2cre allele results in a predicted Pms2 containing the C-terminus, which contains the Mlh1-interaction domain, a possible candidate for stabilizing Mlh1 levels. To study further the basis of male fertility, we examined Mlh1 levels in testes and found that whereas Pms2 loss in Pms2ko/ko mice results in severely reduced levels of Mlh1 expression in the testes, Mlh1 levels in Pms2cre/cre testes were reduced to a lesser extent. Thus, we propose that a primary function of Pms2 during spermatogenesis is to stabilize Mlh1 levels prior to its critical crossing over function with Mlh3. PMID:26753533

An intact Pms2 ATPase domain is not essential for male fertility.

PubMed

Fischer, Jared M; Dudley, Sandra; Miller, Ashleigh J; Liskay, R Michael

2016-03-01

The DNA mismatch repair (MMR) machinery in mammals plays critical roles in both mutation avoidance and spermatogenesis. Meiotic analysis of knockout mice of two different MMR genes, Mlh1 and Mlh3, revealed both male and female infertility associated with a defect in meiotic crossing over. In contrast, another MMR gene knockout, Pms2 (Pms2(ko/ko)), which contained a deletion of a portion of the ATPase domain, produced animals that were male sterile but female fertile. However, the meiotic phenotype of Pms2(ko/ko) males was less clear-cut than for Mlh1- or Mlh3-deficient meiosis. More recently, we generated a different Pms2 mutant allele (Pms2(cre)), which results in deletion of the same portion of the ATPase domain. Surprisingly, Pms2(cre/cre) male mice were completely fertile, suggesting that the ATPase domain of Pms2 is not required for male fertility. To explore the difference in male fertility, we examined the Pms2 RNA and found that alternative splicing of the Pms2(cre) allele results in a predicted Pms2 containing the C-terminus, which contains the Mlh1-interaction domain, a possible candidate for stabilizing Mlh1 levels. To study further the basis of male fertility, we examined Mlh1 levels in testes and found that whereas Pms2 loss in Pms2(ko/ko) mice results in severely reduced levels of Mlh1 expression in the testes, Mlh1 levels in Pms2(cre/cre) testes were reduced to a lesser extent. Thus, we propose that a primary function of Pms2 during spermatogenesis is to stabilize Mlh1 levels prior to its critical crossing over function with Mlh3. Copyright © 2015 Elsevier B.V. All rights reserved.

Comprehensive analysis of the MLH1 promoter region in 480 patients with colorectal cancer and 1150 controls reveals new variants including one with a heritable constitutional MLH1 epimutation.

PubMed

Morak, Monika; Ibisler, Ayseguel; Keller, Gisela; Jessen, Ellen; Laner, Andreas; Gonzales-Fassrainer, Daniela; Locher, Melanie; Massdorf, Trisari; Nissen, Anke M; Benet-Pagès, Anna; Holinski-Feder, Elke

2018-04-01

Germline defects in MLH1 , MSH2 , MSH6 and PMS2 predisposing for Lynch syndrome (LS) are mainly based on sequence changes, whereas a constitutional epimutation of MLH1 (CEM) is exceptionally rare. This abnormal MLH1 promoter methylation is not hereditary when arising de novo, whereas a stably heritable and variant-induced CEM was described for one single allele. We searched for MLH1 promoter variants causing a germline or somatic methylation induction or transcriptional repression. We analysed the MLH1 promoter sequence in five different patient groups with colorectal cancer (CRC) (n=480) composed of patients with i) CEM (n=16), ii) unsolved loss of MLH1 expression in CRC (n=37), iii) CpG-island methylator-phenotype CRC (n=102), iv) patients with LS (n=83) and v) MLH1-proficient CRC (n=242) as controls. 1150 patients with non-LS tumours also served as controls to correctly judge the results. We detected 10 rare MLH1 promoter variants. One novel, complex MLH1 variant c.-63_-58delins18 is present in a patient with CRC with CEM and his sister, both showing a complete allele-specific promoter methylation and transcriptional silencing. The other nine promoter variants detected in 17 individuals were not associated with methylation. For four of these, a normal, biallelic MLH1 expression was found in the patients' cDNA. We report the second promoter variant stably inducing a hereditary CEM. Concerning the classification of promoter variants, we discuss contradictory results from the literature for two variants, describe classification discrepancies between existing rules for five variants, suggest the (re-)classification of five promoter variants to (likely) benign and regard four variants as functionally unclear. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

The MLH1 c.-27C>A and c.85G>T variants are linked to dominantly inherited MLH1 epimutation and are borne on a European ancestral haplotype.

PubMed

Kwok, Chau-To; Vogelaar, Ingrid P; van Zelst-Stams, Wendy A; Mensenkamp, Arjen R; Ligtenberg, Marjolijn J; Rapkins, Robert W; Ward, Robyn L; Chun, Nicolette; Ford, James M; Ladabaum, Uri; McKinnon, Wendy C; Greenblatt, Marc S; Hitchins, Megan P

2014-05-01

Germline mutations of the DNA mismatch repair genes MLH1, MSH2, MSH6 or PMS2, and deletions affecting the EPCAM gene adjacent to MSH2, underlie Lynch syndrome by predisposing to early-onset colorectal, endometrial and other cancers. An alternative but rare cause of Lynch syndrome is constitutional epimutation of MLH1, whereby promoter methylation and transcriptional silencing of one allele occurs throughout normal tissues. A dominantly transmitted constitutional MLH1 epimutation has been linked to an MLH1 haplotype bearing two single-nucleotide variants, NM_000249.2: c.-27C>A and c.85G>T, in a Caucasian family with Lynch syndrome from Western Australia. Subsequently, a second seemingly unrelated Caucasian Australian case with the same MLH1 haplotype and concomitant epimutation was reported. We now describe three additional, ostensibly unrelated, cancer-affected families of European heritage with this MLH1 haplotype in association with constitutional epimutation, bringing the number of index cases reported to five. Array-based genotyping in four of these families revealed shared haplotypes between individual families that extended across ≤2.6-≤6.4 megabase regions of chromosome 3p, indicating common ancestry. A minimal ≤2.6 megabase founder haplotype common to all four families was identified, which encompassed MLH1 and additional flanking genes and segregated with the MLH1 epimutation in each family. Our findings indicate that the MLH1 c.-27C>A and c.85G>T variants are borne on a European ancestral haplotype and provide conclusive evidence for its pathogenicity via a mechanism of epigenetic silencing of MLH1 within normal tissues. Additional descendants bearing this founder haplotype may exist who are also at high risk of developing Lynch syndrome-related cancers.

Germline mutations in PMS2 and MLH1 in individuals with solitary loss of PMS2 expression in colorectal carcinomas from the Colon Cancer Family Registry Cohort.

PubMed

Rosty, Christophe; Clendenning, Mark; Walsh, Michael D; Eriksen, Stine V; Southey, Melissa C; Winship, Ingrid M; Macrae, Finlay A; Boussioutas, Alex; Poplawski, Nicola K; Parry, Susan; Arnold, Julie; Young, Joanne P; Casey, Graham; Haile, Robert W; Gallinger, Steven; Le Marchand, Loïc; Newcomb, Polly A; Potter, John D; DeRycke, Melissa; Lindor, Noralane M; Thibodeau, Stephen N; Baron, John A; Win, Aung Ko; Hopper, John L; Jenkins, Mark A; Buchanan, Daniel D

2016-02-19

Immunohistochemistry for DNA mismatch repair proteins is used to screen for Lynch syndrome in individuals with colorectal carcinoma (CRC). Although solitary loss of PMS2 expression is indicative of carrying a germline mutation in PMS2, previous studies reported MLH1 mutation in some cases. We determined the prevalence of MLH1 germline mutations in a large cohort of individuals with a CRC demonstrating solitary loss of PMS2 expression. This cohort study included 88 individuals affected with a PMS2-deficient CRC from the Colon Cancer Family Registry Cohort. Germline PMS2 mutation analysis (long-range PCR and multiplex ligation-dependent probe amplification) was followed by MLH1 mutation testing (Sanger sequencing and multiplex ligation-dependent probe amplification). Of the 66 individuals with complete mutation screening, we identified a pathogenic PMS2 mutation in 49 (74%), a pathogenic MLH1 mutation in 8 (12%) and a MLH1 variant of uncertain clinical significance predicted to be damaging by in silico analysis in 3 (4%); 6 (9%) carried variants likely to have no clinical significance. Missense point mutations accounted for most alterations (83%; 9/11) in MLH1. The MLH1 c.113A> G p.Asn38Ser mutation was found in 2 related individuals. One individual who carried the MLH1 intronic mutation c.677+3A>G p.Gln197Argfs*8 leading to the skipping of exon 8, developed 2 tumours, both of which retained MLH1 expression. A substantial proportion of CRCs with solitary loss of PMS2 expression are associated with a deleterious MLH1 germline mutation supporting the screening for MLH1 in individuals with tumours of this immunophenotype, when no PMS2 mutation has been identified. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Germline mutations in PMS2 and MLH1 in individuals with solitary loss of PMS2 expression in colorectal carcinomas from the Colon Cancer Family Registry Cohort

PubMed Central

Rosty, Christophe; Clendenning, Mark; Walsh, Michael D; Eriksen, Stine V; Southey, Melissa C; Winship, Ingrid M; Macrae, Finlay A; Boussioutas, Alex; Parry, Susan; Arnold, Julie; Young, Joanne P; Casey, Graham; Haile, Robert W; Gallinger, Steven; Le Marchand, Loïc; Newcomb, Polly A; Potter, John D; DeRycke, Melissa; Lindor, Noralane M; Thibodeau, Stephen N; Baron, John A; Win, Aung Ko; Hopper, John L; Jenkins, Mark A; Buchanan, Daniel D

2016-01-01

Objectives Immunohistochemistry for DNA mismatch repair proteins is used to screen for Lynch syndrome in individuals with colorectal carcinoma (CRC). Although solitary loss of PMS2 expression is indicative of carrying a germline mutation in PMS2, previous studies reported MLH1 mutation in some cases. We determined the prevalence of MLH1 germline mutations in a large cohort of individuals with a CRC demonstrating solitary loss of PMS2 expression. Design This cohort study included 88 individuals affected with a PMS2-deficient CRC from the Colon Cancer Family Registry Cohort. Germline PMS2 mutation analysis (long-range PCR and multiplex ligation-dependent probe amplification) was followed by MLH1 mutation testing (Sanger sequencing and multiplex ligation-dependent probe amplification). Results Of the 66 individuals with complete mutation screening, we identified a pathogenic PMS2 mutation in 49 (74%), a pathogenic MLH1 mutation in 8 (12%) and a MLH1 variant of uncertain clinical significance predicted to be damaging by in silico analysis in 3 (4%); 6 (9%) carried variants likely to have no clinical significance. Missense point mutations accounted for most alterations (83%; 9/11) in MLH1. The MLH1 c.113A> G p.Asn38Ser mutation was found in 2 related individuals. One individual who carried the MLH1 intronic mutation c.677+3A>G p.Gln197Argfs*8 leading to the skipping of exon 8, developed 2 tumours, both of which retained MLH1 expression. Conclusions A substantial proportion of CRCs with solitary loss of PMS2 expression are associated with a deleterious MLH1 germline mutation supporting the screening for MLH1 in individuals with tumours of this immunophenotype, when no PMS2 mutation has been identified. PMID:26895986

Novel DNA variants and mutation frequencies of hMLH1 and hMSH2 genes in colorectal cancer in the Northeast China population.

PubMed

Hu, Fulan; Li, Dandan; Wang, Yibaina; Yao, Xiaoping; Zhang, Wencui; Liang, Jing; Lin, Chunqing; Ren, Jiaojiao; Zhu, Lin; Wu, Zhiwei; Li, Shuying; Li, Ye; Zhao, Xiaojuan; Cui, Binbin; Dong, Xinshu; Tian, Suli; Zhao, Yashuang

2013-01-01

Research on hMLH1 and hMSH2 mutations tend to focus on Lynch syndrome (LS) and LS-like colorectal cancer (CRC). No studies to date have assessed the role of hMLH1 and hMSH2 genes in mass sporadic CRC (without preselection by MSI or early age of onset). We aimed to identify novel hMLH1 and hMSH2 DNA variants, to determine the mutation frequencies and sites in both sporadic and LS CRC and their relationships with clinicopathological characteristics of CRC in Northeast of China. 452 sporadic and 21 LS CRC patients were screened for germline and somatic mutations in hMLH1 and hMSH2 genes with PCR-SSCP sequencing. We identified 11 hMLH1 and seven hMSH2 DNA variants in our study cohort. Six of them were novel: four in hMLH1 gene (IVS8-16 A>T, c.644 GAT>GTT, c.1529 CAG>CGG and c.1831 ATT>TTT) and two in hMSH2 gene (-39 C>T, insertion AACAACA at c.1127 and deletion AAG at c.1129). In sporadic CRC, germline and somatic mutation frequencies of hMLH1/hMSH2 gene were 15.59% and 17.54%, respectively (p = 0.52). Germline mutations present in hMLH1 and hMSH2 genes were 5.28% and 10.78%, respectively (p<0.01). Somatic mutations in hMLH1 and hMSH2 genes were 6.73% and 11.70%, respectively (p = 0.02). In LS CRC, both germline and somatic mutation frequencies of hMLH1/hMSH2 gene were 28.57%. The most prevalent germline mutation site in hMSH2 gene was c.1168 CTT>TTT (3.90%), a polymorphism. Somatic mutation frequency of hMLH1/hMSH2 gene was significantly different in proximal, distal colon and rectal cancer (p = 0.03). Our findings elucidate the mutation spectrum and frequency of hMLH1 and hMSH2 genes in sporadic and LS CRC, and their relationships with clinicopathological characteristics of CRC.

Interdependence of DNA mismatch repair proteins MLH1 and MSH2 in apoptosis in human colorectal carcinoma cell lines.

PubMed

Hassen, Samar; Ali, Akhtar A; Kilaparty, Surya P; Al-Anbaky, Qudes A; Majeed, Waqar; Boman, Bruce M; Fields, Jeremy Z; Ali, Nawab

2016-01-01

The mammalian DNA mismatch repair (MMR) system consists of a number of proteins that play important roles in repair of base pair mismatch mutations and in maintenance of genomic integrity. A defect in this system can cause genetic instability, which can lead to carcinogenesis. For instance, a germline mutation in one of the mismatch repair proteins, especially MLH1 or MSH2, is responsible for hereditary non-polyposis colorectal cancer. These MMR proteins also play an important role in the induction of apoptosis. Accordingly, altered expression of or a defect in MLH1 or MSH2 may confer resistance to anti-cancer drugs used in chemotherapy. We hypothesized that the ability of these two MMR proteins to regulate apoptosis are interdependent. Moreover, a defect in either one may confer resistance to chemotherapy by an inability to trigger apoptosis. To this end, we studied three cell lines-SW480, LoVo, and HTC116. These cell lines were selected based on their differential expression of MLH1 and MSH2 proteins. SW480 expresses both MLH1 and MSH2; LoVo expresses only MLH1 but not MSH2; HCT116 expresses only MSH2 but not MLH1 protein. MTT assays, a measure of cytotoxicity, showed that there were different cytotoxic effects of an anti-cancer drug, etoposide, on these cell lines, effects that were correlated with the MMR status of the cells. Cells that are deficient in MLH1 protein (HCT116 cells) were resistant to the drug. Cells that express both MLH1 and MSH2 proteins (SW480 cells) showed caspase-3 cleavage, an indicator of apoptosis. Cells that lack MLH1 (HCT116 cells) did not show any caspase-3 cleavage. Expression of full-length MLH1 protein was decreased in MMR proficient (SW480) cells during apoptosis; it remained unchanged in cells that lack MSH2 (LoVo cells). The expression of MSH2 protein remained unchanged during apoptosis both in MMR proficient (SW480) and deficient (HCT116) cells. Studies on translocation of MLH1 protein from nucleus to cytosolic fraction, an indicator of apoptosis, showed that MLH1 translocation only occurred in MMR proficient (SW480) cells upon induction of apoptosis further suggested a MSH2 dependent role of MLH1 in apoptosis. These data suggest a role of MLH1 in mediation of apoptosis in a MSH2-dependent manner. Taken together, our data supported an interdependence of mismatch repair proteins, particularly MLH1 and MSH2, in the mediation of apoptosis in human colorectal carcinoma cell lines.

Concomitant mutation and epimutation of the MLH1 gene in a Lynch syndrome family.

PubMed

Cini, Giulia; Carnevali, Ileana; Quaia, Michele; Chiaravalli, Anna Maria; Sala, Paola; Giacomini, Elisa; Maestro, Roberta; Tibiletti, Maria Grazia; Viel, Alessandra

2015-04-01

Lynch syndrome (LS) is an inherited predisposition cancer syndrome, typically caused by germline mutations in the mismatch repair genes MLH1, MSH2, MSH6 and PMS2. In the last years, a role for epimutations of the same genes has also been reported. MLH1 promoter methylation is a well known mechanism of somatic inactivation in tumors, and more recently, several cases of constitutional methylation have been identified. In four subjects affected by multiple tumors and belonging to a suspected LS family, we detected a novel secondary MLH1 gene epimutation. The methylation of MLH1 promoter was always linked in cis with a 997 bp-deletion (c.-168_c.116+713del), that removed exon 1 and partially involved the promoter of the same gene. Differently from cases with constitutional primary MLH1 inactivation, this secondary methylation was allele-specific and CpGs of the residual promoter region were totally methylated, leading to complete allele silencing. In the colon tumor of the proband, MLH1 and PMS2 expression was completely lost as a consequence of a pathogenic somatic point mutation (MLH1 c.199G>A, p.Gly67Arg) that also abrogated local methylation by destroying a CpG site. The evidences obtained highlight how MLH1 mutations and epimutations can reciprocally influence each other and suggest that an altered structure of the MLH1 locus results in epigenetic alteration. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

MLH1 constitutional and somatic methylation in patients with MLH1 negative tumors fulfilling the revised Bethesda criteria.

PubMed

Crucianelli, Francesca; Tricarico, Rossella; Turchetti, Daniela; Gorelli, Greta; Gensini, Francesca; Sestini, Roberta; Giunti, Laura; Pedroni, Monica; Ponz de Leon, Maurizio; Civitelli, Serenella; Genuardi, Maurizio

2014-10-01

Lynch syndrome (LS) is a tumor predisposing condition caused by constitutional defects in genes coding for components of the mismatch repair (MMR) apparatus. While hypermethylation of the promoter of the MMR gene MLH1 occurs in about 15% of colorectal cancer samples, it has also been observed as a constitutional alteration, in the absence of DNA sequence mutations, in a small number of LS patients. In order to obtain further insights on the phenotypic characteristics of MLH1 epimutation carriers, we investigated the somatic and constitutional MLH1 methylation status of 14 unrelated subjects with a suspicion of LS who were negative for MMR gene constitutional mutations and whose tumors did not express the MLH1 protein. A novel case of constitutional MLH1 epimutation was identified. This patient was affected with multiple primary tumors, including breast cancer, diagnosed starting from the age of 55 y. Investigation of her offspring by allele specific expression revealed that the epimutation was not stable across generations. We also found MLH1 hypermethylation in cancer samples from 4 additional patients who did not have evidence of constitutional defects. These patients had some characteristics of LS, namely early age at onset and/or positive family history, raising the possibility of genetic influences in the establishment of somatic MLH1 methylation.

MLH1 constitutional and somatic methylation in patients with MLH1 negative tumors fulfilling the revised Bethesda criteria

PubMed Central

Crucianelli, Francesca; Tricarico, Rossella; Turchetti, Daniela; Gorelli, Greta; Gensini, Francesca; Sestini, Roberta; Giunti, Laura; Pedroni, Monica; Ponz de Leon, Maurizio; Civitelli, Serenella; Genuardi, Maurizio

2014-01-01

Lynch syndrome (LS) is a tumor predisposing condition caused by constitutional defects in genes coding for components of the mismatch repair (MMR) apparatus. While hypermethylation of the promoter of the MMR gene MLH1 occurs in about 15% of colorectal cancer samples, it has also been observed as a constitutional alteration, in the absence of DNA sequence mutations, in a small number of LS patients. In order to obtain further insights on the phenotypic characteristics of MLH1 epimutation carriers, we investigated the somatic and constitutional MLH1 methylation status of 14 unrelated subjects with a suspicion of LS who were negative for MMR gene constitutional mutations and whose tumors did not express the MLH1 protein. A novel case of constitutional MLH1 epimutation was identified. This patient was affected with multiple primary tumors, including breast cancer, diagnosed starting from the age of 55 y. Investigation of her offspring by allele specific expression revealed that the epimutation was not stable across generations. We also found MLH1 hypermethylation in cancer samples from 4 additional patients who did not have evidence of constitutional defects. These patients had some characteristics of LS, namely early age at onset and/or positive family history, raising the possibility of genetic influences in the establishment of somatic MLH1 methylation. PMID:25437057

The mRNA level of MLH1 in peripheral blood is a biomarker for the diagnosis of hereditary nonpolyposis colorectal cancer.

PubMed

Yu, Hong; Li, Hui; Cui, Yongan; Xiao, Wei; Dai, Guihong; Huang, Junxing; Wang, Chaofu

2016-01-01

Hereditary nonpolyposis colorectal cancer (HNPCC) is caused by functional defects in mismatch repair (MMR) genes, including mutL homolog 1 (MLH1) and mutS homolog 2 (MSH2). This study aimed to assess whether the mRNA expression of MLH1 in peripheral blood could be used as a biomarkers for the diagnosis of HNPCC. The mRNA level of MLH1 was determined in 19 HNPCC families (46 members) using real-time quantitative polymerase chain reaction (qPCR). The mRNA levels of MLH1 in HNPCC were significantly lower than controls (P < 0.001). Receiver operating characteristic (ROC) curve showed a high diagnostic value of the mRNA level of MLH1 for the diagnosis of HNPCC with the area under curve of 0.858. At an optimal cut-off value (0.511), the mRNA level of MLH1 had a sensitivity of 81.3% and a specificity of 86.7% for distinguishing HNPCC from controls. In conclusion, the mRNA expression of MLH1 in peripheral blood may serve as a biomarker for the diagnosis of HNPCC.

MLH1 Promoter Methylation Frequency in Colorectal Cancer Patients and Related Clinicopathological and Molecular Features

PubMed Central

Li, Xia; Yao, Xiaoping; Wang, Yibaina; Hu, Fulan; Wang, Fan; Jiang, Liying; Liu, Yupeng; Wang, Da; Sun, Guizhi; Zhao, Yashuang

2013-01-01

Purpose To describe the frequency of MLH1 promoter methylation in colorectal cancer (CRC); to explore the associations between MLH1 promoter methylation and clinicopathological and molecular factors using a systematic review and meta-analysis. Methods A literature search of the PubMed and Embase databases was conducted to identify relevant articles published up to September 7, 2012 that described the frequency of MLH1 promoter methylation or its associations with clinicopathological and molecular factors in CRC. The pooled frequency, odds ratio (OR) and 95% confidence intervals (95% CI) were calculated. Results The pooled frequency of MLH1 promoter methylation in unselected CRC was 20.3% (95% CI: 16.8–24.1%). They were 18.7% (95% CI: 14.7–23.6%) and 16.4% (95% CI: 11.9–22.0%) in sporadic and Lynch syndrome (LS) CRC, respectively. Significant associations were observed between MLH1 promoter methylation and gender (pooled OR = 1.641, 95% CI: 1.215–2.215; P = 0.001), tumor location (pooled OR = 3.804, 95% CI: 2.715–5.329; P<0.001), tumor differentiation (pooled OR = 2.131, 95% CI: 1.464–3.102; P<0.001), MSI (OR: 27.096, 95% CI: 13.717–53.526; P<0.001). Significant associations were also observed between MLH1 promoter methylation and MLH1 protein expression, BRAF mutation (OR = 14.919 (95% CI: 6.427–34.631; P<0.001) and 9.419 (95% CI: 2.613–33.953; P = 0.001), respectively). Conclusion The frequency of MLH1 promoter methylation in unselected CRC was 20.3%. They were 18.7% in sporadic CRC and 16.4% in LS CRC, respectively. MLH1 promoter methylation may be significantly associated with gender, tumor location, tumor differentiation, MSI, MLH1 protein expression, and BRAF mutation. PMID:23555617

Activation of Saccharomyces cerevisiae Mlh1-Pms1 Endonuclease in a Reconstituted Mismatch Repair System.

PubMed

Smith, Catherine E; Bowen, Nikki; Graham, William J; Goellner, Eva M; Srivatsan, Anjana; Kolodner, Richard D

2015-08-28

Previous studies reported the reconstitution of an Mlh1-Pms1-independent 5' nick-directed mismatch repair (MMR) reaction using Saccharomyces cerevisiae proteins. Here we describe the reconstitution of a mispair-dependent Mlh1-Pms1 endonuclease activation reaction requiring Msh2-Msh6 (or Msh2-Msh3), proliferating cell nuclear antigen (PCNA), and replication factor C (RFC) and a reconstituted Mlh1-Pms1-dependent 3' nick-directed MMR reaction requiring Msh2-Msh6 (or Msh2-Msh3), exonuclease 1 (Exo1), replication protein A (RPA), RFC, PCNA, and DNA polymerase δ. Both reactions required Mg(2+) and Mn(2+) for optimal activity. The MMR reaction also required two reaction stages in which the first stage required incubation of Mlh1-Pms1 with substrate DNA, with or without Msh2-Msh6 (or Msh2-Msh3), PCNA, and RFC but did not require nicking of the substrate, followed by a second stage in which other proteins were added. Analysis of different mutant proteins demonstrated that both reactions required a functional Mlh1-Pms1 endonuclease active site, as well as mispair recognition and Mlh1-Pms1 recruitment by Msh2-Msh6 but not sliding clamp formation. Mutant Mlh1-Pms1 and PCNA proteins that were defective for Exo1-independent but not Exo1-dependent MMR in vivo were partially defective in the Mlh1-Pms1 endonuclease and MMR reactions, suggesting that both reactions reflect the activation of Mlh1-Pms1 seen in Exo1-independent MMR in vivo. The availability of this reconstituted MMR reaction should now make it possible to better study both Exo1-independent and Exo1-dependent MMR. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Activation of Saccharomyces cerevisiae Mlh1-Pms1 Endonuclease in a Reconstituted Mismatch Repair System*

PubMed Central

Smith, Catherine E.; Bowen, Nikki; Graham, William J.; Goellner, Eva M.; Srivatsan, Anjana; Kolodner, Richard D.

2015-01-01

Previous studies reported the reconstitution of an Mlh1-Pms1-independent 5′ nick-directed mismatch repair (MMR) reaction using Saccharomyces cerevisiae proteins. Here we describe the reconstitution of a mispair-dependent Mlh1-Pms1 endonuclease activation reaction requiring Msh2-Msh6 (or Msh2-Msh3), proliferating cell nuclear antigen (PCNA), and replication factor C (RFC) and a reconstituted Mlh1-Pms1-dependent 3′ nick-directed MMR reaction requiring Msh2-Msh6 (or Msh2-Msh3), exonuclease 1 (Exo1), replication protein A (RPA), RFC, PCNA, and DNA polymerase δ. Both reactions required Mg2+ and Mn2+ for optimal activity. The MMR reaction also required two reaction stages in which the first stage required incubation of Mlh1-Pms1 with substrate DNA, with or without Msh2-Msh6 (or Msh2-Msh3), PCNA, and RFC but did not require nicking of the substrate, followed by a second stage in which other proteins were added. Analysis of different mutant proteins demonstrated that both reactions required a functional Mlh1-Pms1 endonuclease active site, as well as mispair recognition and Mlh1-Pms1 recruitment by Msh2-Msh6 but not sliding clamp formation. Mutant Mlh1-Pms1 and PCNA proteins that were defective for Exo1-independent but not Exo1-dependent MMR in vivo were partially defective in the Mlh1-Pms1 endonuclease and MMR reactions, suggesting that both reactions reflect the activation of Mlh1-Pms1 seen in Exo1-independent MMR in vivo. The availability of this reconstituted MMR reaction should now make it possible to better study both Exo1-independent and Exo1-dependent MMR. PMID:26170454

Endometrial tumour BRAF mutations and MLH1 promoter methylation as predictors of germline mismatch repair gene mutation status: a literature review.

PubMed

Metcalf, Alexander M; Spurdle, Amanda B

2014-03-01

Colorectal cancer (CRC) that displays high microsatellite instability (MSI-H) can be caused by either germline mutations in mismatch repair (MMR) genes, or non-inherited transcriptional silencing of the MLH1 promoter. A correlation between MLH1 promoter methylation, specifically the 'C' region, and BRAF V600E status has been reported in CRC studies. Germline MMR mutations also greatly increase risk of endometrial cancer (EC), but no systematic review has been undertaken to determine if these tumour markers may be useful predictors of MMR mutation status in EC patients. Endometrial cancer cohorts meeting review inclusion criteria encompassed 2675 tumours from 20 studies for BRAF V600E, and 447 tumours from 11 studies for MLH1 methylation testing. BRAF V600E mutations were reported in 4/2675 (0.1%) endometrial tumours of unknown MMR mutation status, and there were 7/823 (0.9%) total sequence variants in exon 11 and 27/1012 (2.7%) in exon 15. Promoter MLH1 methylation was not observed in tumours from 32 MLH1 mutation carriers, or for 13 MSH2 or MSH6 mutation carriers. MMR mutation-negative individuals with tumour MLH1 and PMS2 IHC loss displayed MLH1 methylation in 48/51 (94%) of tumours. We have also detailed specific examples that show the importance of MLH1 promoter region, assay design, and quantification of methylation. This review shows that BRAF mutations occurs so infrequently in endometrial tumours they can be discounted as a useful marker for predicting MMR-negative mutation status, and further studies of endometrial cohorts with known MMR mutation status are necessary to quantify the utility of tumour MLH1 promoter methylation as a marker of negative germline MMR mutation status in EC patients.

CpG Island Methylator Phenotype Positive Tumors in the Absence of MLH1 Methylation Constitute a Distinct Subset of Duodenal Adenocarcinomas and Are Associated with Poor Prognosis

PubMed Central

Fu, Tao; Pappou, Emmanouil P.; Guzzetta, Angela A.; Jeschke, Jana; Kwak, Ruby; Dave, Pujan; Hooker, Craig M.; Morgan, Richard; Baylin, Stephen B.; Iacobuzio-Donahue, Christine A.; Wolfgang, Christopher L.; Ahuja, Nita

2012-01-01

Purpose Little information is available on genetic and epigenetic changes in duodenal adenocarcinomas. The purpose was to identify possible subsets of duodenal adenocarcinomas based on microsatellite instability (MSI), DNA methylation, mutations in the KRAS and BRAF genes, clinicopathologic features, and prognosis. Experimental Design Demographics, tumor characteristics and survival were available for 99 duodenal adenocarcinoma patients. Testing for KRAS and BRAF mutations, MSI, MLH1 methylation and CpG island methylator phenotype (CIMP) status was performed. A Cox proportional hazard model was built to predict survival. Results CIMP+ was detected in 27 of 99 (27.3%) duodenal adenocarcinomas, and was associated with MSI (P = 0.011) and MLH1 methylation (P < 0.001), but not with KRAS mutations (P = 0.114), as compared to CIMP− tumors. No BRAF V600E mutation was detected. Among the CIMP+ tumors, 15 (55.6%) were CIMP+/MLH1-unmethylated (MLH1-U). Kaplan-Meier analysis showed tumors classified by CIMP, CIMP/MLH1 methylation status or CIMP/MSI status could predict overall survival (OS; P = 0.047, 0.002, and 0.002, respectively), while CIMP/MLH1 methylation status could also predict time-to-recurrence (TTR; P = 0.016). In multivariate analysis, CIMP/MLH1 methylation status showed a significant prognostic value regarding both OS (P < 0.001) and TTR (P = 0.023). Patients with CIMP+/MLH1-U tumors had the worst OS and TTR. Conclusions Our results demonstrate existence of CIMP in duodenal adenocarcinomas. The combination of CIMP+/MLH1-U appears to be independently associated with poor prognosis in patients with duodenal adenocarcinomas. This study also suggests that BRAF mutations are not involved in duodenal tumorigenesis, MSI or CIMP development. PMID:22825585

Abrupt loss of MLH1 and PMS2 expression in endometrial carcinoma: molecular and morphologic analysis of 6 cases.

PubMed

Pai, Rish K; Plesec, Thomas P; Abdul-Karim, Fadi W; Yang, Bin; Marquard, Jessica; Shadrach, Bonnie; Roma, Andres R

2015-07-01

Given that endometrial cancer (EC) is often the sentinel cancer for female Lynch syndrome patients, we have successfully implemented universal screening of ECs and have previously shown that this is the preferred method to identify these patients. However, during the course of universal screening of EC, we encountered 6 cases with an unusual pattern of mismatch-repair protein immunohistochemistry that has not been previously described in this setting. In these 6 cases, there was an abrupt loss of MLH1 and PMS2 expression in a portion of the tumor. In 3 cases, marked histologic differences were identified between the areas of the tumor with retained expression and areas with loss of expression. In 2 cases, the areas with loss of expression were of higher grade (1 demonstrated solid growth and the other demonstrated increased nuclear atypia with diffuse p53 expression). In 4 tumors, histologic features associated with microsatellite instability (MSI) were present, including increased intraepithelial lymphocytes. The areas with loss of and retained MLH1/PMS2 expression were separately microdissected and assessed for MSI and MLH1 promoter methylation. The areas with loss of MLH1 and PMS2 more commonly demonstrated MSI compared with the areas with intact expression (83% vs. 33%). MLH1 promoter methylation analysis demonstrated heterogenous hypermethylation, as all areas with loss of MLH1/PMS2 expression had more extensive methylation of MLH1 compared with those areas with retained expression. In summary, we describe the histologic and molecular features of 6 cases of EC with abrupt loss of MLH1 and PMS2 expression and demonstrate that heterogenous methylation of the MLH1 promoter results in this distinct and unusual pattern of immunohistochemical expression.

DNA mismatch repair proteins MLH1 and PMS2 can be imported to the nucleus by a classical nuclear import pathway.

PubMed

de Barros, Andrea C; Takeda, Agnes A S; Dreyer, Thiago R; Velazquez-Campoy, Adrian; Kobe, Boštjan; Fontes, Marcos R M

2018-03-01

MLH1 and PMS2 proteins form the MutLα heterodimer, which plays a major role in DNA mismatch repair (MMR) in humans. Mutations in MMR-related proteins are associated with cancer, especially with colon cancer. The N-terminal region of MutLα comprises the N-termini of PMS2 and MLH1 and, similarly, the C-terminal region of MutLα is composed by the C-termini of PMS2 and MLH1, and the two are connected by linker region. The nuclear localization sequences (NLSs) necessary for the nuclear transport of the two proteins are found in this linker region. However, the exact NLS sequences have been controversial, with different sequences reported, particularly for MLH1. The individual components are not imported efficiently, presumably due to their C-termini masking their NLSs. In order to gain insights into the nuclear transport of these proteins, we solved the crystal structures of importin-α bound to peptides corresponding to the supposed NLSs of MLH1 and PMS2 and performed isothermal titration calorimetry to study their binding affinities. Both putative MLH1 and PMS2 NLSs can bind to importin-α as monopartite NLSs, which is in agreement with some previous studies. However, MLH1-NLS has the highest affinity measured by a natural NLS peptide, suggesting a major role of MLH1 protein in nuclear import compared to PMS2. Finally, the role of MLH1 and PMS2 in the nuclear transport of the MutLα heterodimer is discussed. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Estrogen enhances mismatch repair by induction of MLH1 expression via estrogen receptor-β

PubMed Central

Lu, Jun-Yu; Jin, Peng; Gao, Wei; Wang, De-Zhi; Sheng, Jian-Qiu

2017-01-01

Epidemiological data demonstrated that hormone replace treatment has protective effect against colorectal cancer (CRC). Our previous studies showed that this effect may be associated with DNA mismatch repair. This study aims to investigate the mechanism of estrogen induction of MLH1, and whether colorectal tumor proliferation can be inhibited through induction of MLH1 by estrogen signal pathway. Human CRC cell lines were used to examine the regulation of MLH1 expression by over-expression and depletion of estrogen receptor-α (ERα) and estrogen receptor-β (ERβ), under the treatment with 17β-estradiol or β-Estradiol 6-(O-carboxy-methyl)oxime:BSA, followed by a real-time Q-PCR and Western blotting analysis. Luciferase reporter and chromatin immunoprecipitation assays were used to identify the estrogen response elements in the proximal promoter of MLH1 gene. Then, the influence of estrogen-induced MLH1 on CRC tumor growth were determined in vitro and in vivo. We found that mismatch repair ability and microsatellite stability of cells were enhanced by estrogen via induction of MLH1 expression, which was mediated by ERβ, through a transcriptional activation process. Furthermore, we identified that ERβ exerted an inhibitory effect on CRC tumor proliferation in vitro and in vivo, combined with 5-FU, through up-regulation of MLH1 expression. Finally, we concluded that estrogen enhances mismatch repair ability and tumor inhibition effect in vitro and in vivo, via induction of MLH1 expression mediated by ERβ. PMID:28404976

Estrogen enhances mismatch repair by induction of MLH1 expression via estrogen receptor-β.

PubMed

Lu, Jun-Yu; Jin, Peng; Gao, Wei; Wang, De-Zhi; Sheng, Jian-Qiu

2017-06-13

Epidemiological data demonstrated that hormone replace treatment has protective effect against colorectal cancer (CRC). Our previous studies showed that this effect may be associated with DNA mismatch repair. This study aims to investigate the mechanism of estrogen induction of MLH1, and whether colorectal tumor proliferation can be inhibited through induction of MLH1 by estrogen signal pathway. Human CRC cell lines were used to examine the regulation of MLH1 expression by over-expression and depletion of estrogen receptor-α (ERα) and estrogen receptor-β (ERβ), under the treatment with 17β-estradiol or β-Estradiol 6-(O-carboxy-methyl)oxime:BSA, followed by a real-time Q-PCR and Western blotting analysis. Luciferase reporter and chromatin immunoprecipitation assays were used to identify the estrogen response elements in the proximal promoter of MLH1 gene. Then, the influence of estrogen-induced MLH1 on CRC tumor growth were determined in vitro and in vivo. We found that mismatch repair ability and microsatellite stability of cells were enhanced by estrogen via induction of MLH1 expression, which was mediated by ERβ, through a transcriptional activation process. Furthermore, we identified that ERβ exerted an inhibitory effect on CRC tumor proliferation in vitro and in vivo, combined with 5-FU, through up-regulation of MLH1 expression. Finally, we concluded that estrogen enhances mismatch repair ability and tumor inhibition effect in vitro and in vivo, via induction of MLH1 expression mediated by ERβ.

Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome

DOE PAGES

Wu, Hong; Zeng, Hong; Lam, Robert; ...

2015-08-01

Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson–Crick base pairs in the genome. Pathogenic mutations in theMLH1gene are associated with a predisposition to Lynch and Turcot's syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. Lastly, the structure shares a high degree of similarity with previously determined prokaryoticMLH1homologs; however, this structure affords a more accurate platform for the classification ofMLH1variants.

Epigenetic silencing of the DNA mismatch repair gene, MLH1, induced by hypoxic stress in a pathway dependent on the histone demethylase, LSD1

PubMed Central

Lu, Yuhong; Wajapeyee, Narendra; Turker, Mitchell S.; Glazer, Peter M.

2014-01-01

SUMMARY Silencing of the MLH1 gene is frequently seen in sporadic cancers. We report that hypoxia causes decreased H3K4 methylation at the MLH1 promoter via the H3K4 demethylases, LSD1 and PLU-1, and promotes long-term silencing of the promoter in a pathway that requires LSD1. Knockdown of LSD1 or its co-repressor, CoREST, also prevents the re-silencing (and cytosine DNA methylation) of the endogenous MLH1 promoter in RKO colon cancer cells following transient reactivation by the DNA methyltransferase inhibitor 5-aza-2′-deoxycytidine (5-aza-dC). The results demonstrate that hypoxia is a critical driving force for silencing of MLH1 through chromatin modification and indicate that the LSD1/CoREST complex is essential for MLH1 silencing. PMID:25043185

MLH1 mutations differentially affect meiotic functions in Saccharomyces cerevisiae.

PubMed Central

Hoffmann, Eva R; Shcherbakova, Polina V; Kunkel, Thomas A; Borts, Rhona H

2003-01-01

To test whether missense mutations in the cancer susceptibility gene MLH1 adversely affect meiosis, we examined 14 yeast MLH1 mutations for effects on meiotic DNA transactions and gamete viability in the yeast Saccharomyces cerevisiae. Mutations analogous to those associated with hereditary nonpolyposis colorectal cancer (HNPCC) or those that reduce Mlh1p interactions with ATP or DNA all impair replicative mismatch repair as measured by increased mutation rates. However, their effects on meiotic heteroduplex repair, crossing over, chromosome segregation, and gametogenesis vary from complete loss of meiotic functions to no meiotic defect, and mutants defective in one meiotic process are not necessarily defective in others. DNA binding and ATP binding but not ATP hydrolysis are required for meiotic crossing over. The results reveal clear separation of different Mlh1p functions in mitosis and meiosis, and they suggest that some, but not all, MLH1 mutations may be a source of human infertility. PMID:12618391

Application of tethered balloon for studying vertical distribution of air pollutants within lower tropsphere of Shanghai

NASA Astrophysics Data System (ADS)

Zhang, K.; Wang, D.; Fu, Q.; Xiu, G.; Duan, Y.

2016-12-01

Tethered balloon-based measurement campaign of particle number concentration (PNC) and particle number size distribution (PNSD) in the range of 15.7-661.2 nm was conducted within the lower troposphere of 1000 m in Shanghai, a Chinses megacity, in December 2015. The meteorological condition, PNC, and PNSD were synchronous measured at ground-based station as well as on the tethered balloon. Overall, the mixing layer height (MLH) showed a peak at about LST 14:00-15:00. On ground level, the 88.2 nm particles had the highest number concentration. The Pearson correlation analysis based on the ground level data shows the Pearson correlation coefficient between PNC and NO2was 0.774. The synchronous measurement of PNC and PNSD on ground level and on the tethered balloon showed the 15.7-200 nm particles had higher PNC on ground level, but the PNC of 200-661.2 nm particles are higher at 400 m. And the wind condition showed a strong influence on PNC.The vertical profiles of meteorological parameters and air pollutants was observed. The particle mass concentration, ozone concentration, temperature, and humidity all showed a quick change when the balloon across the atmosphere boundary layer. One episodic haze event (Dec 22nd-Dec 23rd) was selected with specific focus on the variation of PNSD and PNC vertical profiles. Before the haze, the PNC at ground was 9281 cm-3. The MaxDm (the particle diameter with the highest number concentration) was 53.3 nm at that time. Due to the shallow MLH, the MaxDm changed rapidly to 126.3 nm at 321 m. During the haze, the MaxDm and the PNC on ground level was 126.3 nm and 18515 cm-3 respectively. And a quick drop of PNC was observed at 553 m. This may due to the change of wind direction, temperature, and relative humidity. At the end of haze, the MaxDm and the PNC on ground level was 126.3 nm and 10711 cm-3 respectively. The highest MaxDm during those three launches all appeared at a high altitude, usually above 300 m. This result is consisted with the synchronous measurement on December 21st to some degree. This study provides a first insight of PNSD vertical profiles over Eastern China, which will greatly improve the kownledge of the characteristics of particles within the lower tropsphere.

Variability of the Mixed-Layer Height Over Mexico City

NASA Astrophysics Data System (ADS)

García-Franco, J. L.; Stremme, W.; Bezanilla, A.; Ruiz-Angulo, A.; Grutter, M.

2018-02-01

The diurnal and seasonal variability of the mixed-layer height in urban areas has implications for ground-level air pollution and the meteorological conditions. Measurements of the backscatter of light pulses with a commercial lidar system were performed for a continuous period of almost six years between 2011 and 2016 in the southern part of Mexico City. The profiles were temporally and vertically smoothed, clouds were filtered out, and the mixed-layer height was determined with an ad hoc treatment of both the filtered and unfiltered profiles. The results are in agreement when compared with values of mixed-layer height reconstructed from, (i) radiosonde data, and (ii) surface and vertical column densities of a trace gas. The daily maxima of the mean mixed-layer height reach values > 3 km above ground level in the months of March-April, and are clearly lower (< 2.7 km ) during the colder months from September-December. Mean daily minima are typically observed at 0700 local time (UTC - 6h), and are lowest during the winter months with values on average below 500 m. The data presented here show an anti-correlation between high-pollution episodes and the height of the mixed layer. The growth rate of the convective mixed-layer height has a seasonal behaviour, which is characterized together with the mixed-layer-height anomalies. A clear residual layer is evident from the backscattered signals recorded in days with specific atmospheric conditions, but also from the cloud-filtered mean diurnal profiles. The occasional presence of a residual layer results in an overestimation of the reported mixed-layer height during the night and early morning hours.

Variability of the Mixed-Layer Height Over Mexico City

NASA Astrophysics Data System (ADS)

García-Franco, J. L.; Stremme, W.; Bezanilla, A.; Ruiz-Angulo, A.; Grutter, M.

2018-06-01

The diurnal and seasonal variability of the mixed-layer height in urban areas has implications for ground-level air pollution and the meteorological conditions. Measurements of the backscatter of light pulses with a commercial lidar system were performed for a continuous period of almost six years between 2011 and 2016 in the southern part of Mexico City. The profiles were temporally and vertically smoothed, clouds were filtered out, and the mixed-layer height was determined with an ad hoc treatment of both the filtered and unfiltered profiles. The results are in agreement when compared with values of mixed-layer height reconstructed from, (i) radiosonde data, and (ii) surface and vertical column densities of a trace gas. The daily maxima of the mean mixed-layer height reach values > 3 km above ground level in the months of March-April, and are clearly lower (< 2.7 km) during the colder months from September-December. Mean daily minima are typically observed at 0700 local time (UTC - 6h), and are lowest during the winter months with values on average below 500 m. The data presented here show an anti-correlation between high-pollution episodes and the height of the mixed layer. The growth rate of the convective mixed-layer height has a seasonal behaviour, which is characterized together with the mixed-layer-height anomalies. A clear residual layer is evident from the backscattered signals recorded in days with specific atmospheric conditions, but also from the cloud-filtered mean diurnal profiles. The occasional presence of a residual layer results in an overestimation of the reported mixed-layer height during the night and early morning hours.

Role of MLH1 methylation in esophageal cancer carcinogenesis and its clinical significance.

PubMed

Li, Jinyun; Ye, Dong; Wang, Lei; Peng, Yingying; Li, Qun; Deng, Hongxia; Zhou, Chongchang

2018-01-01

The mutL homolog-1 ( MLH1 ) is a DNA mismatch repair gene and has been reported to be frequently methylated in numerous cancers. However, the association between MLH1 methylation and esophageal cancer (EC), as well as its clinical significance, remains unclear. Hence, we conducted a systematic meta-analysis based on 19 articles (including 1384 ECs, 345 premalignant lesions, and 1244 healthy controls). Our analysis revealed that the frequency of MLH1 methylation was significantly elevated during EC carcinogenesis. In addition, we observed that MLH1 promoter methylation was associated with age (odds ratio [OR]=1.79; 95% CI =1.20-2.66), advanced tumor grade (OR=3.7; 95% CI =2.37-5.77), lymph node metastasis (OR=2.65; 95% CI =1.81-3.88), distant metastasis (OR=7.60; 95% CI =1.23-47.19), advanced clinical stage (OR=4.46; 95% CI =2.88-6.91), and poor prognosis in EC patients (hazard ratio =1.64, 95% CI =1.00-2.69). The pooled sensitivity, specificity, and area under the curve of MLH1 methylation in EC patients versus healthy individuals were 0.15, 0.99, and 0.77, respectively. Our findings indicate that MLH1 methylation is involved in the carcinogenesis, progression, and metastasis of EC. Moreover, methylated MLH1 could be a potential diagnostic and prognostic biomarker for EC.

Patients with colorectal cancer associated with Lynch syndrome and MLH1 promoter hypermethylation have similar prognoses.

PubMed

Haraldsdottir, Sigurdis; Hampel, Heather; Wu, Christina; Weng, Daniel Y; Shields, Peter G; Frankel, Wendy L; Pan, Xueliang; de la Chapelle, Albert; Goldberg, Richard M; Bekaii-Saab, Tanios

2016-09-01

Mismatch repair-deficient (dMMR) colorectal cancer (CRC) is caused by Lynch syndrome (LS) in 3% and sporadic inactivation of MLH1 by hypermethylation (MLH1-hm) in 12% of cases. It is not clear whether outcomes between LS-associated and MLH1-hm CRC differ. The objective of this study was to explore differences in clinical factors and outcomes in these two groups. Patients with dMMR CRC identified by immunohistochemistry staining and treated at a single institution from 1998 to 2012 were included. MLH1-hm was established with BRAF mutational analysis or hypermethylation testing. Patients' charts were accessed for information on pathology, germ-line MMR mutation testing, and clinical course. A total of 143 patients had CRC associated with LS (37 patients, 26%) or MLH1-hm (106 patients, 74%). Patients with LS were younger, more often male, presented more often with stage III disease, and had more metachronous disease than patients with MLH1-hm tumors. There was no difference in cancer-specific survival (CSS) between the groups; overall survival was longer in patients with LS, but this difference was minimal after adjusting for age and stage at diagnosis. CSS did not differ in LS-associated CRC compared with MLH1-hm CRC, suggesting that they carry a similar prognosis.Genet Med 18 9, 863-868.

Role of MLH1 methylation in esophageal cancer carcinogenesis and its clinical significance

PubMed Central

Li, Jinyun; Ye, Dong; Wang, Lei; Peng, Yingying; Li, Qun; Deng, Hongxia

2018-01-01

The mutL homolog-1 (MLH1) is a DNA mismatch repair gene and has been reported to be frequently methylated in numerous cancers. However, the association between MLH1 methylation and esophageal cancer (EC), as well as its clinical significance, remains unclear. Hence, we conducted a systematic meta-analysis based on 19 articles (including 1384 ECs, 345 premalignant lesions, and 1244 healthy controls). Our analysis revealed that the frequency of MLH1 methylation was significantly elevated during EC carcinogenesis. In addition, we observed that MLH1 promoter methylation was associated with age (odds ratio [OR]=1.79; 95% CI =1.20–2.66), advanced tumor grade (OR=3.7; 95% CI =2.37–5.77), lymph node metastasis (OR=2.65; 95% CI =1.81–3.88), distant metastasis (OR=7.60; 95% CI =1.23–47.19), advanced clinical stage (OR=4.46; 95% CI =2.88–6.91), and poor prognosis in EC patients (hazard ratio =1.64, 95% CI =1.00–2.69). The pooled sensitivity, specificity, and area under the curve of MLH1 methylation in EC patients versus healthy individuals were 0.15, 0.99, and 0.77, respectively. Our findings indicate that MLH1 methylation is involved in the carcinogenesis, progression, and metastasis of EC. Moreover, methylated MLH1 could be a potential diagnostic and prognostic biomarker for EC. PMID:29440913

Distinct DNA-binding surfaces in the ATPase and linker domains of MutLγ determine its substrate specificities and exert separable functions in meiotic recombination and mismatch repair

PubMed Central

2017-01-01

Mlh1-Mlh3 (MutLγ) is a mismatch repair factor with a central role in formation of meiotic crossovers, presumably through resolution of double Holliday junctions. MutLγ has DNA-binding, nuclease, and ATPase activities, but how these relate to one another and to in vivo functions are unclear. Here, we combine biochemical and genetic analyses to characterize Saccharomyces cerevisiae MutLγ. Limited proteolysis and atomic force microscopy showed that purified recombinant MutLγ undergoes ATP-driven conformational changes. In vitro, MutLγ displayed separable DNA-binding activities toward Holliday junctions (HJ) and, surprisingly, single-stranded DNA (ssDNA), which was not predicted from current models. MutLγ bound DNA cooperatively, could bind multiple substrates simultaneously, and formed higher-order complexes. FeBABE hydroxyl radical footprinting indicated that the DNA-binding interfaces of MutLγ for ssDNA and HJ substrates only partially overlap. Most contacts with HJ substrates were located in the linker regions of MutLγ, whereas ssDNA contacts mapped within linker regions as well as the N-terminal ATPase domains. Using yeast genetic assays for mismatch repair and meiotic recombination, we found that mutations within different DNA-binding surfaces exert separable effects in vivo. For example, mutations within the Mlh1 linker conferred little or no meiotic phenotype but led to mismatch repair deficiency. Interestingly, mutations in the N-terminal domain of Mlh1 caused a stronger meiotic defect than mlh1Δ, suggesting that the mutant proteins retain an activity that interferes with alternative recombination pathways. Furthermore, mlh3Δ caused more chromosome missegregation than mlh1Δ, whereas mlh1Δ but not mlh3Δ partially alleviated meiotic defects of msh5Δ mutants. These findings illustrate functional differences between Mlh1 and Mlh3 during meiosis and suggest that their absence impinges on chromosome segregation not only via reduced formation of crossovers. Taken together, our results offer insights into the structure-function relationships of the MutLγ complex and reveal unanticipated genetic relationships between components of the meiotic recombination machinery. PMID:28505149

Adjustment of a Population of South African Children of Mothers Living With/and Without HIV Through Three Years Post-Birth.

PubMed

Rotheram-Borus, Mary Jane; Tomlinson, Mark; Scheffler, Aaron; Harris, Danielle M; Nelson, Sandahl

2017-06-01

Mothers living with HIV (MLH) and their children are typically studied to ensure that perinatal HIV transmission is blocked. Yet, HIV impacts MLH and their children lifelong. We examine child outcomes from pregnancy to 3 years post-birth among a peri-urban population of pregnant MLH and mothers without HIV (MWOH). Almost all pregnant women in 12 neighborhoods (98 %; N = 584) in Cape Town, South Africa were recruited and repeatedly assessed within 2 weeks of birth (92 %), at 6 months (88 %), 18 months (84 %), and 3 years post-birth (86 %). There were 186 MLH and 398 MWOH. Controlling for neighborhood and repeated measures, child and maternal outcomes were contrasted over time using longitudinal random effects regression analyses. For measures collected only at 3 years, outcomes were analyzed using multiple regressions. Compared to MWOH, MLH had less income, more informal housing and food insecurity, used alcohol more often during pregnancy, and were more depressed during pregnancy and over time. Only 4.8 % of MLH's children were seropositive; seropositive children were excluded from additional analyses. Children of MLH tended to have significantly lower weights (p < .10) over time (i.e., lower weight-for-age Z-scores) and were also hospitalized significantly more often than children of MWOH (p < .01). Children of MLH and MWOH died at similar rates (8.5 %) and were similar in social and behavioral adjustment, vocabulary, and executive functioning at 3 years post-birth. Despite living in households with fewer resources and having more depressed mothers, only the physical health of children of MLH is compromised, compared to children of MWOH. In township neighborhoods with extreme poverty, social, behavioral, language, and cognitive functioning appear similar over the first three years of life between children of MLH and MWOH.

Germline MLH1 Mutations Are Frequently Identified in Lynch Syndrome Patients With Colorectal and Endometrial Carcinoma Demonstrating Isolated Loss of PMS2 Immunohistochemical Expression.

PubMed

Dudley, Beth; Brand, Randall E; Thull, Darcy; Bahary, Nathan; Nikiforova, Marina N; Pai, Reetesh K

2015-08-01

Current guidelines on germline mutation testing for patients suspected of having Lynch syndrome are not entirely clear in patients with tumors demonstrating isolated loss of PMS2 immunohistochemical expression. We analyzed the clinical and pathologic features of patients with tumors demonstrating isolated loss of PMS2 expression in an attempt to (1) determine the frequency of germline MLH1 and PMS2 mutations and (2) correlate mismatch-repair protein immunohistochemistry and tumor histology with germline mutation results. A total of 3213 consecutive colorectal carcinomas and 215 consecutive endometrial carcinomas were prospectively analyzed for DNA mismatch-repair protein expression by immunohistochemistry. In total, 32 tumors from 31 patients demonstrated isolated loss of PMS2 immunohistochemical expression, including 16 colorectal carcinomas and 16 endometrial carcinomas. Microsatellite instability (MSI) polymerase chain reaction was performed in 29 tumors from 28 patients with the following results: 28 tumors demonstrated high-level MSI, and 1 tumor demonstrated low-level MSI. Twenty of 31 (65%) patients in the study group had tumors demonstrating histopathology associated with high-level MSI. Seventeen patients underwent germline mutation analysis with the following results: 24% with MLH1 mutations, 35% with PMS2 mutations, 12% with PMS2 variants of undetermined significance, and 29% with no mutations in either MLH1 or PMS2. Three of the 4 patients with MLH1 germline mutations had a mutation that results in decreased stability and quantity of the MLH1 protein that compromises the MLH1-PMS2 protein complex, helping to explain the presence of immunogenic but functionally inactive MLH1 protein within the tumor. The high frequency of MLH1 germline mutations identified in our study has important implications for testing strategies in patients suspected of having Lynch syndrome and indicates that patients with tumors demonstrating isolated loss of PMS2 expression without a germline PMS2 mutation must have MLH1 mutation analysis performed.

Ovarian metastasis from uveal melanoma with MLH1/PMS2 protein loss in a patient with germline MLH1 mutated Lynch syndrome: consequence or coincidence?

PubMed

Lobo, João; Pinto, Carla; Freitas, Micaela; Pinheiro, Manuela; Vizcaino, Rámon; Oliva, Esther; Teixeira, Manuel R; Jerónimo, Carmen; Bartosch, Carla

2017-03-01

Currently, uveal melanoma is not considered within the Lynch syndrome tumor spectrum. However, there are studies suggesting a contribution of microsatellite instability in sporadic uveal melanoma tumorigenesis. We report a 45-year-old woman who was referred for genetic counseling due to a family history of Lynch syndrome caused by a MLH1 mutation. She originally underwent enucleation of the right eye secondary to a uveal spindle cell melanoma diagnosed at age 25. The tumor recurred 22 years later presenting as an ovarian metastasis and concurrently a microscopic endometrial endometrioid carcinoma, grade 1/3 was diagnosed. Subsequent studies highlighted that the uveal melanoma showed high microsatellite instability and loss of MLH1 and PMS2 protein expression, with no MLH1 promoter methylation or BRAF mutation. Additionally, a GNAQ mutation was found. We conclude that our patient's uveal melanoma is most likely related to MLH1 germline mutation and thus Lynch syndrome related. To the best of our knowledge, this is the first report of uveal melanoma showing MLH1/PMS2 protein loss in the context of Lynch syndrome.

Comparison of dust-layer heights from active and passive satellite sensors

NASA Astrophysics Data System (ADS)

Kylling, Arve; Vandenbussche, Sophie; Capelle, Virginie; Cuesta, Juan; Klüser, Lars; Lelli, Luca; Popp, Thomas; Stebel, Kerstin; Veefkind, Pepijn

2018-05-01

Aerosol-layer height is essential for understanding the impact of aerosols on the climate system. As part of the European Space Agency Aerosol_cci project, aerosol-layer height as derived from passive thermal and solar satellite sensors measurements have been compared with aerosol-layer heights estimated from CALIOP measurements. The Aerosol_cci project targeted dust-type aerosol for this study. This ensures relatively unambiguous aerosol identification by the CALIOP processing chain. Dust-layer height was estimated from thermal IASI measurements using four different algorithms (from BIRA-IASB, DLR, LMD, LISA) and from solar GOME-2 (KNMI) and SCIAMACHY (IUP) measurements. Due to differences in overpass time of the various satellites, a trajectory model was used to move the CALIOP-derived dust heights in space and time to the IASI, GOME-2 and SCIAMACHY dust height pixels. It is not possible to construct a unique dust-layer height from the CALIOP data. Thus two CALIOP-derived layer heights were used: the cumulative extinction height defined as the height where the CALIOP extinction column is half of the total extinction column, and the geometric mean height, which is defined as the geometrical mean of the top and bottom heights of the dust layer. In statistical average over all IASI data there is a general tendency to a positive bias of 0.5-0.8 km against CALIOP extinction-weighted height for three of the four algorithms assessed, while the fourth algorithm has almost no bias. When comparing geometric mean height there is a shift of -0.5 km for all algorithms (getting close to zero for the three algorithms and turning negative for the fourth). The standard deviation of all algorithms is quite similar and ranges between 1.0 and 1.3 km. When looking at different conditions (day, night, land, ocean), there is more detail in variabilities (e.g. all algorithms overestimate more at night than during the day). For the solar sensors it is found that on average SCIAMACHY data are lower by -1.097 km (-0.961 km) compared to the CALIOP geometric mean (cumulative extinction) height, and GOME-2 data are lower by -1.393 km (-0.818 km).

MLH1 Promoter Methylation and Prediction/Prognosis of Gastric Cancer: A Systematic Review and Meta and Bioinformatic Analysis.

PubMed

Shen, Shixuan; Chen, Xiaohui; Li, Hao; Sun, Liping; Yuan, Yuan

2018-01-01

Background: The promoter methylation of MLH1 gene and gastric cancer (GC)has been investigated previously. To get a more credible conclusion, we performed a systematic review and meta and bioinformatic analysis to clarify the role of MLH1 methylation in the prediction and prognosis of GC. Methods: Eligible studies were targeted after searching the PubMed, Web of Science, Embase, BIOSIS, CNKI and Wanfang Data to collect the information of MLH1 methylation and GC. The link strength between the two was estimated by odds ratio with its 95% confidence interval. The Newcastle-Ottawa scale was used for quantity assessment . Subgroup and sensitivity analysis were conducted to explore sources of heterogeneity. The Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) were employed for bioinformatics analysis on the correlation between MLH1 methylation and GC risk, clinicopathological behavior as well as prognosis. Results: 2365 GC and 1563 controls were included in the meta-analysis. The pooled OR of MLH1 methylation in GC was 4.895 (95% CI: 3.149-7.611, P<0.001), which considerably associated with increased GC risk. No significant difference was found in relation to Lauren classification, tumor invasion, lymph node/distant metastasis and tumor stage in GC. Analysis based on GEO and TCGA showed that high MLH1 methylation enhanced GC risk but might not related with GC clinicopathological features and prognosis. Conclusion: MLH1 methylation is an alive biomarker for the prediction of GC and it might not affect GC behavior. Further study could be conducted to verify the impact of MLH1 methylation on GC prognosis.

MLH1 Promoter Methylation and Prediction/Prognosis of Gastric Cancer: A Systematic Review and Meta and Bioinformatic Analysis

PubMed Central

Shen, Shixuan; Chen, Xiaohui; Li, Hao; Sun, Liping; Yuan, Yuan

2018-01-01

Background: The promoter methylation of MLH1 gene and gastric cancer (GC)has been investigated previously. To get a more credible conclusion, we performed a systematic review and meta and bioinformatic analysis to clarify the role of MLH1 methylation in the prediction and prognosis of GC. Methods: Eligible studies were targeted after searching the PubMed, Web of Science, Embase, BIOSIS, CNKI and Wanfang Data to collect the information of MLH1 methylation and GC. The link strength between the two was estimated by odds ratio with its 95% confidence interval. The Newcastle-Ottawa scale was used for quantity assessment. Subgroup and sensitivity analysis were conducted to explore sources of heterogeneity. The Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) were employed for bioinformatics analysis on the correlation between MLH1 methylation and GC risk, clinicopathological behavior as well as prognosis. Results: 2365 GC and 1563 controls were included in the meta-analysis. The pooled OR of MLH1 methylation in GC was 4.895 (95% CI: 3.149-7.611, P<0.001), which considerably associated with increased GC risk. No significant difference was found in relation to Lauren classification, tumor invasion, lymph node/distant metastasis and tumor stage in GC. Analysis based on GEO and TCGA showed that high MLH1 methylation enhanced GC risk but might not related with GC clinicopathological features and prognosis. Conclusion: MLH1 methylation is an alive biomarker for the prediction of GC and it might not affect GC behavior. Further study could be conducted to verify the impact of MLH1 methylation on GC prognosis. PMID:29896277

Mlh1 is required for female fertility in Drosophila melanogaster: An outcome of effects on meiotic crossing over, ovarian follicles and egg activation.

PubMed

Vimal, Divya; Kumar, Saurabh; Pandey, Ashutosh; Sharma, Divya; Saini, Sanjay; Gupta, Snigdha; Ravi Ram, Kristipati; Chowdhuri, Debapratim Kar

2018-03-01

Mismatch repair (MMR) system, a conserved DNA repair pathway, plays crucial role in DNA recombination and is involved in gametogenesis. The impact of alterations in MMR family of proteins (bacterial MutS and MutL homologues) on mammalian fertility is well documented. However, an insight to the role of MMR in reproduction of non-mammalian organisms is limited. Hence, in the present study, we analysed the impact of mlh1 (a MutL homologue) on meiotic crossing over/recombination and fertility in a genetically tractable model, Drosophila melanogaster. Using mlh1 e00130 hypomorphic allele, we report female specific adverse reproductive outcome for reduced mlh1 in Drosophila: mlh1 e00130 homozygous females had severely reduced fertility while males were fertile. Further, mlh1 e00130 females contained small ovaries with large number of early stages as well as significantly reduced mature oocytes, and laid fewer eggs, indicating discrepancies in egg production and ovulation. These observations contrast the sex independent and/or male specific sterility and normal follicular development as well as ovulation reported so far for MMR family proteins in mammals. However, analogous to the role(s) of mlh1 in meiotic crossing over and DNA repair processes underlying mammalian fertility, ovarian follicles from mlh1 e00130 females contained significantly increased DNA double strand breaks (DSBs) and reduced synaptonemal complex foci. In addition, large proportion of fertilized eggs display discrepancies in egg activation and fail to proceed beyond stage 5 of embryogenesis. Hence, reduction of the Mlh1 protein level leads to defective oocytes that fail to complete embryogenesis after fertilization thereby reducing female fertility. Copyright © 2017 Elsevier GmbH. All rights reserved.

Expression of DNA mismatch repair proteins MLH1, MSH2, and MSH6 in recurrent glioblastoma.

PubMed

Stark, Andreas M; Doukas, Alexander; Hugo, Heinz-Herrmann; Hedderich, Jürgen; Hattermann, Kirsten; Maximilian Mehdorn, H; Held-Feindt, Janka

2015-02-01

Methylated O6-methylguanin-DNA-methytransferase (MGMT) promoter methylation is associated with survival in patients with glioblastoma. Current evidence suggests that further mismatch repair genes play a pivotal role in the tumor response to treatment. Candidate genes are MLH1, MSH2, and MSH6. Formerly, we found evidence of prognostic impact of MLH1 and MSH6 immunohistochemical expression in a small series of patients with initial glioblastoma. Two hundred and eleven patients were included who underwent macroscopically total removal of primary glioblastoma and at least one re-craniotomy for recurrence. Immunohistochemical staining was performed on paraffin-embedded specimens of initial tumors with specific antibodies against MLH1, MSH2, and MSH6. RESULTS were compared to the Ki67 proliferation index and patient survival. Additionally, fresh frozen samples from 16 paired initial and recurrent specimens were examined using real-time reverse transcription polymerase chain reaction (RT-PCR) with specific primers against MLH1, MSH2, and MSH6. RESULTS were compared to MGMT status and survival. (1) Immunohistochemical expression of MSH6 was significantly associated with the Ki67 proliferation index (P<0.001) but not with survival. (2) PCR revealed two patients with increasing expression of MLH1, MLH2, and MSH6 over treatment combined with lacking MGMT methylation. In another two patients, decreased MLH1, MSH2, and MSH6 expression was observed in combination with MGMT promoter methylation. Our data indicate that there may be glioblastoma patient subgroups characterized by MMR-expression changes beyond MGMT promoter methylation. The immunohistochemical expression of MLH1, MSH2, and MSH6 in initial glioblastoma is not associated with patient survival.

Tumour MLH1 promoter region methylation testing is an effective pre-screen for Lynch Syndrome (HNPCC)

PubMed Central

Newton, K; Jorgensen, NM; Wallace, AJ; Buchanan, DD; Lalloo, F; McMahon, RFT; Hill, J; Evans, DG

2016-01-01

Background & Aims Lynch syndrome patients have DNA mismatch repair deficiency and up to 80% life-time risk of colorectal cancer. Screening of mutation carriers reduces colorectal cancer incidence and mortality. Selection for constitutional mutation testing relies on family history (Amsterdam and Bethesda Guidelines) and tumour derived biomarkers. Initial biomarker analysis uses mismatch repair protein immunohistochemistry and microsatellite instability. Abnormalities in either identify mismatch repair deficiency but do not differentiate sporadic epigenetic defects, due to MLH1 promoter region methylation (13% of CRCs) from Lynch Syndrome (4% of CRCs). A diagnostic biomarker capable of making this distinction would be valuable. This study compared two biomarkers in tumours with mismatch repair deficiency; quantification of methylation of the MLH1 promoter region using a novel assay and BRAF c.1799T>A, p.(Val600Glu) mutation status in the identification of constitutional mutations. Methods Tumour DNA was extracted (FFPE tissue) and pyrosequencing used to test for MLH1 promoter methylation and presence of the BRAF c.1799T>A, p.(Val600Glu) mutation 71 CRCs from individuals with pathogenic MLH1 mutations and 73 CRCs with sporadic MLH1 loss. Specificity and sensitivity was compared. Findings Unmethylated MLH1 promoter: sensitivity 94.4% (95% CI 86.2–98.4%), specificity 87.7% (95% CI 77.9–94.2%), Wild-type BRAF (codon 600): sensitivity 65.8% (95% CI 53.7–76.5%), specificity 98.6% (95% CI 92.4–100.0%) for the identification of those with pathogenic MLH1 mutations. Conclusions Quantitative MLH1 promoter region methylation using pyrosequencing is superior to BRAF codon 600 mutation status in identifying constitutional mutations in mismatch repair deficient tumours. PMID:25280751

De novo constitutional MLH1 epimutations confer early-onset colorectal cancer in two new sporadic Lynch syndrome cases, with derivation of the epimutation on the paternal allele in one.

PubMed

Goel, Ajay; Nguyen, Thuy-Phuong; Leung, Hon-Chiu E; Nagasaka, Takeshi; Rhees, Jennifer; Hotchkiss, Erin; Arnold, Mildred; Banerji, Pia; Koi, Minoru; Kwok, Chau-To; Packham, Deborah; Lipton, Lara; Boland, C Richard; Ward, Robyn L; Hitchins, Megan P

2011-02-15

Lynch syndrome is an autosomal dominant cancer predisposition syndrome classically caused by germline mutations of the mismatch repair genes, MLH1, MSH2, MSH6 and PMS2. Constitutional epimutations of the MLH1 gene, characterized by soma-wide methylation of a single allele of the promoter and allelic transcriptional silencing, have been identified in a subset of Lynch syndrome cases lacking a sequence mutation in MLH1. We report two individuals with no family history of colorectal cancer who developed that disease at age 18 and 20 years. In both cases, cancer had arisen because of the de novo occurrence of a constitutional MLH1 epimutation and somatic loss-of-heterozygosity of the functional allele in the tumors. We show for the first time that the epimutation in one case arose on the paternally inherited allele. Analysis of 13 tumors from seven individuals with constitutional MLH1 epimutations showed eight tumors had lost the second MLH1 allele, two tumors had a novel pathogenic missense mutation and three had retained heterozygosity. Only 1 of 12 tumors demonstrated the BRAF V600E mutation and 3 of 11 tumors harbored a mutation in KRAS. The finding that epimutations can originate on the paternal allele provides important new insights into the mechanism of origin of epimutations. It is clear that the second hit in MLH1 epimutation-associated tumors typically has a genetic not epigenetic basis. Individuals with mismatch repair-deficient cancers without the BRAF V600E mutation are candidates for germline screening for sequence or methylation changes in MLH1. Copyright © 2010 UICC.

De novo constitutional MLH1 epimutations confer early-onset colorectal cancer in two new sporadic Lynch syndrome cases, with derivation of the epimutation on the paternal allele in one

PubMed Central

Goel, Ajay; Nguyen, Thuy-Phuong; Leung, Hon-Chiu E.; Nagasaka, Takeshi; Rhees, Jennifer; Hotchkiss, Erin; Arnold, Mildred; Banerji, Pia; Koi, Minoru; Kwok, Chau-To; Packham, Deborah; Lipton, Lara; Boland, C. Richard; Ward, Robyn L.; Hitchins, Megan P.

2013-01-01

Lynch syndrome is an autosomal dominant cancer predisposition syndrome classically caused by germline mutations of the mismatch repair genes, MLH1, MSH2, MSH6 and PMS2. Constitutional epimutations of the MLH1 gene, characterized by soma-wide methylation of a single allele of the promoter and allelic transcriptional silencing, have been identified in a subset of Lynch syndrome cases lacking a sequence mutation in MLH1. We report two individuals with no family history of colorectal cancer who developed that disease at age 18 and 20 years. In both cases, cancer had arisen because of the de novo occurrence of a constitutional MLH1 epimutation and somatic loss-of-heterozygosity of the functional allele in the tumors. We show for the first time that the epimutation in one case arose on the paternally inherited allele. Analysis of 13 tumors from seven individuals with constitutional MLH1 epimutations showed eight tumors had lost the second MLH1 allele, two tumors had a novel pathogenic missense mutation and three had retained heterozygosity. Only 1 of 12 tumors demonstrated the BRAF V600E mutation and 3 of 11 tumors harbored a mutation in KRAS. The finding that epimutations can originate on the paternal allele provides important new insights into the mechanism of origin of epimutations. It is clear that the second hit in MLH1 epimutation-associated tumors typically has a genetic not epigenetic basis. Individuals with mismatch repair–deficient cancers without the BRAF V600E mutation are candidates for germline screening for sequence or methylation changes in MLH1. PMID:20473912

Epitope-positive truncating MLH1 mutation and loss of PMS2: implications for IHC-directed genetic testing for Lynch syndrome.

PubMed

Zighelboim, Israel; Powell, Matthew A; Babb, Sheri A; Whelan, Alison J; Schmidt, Amy P; Clendenning, Mark; Senter, Leigha; Thibodeau, Stephen N; de la Chapelle, Albert; Goodfellow, Paul J

2009-01-01

We assessed mismatch repair by immunohistochemistry (IHC) and microsatellite instability (MSI) analysis in an early onset endometrial cancer and a sister's colon cancer. We demonstrated high-level MSI and normal expression for MLH1, MSH2 and MSH6. PMS2 failed to stain in both tumors, strongly implicating a PMS2 defect. This family did not meet clinical criteria for Lynch syndrome. However, early onset endometrial cancers in the proband and her sister, a metachronous colorectal cancer in the sister as well as MSI in endometrial and colonic tumors suggested a heritable mismatch repair defect. PCR-based direct exonic sequencing and multiplex ligation-dependent probe amplification (MLPA) were undertaken to search for PMS2 mutations in the germline DNA from the proband and her sister. No mutation was identified in the PMS2 gene. However, PMS2 exons 3, 4, 13, 14, 15 were not evaluated by MLPA and as such, rearrangements involving those exons cannot be excluded. Clinical testing for MLH1 and MSH2 mutation revealed a germline deletion of MLH1 exons 14 and 15. This MLH1 germline deletion leads to an immunodetectable stable C-terminal truncated MLH1 protein which based on the IHC staining must abrogate PMS2 stabilization. To the best of our knowledge, loss of PMS2 in MLH1 truncating mutation carriers that express MLH1 in their tumors has not been previously reported. This family points to a potential limitation of IHC-directed gene testing for suspected Lynch syndrome and the need to consider comprehensive MLH1 testing for individuals whose tumors lack PMS2 but for whom PMS2 mutations are not identified.

Estimation of the mixing layer height over a high altitude site in Central Himalayan region by using Doppler lidar

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shukla, K. K.; Phanikumar, D. V.; Newsom, Rob K.

2014-03-01

A Doppler lidar was installed at Manora Peak, Nainital (29.4 N; 79.2 E, 1958 amsl) to estimate mixing layer height for the first time by using vertical velocity variance as basic measurement parameter for the period September-November 2011. Mixing layer height is found to be located ~0.57 +/- 0.1and 0.45 +/- 0.05km AGL during day and nighttime, respectively. The estimation of mixing layer height shows good correlation (R>0.8) between different instruments and with different methods. Our results show that wavelet co-variance transform is a robust method for mixing layer height estimation.

Diversity of genetic events associated with MLH1 promoter methylation in Lynch syndrome families with heritable constitutional epimutation.

PubMed

Leclerc, Julie; Flament, Cathy; Lovecchio, Tonio; Delattre, Lucie; Ait Yahya, Emilie; Baert-Desurmont, Stéphanie; Burnichon, Nelly; Bronner, Myriam; Cabaret, Odile; Lejeune, Sophie; Guimbaud, Rosine; Morin, Gilles; Mauillon, Jacques; Jonveaux, Philippe; Laurent-Puig, Pierre; Frébourg, Thierry; Porchet, Nicole; Buisine, Marie-Pierre

2018-04-12

PurposeConstitutional epimutations are an alternative to genetic mutations in the etiology of genetic diseases. Some of these epimutations, termed secondary, correspond to the epigenetic effects of cis-acting genetic defects transmitted to the offspring following a Mendelian inheritance pattern. In Lynch syndrome, a few families with such apparently heritable MLH1 epimutations have been reported so far.MethodsWe designed a long-range polymerase chain reaction next-generation sequencing strategy to screen MLH1 entire gene and applied it to 4 French families with heritable epimutations and 10 additional patients with no proven transmission of their epimutations.ResultsThis strategy successfully detected the insertion of an Alu element in MLH1 coding sequence in one family. Two previously unreported MLH1 variants were also identified in other epimutation carriers: a nucleotide substitution within intron 1 and a single-nucleotide deletion in the 5'-UTR. Detection of a partial MLH1 duplication in another family required multiplex ligation-dependent probe amplification technology. We demonstrated the segregation of these variants with MLH1 methylation and studied the functional consequences of these defects on transcription.ConclusionThis is the largest cohort of patients with MLH1 secondary epimutations associated with a broad spectrum of genetic defects. This study provides further insight into the complexity of molecular mechanisms leading to secondary epimutations.GENETICS in MEDICINE advance online publication, 12 April 2018; doi:10.1038/gim.2018.47.

Repair genes expression profile of MLH1, MSH2 and ATM in the normal oral mucosa of chronic smokers.

PubMed

Alves, Mônica Ghislaine Oliveira; Carta, Celina Faig Lima; de Barros, Patrícia Pimentel; Issa, Jaqueline Scholz; Nunes, Fábio Daumas; Almeida, Janete Dias

2017-01-01

The aim of this study was to evaluate the effect of chronic smoking on the expression profile of the repair genes MLH1, MSH2 and ATM in the normal oral mucosa of chronic smokers and never smokers. The sample consisted of thirty exfoliative cytology smears per group obtained from Smokers and Never Smokers. Total RNA was extracted and expression of the MLH1, MSH2 and ATM genes were evaluated by quantitative real-time and immunocytochemistry. The gene and protein expression data were correlated to the clinical data. Gene expression was analyzed statistically using the Student t-test and Pearson's correlation coefficient, with p<0.05. MLH1, MSH2 and ATM genes were downregulated in the smoking group compared to the control with significant values for MLH1 (p=0.006), MSH2 (p=0.0001) and ATM (p=0.0001). Immunocytochemical staining for anti-MLH1, anti-MSH2 and anti-ATM was negative in Never Smokers; in Smokers it was rarely positive. No significant correlation was observed among the expression of MLH1, MSH2, ATM and age, number of cigarettes consumed per day, time of smoking during life, smoking history or levels of CO in expired air. The expression of genes and proteins related to DNA repair mechanism MLH1, MSH2 and ATM in the normal oral mucosa of chronic smokers was reduced. Copyright © 2016 Elsevier Ltd. All rights reserved.

Expression of MLH1 and MSH2 in urothelial carcinoma of the renal pelvis.

PubMed

Ehsani, Laleh; Osunkoya, Adeboye O

2014-09-01

In this study, we investigated microsatellite instability in urothelial carcinoma of the renal pelvis by lack of immunohistochemical staining for MLH1 and MSH2. The study included 44 cases of urothelial carcinoma of the renal pelvis obtained from radical nephroureterectomy specimens at our institution. We evaluated the loss of nuclear immunohistochemical staining of MLH1 and MSH2. Eight of 44 (18 %) patients had negative MLH1 expression and 25/44 (57 %) patients had negative MSH2 expression. Six of 8 (75 %) patients with negative MLH1 expression were male and 2/8 (25 %) patients were female. Nineteen of 25 (75 %) patients with negative MSH2 expression were male, and 6/25 (24 %) patients were female. Seven of 8 (88 %) cases with negative MLH1 expression were high-grade urothelial carcinoma, and 21/25 (84 %) cases with negative MSH2 expression were high-grade urothelial carcinoma. Twenty-one of 44 (48 %) cases had an inverted growth pattern, of which 3/21 (14 %) cases had negative MLH1 expression and 14/21 (67 %) cases had negative MSH2 expression. Our study showed that microsatellite instability based on negative expression of MLH1 and MSH2 was more common in male patients with high-grade urothelial carcinoma. There is a strong correlation between inverted growth pattern and negative MSH2 expression. Microsatellite instability testing should be performed in patients with upper urinary tract carcinoma and may have prognostic value.

Lynch syndrome associated with two MLH1 promoter variants and allelic imbalance of MLH1 expression.

PubMed

Hesson, Luke B; Packham, Deborah; Kwok, Chau-To; Nunez, Andrea C; Ng, Benedict; Schmidt, Christa; Fields, Michael; Wong, Jason W H; Sloane, Mathew A; Ward, Robyn L

2015-06-01

Lynch syndrome is a hereditary cancer syndrome caused by a constitutional mutation in one of the mismatch repair genes. The implementation of predictive testing and targeted preventative surveillance is hindered by the frequent finding of sequence variants of uncertain significance in these genes. We aimed to determine the pathogenicity of previously reported variants (c.-28A>G and c.-7C>T) within the MLH1 5'untranslated region (UTR) in two individuals from unrelated suspected Lynch syndrome families. We investigated whether these variants were associated with other pathogenic alterations using targeted high-throughput sequencing of the MLH1 locus. We also determined their relationship to gene expression and epigenetic alterations at the promoter. Sequencing revealed that the c.-28A>G and c.-7C>T variants were the only potentially pathogenic alterations within the MLH1 gene. In both individuals, the levels of transcription from the variant allele were reduced to 50% compared with the wild-type allele. Partial loss of expression occurred in the absence of constitutional epigenetic alterations within the MLH1 promoter. We propose that these variants may be pathogenic due to constitutional partial loss of MLH1 expression, and that this may be associated with intermediate penetrance of a Lynch syndrome phenotype. Our findings provide further evidence of the potential importance of noncoding variants in the MLH1 5'UTR in the pathogenesis of Lynch syndrome. © 2015 The Authors. **Human Mutation published by Wiley Periodicals, Inc.

Lynch Syndrome Associated with Two MLH1 Promoter Variants and Allelic Imbalance of MLH1 Expression

PubMed Central

Hesson, Luke B; Packham, Deborah; Kwok, Chau-To; Nunez, Andrea C; Ng, Benedict; Schmidt, Christa; Fields, Michael; Wong, Jason WH; Sloane, Mathew A; Ward, Robyn L

2015-01-01

Lynch syndrome is a hereditary cancer syndrome caused by a constitutional mutation in one of the mismatch repair genes. The implementation of predictive testing and targeted preventative surveillance is hindered by the frequent finding of sequence variants of uncertain significance in these genes. We aimed to determine the pathogenicity of previously reported variants (c.-28A>G and c.-7C>T) within the MLH1 5′untranslated region (UTR) in two individuals from unrelated suspected Lynch syndrome families. We investigated whether these variants were associated with other pathogenic alterations using targeted high-throughput sequencing of the MLH1 locus. We also determined their relationship to gene expression and epigenetic alterations at the promoter. Sequencing revealed that the c.-28A>G and c.-7C>T variants were the only potentially pathogenic alterations within the MLH1 gene. In both individuals, the levels of transcription from the variant allele were reduced to 50% compared with the wild-type allele. Partial loss of expression occurred in the absence of constitutional epigenetic alterations within the MLH1 promoter. We propose that these variants may be pathogenic due to constitutional partial loss of MLH1 expression, and that this may be associated with intermediate penetrance of a Lynch syndrome phenotype. Our findings provide further evidence of the potential importance of noncoding variants in the MLH1 5′UTR in the pathogenesis of Lynch syndrome. PMID:25762362

Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair

PubMed Central

Kosinski, Jan; Hinrichsen, Inga; Bujnicki, Janusz M.; Friedhoff, Peter; Plotz, Guido

2010-01-01

Missense alterations of the mismatch repair gene MLH1 have been identified in a significant proportion of individuals suspected of having Lynch syndrome, a hereditary syndrome which predisposes for cancer of colon and endometrium. The pathogenicity of many of these alterations, however, is unclear. A number of MLH1 alterations are located in the C-terminal domain (CTD) of MLH1, which is responsible for constitutive dimerization with PMS2. We analyzed which alterations may result in pathogenic effects due to interference with dimerization. We used a structural model of CTD of MLH1-PMS2 heterodimer to select 19 MLH1 alterations located inside and outside two candidate dimerization interfaces in the MLH1-CTD. Three alterations (p.Gln542Leu, p.Leu749Pro, p.Tyr750X) caused decreased co-expression of PMS2, which is unstable in the absence of interaction with MLH1, suggesting that these alterations interfere with dimerization. All three alterations are located within the dimerization interface suggested by our model. They also compromised mismatch repair, suggesting that defects in dimerization abrogate repair and confirming that all three alterations are pathogenic. Additionally, we provided biochemical evidence that four alterations with uncertain pathogenicity (p.Ala586Pro, p.Leu636Pro, p.Thr662Pro, and p.Arg755Trp) are deleterious because of poor expression or poor repair efficiency, and confirm the deleterious effect of eight further alterations. PMID:20533529

Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair.

PubMed

Kosinski, Jan; Hinrichsen, Inga; Bujnicki, Janusz M; Friedhoff, Peter; Plotz, Guido

2010-08-01

Missense alterations of the mismatch repair gene MLH1 have been identified in a significant proportion of individuals suspected of having Lynch syndrome, a hereditary syndrome that predisposes for cancer of colon and endometrium. The pathogenicity of many of these alterations, however, is unclear. A number of MLH1 alterations are located in the C-terminal domain (CTD) of MLH1, which is responsible for constitutive dimerization with PMS2. We analyzed which alterations may result in pathogenic effects due to interference with dimerization. We used a structural model of CTD of MLH1-PMS2 heterodimer to select 19 MLH1 alterations located inside and outside two candidate dimerization interfaces in the MLH1-CTD. Three alterations (p.Gln542Leu, p.Leu749Pro, p.Tyr750X) caused decreased coexpression of PMS2, which is unstable in the absence of interaction with MLH1, suggesting that these alterations interfere with dimerization. All three alterations are located within the dimerization interface suggested by our model. They also compromised mismatch repair, suggesting that defects in dimerization abrogate repair and confirming that all three alterations are pathogenic. Additionally, we provided biochemical evidence that four alterations with uncertain pathogenicity (p.Ala586Pro, p.Leu636Pro, p.Thr662Pro, and p.Arg755Trp) are deleterious because of poor expression or poor repair efficiency, and confirm the deleterious effect of eight further alterations.

An Algorithm for the Vertical Structure of Aerosol Extinction in the Lowest Kilometer of the Atmosphere: Rev. 1

DTIC Science & Technology

2017-11-01

inversion layer, or the well-mixed boundary layer. In such cases a low cloud ceiling is not present. In all instances the atmospheric extinction profiles...height, radiation fog depth, or the inversion layer height. The visibility regions and several representative vertical profiles of extinction are...the coefficient B can be found by B = ln(D/A) . (2) The coefficient B is sometimes a function of the cloud ceiling height, the inversion layer height

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Hong; Zeng, Hong; Lam, Robert

Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson–Crick base pairs in the genome. Pathogenic mutations in theMLH1gene are associated with a predisposition to Lynch and Turcot's syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. Lastly, the structure shares a high degree of similarity with previously determined prokaryoticMLH1homologs; however, this structure affords a more accurate platform for the classification ofMLH1variants.

A Novel Functional Screen for New Breast Cancer Genes

DTIC Science & Technology

2005-09-01

remaining three mammalian MutL homologs [19- 21]. The heterodimer of MLH1 and PMS2 , MutLa, is the major player in mammalian mismatch 4 repair...in MSH2 [39-41], 30% in MLH1 [42], and less than 10% in PMS1 or PMS2 [43]. Mice with homozygous deletions in either MSH2 or MLH1 also have increased...cancer susceptibility. In many nonfamilial colon tumors with MSI, somatic mutations have been identified in MSH2, in MLH1, and occasionally in PMS2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Hong; Zeng, Hong; Lam, Robert

The crystal structure of the human MLH1 N-terminus is reported at 2.30 Å resolution. The overall structure is described along with an analysis of two clinically important mutations. Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson–Crick base pairs in the genome. Pathogenic mutations in the MLH1 gene are associated with a predisposition to Lynch and Turcot’s syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. The structure shares a high degree ofmore » similarity with previously determined prokaryotic MLH1 homologs; however, this structure affords a more accurate platform for the classification of MLH1 variants.« less

Constitutional MLH1 methylation presenting with colonic polyposis syndrome and not Lynch syndrome.

PubMed

Kidambi, Trilokesh D; Blanco, Amie; Van Ziffle, Jessica; Terdiman, Jonathan P

2016-04-01

At least one-third of patients meeting clinical criteria for Lynch syndrome will have no germline mutation and constitutional epimutations leading to promoter methylation of MLH1 have been identified in a subset of these patients. We report the first case of constitutional MLH1 promoter methylation associated with a colonic polyposis syndrome in a 39 year-old man with a family history of colorectal cancer (CRC) and a personal history of 21 polyps identified over 8 years as well as the development of two synchronous CRCs over 16 months who was evaluated for a hereditary cancer syndrome. Immunohistochemistry (IHC) of multiple tumors showed absent MLH1 and PMS2 expression, though germline testing with Sanger sequencing and multiplex ligation-dependent probe amplification of these mismatch repair genes (MMR) genes was negative. A next generation sequencing panel of 29 genes also failed to identify a pathogenic mutation. Hypermethylation was identified in MLH1 intron 1 in tumor specimens along with buccal cells and peripheral white blood cells, confirming the diagnosis of constitutional MLH1 promoter methylation. This case highlights that constitutional MLH1 methylation should be considered in the differential diagnosis for a polyposis syndrome if IHC staining shows absent MMR gene expression.

Reduced MLH3 Expression in the Syndrome of Gan-Shen Yin Deficiency in Patients with Different Diseases.

PubMed

Du, Juan; Zhong, Maofeng; Liu, Dong; Liang, Shufang; Liu, Xiaolin; Cheng, Binbin; Zhang, Yani; Yin, Zifei; Wang, Yuan; Ling, Changquan

2017-01-01

Traditional Chinese medicine formulates treatment according to body constitution (BC) differentiation. Different constitutions have specific metabolic characteristics and different susceptibility to certain diseases. This study aimed to assess the characteristic genes of gan-shen Yin deficiency constitution in different diseases. Fifty primary liver cancer (PLC) patients, 94 hypertension (HBP) patients, and 100 diabetes mellitus (DM) patients were enrolled and classified into gan-shen Yin deficiency group and non-gan-shen Yin deficiency group according to the body constitution questionnaire to assess the clinical manifestation of patients. The mRNA expressions of 17 genes in PLC patients with gan-shen Yin deficiency were different from those without gan-shen Yin deficiency. However, considering all patients with PLC, HBP, and DM, only MLH3 was significantly lower in gan-shen Yin deficiency group than that in non-gen-shen Yin deficiency. By ROC analysis, the relationship between MLH3 and gan-shen Yin deficiency constitution was confirmed. Treatment of MLH3 (-/- and -/+) mice with Liuweidihuang wan, classical prescriptions for Yin deficiency, partly ameliorates the body constitution of Yin deficiency in MLH3 (-/+) mice, but not in MLH3 (-/-) mice. MLH3 might be one of material bases of gan-shen Yin deficiency constitution.

Gene Expression, DNA Methylation and Prognostic Significance of DNA Repair Genes in Human Bladder Cancer.

PubMed

Wojtczyk-Miaskowska, Anita; Presler, Malgorzata; Michajlowski, Jerzy; Matuszewski, Marcin; Schlichtholz, Beata

2017-01-01

This study investigated the gene expression and DNA methylation of selected DNA repair genes (MBD4, TDG, MLH1, MLH3) and DNMT1 in human bladder cancer in the context of pathophysiological and prognostic significance. To determine the relationship between the gene expression pattern, global methylation and promoter methylation status, we performed real-time PCR to quantify the mRNA of selected genes in 50 samples of bladder cancer and adjacent non-cancerous tissue. The methylation status was analyzed by methylation-specific polymerase chain reaction (MSP) or digestion of genomic DNA with a methylation-sensitive restriction enzyme and PCR with gene-specific primers (MSRE-PCR). The global DNA methylation level was measured using the antibody-based 5-mC detection method. The relative levels of mRNA for MBD4, MLH3, and MLH1 were decreased in 28% (14/50), 34% (17/50) and 36% (18/50) of tumor samples, respectively. The MBD4 mRNA expression was decreased in 46% of non-muscle invasive tumors (Ta/T1) compared with 11% found in muscle invasive tumors (T2-T4) (P<0.003). Analysis of mRNA expression for TDG did not show any significant differences between Ta/T1 and T2-T4 tumors. The frequency of increased DNMT1 mRNA expression was higher in T2-T4 (52%) comparing to Ta/T1 (16%). The overall methylation rates in tumor tissue were 18% for MBD4, 25% for MLH1 and there was no evidence of MLH3 promoter methylation. High grade tumors had significantly lower levels of global DNA methylation (P=0.04). There was a significant association between shorter survival and increased expression of DNMT1 mRNA (P=0.002), decreased expression of MLH1 mRNA (P=0.032) and the presence of MLH1 promoter methylation (P=0.006). This study highlights the importance of DNA repair pathways and provides the first evidence of the role of MBD4 and MLH3 in bladder cancer. In addition, our findings suggest that DNMT1 mRNA and MLH1 mRNA expression, as well as the status of MLH1 promoter methylation, are attractive prognostic markers in this pathology. © 2017 The Author(s). Published by S. Karger AG, Basel.

Expression of the DNA repair gene MLH1 correlates with survival in patients who have resected pancreatic cancer and have received adjuvant chemoradiation: NRG Oncology RTOG Study 9704.

PubMed

Lawrence, Yaacov R; Moughan, Jennifer; Magliocco, Anthony M; Klimowicz, Alexander C; Regine, William F; Mowat, Rex B; DiPetrillo, Thomas A; Small, William; Simko, Jeffry P; Golan, Talia; Winter, Kathryn A; Guha, Chandan; Crane, Christopher H; Dicker, Adam P

2018-02-01

The majority of patients with pancreatic cancer who undergo curative resection experience rapid disease recurrence. In previous small studies, high expression of the mismatch-repair protein mutL protein homolog 1 (MLH1) in pancreatic cancers was associated with better outcomes. The objective of this study was to validate the association between MLH1 expression and survival in patients who underwent resection of pancreatic cancer and received adjuvant chemoradiation. Samples were obtained from the NRG Oncology Radiation Therapy Oncology Group 9704 prospective, randomized trial (clinicaltrials.gov identifier NCT00003216), which compared 2 adjuvant protocols in patients with pancreatic cancer who underwent resection. Tissue microarrays were prepared from formalin-fixed, paraffin-embedded, resected tumor tissues. MLH1 expression was quantified using fluorescence immunohistochemistry and automated quantitative analysis, and expression was dichotomized above and below the median value. Immunohistochemical staining was successfully performed on 117 patients for MLH1 (60 and 57 patients from the 2 arms). The characteristics of the participants who had tissue samples available were similar to those of the trial population as a whole. At the time of analysis, 84% of participants had died, with a median survival of 17 months. Elevated MLH1 expression levels in tumor nuclei were significantly correlated with longer disease-free and overall survival in each arm individually and in both arms combined. Two-year overall survival was 16% in patients who had low MLH1 expression levels and 53% in those who had high MLH1 expression levels (P < .0001 for both arms combined). This association remained true on a multivariate analysis that allowed for lymph node status (hazard ratio, 0.41; 95% confidence interval, 0.27-0.63; P < .0001). In the current sample, MLH1 expression was correlated with long-term survival. Further studies should assess whether MLH1 expression predicts which patients with localized pancreatic cancer may benefit most from aggressive, multimodality treatment. Cancer 2018;124:491-8. © 2017 American Cancer Society. © 2017 American Cancer Society.

Dominant Mutations in S. cerevisiae PMS1 Identify the Mlh1-Pms1 Endonuclease Active Site and an Exonuclease 1-Independent Mismatch Repair Pathway

PubMed Central

Smith, Catherine E.; Mendillo, Marc L.; Bowen, Nikki; Hombauer, Hans; Campbell, Christopher S.; Desai, Arshad; Putnam, Christopher D.; Kolodner, Richard D.

2013-01-01

Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC) is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR) caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. To better understand the function of Mlh1-Pms1 in MMR, we used Saccharomyces cerevisiae to identify six pms1 mutations (pms1-G683E, pms1-C817R, pms1-C848S, pms1-H850R, pms1-H703A and pms1-E707A) that were weakly dominant in wild-type cells, which surprisingly caused a strong MMR defect when present on low copy plasmids in an exo1Δ mutant. Molecular modeling showed these mutations caused amino acid substitutions in the metal coordination pocket of the Pms1 endonuclease active site and biochemical studies showed that they inactivated the endonuclease activity. This model of Mlh1-Pms1 suggested that the Mlh1-FERC motif contributes to the endonuclease active site. Consistent with this, the mlh1-E767stp mutation caused both MMR and endonuclease defects similar to those caused by the dominant pms1 mutations whereas mutations affecting the predicted metal coordinating residue Mlh1-C769 had no effect. These studies establish that the Mlh1-Pms1 endonuclease is required for MMR in a previously uncharacterized Exo1-independent MMR pathway. PMID:24204293

Clinical and prognosis value of the CIMP status combined with MLH1 or p16 INK4a methylation in colorectal cancer.

PubMed

Saadallah-Kallel, Amana; Abdelmaksoud-Dammak, Rania; Triki, Mouna; Charfi, Slim; Khabir, Abdelmajid; Sallemi-Boudawara, Tahia; Mokdad-Gargouri, Raja

2017-08-01

Aberrant DNA methylation of CpG islands occurred frequently in CRC and associated with transcriptional silencing of key genes. In this study, the CIMP combined with MLH1 or p16 INK4a methylation status was determined in CRC patients and correlated with clinicopathological parameters and overall survival. Our data showed that CIMP+ CRCs were identified in 32.9% of cases and that CACNAG1 is the most frequently methylated promoter. When we combined the CIMP with the MLH1 or the p16 INK4a methylation status, we found that CIMP-/MLH1-U (37.8%) and CIMP-/p16 INK4a -U (35.4%) tumors were the most frequent among the four subtypes. Statistical analysis showed that tumor location, lymphovascular invasion, TNM stage, and MSI differed among the group of patients. Kaplan-Meier analyses revealed differences in overall survival according to the CIMP combined with MLH1 or p16 INK4a methylation status. In a multivariate analysis, CIMP/MLH1 and CIMP/p16 INK4a methylation statuses were predictive of prognosis, and the OS was longer for patients with tumors CIMP-/MLH1-M, as well as CIMP-/p16 INK4a -M. Furthermore, DNMT1 is significantly overexpressed in tumors than in normal tissues as well as in CIMP+ than CIMP- tumors. Our results suggest that tumor classification based on the CIMP status combined with MLH1 or p16 INK4a methylation is useful to predict prognosis in CRC patients.

Dominant mutations in S. cerevisiae PMS1 identify the Mlh1-Pms1 endonuclease active site and an exonuclease 1-independent mismatch repair pathway.

PubMed

Smith, Catherine E; Mendillo, Marc L; Bowen, Nikki; Hombauer, Hans; Campbell, Christopher S; Desai, Arshad; Putnam, Christopher D; Kolodner, Richard D

2013-10-01

Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC) is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR) caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. To better understand the function of Mlh1-Pms1 in MMR, we used Saccharomyces cerevisiae to identify six pms1 mutations (pms1-G683E, pms1-C817R, pms1-C848S, pms1-H850R, pms1-H703A and pms1-E707A) that were weakly dominant in wild-type cells, which surprisingly caused a strong MMR defect when present on low copy plasmids in an exo1Δ mutant. Molecular modeling showed these mutations caused amino acid substitutions in the metal coordination pocket of the Pms1 endonuclease active site and biochemical studies showed that they inactivated the endonuclease activity. This model of Mlh1-Pms1 suggested that the Mlh1-FERC motif contributes to the endonuclease active site. Consistent with this, the mlh1-E767stp mutation caused both MMR and endonuclease defects similar to those caused by the dominant pms1 mutations whereas mutations affecting the predicted metal coordinating residue Mlh1-C769 had no effect. These studies establish that the Mlh1-Pms1 endonuclease is required for MMR in a previously uncharacterized Exo1-independent MMR pathway.

Intervening on Conflict, Parental Bonds, and Sexual Risk Acts among Adolescent Children of Mothers Living with HIV

PubMed Central

Rotheram-Borus, Mary Jane; Stein, Judith A.; Rice, Eric

2014-01-01

Objective In 1993–1994, a psychosocial intervention conducted in New York City significantly improved outcomes for parents living with HIV and their adolescent children over six years. We examine if the intervention benefits are similar for adolescents of mothers living with HIV (MLH) in 2004–2005 in Los Angeles when MLH’s survival had increased substantially. Methods Adolescents of MLH in Los Angeles (N = 256) aged 12–20 years old were randomized with their MLH to either: 1) a standard care condition (n = 120 adolescent-MLH dyads); or 2) an intervention condition consisting of small group activities to build coping skills (n = 136 adolescent-MLH dyads, 78% attended the intervention). At 18 months, 94.7% of adolescents were reassessed. Longitudinal structural equation modeling examined if intervention participation impacted adolescents’ relationships with parents and their sexual risk behaviors. Results Compared to the standard care, adolescents in the intervention condition reported significantly more positive family bonds 18 months later. Greater participation by MLH predicted fewer family conflicts, and was indirectly associated with less adolescent sexual risk behavior at the 18 month follow-up assessment. Anticipated developmental patterns were observed - sexual risk acts increased with age. Reports were also consistent with anticipated gender roles; girls reported better bonds with their mothers at 18 months, compared to boys. Conclusions Adolescents of MLH have better bonds with their mothers as a function of participating in a coping skills intervention and reduced sexual risk-taking as a function of MLH intervention involvement. PMID:25010119

Tumour MLH1 promoter region methylation testing is an effective prescreen for Lynch Syndrome (HNPCC).

PubMed

Newton, K; Jorgensen, N M; Wallace, A J; Buchanan, D D; Lalloo, F; McMahon, R F T; Hill, J; Evans, D G

2014-12-01

Lynch syndrome (LS) patients have DNA mismatch repair deficiency and up to 80% lifetime risk of colorectal cancer (CRC). Screening of mutation carriers reduces CRC incidence and mortality. Selection for constitutional mutation testing relies on family history (Amsterdam and Bethesda Guidelines) and tumour-derived biomarkers. Initial biomarker analysis uses mismatch repair protein immunohistochemistry and microsatellite instability. Abnormalities in either identify mismatch repair deficiency but do not differentiate sporadic epigenetic defects, due to MLH1 promoter region methylation (13% of CRCs) from LS (4% of CRCs). A diagnostic biomarker capable of making this distinction would be valuable. This study compared two biomarkers in tumours with mismatch repair deficiency; quantification of methylation of the MLH1 promoter region using a novel assay and BRAF c.1799T>A, p.(Val600Glu) mutation status in the identification of constitutional mutations. Tumour DNA was extracted (formalin fixed, paraffin embedded, FFPE tissue) and pyrosequencing used to test for MLH1 promoter methylation and presence of the BRAF c.1799T>A, p.(Val600Glu) mutation 71 CRCs from individuals with pathogenic MLH1 mutations and 73 CRCs with sporadic MLH1 loss. Specificity and sensitivity was compared. Unmethylated MLH1 promoter: sensitivity 94.4% (95% CI 86.2% to 98.4%), specificity 87.7% (95% CI 77.9% to 94.2%), Wild-type BRAF (codon 600): sensitivity 65.8% (95% CI 53.7% to 76.5%), specificity 98.6% (95% CI 92.4% to 100.0%) for the identification of those with pathogenic MLH1 mutations. Quantitative MLH1 promoter region methylation using pyrosequencing is superior to BRAF codon 600 mutation status in identifying constitutional mutations in mismatch repair deficient tumours. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

MutLα Heterodimers Modify the Molecular Phenotype of Friedreich Ataxia

PubMed Central

Ezzatizadeh, Vahid; Sandi, Chiranjeevi; Sandi, Madhavi; Anjomani-Virmouni, Sara; Al-Mahdawi, Sahar; Pook, Mark A.

2014-01-01

Background Friedreich ataxia (FRDA), the most common autosomal recessive ataxia disorder, is caused by a dynamic GAA repeat expansion mutation within intron 1 of FXN gene, resulting in down-regulation of frataxin expression. Studies of cell and mouse models have revealed a role for the mismatch repair (MMR) MutS-heterodimer complexes and the PMS2 component of the MutLα complex in the dynamics of intergenerational and somatic GAA repeat expansions: MSH2, MSH3 and MSH6 promote GAA repeat expansions, while PMS2 inhibits GAA repeat expansions. Methodology/Principal Findings To determine the potential role of the other component of the MutLα complex, MLH1, in GAA repeat instability in FRDA, we have analyzed intergenerational and somatic GAA repeat expansions from FXN transgenic mice that have been crossed with Mlh1 deficient mice. We find that loss of Mlh1 activity reduces both intergenerational and somatic GAA repeat expansions. However, we also find that loss of either Mlh1 or Pms2 reduces FXN transcription, suggesting different mechanisms of action for Mlh1 and Pms2 on GAA repeat expansion dynamics and regulation of FXN transcription. Conclusions/Significance Both MutLα components, PMS2 and MLH1, have now been shown to modify the molecular phenotype of FRDA. We propose that upregulation of MLH1 or PMS2 could be potential FRDA therapeutic approaches to increase FXN transcription. PMID:24971578

Epigenetic Silencing of the MLH1 Promoter in Relation to the Development of Gastric Cancer and its use as a Biomarker for Patients with Microsatellite Instability: a Systematic Analysis.

PubMed

Hu, Guimei; Qin, Lijun; Zhang, Xinjun; Ye, Guoliang; Huang, Tao

2018-01-01

Human mutL homolog 1 (MLH1) promoter methylation was reported in gastric cancer (GC). This study determined the clinicopathological, prognostic, and diagnostic effects of MLH1 promoter methylation in GC. The combined odds ratio (OR) or hazard ratio (HR) and their corresponding 95% confidence intervals (95% CI) were calculated. The pooled sensitivity, specificity, and area under the curve (AUC) were analyzed. A total of 4654 GC patients and 3669 non-malignant controls were identified in this systematic analysis. MLH1 promoter methylation was significantly higher in GC samples than in gastric adenomas, chronic gastritis, adjacent tissues, normal gastric mucosa, and normal healthy blood samples, but it exhibited a similar frequency in GC vs. intestinal metaplasia and dysplasia samples. MLH1 promoter methylation correlated with age and microsatellite instability (MSI), but it was not associated with gender, H. pylori infection, smoking, drinking behaviors, pathological histology, tumor differentiation, clinical stage, lymph node status, distant metastasis, or overall survival of GC. MLH1 promoter methylation exhibited a poor sensitivity value (< 0.5) in patients with GC compared with adjacent tissues, gastric adenomas, chronic gastritis, normal gastric mucosa, and normal healthy blood samples. The pooled sensitivity, specificity, and AUC of MLH1 promoter methylation in GC with MSI vs. GC with microsatellite stability (MSS) samples were 0.64, 0.96, and 0.90, respectively. Our results suggest that the detection of MLH1 promoter methylation may be a potential prognostic biomarker for GC patients with MSI. © 2018 The Author(s). Published by S. Karger AG, Basel.

GLI1 interferes with the DNA mismatch repair system in pancreatic cancer through BHLHE41-mediated suppression of MLH1.

PubMed

Inaguma, Shingo; Riku, Miho; Hashimoto, Mitsuyoshi; Murakami, Hideki; Saga, Shinsuke; Ikeda, Hiroshi; Kasai, Kenji

2013-12-15

The mismatch repair (MMR) system is indispensable for the fidelity of DNA replication, the impairment of which predisposes to the development and progression of many types of cancers. To date, GLI1 transcription factor, a key molecule of the Hedgehog signaling pathway, has been shown to regulate the expression of several genes crucial for a variety of cancer cell properties in many types of cancers, including pancreatic ductal adenocarcinoma (PDAC), but whether GLI1 could control the MMR system was not known. Here, we showed that GLI1 and GLI2 indirectly suppressed the expression of MLH1 in PDAC cells. Through GLI1 target gene screening, we found that GLI1 and GLI2 activated the expression of a basic helix-loop-helix type suppressor BHLHE41/DEC2/SHARP1 through a GLI-binding site in the promoter. Consistent with a previous report that BHLHE41 suppresses the MLH1 promoter activity, we found that the activation of GLI1 led to the BHLHE41-dependent suppression of MLH1, and a double knockdown of GLI1 and GLI2 conversely increased the MLH1 protein in PDAC cells. Using TALEN-based modification of the MLH1 gene, we further showed that GLI1 expression was indeed associated with an increased tolerance to a methylating agent, methylnitrosourea cooperatively with a lower copy number status of MLH1. Finally, GLI1 expression was immunohistochemically related positively with BHLHE41 and inversely with MLH1 in PDAC cells and precancerous lesions of the pancreas. On the basis of these results, we propose that GLI1 depresses the MMR activity and might contribute to the development and progression of PDAC. ©2013 AACR.

Correlation of MLH1 and MGMT methylation levels between peripheral blood leukocytes and colorectal tissue DNA samples in colorectal cancer patients.

PubMed

Li, Xia; Wang, Yibaina; Zhang, Zuoming; Yao, Xiaoping; Ge, Jie; Zhao, Yashuang

2013-11-01

CpG island methylation in the promoter regions of the DNA mismatch repair gene mutator L homologue 1 ( MLH1 ) and DNA repair gene O 6 -methylguanine-DNA methyltransferase ( MGMT ) genes has been shown to occur in the leukocytes of peripheral blood and colorectal tissue. However, it is unclear whether the methylation levels in the blood leukocytes and colorectal tissue are correlated. The present study analyzed and compared the levels of MGMT and MLH1 gene methylation in the leukocytes of peripheral blood and colorectal tissues obtained from patients with colorectal cancer (CRC). The methylation levels of MGMT and MLH1 were examined using methylation-sensitive high-resolution melting (MS-HRM) analysis. A total of 44 patients with CRC were selected based on the MLH1 and MGMT gene methylation levels in the leukocytes of the peripheral blood. Corresponding colorectal tumor and normal tissues were obtained from each patient and the DNA methylation levels were determined. The correlation coefficients were evaluated using Spearman's rank test. Agreement was determined by generalized κ-statistics. Spearman's rank correlation coefficients (r) for the methylation levels of the MGMT and MLH1 genes in the leukocytes of the peripheral blood and normal colorectal tissue were 0.475 and 0.362, respectively (P=0.001 and 0.016, respectively). The agreement of the MGMT and MLH1 gene methylation levels in the leukocytes of the peripheral blood and normal colorectal tissue were graded as fair and poor (κ=0.299 and 0.126, respectively). The methylation levels of MGMT and MLH1 were moderately and weakly correlated between the patient-matched leukocytes and the normal colorectal tissue, respectively. Blood-derived DNA methylation measurements may not always represent the levels of normal colorectal tissue methylation.

Molecular analysis of MLH1 variants in Chinese sporadic colorectal cancer patients.

PubMed

Peng, H X; Xu, X; Yang, R; Chu, Y M; Yang, D M; Xu, Y; Zhou, F L; Ma, W Z; Zhang, X J; Guan, M; Yang, Z H; Jin, Z D

2016-04-26

Single nucleotide polymorphisms (SNPs) in mismatch repair genes, especially in the MLH1 gene, are closely associated with susceptibility to hereditary nonpolyposis colorectal cancer. However, few relevant findings are available regarding the association between sporadic colorectal cancer (SCRC) and SNPs of MLH1 in Chinese patients. Therefore, the present study aimed to describe the pathogenic association between three important MLH1 polymorphisms and SCRC in the Chinese population. Peripheral blood samples from 156 SCRC patients and 311 healthy controls were collected. DNA was purified from peripheral blood, and the V384D, R217C, and I219V polymorphisms were evaluated using high-resolution melting analysis and direct sequencing. The association between the three important MLH1 polymorphisms and clinical pathological features of the SCRC patients was analyzed. In addition, PMS2-MLH1 protein interactions were determined by co-immunoprecipitation (Co-IP) to determine the protein functional alteration induced by these SNPs. Among the three polymorphisms, V384D was significantly associated with the risk of SCRC (OR = 31.36, P < 0.0001). The allele frequencies were 4.81 and 0.16% in the SCRC group. No association was found between SCRC and R217C, or between SCRC and I219V. Moreover, the allele frequency of R217C was significantly higher in the SCRC patients younger than 60 years than in those older than 60 years. Co-IP showed that the MLH1 R217C, V384D, and I219V variants had relative binding abilities with PMS2 of 0.59, 0.70, and 0.80, respectively, compared with the wild-type. These findings suggest that MLH1 V384D could be a promising genetic marker for susceptibility to SCRC.

Quantitative high resolution mapping of HvMLH3 foci in barley pachytene nuclei reveals a strong distal bias and weak interference

PubMed Central

Phillips, Dylan; Wnetrzak, Joanna; Nibau, Candida; Barakate, Abdellah; Ramsay, Luke; Wright, Frank; Higgins, James D.; Perry, Ruth M.; Jenkins, Glyn

2013-01-01

In barley (Hordeum vulgare L.), chiasmata (the physical sites of genetic crossovers) are skewed towards the distal ends of chromosomes, effectively consigning a large proportion of genes to recombination coldspots. This has the effect of limiting potential genetic variability, and of reducing the efficiency of map-based cloning and breeding approaches for this crop. Shifting the sites of recombination to more proximal chromosome regions by forward and reverse genetic means may be profitable in terms of realizing the genetic potential of the species, but is predicated upon a better understanding of the mechanisms governing the sites of these events, and upon the ability to recognize real changes in recombination patterns. The barley MutL Homologue (HvMLH3), a marker for class I interfering crossovers, has been isolated and a specific antibody has been raised. Immunolocalization of HvMLH3 along with the synaptonemal complex transverse filament protein ZYP1, used in conjunction with fluorescence in situ hybridization (FISH) tagging of specific barley chromosomes, has enabled access to the physical recombination landscape of the barley cultivars Morex and Bowman. Consistent distal localization of HvMLH3 foci throughout the genome, and similar patterns of HvMLH3 foci within bivalents 2H and 3H have been observed. A difference in total numbers of HvMLH3 foci between these two cultivars has been quantified, which is interpreted as representing genotypic variation in class I crossover frequency. Discrepancies between the frequencies of HvMLH3 foci and crossover frequencies derived from linkage analysis point to the existence of at least two crossover pathways in barley. It is also shown that interference of HvMLH3 foci is relatively weak compared with other plant species. PMID:23554258

Lynch syndrome: the influence of environmental factors on extracolonic cancer risk in hMLH1 c.C1528T mutation carriers and their mutation-negative sisters.

PubMed

Blokhuis, M M; Pietersen, G E; Goldberg, P A; Algar, U; Van der Merwe, L; Mbatani, N; Vorster, A A; Ramesar, R S

2010-09-01

Lynch Syndrome (LS) is a cancer susceptibility syndrome caused mostly by mutations in the mismatch repair genes, hMLH1, hMSH2 and hMSH6. Mutation carriers are at risk of colorectal and endometrial cancer and, less frequently, cancer of the ovaries, stomach, small bowel, hepatobiliary tract, ureter, renal pelvis and brain. The influence of environmental factors on extracolonic cancer risk in LS patients has not been investigated thus far. The aim of this study was to investigate some of these factors in South African females carrying the hMLH1 c.C1528T mutation and their mutation-negative relatives. Data were collected from 87 mutation-positive females and 121 mutation-negative female relatives regarding age, cancer history, hormonal contraceptive use, parity, duration of breast feeding, height, weight and age at first birth, last birth, menarche and menopause. Influence of these factors on cancer risk was analysed by mixed-effects generalised linear models. Extracolonic cancer occurred in 14% (12/87) of mutation-positive females versus 7% (8/121) of mutation-negative females, (P = 0.0279, adjusted for age and relatedness between women). Breast cancer was the most common extracolonic cancer. An association was found for oral contraceptive use and extracolonic cancer risk in mutation-negative females only. No association was found for any of the other risk factors investigated, when adjusted for age. This might be due to the scarcity of extracolonic cancers in our data. Future knowledge on the influence of additional environmental factors on cancer risk in LS females can lead to evidence-based lifestyle advice for mutation carriers, thereby complementing the prevention strategies available today. In addition, it can contribute to an integrated model of cancer aetiology. Therefore, this study should be taken as a thrust for further research.

Human MLH1 suppresses the insertion of telomeric sequences at intra-chromosomal sites in telomerase-expressing cells

PubMed Central

Jia, Pingping; Chastain, Megan; Zou, Ying; Her, Chengtao

2017-01-01

Abstract Aberrant formation of interstitial telomeric sequences (ITSs) promotes genome instabilities. However, it is unclear how aberrant ITS formation is suppressed in human cells. Here, we report that MLH1, a key protein involved in mismatch repair (MMR), suppresses telomeric sequence insertion (TSI) at intra-chromosomal regions. The frequency of TSI can be elevated by double-strand break (DSB) inducer and abolished by ATM/ATR inhibition. Suppression of TSI requires MLH1 recruitment to DSBs, indicating that MLH1's role in DSB response/repair is important for suppressing TSI. Moreover, TSI requires telomerase activity but is independent of the functional status of p53 and Rb. Lastly, we show that TSI is associated with chromosome instabilities including chromosome loss, micronuclei formation and chromosome breakage that are further elevated by replication stress. Our studies uncover a novel link between MLH1, telomerase, telomere and genome stability. PMID:28180301

Reduction of MLH1 and PMS2 confers temozolomide resistance and is associated with recurrence of glioblastoma

PubMed Central

Shinsato, Yoshinari; Furukawa, Tatsuhiko; Yunoue, Shunji; Yonezawa, Hajime; Minami, Kentarou; Nishizawa, Yukihiko; Ikeda, Ryuji; Kawahara, Kohichi; Yamamoto, Masatatsu; Hirano, Hirofumi; Tokimura, Hiroshi; Arita, Kazunori

2013-01-01

Although there is a relationship between DNA repair deficiency and temozolomide (TMZ) resistance in glioblastoma (GBM), it remains unclear which molecule is associated with GBM recurrence. We isolated three TMZ-resistant human GBM cell lines and examined the expression of O6-methylguanine-DNA methyltransferase (MGMT) and mismatch repair (MMR) components. We used immunohistochemical analysis to compare MutL homolog 1 (MLH1), postmeiotic segregation increased 2 (PMS2) and MGMT expression in primary and recurrent GBM specimens obtained from GBM patients during TMZ treatment. We found a reduction in MLH1 expression and a subsequent reduction in PMS2 protein levels in TMZ-resistant cells. Furthermore, MLH1 or PMS2 knockdown confered TMZ resistance. In recurrent GBM tumours, the expression of MLH1 and PMS2 was reduced when compared to primary tumours. PMID:24259277

Reduction of MLH1 and PMS2 confers temozolomide resistance and is associated with recurrence of glioblastoma.

PubMed

Shinsato, Yoshinari; Furukawa, Tatsuhiko; Yunoue, Shunji; Yonezawa, Hajime; Minami, Kentarou; Nishizawa, Yukihiko; Ikeda, Ryuji; Kawahara, Kohichi; Yamamoto, Masatatsu; Hirano, Hirofumi; Tokimura, Hiroshi; Arita, Kazunori

2013-12-01

Although there is a relationship between DNA repair deficiency and temozolomide (TMZ) resistance in glioblastoma (GBM), it remains unclear which molecule is associated with GBM recurrence. We isolated three TMZ-resistant human GBM cell lines and examined the expression of O6-methylguanine-DNA methyltransferase (MGMT) and mismatch repair (MMR) components. We used immunohistochemical analysis to compare MutL homolog 1 (MLH1), postmeiotic segregation increased 2 (PMS2) and MGMT expression in primary and recurrent GBM specimens obtained from GBM patients during TMZ treatment. We found a reduction in MLH1 expression and a subsequent reduction in PMS2 protein levels in TMZ-resistant cells. Furthermore, MLH1 or PMS2 knockdown confered TMZ resistance. In recurrent GBM tumours, the expression of MLH1 and PMS2 was reduced when compared to primary tumours.

A novel deletion in the splice donor site of MLH1 exon 6 in a Japanese colon cancer patient with Lynch syndrome.

PubMed

Yamaguchi, Junya; Sato, Yuri; Kita, Mizuho; Nomura, Sachio; Yamamoto, Noriko; Kato, Yo; Ishikawa, Yuichi; Arai, Masami

2015-10-01

Lynch syndrome is an autosomal dominantly inherited disease that is characterized by a predisposition to cancers, mainly colorectal cancer. Germline mutations of DNA mismatch repair genes such as MLH1, MSH2, MSH6 and PMS2 have been described in patients with Lynch syndrome. Here, we report deletion of 2 bp in the splice donor site of the MLH1 exon 6 (c.545+4_545+5delCA) in a 48-year-old Japanese woman with Lynch syndrome. RT-PCR direct sequencing analysis revealed that this mutation led to an increase in the level of an MLH1 transcript in which exon 6 was skipped, and may cause a frameshift (p.E153FfsX8). Therefore, this mutation appears to be pathogenic and is responsible for Lynch syndrome. Additionally, analysis of the patient's tumor cells indicated microsatellite instability high phenotype and loss of the MLH1 and PMS2 proteins. To our knowledge, this is a germline splice site mutation of MLH1 that has not been reported previously. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Promoter hypermethylation of CDKN2A, MGMT, MLH1, and DAPK genes in laryngeal squamous cell carcinoma and their associations with clinical profiles of the patients.

PubMed

Pierini, Stefano; Jordanov, Stanislav H; Mitkova, Atanaska V; Chalakov, Ivan J; Melnicharov, Mincho B; Kunev, Kuncho V; Mitev, Vanio I; Kaneva, Radka P; Goranova, Teodora E

2014-08-01

Laryngeal squamous cell carcinoma (laryngeal SCC) is a frequently occurring cancer of the head and neck area. Epigenetic changes of tumor-related genes contribute to its genesis and progression. We assessed promoter methylation status of the selected genes (CDKN2A, MGMT, MLH1, and DAPK) using methylation-sensitive high resolution melting (MS-HRM) in 100 patients with laryngeal SCC and studied the correlations with clinical characteristics. The prevalence of promoter methylation in MGMT, CDKN2A, MLH1, and DAPK was 59 of 97 (60.8%), 46 of 97 (47.4%), 45 of 97 (46.4%), and 41 of 97 patients (42.3%), respectively. Significantly increased methylation of CDKN2A was observed in heavy smokers. Epigenetic inactivation of CDKN2A and MLH1 were found to be associated with lymph node involvement. An inverse correlation was present between MLH1 methylation and alcohol consumption. Our results strongly suggest that deregulation of p16-associated, and MLH1-associated pathways, because of promoter hypermethylation, is associated with increased cancer cell migration, tumor invasiveness, and, thus, aggressive phenotype. Copyright © 2013 Wiley Periodicals, Inc.

Excess of extracolonic non-endometrial multiple primary cancers in MSH2 germline mutation carriers over MLH1.

PubMed

Lin-Hurtubise, Kevin M; Yheulon, Christopher G; Gagliano, Ronald A; Lynch, Henry T

2013-12-01

The lynch syndrome (LS) tumor spectrum involves colorectal cancer (CRC), endometrial cancer (EC), and less frequently various extracolonic non-endometrial cancers (non-EC). The organ-specific survival rates of these patients are well defined, however, the collective survival of all-cancers combined (CRC + EC + non-EC) are unclear. Fifty-two MSH2 patients and 68 MLH1 patients were followed for a median of 6.3 years after diagnosis of first cancer, regardless of type. The proportions of CRC only, EC, non-EC, and multiple primary cancers were compared between the two genotypes. Kaplan-Meier curves were developed for survival comparisons. MSH2 patients present less frequently with only CRC (37% MSH2, 62% MLH1, P = 0.0096), manifest more multiple primary cancers (38% MSH2, 18% MLH1, P = 0.013), develop more extracolonic cancers (62% MSH2, 38% MLH1, P = 0.003), non-EC only cancers (46% MSH2, 24% MLH1, P = 0.028) and carry a greater risk for urinary tract cancer (UTC) (13.4% MSH2, 1.5% MLH1, P = 0.024). There was no difference in 10-year survival between the two groups (P = 0.4). The additional propensity for UTC in MSH2 carriers argues in favor of UTC screening in MSH2 individuals. Other types of cancer screening should be tailored to the expression history of the specific LS mutation. © 2013 Wiley Periodicals, Inc.

Single nucleotide polymorphisms of DNA mismatch repair genes MSH2 and MLH1 confer susceptibility to esophageal cancer.

PubMed

Sun, Ming-Zhong; Ju, Hui-Xiang; Zhou, Zhong-Wei; Jin, Hao; Zhu, Rong

2014-01-01

Defects in DNA mismatch repair genes like MSH2 and MLH1 confer increased risk of cancers. Here, single nucleotide polymorphisms (SNPs) in MSH2 and MLH1 were investigated for their potential contribution to the risk of esophageal cancer. This study recruited 614 participants from Affiliated Yancheng Hospital, School of Medicine, Southeast University, of which 289 were patients with esophageal cancer, and the remainder was healthy individuals who served as a control group. Two SNPs, MSH2 c.2063T>G and MLH1 IVS14-19A>G, were genotyped using PCR-RFLP. Statistical analysis was performed using chi-square test and logistic regression analysis. Carriers of the MSH2 c.2063G allele were at significantly higher risk for esophageal cancer compared to individuals with the TT genotype [OR = 3.36, 95% confidence interval (CI): 1.18-11.03]. The MLH1 IVS14-19A>G allele also conferred significantly increased (1.70-fold) for esophageal cancer compared to the AA genotype (OR = 1.70, 95% CI: 1.13-5.06). Further, the variant alleles interacted such that individuals with the susceptible genotypes at both MSH2 and MLH1 had a significantly exacerbated risk for esophageal cancer (OR = 12.38, 95% CI: 3.09-63.11). In brief, SNPs in the DNA mismatch repair genes MSH2 and MLH1 increase the risk of esophageal cancer. Molecular investigations are needed to uncover the mechanism behind their interaction effect.

MLH1 V384D polymorphism associates with poor response to EGFR tyrosine kinase inhibitors in patients with EGFR L858R-positive lung adenocarcinoma.

PubMed

Chiu, Chao-Hua; Ho, Hsiang-Ling; Doong, Howard; Yeh, Yi-Chen; Chen, Mei-Yu; Chou, Teh-Ying; Tsai, Chun-Ming

2015-04-10

A significant fraction of patients with lung adenocarcinomas harboring activating epidermal growth factor receptor (EGFR) mutations do not experience clinical benefits from EGFR tyrosine kinase inhibitor (TKI) therapy. Using next-generation sequencing, we screened 739 mutation hotspots in 46 cancer-related genes in EGFR L858R-mutant lung adenocarcinomas from 29 patients who received EGFR-TKI therapy; 13 had short (< 3 months) and 16 had long (> 1 year) progression-free survival (PFS). We discovered MLH1 V384D as a genetic variant enriched in the group of patients with short PFS. Next, we investigated this genetic variation in 158 lung adenocarcinomas with the EGFR L858R mutation and found 14 (8.9%) patients had MLH1 V384D; available blood or non-tumor tissues from patients were also tested positive for MLH1 V384D. Patients with MLH1 V384D had a significantly shorter median PFS than those without (5.1 vs. 10.6 months; P= 0.001). Multivariate analysis showed that MLH1 V384D polymorphism was an independent predictor for a reduced PFS time (hazard ratio, 3.5; 95% confidence interval, 1.7 to 7.2; P= 0.001). In conclusion, MLH1 V384D polymorphism is associated with primary resistance to EGFR-TKIs in patients with EGFR L858R-positive lung adenocarcinoma and may potentially be a novel biomarker to guide treatment decisions.

Spatiotemporal Variability in Observations of Urban Mixed-Layer Heights from Surface-based Lidar Systems during DISCOVER-AQ 2011

NASA Astrophysics Data System (ADS)

Lewis, J. R.; Banks, R. F.; Berkoff, T.; Welton, E. J.; Joseph, E.; Thompson, A. M.; Decola, P.; Hegarty, J. D.

2015-12-01

Accurate characterization of the planetary boundary layer height is crucial for numerical weather prediction, estimating pollution emissions and modeling air quality. More so, given the increasing trend in global urban populations, there is a growing need to improve our understanding of the urban boundary layer structure and development. The Deriving Information on Surface conditions from COlumn and VERtically resolved observations relevant to Air Quality (DISCOVER-AQ) 2011 field campaign, which took place in the Baltimore-Washington DC region, offered a unique opportunity to study boundary layer processes in an urban area using a geographically dense collection of surface-based lidar systems (see figure). Lidars use aerosols as tracers for atmospheric boundary layer dynamics with high vertical and temporal resolutions. In this study, we use data from two permanent Micropulse Lidar Network (MPLNET) sites and five field deployed Micropulse lidar (MPL) systems in order to observe spatiotemporal variations in the daytime mixed layer height. We present and compare lidar-derived retrievals of the mixed layer height using two different methods. The first method uses the wavelet covariance transform and a "fuzzy logic" attribution scheme in order to determine the mixed layer height. The second method uses an objective approach utilizing a time-adaptive extended Kalman filter. Independent measurements of the boundary layer height are obtained using profiles from ozonesonde launches at the Beltsville and Edgewood sites for comparison with lidar observations.

The silent mutation MLH1 c.543C>T resulting in aberrant splicing can cause Lynch syndrome: a case report.

PubMed

Yamaguchi, Tatsuro; Wakatsuki, Tomokazu; Kikuchi, Mari; Horiguchi, Shin-Ichiro; Akagi, Kiwamu

2017-06-01

The proband was a 67-year-old man with transverse and sigmoid colon cancer. Microsatellite instability analysis revealed a high frequency of microsatellite instability, and immunohistochemical staining showed the absence of both MLH1 and PMS2 proteins in the sigmoid colon cancer tissue specimens from the patient. DNA sequencing revealed a nucleotide substitution c.543C>T in MLH1, but this variant did not substitute an amino acid. The MLH1 c.543C>T variant was located 3 bases upstream from the end of exon 6 and created a new splice donor site 4 bases upstream from the end of exon 6. Consequently, the last 4 bases of exon 6 were deleted and frameshift occurred. Thus, the MLH1 c.543C>T silent mutation is considered 'pathogenic'. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Pediatric renal cell carcinomas with Xp11.2 rearrangements are immunoreactive for hMLH1 and hMSH2 proteins.

PubMed

Rakheja, Dinesh; Kapur, Payal; Tomlinson, Gail E; Margraf, Linda R

2005-01-01

Alveolar soft part sarcoma and pediatric renal cell carcinoma share a similar chromosomal abnormality, t(X;17)(p11.2;q25). Recently, it has been suggested that the inactivation of DNA mismatch repair genes hMLH1 and hMSH2 may play an additional role in the pathogenesis of alveolar soft part sarcoma. Immunohistochemical expression of the proteins hMLH1 and hMSH2 is indicative of the activation status of the corresponding genes. We performed immunohistochemistry for hMLH1 and hMSH2 in 4 cases of pediatric renal cell carcinomas with Xp11.2 rearrangements. All cases showed nuclear immunoreactivity for both proteins, although the staining was patchy. Our study demonstrates that inactivation of the DNA mismatch repair genes hMLH1 and hMSH2 does not appear to play a role in the tumorigenesis of pediatric renal cell carcinomas with Xp11.2 rearrangements.

Quest: A New Approach to Molecular Staging of Tumors

DTIC Science & Technology

2004-08-01

121). Germline heterozygous inactivating mutations in MLH1 cause inefficient DNA mismatch repair, with the consequent increase in mutation frequency and... MLH1 heterozygous first cousins each produced two children with NFI disease and hematological malignancies (120, 121). The parents had no signs of NFl...Ozdag, H., Tuncer, M., Gurgey, A., Uzunalimoglu, 0., Cetinkaya, H., Tanyeli, A., Erken, E., Ozturk, M. Human MLH1 deficiency predisposes to hematological

Nuclear import of human MLH1, PMS2, and MutLalpha: redundancy is the key.

PubMed

Leong, Vivian; Lorenowicz, Jessica; Kozij, Natalie; Guarné, Alba

2009-08-01

DNA mismatch repair maintains genomic stability by correcting errors that have escaped polymerase proofreading. Defects on mismatch repair genes lead to an increased mutation rate, microsatellite instability and predisposition to human non-polyposis colorectal cancer (HNPCC). Human MutLalpha is a heterodimer formed by the interaction of MLH1 and PMS2 that coordinates a series of key events in mismatch repair. It has been proposed that nuclear import of MutLalpha may be the first regulatory step on the activation of the mismatch repair pathway. Using confocal microscopy and mismatch repair deficient cells, we have identified the sequence determinants that drive nuclear import of human MLH1, PMS2, and MutLalpha. Transient transfection of the individual proteins reveals that MLH1 has a bipartite and PMS2 has a single monopartite nuclear localization signal. Although dimerization is not required for nuclear localization, the MutLalpha heterodimer is imported more efficiently than the MLH1 or PMS2 monomers. Interestingly, the bipartite localization signal of MLH1 can direct import of MutLalpha even when PMS2 encompasses a mutated localization signal. Hence we conclude that the presence of redundant nuclear localization signals guarantees nuclear transport of MutLalpha and, consequently, efficient mismatch repair.

Retrieving the Height of Smoke and Dust Aerosols by Synergistic Use of VIIRS, OMPS, and CALIOP Observations

NASA Technical Reports Server (NTRS)

Lee, Jaehwa; Hsu, N. Christina; Bettenhausen, Corey; Sayer, Andrew M.; Seftor, Colin J.; Jeong, Myeong-Jae

2015-01-01

Aerosol Single scattering albedo and Height Estimation (ASHE) algorithm was first introduced in Jeong and Hsu (2008) to provide aerosol layer height as well as single scattering albedo (SSA) for biomass burning smoke aerosols. One of the advantages of this algorithm was that the aerosol layer height can be retrieved over broad areas, which had not been available from lidar observations only. The algorithm utilized aerosol properties from three different satellite sensors, i.e., aerosol optical depth (AOD) and Ångström exponent (AE) from Moderate Resolution Imaging Spectroradiometer (MODIS), UV aerosol index (UVAI) from Ozone Monitoring Instrument (OMI), and aerosol layer height from Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP). Here, we extend the application of the algorithm to Visible Infrared Imaging Radiometer Suite (VIIRS) and Ozone Mapping and Profiler Suite (OMPS) data. We also now include dust layers as well as smoke. Other updates include improvements in retrieving the AOD of nonspherical dust from VIIRS, better determination of the aerosol layer height from CALIOP, and more realistic input aerosol profiles in the forward model for better accuracy.

An Investigation of Instantaneous Plume Rise from Rocket Exhaust

DTIC Science & Technology

1996-12-01

METERS) TOP = 2973.48 BASE= 210.62 SIGMAR (AZ) AT THE SURFACE (DEGREES) 13.5054 SIGMER(EL) AT THE SURFACE (DEGREES) 2.9738 MET. WIND WIND LAYER WIND SPEED...SELECTED LAYER HEIGHT- (METERS) TOP = 2973.48 BASE= 210.62 SIGMAR (AZ) AT THE SURFACE (DEGREES) 13.6911 SIGMER(EL) AT THE SURFACE (DEGREES) 2.9738 MET...TIME (SECS) 368.08 FIRST MIXING LAYER HEIGHT- (METERS) TOP = 210.62 BASE= 0.00 SECOND SELECTED LAYER HEIGHT- (METERS) TOP = 2973.48 BASE= 210.62 SIGMAR

Immunohistochemical analysis of expression and allelotype of mismatch repair genes (hMLH1 and hMSH2) in bladder cancer

PubMed Central

Kassem, H Sh; Varley, J M; Hamam, S M; Margison, G P

2001-01-01

Mutation of human homologues of DNA mismatch repair (MMR) genes in tumours has been shown to be associated with the phenomenon of microsatellite instability (MSI). Several studies have reported the occurrence of MSI in bladder cancer, but evidence of involvement of MMR genes in the pathogenesis of this cancer is still unclear. We therefore utilized quantitative immunohistochemical (IHC) image analysis and PCR-based allelotype analysis to determine hMLH1 and hMSH2 genes alteration in a cohort of Egyptian bladder cancer samples. IHC analysis of 24 TCC and 12 SCC revealed marked- intra and intertumour heterogeneity in the levels of expression of the two MMR proteins. One TCC lost MLH1 expression and one lost MSH2, (1/24, 4%), and one SCC lost MSH2 (1/12, 8%). A large proportion of analysed tumours revealed a percentage positivity of less than 50% for MLH1 and MSH2 expression (44% and 69%, respectively). Complete loss of heterozygosity in three dinucleotide repeats lying within, or in close proximity to, hMLH1 and hMSH2 was rare (2/57, (4%) for MLH1; and 1/55, (2%) for MSH2), however allelic imbalance was detected in 11/57 (hMLH1) and 10/55 (hMSH2) at any of the informative microsatellite loci. These alterations in structure and expression of DNA MMR genes suggest their possible involvement in the tumorigenesis and/or progression of bladder cancer. © 2001 Cancer Research Campaign http://www.bjcancer.com PMID:11161395

Chronic exposure to arsenic, estrogen, and their combination causes increased growth and transformation in human prostate epithelial cells potentially by hypermethylation-mediated silencing of MLH1.

PubMed

Treas, Justin; Tyagi, Tulika; Singh, Kamaleshwar P

2013-11-01

Chronic exposure to arsenic and estrogen is associated with risk of prostate cancer, but their mechanism is not fully understood. Additionally, the carcinogenic effects of their co-exposure are not known. Therefore, the objective of this study was to evaluate the effects of chronic exposure to arsenic, estrogen, and their combination, on cell growth and transformation, and identify the mechanism behind these effects. RWPE-1 human prostate epithelial cells were chronically exposed to arsenic and estrogen alone and in combination. Cell growth was measured by cell count and cell cycle, whereas cell transformation was evaluated by colony formation assay. Gene expression was measured by quantitative real-time PCR and confirmed at protein level by Western blot analysis. MLH1 promoter methylation was determined by pyrosequencing method. Exposure to arsenic, estrogen, and their combinations increases cell growth and transformation in RWPE-1 cells. Increased expression of Cyclin D1 and Bcl2, whereas decreased expression of mismatch repair genes MSH4, MSH6, and MLH1 was also observed. Hypermethylation of MLH1 promoter further suggested the epigenetic inactivation of MLH1 expression in arsenic and estrogen treated cells. Arsenic and estrogen combination caused greater changes than their individual treatments. Findings of this study for the first time suggest that arsenic and estrogen exposures cause increased cell growth and survival potentially through epigenetic inactivation of MLH1 resulting in decreased MLH1-mediated apoptotic response, and consequently increased cellular transformation. © 2013 Wiley Periodicals, Inc.

Four novel germline mutations in the MLH1 and PMS2 mismatch repair genes in patients with hereditary nonpolyposis colorectal cancer.

PubMed

Montazer Haghighi, Mahdi; Radpour, Ramin; Aghajani, Katayoun; Zali, Narges; Molaei, Mahsa; Zali, Mohammad Reza

2009-08-01

Hereditary nonpolyposis colorectal cancer (HNPCC) is the most common cause of early onset hereditary colorectal cancer. In the majority of HNPCC families, microsatellite instability (MSI) and germline mutation in one of the DNA mismatch repair (MMR) genes are found. The entire coding sequence of MMR genes (MLH1, MLH2, MLH6, and PMS2) was analyzed using direct sequencing. Also, tumor tests were done as MSI and immunohistochemistry testing. We were able to find three novel MLH1 and one novel PMS2 germline mutations in three Iranian HNPCC patients. The first was a transversion mutation c.346A>C (T116P) and happened in the highly conserved HATPase-c region of MLH1 protein. The second was a transversion mutation c.736A>T (I246L), which caused an amino acid change of isoleucine to leucine. The third mutation (c.2145,6 delTG) was frameshift and resulted in an immature stop codon in five codons downstream. All of these three mutations were detected in the MLH1 gene. The other mutation was a transition mutation, c.676G>A (G207E), which has been found in exon six of the PMS2 gene and caused an amino acid change of glycine to glutamic acid. MSI assay revealed high instability in microsatellite for two patients and microsatellite stable for one patient. In all patients, an abnormal expression of the MMR proteins in HNPCC was related to the above novel mutations.

BRCA2, EGFR, and NTRK mutations in mismatch repair-deficient colorectal cancers with MSH2 or MLH1 mutations.

PubMed

Deihimi, Safoora; Lev, Avital; Slifker, Michael; Shagisultanova, Elena; Xu, Qifang; Jung, Kyungsuk; Vijayvergia, Namrata; Ross, Eric A; Xiu, Joanne; Swensen, Jeffrey; Gatalica, Zoran; Andrake, Mark; Dunbrack, Roland L; El-Deiry, Wafik S

2017-06-20

Deficient mismatch repair (MMR) and microsatellite instability (MSI) contribute to ~15% of colorectal cancer (CRCs). We hypothesized MSI leads to mutations in DNA repair proteins including BRCA2 and cancer drivers including EGFR. We analyzed mutations among a discovery cohort of 26 MSI-High (MSI-H) and 558 non-MSI-H CRCs profiled at Caris Life Sciences. Caris-profiled MSI-H CRCs had high mutation rates (50% vs 14% in non-MSI-H, P < 0.0001) in BRCA2. Of 1104 profiled CRCs from a second cohort (COSMIC), MSH2/MLH1-mutant CRCs showed higher mutation rates in BRCA2 compared to non-MSH2/MLH1-mutant tumors (38% vs 6%, P < 0.0000001). BRCA2 mutations in MSH2/MLH1-mutant CRCs included 75 unique mutations not known to occur in breast or pancreatic cancer per COSMIC v73. Only 5 deleterious BRCA2 mutations in CRC were previously reported in the BIC database as germ-line mutations in breast cancer. Some BRCA2 mutations were predicted to disrupt interactions with partner proteins DSS1 and RAD51. Some CRCs harbored multiple BRCA2 mutations. EGFR was mutated in 45.5% of MSH2/MLH1-mutant and 6.5% of non-MSH2/MLH1-mutant tumors (P < 0.0000001). Approximately 15% of EGFR mutations found may be actionable through TKI therapy, including N700D, G719D, T725M, T790M, and E884K. NTRK gene mutations were identified in MSH2/MLH1-mutant CRC including NTRK1 I699V, NTRK2 P716S, and NTRK3 R745L. Our findings have clinical relevance regarding therapeutic targeting of BRCA2 vulnerabilities, EGFR mutations or other identified oncogenic drivers such as NTRK in MSH2/MLH1-mutant CRCs or other tumors with mismatch repair deficiency.

Sessile serrated adenomas with dysplasia: morphological patterns and correlations with MLH1 immunohistochemistry.

PubMed

Liu, Cheng; Walker, Neal I; Leggett, Barbara A; Whitehall, Vicki Lj; Bettington, Mark L; Rosty, Christophe

2017-12-01

Sessile serrated adenomas are the precursor polyp of approximately 20% of colorectal carcinomas. Sessile serrated adenomas with dysplasia are rarely encountered and represent an intermediate step to malignant progression, frequently associated with loss of MLH1 expression. Accurate diagnosis of these lesions is important to facilitate appropriate surveillance, particularly because progression from dysplasia to carcinoma can be rapid. The current World Health Organization classification describes two main patterns of dysplasia occurring in sessile serrated adenomas, namely, serrated and conventional. However, this may not adequately reflect the spectrum of changes seen by pathologists in routine practice. Furthermore, subtle patterns of dysplasia that are nevertheless associated with loss of MLH1 expression are not encompassed in this classification. We performed a morphological analysis of 266 sessile serrated adenomas with dysplasia with concurrent MLH1 immunohistochemistry with the aims of better defining the spectrum of dysplasia occurring in these lesions and correlating dysplasia patterns with MLH1 expression. We found that dysplasia can be divided morphologically into four major patterns, comprising minimal deviation (19%), serrated (12%), adenomatous (8%) and not otherwise specified (79%) groups. Minimal deviation dysplasia is defined by minor architectural and cytological changes that typically requires loss of MLH1 immunohistochemical expression to support the diagnosis. Serrated dysplasia and adenomatous dysplasia have distinctive histological features and are less frequently associated with loss of MLH1 expression (13 and 5%, respectively). Finally, dysplasia not otherwise specified encompasses most cases and shows a diverse range of morphological changes that do not fall into the other subgroups and are frequently associated with loss of MLH1 expression (83%). This morphological classification of sessile serrated adenomas with dysplasia may represent an improvement on the current description as it correlates with the underlying mismatch repair protein status of the polyps and better highlights the range of morphologies seen by pathologists.

The mutational profile and infiltration pattern of murine MLH1-/- tumors: concurrences, disparities and cell line establishment for functional analysis.

PubMed

Maletzki, Claudia; Beyrich, Franziska; Hühns, Maja; Klar, Ernst; Linnebacher, Michael

2016-08-16

Mice lines homozygous negative for one of the four DNA mismatch repair (MMR) genes (MLH1, MSH2, PMS2, MSH6) were generated as models for MMR deficient (MMR-D) diseases. Clinically, hereditary forms of MMR-D include Lynch syndrome (characterized by a germline MMR gene defect) and constitutional MMR-D, the biallelic form. MMR-D knockout mice may be representative for both diseases. Here, we aimed at characterizing the MLH1-/- model focusing on tumor-immune microenvironment and identification of coding microsatellite mutations in lymphomas and gastrointestinal tumors (GIT).All tumors showed microsatellite instability (MSI) in non-coding mononucleotide markers. Mutational profiling of 26 coding loci in MSI+ GIT and lymphomas revealed instability in half of the microsatellites, two of them (Rfc3 and Rasal2) shared between both entities. MLH1-/- tumors of both entities displayed a similar phenotype (high CD71, FasL, PD-L1 and CTLA-4 expression). Additional immunofluorescence verified the tumors' natural immunosuppressive character (marked CD11b/CD200R infiltration). Vice versa, CD3+ T cells as well as immune checkpoints molecules were detectable, indicative for an active immune microenvironment. For functional analysis, a permanent cell line from an MLH1-/- GIT was established. The newly developed MLH1-/- A7450 cells exhibit stable in vitro growth, strong invasive potential and heterogeneous drug response. Moreover, four additional MSI target genes (Nktr1, C8a, Taf1b, and Lig4) not recognized in the primary were identified in this cell line.Summing up, molecular and immunological mechanisms of MLH1-/- driven carcinogenesis correlate well with clinical features of MMR-D. MLH1-/- knockout mice combine characteristics of Lynch syndrome and constitutional MMR-D, making them suitable models for preclinical research aiming at MMR-D related diseases.

The mutational profile and infiltration pattern of murine MLH1-/- tumors: concurrences, disparities and cell line establishment for functional analysis

PubMed Central

Hühns, Maja; Klar, Ernst; Linnebacher, Michael

2016-01-01

Mice lines homozygous negative for one of the four DNA mismatch repair (MMR) genes (MLH1, MSH2, PMS2, MSH6) were generated as models for MMR deficient (MMR-D) diseases. Clinically, hereditary forms of MMR-D include Lynch syndrome (characterized by a germline MMR gene defect) and constitutional MMR-D, the biallelic form. MMR-D knockout mice may be representative for both diseases. Here, we aimed at characterizing the MLH1-/- model focusing on tumor-immune microenvironment and identification of coding microsatellite mutations in lymphomas and gastrointestinal tumors (GIT). All tumors showed microsatellite instability (MSI) in non-coding mononucleotide markers. Mutational profiling of 26 coding loci in MSI+ GIT and lymphomas revealed instability in half of the microsatellites, two of them (Rfc3 and Rasal2) shared between both entities. MLH1-/- tumors of both entities displayed a similar phenotype (high CD71, FasL, PD-L1 and CTLA-4 expression). Additional immunofluorescence verified the tumors’ natural immunosuppressive character (marked CD11b/CD200R infiltration). Vice versa, CD3+ T cells as well as immune checkpoints molecules were detectable, indicative for an active immune microenvironment. For functional analysis, a permanent cell line from an MLH1-/- GIT was established. The newly developed MLH1-/- A7450 cells exhibit stable in vitro growth, strong invasive potential and heterogeneous drug response. Moreover, four additional MSI target genes (Nktr1, C8a, Taf1b, and Lig4) not recognized in the primary were identified in this cell line. Summing up, molecular and immunological mechanisms of MLH1-/- driven carcinogenesis correlate well with clinical features of MMR-D. MLH1-/- knockout mice combine characteristics of Lynch syndrome and constitutional MMR-D, making them suitable models for preclinical research aiming at MMR-D related diseases. PMID:27447752

Small suitability of the DLEC1, MLH1 and TUSC4 mRNA expression analysis as potential prognostic or differentiating markers for NSCLC patients in the Polish population.

PubMed

Kordiak, Jacek; Czarnecka, Karolina H; Pastuszak-Lewandoska, Dorota; Antczak, Adam; Migdalska-Sęk, Monika; Nawrot, Ewa; Domańska-Senderowska, Daria; Kiszałkiewicz, Justyna; Brzeziańska-Lasota, Ewa

2017-06-01

According to the latest data, lung cancer is one of the most common cancer worldwide, men contributing nearly 21.2% and women 8.6% of all diagnosed cancers. Late detection of tumour drastically reduces the chance for a cure. Thus, it is important to search for candidate biomarkers for screening of early stage nonsmall cell lung carcinoma (NSCLC). Tumour suppressor genes, DLEC1, TUSC4 and MLH1, localized on 3p21 are recognized to play a role in NSCLC carcinogenesis. The aim of this study was to assess the relationship between the DLEC1, TUSC4 and MLH1 mRNA expression, and clinical features of NSCLC patients, tobacco addiction, and tumour histopathological characteristics. The DLEC1, TUSC4 and MLH1 expression was analysed in lung tumour tissue samples obtained from 69 patients diagnosed with NSCLC: squamous cell carcinoma (n = 34), adenocarcinoma (n = 24), large cell carcinoma (n = 5), carcinoma adenosquamosum (n = 5). A decreased gene expression (RQ < 0.7) was observed for DLEC1 in 60.9% of tumour samples, for MLH1 in 50.7% and for TUSC4 in 26% of NSCLC samples. DLEC1 was decreased in more aggressive subtypes: large cell carcinoma and adenocarcinoma-squamous cell carcinoma. The simultaneous downregulation of two of the studied genes, DLEC1 andMLH1,was observed in 30.4% of NSCLCsamples, highlighting the importance of these two genes in lung carcinogenesis. We found no correlation between the DLEC1, TUSC4 and MLH1 gene expression and NSCLC patient characteristics (gender, age and smoking) or cancer histopathology. No significant differences in the gene expression among NSCLC subtypes indicate the weakness of DLEC1, TUSC4 and MLH1 expression analysis as potential differentiating markers of NSCLC subtypes in the Polish population.

Retrieving the Height of Smoke and Dust Aerosols by Synergistic Use of Multiple Satellite Sensors

NASA Technical Reports Server (NTRS)

Lee, Jaehwa; Hsu, N. Christina; Bettenhausen, Corey; Sayer, Andrew M.; Seftor, Colin J.; Jeong, Myeong-Jae

2016-01-01

The Aerosol Single scattering albedo and Height Estimation (ASHE) algorithm was first introduced in Jeong and Hsu (2008) to provide aerosol layer height and single scattering albedo (SSA) for biomass burning smoke aerosols. By using multiple satellite sensors synergistically, ASHE can provide the height information over much broader areas than lidar observations alone. The complete ASHE algorithm uses aerosol data from MODIS or VIIRS, OMI or OMPS, and CALIOP. A simplified algorithm also exists that does not require CALIOP data as long as the SSA of the aerosol layer is provided by another source. Several updates have recently been made: inclusion of dust layers in the retrieval process, better determination of the input aerosol layer height from CALIOP, improvement in aerosol optical depth (AOD) for nonspherical dust, development of quality assurance (QA) procedure, etc.

Hypoxia in Invasion and Metastasis

DTIC Science & Technology

2007-08-01

hypoxia and activating HIF-1 downregulate the DNA mismatch repair proteins ( mlh1 and/or msh2), a group of important proteins for maintaining genetic...Investigate the hypoxia and activating HIF-1 downregulate the DNA mismatch repair proteins ( mlh1 and/or msh2) (Month 7-12) Methods: We performed a parallel...inducible factors from invasive tumor cells. Changes in the level of multiple hypoxia related factor (HIF-1) and DNA mismatch repair proteins ( MLH1 , MSH2

Passive remote sensing of aerosol layer height using near-UV multiangle polarization measurements

NASA Astrophysics Data System (ADS)

Wu, Lianghai; Hasekamp, Otto; van Diedenhoven, Bastiaan; Cairns, Brian; Yorks, John E.; Chowdhary, Jacek

2016-08-01

We demonstrate that multiangle polarization measurements in the near-UV and blue part of the spectrum are very well suited for passive remote sensing of aerosol layer height. For this purpose we use simulated measurements with different setups (different wavelength ranges, with and without polarization, different polarimetric accuracies) as well as airborne measurements from the Research Scanning Polarimeter (RSP) obtained over the continental USA. We find good agreement of the retrieved aerosol layer height from RSP with measurements from the Cloud Physics Lidar showing a mean absolute difference of less than 1 km. Furthermore, we found that the information on aerosol layer height is provided for large part by the multiangle polarization measurements with high accuracy rather than the multiangle intensity measurements. The information on aerosol layer height is significantly decreased when the shortest RSP wavelength (410 nm) is excluded from the retrieval and is virtually absent when 550 nm is used as shortest wavelength.

Effect of an isolated semi-arid pine forest on the boundary layer height

NASA Astrophysics Data System (ADS)

Brugger, Peter; Banerjee, Tirtha; Kröniger, Konstantin; Preisler, Yakir; Rotenberg, Eyal; Tatarinov, Fedor; Yakir, Dan; Mauder, Matthias

2017-04-01

Forests play an important role for earth's climate by influencing the surface energy balance and CO2 concentrations in the atmosphere. Semi-arid forests and their effects on the local and regional climate are studied within the CliFF project (Climate Feedbacks and benefits of semi-arid Forests). This requires understanding of the atmospheric boundary layer over semi-arid forests, because it links the surface and the free atmosphere and determines the exchange of momentum, heat and trace gases. Our study site, Yatir, is a semi-arid isolated pine forest in the Negev desert in Israel. Higher roughness and lower albedo compared to the surrounding shrubland make it interesting to study the influences of the semi-arid Yatir forest on the boundary layer. Previous studies of the forest focused on the energy balance and secondary circulations. This study focuses on the boundary layer structure above the forest, in particular the boundary layer height. The boundary layer height is an essential parameter for many applications (e.g. construction of convective scaling parameters or air pollution modeling). We measured the boundary layer height upwind, over and downwind of the forest. In addition we measured at two sites wind profiles within the boundary layer and turbulent fluxes at the surface. This allows us to quantify the effects of the forest on boundary layer compared to the surrounding shrubland. Results show that the forest increases the boundary layer height in absence of a strong boundary layer top inversion. A model of the boundary layer height based on eddy-covariance data shows some agreement to the measurements, but fails during anticyclonic conditions and the transition to the nocturnal boundary layer. More complex models accounting for large scale influences are investigated. Further influences of the forest and surrounding shrubland on the turbulent transport of energy are discussed in a companion presentation (EGU2017-2219).

The dynamic DNA methylation landscape of the mutL homolog 1 shore is altered by MLH1-93G>A polymorphism in normal tissues and colorectal cancer.

PubMed

Savio, Andrea J; Mrkonjic, Miralem; Lemire, Mathieu; Gallinger, Steven; Knight, Julia A; Bapat, Bharat

2017-01-01

Colorectal cancers (CRCs) undergo distinct genetic and epigenetic alterations. Expression of mutL homolog 1 ( MLH1 ), a mismatch repair gene that corrects DNA replication errors, is lost in up to 15% of sporadic tumours due to mutation or, more commonly, due to DNA methylation of its promoter CpG island. A single nucleotide polymorphism (SNP) in the CpG island of MLH1 ( MLH1 -93G>A or rs1800734) is associated with CpG island hypermethylation and decreased MLH1 expression in CRC tumours. Further, in peripheral blood mononuclear cell (PBMC) DNA of both CRC cases and non-cancer controls, the variant allele of rs1800734 is associated with hypomethylation at the MLH1 shore, a region upstream of its CpG island that is less dense in CpG sites . To determine whether this genotype-epigenotype association is present in other tissue types, including colorectal tumours, we assessed DNA methylation in matched normal colorectal tissue, tumour, and PBMC DNA from 349 population-based CRC cases recruited from the Ontario Familial Colorectal Cancer Registry. Using the semi-quantitative real-time PCR-based MethyLight assay, MLH1 shore methylation was significantly higher in tumour tissue than normal colon or PBMCs ( P  < 0.01). When shore methylation levels were stratified by SNP genotype, normal colorectal DNA and PBMC DNA were significantly hypomethylated in association with variant SNP genotype ( P  < 0.05). However, this association was lost in tumour DNA. Among distinct stages of CRC, metastatic stage IV CRC tumours incurred significant hypomethylation compared to stage I-III cases, irrespective of genotype status. Shore methylation of MLH1 was not associated with MSI status or promoter CpG island hypermethylation, regardless of genotype. To confirm these results, bisulfite sequencing was performed in matched tumour and normal colorectal specimens from six CRC cases, including two cases per genotype (wildtype, heterozygous, and homozygous variant). Bisulfite sequencing results corroborated the methylation patterns found by MethyLight, with significant hypomethylation in normal colorectal tissue of variant SNP allele carriers. These results indicate that the normal tissue types tested (colorectum and PBMC) experience dynamic genotype-associated epigenetic alterations at the MLH1 shore, whereas tumour DNA incurs aberrant hypermethylation compared to normal DNA.

MGMT and MLH1 methylation in Helicobacter pylori-infected children and adults.

PubMed

Alvarez, Marisa C; Santos, Juliana C; Maniezzo, Nathália; Ladeira, Marcelo S; da Silva, Artur L C; Scaletsky, Isabel C A; Pedrazzoli, José; Ribeiro, Marcelo L

2013-05-28

To evaluate the association between Helicobacter pylori (H. pylori) infection and MLH1 and MGMT methylation and its relationship with microsatellite instability (MSI). The methylation status of the MLH1 and MGMT promoter region was analysed by methylation specific methylation-polymerase chain reaction (MSP-PCR) in gastric biopsy samples from uninfected or H. pylori-infected children (n = 50), from adults with chronic gastritis (n = 97) and from adults with gastric cancer (n = 92). MLH1 and MGMT mRNA expression were measured by real-time PCR and normalised to a constitutive gene (β actin). MSI analysis was performed by screening MSI markers at 4 loci (Bat-25, Bat-26, D17S250 and D2S123) with PCR; PCR products were analysed by single strand conformation polymorphism followed by silver staining. Statistical analyses were performed with either the χ(2) test with Yates continuity correction or Fisher's exact test, and statistical significance for expression analysis was assessed using an unpaired Student's t-test. Methylation was not detected in the promoter regions of MLH1 and MGMT in gastric biopsy samples from children, regardless of H. pylori infection status. The MGMT promoter was methylated in 51% of chronic gastritis adult patients and was associated with H. pylori infection (P < 0.05); this region was methylated in 66% of gastric cancer patients, and the difference in the percentage of methylated samples between these patients and those from H. pylori-infected chronic gastritis patients was statistically significant (P < 0.05). MLH1 methylation frequencies among H. pylori-infected and non-infected chronic gastritis adult patients were 13% and 7%, respectively. We observed methylation of the MLH1 promoter (39%) and increased MSI levels (68%) in samples from gastric cancer patients in comparison to samples from H. pylori-infected adult chronic gastritis patients (P < 0.001 and P < 0.01, respectively). The frequency of promoter methylation for both genes was higher in gastric cancer samples than in H. pylori-positive chronic gastritis samples (P < 0.05). The levels of MLH1 and MGMT mRNA were significantly reduced in chronic gastritis samples that were also hypermethylated (P < 0.01). In summary, MGMT and MLH1 methylation did not occur in earlier-stage H. pylori infections and thus might depend on the duration of infection.

The importance of proper bioinformatics analysis and clinical interpretation of tumor genomic profiling: a case study of undifferentiated sarcoma and a constitutional pathogenic BRCA2 mutation and an MLH1 variant of uncertain significance.

PubMed

Varga, Elizabeth; Chao, Elizabeth C; Yeager, Nicholas D

2015-09-01

Next-generation sequencing (NGS) technology is increasingly utilized to identify therapeutic targets for patients with malignancy. This technology also has the capability to reveal the presence of constitutional genetic alterations, which may have significant implications for patients and their family members. Here we present the case of a 23 year old Caucasian patient with recurrent undifferentiated sarcoma who had NGS-based tumor analysis using an assay which simultaneously analyzed the entire coding sequence of 236 cancer-related genes (3769 exons) plus 47 introns from 19 genes often rearranged or altered in cancer. Pathogenic alterations were reported in tumor as the predicted protein alterations, BRCA2 "R645fs*15″ and MLH1 "E694*". Because constitutional BRCA2 and MLH1 gene mutations are associated with Hereditary Breast Ovarian Cancer Syndrome (HBOCS) and Lynch syndrome respectively, sequence analysis of DNA isolated from peripheral blood was performed. The presence of the alterations, BRCA2 c.1929delG and MLH1 c.2080G>T, corresponding to the previously reported predicted protein alterations, were confirmed by Sanger sequencing in the constitutional DNA. An additional DNA finding was reported in this analysis, MLH1 c.2081A>C at the neighboring nucleotide. Further evaluation of the family revealed that all alterations were paternally inherited and the two MLH1 substitutions were in cis, more appropriately referred to as MLH1 c.2080_2081delGAinsTC, which is classified as a variant of uncertain significance. This case illustrates important considerations related to appropriate interpretation of NGS tumor results and follow-up of patients with potentially deleterious constitutional alterations.

Ionizing radiation, inflammation, and their interactions in colon carcinogenesis in Mlh1-deficient mice.

PubMed

Morioka, Takamitsu; Miyoshi-Imamura, Tomoko; Blyth, Benjamin J; Kaminishi, Mutsumi; Kokubo, Toshiaki; Nishimura, Mayumi; Kito, Seiji; Tokairin, Yutaka; Tani, Shusuke; Murakami-Murofushi, Kimiko; Yoshimi, Naoki; Shimada, Yoshiya; Kakinuma, Shizuko

2015-03-01

Genetic, physiological and environmental factors are implicated in colorectal carcinogenesis. Mutations in the mutL homolog 1 (MLH1) gene, one of the DNA mismatch repair genes, are a main cause of hereditary colon cancer syndromes such as Lynch syndrome. Long-term chronic inflammation is also a key risk factor, responsible for colitis-associated colorectal cancer; radiation exposure is also known to increase colorectal cancer risk. Here, we studied the effects of radiation exposure on inflammation-induced colon carcinogenesis in DNA mismatch repair-proficient and repair-deficient mice. Male and female Mlh1(-/-) and Mlh1(+/+) mice were irradiated with 2 Gy X-rays when aged 2 weeks or 7 weeks and/or were treated with 1% dextran sodium sulfate (DSS) in drinking water for 7 days at 10 weeks old to induce mild inflammatory colitis. No colon tumors developed after X-rays and/or DSS treatment in Mlh1(+/+) mice. Colon tumors developed after DSS treatment alone in Mlh1(-/-) mice, and exposure to radiation prior to DSS treatment increased the number of tumors. Histologically, colon tumors in the mice resembled the subtype of well-to-moderately differentiated adenocarcinomas with tumor-infiltrating lymphocytes of human Lynch syndrome. Immunohistochemistry revealed that expression of both p53 and β-catenin and loss of p21 and adenomatosis polyposis coli proteins were observed at the later stages of carcinogenesis, suggesting a course of molecular pathogenesis distinct from typical sporadic or colitis-associated colon cancer in humans. In conclusion, radiation exposure could further increase the risk of colorectal carcinogenesis induced by inflammation under the conditions of Mlh1 deficiency. © 2014 The Authors. Cancer Science published by Wiley Publishing Asia Pty Ltd on behalf of Japanese Cancer Association.

Cancer-Predicting Gene Expression Changes in Colonic Mucosa of Western Diet Fed Mlh1 +/- Mice

PubMed Central

Dermadi Bebek, Denis; Valo, Satu; Reyhani, Nima; Ollila, Saara; Päivärinta, Essi; Peltomäki, Päivi; Mutanen, Marja; Nyström, Minna

2013-01-01

Colorectal cancer (CRC) is the second most common cause of cancer-related deaths in the Western world and interactions between genetic and environmental factors, including diet, are suggested to play a critical role in its etiology. We conducted a long-term feeding experiment in the mouse to address gene expression and methylation changes arising in histologically normal colonic mucosa as putative cancer-predisposing events available for early detection. The expression of 94 growth-regulatory genes previously linked to human CRC was studied at two time points (5 weeks and 12 months of age) in the heterozygote Mlh1 +/- mice, an animal model for human Lynch syndrome (LS), and wild type Mlh1 +/+ littermates, fed by either Western-style (WD) or AIN-93G control diet. In mice fed with WD, proximal colon mucosa, the predominant site of cancer formation in LS, exhibited a significant expression decrease in tumor suppressor genes, Dkk1, Hoxd1, Slc5a8, and Socs1, the latter two only in the Mlh1 +/- mice. Reduced mRNA expression was accompanied by increased promoter methylation of the respective genes. The strongest expression decrease (7.3 fold) together with a significant increase in its promoter methylation was seen in Dkk1, an antagonist of the canonical Wnt signaling pathway. Furthermore, the inactivation of Dkk1 seems to predispose to neoplasias in the proximal colon. This and the fact that Mlh1 which showed only modest methylation was still expressed in both Mlh1 +/- and Mlh1 +/+ mice indicate that the expression decreases and the inactivation of Dkk1 in particular is a prominent early marker for colon oncogenesis. PMID:24204690

Ionizing radiation, inflammation, and their interactions in colon carcinogenesis in Mlh1-deficient mice

PubMed Central

Morioka, Takamitsu; Miyoshi-Imamura, Tomoko; Blyth, Benjamin J; Kaminishi, Mutsumi; Kokubo, Toshiaki; Nishimura, Mayumi; Kito, Seiji; Tokairin, Yutaka; Tani, Shusuke; Murakami-Murofushi, Kimiko; Yoshimi, Naoki; Shimada, Yoshiya; Kakinuma, Shizuko

2015-01-01

Genetic, physiological and environmental factors are implicated in colorectal carcinogenesis. Mutations in the mutL homolog 1 (MLH1) gene, one of the DNA mismatch repair genes, are a main cause of hereditary colon cancer syndromes such as Lynch syndrome. Long-term chronic inflammation is also a key risk factor, responsible for colitis-associated colorectal cancer; radiation exposure is also known to increase colorectal cancer risk. Here, we studied the effects of radiation exposure on inflammation-induced colon carcinogenesis in DNA mismatch repair-proficient and repair-deficient mice. Male and female Mlh1−/− and Mlh1+/+ mice were irradiated with 2 Gy X-rays when aged 2 weeks or 7 weeks and/or were treated with 1% dextran sodium sulfate (DSS) in drinking water for 7 days at 10 weeks old to induce mild inflammatory colitis. No colon tumors developed after X-rays and/or DSS treatment in Mlh1+/+ mice. Colon tumors developed after DSS treatment alone in Mlh1−/− mice, and exposure to radiation prior to DSS treatment increased the number of tumors. Histologically, colon tumors in the mice resembled the subtype of well-to-moderately differentiated adenocarcinomas with tumor-infiltrating lymphocytes of human Lynch syndrome. Immunohistochemistry revealed that expression of both p53 and β-catenin and loss of p21 and adenomatosis polyposis coli proteins were observed at the later stages of carcinogenesis, suggesting a course of molecular pathogenesis distinct from typical sporadic or colitis-associated colon cancer in humans. In conclusion, radiation exposure could further increase the risk of colorectal carcinogenesis induced by inflammation under the conditions of Mlh1 deficiency. PMID:25529563

Expression of DNA repair proteins MSH2, MLH1 and MGMT in human benign and malignant thyroid lesions: An immunohistochemical study

PubMed Central

Giaginis, Constantinos; Michailidi, Christina; Stolakis, Vasileios; Alexandrou, Paraskevi; Tsourouflis, Gerasimos; Klijanienko, Jerzy; Delladetsima, Ioanna; Theocharis, Stamatios

2011-01-01

Summary Background DNA repair is a major defense mechanism, which contributes to the maintenance of genetic sequence, and minimizes cell death, mutation rates, replication errors, DNA damage persistence and genomic instability. Alterations in the expression levels of proteins participating in DNA repair mechanisms have been associated with several aspects of cancer biology. The present study aimed to evaluate the clinical significance of DNA repair proteins MSH2, MLH1 and MGMT in benign and malignant thyroid lesions. Material/Methods MSH2, MLH1 and MGMT protein expression was assessed immunohistochemically on paraffin-embedded thyroid tissues from 90 patients with benign and malignant lesions. Results The expression levels of MLH1 was significantly upregulated in cases with malignant compared to those with benign thyroid lesions (p=0.038). The expression levels of MGMT was significantly downregulated in malignant compared to benign thyroid lesions (p=0.001). Similar associations for both MLH1 and MGMT between cases with papillary carcinoma and hyperplastic nodules were also noted (p=0.014 and p=0.026, respectively). In the subgroup of malignant thyroid lesions, MSH2 downregulation was significantly associated with larger tumor size (p=0.031), while MLH1 upregulation was significantly associated with the presence of lymphatic and vascular invasion (p=0.006 and p=0.002, respectively). Conclusions Alterations in the mismatch repair proteins MSH2 and MLH1 and the direct repair protein MGMT may result from tumor development and/or progression. Further studies are recommended to draw definite conclusions on the clinical significance of DNA repair proteins in thyroid neoplasia. PMID:21358597

Efficient molecular screening of Lynch syndrome by specific 3' promoter methylation of the MLH1 or BRAF mutation in colorectal cancer with high-frequency microsatellite instability.

PubMed

Nakagawa, Hitoshi; Nagasaka, Takeshi; Cullings, Harry M; Notohara, Kenji; Hoshijima, Naoko; Young, Joanne; Lynch, Henry T; Tanaka, Noriaki; Matsubara, Nagahide

2009-06-01

It is sometimes difficult to diagnose Lynch syndrome by the simple but strict clinical criteria, or even by the definitive genetic testing for causative germline mutation of mismatch repair genes. Thus, some practical and efficient screening strategy to select highly possible Lynch syndrome patients is exceedingly desirable. We performed a comprehensive study to evaluate the methylation status of whole MLH1 promoter region by direct bisulfite sequencing of the entire MLH1 promoter regions on Lynch and non-Lynch colorectal cancers (CRCs). Then, we established a convenient assay to detect methylation in key CpG islands responsible for the silencing of MLH1 expression. We studied the methylation status of MLH1 as well as the CpG island methylator phenotype (CIMP) and immunohistochemical analysis of mismatch repair proteins on 16 cases of Lynch CRC and 19 cases of sporadic CRCs with high-frequency microsatellite instability (MSI-H). Sensitivity to detect Lynch syndrome by MLH1 (CCAAT) methylation was 88% and the specificity was 84%. Positive likelihood ratio (PLR) was 5.5 and negative likelihood ratio (NLR) was 0.15. Sensitivity by mutational analysis of BRAF was 100%, specificity was 84%, PLR was 6.3 and NLR was zero. By CIMP analysis; sensitivity was 88%, specificity was 79%, PLR was 4.2, and NLR was 0.16. BRAF mutation or MLH1 methylation analysis combined with MSI testing could be a good alternative to screen Lynch syndrome patients in a cost effective manner. Although the assay for CIMP status also showed acceptable sensitivity and specificity, it may not be practical because of its rather complicated assay.

Universal screening for Lynch syndrome in endometrial cancers: frequency of germline mutations and identification of patients with Lynch-like syndrome.

PubMed

Dillon, Jessica L; Gonzalez, Jorge L; DeMars, Leslie; Bloch, Katarzyna J; Tafe, Laura J

2017-12-01

Lynch syndrome (LS) is an inherited clinical syndrome characterized by a high risk of colorectal, endometrial (lifetime risk of up to 60%), ovarian, and urinary tract cancers. The diagnosis is confirmed by identification of germline mutations in the DNA mismatch repair genes MLH1, PMS2, MSH2, MSH6, or EPCAM. In 2015, our institution implemented universal screening of endometrial cancer (EC) hysterectomy specimens by mismatch repair immunohistochemistry (IHC) with reflex MLH1 promoter hypermethylation analysis for tumors with loss of MLH1/PMS2 expression. Patients with tumors negative for MLH1 methylation and those with a loss of the heterodimer pair MSH2 and MSH6, or isolated loss of either PMS2 or MSH6 were referred to the Familial Cancer Program for genetic counseling and consideration of germline testing. Between May 2015 to Dec 2016, 233 EC patients were screened by IHC for LS with a median age of 63 years. Sixty tumors (27%) had abnormal IHC staining results. Fifty-one (22%) harbored heterodimeric loss of MLH1 and PMS2, 49 of which showed MLH1 promoter methylation (1 failure, 1 negative). One showed loss of MLH1/PMS2 and MSH6, 2 showed loss of MSH2/MSH6, and 6 had isolated loss of MSH6 only. Ten patients underwent genetic counseling, and germline testing was performed in 8; LS was confirmed in 5 patients (2.1%). In addition, 3 patients with negative germline testing and presumed Lynch-like syndrome were identified and offered additional somatic testing. Universal screening for LS in EC patients has yielded positive results for identification of patients at risk for this inherited syndrome. Copyright © 2017 Elsevier Inc. All rights reserved.

MSH3 protein expression and nodal status in MLH1-deficient colorectal cancers.

PubMed

Laghi, Luigi; Bianchi, Paolo; Delconte, Gabriele; Celesti, Giuseppe; Di Caro, Giuseppe; Pedroni, Monica; Chiaravalli, Anna Maria; Jung, Barbara; Capella, Carlo; de Leon, Maurizio Ponz; Malesci, Alberto

2012-06-01

Patients with colorectal cancers (CRC) and high microsatellite instability (MSI) have a better outcome than their chromosome-unstable counterpart. Given the heterogeneity of microsatellite-unstable CRCs, we wanted to see whether any MSI-associated molecular features are specifically associated with prognosis. One hundred and nine MSI-high CRCs were typed for primary mismatch repair (MMR) defect and for secondary loss of MMR proteins. Frameshifts at seven target genes, mutations in the RAS pathway, and methylation at MLH1/CDKN2A promoters were also searched. The interplay of molecular findings with clinicopathologic features and patient survival was analyzed. Of 84 MLH1-deficient CRCs, 31 (36.9%) had MSH3 and 11 (13.1%) had MSH6 loss (P < 0.001), biallelic frameshift mutations at mononucleotide repeats accounting for most (78%) MSH3 losses. As compared with MSH3-retaining cancers, MLH1-deficient tumors with MSH3 loss showed a higher number of mutated target genes (3.94 ± 1.56 vs. 2.79 ± 1.75; P = 0.001), absence of nodal involvement at pathology [N0; OR, 0.11; 95% confidence interval (CI), 0.04-0.43, P < 0.001], and better disease-free survival (P = 0.06). No prognostic value was observed for KRAS status and for MLH1/CDKN2A promoter methylation. The association between MSH3 loss and N0 was confirmed in an independent cohort of 71 MLH1-deficient CRCs (OR, 0.23; 95% CI, 0.06-0.83, P = 0.02). MLH1-deficient CRCs not expressing MSH3 have a more severe MSI, a lower rate of nodal involvement, and a better postsurgical outcome.

Analysis of hMLH1 missense mutations in East Asian patients with suspected hereditary nonpolyposis colorectal cancer.

PubMed

Fan, Yimei; Wang, Wei; Zhu, Ming; Zhou, Jiji; Peng, Jingyuan; Xu, Lizhi; Hua, Zichun; Gao, Xiang; Wang, Yaping

2007-12-15

Germ line mutations in the DNA mismatch repair gene hMLH1 are a frequent cause of hereditary nonpolyposis colorectal cancer and about one-third of these are missense mutations. Several missense mutations in hMLH1 have frequently been detected in East Asian patients with suspected hereditary nonpolyposis colorectal cancer, but their pathogenic role has not been extensively assessed. The aim of this study was to perform functional analyses of these variants and their association with gastrointestinal cancer in East Asians. Altogether, 10 hMLH1 variants were analyzed by yeast two-hybrid and coimmunoprecipitation assays. The carboxyl-terminal replacements Q542L, L549P, L574P, and P581L in hMLH1 resulted in complete loss of activity in both yeast two-hybrid and coimmunoprecipitation tests and thus might be considered as pathogenic. The amino-terminal variants S46I, G65D, G67R, and R217C did not affect complex formation with hPMS2 in coimmunoprecipitation, but partly or fully lost their activity in yeast two-hybrid assay, and we suggested that these variants might reduce the efficiency of the heterodimer to go into the nucleus and thus the mismatch repair function might be blocked or reduced. The V384D and the Q701K variant resulted in the interaction of hMLH1 with hPMS2 at reduced efficiency and might raise the gastrointestinal cancer risk of the mutation carriers. This work availably evaluated the functional consequences of some missense mutations not previously determined in the hMLH1 gene and might be useful for the clinical diagnosis of hereditary gastrointestinal cancer, especially in East Asians.

Phosphorylation-dependent signaling controls degradation of DNA mismatch repair protein PMS2.

PubMed

Hinrichsen, Inga; Weßbecher, Isabel M; Huhn, Meik; Passmann, Sandra; Zeuzem, Stefan; Plotz, Guido; Biondi, Ricardo M; Brieger, Angela

2017-12-01

MutLα, a heterodimer consisting of MLH1 and PMS2, plays an important role in DNA mismatch repair and has been shown to be additionally involved in several other important cellular mechanisms. Previous work indicated that AKT could modulate PMS2 stability by phosphorylation. Still, the mechanisms of regulation of MutLα remain unclear. The stability of MutLα subunits was investigated by transiently overexpression of wild type and mutant forms of MLH1 and PMS2 using immunoblotting for measuring the protein levels after treatment. We found that treatment with the cell-permeable serine/threonine phosphatase inhibitor, Calyculin, leads to degradation of PMS2 when MLH1 or its C-terminal domain is missing or if amino acids of MLH1 essential for PMS2 interaction are mutated. In addition, we discovered that the C-terminal tail of PMS2 is relevant for this Calyculin-dependent degradation. A direct involvement of AKT, which was previously described to be responsible for PMS2 degradation, could not be detected. The multi-kinase inhibitor Sorafenib, in contrast, was able to avoid the degradation of PMS2 which postulates that cellular phosphorylation is involved in this process. Together, we show that pharmacologically induced phosphorylation by Calyculin can induce the selective proteasome-dependent degradation of PMS2 but not of MLH1 and that the PMS2 degradation could be blocked by Sorafenib treatment. Curiously, the C-terminal Lynch Syndrome-variants MLH1 L749P and MLH1 Y750X make PMS2 prone to Calyculin induced degradation. Therefore, we conclude that the specific degradation of PMS2 may represent a new mechanism to regulate MutLα. © 2017 Wiley Periodicals, Inc.

Environmentally Induced Gene Silencing in Breast Cancer

DTIC Science & Technology

2007-07-01

fibrosarcoma cell line (HTD114), and a human breast cancer cell line (MCF7). The MLH1 promoter was only tested in the MCG7 cells. The control TRE-Luc...TRE- Luc MLH1 - Luc step in silencing is quite unstable. Nonetheless, cells that exhibit stable silencing of the HPRT construct can arise in...mechanism (i.e., gene repression). Finally, during the last year we have isolated or acquired functional promoters for the BRCA-1, MLH1 , and E

Link between immunoexpression of hMLH1 and hMSH2 proteins and clinical-epidemiological aspects of actinic cheilitis*

PubMed Central

Sarmento, Dmitry José de Santana; Godoy, Gustavo Pina; Miguel, Márcia Cristina da Costa; da Silveira, Éricka Janine Dantas

2016-01-01

Background The studies found in the literature associate the immunoexpression of hMLH1 and hMSH2 proteins with histologic aspects, but do not correlate it with clinical and epidemiological data. Objective To evaluate the immunoexpression of hMLH1 and hMSH2 in actinic cheilitis, correlating it with clinical characteristics. Methods We analyzed 40 cases. Histological and immunohistochemical analyses were performed. The following clinical variables were evaluated: gender, age range, ethnicity, clinical aspect and occupational sunlight exposure. Statistical evaluation included the Student t-test, while the significance level was set at 5%. Results Greater immunoexpression of hMLH1 and hMSH2 was observed in females, individuals aged over 40, and mixed-race/black patients. Furthermore, the immunoexpression of these proteins was greater in actinic cheilitis with a white-colored appearance and in patients without occupational sunlight exposure. No statistical differences were observed for the variables studied. Conclusion This study uncovered variations of hMLH1 and hMSH2 protein expression upon evaluation of clinical aspects in actinic cheilitis. PMID:27579741

Link between immunoexpression of hMLH1 and hMSH2 proteins and clinical-epidemiological aspects of actinic cheilitis.

PubMed

Sarmento, Dmitry José de Santana; Godoy, Gustavo Pina; Miguel, Márcia Cristina da Costa; Silveira, Éricka Janine Dantas da

2016-01-01

The studies found in the literature associate the immunoexpression of hMLH1 and hMSH2 proteins with histologic aspects, but do not correlate it with clinical and epidemiological data. To evaluate the immunoexpression of hMLH1 and hMSH2 in actinic cheilitis, correlating it with clinical characteristics. We analyzed 40 cases. Histological and immunohistochemical analyses were performed. The following clinical variables were evaluated: gender, age range, ethnicity, clinical aspect and occupational sunlight exposure. Statistical evaluation included the Student t-test, while the significance level was set at 5%. Greater immunoexpression of hMLH1 and hMSH2 was observed in females, individuals aged over 40, and mixed-race/black patients. Furthermore, the immunoexpression of these proteins was greater in actinic cheilitis with a white-colored appearance and in patients without occupational sunlight exposure. No statistical differences were observed for the variables studied. This study uncovered variations of hMLH1 and hMSH2 protein expression upon evaluation of clinical aspects in actinic cheilitis.

[Comparison of the sensibility and specificity between single-stranded conformation polymorphism and denaturing high-performance liquid chromatography in screening hMSH2 and hMLH1 gene mutations in hereditary non-polyposis colorectal cancer].

PubMed

Wei, Guang-hui; Zhao, Bo; Wang, Zhen-jun

2008-09-01

To compare the sensibility and specificity between single-stranded conformation polymorphism (SSCP) and denaturing high-performance liquid chromatography (DHPLC) in screening hMSH2 and hMLH1 gene mutations for the diagnosis of hereditary non-polyposis colorectal cancer (HNPCC). Seven Chinese HNPCC kindreds were collected. PCR-SSCP and DHPLC were used to screen the coding regions of hMSH2 and hMLH1 genes and the abnormal profiles were sequenced by a 377 DNA sequencer. Seven gene sequence variations of hMSH2 or hMLH1 were found. Among them, 4 variations were not found by SSCP, but by DHPLC. The sensibility of SSCP and DHPLC were 51.6% and 100% respectively, and the specificity were 66.6% and 93.3% respectively. DHPLC has better sensibility and specificity in screening hMSH2 and hMLH1 gene mutation as compared to SSCP. DHPLC is an ideal method in the diagnosis of HNPCC.

Predicting Breast Cancer Risk by Assaying Peripheral Blood Methylation. Addendum

DTIC Science & Technology

2007-10-01

tumor suppressor genes such as the cell cycle inhibitor p16INK4a , the DNA repair genes BRCA1, MLH1 , and MGMT , and the p53 regulator p14ARF , has been... MLH1 . Int J Cancer 2007;120:1684–8. Chong S, Youngson NA,Whitelaw E. Heritable germline epimutation is not the same as transgenerational epigenetic...hypermethylation of the MLH1 gene in normal tissue and loss of heterozygosity of the unmethylated allele in the resulting microsatellite instability-high tumor

Breast Cancer in Three Dimensions: Revealing Telomere Dysfunction in Breast Cancer

DTIC Science & Technology

2006-09-01

suppressor PTEN and the glypican 3 (GPC3) gene in patients diagnosed with Proteus syndrome . Am J Med Genet, 1: 123-7, 2004. 101. Oros KK, Ghadirian...characterization of the spectrum of genomic deletions in the mismatch repair genes MSH2, MLH1, MSH6, and PMS2 responsible for hereditary nonpolyposis colorectal...Distinct patterns of Germ-Line Deletions in MLH1 and MLH2 : the Implication of Alu Repetitive Element in the genetic etiology of Lynch Syndrome

Laboratory simulations of the atmospheric mixed-layer in flow ...

EPA Pesticide Factsheets

A laboratory study of the influence of complex terrain on the interface between a well-mixed boundary layer and an elevated stratified layer was conducted in the towing-tank facility of the U.S. Environmental Protection Agency. The height of the mixed layer in the daytime boundary layer can have a strong influence on the concentration of pollutants within this layer. Deflections of streamlines at the height of the interface are primarily a function of hill Froude number (Fr), the ratio of mixed-layer height (zi) to terrain height (h), and the crosswind dimension of the terrain. The magnitude of the deflections increases as Fr increases and zi / h decreases. For mixing-height streamlines that are initially below the terrain top, the response is linear with Fr; for those initially above the terrain feature the response to Fr is more complex. Once Fr exceeds about 2, the terrain related response of the mixed layer interface decreases somewhat with increasing Fr (toward more neutral flow). Deflections are also shown to increase as the crosswind dimensions of the terrain increases. Comparisons with numerical modeling, limited field data and other laboratory measurements reported in the literature are favorable. Additionally, visual observations of dye streamers suggests that the flow structure exhibited for our elevated inversions passing over three dimensional hills is similar to that reported in the literature for continuously stratified flow over two-dimensional h

Outer layer effects in wind-farm boundary layers: Coriolis forces and boundary layer height

NASA Astrophysics Data System (ADS)

Allaerts, Dries; Meyers, Johan

2015-11-01

In LES studies of wind-farm boundary layers, scale separation between the inner and outer region of the atmospheric boundary layer (ABL) is frequently assumed, i.e., wind turbines are presumed to fall within the inner layer and are not affected by outer layer effects. However, modern wind turbine and wind farm design tends towards larger rotor diameters and farm sizes, which means that outer layer effects will become more important. In a prior study, it was already shown for fully-developed wind farms that the ABL height influences the power performance. In this study, we use the in-house LES code SP-Wind to investigate the importance of outer layer effects on wind-farm boundary layers. In a suite of LES cases, the ABL height is varied by imposing a capping inversion with varying inversion strengths. Results indicate the growth of an internal boundary layer (IBL), which is limited in cases with low inversion layers. We further find that flow deceleration combined with Coriolis effects causes a change in wind direction throughout the farm. This effect increases with decreasing boundary layer height, and can result in considerable turbine wake deflection near the end of the farm. The authors are supported by the ERC (ActiveWindFarms, grant no: 306471). Computations were performed on VSC infrastructiure (Flemish Supercomputer Center), funded by the Hercules Foundation and the Flemish Government-department EWI.

A modified S-DIMM+: applying additional height grids for characterizing daytime seeing profiles

NASA Astrophysics Data System (ADS)

Wang, Zhiyong; Zhang, Lanqiang; Kong, Lin; Bao, Hua; Guo, Youming; Rao, Xuejun; Zhong, Libo; Zhu, Lei; Rao, Changhui

2018-07-01

Characterization of daytime atmospheric turbulence profiles is needed for the design of a multi-conjugate adaptive optical system. S-DIMM+ (solar differential image motion monitor+) is a technique to measure vertical seeing profiles. However, the number of height grids will be limited by the lenslet array of the wide-field Shack-Hartmann wavefront sensor (SHWFS). A small number of subaperture lenslet arrays will lead to a coarse height grid over the atmosphere, which can result in difficulty in finding the location of strong-turbulence layers and overestimates of the turbulence strength for the measured layers. To address this problem, we propose a modified S-DIMM+ method to measure seeing profiles iteratively with decreasing altitude range for a given number of height grids; finally they will be combined as a new seeing profile, with a denser and more uniform distribution of height grids. This method is tested with simulations and recovers the input height and contribution perfectly. Furthermore, this method is applied to the 102 data-sequences recorded from the 1-m New Vacuum Solar Telescope at Fuxian Solar Observatory, 55 of which were recorded at local time between 13:40 and 14:35 on 2016 October 6, and the other 47 between 12:50 and 13:40 on 2017 October 5. A 7x7 lenslet array of SHWFS is used to generate a 16-layer height grid to 15 km, each with 1 km height separation. The experimental results show that the turbulence has three origins in the lower (0-2 km) layers, the higher (3-6 km) layers and the uppermost (≥7 km) layers.

Predictive value of CHFR and MLH1 methylation in human gastric cancer.

PubMed

Li, Yazhuo; Yang, Yunsheng; Lu, Youyong; Herman, James G; Brock, Malcolm V; Zhao, Po; Guo, Mingzhou

2015-04-01

Gastric carcinoma (GC) has one of the highest mortality rates of cancer diseases and has a high incidence rate in China. Palliative chemotherapy is the main treatment for advanced gastric cancer. It is necessary to compare the effectiveness and toxicities of different regimens. This study explores the possibility of methylation of DNA damage repair genes serving as a prognostic and chemo-sensitive marker in human gastric cancer. The methylation status of five DNA damage repair genes (CHFR, FANCF, MGMT, MLH1, and RASSF1A) was detected by nested methylation-specific PCR in 102 paraffin-embedded gastric cancer samples. Chi-square or Fisher's exact tests were used to evaluate the association of methylation status and clinic-pathological factors. The Kaplan-Meier method and Cox proportional hazards models were employed to analyze the association of methylation status and chemo-sensitivity. The results indicate that CHFR, MLH1, RASSF1A, MGMT, and FANCF were methylated in 34.3% (35/102), 21.6% (22/102), 12.7% (13/102), 9.8% (10/102), and 0% (0/102) of samples, respectively. No association was found between methylation of CHFR, MLH1, RASSF1A, MGMT, or FANCF with gender, age, tumor size, tumor differentiation, lymph node metastasis, and TNM stage. In docetaxel-treated gastric cancer patients, resistance to docetaxel was found in CHFR unmethylated patients by Cox proportional hazards model (HR 0.243, 95% CI, 0.069-0.859, p = 0.028), and overall survival is longer in the CHFR methylated group compared with the CHFR unmethylated group (log-rank, p = 0.036). In oxaliplatin-treated gastric cancer patients, resistance to oxaliplatin was found in MLH1 methylated patients (HR 2.988, 95% CI, 1.064-8.394, p = 0.038), and overall survival was longer in the MLH1 unmethylated group compared with the MLH1 methylated group (log-rank, p = 0.046). CHFR is frequently methylated in human gastric cancer, and CHFR methylation may serve as a docetaxel-sensitive marker. MLH1 methylation was related to oxaliplatin resistance in gastric cancer patients.

Height Distribution Between Cloud and Aerosol Layers from the GLAS Spaceborne Lidar in the Indian Ocean Region

NASA Technical Reports Server (NTRS)

Hart, William D.; Spinhirne, James D.; Palm, Steven P.; Hlavka, Dennis L.

2005-01-01

The Geoscience Laser Altimeter System (GLAS), a nadir pointing lidar on the Ice Cloud and land Elevation Satellite (ICESat) launched in 2003, now provides important new global measurements of the relationship between the height distribution of cloud and aerosol layers. GLAS data have the capability to detect, locate, and distinguish between cloud and aerosol layers in the atmosphere up to 40 km altitude. The data product algorithm tests the product of the maximum attenuated backscatter coefficient b'(r) and the vertical gradient of b'(r) within a layer against a predetermined threshold. An initial case result for the critical Indian Ocean region is presented. From the results the relative height distribution between collocated aerosol and cloud shows extensive regions where cloud formation is well within dense aerosol scattering layers at the surface. Citation: Hart, W. D., J. D. Spinhime, S. P. Palm, and D. L. Hlavka (2005), Height distribution between cloud and aerosol layers from the GLAS spaceborne lidar in the Indian Ocean region,

Planetary Boundary Layer from AERI and MPL

DOE Data Explorer

Sawyer, Virginia

2014-02-13

The distribution and transport of aerosol emitted to the lower troposphere is governed by the height of the planetary boundary layer (PBL), which limits the dilution of pollutants and influences boundary-layer convection. Because radiative heating and cooling of the surface strongly affect the PBL top height, it follows diurnal and seasonal cycles and may vary by hundreds of meters over a 24-hour period. The cap the PBL imposes on low-level aerosol transport makes aerosol concentration an effective proxy for PBL height: the top of the PBL is marked by a rapid transition from polluted, well-mixed boundary-layer air to the cleaner, more stratified free troposphere. Micropulse lidar (MPL) can provide much higher temporal resolution than radiosonde and better vertical resolution than infrared spectrometer (AERI), but PBL heights from all three instruments at the ARM SGP site are compared to one another for validation. If there is agreement among them, the higher-resolution remote sensing-derived PBL heights can accurately fill in the gaps left by the low frequency of radiosonde launches, and thus improve model parameterizations and our understanding of boundary-layer processes.

The seasonal cycle of the mixing layer height and its impact on black carbon concentrations in the Kathmandu Valley (Nepal)

NASA Astrophysics Data System (ADS)

Mues, Andrea; Rupakheti, Maheswar; Hoor, Peter; Bozem, Heiko; Münkel, Christoph; Lauer, Axel; Butler, Tim

2016-04-01

The properties and the vertical structure of the mixing layer as part of the planetary boundary layer are of key importance for local air quality. They have a substantial impact on the vertical dispersion of pollutants in the lower atmosphere and thus on their concentrations near the surface. In this study, ceilometer measurements taken within the framework of the SusKat project (Sustainable Atmosphere for the Kathmandu Valley) are used to investigate the mixing layer height in the Kathmandu Valley, Nepal. The applied method is based on the assumption that the aerosol concentration is nearly constant in the vertical and distinctly higher within the mixing layer than in the air above. Thus, the height with the steepest gradient within the ceilometer backscatter profile marks the top of the mixing layer. Ceilometer and black carbon (BC) measurements conducted from March 2013 through February 2014 provide a unique and important dataset for the analysis of the meteorological and air quality conditions in the Kathmandu Valley. In this study the mean diurnal cycle of the mixing layer height in the Kathmandu Valley for each season (pre-monsoon, monsoon, post-monsoon and winter season) and its dependency on the meteorological situation is investigated. In addition, the impact of the mixing layer height on the BC concentration is analyzed and compared to the relevance of other important processes such as emissions, horizontal advection and deposition. In all seasons the diurnal cycle is typically characterized by low mixing heights during the night, gradually increasing after sun rise reaching to maximum values in the afternoon before decreasing again. Seasonal differences can be seen particularly in the height of the mixing layer, e.g. from on average 153/1200 m (pre-monsoon) to 241/755 m (monsoon season) during the night/day, and the duration of enhanced mixing layer heights during daytime (around 12 hours (pre-monsoon season) to 8 hours (winter)). During the monsoon season, the observed diurnal cycle typically shows the lowest amplitude and the lowest mixing height during the day and the highest in the night and morning hours of all seasons. These characteristics can mainly be explained with frequently present clouds and the associated lack of incoming solar radiation and outgoing longwave radiation. In general there is a clear anti-correlation of the BC concentration and the mixing layer height although this relation is less pronounced in the monsoon season. The shape and magnitude of the BC diurnal cycle differs between the seasons (e.g., daily maximum concentration from around 6 to 50 μg/m3 depending on the season). This is partly due to the different meteorological conditions including the mixing layer height but also caused by the different (seasonal and diurnal) time profiles of the main emission sources. From late December to April, for instance, brick kilns are major emitters of black carbon. The brick kilns emit continuously throughout the day whereas in the other months sources with more pronounced diurnal cycles, such as traffic and cooking activities, are dominating the total emissions.

Methylation Analysis of DNA Mismatch Repair Genes Using DNA Derived from the Peripheral Blood of Patients with Endometrial Cancer: Epimutation in Endometrial Carcinogenesis.

PubMed

Takeda, Takashi; Banno, Kouji; Yanokura, Megumi; Adachi, Masataka; Iijima, Moito; Kunitomi, Haruko; Nakamura, Kanako; Iida, Miho; Nogami, Yuya; Umene, Kiyoko; Masuda, Kenta; Kobayashi, Yusuke; Yamagami, Wataru; Hirasawa, Akira; Tominaga, Eiichiro; Susumu, Nobuyuki; Aoki, Daisuke

2016-10-14

Germline mutation of DNA mismatch repair (MMR) genes is a cause of Lynch syndrome. Methylation of MutL homolog 1 ( MLH1 ) and MutS homolog 2 ( MSH2 ) has been detected in peripheral blood cells of patients with colorectal cancer. This methylation is referred to as epimutation. Methylation of these genes has not been studied in an unselected series of endometrial cancer cases. Therefore, we examined methylation of MLH1 , MSH2 , and MSH6 promoter regions of peripheral blood cells in 206 patients with endometrial cancer using a methylation-specific polymerase chain reaction (MSP). Germline mutation of MMR genes, microsatellite instability (MSI), and immunohistochemistry (IHC) were also analyzed in each case with epimutation. MLH1 epimutation was detected in a single patient out of a total of 206 (0.49%)-1 out of 58 (1.72%) with an onset age of less than 50 years. The patient with MLH1 epimutation showed high level MSI (MSI-H), loss of MLH1 expression and had developed endometrial cancer at 46 years old, complicated with colorectal cancer. No case had epimutation of MSH2 or MSH6 . The MLH1 epimutation detected in a patient with endometrial cancer may be a cause of endometrial carcinogenesis. This result indicates that it is important to check epimutation in patients with endometrial cancer without a germline mutation of MMR genes.

Methylation variable position profiles of hMLH1 promoter CpG islands in human sporadic colorectal carcinoma.

PubMed

Huang, Qing; Huang, Jun-Fu; Zhang, Bo; Baum, Larry; Fu, Wei-Ling

2012-03-01

Aberrant hypermethylation of CpG islands (CGIs) in hMLH1 promoter regions has been well known to play an important role in the tumorigenesis of human sporadic colorectal carcinoma (SCRC). In this study, bisulfite sequencing was performed to analyze the methylation variable positions (MVPs) profiles of hMLH1 promoter CGIs in 30 clinical SCRC patients, and further analysis was carried out to evaluate the associations between the CGI methylation and the clinicopathological features in SCRC. Among the 2 CGIs in the hMLH1 promoter, that is, CGI-I and CGI-II, 20% (6/30) and 13% (4/30) of the patients had methylated CGI-I and CGI-II, respectively. Suppressed expression of hMLH1was significantly correlated with methylation of CGI-I but not CGI-II. Further analysis of the MVP profiles of CGI-I showed that most of the MVPs were hypermethylated and others were poorly methylated or unmethylated. The profiles could be classified into at least 4 groups based on the methylation status of 3 MVPs at positions 21 to 23 in CGI-I. All 6 patients with methylated CGI-I belonged to group I. This result suggests that the above 3 MVPs in CGI-I should be a targeted region to further analyze the epigenetic features of hMLH1 in human SCRC. Our results further suggest that MVP profiling is useful for identifying the aberrantly methylated CGIs associated with suppressed gene expression.

BEHAVIORAL AND NEUROCHEMICAL CHARACTERIZATION OF THE mlh MUTANT MICE LACKING OTOCONIA.

PubMed

Manes, Marianna; Garcia-Gomes, Mariana de Souza Aranha; Sandini, Thaísa Meira; Zaccarelli-Magalhães, J; Florio, J C; Alexandre-Ribeiro, Sandra Regina; Wadt, Danilo; Bernardi, Maria Martha; Massironi, Silvia Maria Gomes; Mori, Claudia Madalena Cabrera

2018-06-15

Otoconia are crucial for the correct processing of positional information and orientation. Mice lacking otoconia cannot sense the direction of the gravity vector and cannot swim properly. This study aims to characterize the behavior of mergulhador (mlh), otoconia-deficient mutant mice. Additionally, the central catecholamine levels were evaluated to investigate possible correlations between behaviors and central neurotransmitters. A sequence of behavioral tests was used to evaluate the parameters related to the general activity, sensory nervous system, psychomotor system, and autonomous nervous system, in addition to measuring the acquisition of spatial and declarative memory, anxiety-like behavior, motor coordination, and swimming behavior of the mlh mutant mice. As well, the neurotransmitter levels in the cerebellum, striatum, frontal cortex, and hippocampus were measured. Relative to BALB/c mice, the mutant mlh mice showed 1) reduced locomotor and rearing behavior, increased auricular and touch reflexes, decreased motor coordination and increased micturition; 2) decreased responses in the T-maze and aversive wooden beam tests; 3) increased time of immobility in the tail suspension test; 4) no effects in the elevated plus maze or object recognition test; 5) an inability to swim; and 6) reduced turnover of dopaminergic system in the cerebellum, striatum, and frontal cortex. Thus, in our mlh mutant mice, otoconia deficiency reduced the motor, sensory and spatial learning behaviors likely by impairing balance. We did not rule out the role of the dopaminergic system in all behavioral deficits of the mlh mutant mice. Copyright © 2018. Published by Elsevier B.V.

Inhibition of colorectal cancer genomic copy number alterations and chromosomal fragile site tumor suppressor FHIT and WWOX deletions by DNA mismatch repair

PubMed Central

Gelincik, Ozkan; Blecua, Pedro; Edelmann, Winfried; Kucherlapati, Raju; Zhou, Kathy; Jasin, Maria; Gümüş, Zeynep H.; Lipkin, Steven M.

2017-01-01

Homologous recombination (HR) enables precise DNA repair after DNA double strand breaks (DSBs) using identical sequence templates, whereas homeologous recombination (HeR) uses only partially homologous sequences. Homeologous recombination introduces mutations through gene conversion and genomic deletions through single-strand annealing (SSA). DNA mismatch repair (MMR) inhibits HeR, but the roles of mammalian MMR MutL homologues (MLH1, PMS2 and MLH3) proteins in HeR suppression are poorly characterized. Here, we demonstrate that mouse embryonic fibroblasts (MEFs) carrying Mlh1, Pms2, and Mlh3 mutations have higher HeR rates, by using 7,863 uniquely mapping paired direct repeat sequences (DRs) in the mouse genome as endogenous gene conversion and SSA reporters. Additionally, when DSBs are induced by gamma-radiation, Mlh1, Pms2 and Mlh3 mutant MEFs have higher DR copy number alterations (CNAs), including DR CNA hotspots previously identified in mouse MMR-deficient colorectal cancer (dMMR CRC). Analysis of The Cancer Genome Atlas CRC data revealed that dMMR CRCs have higher genome-wide DR HeR rates than MMR proficient CRCs, and that dMMR CRCs have deletion hotspots in tumor suppressors FHIT/WWOX at chromosomal fragile sites FRA3B and FRA16D (which have elevated DSB rates) flanked by paired homologous DRs and inverted repeats (IR). Overall, these data provide novel insights into the MMR-dependent HeR inhibition mechanism and its role in tumor suppression. PMID:29069730

Genesis of Atlantic Lows Experiment NASA Electra Boundary Layer Flights Data Report

NASA Technical Reports Server (NTRS)

Palm, Stephen P.; Melfi, S. H.; Boers, Reinout

1988-01-01

The objective of this research was to obtain high resolution measurements of the height of the Marine Atmospheric Boundary Layer (MABL) during cold air outbreaks using an Airborne Lidar System. The research was coordinated with other investigators participating in the Genesis of Atlantic Lows Experiment (GALE). An objective computerized scheme was developed to obtain the Boundary Layer Height from the Lidar Data. The algorithm was used on each of the four flight days producing a high resolution data set of the MABL height over the GALE experiment area. Plots of the retrieved MABL height as well as tabular data summaries are presented.

Lessons learnt from implementation of a Lynch syndrome screening program for patients with gynaecological malignancy.

PubMed

Najdawi, Fedaa; Crook, Ashley; Maidens, Jayne; McEvoy, Christopher; Fellowes, Andrew; Pickett, Justine; Ho, Musei; Nevell, David; McIlroy, Kirsten; Sheen, Amy; Sioson, Loretta; Ahadi, Mahsa; Turchini, John; Clarkson, Adele; Hogg, Russell; Valmadre, Sue; Gard, Greg; Dooley, Susan J; Scott, Rodney J; Fox, Stephen B; Field, Michael; Gill, Anthony J

2017-08-01

Despite a trend towards universal testing, best practice to screen patients presenting with gynaecological malignancy for Lynch syndrome (LS) is uncertain. We report our institutional experience of a co-ordinated gynaecological LS screening program. All patients with endometrial carcinoma or carcinosarcoma, or gynaecological endometrioid or clear cell carcinomas undergo reflex four panel immunohistochemistry (IHC) for MLH1, PMS2, MSH2 and MSH6 followed by cascade somatic hypermethylation analysis of the MLH1 promoter locus for dual MLH1/PMS2 negative tumours. On the basis of these results, genetic counselling and targeted germline mutation testing is then offered to patients considered at high risk of LS. From 1 August 2013 to 31 December 2015, 124 patients were screened (mean age 64.6 years). Thirty-six (29.0%) demonstrated abnormal MMR IHC: 26 (72.2%) showed dual loss of MLH1/PMS2, five (13.9%) dual loss of MSH2/MSH6, three (8.3%) isolated loss of MSH6, and two (5.6%) isolated loss of PMS2. Twenty-five of 26 (96.1%) patients with dual MLH1/PMS2 loss demonstrated MLH1 promoter methylation. Therefore, 11 (8.9%) patients screened were classified as high risk for LS, of whom nine (81.8%) accepted germline mutation testing. Three (2.4% of total screened) were confirmed to have LS, two with germline PMS2 and one with germline MSH2 mutation. Massive parallel sequencing of tumour tissue demonstrated somatic mutations which were concordant with the IHC results in the remainder. Interestingly, the one MLH1/PMS2 IHC negative but not hypermethylated tumour harboured only somatic MLH1 mutations, indicating that universal cascade methylation testing in MLH1/PMS2 IHC negative tumours is very low yield and could be reconsidered in a resource-poor setting. In conclusion, universal screening for LS in patients presenting with gynaecological malignancy using the algorithm described above identified LS in three of 124 (2.4%) of our population. Only three of nine (33.3%) patients considered at high risk for LS by combined IHC and hypermethylation analysis were proven to have LS. Only one of the LS patients was less than 50 years of age and none of these patients would have been identified had more restrictive Amsterdam or Bethesda criteria been applied. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

MLH1 Region Polymorphisms Show a Significant Association with CpG Island Shore Methylation in a Large Cohort of Healthy Individuals

PubMed Central

Savio, Andrea J.; Lemire, Mathieu; Mrkonjic, Miralem; Gallinger, Steven; Zanke, Brent W.; Hudson, Thomas J.; Bapat, Bharati

2012-01-01

Single nucleotide polymorphisms (SNPs) are the most common form of genetic variation. We previously demonstrated that SNPs (rs1800734, rs749072, and rs13098279) in the MLH1 gene region are associated with MLH1 promoter island methylation, loss of MLH1 protein expression, and microsatellite instability (MSI) in colorectal cancer (CRC) patients. Recent studies have identified less CpG-dense “shore” regions flanking many CpG islands. These shores often exhibit distinct methylation profiles between different tissues and matched normal versus tumor cells of patients. To date, most epigenetic studies have focused on somatic methylation events occurring within solid tumors; less is known of the contributions of peripheral blood cell (PBC) methylation to processes such as aging and tumorigenesis. To address whether MLH1 methylation in PBCs is correlated with tumorigenesis we utilized the Illumina 450 K microarrays to measure methylation in PBC DNA of 846 healthy controls and 252 CRC patients from Ontario, Canada. Analysis of a region of chromosome 3p21 spanning the MLH1 locus in healthy controls revealed that a CpG island shore 1 kb upstream of the MLH1 gene exhibits different methylation profiles when stratified by SNP genotypes (rs1800734, rs749072, and rs13098279). Individuals with wild-type genotypes incur significantly higher PBC shore methylation than heterozygous or homozygous variant carriers (p<1.1×10−6; ANOVA). This trend is also seen in CRC cases (p<0.096; ANOVA). Shore methylation also decreases significantly with increasing age in cases and controls. This is the first study of its kind to integrate PBC methylation at a CpG island shore with SNP genotype status in CRC cases and controls. These results indicate that CpG island shore methylation in PBCs may be influenced by genotype as well as the normal aging process. PMID:23240038

Cloning of rat MLH1 and expression analysis of MSH2, MSH3, MSH6, and MLH1 during spermatogenesis.

PubMed

Geeta Vani, R; Varghese, C M; Rao, M R

1999-12-15

The mismatch repair system has been highly conserved in various species. In eukaryotic cells, the Mut S and Mut L homologues play crucial roles in both DNA mismatch repair and meiotic recombination. A full-length rat cDNA clone for rat MLH1 has been constructed using the RT-PCR method. The cDNA has an open reading frame of 2274 nucleotides for a protein of 757 amino acids. We have also obtained partial cDNA clones for MSH3 and MSH6. Northern blot analysis of rat MLH1, MSH2, MSH3, and MSH6 in the testes of rats of different ages showed differential expression of these genes as a function of developmental maturation of the testes. The expression analysis suggests that MSH3 may have a more predominant role in the meiotic recombination process. Copyright 1999 Academic Press.

Artefactual punctate MLH1 staining can lead to erroneous reporting of isolated PMS2 loss.

PubMed

Niu, Bonnie T; Hammond, Rory F L; Leen, Sarah L S; Faruqi, Asma Z; Trevisan, Giorgia; Gilks, C Blake; Singh, Naveena

2018-05-31

Germline mutations in the PMS2 gene are an uncommon cause of Lynch Syndrome (LS), present in <5% of LS-associated endometrial carcinomas (EC) 1,2 . Isolated loss of PMS2 immunohistochemical expression, with retained MLH1 expression, triggers referral to genetics services due to the significant risk of LS 3 . As detection of PMS2 germline mutations is problematic 4 , this may result in patients being labeled as "Lynch-like", with implications for future surveillance 5 . A recent study suggested that some cases of isolated PMS2 loss result from MLH1 promoter methylation and are sporadic rather than likely LS 6 ; they therefore recommended MLH1 promoter methylation testing in all cases of isolated PMS2 loss 6 . This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Choice of optimum heights for registration of ionospheric response onto earthquakes

NASA Astrophysics Data System (ADS)

Krasnov, Valerii; Gotur, Ivan; Kuleshov, Yurii; Cherny, Sergei

2017-10-01

To investigate the dependence of ionospheric disturbances on height we used model calculations, and the data of seismic and ionospheric observations during the Tohoku-Oki earthquake. High-altitude dependences of "portraits" of ionospheric disturbances are calculated for a case of influence of a seismic P-wave onto the ionosphere. We compared the "portraits" of ionospheric disturbances with the "portraits" of the seismic recording. The correlation coefficient of the recordings for the height of 100 km was about 0.81, for 130 km - 0.85, for 160 km - 0.77, for 180 km - 0.76, for 200 km - 0.7, for 230 km -0.54 and for 250 km - 0.41. At the same time the maximum of F2-layer was at the height about 250 km. Thus, the height of a maximum of F2-layer was not optimum for registration of ionospheric disturbances due to the earthquake. It was preferable to carry out measurements of the ionospheric disturbances at the heights below 200 km. The profile of amplitude of the ionospheric disturbance had no sharply expressed maximum at the height of a maximum of F2-layer. Therefore it is problematic to use the approach of the thin layer for interpretation of TEC disturbances.

On the Creation of An Urban Boundary Layer Product Using The Radar Wind Profiler of the New York City Meteorological Network

NASA Astrophysics Data System (ADS)

Dempsey, M. J.; Booth, J.; Arend, M.; Melecio-Vazquez, D.

2016-12-01

The radar wind profiler (RWP) located on the Liberty Science Center in Jersey City, NJ is a part of the New York City Meteorological Network (NYCMetNet). An automatic algorithm based on those by Angevine [1] and Molod [2] is expanded upon and implemented to take RWP signal to noise ratio data and create an urban boundary layer (UBL) height product. Time series of the RWP UBL heights from clear and cloudy days are examined and compared to UBL height time series calculated from thermal data obtained from a NYCMetNet radiometer located on the roof of the Grove School of Engineering at The City College of New York. UBL data from the RWP are also compared to the MERRA (Modern Era Retrospective Analysis for Research and Applications) planetary boundary layer height time series product. A limited seasonal climatology is created from the available RWP data for clear and cloudy days and then compared to a limited seasonal climatology produced from boundary layer data obtained from MERRA and boundary layer data calculated from the CCNY radiometer. As with wind profilers in the NOAA wind profiler network, the signal return to the lowest range gates is not always the result of turbulent scattering, but from scattering from other targets such as the building itself, birds and insects. The algorithm attempts to address this during the daytime, when strong signal returns at the lowest range gates mask the SNR maxima above which are representative of the actual UBL height. Detecting the collapse and fall of the boundary layer meets with limited success, also, from the hours of 2:30pm to 5:00pm. Upper and lower range gates from the wind profiler limit observation of the nighttime boundary layer for heights falling below the lowest range gate and daytime convective boundary layer maxima rising above the highest. Due to the constraints of the instrument and the algorithm it is recommended that the boundary layer height product be constrained to the hours of 8am to 7pm.

Haplotype analysis suggest that the MLH1 c.2059C > T mutation is a Swedish founder mutation.

PubMed

von Salomé, Jenny; Liu, Tao; Keihäs, Markku; Morak, Moni; Holinski-Feder, Elke; Berry, Ian R; Moilanen, Jukka S; Baert-Desurmont, Stéphanie; Lindblom, Annika; Lagerstedt-Robinson, Kristina

2017-12-29

Lynch syndrome (LS) predisposes to a spectrum of cancers and increases the lifetime risk of developing colorectal- or endometrial cancer to over 50%. Lynch syndrome is dominantly inherited and is caused by defects in DNA mismatch-repair genes MLH1, MSH2, MSH6 or PMS2, with the vast majority detected in MLH1 and MSH2. Recurrent LS-associated variants observed in apparently unrelated individuals, have either arisen de novo in different families due to mutation hotspots, or are inherited from a founder (a common ancestor) that lived several generations back. There are variants that recur in some populations while also acting as founders in other ethnic groups. Testing for founder mutations can facilitate molecular diagnosis of Lynch Syndrome more efficiently and more cost effective than screening for all possible mutations. Here we report a study of the missense mutation MLH1 c.2059C > T (p.Arg687Trp), a potential founder mutation identified in eight Swedish families and one Finnish family with Swedish ancestors. Haplotype analysis confirmed that the Finnish and Swedish families shared a haplotype of between 0.9 and 2.8 Mb. While MLH1 c.2059C > T exists worldwide, the Swedish haplotype was not found among mutation carriers from Germany or France, which indicates a common founder in the Swedish population. The geographic distribution of MLH1 c.2059C > T in Sweden suggests a single, ancient mutational event in the northern part of Sweden.

Montmorillonite-lipid hybrid carriers for ionizable and neutral poorly water-soluble drugs: Formulation, characterization and in vitro lipolysis studies.

PubMed

Dening, Tahnee J; Rao, Shasha; Thomas, Nicky; Prestidge, Clive A

2017-06-30

Lipid-based formulations (LBFs) are a popular strategy for enhancing the gastrointestinal solubilization and absorption of poorly water-soluble drugs. In light of this, montmorillonite-lipid hybrid (MLH) particles, composed of medium-chain triglycerides, lecithin and montmorillonite clay platelets, have been developed as a novel solid-state LBF. Owing to the unique charge properties of montmorillonite, whereby the clay platelet surfaces carry a permanent negative charge and the platelet edges carry a pH-dependent charge, three model poorly water-soluble drugs with different charge properties; blonanserin (weak base, pKa 7.7), ibuprofen (weak acid, pKa 4.5) and fenofibrate (neutral), were formulated as MLH particles and their performance during biorelevant in vitro lipolysis at pH 7.5 was investigated. For blonanserin, drug solubilization during in vitro lipolysis was significantly reduced 3.4-fold and 3.2-fold for MLH particles in comparison to a control lipid solution and silica-lipid hybrid (SLH) particles, respectively. It was hypothesized that strong electrostatic interactions between the anionic montmorillonite platelet surfaces and cationic blonanserin molecules were responsible for the inferior performance of MLH particles. In contrast, no significant influence on drug solubilization was observed for ibuprofen- and fenofibrate-loaded MLH particles. The results of the current study indicate that whilst MLH particles are a promising novel formulation strategy for poorly water-soluble drugs, drug ionization tendency and the potential for drug-clay interactions must be taken into consideration to ensure an appropriate performance. Copyright © 2017 Elsevier B.V. All rights reserved.

Evaluation of the operational Aerosol Layer Height retrieval algorithm for Sentinel-5 Precursor: application to O2 A band observations from GOME-2A

NASA Astrophysics Data System (ADS)

Sanders, A. F. J.; de Haan, J. F.; Sneep, M.; Apituley, A.; Stammes, P.; Vieitez, M. O.; Tilstra, L. G.; Tuinder, O. N. E.; Koning, C. E.; Veefkind, J. P.

2015-06-01

An algorithm setup for the operational Aerosol Layer Height product for TROPOMI on the Sentinel-5 Precursor mission is described and discussed, applied to GOME-2A data, and evaluated with lidar measurements. The algorithm makes a spectral fit of reflectance at the O2 A band in the near-infrared and the fit window runs from 758 to 770 nm. The aerosol profile is parameterized by a scattering layer with constant aerosol volume extinction coefficient and aerosol single scattering albedo and with a fixed pressure thickness. The algorithm's target parameter is the height of this layer. In this paper, we apply the algorithm to observations from GOME-2A in a number of systematic and extensive case studies and we compare retrieved aerosol layer heights with lidar measurements. Aerosol scenes cover various aerosol types, both elevated and boundary layer aerosols, and land and sea surfaces. The aerosol optical thicknesses for these scenes are relatively moderate. Retrieval experiments with GOME-2A spectra are used to investigate various sensitivities, in which particular attention is given to the role of the surface albedo. From retrieval simulations with the single-layer model, we learn that the surface albedo should be a fit parameter when retrieving aerosol layer height from the O2 A band. Current uncertainties in surface albedo climatologies cause biases and non-convergences when the surface albedo is fixed in the retrieval. Biases disappear and convergence improves when the surface albedo is fitted, while precision of retrieved aerosol layer pressure is still largely within requirement levels. Moreover, we show that fitting the surface albedo helps to ameliorate biases in retrieved aerosol layer height when the assumed aerosol model is inaccurate. Subsequent retrievals with GOME-2A spectra confirm that convergence is better when the surface albedo is retrieved simultaneously with aerosol parameters. However, retrieved aerosol layer pressures are systematically low (i.e., layer high in the atmosphere) to the extent that retrieved values are not realistically representing actual extinction profiles anymore. When the surface albedo is fixed in retrievals with GOME-2A spectra, convergence deteriorates as expected, but retrieved aerosol layer pressures become much higher (i.e., layer lower in atmosphere). The comparison with lidar measurements indicates that retrieved aerosol layer heights are indeed representative of the underlying profile in that case. Finally, subsequent retrieval simulations with two-layer aerosol profiles show that a model error in the assumed profile (two layers in the simulation but only one in the retrieval) is partly absorbed by the surface albedo when this parameter is fitted. This is expected in view of the correlations between errors in fit parameters and the effect is relatively small for elevated layers (less than 100 hPa). In case one of the scattering layers is near the surface (boundary layer aerosols), the effect becomes surprisingly large such that the retrieved height of the single layer is above the two-layer profile. Furthermore, we find that the retrieval solution, once retrieval converges, hardly depends on the starting values for the fit. Sensitivity experiments with GOME-2A spectra also show that aerosol layer height is indeed relatively robust against inaccuracies in the assumed aerosol model, even when the surface albedo is not fitted. We show spectral fit residuals, which can be used for further investigations. Fit residuals may be partly explained by spectroscopic uncertainties, which is suggested by an experiment showing the improvement of convergence when the absorption cross section is scaled in agreement with Butz et al. (2012) and Crisp et al. (2012) and a temperature offset to the a priori ECMWF temperature profile is fitted. Retrieved temperature offsets are always negative and quite large (ranging between -4 and -8 K), which is not expected if temperature offsets absorb remaining inaccuracies in meteorological data. Other sensitivity experiments investigate fitting of stray light and fluorescence emissions. We find negative radiance offsets and negative fluorescence emissions, also for non-vegetated areas, but from the results it is not clear whether fitting these parameters improves the retrieval. Based on the present results, the operational baseline for the Aerosol Layer Height product currently will not fit the surface albedo. The product will be particularly suited for elevated, optically thick aerosol layers. In addition to its scientific value in climate research, anticipated applications of the product for TROPOMI are providing aerosol height information for aviation safety and improving interpretation of the Absorbing Aerosol Index.

Evaluation of the operational Aerosol Layer Height retrieval algorithm for Sentinel-5 Precursor: application to O2 A band observations from GOME-2A

NASA Astrophysics Data System (ADS)

Sanders, A. F. J.; de Haan, J. F.; Sneep, M.; Apituley, A.; Stammes, P.; Vieitez, M. O.; Tilstra, L. G.; Tuinder, O. N. E.; Koning, C. E.; Veefkind, J. P.

2015-11-01

An algorithm setup for the operational Aerosol Layer Height product for TROPOMI on the Sentinel-5 Precursor mission is described and discussed, applied to GOME-2A data, and evaluated with lidar measurements. The algorithm makes a spectral fit of reflectance at the O2 A band in the near-infrared and the fit window runs from 758 to 770 nm. The aerosol profile is parameterised by a scattering layer with constant aerosol volume extinction coefficient and aerosol single scattering albedo and with a fixed pressure thickness. The algorithm's target parameter is the height of this layer. In this paper, we apply the algorithm to observations from GOME-2A in a number of systematic and extensive case studies, and we compare retrieved aerosol layer heights with lidar measurements. Aerosol scenes cover various aerosol types, both elevated and boundary layer aerosols, and land and sea surfaces. The aerosol optical thicknesses for these scenes are relatively moderate. Retrieval experiments with GOME-2A spectra are used to investigate various sensitivities, in which particular attention is given to the role of the surface albedo. From retrieval simulations with the single-layer model, we learn that the surface albedo should be a fit parameter when retrieving aerosol layer height from the O2 A band. Current uncertainties in surface albedo climatologies cause biases and non-convergences when the surface albedo is fixed in the retrieval. Biases disappear and convergence improves when the surface albedo is fitted, while precision of retrieved aerosol layer pressure is still largely within requirement levels. Moreover, we show that fitting the surface albedo helps to ameliorate biases in retrieved aerosol layer height when the assumed aerosol model is inaccurate. Subsequent retrievals with GOME-2A spectra confirm that convergence is better when the surface albedo is retrieved simultaneously with aerosol parameters. However, retrieved aerosol layer pressures are systematically low (i.e., layer high in the atmosphere) to the extent that retrieved values no longer realistically represent actual extinction profiles. When the surface albedo is fixed in retrievals with GOME-2A spectra, convergence deteriorates as expected, but retrieved aerosol layer pressures become much higher (i.e., layer lower in atmosphere). The comparison with lidar measurements indicates that retrieved aerosol layer heights are indeed representative of the underlying profile in that case. Finally, subsequent retrieval simulations with two-layer aerosol profiles show that a model error in the assumed profile (two layers in the simulation but only one in the retrieval) is partly absorbed by the surface albedo when this parameter is fitted. This is expected in view of the correlations between errors in fit parameters and the effect is relatively small for elevated layers (less than 100 hPa). If one of the scattering layers is near the surface (boundary layer aerosols), the effect becomes surprisingly large, in such a way that the retrieved height of the single layer is above the two-layer profile. Furthermore, we find that the retrieval solution, once retrieval converges, hardly depends on the starting values for the fit. Sensitivity experiments with GOME-2A spectra also show that aerosol layer height is indeed relatively robust against inaccuracies in the assumed aerosol model, even when the surface albedo is not fitted. We show spectral fit residuals, which can be used for further investigations. Fit residuals may be partly explained by spectroscopic uncertainties, which is suggested by an experiment showing the improvement of convergence when the absorption cross section is scaled in agreement with Butz et al. (2013) and Crisp et al. (2012), and a temperature offset to the a priori ECMWF temperature profile is fitted. Retrieved temperature offsets are always negative and quite large (ranging between -4 and -8 K), which is not expected if temperature offsets absorb remaining inaccuracies in meteorological data. Other sensitivity experiments investigate fitting of stray light and fluorescence emissions. We find negative radiance offsets and negative fluorescence emissions, also for non-vegetated areas, but from the results it is not clear whether fitting these parameters improves the retrieval. Based on the present results, the operational baseline for the Aerosol Layer Height product currently will not fit the surface albedo. The product will be particularly suited for elevated, optically thick aerosol layers. In addition to its scientific value in climate research, anticipated applications of the product for TROPOMI are providing aerosol height information for aviation safety and improving interpretation of the Absorbing Aerosol Index.

Learning about Colon Cancer

MedlinePlus

... MSH2 on chromosome 2 MLH1 on chromosome 3 PMS2 on chromosome 7 MSH6 on chromosome 2 PMS1 ... are associated with HNPCC - MLH1 , MSH2 , MSH6 , and PMS2 . Individuals in families at high risk of genetic ...

MSH3 Mismatch Repair Protein Regulates Sensitivity to Cytotoxic Drugs and a Histone Deacetylase Inhibitor in Human Colon Carcinoma Cells

PubMed Central

Park, Jae Myung; Huang, Shengbing; Tougeron, David; Sinicrope, Frank A.

2013-01-01

Background MSH3 is a DNA mismatch repair (MMR) gene that undergoes frequent somatic mutation in colorectal cancers (CRCs) with MMR deficiency. MSH3, together with MSH2, forms the MutSβ heteroduplex that interacts with interstrand cross-links induced by drugs such as cisplatin. To date, the impact of MSH3 on chemosensitivity is unknown. Methods We utilized isogenic HCT116 (MLH1−/MSH3−) cells where MLH1 is restored by transfer of chromosome 3 (HCT116+ch3) and also MSH3 by chromosome 5 (HCT116+3+5). We generated HCT116+3+5, SW480 (MLH1+/MSH3+) and SW48 (MLH1−/MSH3+) cells with shRNA knockdown of MSH3. Cells were treated with 5-fluorouracil (5-FU), SN-38, oxaliplatin, or the histone deacetylase (HDAC) inhibitor PCI-24781 and cell viability, clonogenic survival, DNA damage and apoptosis were analyzed. Results MSH3-deficient vs proficient CRC cells showed increased sensitivity to the irinotecan metabolite SN-38 and to oxaliplatin, but not 5-FU, as shown in assays for apoptosis and clonogenic survival. In contrast, suppression of MLH1 attenuated the cytotoxic effect of 5-FU, but did not alter sensitivity to SN-38 or oxaliplatin. The impact of MSH3 knockdown on chemosensitivity to SN-38 and oxaliplatin was maintained independent of MLH1 status. In MSH3-deficient vs proficient cells, SN-38 and oxaliplatin induced higher levels of phosphorylated histone H2AX and Chk2, and similar results were found in MLH1-proficient SW480 cells. MSH3-deficient vs proficient cells showed increased 53BP1 nuclear foci after irradiation, suggesting that MSH3 can regulate DNA double strand break (DSB) repair. We then utilized PCI-24781 that interferes with homologous recombination (HR) indicated by a reduction in Rad51 expression. The addition of PCI-24781 to oxaliplatin enhanced cytotoxicity to a greater extent compared to either drug alone. Conclusion MSH3 status can regulate the DNA damage response and extent of apoptosis induced by chemotherapy. The ability of MSH3 to regulate chemosensitivity was independent of MLH1 status. PCI-24781-mediated impairment of HR enhanced oxaliplatin sensitivity, suggesting that reduced DSB repair capacity may be contributory. PMID:23724141

MSH3 mismatch repair protein regulates sensitivity to cytotoxic drugs and a histone deacetylase inhibitor in human colon carcinoma cells.

PubMed

Park, Jae Myung; Huang, Shengbing; Tougeron, David; Sinicrope, Frank A

2013-01-01

MSH3 is a DNA mismatch repair (MMR) gene that undergoes frequent somatic mutation in colorectal cancers (CRCs) with MMR deficiency. MSH3, together with MSH2, forms the MutSβ heteroduplex that interacts with interstrand cross-links induced by drugs such as cisplatin. To date, the impact of MSH3 on chemosensitivity is unknown. We utilized isogenic HCT116 (MLH1-/MSH3-) cells where MLH1 is restored by transfer of chromosome 3 (HCT116+ch3) and also MSH3 by chromosome 5 (HCT116+3+5). We generated HCT116+3+5, SW480 (MLH1+/MSH3+) and SW48 (MLH1-/MSH3+) cells with shRNA knockdown of MSH3. Cells were treated with 5-fluorouracil (5-FU), SN-38, oxaliplatin, or the histone deacetylase (HDAC) inhibitor PCI-24781 and cell viability, clonogenic survival, DNA damage and apoptosis were analyzed. MSH3-deficient vs proficient CRC cells showed increased sensitivity to the irinotecan metabolite SN-38 and to oxaliplatin, but not 5-FU, as shown in assays for apoptosis and clonogenic survival. In contrast, suppression of MLH1 attenuated the cytotoxic effect of 5-FU, but did not alter sensitivity to SN-38 or oxaliplatin. The impact of MSH3 knockdown on chemosensitivity to SN-38 and oxaliplatin was maintained independent of MLH1 status. In MSH3-deficient vs proficient cells, SN-38 and oxaliplatin induced higher levels of phosphorylated histone H2AX and Chk2, and similar results were found in MLH1-proficient SW480 cells. MSH3-deficient vs proficient cells showed increased 53BP1 nuclear foci after irradiation, suggesting that MSH3 can regulate DNA double strand break (DSB) repair. We then utilized PCI-24781 that interferes with homologous recombination (HR) indicated by a reduction in Rad51 expression. The addition of PCI-24781 to oxaliplatin enhanced cytotoxicity to a greater extent compared to either drug alone. MSH3 status can regulate the DNA damage response and extent of apoptosis induced by chemotherapy. The ability of MSH3 to regulate chemosensitivity was independent of MLH1 status. PCI-24781-mediated impairment of HR enhanced oxaliplatin sensitivity, suggesting that reduced DSB repair capacity may be contributory.

Observing the Vertical Extent of the Urban Boundary Layer Over Jersey City, NJ: A Diurnal and Seasonal Analysis

NASA Astrophysics Data System (ADS)

Dempsey, M. J.; Booth, J.; Arend, M.; Melecio-Vazquez, D.; Gonzalez, J.

2015-12-01

The atmospheric boundary remains one of the more difficult components of the climate system to classify. One of the most important characteristics is the boundary layer height, especially in urban settings. The current study examines the boundary layer height using the the New York City Meteorological Network or NYCMetNet. NYCMetNet is a network of weather stations, which report meteorological conditions in and around New York City, as part of the Optical Remote Sensing Laboratory of The City College of New York (ORSL). Of interest to this study is the data obtained from wind profiler station LSC01. The 915 MHz wind profiler is located 30m above the ground on the roof of the Liberty Science Center in Jersey City, NJ. It is a Vaisala Wind Profiler LAP 3000 with a wavelength of ~34cm, which means that the instrument responds primarily to Bragg backscattering. Can a seasonal urban boundary layer climatology be extrapolated from the data obtained from the wind profiler? What is the timing of boundary layer evolution and collapse over Jersey City? How effective is the profiler under cloudy skies and even in light rain or snow? This study examines the entire time period covered by the wind profile (2007 to present) and selects a series of clear days and a series of cloudy days. The top of the urban boundary layer is subjectively located from each half hour time stamp of signal to noise values. The urban boundary layer heights are recorded for clear and then cloudy days. Then the days are sorted seasonally (DJF, MAM, JJA, SON). A seasonal mean is calculated for every half hour time step. Finally a time series of seasonal urban boundary layer heights is constructed, and the timing of the urban boundary layer height maximum and time evolution and collapse of the boundary layer are generalized. A comparison is made against urban boundary layer heights obtained from Modern-Era Retrospective Analysis For Research And Applications (MERRA).

[Characteristics of main layer and regeneration layer of Haloxylon ammodendron plantations at different ages on the southern edge of the Gurbantunggut Desert, Northwest China].

PubMed

Chen, Qi Min; Luo, Qing Hong; Ning, Hu Sen; Zhao, Cheng Yi; Duan, Wen Biao

2017-03-18

The population structure characteristics, natural regeneration, and the influential factors of Haloxylon ammodendron plantations at six different stand ages on the southern edge of the Gurbantunggut Desert were studied. The results showed that H. ammodendron plantation at the stand age of 7 could naturally regenerate. At the stand age of 17, the densities of the seedlings (＜30 cm height), saplings (30≤H＜50 height), and small trees (≥50 cm height) reached optimal class, and the mean height and base diameter of the small tress reached 1.10 m and 1.91 cm, respectively. The parent trees in H. ammodendron plantation at the stand age of 20 grew best. The height of 35% individuals grew up to 2.50-3.00 m, and the basal stem diameter of 23.1% individuals grew up to 8.00-10.00 cm. The height and diameter growth of the parent trees in H. ammodendron plantation at the stand age of 33 apparently declined, but the regeneration ability by natural seed dispersal was still strong. The regeneration density of natural seed dispersal showed the greatest correlation with the available nitrogen content in 0-100 cm soil layer (0.87), followed by the soil rapidly available phosphorus content (0.84) and the soil water content (0.79). The soils with pH 8.1-8.6 did not limit the nutrient growth of the regeneration layer. In the main stand layer, the individual density of whole regeneration layer showed the greatest correlation with the biomass of the parent trees (0.77), while the density of regeneration layer of the small trees showed the greatest correlation with the planting density (0.71) and the age of the parent trees (0.70).

On the performance of surface renewal analysis to estimate sensible heat flux over two growing rice fields under the influence of regional advection

NASA Astrophysics Data System (ADS)

Castellví, F.; Snyder, R. L.

2009-09-01

SummaryHigh-frequency temperature data were recorded at one height and they were used in Surface Renewal (SR) analysis to estimate sensible heat flux during the full growing season of two rice fields located north-northeast of Colusa, CA (in the Sacramento Valley). One of the fields was seeded into a flooded paddy and the other was drill seeded before flooding. To minimize fetch requirements, the measurement height was selected to be close to the maximum expected canopy height. The roughness sub-layer depth was estimated to discriminate if the temperature data came from the inertial or roughness sub-layer. The equation to estimate the roughness sub-layer depth was derived by combining simple mixing-length theory, mixing-layer analogy, equations to account for stable atmospheric surface layer conditions, and semi-empirical canopy-architecture relationships. The potential for SR analysis as a method that operates in the full surface boundary layer was tested using data collected over growing vegetation at a site influenced by regional advection of sensible heat flux. The inputs used to estimate the sensible heat fluxes included air temperature sampled at 10 Hz, the mean and variance of the horizontal wind speed, the canopy height, and the plant area index for a given intermediate height of the canopy. Regardless of the stability conditions and measurement height above the canopy, sensible heat flux estimates using SR analysis gave results that were similar to those measured with the eddy covariance method. Under unstable cases, it was shown that the performance was sensitive to estimation of the roughness sub-layer depth. However, an expression was provided to select the crucial scale required for its estimation.

Evidence of constitutional MLH1 epimutation associated to transgenerational inheritance of cancer susceptibility.

PubMed

Crépin, Michel; Dieu, Marie-Claire; Lejeune, Sophie; Escande, Fabienne; Boidin, Denis; Porchet, Nicole; Morin, Gilles; Manouvrier, Sylvie; Mathieu, Michèle; Buisine, Marie-Pierre

2012-01-01

Constitutional epimutations of DNA mismatch repair (MMR) genes have been recently reported as a possible cause of Lynch syndrome. However, little is known about their prevalence, the risk of transmission through the germline and the risk for carriers to develop cancers. In this study, we evaluated the contribution of constitutional epimutations of MMR genes in Lynch syndrome. A cohort of 134 unrelated Lynch syndrome-suspected patients without MMR germline mutation was screened for constitutional epimutations of MLH1 and MSH2 by quantitative bisulfite pyrosequencing. Patients were also screened for the presence of EPCAM deletions, a possible cause of MSH2 methylation. Tumors from patients with constitutional epimutations were extensively analyzed. We identified a constitutional MLH1 epimutation in two proband patients. For one of them, we report for the first time evidence of transmission to two children who also developed early colonic tumors, indicating that constitutional MLH1 epimutations are associated to a real risk of transgenerational inheritance of cancer susceptibility. Moreover, a somatic BRAF mutation was detected in one affected child, indicating that tumors from patients carrying constitutional MLH1 epimutation can mimic MSI-high sporadic tumors. These findings may have important implications for future diagnostic strategies and genetic counseling. © 2011 Wiley Periodicals, Inc.

Parenting Deficits of Mothers Living with HIV/AIDS who have Young Children

PubMed Central

Murphy, Debra A.; Armistead, Lisa; Marelich, William D.; Herbeck, Diane M.

2014-01-01

The purpose of this study was to examine a model of the relationships between parenting deficits and skills, along with child outcomes, in a sample of mothers living with HIV (MLH) and their 6 to 14 year old children. Sixty-two MLH (61% Latina, 26% black, 3% white, & 10% multiracial) and their well children (age 6 – 14) were recruited from the greater Los Angeles, California, region to participate in an intervention (IMAGE: Improving Mothers’ parenting Abilities, Growth, and Effectiveness) designed to assist MLH with parenting and self-care skills. Constructs examined included parenting deficits, parenting skills, and child outcomes. Covariance structural modeling was used for the analyses. Covariance structural modeling confirmed the hypothesized set of construct associations. As predicted, fewer parenting deficits were associated with better parenting skills, which, in turn, were associated with better child outcomes. This study delineated further the parenting issues with which MLH struggle, providing information on the interventions needed for this population. MLH who have little confidence they can enact parenting skills and limited knowledge of basic parenting practices appear to be less likely to provide family routines consistently, monitor their children, or to engender family cohesion or a close parent-child relationship. Such parenting skills were found to be associated with child functioning. PMID:25620995

Mutational Analysis of Mismatch Repair Genes, hMLH1 and hMSH2, in Sporadic Endometrial Carcinomas with Microsatellite Instability

PubMed Central

Kobayashi, Kanji; Matsushima, Mieko; Koi, Sumiko; Saito, Hiroko; Sagae, Satoru; Kudo, Ryuichi

1996-01-01

Microsatellite instability, monitored by replication error (RER), bas been observed in both sporadic and hereditary types of endometrial carcinoma. In the hereditary tumors, this instability is considered to be caused by a germline defect in the DNA mismatch‐repair system. We previously reported that nearly one‐quarter of sporadic endometrial carcinomas examined revealed an RER‐positive phenotype at multiple microsatellite loci. To investigate the role of genetic alterations of DNA mismatch‐repair genes in sporadic endometrial carcinomas, we screened 18 RER(+) endometrial carcinomas for mutations of hMLH1 and hMSH2. Although we found no germline mutations, we detected two somatic mutations of hMLH1 in a single endometrial cancer; these two mutations had occurred on different alleles, suggesting that two separate mutational events had affected both copies of hMLH1 in this particular tumor. These data implied that mutations of hMLH1 or hMSH2 play limited roles in the development of sporadic endometrial carcinomas, and that the tumors with genetic instability might have alterations of other mismatch‐repair genes, such as hPMS1 and hPMS2, or of unknown genes related to the mismatch‐repair system. PMID:8609062

A Lidar Point Cloud Based Procedure for Vertical Canopy Structure Analysis And 3D Single Tree Modelling in Forest

PubMed Central

Wang, Yunsheng; Weinacker, Holger; Koch, Barbara

2008-01-01

A procedure for both vertical canopy structure analysis and 3D single tree modelling based on Lidar point cloud is presented in this paper. The whole area of research is segmented into small study cells by a raster net. For each cell, a normalized point cloud whose point heights represent the absolute heights of the ground objects is generated from the original Lidar raw point cloud. The main tree canopy layers and the height ranges of the layers are detected according to a statistical analysis of the height distribution probability of the normalized raw points. For the 3D modelling of individual trees, individual trees are detected and delineated not only from the top canopy layer but also from the sub canopy layer. The normalized points are resampled into a local voxel space. A series of horizontal 2D projection images at the different height levels are then generated respect to the voxel space. Tree crown regions are detected from the projection images. Individual trees are then extracted by means of a pre-order forest traversal process through all the tree crown regions at the different height levels. Finally, 3D tree crown models of the extracted individual trees are reconstructed. With further analyses on the 3D models of individual tree crowns, important parameters such as crown height range, crown volume and crown contours at the different height levels can be derived. PMID:27879916

Estimating Mixing Heights Using Microwave Temperature Profiler

NASA Technical Reports Server (NTRS)

Nielson-Gammon, John; Powell, Christina; Mahoney, Michael; Angevine, Wayne

2008-01-01

A paper describes the Microwave Temperature Profiler (MTP) for making measurements of the planetary boundary layer thermal structure data necessary for air quality forecasting as the Mixing Layer (ML) height determines the volume in which daytime pollution is primarily concentrated. This is the first time that an airborne temperature profiler has been used to measure the mixing layer height. Normally, this is done using a radar wind profiler, which is both noisy and large. The MTP was deployed during the Texas 2000 Air Quality Study (TexAQS-2000). An objective technique was developed and tested for estimating the ML height from the MTP vertical temperature profiles. In order to calibrate the technique and evaluate the usefulness of this approach, estimates from a variety of measurements during the TexAQS-2000 were compared. Estimates of ML height were used from radiosondes, radar wind profilers, an aerosol backscatter lidar, and in-situ aircraft measurements in addition to those from the MTP.

HSTRESS: A computer program to calculate the height of a hydraulic fracture in a multi-layered stress medium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Warpinski, N.R.

A computer code for calculating hydraulic fracture height and width in a stressed-layer medium has been modified for easy use on a personal computer. HSTRESS allows for up to 51 layers having different thicknesses, stresses and fracture toughnesses. The code can calculate fracture height versus pressure or pressure versus fracture height, depending on the design model in which the data will be used. At any pressure/height, a width profile is calculated and an equivalent width factor and flow resistance factor are determined. This program is written in FORTRAN. Graphics use PLOT88 software by Plotworks, Inc., but the graphics software mustmore » be obtained by the user because of licensing restrictions. A version without graphics can also be run. This code is available through the National Energy Software Center (NESC), operated by Argonne National Laboratory. 14 refs., 21 figs.« less

MLH1-Silenced and Non-Silenced Subgroups of Hypermutated Colorectal Carcinomas Have Distinct Mutational Landscapes

PubMed Central

Donehower, Lawrence A.; Creighton, Chad J.; Schultz, Nikolaus; Shinbrot, Eve; Chang, Kyle; Gunaratne, Preethi H.; Muzny, Donna; Sander, Chris; Hamilton, Stanley R.; Gibbs, Richard A.; Wheeler, David

2014-01-01

Approximately 15% of colorectal carcinomas (CRC) exhibit a hypermutated genotype accompanied by high levels of microsatellite instability (MSI-H) and defects in DNA mismatch repair. These tumors, unlike the majority of colorectal carcinomas, are often diploid, exhibit frequent epigenetic silencing of the MLH1 DNA mismatch repair gene, and have a better clinical prognosis. As an adjunct study to The Cancer Genome Atlas consortium that recently analyzed 224 colorectal cancers by whole exome sequencing, we compared the 35 CRC (15.6%) with a hypermutated genotype to those with a non-hypermutated genotype. We found that 22 (63%) of hypermutated CRC exhibited transcriptional silencing of the MLH1 gene, a high frequency of BRAF V600E gene mutations and infrequent APC and KRAS mutations, a mutational pattern significantly different from their non-hypermutated counterparts. However, the remaining 13 (37%) hypermutated CRC lacked MLH1 silencing, contained tumors with the highest mutation rates (“ultramutated” CRC), and exhibited higher incidences of APC and KRAS mutations, but infrequent BRAF mutations. These patterns were confirmed in an independent validation set of 250 exome-sequenced CRC. Analysis of mRNA and microRNA expression signatures revealed that hypermutated CRC with MLH1 silencing had greatly reduced levels of WNT signaling and increased BRAF signaling relative non-hypermutated CRC. Our findings suggest that hypermutated CRC include one subgroup with fundamentally different pathways to malignancy than the majority of CRC. Examination of MLH1 expression status and frequencies of APC, KRAS, and BRAF mutation in CRC may provide a useful diagnostic tool that could supplement the standard microsatellite instability assays and influence therapeutic decisions. PMID:22899370

MLH1-rheMac hereditary nonpolyposis colorectal cancer syndrome in rhesus macaques.

PubMed

Brammer, David W; Gillespie, Patrick J; Tian, Mei; Young, Daniel; Raveendran, Muthuswamy; Williams, Lawrence E; Gagea, Mihai; Benavides, Fernando J; Perez, Carlos J; Broaddus, Russell R; Bernacky, Bruce J; Barnhart, Kirstin F; Alauddin, Mian M; Bhutani, Manoop S; Gibbs, Richard A; Sidman, Richard L; Pasqualini, Renata; Arap, Wadih; Rogers, Jeffrey; Abee, Christian R; Gelovani, Juri G

2018-03-13

Over the past two decades, 33 cases of colonic adenocarcinomas have been diagnosed in rhesus macaques ( Macaca mulatta ) at the nonhuman primate colony of the Keeling Center for Comparative Medicine and Research at The University of Texas MD Anderson Cancer Center. The distinctive feature in these cases, based on PET/computed tomography (CT) imaging, was the presence of two or three tumor lesions in different locations, including proximal to the ileocecal juncture, proximal to the hepatic flexure, and/or in the sigmoid colon. These colon carcinoma lesions selectively accumulated [ 18 F]fluorodeoxyglucose ([ 18 F]FDG) and [ 18 F]fluoroacetate ([ 18 F]FACE) at high levels, reflecting elevated carbohydrate and fatty acid metabolism in these tumors. In contrast, the accumulation of [ 18 F]fluorothymidine ([ 18 F]FLT) was less significant, reflecting slow proliferative activity in these tumors. The diagnoses of colon carcinomas were confirmed by endoscopy. The expression of MLH1, MSH2, and MSH6 proteins and the degree of microsatellite instability (MSI) was assessed in colon carcinomas. The loss of MLH1 protein expression was observed in all tumors and was associated with a deletion mutation in the MLH1 promoter region and/or multiple single-nucleotide polymorphism (SNP) mutations in the MLH1 gene. All tumors exhibited various degrees of MSI. The pedigree analysis of this rhesus macaque population revealed several clusters of affected animals related to each other over several generations, suggesting an autosomal dominant transmission of susceptibility for colon cancer. The newly discovered hereditary nonpolyposis colorectal cancer syndrome in rhesus macaques, termed MLH1 -rheMac, may serve as a model for development of novel approaches to diagnosis and therapy of Lynch syndrome in humans. Copyright © 2018 the Author(s). Published by PNAS.

Performance of Lynch syndrome predictive models in quantifying the likelihood of germline mutations in patients with abnormal MLH1 immunoexpression.

PubMed

Cabreira, Verónica; Pinto, Carla; Pinheiro, Manuela; Lopes, Paula; Peixoto, Ana; Santos, Catarina; Veiga, Isabel; Rocha, Patrícia; Pinto, Pedro; Henrique, Rui; Teixeira, Manuel R

2017-01-01

Lynch syndrome (LS) accounts for up to 4 % of all colorectal cancers (CRC). Detection of a pathogenic germline mutation in one of the mismatch repair genes is the definitive criterion for LS diagnosis, but it is time-consuming and expensive. Immunohistochemistry is the most sensitive prescreening test and its predictive value is very high for loss of expression of MSH2, MSH6, and (isolated) PMS2, but not for MLH1. We evaluated if LS predictive models have a role to improve the molecular testing algorithm in this specific setting by studying 38 individuals referred for molecular testing and who were subsequently shown to have loss of MLH1 immunoexpression in their tumors. For each proband we calculated a risk score, which represents the probability that the patient with CRC carries a pathogenic MLH1 germline mutation, using the PREMM 1,2,6 and MMRpro predictive models. Of the 38 individuals, 18.4 % had a pathogenic MLH1 germline mutation. MMRpro performed better for the purpose of this study, presenting a AUC of 0.83 (95 % CI 0.67-0.9; P < 0.001) compared with a AUC of 0.68 (95 % CI 0.51-0.82, P = 0.09) for PREMM 1,2,6 . Considering a threshold of 5 %, MMRpro would eliminate unnecessary germline mutation analysis in a significant proportion of cases while keeping very high sensitivity. We conclude that MMRpro is useful to correctly predict who should be screened for a germline MLH1 gene mutation and propose an algorithm to improve the cost-effectiveness of LS diagnosis.

Germline MLH1, MSH2 and MSH6 variants in Brazilian patients with colorectal cancer and clinical features suggestive of Lynch Syndrome.

PubMed

Schneider, Nayê Balzan; Pastor, Tatiane; Paula, André Escremim de; Achatz, Maria Isabel; Santos, Ândrea Ribeiro Dos; Vianna, Fernanda Sales Luiz; Rosset, Clévia; Pinheiro, Manuela; Ashton-Prolla, Patricia; Moreira, Miguel Ângelo Martins; Palmero, Edenir Inêz

2018-05-01

Lynch syndrome (LS) is the most common hereditary colorectal cancer syndrome, caused by germline mutations in one of the major genes involved in mismatch repair (MMR): MLH1, MSH2, MSH6 and more rarely, PMS2. Recently, germline deletions in EPCAM have been also associated to the syndrome. Most of the pathogenic MMR mutations found in LS families occur in MLH1 or MSH2. Gene variants include missense, nonsense, frameshift mutations, large genomic rearrangements and splice-site variants and most of the studies reporting the molecular characterization of LS families have been conducted outside South America. In this study, we analyzed 60 unrelated probands diagnosed with colorectal cancer and LS criteria. Testing for germline mutations and/or rearrangements in the most commonly affected MMR genes (MLH1, MSH2, EPCAM and MSH6) was done by Sanger sequencing and MLPA. Pathogenic or likely pathogenic variants were identified in MLH1 or MSH2 in 21 probands (35.0%). Of these, approximately one-third were gene rearrangements. In addition, nine variants of uncertain significance (VUS) were identified in 10 (16.6%) of the sixty probands analyzed. Other four novel variants were identified, only in MLH1. Our results suggest that MSH6 pathogenic variants are not common among Brazilian LS probands diagnosed with CRC and that MMR gene rearrangements account for a significant proportion of the germline variants in this population underscoring the need to include rearrangement analysis in the molecular testing of Brazilian individuals with suspected Lynch syndrome. © 2018 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

The effects of anticancer drugs TSA and GSK on spermatogenesis in male mice.

PubMed

Song, Wen-Yan; Yang, Qing-Ling; Zhao, Wan-Li; Jin, Hai-Xia; Yao, Gui-Dong; Peng, Zhao-Feng; Shi, Sen-Lin; Yang, Hong-Yi; Zhang, Xiang-Yang; Sun, Ying-Pu

2016-01-01

The effect of anticancer drugs Trichostation A (TSA) and GSK2126458 (GSK) on genetic recombination of sperm meiosis in mice was investigated, and their clinical feasibility of fertility preservation in cancer patients was also assessed. Eighteen Kunming mice were randomly given TSA or GSK at the concentrations of 0, 0.1 and 0.2 umol/L for three months. Immunofluorescence was used to evaluate the genetic recombination of homologous chromosomes and fidelity of chromosome synapsis. Sperm density, motility and viability were also examined to investigate the spermatogenic function. The average number of MLH1 foci in each spermatocyte was greatly higher in TSA (0.1) group than that in control (P<0.05), but no difference with the TSA (0.2) group (P>0.05). The frequency of SC with no MLH1 foci was lower while the frequency of SC with one MLH1 foci was higher in spermatocyte of mice with different doses of TSA compared with controls (P<0.05). The weight of left testis in TSA (0.1) group was significant decreased compared with that in control (P<0.05). However, no significant differences were observed in average number of MLH1, frequency of SC with 0-3 MLH1 foci, spermatocyte percentage of XY chromosomes containing MLH1 foci and percentages of cells containing gaps and splits among groups with or without the treatment of GSK. Furthermore, there were no statistical differences in body weight, testicular weight, sperm density, sperm motility and sperm viability among the three groups. TSA increased genetic recombination frequency of spermatocyte meiosis. GSK had no significant effect on genetic recombination frequency of spermatocyte meiosis and spermatogenic function.

Enhancement of MSH2-MSH3-mediated mismatch recognition by the yeast MLH1-PMS1 complex.

PubMed

Habraken, Y; Sung, P; Prakash, L; Prakash, S

1997-10-01

DNA mismatch repair has a key role in maintaining genomic stability. Defects in mismatch repair cause elevated spontaneous mutation rates and increased instability of simple repetitive sequences, while mutations in human mismatch repair genes result in hereditary nonpolyposis colorectal cancers. Mismatch recognition represents the first critical step of mismatch repair. Genetic and biochemical studies in yeast and humans have indicated a requirement for MSH2-MSH3 and MSH2-MSH6 heterodimers in mismatch recognition. These complexes have, to some extent, overlapping mismatch binding specificities. MLH1 and PMS1 are the other essential components of mismatch repair, but how they function in this process is not known. We have purified the yeast MLH1-PMS1 heterodimer to near homogeneity, and examined its effect on MSH2-MSH3 binding to DNA mismatches. By itself, the MLH1-PMS1 complex shows no affinity for mismatched DNA, but it greatly enhances the mismatch binding ability of MSH2-MSH3.

[Expression difference of DNA mismatch repair gene hMLH1 and hMSH2 between schistosomiasis-associated colorectal cancer and sporadic colorectal cancer].

PubMed

Chen, Yinbo; Liu, Zhuo; Qian, Jun; Feng, Haiyang; Li, Dechuan; Fan, Yongtian

2016-01-01

To investigate the expression difference of DNA mismatch repair gene hMLH1 and hMSH2 between schistosomiasis-associated colorectal cancer and sporadic colorectal cancer. Clinical and pathological data of colorectal cancer patients receiving operations in Zhejiang Cancer Hospital between January 2008 and December 2010 were retrospectively analyzed. Patients were divided into schistosomiasis group(n=80) and sporadic group (n=258) according to the preoperative history and pathologic results. Pathological specimens were collected and tissue chips were made to analyze the expression of hMLH1 and hMSH2 by immunohistochemistr. Compared with sporadic group, older age [(62.2 ± 9.6) year vs. (57.2 ± 11.7) year, P=0.000)], lower platelet level [(197.0 ± 59.6) × 10(9)/L vs. (217.0 ± 84.3) × 10(9)/L, P=0.02] and lower WBC level [(5.9 ± 1.9) × 10(9)/L vs. (6.6 ± 2.8) × 10(9)/L, P=0.02] were found in schistosomiasis group. Ratio of low differentiation-undifferentiation tumor was significantly higher in schistosomiasis group [44.2% (34/77) vs. 4.9% (12/247), P<0.05]. Lower positive rate of hMLH1 expression [77.5% (62/80) vs. 98.1% (253/258), P=0.000] and hMSH2 expression [75.0% (60/80) vs. 95.3% (246/258), P=0.000] was found in schistosomiasis group compared with sporadic group. Concurrent schistosomiasis was one of the risk factors of hMLH1/hMSH2 deficiency (RR: 0.913, 95% CI: 0.836-0.997, P=0.043), but not an independent factor (RR: 0.951, 95% CI: 0.867-1.043, P=0.286). Schistosomiasis is associated with lower positive expression of hMLH1 and hMSH2, which indicates that hMLH1/hMSH2 deficiency may be a potential mechanism of schistosomiasis inducing carcinogenesis of colorectal cancer.

Transgenerational Radiation Epigenetics

DTIC Science & Technology

2014-11-01

Cxcl12, Cyp1b1, Fhit, Mlh1 , Mthfr, Prdm2, Rarb, Rassf1, Rassf2, Sema3b, Slit2, Sfrp1, Tcf21; Genes with Metastatic Potential: Anxa5, Dlg2, Dusp6...Anxa5, Apc, Bcl2, Birc5, Braf, Cadm1, Cdh1, Cdh13, Cdkn2a, Dlc1, Egfr, Erbb2, Erbb3, Hgf, Hras1, Kras, Lck, Mlh1 , Mmp9, Nf1, Nfkb1, Ptgs2, Sema3b...Trp53; Immune response genes: Bcl2, Cadm1, Csf3, Cxcl12, Cxcl13, Irf4, Lck, Mlh1 , Nfkb1, Pax5, Stat1, Stat2, Tgfb1, Tnf, Trp53, Vegfa; and

Assumptions about footprint layer heights influence the quantification of emission sources: a case study for Cyprus

NASA Astrophysics Data System (ADS)

Hüser, Imke; Harder, Hartwig; Heil, Angelika; Kaiser, Johannes W.

2017-09-01

Lagrangian particle dispersion models (LPDMs) in backward mode are widely used to quantify the impact of transboundary pollution on downwind sites. Most LPDM applications count particles with a technique that introduces a so-called footprint layer (FL) with constant height, in which passing air tracer particles are assumed to be affected by surface emissions. The mixing layer dynamics are represented by the underlying meteorological model. This particle counting technique implicitly assumes that the atmosphere is well mixed in the FL. We have performed backward trajectory simulations with the FLEXPART model starting at Cyprus to calculate the sensitivity to emissions of upwind pollution sources. The emission sensitivity is used to quantify source contributions at the receptor and support the interpretation of ground measurements carried out during the CYPHEX campaign in July 2014. Here we analyse the effects of different constant and dynamic FL height assumptions. The results show that calculations with FL heights of 100 and 300 m yield similar but still discernible results. Comparison of calculations with FL heights constant at 300 m and dynamically following the planetary boundary layer (PBL) height exhibits systematic differences, with daytime and night-time sensitivity differences compensating for each other. The differences at daytime when a well-mixed PBL can be assumed indicate that residual inaccuracies in the representation of the mixing layer dynamics in the trajectories may introduce errors in the impact assessment on downwind sites. Emissions from vegetation fires are mixed up by pyrogenic convection which is not represented in FLEXPART. Neglecting this convection may lead to severe over- or underestimations of the downwind smoke concentrations. Introducing an extreme fire source from a different year in our study period and using fire-observation-based plume heights as reference, we find an overestimation of more than 60  % by the constant FL height assumptions used for surface emissions. Assuming a FL that follows the PBL may reproduce the peak of the smoke plume passing through but erroneously elevates the background for shallow stable PBL heights. It might thus be a reasonable assumption for open biomass burning emissions wherever observation-based injection heights are not available.

Clinical Significance of MLH1 Methylation and CpG Island Methylator Phenotype as Prognostic Markers in Patients with Gastric Cancer

PubMed Central

Shigeyasu, Kunitoshi; Nagasaka, Takeshi; Mori, Yoshiko; Yokomichi, Naosuke; Kawai, Takashi; Fuji, Tomokazu; Kimura, Keisuke; Umeda, Yuzo; Kagawa, Shunsuke; Goel, Ajay; Fujiwara, Toshiyoshi

2015-01-01

Background To improve the outcome of patients suffering from gastric cancer, a better understanding of underlying genetic and epigenetic events in this malignancy is required. Although CpG island methylator phenotype (CIMP) and microsatellite instability (MSI) have been shown to play pivotal roles in gastric cancer pathogenesis, the clinical significance of these events on survival outcomes in patients with gastric cancer remains unknown. Methods This study included a patient cohort with pathologically confirmed gastric cancer who had surgical resections. A cohort of 68 gastric cancers was analyzed. CIMP and MSI statuses were determined by analyzing promoter CpG island methylation status of 28 genes/loci, and genomic instability at 10 microsatellite markers, respectively. A Cox’s proportional hazards model was performed for multivariate analysis including age, stage, tumor differentiation, KRAS mutation status, and combined CIMP/MLH1 methylation status in relation to overall survival (OS). Results By multivariate analysis, longer OS was significantly correlated with lower pathologic stage (P = 0.0088), better tumor differentiation (P = 0.0267) and CIMP-high and MLH1 3' methylated status (P = 0.0312). Stratification of CIMP status with regards to MLH1 methylation status further enabled prediction of gastric cancer prognosis. Conclusions CIMP and/or MLH1 methylation status may have a potential to be prognostic biomarkers for patients with gastric cancer. PMID:26121593

Constitutional mismatch repair deficiency and Lynch syndrome among consecutive Arab Bedouins with colorectal cancer in Israel.

PubMed

Abu Freha, Naim; Leibovici Weissman, Yaara; Fich, Alexander; Barnes Kedar, Inbal; Halpern, Marisa; Sztarkier, Ignacio; Behar, Doron M; Arbib Sneh, Orly; Vilkin, Alex; Baris, Hagit N; Gingold, Rachel; Lejbkowicz, Flavio; Niv, Yaron; Goldberg, Yael; Levi, Zohar

2018-01-01

We assessed the molecular characteristics and the frequency of mutations in mismatch-repair genes among Bedouin patients with colorectal cancer (CRC) in Israel. Bedouin patients with a diagnosis of CRC at a major hospital in the southern part of Israel were deemed eligible for this study. The primary screening method was immunohistochemical staining for mismatch-repair proteins (MLH1, MSH2, MSH6, and PMS2). For subjects with abnormal immunohistochemical staining, we performed microsatellite instability (MSI) analyses, and for tumors with a loss of MLH1 expression we also performed BRAF testing. In MSI high cases we searched further for germline mutations. Of the 24 patients enrolled, four subjects (16.7%) had MSI high tumors: one subject was found to harbor a biallelic PMS2 mutation, one subject had Lynch syndrome (LS) with MSH6 mutation and two subjects had a loss of MLH1/PMS2 proteins/BRAF wild type /normal MLH1 sequence. Ten patients (41.7%) were younger than 50 at the time of diagnosis and none had first degree relatives with CRC. In conclusion, in this cohort of 24 consecutive Arab Bedouins with CRC, one patient was found to harbor a constitutional mismatch repair deficiency, one patient had LS with MSH6 mutation, and two patients had unresolved loss of MLH1/PMS2 proteins/BRAF wild type phenotype.

Planetary Boundary Layer Patterns, Height Variability and their Controls over the Indian Subcontinent with respect to Monsoon

NASA Astrophysics Data System (ADS)

Sathyanadh, A.; Karipot, A.; Prabhakaran, T.

2016-12-01

Planetary boundary layer (PBL) height and its controlling factors undergo large variations at different spatio-temporal scales over land regions. In the present study, Modern Era Retrospective analysis for Research and Applications (MERRA) data products are used to investigate variations of PBL height and its controls in relation to different phases of Indian monsoon. MERRA PBL height validations carried out against those estimated from radiosonde and Global Positioning System Radio Occultation atmospheric profiles revealed fairly good agreement. Different PBL patterns are identified in terms of maximum height, its time of occurrence and growth rate, and they vary with respect to geographical locations, terrain characteristics and monsoon circulation. The pre-monsoon boundary layers are the deepest over the region, often exceeding 4 km and grow at a rate of approximately 400 m hr-1. Large nocturnal BL depths, possibly related to weakly convective residual layers, are another feature noted during dry conditions. Monsoon BLs are generally shallower, except where rainfall is scanty. The break-monsoon periods have slightly deeper BLs than the active monsoon phase. The controlling factors for the observed boundary layer behaviour are investigated using supplementary MERRA datasets. Evaporative fraction is found to have dominant control on the PBL height varying with seasons and regions. The characteristics and controls of wet and dry boundary layer regimes over inland and coastal locations are different. The fractional diffusion (ratio of non-local and total diffusion) coefficient analyses indicated that enhanced entrainment during monsoon contributes to reduction in PBLH unlike in the dry period. The relationship between controls and PBLH are better defined over inland than coastal regions. The wavelet cross spectral analysis revealed temporal variations in dominant contributions from the controlling factors at different periodicities during the course of the year.

Assessment of mixed-layer height estimation from single-wavelength ceilometer profiles

EPA Science Inventory

Differing boundary/mixed-layer height measurement methods were assessed in moderately polluted and clean environments, with a focus on the Vaisala CL51 ceilometer. This intercomparison was performed as part of ongoing measurements at the Chemistry And Physics of the Atmospheric B...

Hyaluronan Tumor Cell Interactions in Prostate Cancer Growth and Survival

DTIC Science & Technology

2008-12-01

different outcomes. For example, colo- rectal cancers can be grouped into DNA mismatch repair-proficient, MLH1 negative and presumed Lynch syndrome. Although...a prognostic factor in DNA-mismatch repair-proficient (MMR-proficient) and presumed Lynch syndrome forms of colorectal cancer but not in MLH1 negative

Optimal control of build height utilizing optical profilometry in cold spray deposits

NASA Astrophysics Data System (ADS)

Chakraborty, Abhijit; Shishkin, Sergey; Birnkrant, Michael J.

2017-04-01

Part-to-part variability and poor part quality due to failure to maintain geometric specifications pose a challenge for adopting Additive Manufacturing (AM) as a viable manufacturing process. In recent years, In-process Monitoring and Control (InPMC) has received a lot of attention as an approach to overcome these obstacles. The ability to sense geometry of the deposited layers accurately enables effective process monitoring and control of AM application. This paper demonstrates an application of geometry sensing technique for the coating deposition Cold Spray process, where solid powders are accelerated through a nozzle, collides with the substrate and adheres to it. Often the deposited surface has shape irregularities. This paper proposes an approach to suppress the iregularities by controlling the deposition height. An analytical control-oriented model is developed that expresses the resulting height of deposit as an integral function of nozzle velocity and angle. In order to obtain height information at each layer, a Micro-Epsilon laser line scanner was used for surface profiling after each deposition. This surface profile information, specifically the layer height, was then fed back to an optimal control algorithm which manipulated the nozzle speed to control the layer height to a pre specified height. While the problem is heavily nonlinear, we were able to transform it into equivalent Optimal Control problem linear w.r.t. input. That enabled development of two solution methods: one is fast and approximate, while another is more accurate but still efficient.

Algae separation from urban landscape water using a high density microbubble layer enhanced by micro-flocculation.

PubMed

Chen, Shuwen; Xu, Jingcheng; Liu, Jia; Wei, Qiaoling; Li, Guangming; Huang, Xiangfeng

2014-01-01

Eutrophication of raw water results in outbreaks of algae, which hinders conventional water treatment. In this study, high density microbubble layers combined with micro-flocculation was adopted to remove algae from urban landscape water, and the effects of pressure, hydraulic loading, microbubble layer height and flocculation dosage on the removal efficiency for algae were studied. The greatest removal efficiency for algae, chemical oxygen demand, nitrogen and phosphorus was obtained at 0.42 MPa with hydraulic loading at 5 m/h and a flocculation dosage of 4 mg/L using a microbubble layer with a height of 130 cm. Moreover, the size, clearance distance and concentration of microbubbles were found to be affected by pressure and the height of the microbubble layer. Based on the study, this method was an alternative for algae separation from urban landscape water and water purification.

Amendment to "Analytical Solution for the Convectively-Mixed Atmospheric Boundary Layer": Inclusion of Subsidence

NASA Astrophysics Data System (ADS)

Ouwersloot, H. G.; de Arellano, J. Vilà-Guerau

2013-09-01

In Ouwersloot and Vilà-Guerau de Arellano (Boundary-Layer Meteorol. doi: 10.1007/s10546-013-9816-z , 2013, this issue), the analytical solutions for the boundary-layer height and scalar evolutions are derived for the convective boundary layer, based on the prognostic equations of mixed-layer slab models without taking subsidence into account. Here, we include and quantify the added effect of subsidence if the subsidence velocity scales linearly with height throughout the atmosphere. This enables analytical analyses for a wider range of observational cases. As a demonstration, the sensitivity of the boundary-layer height and the potential temperature jump to subsidence and the free tropospheric stability is graphically presented. The new relations show the importance of the temporal distribution of the surface buoyancy flux in determining the evolution if there is subsidence.

Variations of Scale Height at F-Region Peak Based on Ionosonde Measurements during Solar Maximum over the Crest of Equatorial Ionization Anomaly Region

PubMed Central

Chuo, Yu-Jung

2014-01-01

Scale height is an important parameter in characterizing the shape of the ionosphere and its physical processes. In this study, we attempt to examine and discuss the variation of scale height, H m, around the F-layer peak height during high solar activity at the northern crest of the equatorial ionization anomaly (EIA) region. H m exhibits day-to-day variation and seasonal variation, with a greater average daily variation during daytime in summer. Furthermore, the diurnal variation of H m exhibits an abnormal peak at presunrise during all the seasons, particularly in winter. This increase is also observed in the F2-layer peak height for the same duration with an upward movement associated with thermospheric wind toward the equator; this upward movement increases the N2/O ratio and H m, but it causes a decrease in the F2-layer maximum critical frequency during the presunrise period. PMID:25162048

The height of electron content changes in the ionosphere from ATS 6 beacon data

NASA Technical Reports Server (NTRS)

Davies, K.; Heron, M. L.

1984-01-01

A technique is described which uses relative changes in Faraday rotation and modulation phase of satellite radio signals to determine the median height of the enhancement (or depletion) in the electron density of the ionosphere. During the post sunrise formation of the F layer the incremental layers have a median height of around 210 km (+ or - 40) and in the afternoon the decremental median is above the peak at 340 km (+ or - 40) on a winter day. A winter nighttime enhancement just after midnight appears as a thick layer extending upwards from the peak, with a median height at about 730 km. The method applies to large scale irregularities but not to small, dense, scintillation-causing irregularities for which Faraday and modulation phases do not represent the total electron content.

Improved boundary layer height measurement using a fuzzy logic method: Diurnal and seasonal variabilities of the convective boundary layer over a tropical station

NASA Astrophysics Data System (ADS)

Allabakash, S.; Yasodha, P.; Bianco, L.; Venkatramana Reddy, S.; Srinivasulu, P.; Lim, S.

2017-09-01

This paper presents the efficacy of a "tuned" fuzzy logic method at determining the height of the boundary layer using the measurements from a 1280 MHz lower atmospheric radar wind profiler located in Gadanki (13.5°N, 79°E, 375 mean sea level), India, and discusses the diurnal and seasonal variations of the measured convective boundary layer over this tropical station. The original fuzzy logic (FL) method estimates the height of the atmospheric boundary layer combining the information from the range-corrected signal-to-noise ratio, the Doppler spectral width of the vertical velocity, and the vertical velocity itself, measured by the radar, through a series of thresholds and rules, which did not prove to be optimal for our radar system and geographical location. For this reason the algorithm was tuned to perform better on our data set. Atmospheric boundary layer heights obtained by this tuned FL method, the original FL method, and by a "standard method" (that only uses the information from the range-corrected signal-to-noise ratio) are compared with those obtained from potential temperature profiles measured by collocated Global Positioning System Radio Sonde during years 2011 and 2013. The comparison shows that the tuned FL method is more accurate than the other methods. Maximum convective boundary layer heights are observed between 14:00 and 15:00 local time (LT = UTC + 5:30) for clear-sky days. These daily maxima are found to be lower during winter and postmonsoon seasons and higher during premonsoon and monsoon seasons, due to net surface radiation and convective processes over this region being more intense during premonsoon and monsoon seasons and less intense in winter and postmonsoon seasons.

Analysis of grating doublets for achromatic beam-splitting

PubMed Central

Pacheco, Shaun; Milster, Tom; Liang, Rongguang

2015-01-01

Achromatic beam-splitting grating doublets are designed for both continuous phase and binary phase gratings. By analyzing the sensitivity to lateral shifts between the two grating layers, it is shown that continuous-profile grating doublets are extremely difficult to fabricate. Achromatic grating doublets that have profiles with a constant first spatial derivative are significantly more resistant to lateral shifts between grating layers, where one design case showed a 17 times improvement in performance. Therefore, binary phase, multi-level phase, and blazed grating doublets perform significantly better than continuous phase grating doublets in the presence of a lateral shift between two grating layers. By studying the sensitivity to fabrication errors in the height of both grating layers, one grating layer height can be adjusted to maintain excellent performance over a large wavelength range if the other grating layer is fabricated incorrectly. It is shown in one design case that the performance of an achromatic Dammann grating doublet can be improved by a factor of 215 if the heights of the grating layers are chosen to minimize the performance change in the presence of fabrication errors. PMID:26368261

Pulse-height defect due to electron interaction in dead layers of Ge/Li/ gamma-ray detectors

NASA Technical Reports Server (NTRS)

Larsen, R. N.; Strauss, M. G.

1969-01-01

Study shows the pulse-height degradation of gamma ray spectra in germanium/lithium detectors to be due to electron interaction in the dead layers that exist in all semiconductor detectors. A pulse shape discrimination technique identifies and eliminates these defective pulses.

Deoxyinosine triphosphate induces MLH1/PMS2- and p53-dependent cell growth arrest and DNA instability in mammalian cells

PubMed Central

Yoneshima, Yasuto; Abolhassani, Nona; Iyama, Teruaki; Sakumi, Kunihiko; Shiomi, Naoko; Mori, Masahiko; Shiomi, Tadahiro; Noda, Tetsuo; Tsuchimoto, Daisuke; Nakabeppu, Yusaku

2016-01-01

Deoxyinosine (dI) occurs in DNA either by oxidative deamination of a previously incorporated deoxyadenosine residue or by misincorporation of deoxyinosine triphosphate (dITP) from the nucleotide pool during replication. To exclude dITP from the pool, mammals possess specific hydrolysing enzymes, such as inosine triphosphatase (ITPA). Previous studies have shown that deficiency in ITPA results in cell growth suppression and DNA instability. To explore the mechanisms of these phenotypes, we analysed ITPA-deficient human and mouse cells. We found that both growth suppression and accumulation of single-strand breaks in nuclear DNA of ITPA-deficient cells depended on MLH1/PMS2. The cell growth suppression of ITPA-deficient cells also depended on p53, but not on MPG, ENDOV or MSH2. ITPA deficiency significantly increased the levels of p53 protein and p21 mRNA/protein, a well-known target of p53, in an MLH1-dependent manner. Furthermore, MLH1 may also contribute to cell growth arrest by increasing the basal level of p53 activity. PMID:27618981

Vitamin E Modifies High-Fat Diet-Induced Increase of DNA Strand Breaks, and Changes in Expression and DNA Methylation of Dnmt1 and MLH1 in C57BL/6J Male Mice.

PubMed

Remely, Marlene; Ferk, Franziska; Sterneder, Sonja; Setayesh, Tahereh; Kepcija, Tatjana; Roth, Sylvia; Noorizadeh, Rahil; Greunz, Martina; Rebhan, Irene; Wagner, Karl-Heinz; Knasmüller, Siegfried; Haslberger, Alexander

2017-06-14

Obesity is associated with low-grade inflammation, increased ROS production and DNA damage. Supplementation with antioxidants might ameliorate DNA damage and support epigenetic regulation of DNA repair. C57BL/6J male mice were fed a high-fat (HFD) or a control diet (CD) with and without vitamin E supplementation (4.5 mg/kg body weight (b.w.)) for four months. DNA damage, DNA promoter methylation and gene expression of Dnmt1 and a DNA repair gene ( MLH1 ) were assayed in liver and colon. The HFD resulted in organ specific changes in DNA damage, the epigenetically important Dnmt1 gene, and the DNA repair gene MLH1 . Vitamin E reduced DNA damage and showed organ-specific effects on MLH1 and Dnmt1 gene expression and methylation. These results suggest that interventions with antioxidants and epigenetic active food ingredients should be developed as an effective prevention for obesity-and oxidative stress-induced health risks.

An Inducible, Isogenic Cancer Cell Line System for Targeting the State of Mismatch Repair Deficiency

PubMed Central

Bailis, Julie M.; Gordon, Marcia L.; Gurgel, Jesse L.; Komor, Alexis C.; Barton, Jacqueline K.; Kirsch, Ilan R.

2013-01-01

The DNA mismatch repair system (MMR) maintains genome stability through recognition and repair of single-base mismatches and small insertion-deletion loops. Inactivation of the MMR pathway causes microsatellite instability and the accumulation of genomic mutations that can cause or contribute to cancer. In fact, 10-20% of certain solid and hematologic cancers are MMR-deficient. MMR-deficient cancers do not respond to some standard of care chemotherapeutics because of presumed increased tolerance of DNA damage, highlighting the need for novel therapeutic drugs. Toward this goal, we generated isogenic cancer cell lines for direct comparison of MMR-proficient and MMR-deficient cells. We engineered NCI-H23 lung adenocarcinoma cells to contain a doxycycline-inducible shRNA designed to suppress the expression of the mismatch repair gene MLH1, and compared single cell subclones that were uninduced (MLH1-proficient) versus induced for the MLH1 shRNA (MLH1-deficient). Here we present the characterization of these MMR-inducible cell lines and validate a novel class of rhodium metalloinsertor compounds that differentially inhibit the proliferation of MMR-deficient cancer cells. PMID:24205301

Delay in onset of metabolic alkalosis during regional citrate anti-coagulation in continuous renal replacement therapy with calcium-free replacement solution.

PubMed

See, Kay Choong; Lee, Margaret; Mukhopadhyay, Amartya

2009-01-01

Regional citrate anti-coagulation for continuous renal replacement therapy chelates calcium to produce the anti- coagulation effect. We hypothesise that a calcium-free replacement solution will require less citrate and produce fewer metabolic side effects. Fifty patients, in a Medical Intensive Care Unit of a tertiary teaching hospital (25 in each group), received continuous venovenous hemofiltration using either calcium-containing or calcium-free replacement solutions. Both groups had no significant differences in filter life, metabolic alkalosis, hypernatremia, hypocalcemia, and hypercalcemia. However, patients using calcium-containing solution developed metabolic alkalosis earlier, compared to patients using calcium-free solution (mean 24.6 hours,CI 0.8-48.4 vs. 37.2 hours, CI 9.4-65, P = 0.020). When calcium-containing replacement solution was used, more citrate was required (mean 280 ml/h, CI 227.2-332.8 vs. 265 ml/h, CI 203.4-326.6, P = 0.069), but less calcium was infused (mean 21.2 ml/h, CI 1.2-21.2 vs 51.6 ml/h, CI 26.8-76.4, P < or = 0.0001).

A biphasic dialytic strategy for the treatment of neonatal hyperammonemia

PubMed Central

Avasare, Sonal; Tsai, Eileen; Yadin, Ora; Zaritsky, Joshua

2018-01-01

Background Neonates with inborn errors of metabolism (IEM) often develop hyperammonemia which, if not corrected quickly, may result in poor neurologic outcomes. As pharmacologic therapy cannot rapidly lower ammonia levels, dialysis is frequently required. Both hemodialysis (HD) and standard-dose continuous renal replacement therapy (CRRT) are effective; however, HD may be followed by post-dialytic ammonia rebound, and standard-dose CRRT may not effect a rapid enough decrease in ammonia levels. Case-Diagnosis/Treatment We present two cases of IEM-associated neonatal hyperammonemia in which we employed a biphasic, high-dose CRRT treatment strategy, initially using dialysate flow rates of 5,000 mL/h (approximately 40,000 mL/h/1.73 m2) in order to rapidly decrease ammonia levels, then decreasing the dialysate flow rates to 500 mL/h (approximately 4,000 mL/h/1.73 m2) in order to prevent ammonia rebound. Conclusions This biphasic dialytic treatment strategy for neonatal hyperammonemia effected rapid ammonia reduction without rebound and accomplished during a single dialysis run without equipment changes. PMID:24122260

Vertical leaf mass per area gradient of mature sugar maple reflects both height-driven increases in vascular tissue and light-driven increases in palisade layer thickness.

PubMed

Coble, Adam P; Cavaleri, Molly A

2017-10-01

A key trait used in canopy and ecosystem function modeling, leaf mass per area (LMA), is influenced by changes in both leaf thickness and leaf density (LMA = Thickness × Density). In tall trees, LMA is understood to increase with height through two primary mechanisms: (i) increasing palisade layer thickness (and thus leaf thickness) in response to light and/or (ii) reduced cell expansion and intercellular air space in response to hydrostatic constraints, leading to increased leaf density. Our objective was to investigate within-canopy gradients in leaf anatomical traits in order to understand environmental factors that influence leaf morphology in a sugar maple (Acer saccharum Marshall) forest canopy. We teased apart the effects of light and height on anatomical traits by sampling at exposed and closed canopies that had different light conditions at similar heights. As expected, palisade layer thickness responded strongly to cumulative light exposure. Mesophyll porosity, however, was weakly and negatively correlated with light and height (i.e., hydrostatic gradients). Reduced mesophyll porosity was not likely caused by limitations on cell expansion; in fact, epidermal cell width increased with height. Palisade layer thickness was better related to LMA, leaf density and leaf thickness than was mesophyll porosity. Vein diameter and fraction of vascular tissue also increased with height and LMA, density and thickness, revealing that greater investment in vascular and support tissue may be a third mechanism for increased LMA with height. Overall, decreasing mesophyll porosity with height was likely due to palisade cells expanding into the available air space and also greater investments in vascular and support tissue, rather than a reduction of cell expansion due to hydrostatic constraints. Our results provide evidence that light influences both palisade layer thickness and mesophyll porosity and indicate that hydrostatic gradients influence leaf vascular and support tissues in mature Acer saccharum trees. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

First description of mutational analysis of MLH1, MSH2 and MSH6 in Algerian families with suspected Lynch syndrome.

PubMed

Ziada-Bouchaar, H; Sifi, K; Filali, T; Hammada, T; Satta, D; Abadi, N

2017-01-01

Hereditary non-polyposis colorectal cancer (HNPCC) is an autosomal dominant disorder characterized by the early onset of colorectal cancer (CRC) linked to germline defects in Mismatch Repair (MMR) genes. We present here, the first molecular study of the correlation between CRC and mutations occurring in these genes performed in twenty-one unrelated Algerian families. The presence of germline mutations in MMR genes, MLH1, MSH2 and MSH6 genes was tested by sequencing all exons plus adjacent intronic sequences and Multiplex ligand-dependent probe amplification (MLPA) for testing large genomic rearrangements. Pathogenic mutations were identified in 20 % of families with clinical suspicion on HNPCC. Two novel variants described for the first time in Algerian families were identified in MLH1, c.881_884delTCAGinsCATTCCT and a large deletion in MSH6 gene from a young onset of CRC. Moreover, the variants of MSH2 gene: c.942+3A>T, c.1030C>T, the most described ones, were also detected in Algerian families. Furthermore, the families HNPCC caused by MSH6 germline mutation may show an age of onset that is comparable to this of patients with MLH1 and MSH2 mutations. In this study, we confirmed that MSH2, MLH1, and MSH6 contribute to CRC susceptibility. This work represents the implementation of a diagnostic algorithm for the identification of Lynch syndrome patients in Algerian families.

Risk of colon cancer in hereditary non-polyposis colorectal cancer patients as predicted by fuzzy modeling: Influence of smoking

PubMed Central

Brand, Rhonda M; Jones, David D; Lynch, Henry T; Brand, Randall E; Watson, Patrice; Ashwathnayaran, Ramesh; Roy, Hemant K

2006-01-01

AIM: To investigate whether a fuzzy logic model could predict colorectal cancer (CRC) risk engendered by smoking in hereditary non-polyposis colorectal cancer (HNPCC) patients. METHODS: Three hundred and forty HNPCC mismatch repair (MMR) mutation carriers from the Creighton University Hereditary Cancer Institute Registry were selected for modeling. Age-dependent curves were generated to elucidate the joint effects between gene mutation (hMLH1 or hMSH2), gender, and smoking status on the probability of developing CRC. RESULTS: Smoking significantly increased CRC risk in male hMSH2 mutation carriers (P < 0.05). hMLH1 mutations augmented CRC risk relative to hMSH2 mutation carriers for males (P < 0.05). Males had a significantly higher risk of CRC than females for hMLH1 non smokers (P < 0.05), hMLH1 smokers (P < 0.1) and hMSH2 smokers (P < 0.1). Smoking promoted CRC in a dose-dependent manner in hMSH2 in males (P < 0.05). Females with hMSH2 mutations and both sexes with the hMLH1 groups only demonstrated a smoking effect after an extensive smoking history (P < 0.05). CONCLUSION: CRC promotion by smoking in HNPCC patients is dependent on gene mutation, gender and age. These data demonstrate that fuzzy modeling may enable formulation of clinical risk scores, thereby allowing individualization of CRC prevention strategies. PMID:16874859

[Promoter hypermethylation status of the mismatch repair gene hMLH1 in patients with sporadic renal cell carcinoma].

PubMed

Salinas-Sánchez, Antonio S; Rubio-del-Campo, Antonio; Sánchez-Sánchez, Francisco; Giménez-Bachs, José M; Donate-Moreno, María J; García-Olmo, Dolores C; Escribano-Martínez, Julio

2006-04-01

Epigenetic inactivation is a gene function abnormality that produces no changes in the DNA sequence, with the most frequent epigenetic alteration being hypermethylation of CpG islands in the promoter regions of the genes. Based on recent indications of a potential relationship between mismatch repair genes and renal cell carcinoma (RCC), we were interested in investigating the existence of promoter hypermethylation of the hMLH1 gene in tumor DNA samples from patients with sporadic RCC. Sixty-five tumor tissue specimens were collected consecutively. The DNA was first obtained and purified, then digested with the restriction enzymes Hpa II and Msp I, followed by polimerase chain reaction amplification of 3 promoter regions of the hMLH1 gene, agarose gel electrophoresis, and densitometric analysis of the images of the amplified bands. Mean patient age was 63.7 years. The most frequent cell type was clear cell carcinoma (67.7%). 73.9% of tumors were diagnosed in stages below pT2, 9.3% had gland involvement and 20%, distant metastasis. No somatic hypermethylation was detected in the promoter region of the hMLH1 gene in any of the patients studied. Our data indicate that promoter hypermethylation of the hMLH1 gene is not implicated in the pathogenesis of sporadic RCC, and therefore the existence of another type of mutation, microsatellite instability and/or loss of heterozygosity should be examined to determine the possible role of this gene in sporadic RCC.

Genetic changes of MLH1 and MSH2 genes could explain constant findings on microsatellite instability in intracranial meningioma.

PubMed

Pećina-Šlaus, Nives; Kafka, Anja; Bukovac, Anja; Vladušić, Tomislav; Tomas, Davor; Hrašćan, Reno

2017-07-01

Postreplicative mismatch repair safeguards the stability of our genome. The defects in its functioning will give rise to microsatellite instability. In this study, 50 meningiomas were investigated for microsatellite instability. Two major mismatch repair genes, MLH1 and MSH2, were analyzed using microsatellite markers D1S1611 and BAT26 amplified by polymerase chain reaction and visualized by gel electrophoresis on high-resolution gels. Furthermore, genes DVL3 (D3S1262), AXIN1 (D16S3399), and CDH1 (D16S752) were also investigated for microsatellite instability. Our study revealed constant presence of microsatellite instability in meningioma patients when compared to their autologous blood DNA. Altogether 38% of meningiomas showed microsatellite instability at one microsatellite locus, 16% on two, and 13.3% on three loci. The percent of detected microsatellite instability for MSH2 gene was 14%, and for MLH1, it was 26%, for DVL3 22.9%, for AXIN1 17.8%, and for CDH1 8.3%. Since markers also allowed for the detection of loss of heterozygosity, gross deletions of MLH1 gene were found in 24% of meningiomas. Genetic changes between MLH1 and MSH2 were significantly positively correlated (p = 0.032). We also noted a positive correlation between genetic changes of MSH2 and DVL3 genes (p = 0.034). No significant associations were observed when MLH1 or MSH2 was tested against specific histopathological meningioma subtype or World Health Organization grade. However, genetic changes in DVL3 were strongly associated with anaplastic histology of meningioma (χ 2  = 9.14; p = 0.01). Our study contributes to better understanding of the genetic profile of human intracranial meningiomas and suggests that meningiomas harbor defective cellular DNA mismatch repair mechanisms.

I219V polymorphism in hMLH1 gene in patients affected with ulcerative colitis.

PubMed

Vietri, Maria Teresa; Riegler, Gabriele; De Paola, Marialaura; Simeone, Serena; Boggia, Maria; Improta, Alessia; Parisi, Mariarita; Molinari, Anna Maria; Cioffi, Michele

2009-04-01

hMLH1 gene, lying on chromosome 3p21-23, is a key factor of the mismatch repair (MMR) complex, which amends DNA replication errors. MMR alterations are involved in the development of both hereditary and sporadic forms of colorectal carcinoma related to ulcerative colitis (UC). I219V Polymorphism is located on exon 8 of hMLH1 and provides an aminoacidic substitution of isoleucine to valine, on the protein codon 219. This may affect the speed and fidelity of protein synthesis because of a tRNA paucity or changes in the mRNA secondary structure. Most of the hereditary nonpolyposis colon cancer-associated missense mutations of hMLH1 cause structural changes of the amino- or carboxy-terminal regions, involving the domains that interact with ATP and hPMS2. In this study, we analyzed the hMLH1 I219V polymorphism frequency in colectomized patients with UC. Venous blood from 100 ulcerative patients and 97 apparently healthy subjects has been collected. Out of 100 patients affected with UC, 75 noncolectomized showed an alternating course of disease, while 25 did not respond to the common drugs, and underwent colectomy. Genotyping was performed by polymerase chain reaction and following enzymatic digestion by BccI. No significant differences were found between patients with UC and controls both for genotype and allele frequencies. However, our data show a significant association when colectomized and noncolectomized patients are compared. The frequencies of G homozygosity were 28% in colectomized and 10.7% in noncolectomized patients (p < 0.05, chi(2) = 4.4, Odds ratio = 3.3). The allele frequencies of allele A were 52% in colectomized and 68% in noncolectomized patients; while those of allele G were 48% and 32%, respectively. I219V polymorphism in hMLH1 could influence the clinical course of the disease and lead to resistance to therapy.

MSH-2 and MLH-1 Protein Expression in Muir Torre Syndrome-Related and Sporadic Sebaceous Neoplasms

PubMed Central

Morales-Burgos, Adisbeth; Sánchez, Jorge L.; Figueroa, Luz D.; De Jesús-Monge, Wilfredo E.; Cruz-Correa, Marcia R.; González-Keelan, Carmen; Nazario, Cruz María

2009-01-01

Background Muir-Torre Syndrome (MTS) is a rare autosomal-dominant disorder characterized by the predisposition to both sebaceous neoplasm and internal malignancies. MTS-associated sebaceous neoplasms reveal mutations in DNA mismatch repair (MMR) genes and microsatellite instability. A significant part of MTS patients represents a phenotypic variant, the hereditary nonpolyposis colorectal cancer (HNPCC). A strong correlation between microsatellite instability and immunostaining has been demonstrated. The early recognition of sebaceous neoplasm as part of MTS, and their differentiation from sporadic sebaceous neoplasm may have an important application in a clinical setting. The absence of MLH-1 or MSH-2 expression by immunostaining identifies tumors with mismatch repair deficiency. Objectives Our aim is to determine whether an immunohistochemical approach, targeting DNA repair proteins MSH-2 and MLH-1 in MTS-related sebaceous neoplasm and their sporadic counterparts, can be used for their identification. Methods We examined 15 sebaceous neoplasms (including 6 internal malignancy- associated sebaceous neoplasms and 8 sporadic sebaceous neoplasms) from 11 patients for the expression of MSH-2 and MLH-1 by immunohistochemistry. Results Four of 5 internal malignancy-associated sebaceous neoplasms showed loss of expression of MSH-2 or MLH-1. Correlation of the immunostaining pattern of the sebaceous neoplasms and the patients’ positive history of colon carcinoma was 80%. Seven of 8 sporadic sebaceous neoplasms showed a positive expression of MSH-2 and MLH-1. The prevalence for loss of expression of MMR proteins in sebaceous neoplasms was 38.5%. MMR immunostaining had 87.5% specificity and 80% sensitivity. Limitations This study is limited by a small sample size, and by bias selection due to the use of non nationwide data-base as the resource of cases. Conclusions Our findings demonstrate that immunohistochemical testing for internal malignancy-associated sebaceous neoplasms is a practical approach to confirm a suspected inherited MMR gene defect, and an accurate method to distinguish between sporadic and MTS-associated sebaceous lesions. PMID:19069357

Screening for germline mutations of MLH1, MSH2, MSH6 and PMS2 genes in Slovenian colorectal cancer patients: implications for a population specific detection strategy of Lynch syndrome.

PubMed

Berginc, Gasper; Bracko, Matej; Ravnik-Glavac, Metka; Glavac, Damjan

2009-01-01

Microsatellite instability (MSI) is present in more than 90% of colorectal cancers of patients with Lynch syndrome, and is therefore a feasible marker for the disease. Mutations in MLH1, MSH2, MSH6 and PMS2, which are one of the main causes of deficient mismatch repair and subsequent MSI, have been linked to the disease. In order to establish the role of each of the 4 genes in Slovenian Lynch syndrome patients, we performed MSI analysis on 593 unselected CRC patients and subsequently searched for the presence of point mutations, larger genomic rearrangements and MLH1 promoter hypermethylation in patients with MSI-high tumours. We detected 43 (7.3%) patients with MSI-H tumours, of which 7 patients (1.3%) harboured germline defects: 2 in MLH1, 4 in MSH2, 1 in PMS2 and none in MSH6. Twenty-nine germline sequence variations of unknown significance and 17 deleterious somatic mutations were found. MLH1 promoter methylation was detected in 56% of patients without detected germline defects and in 1 (14%) suspected Lynch syndrome. Due to the minor role of germline MSH6 mutations, we adapted the Lynch syndrome detection strategy for the Slovenian population of CRC patients, whereby germline alterations should be first sought in MLH1 and MSH2 followed by a search for larger genomic rearrangements in these two genes. When no germline mutations are found tumors should be further tested for the presence of germline defects in PMS2 and MSH6. The choice about which gene should be tested first can be guided more accurately by the immunohistochemical analysis. Our study demonstrates that the incidence of MMR mutations in a population should be known prior to the application of one of several suggested strategies for detection of Lynch syndrome.

Using Four-Layer Sculpted Rib Cartilage Framework to Increase Transverse Height of the Reconstructive Ear in One Operative Stage for Microtia Patients.

PubMed

Wan, Rui; Pang, Xingyuan; Ren, Jun

2018-02-01

This case study improves an operative method of ear reconstruction for microtia patients by using a four-layer rib cartilage framework to increase transverse height of the reconstructive ear to a natural level in one operative stage. The procedures of ear reconstruction were conducted from February 2014 to May 2016. The ear framework used in the procedures was fabricated from autologous rib cartilage into a four-layer spliced sculpture. Totally 23 patients with unilateral microtia were willing to be enrolled in this study. After the operation, 23 patients achieved 2.3-2.8 cm transverse height of reconstructed ears, which was basically the same as the normal side. Both patients and their families felt satisfied with the results. Follow-up was performed at 6-16 months after the procedures. Only one case showed significantly lowered transverse height of the reconstructed ear, compared to the normal one. It was due to the sleeping position of the patient (10-year-old boy), which put the reconstructed ear under pressure and reduced the transverse height of the ear. The method of four-layer sculpted autologous rib cartilage ear reconstruction has good clinical effect. It can provide a reconstructed ear that reaches normal transverse height and avoids a third operation to increase the transverse height by rib cartilage transplantation. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

BOREAS AFM-6 Boundary Layer Height Data

NASA Technical Reports Server (NTRS)

Wilczak, James; Hall, Forrest G. (Editor); Newcomer, Jeffrey A. (Editor); Smith, David E. (Technical Monitor)

2000-01-01

The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-6 team from National Oceanic and Atmospheric Adminsitration/Environment Technology Laboratory (NOAA/ETL) operated a 915-MHz wind/Radio Acoustic Sounding System (RASS) profiler system in the Southern Study Area (SSA) near the Old Jack Pine (OJP) site. This data set provides boundary layer height information over the site. The data were collected from 21 May 1994 to 20 Sep 1994 and are stored in tabular ASCII files. The boundary layer height data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

Measurements of aerosol layer height and vertical profiles by lidar over Jinhua City

NASA Astrophysics Data System (ADS)

Yu, Siqi; Liu, Dong; Wang, Zhenzhu; Xu, Jiwei; Tian, Xiaomin; Wu, Decheng; Xie, Chenbo; Wang, Yingjian

2018-03-01

The vertical distribution of the aerosol layers is depicted by using the lidar data in Jinhua city from 2013 to 2014. The lidar installed in Jinhua is a dual-wavelength Mie polarization Raman lidar. Aerosol layers are searched through gradient method. At the same time, HYSPLIT model is used to tracing the aerosol trajectories. The results show that different heights of aerosol layers have different transportation route. By a case study, the lidar data on December 30, 2013 and May 1, 2014 reveal several vertical aerosol layers. According to the 24-hour backward trajectory of HYSPLIT model, different aerosol layers comes from different places, and this may relate to the winter monsoon in China.

Study of Semi-Span Model Testing Techniques

NASA Technical Reports Server (NTRS)

Gatlin, Gregory M.; McGhee, Robert J.

1996-01-01

An investigation has been conducted in the NASA Langley 14- by 22-Foot Subsonic Tunnel in order to further the development of semi-span testing capabilities. A twin engine, energy efficient transport (EET) model with a four-element wing in a takeoff configuration was used for this investigation. Initially a full span configuration was tested and force and moment data, wing and fuselage surface pressure data, and fuselage boundary layer measurements were obtained as a baseline data set. The semi-span configurations were then mounted on the wind tunnel floor, and the effects of fuselage standoff height and shape as well as the effects of the tunnel floor boundary layer height were investigated. The effectiveness of tangential blowing at the standoff/floor juncture as an active boundary-layer control technique was also studied. Results indicate that the semi-span configuration was more sensitive to variations in standoff height than to variations in floor boundary layer height. A standoff height equivalent to 30 percent of the fuselage radius resulted in better correlation with full span data than no standoff or the larger standoff configurations investigated. Undercut standoff leading edges or the use of tangential blowing in the standoff/ floor juncture improved correlation of semi-span data with full span data in the region of maximum lift coefficient.

Genetics Home Reference: Lynch syndrome

MedlinePlus

... or EPCAM gene increase the risk of developing Lynch syndrome . The MLH1 , MSH2 , MSH6 , and PMS2 genes are involved in the repair of errors that ... B, Eisinger F, Hutter P, Olschwang S. Clinical utility gene card for: Lynch syndrome (MLH1, MSH2, MSH6, PMS2, EPCAM) - update 2012. Eur J Hum Genet. 2013 ...

Fermi level de-pinning of aluminium contacts to n-type germanium using thin atomic layer deposited layers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gajula, D. R., E-mail: dgajula01@qub.ac.uk; Baine, P.; Armstrong, B. M.

Fermi-level pinning of aluminium on n-type germanium (n-Ge) was reduced by insertion of a thin interfacial dielectric by atomic layer deposition. The barrier height for aluminium contacts on n-Ge was reduced from 0.7 eV to a value of 0.28 eV for a thin Al{sub 2}O{sub 3} interfacial layer (∼2.8 nm). For diodes with an Al{sub 2}O{sub 3} interfacial layer, the contact resistance started to increase for layer thicknesses above 2.8 nm. For diodes with a HfO{sub 2} interfacial layer, the barrier height was also reduced but the contact resistance increased dramatically for layer thicknesses above 1.5 nm.

The Martian atmospheric planetary boundary layer stability, fluxes, spectra, and similarity

NASA Technical Reports Server (NTRS)

Tillman, James E.

1994-01-01

This is the first analysis of the high frequency data from the Viking lander and spectra of wind, in the Martian atmospheric surface layer, along with the diurnal variation of the height of the mixed surface layer, are calculated for the first time for Mars. Heat and momentum fluxes, stability, and z(sub O) are estimated for early spring, from a surface temperature model and from Viking Lander 2 temperatures and winds at 44 deg N, using Monin-Obukhov similarity theory. The afternoon maximum height of the mixed layer for these seasons and conditions is estimated to lie between 3.6 and 9.2 km. Estimations of this height is of primary importance to all models of the boundary layer and Martian General Circulation Models (GCM's). Model spectra for two measuring heights and three surface roughnesses are calculated using the depth of the mixed layer, and the surface layer parameters and flow distortion by the lander is also taken into account. These experiments indicate that z(sub O), probably lies between 1.0 and 3.0 cm, and most likely is closer to 1.0 cm. The spectra are adjusted to simulate aliasing and high frequency rolloff, the latter caused both by the sensor response and the large Kolmogorov length on Mars. Since the spectral models depend on the surface parameters, including the estimated surface temperature, their agreement with the calculated spectra indicates that the surface layer estimates are self consistent. This agreement is especially noteworthy in that the inertial subrange is virtually absent in the Martian atmosphere at this height, due to the large Kolmogorov length scale. These analyses extend the range of applicability of terrestrial results and demonstrate that it is possible to estimate the effects of severe aliasing of wind measurements, to produce a models which agree well with the measured spectra. The results show that similarity theory developed for Earth applies to Mars, and that the spectral models are universal.

Characteristics of nocturnal coastal boundary layer in Ahtopol based on averaged SODAR profiles

NASA Astrophysics Data System (ADS)

Barantiev, Damyan; Batchvarova, Ekaterina; Novitzky, Mikhail

2014-05-01

The ground-based remote sensing instruments allow studying the wind regime and the turbulent characteristics of the atmosphere with height, achieving new knowledge and solving practical problems, such as air quality assessments, mesoscale models evaluation with high resolution data, characterization of the exchange processes between the surface and the atmosphere, the climate comfort conditions and the risk for extreme events, etc. Very important parameter in such studies is the height of the atmospheric boundary layer. Acoustic remote sensing data of the coastal atmospheric boundary layer were explored based on over 4-years continuous measurements at the meteorological observatory of Ahtopol (Bulgarian Southern Black Sea Coast) under Bulgarian - Russian scientific agreement. Profiles of 12 parameters from a mid-range acoustic sounding instrument type SCINTEC MFAS are derived and averaged up to about 600 m according filtering based on wind direction (land or sea type of night fowls). From the whole investigated period of 1454 days with 10-minute resolution SODAR data 2296 profiles represented night marine air masses and 1975 profiles represented the night flow from land during the months May to September. Graphics of averaged profiles of 12 SODAR output parameters with different availability of data in height are analyzed for both cases. A marine boundary-layer height of about 300 m is identified in the profiles of standard deviation of vertical wind speed (σw), Turbulent Kinetic Energy (TKE) and eddy dissipation rate (EDR). A nocturnal boundary-layer height of about 420 m was identified from the profiles of the same parameters under flows from land condition. In addition, the Buoyancy Production (BP= σw3/z) profiles were calculated from the standard deviation of the vertical wind speed and the height z above ground.

Observational Characteristics of the Tropopause Inversion Layer derived from CHAMP/GRACE Radio Occultations and MOZAIC Aircraft Data

NASA Astrophysics Data System (ADS)

Schmidt, T.; Cammas, J.; Heise, S.; Wickert, J.; Haser, A.

2010-12-01

In this study we discuss characteristics of the northern hemisphere (NH) midlatitude (40°N-60°N) tropopause inversion layer (TIL) based on two datasets. First, temperature measurements from GPS radio occultation data (CHAMP and GRACE) for the time interval 2001-2009 are used to exhibit seasonal properties of the TIL bottom height defined here as the height of the squared buoyancy frequency minimum N2 below the thermal tropopause, the TIL maximum height as the height of the N2 maximum above the tropopause and the TIL top height as the height of the temperature maximum above the tropopause. Mean values of the TIL bottom, TIL maximum and TIL top heights relative to the thermal tropopause for the NH midlatitudes are (-2.08±0.35) km, (0.52±0.10) km and (2.10±0.23) km, respectively. A seasonal cycle of the TIL bottom and TIL top height is observed with values closer to the thermal tropopause during summer. Secondly, high-resolution temperature and trace gas profile measurements onboard commercial aircrafts (MOZAIC program) from 2001-2008 for the NH midlatitude (40°N-60°N) region are used to characterize the TIL as a mixing layer around the tropopause. Mean TIL bottom, TIL maximum and TIL top heights based on the MOZAIC temperature (N2) measurements confirm the results from the GPS data, even though most of the MOZAIC profiles used here are available under cyclonic situations. Further, we demonstrate that the mixing ratio gradients of ozone (O3) and carbon monoxide (CO) are suitable parameters for characterizing the TIL structure. Using O3-CO correlations we also show that on average the highest mixing occurs in a layer less than 1 km above the thermal tropopause, i.e., within the TIL.

Characterization of the planetary boundary layer height and structure by Raman lidar: comparison of different approaches

NASA Astrophysics Data System (ADS)

Summa, D.; Di Girolamo, P.; Stelitano, D.; Cacciani, M.

2013-12-01

The planetary boundary layer (PBL) includes the portion of the atmosphere which is directly influenced by the presence of the earth's surface. Aerosol particles trapped within the PBL can be used as tracers to study the boundary-layer vertical structure and time variability. As a result of this, elastic backscatter signals collected by lidar systems can be used to determine the height and the internal structure of the PBL. The present analysis considers three different methods to estimate the PBL height. The first method is based on the determination of the first-order derivative of the logarithm of the range-corrected elastic lidar signals. Estimates of the PBL height for specific case studies obtained through this approach are compared with simultaneous estimates from the potential temperature profiles measured by radiosondes launched simultaneously to lidar operation. Additional estimates of the boundary layer height are based on the determination of the first-order derivative of the range-corrected rotational Raman lidar signals. This latter approach results to be successfully applicable also in the afternoon-evening decaying phase of the PBL, when the effectiveness of the approach based on the elastic lidar signals may be compromised or altered by the presence of the residual layer. Results from these different approaches are compared and discussed in the paper, with a specific focus on selected case studies collected by the University of Basilicata Raman lidar system BASIL during the Convective and Orographically-induced Precipitation Study (COPS).

Characterization of the planetary boundary layer height and structure by Raman lidar: comparison of different approaches

NASA Astrophysics Data System (ADS)

Summa, D.; Di Girolamo, P.; Stelitano, D.; Cacciani, M.

2013-06-01

The Planetary Boundary Layer (PBL) includes the portion of the atmosphere which is directly influenced by the presence of the Earth's surface. Aerosol particles trapped within the PBL can be used as tracers to study the boundary-layer vertical structure and time variability. As a result of this, elastic backscatter signals collected by lidar systems can be used to determine the height and the internal structure of the PBL. The present analysis considers three different methods to estimate the PBL height. A first method is based on the determination of the first order derivative of the logarithm of the range-corrected elastic lidar signals. Estimates of the PBL height for specific case studies obtained from this approach are compared with simultaneous estimates from the potential temperature profiles measured by radiosondes launched simultaneously to lidar operation. Additional estimates of the boundary layer height are based on the determination of the first order derivative of the range-corrected rotational Raman lidar signals. This latter approach results to be successfully applicable also in the afternoon-evening decaying phase of the PBL, when the effectiveness of the approach based on the elastic lidar signals may be compromised or altered by the presence of the residual layer. Results from these different approaches are compared and discussed in the paper, with a specific focus on selected case studies collected by the University of Basilicata Raman lidar system BASIL during the Convective and Orographically-induced Precipitation Study (COPS).

Systems and methods that generate height map models for efficient three dimensional reconstruction from depth information

DOEpatents

Frahm, Jan-Michael; Pollefeys, Marc Andre Leon; Gallup, David Robert

2015-12-08

Methods of generating a three dimensional representation of an object in a reference plane from a depth map including distances from a reference point to pixels in an image of the object taken from a reference point. Weights are assigned to respective voxels in a three dimensional grid along rays extending from the reference point through the pixels in the image based on the distances in the depth map from the reference point to the respective pixels, and a height map including an array of height values in the reference plane is formed based on the assigned weights. An n-layer height map may be constructed by generating a probabilistic occupancy grid for the voxels and forming an n-dimensional height map comprising an array of layer height values in the reference plane based on the probabilistic occupancy grid.

Moment expansion for ionospheric range error

NASA Technical Reports Server (NTRS)

Mallinckrodt, A.; Reich, R.; Parker, H.; Berbert, J.

1972-01-01

On a plane earth, the ionospheric or tropospheric range error depends only on the total refractivity content or zeroth moment of the refracting layer and the elevation angle. On a spherical earth, however, the dependence is more complex; so for more accurate results it has been necessary to resort to complex ray-tracing calculations. A simple, high-accuracy alternative to the ray-tracing calculation is presented. By appropriate expansion of the angular dependence in the ray-tracing integral in a power series in height, an expression is obtained for the range error in terms of a simple function of elevation angle, E, at the expansion height and of the mth moment of the refractivity, N, distribution about the expansion height. The rapidity of convergence is heavily dependent on the choice of expansion height. For expansion heights in the neighborhood of the centroid of the layer (300-490 km), the expansion to N = 2 (three terms) gives results accurate to about 0.4% at E = 10 deg. As an analytic tool, the expansion affords some insight on the influence of layer shape on range errors in special problems.

Detailed characterization of MLH1 p.D41H and p.N710D variants coexisting in a Lynch syndrome family with conserved MLH1 expression tumors.

PubMed

Pineda, M; González-Acosta, M; Thompson, B A; Sánchez, R; Gómez, C; Martínez-López, J; Perea, J; Caldés, T; Rodríguez, Y; Landolfi, S; Balmaña, J; Lázaro, C; Robles, L; Capellá, G; Rueda, D

2015-06-01

Lynch syndrome (LS) is an autosomal dominant cancer-susceptibility disease caused by inactivating germline mutations in mismatch repair (MMR) genes. Variants of unknown significance (VUS) are often detected in mutational analysis of MMR genes. Here we describe a large family fulfilling Amsterdam I criteria carrying two rare VUS in the MLH1 gene: c.121G > C (p.D41H) and c.2128A > G (p.N710D). Collection of clinico-pathological data, multifactorial analysis, in silico predictions, and functional analyses were used to elucidate the clinical significance of the identified MLH1 VUS. Only the c.121G > C variant cosegregated with LS-associated tumors in the family. Diagnosed colorectal tumors were microsatellite unstable although immunohistochemical staining revealed no loss of MMR proteins expression. Multifactorial likelihood analysis classified c.2128A > G as a non-pathogenic variant and c.121G > C as pathogenic. In vitro functional tests revealed impaired MMR activity and diminished expression of c.121G > C. Accordingly, the N710 residue is located in the unconserved MLH1 C-terminal domain, whereas D41 is highly conserved and located in the ATPase domain. The obtained results will enable adequate genetic counseling of c.121G > C and c.2128A > G variant carriers and their families. Furthermore, they exemplify how cumulative data and comprehensive analyses are mandatory to refine the classification of MMR variants. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Loss of mutL homolog-1 (MLH1) expression promotes acquisition of oncogenic and inhibitor-resistant point mutations in tyrosine kinases.

PubMed

Springuel, Lorraine; Losdyck, Elisabeth; Saussoy, Pascale; Turcq, Béatrice; Mahon, François-Xavier; Knoops, Laurent; Renauld, Jean-Christophe

2016-12-01

Genomic instability drives cancer progression by promoting genetic abnormalities that allow for the multi-step clonal selection of cells with growth advantages. We previously reported that the IL-9-dependent TS1 cell line sequentially acquired activating substitutions in JAK1 and JAK3 upon successive selections for growth factor independent and JAK inhibitor-resistant cells, suggestive of a defect in mutation avoidance mechanisms. In the first part of this paper, we discovered that the gene encoding mutL homolog-1 (MLH1), a key component of the DNA mismatch repair system, is silenced by promoter methylation in TS1 cells. By means of stable ectopic expression and RNA interference methods, we showed that the high frequencies of growth factor-independent and inhibitor-resistant cells with activating JAK mutations can be attributed to the absence of MLH1 expression. In the second part of this paper, we confirm the clinical relevance of our findings by showing that chronic myeloid leukemia relapses upon ABL-targeted therapy correlated with a lower expression of MLH1 messenger RNA. Interestingly, the mutational profile observed in our TS1 model, characterized by a strong predominance of T:A>C:G transitions, was identical to the one described in the literature for primitive cells derived from chronic myeloid leukemia patients. Taken together, our observations demonstrate for the first time a causal relationship between MLH1-deficiency and incidence of oncogenic point mutations in tyrosine kinases driving cell transformation and acquired resistance to kinase-targeted cancer therapies.

The Germline MLH1 K618A Variant and Susceptibility to Lynch Syndrome-Associated Tumors

PubMed Central

Medeiros, Fabiola; Lindor, Noralane M.; Couch, Fergus J.; Highsmith, W. Edward

2013-01-01

Missense variants discovered during sequencing of cancer susceptibility genes can be problematic for clinical interpretation. MLH1 K618A, which results from a 2-bp alteration (AAG→GCG) leading to a substitution of lysine to alanine in codon 618, has variously been interpreted as a pathogenic mutation, a variant of unknown significance, and a benign polymorphism. We evaluated the role of MLH1 K618A in predisposition to cancer by genotyping 1512 control subjects to assess its frequency in the general population. We also reviewed the literature concerning MLH1 K618A in families with colorectal cancer. The measured allele frequency of the K618A variant was 0.40%, which is remarkably close to the 0.44% summarized from 2491 control subjects in the literature. K618A was over-represented in families with suspected Lynch syndrome. In 1366 families, the allele frequency was 0.88% (OR = 2.1, 95% CI = 1.3 to 3.5; P = 0.006). In studies of sporadic cancers of the type associated with Lynch syndrome, K618A was over-represented in 1742 cases (allele frequency of 0.83) (OR = 2.0, 95% CI = 1.2 to 3.2; P = 0.008). We conclude that MLH1 K618A is not a fully penetrant Lynch syndrome mutation, although it is not without effect, appearing to increase the risk of Lynch syndrome-associated tumors approximately twofold. Our systematic assessment approach may be useful for variants in other genes. PMID:22426235

Mlh1 deficiency in normal mouse colon mucosa associates with chromosomally unstable colon cancer

PubMed Central

Pussila, Marjaana; Törönen, Petri; Einarsdottir, Elisabet; Katayama, Shintaro; Krjutškov, Kaarel; Holm, Liisa; Kere, Juha; Peltomäki, Päivi; Mäkinen, Markus J; Linden, Jere; Nyström, Minna

2018-01-01

Abstract Colorectal cancer (CRC) genome is unstable and different types of instabilities, such as chromosomal instability (CIN) and microsatellite instability (MSI) are thought to reflect distinct cancer initiating mechanisms. Although 85% of sporadic CRC reveal CIN, 15% reveal mismatch repair (MMR) malfunction and MSI, the hallmarks of Lynch syndrome with inherited heterozygous germline mutations in MMR genes. Our study was designed to comprehensively follow genome-wide expression changes and their implications during colon tumorigenesis. We conducted a long-term feeding experiment in the mouse to address expression changes arising in histologically normal colonic mucosa as putative cancer preceding events, and the effect of inherited predisposition (Mlh1+/−) and Western-style diet (WD) on those. During the 21-month experiment, carcinomas developed mainly in WD-fed mice and were evenly distributed between genotypes. Unexpectedly, the heterozygote (B6.129-Mlh1tm1Rak) mice did not show MSI in their CRCs. Instead, both wildtype and heterozygote CRC mice showed a distinct mRNA expression profile and shortage of several chromosomal segregation gene-specific transcripts (Mlh1, Bub1, Mis18a, Tpx2, Rad9a, Pms2, Cenpe, Ncapd3, Odf2 and Dclre1b) in their colon mucosa, as well as an increased mitotic activity and abundant numbers of unbalanced/atypical mitoses in tumours. Our genome-wide expression profiling experiment demonstrates that cancer preceding changes are already seen in histologically normal colon mucosa and that decreased expressions of Mlh1 and other chromosomal segregation genes may form a field-defect in mucosa, which trigger MMR-proficient, chromosomally unstable CRC. PMID:29701748

Promoter methylation profile in gallbladder cancer.

PubMed

Roa, Juan Carlos; Anabalón, Leonardo; Roa, Iván; Melo, Angélica; Araya, Juan Carlos; Tapia, Oscar; de Aretxabala, Xavier; Muñoz, Sergio; Schneider, Barbara

2006-03-01

Methylation in the promoter region of genes is an important mechanism of inactivation of tumor suppressor genes. Our objective was to analyze the methylation pattern of some of the genes involved in carcinogenesis of the gallbladder, examining the immunohistochemical expression of proteins, clinical features, and patient survival time. Twenty cases of gallbladder cancer were selected from the frozen tumor bank. The DNA extracted was analyzed by means of a methylation-specific polymerase chain reaction test for the CDKN2A (p16), MLH1, APC, FHIT, and CDH1 (E-cadherin) genes. Morphological and clinical data and follow-up information were obtained. All cases were in an advanced stage: histologically moderate or poorly differentiated tumors (95%). Methylation of the promoter area of genes was observed in 5%, 20%, 30%, 40%, and 65% of cases, and an altered immunohistochemical pattern (AIP) in 5%, 35%, 21%, 25%, and 66% for the MLH1, CDKN2A, FHIT, APC, and CDH1 genes, respectively. The Kappa concordance index between methylation of the promoter area and AIP for the MLH1 and CDH1 genes was very high (K > 0.75) and substantial for APC (K > 0.45). No correlation was found between survival time and the methylation of the genes studied. The high frequency of gene methylation (with the exception of MLH1) and the high agreement between AIP and methylation of the gene promoter area for the MLH1, APC, and CDH1 genes suggest that the inactivation of tumor suppressor genes and of the genes related to the control of cellular proliferation through this mechanism is involved in gallbladder carcinogenesis.

Estimating the atmospheric boundary layer height over sloped, forested terrain from surface spectral analysis during BEARPEX

NASA Astrophysics Data System (ADS)

Choi, W.; Faloona, I. C.; McKay, M.; Goldstein, A. H.; Baker, B.

2011-07-01

The atmospheric boundary layer (ABL) height (zi) over complex, forested terrain is estimated based on the power spectra and the integral length scale of cross-stream winds obtained from a three-axis sonic anemometer during the two summers of the BEARPEX (Biosphere Effects on Aerosol and Photochemistry) Experiment. The zi values estimated with this technique show very good agreement with observations obtained from balloon tether sondes (2007) and rawinsondes (2009) under unstable conditions (z/L < 0) at the coniferous forest in the California Sierra Nevada. On the other hand, the low frequency behavior of the streamwise upslope winds did not exhibit significant variations and was therefore not useful in predicting boundary layer height. The behavior of the nocturnal boundary layer height (h) with respect to the power spectra of the v-wind component and temperature under stable conditions (z/L > 0) is also presented. The nocturnal boundary layer height is found to be fairly well predicted by a recent interpolation formula proposed by Zilitinkevich et al. (2007), although it was observed to only vary from 60-80 m during the 2009 experiment in which it was measured. Finally, significant directional wind shear was observed during both day and night soundings. The winds were found to be consistently backing from the prevailing west-southwesterlies within the ABL (the anabatic cross-valley circulation) to southerlies in a layer ~1-2 km thick just above the ABL before veering to the prevailing westerlies further aloft. This shear pattern is shown to be consistent with the forcing of a thermal wind driven by the regional temperature gradient directed east-southeast in the lower troposphere.

Influence of AZO stair-like transparent layers on GaN-based light-emitting diodes

NASA Astrophysics Data System (ADS)

Liou, Syuan-Hao; Tsai, Jung-Hui; Liu, Wen-Chau; Lin, Pao-Sheng; Chen, Yu-Chi

2017-10-01

The GaN-based light-emitting diodes (LEDs) with various height ratios of aluminum-doped zinc oxide (AZO) stair-like transparent layers are fabricated and comparatively investigated. The characteristics of the LEDs with conventional plane AZO transparent layer (device A) and AZO stair-like transparent layers having height ratios of 1:1:1 (device B), 1.5:1:0.5 (device C), and 0.5:1:1.5 (device D) are compared. Attributed that the lower resistance is formed in the thinner AZO film of the stair-like structure, the current crowding effect is improved for extending the whole current-spreading area. Experimentally, the forward turn-on voltages of the LEDs are reduced from 3.68 V to 3.42 V as the plane AZO transparent layer is processed to form the stair-like transparent layers with height ratio of 1:1:1. In addition, the light luminous flux, output power, external quantum efficiency, and wall-plug efficiency of the device B are enhanced by 30.5, 12.1, 22.2, and 20.7%, respectively, as compared to the traditional device with plane AZO transparent layer.

The Role of Histone Deacetylase and DNA Methylation in Estrogen a Expression in Breast Cancer

DTIC Science & Technology

2001-06-01

ever, in other cases, both demethylation and HDAC inhibition appear to be necessary. For example, certain hypermethylated genes like 231C MLH1 , TIMP3...Treatment of these cells with the demethylat- permethylated genes, such as MLH1 , TIMP3, INK4B ing agent, deoxyC, led to partial demethylation of the (p15

Elucidation of Chromatin Remodeling Machinery Involved in Regulation of Estrogen Receptor Alpha Expression in Human Breast Cancer Cells

DTIC Science & Technology

2006-08-01

depsipeptide with 5-aza-dC has been shown to synergistically reactivate silenced tumor suppressor genes in human cancer cells, including MLH1 , TIMP3...depsipeptide with 5- aza-dC has been shown to synergistically reactivate silenced tumor suppressor genes in human cancer cells, including MLH1 , TIMP3

Pilot Trial of a Parenting and Self-Care Intervention for HIV-Positive Mothers: The IMAGE Program

PubMed Central

Murphy, Debra A.; Armistead, Lisa; Payne, Diana L.; Marelich, William D.; Herbeck, Diane M.

2016-01-01

A pilot study was conducted to assess the effects of the IMAGE pilot intervention (Improving Mothers’ parenting Abilities, Growth, and Effectiveness) on mothers living with HIV (MLH). Based on Fisher and Fisher's IMB model (1992), the intervention focused on self-care and parenting behavior skills of MLH that affect maternal, child, and family outcomes. A randomized pretest-posttest two-group design with repeated assessments was used. MLH (n = 62) and their children ages 6 - 14 (n = 62; total N = 124) were recruited for the trial and randomized to the theory-based skills training condition or a standard care control condition. Assessments were conducted at baseline with follow-ups at 3, 6, and 12 months. Maternal, child, and family outcomes were assessed. Results show significant effects of the intervention for improving parenting practices for mothers. The intervention also improved family outcomes, and showed improvements in the parent-child relationship. IMAGE had a positive impact on parenting behaviors, and on maternal, child, and family outcomes. Given MLH can be challenged by their illness and also live in under-resourced environments, IMAGE may be viewed as a viable way to improve quality of life and family outcomes. PMID:27377577

Measurement of net whole-body transcapillary fluid transport and effective vascular compliance in humans

NASA Technical Reports Server (NTRS)

Watenpaugh, D. E.; Gaffney, F. A.; Schneider, S. M. (Principal Investigator)

1998-01-01

BACKGROUND: Net whole-body transcapillary fluid transport (TFT) between the circulation and the interstitial (extravascular) space may be calculated as: IV - deltaPV - UV - IL, where IV=infused or ingested volume (when applicable), deltaPV = change in plasma volume, UV=urine volume, and IL=insensible loss. RESULTS: Infusion of 30 mL/kg isotonic saline over 25 minutes increased supine TFT from a basal capillary reabsorption of -106+/-24 mL/h (mean+/-SE) to a net filtration of 1,229+/-124 mL/h. One hour after infusion, reabsorption of -236+/-102 mL/h was seen, and control reabsorption levels returned by 3 hours. Four hours of 30 mm Hg lower body negative pressure (LBNP) elicited no net TFT, probably because of upper body reabsorptive compensation for lower body capillary filtration. When ingestion of 1 L of isotonic saline accompanied LBNP, filtration of 145+/-10 mL/h occurred. Reabsorption of extravascular fluid into the circulation always followed LBNP. CONCLUSION: Application of this technique could aid understanding of physiologic conditions, experimental interventions, disease states, and therapies that cause or are influenced by fluid shifts between intravascular and interstitial compartments.

Meiotic Recombination in the Giraffe (G. reticulata).

PubMed

Vozdova, Miluse; Fröhlich, Jan; Kubickova, Svatava; Sebestova, Hana; Rubes, Jiri

2017-01-01

Recently, the reticulated giraffe (G. reticulata) was identified as a distinct species, which emphasized the need for intensive research in this interesting animal. To shed light on the meiotic process as a source of biodiversity, we analysed the frequency and distribution of meiotic recombination in 2 reticulated giraffe males. We used immunofluorescence detection of synaptonemal complex protein (SYCP3), meiotic double strand breaks (DSB, marked as RAD51 foci) in leptonema, and crossovers (COs, as MLH1 foci) in pachynema. The mean number of autosomal MLH1 foci per cell (27), which resulted from a single, distally located MLH1 focus observed on most chromosome arms, is one of the lowest among mammalian species analysed so far. The CO/DSB conversion ratio was 0.32. The pseudoautosomal region was localised in the Xq and Yp termini by FISH and showed an MLH1 focus in 83% of the pachytene cells. Chromatin structures corresponding to the nucleolus organiser regions were observed in the pachytene spermatocytes. The results are discussed in the context of known data on meiosis in Cetartiodactyla, depicting that the variation in CO frequency among species of this taxonomic group is mostly associated with their diploid chromosome number. © 2017 S. Karger AG, Basel.

Forward-facing steps induced transition in a subsonic boundary layer

NASA Astrophysics Data System (ADS)

Zh, Hui; Fu, Song

2017-10-01

A forward-facing step (FFS) immersed in a subsonic boundary layer is studied through a high-order flux reconstruction (FR) method to highlight the flow transition induced by the step. The step height is a third of the local boundary-layer thickness. The Reynolds number based on the step height is 720. Inlet disturbances are introduced giving rise to streamwise vortices upstream of the step. It is observed that these small-scale streamwise structures interact with the step and hairpin vortices are quickly developed after the step leading to flow transition in the boundary layer.

Utilization of O4 slant column density to derive aerosol layer height from a space-borne UV-visible hyperspectral sensor: sensitivity and case study

NASA Astrophysics Data System (ADS)

Park, Sang Seo; Kim, Jhoon; Lee, Hanlim; Torres, Omar; Lee, Kwang-Mog; Lee, Sang Deok

2016-02-01

The sensitivities of oxygen-dimer (O4) slant column densities (SCDs) to changes in aerosol layer height are investigated using the simulated radiances by a radiative transfer model, the linearized pseudo-spherical vector discrete ordinate radiative transfer (VLIDORT), and the differential optical absorption spectroscopy (DOAS) technique. The sensitivities of the O4 index (O4I), which is defined as dividing O4 SCD by 1040 molecules2 cm-5, to aerosol types and optical properties are also evaluated and compared. Among the O4 absorption bands at 340, 360, 380, and 477 nm, the O4 absorption band at 477 nm is found to be the most suitable to retrieve the aerosol effective height. However, the O4I at 477 nm is significantly influenced not only by the aerosol layer effective height but also by aerosol vertical profiles, optical properties including single scattering albedo (SSA), aerosol optical depth (AOD), particle size, and surface albedo. Overall, the error of the retrieved aerosol effective height is estimated to be 1276, 846, and 739 m for dust, non-absorbing, and absorbing aerosol, respectively, assuming knowledge on the aerosol vertical distribution shape. Using radiance data from the Ozone Monitoring Instrument (OMI), a new algorithm is developed to derive the aerosol effective height over East Asia after the determination of the aerosol type and AOD from the MODerate resolution Imaging Spectroradiometer (MODIS). About 80 % of retrieved aerosol effective heights are within the error range of 1 km compared to those obtained from the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) measurements on thick aerosol layer cases.

Utilization of O4 Slant Column Density to Derive Aerosol Layer Height from a Space-Borne UV-Visible Hyperspectral Sensor: Sensitivity and Case Study

NASA Technical Reports Server (NTRS)

Park, Sang Seo; Kim, Jhoon; Lee, Hanlim; Torres, Omar; Lee, Kwang-Mog; Lee, Sang Deok

2016-01-01

The sensitivities of oxygen-dimer (O4) slant column densities (SCDs) to changes in aerosol layer height are investigated using the simulated radiances by a radiative transfer model, the linearized pseudo-spherical vector discrete ordinate radiative transfer (VLIDORT), and the differential optical absorption spectroscopy (DOAS) technique. The sensitivities of the O4 index (O4I), which is defined as dividing O4 SCD by 10(sup 40) molecules (sup 2) per centimeters(sup -5), to aerosol types and optical properties are also evaluated and compared. Among the O4 absorption bands at 340, 360, 380, and 477 nanometers, the O4 absorption band at 477 nanometers is found to be the most suitable to retrieve the aerosol effective height. However, the O4I at 477 nanometers is significantly influenced not only by the aerosol layer effective height but also by aerosol vertical profiles, optical properties including single scattering albedo (SSA), aerosol optical depth (AOD), particle size, and surface albedo. Overall, the error of the retrieved aerosol effective height is estimated to be 1276, 846, and 739 meters for dust, non-absorbing, and absorbing aerosol, respectively, assuming knowledge on the aerosol vertical distribution shape. Using radiance data from the Ozone Monitoring Instrument (OMI), a new algorithm is developed to derive the aerosol effective height over East Asia after the determination of the aerosol type and AOD from the MODerate resolution Imaging Spectroradiometer (MODIS). About 80 percent of retrieved aerosol effective heights are within the error range of 1 kilometer compared to those obtained from the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) measurements on thick aerosol layer cases.

Utilization of O4 Slant Column Density to Derive Aerosol Layer Height from a Spaceborne UV-Visible Hyperspectral Sensor: Sensitivity and Case Study

NASA Technical Reports Server (NTRS)

Park, Sang Seo; Kim, Jhoon; Lee, Hanlim; Torres, Omar; Lee, Kwang-Mog; Lee, Sang Deok

2016-01-01

The sensitivities of oxygen-dimer (O4) slant column densities (SCDs) to changes in aerosol layer height are investigated using the simulated radiances by a radiative transfer model, the linearized pseudo-spherical vector discrete ordinate radiative transfer (VLIDORT), and the Differential Optical Absorption Spectroscopy (DOAS) technique. The sensitivities of the O4 index (O4I), which is defined as dividing O4 SCD by 10(exp 40) sq molecules cm(exp -5), to aerosol types and optical properties are also evaluated and compared. Among the O4 absorption bands at 340, 360, 380, and 477 nm, the O4 absorption band at 477 nm is found to be the most suitable to retrieve the aerosol effective height. However, the O4I at 477 nm is significantly influenced not only by the aerosol layer effective height but also by aerosol vertical profiles, optical properties including single scattering albedo (SSA), aerosol optical depth (AOD), particle size, and surface albedo. Overall, the error of the retrieved aerosol effective height is estimated to be 1276, 846, and 739 m for dust, non-absorbing, and absorbing aerosol, respectively, assuming knowledge on the aerosol vertical distribution shape. Using radiance data from the Ozone Monitoring Instrument (OMI), a new algorithm is developed to derive the aerosol effective height over East Asia after the determination of the aerosol type and AOD from the MODerate resolution Imaging Spectroradiometer (MODIS). About 80% of retrieved aerosol effective heights are within the error range of 1 km compared to those obtained from the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) measurements on thick aerosol layer cases.

Estimating Planetary Boundary Layer Heights from NOAA Profiler Network Wind Profiler Data

NASA Technical Reports Server (NTRS)

Molod, Andrea M.; Salmun, H.; Dempsey, M

2015-01-01

An algorithm was developed to estimate planetary boundary layer (PBL) heights from hourly archived wind profiler data from the NOAA Profiler Network (NPN) sites located throughout the central United States. Unlike previous studies, the present algorithm has been applied to a long record of publicly available wind profiler signal backscatter data. Under clear conditions, summertime averaged hourly time series of PBL heights compare well with Richardson-number based estimates at the few NPN stations with hourly temperature measurements. Comparisons with clear sky reanalysis based estimates show that the wind profiler PBL heights are lower by approximately 250-500 m. The geographical distribution of daily maximum PBL heights corresponds well with the expected distribution based on patterns of surface temperature and soil moisture. Wind profiler PBL heights were also estimated under mostly cloudy conditions, and are generally higher than both the Richardson number based and reanalysis PBL heights, resulting in a smaller clear-cloudy condition difference. The algorithm presented here was shown to provide a reliable summertime climatology of daytime hourly PBL heights throughout the central United States.

Physical modeling of the atmospheric boundary layer in the UNH Flow Physics Facility

NASA Astrophysics Data System (ADS)

Taylor-Power, Gregory; Gilooly, Stephanie; Wosnik, Martin; Klewicki, Joe; Turner, John

2016-11-01

The Flow Physics Facility (FPF) at UNH has test section dimensions W =6.0m, H =2.7m, L =72m. It can achieve high Reynolds number boundary layers, enabling turbulent boundary layer, wind energy and wind engineering research with exceptional spatial and temporal instrument resolution. We examined the FPF's ability to experimentally simulate different types of the atmospheric boundary layer (ABL) using upstream roughness arrays. The American Society for Civil Engineers defines standards for simulating ABLs for different terrain types, from open sea to dense city areas (ASCE 49-12). The standards require the boundary layer to match a power law shape, roughness height, and power spectral density criteria. Each boundary layer type has a corresponding power law exponent and roughness height. The exponent and roughness height both increase with increasing roughness. A suburban boundary layer was chosen for simulation and a roughness element fetch was created. Several fetch lengths were experimented with and the resulting boundary layers were measured and compared to standards in ASCE 49-12: Wind Tunnel Testing for Buildings and Other Structures. Pitot tube and hot wire anemometers were used to measure average and fluctuating flow characteristics. Velocity profiles, turbulence intensity and velocity spectra were found to compare favorably.

PathfinderTURB: an automatic boundary layer algorithm. Development, validation and application to study the impact on in situ measurements at the Jungfraujoch

NASA Astrophysics Data System (ADS)

Poltera, Yann; Martucci, Giovanni; Collaud Coen, Martine; Hervo, Maxime; Emmenegger, Lukas; Henne, Stephan; Brunner, Dominik; Haefele, Alexander

2017-08-01

We present the development of the PathfinderTURB algorithm for the analysis of ceilometer backscatter data and the real-time detection of the vertical structure of the planetary boundary layer. Two aerosol layer heights are retrieved by PathfinderTURB: the convective boundary layer (CBL) and the continuous aerosol layer (CAL). PathfinderTURB combines the strengths of gradient- and variance-based methods and addresses the layer attribution problem by adopting a geodesic approach. The algorithm has been applied to 1 year of data measured by two ceilometers of type CHM15k, one operated at the Aerological Observatory of Payerne (491 m a.s.l.) on the Swiss plateau and one at the Kleine Scheidegg (2061 m a.s.l.) in the Swiss Alps. The retrieval of the CBL has been validated at Payerne using two reference methods: (1) manual detections of the CBL height performed by human experts using the ceilometer backscatter data; (2) values of CBL heights calculated using the Richardson's method from co-located radio sounding data. We found average biases as small as 27 m (53 m) with respect to reference method 1 (method 2). Based on the excellent agreement between the two reference methods, PathfinderTURB has been applied to the ceilometer data at the mountainous site of the Kleine Scheidegg for the period September 2014 to November 2015. At this site, the CHM15k is operated in a tilted configuration at 71° zenith angle to probe the atmosphere next to the Sphinx Observatory (3580 m a.s.l.) on the Jungfraujoch (JFJ). The analysis of the retrieved layers led to the following results: the CAL reaches the JFJ 41 % of the time in summer and 21 % of the time in winter for a total of 97 days during the two seasons. The season-averaged daily cycles show that the CBL height reaches the JFJ only during short periods (4 % of the time), but on 20 individual days in summer and never during winter. During summer in particular, the CBL and the CAL modify the air sampled in situ at JFJ, resulting in an unequivocal dependence of the measured absorption coefficient on the height of both layers. This highlights the relevance of retrieving the height of CAL and CBL automatically at the JFJ.

Analysis of vertical distributions and effective flight layers of insects: three-dimensional simulation of flying insects and catch at trap heights

USDA-ARS?s Scientific Manuscript database

The mean height and standard deviation (SD) of flight is calculated for over 100 insect species from their catches on trap heights reported in the literature. The iterative equations for calculating mean height and SD are presented. The mean flight height for 95% of the studies varied from 0.17 to 5...

Mid-latitude empirical model of the height distribution of atomic oxygen in the MLT region for different solar and geophysical conditions

NASA Astrophysics Data System (ADS)

Semenov, A.; Shefov, N.; Fadel, Kh.

The model of altitude distributions of atomic oxygen in the region of the mesopause and lower thermosphere (MLT) is constructed on the basis of empirical models of variations of the intensities, temperatures and altitudes of maximum of the layers of the emissions of atomic oxygen at 557.7 nm, hydroxyl and Atmospheric system of molecular oxygen. An altitude concentration distribution of neutral components is determined on the basis of systematization of the long-term data of temperature of the middle atmosphere from rocket, nightglow and ionospheric measurements at heights of 30-110 km in middle latitudes. They include dependence on a season, solar activity and a long-term trend. Examples of results of calculation for different months of year for conditions of the lower and higher solar activity are presented. With increasing of solar activity, the height of a layer of a maximum of atomic oxygen becomes lower, and the thickness of the layer increases. There is a high correlation between characteristics of a layer of atomic oxygen and a maximum of temperature at heights of the mesopause and lower thermosphere. This work is supported by grant of ISTC No. 2274.

Colorectal cancer incidence in path_MLH1 carriers subjected to different follow-up protocols: a Prospective Lynch Syndrome Database report.

PubMed

Seppälä, Toni; Pylvänäinen, Kirsi; Evans, Dafydd Gareth; Järvinen, Heikki; Renkonen-Sinisalo, Laura; Bernstein, Inge; Holinski-Feder, Elke; Sala, Paola; Lindblom, Annika; Macrae, Finlay; Blanco, Ignacio; Sijmons, Rolf; Jeffries, Jacqueline; Vasen, Hans; Burn, John; Nakken, Sigve; Hovig, Eivind; Rødland, Einar Andreas; Tharmaratnam, Kukatharmini; de Vos Tot Nederveen Cappel, Wouter H; Hill, James; Wijnen, Juul; Jenkins, Mark; Genuardi, Maurizio; Green, Kate; Lalloo, Fiona; Sunde, Lone; Mints, Miriam; Bertario, Lucio; Pineda, Marta; Navarro, Matilde; Morak, Monika; Frayling, Ian M; Plazzer, John-Paul; Sampson, Julian R; Capella, Gabriel; Möslein, Gabriela; Mecklin, Jukka-Pekka; Møller, Pål

2017-01-01

We have previously reported a high incidence of colorectal cancer (CRC) in carriers of pathogenic MLH1 variants (path_MLH1 ) despite follow-up with colonoscopy including polypectomy. The cohort included Finnish carriers enrolled in 3-yearly colonoscopy ( n  = 505; 4625 observation years) and carriers from other countries enrolled in colonoscopy 2-yearly or more frequently ( n  = 439; 3299 observation years). We examined whether the longer interval between colonoscopies in Finland could explain the high incidence of CRC and whether disease expression correlated with differences in population CRC incidence. Cumulative CRC incidences in carriers of path_MLH1 at 70-years of age were 41% for males and 36% for females in the Finnish series and 58% and 55% in the non-Finnish series, respectively ( p  > 0.05). Mean time from last colonoscopy to CRC was 32.7 months in the Finnish compared to 31.0 months in the non-Finnish (p > 0.05) and was therefore unaffected by the recommended colonoscopy interval. Differences in population incidence of CRC could not explain the lower point estimates for CRC in the Finnish series. Ten-year overall survival after CRC was similar for the Finnish and non-Finnish series (88% and 91%, respectively; p > 0.05). The hypothesis that the high incidence of CRC in path_MLH1 carriers was caused by a higher incidence in the Finnish series was not valid. We discuss whether the results were influenced by methodological shortcomings in our study or whether the assumption that a shorter interval between colonoscopies leads to a lower CRC incidence may be wrong. This second possibility is intriguing, because it suggests the dogma that CRC in path_MLH1 carriers develops from polyps that can be detected at colonoscopy and removed to prevent CRC may be erroneous. In view of the excellent 10-year overall survival in the Finnish and non-Finnish series we remain strong advocates of current surveillance practices for those with LS pending studies that will inform new recommendations on the best surveillance interval.

Clinical and molecular characterisation of hereditary and sporadic metastatic colorectal cancers harbouring microsatellite instability/DNA mismatch repair deficiency.

PubMed

Cohen, R; Buhard, O; Cervera, P; Hain, E; Dumont, S; Bardier, A; Bachet, J-B; Gornet, J-M; Lopez-Trabada, D; Dumont, S; Kaci, R; Bertheau, P; Renaud, F; Bibeau, F; Parc, Y; Vernerey, D; Duval, A; Svrcek, M; André, Thierry

2017-11-01

Patients treated with chemotherapy for microsatellite unstable (MSI) and/or mismatch repair deficient (dMMR) cancer metastatic colorectal cancer (mCRC) exhibit poor prognosis. We aimed to evaluate the relevance of distinguishing sporadic from Lynch syndrome (LS)-like mCRCs. MSI/dMMR mCRC patients were retrospectively identified in six French hospitals. Tumour samples were screened for MSI, dMMR, RAS/RAF mutations and MLH1 methylation. Sporadic cases were molecularly defined as those displaying MLH1/PMS2 loss of expression with BRAFV600E and/or MLH1 hypermethylation and no MMR germline mutation. Among 129 MSI/dMMR mCRC patients, 81 (63%) were LS-like and 48 (37%) had sporadic tumours; 22% of MLH1/PMS2-negative mCRCs would have been misclassified using an algorithm based on local medical records (age, Amsterdam II criteria, BRAF and MMR statuses when locally tested), compared to a systematical assessment of MMR, BRAF and MLH1 methylation statuses. In univariate analysis, parameters associated with better overall survival were age (P < 0.0001), metastatic resection (P = 0.001) and LS-like mCRC (P = 0.01), but not BRAFV600E. In multivariate analysis, age (hazard ratio (HR) = 3.19, P = 0.01) and metastatic resection (HR = 4.2, P = 0.001) were associated with overall survival, but not LS. LS-like patients were associated with more frequent liver involvement, metastatic resection and better disease-free survival after metastasectomy (HR = 0.28, P = 0.01). Median progression-free survival of first-line chemotherapy was similar between the two groups (4.2 and 4.2 months; P = 0.44). LS-like and sporadic MSI/dMMR mCRCs display distinct natural histories. MMR, BRAF mutation and MLH1 methylation testing should be mandatory to differentiate LS-like and sporadic MSI/dMMR mCRC, to determine in particular whether immune checkpoint inhibitors efficacy differs in these two populations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Features of the amplitude-height-frequency characteristics of midlatitude sporadic-E layer

NASA Astrophysics Data System (ADS)

Yusupov, Kamil; Akchurin, Adel

2012-07-01

At early investigation of an ionosphere the vertical pulse sounding was without separation magnetoionic components and such conditions allowed to observe interferential beatings or polarized fading over frequencies where traces of various magnetoionic component was crossing (overlapping). The beatings in F layer traces are often observed and their origin easily are explain by an interference o - and x-mode whereas in sporadic-E layer traces even observability of beatings of o- and x-modes is in doubt. Absence of experimental evidences of beatings is explain that measurements did not manage to be performed over the necessary time moment because of randomness and a rarity of occurrence high-intensity sporadic-E layers (without properties of scattering on small scale irregularities) and because of high labour input at recording and processing of amplitude-frequency characteristics. The direct observation of interferential beatings became problematic when ionosondes with separations of magnetoionic components appeared. Moreover because of relative vicinity of gyro and background plasma frequencies and also the steep electron profile gradient the beatings in sporadic-E traces should occur between two o-modes because in typical diurnal low-intensity sporadic-E layers (foEs<5MHz) x-mode will be strongly absorbed and the steep gradient on the bottom of sporadic-E layer will strengthen magnetoionic coupling (between o- and x-modes) and lead occurrence of so-called z-mode. The z-mode (extraordinary mode with ordinary polarization) reflected in higher height again takes the form of ordinary mode after passage of height of reflection of ordinary mode and interferes with ordinary mode. However our observations show that beating in sporadic-E traces mostly occur because of interference about o- and x-modes. For detailed research of interference conditions the approximation of width of interference fringes (distance between consecutive minima in interference pattern) as a function of sounding frequency was performed. This information can be also applied to determination of parameters of the height electron profile used in IRI model. For exact profile restoration it is necessary to use all information from ionogram. Besides the specified approximation of width of interference fringes it is necessary to determine also frequency dependences of the virtual height of reflection of sporadic-E layers for o- and x-modes accurate within 300 m. First of all it concerns to cusp in the beginning of sporadic-E traces. For approximation of this dependence the modernized model of a parabolic layer for o- and x-modes with various half-thickness of layer has been used. Comparison with experimental data gives half-thickness are approximately equal 5 and 25 km accordingly. All three approximations of interference fringe widths and of reflection heights will be used for determination of height electron density profile with improved precision below maximum of sporadic-E layer.

Pulse width and height modulation for multi-level resistance in bi-layer TaOx based RRAM

NASA Astrophysics Data System (ADS)

Alamgir, Zahiruddin; Beckmann, Karsten; Holt, Joshua; Cady, Nathaniel C.

2017-08-01

Mutli-level switching in resistive memory devices enables a wide range of computational paradigms, including neuromorphic and cognitive computing. To this end, we have developed a bi-layer tantalum oxide based resistive random access memory device using Hf as the oxygen exchange layer. Multiple, discrete resistance levels were achieved by modulating the RESET pulse width and height, ranging from 2 kΩ to several MΩ. For a fixed pulse height, OFF state resistance was found to increase gradually with the increase in the pulse width, whereas for a fixed pulse width, the increase in the pulse height resulted in drastic changes in resistance. Resistive switching in these devices transitioned from Schottky emission in the OFF state to tunneling based conduction in the ON state, based on I-V curve fitting and temperature dependent current measurements. These devices also demonstrated endurance of more than 108 cycles with a satisfactory Roff/Ron ratio and retention greater than 104 s.

Reduction of FeO contents in sinter under high bed operation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fujii, K.; Hazama, K.; Hoshikuma, Y.

1996-12-31

High-bed operation (bed height more than 700 mm) is currently being carried out at the Kure No. 1 sintering plant. Before initiating this high-bed operation, the authors conducted sinter pot tests at various bed heights to investigate the effect of bed height on sintering. The following results were obtained from these pot tests: Heightening of the sinter bed increased yield at the upper layer, but at the lower layer, the yield reached a maximum value at a certain bed height. From observation of the sinter cakes, the reduction in yield is attributed to uneven burn caused by surplus heat atmore » the lower layers. Therefore, when high-bed operation is carried out, reduction of the burning energy (reduction of the FeO content in the sinter) is required. This high-bed operation with lower FeO content has enabled the company to reduce fuel consumption and SiO{sub 2} content, while maintaining high yield and high sinter quality.« less

Observational characteristics of the tropopause inversion layer derived from CHAMP/GRACE radio occultations and MOZAIC aircraft data

NASA Astrophysics Data System (ADS)

Schmidt, T.; Cammas, J.-P.; Smit, H. G. J.; Heise, S.; Wickert, J.; Haser, A.

2010-12-01

In this study we discuss characteristics of the Northern Hemisphere (NH) midlatitude (40°N-60°N) tropopause inversion layer (TIL) based on two data sets. First, temperature measurements from GPS radio occultation data (CHAMP and GRACE) for the time interval 2001-2009 are used to exhibit seasonal properties of the TIL bottom height defined here as the height of the squared buoyancy frequency minimum N2 below the thermal tropopause, the TIL maximum height as the height of the N2 maximum above the tropopause, and the TIL top height as the height of the temperature maximum above the tropopause. Mean values of the TIL bottom, TIL maximum, and TIL top heights relative to the thermal tropopause for the NH midlatitudes are (-2.08 ± 0.35) km, (0.52 ± 0.10) km and (2.10 ± 0.23) km, respectively. A seasonal cycle of the TIL bottom and TIL top height is observed with values closer to the thermal tropopause during summer. Secondly, high-resolution temperature and trace gas profile measurements on board commercial aircrafts (Measurement of Ozone and Water Vapor by Airbus In-Service Aircraft (MOZAIC) program) from 2001-2008 for the NH midlatitude (40°N-60°N) region are used to characterize the TIL as a mixing layer around the tropopause. Mean TIL bottom, TIL maximum, and TIL top heights based on the MOZAIC temperature (N2) measurements confirm the results from the GPS data, even though most of the MOZAIC profiles used here are available under cyclonic situations. Further, we demonstrate that the mixing ratio gradients of ozone (O3) and carbon monoxide (CO) are suitable parameters for characterizing the TIL structure.

Reaction mechanism of CO oxidation on Cu2O(111): A density functional study

NASA Astrophysics Data System (ADS)

Sun, Bao-Zhen; Chen, Wen-Kai; Xu, Yi-Jun

2010-10-01

The possible reaction mechanisms for CO oxidation on the perfect Cu2O(111) surface have been investigated by performing periodic density functional theoretical calculations. We find that Cu2O(111) is able to facilitate the CO oxidation with different mechanisms. Four possible mechanisms are explored (denoted as MER1, MER2, MLH1, and MLH2, respectively): MER1 is CO(gas)+O2(ads)-->CO2(gas) MER2 is CO(gas)+O2(ads)-->CO3(ads)-->O(ads)+CO2(gas) MLH1 refers to CO(ads)+O2(ads)-->O(ads)+CO2(ads) and MLH2 refers to CO(ads)+O2(ads)-->OOCO(ads)-->O(ads)+CO2(ads). Our transition state calculations clearly reveal that MER1 and MLH2 are both viable; but MER1 mechanism preferentially operates, in which only a moderate energy barrier (60.22 kJ/mol) needs to be overcome. When CO oxidation takes place along MER2 path, it is facile for CO3 formation, but is difficult for its decomposition, thereby CO3 species can stably exist on Cu2O(111). Of course, the reaction of CO with lattice O of Cu2O(111) is also considered. However, the calculated barrier is 600.00 kJ/mol, which is too large to make the path feasible. So, we believe that on Cu2O(111), CO reacts with adsorbed O, rather than lattice O, to form CO2. This is different from the usual Mars-van Krevene mechanism. The present results enrich our understanding of the catalytic oxidation of CO by copper-based and metal-oxide catalysts.

A modifier of Huntington's disease onset at the MLH1 locus.

PubMed

Lee, Jong-Min; Chao, Michael J; Harold, Denise; Abu Elneel, Kawther; Gillis, Tammy; Holmans, Peter; Jones, Lesley; Orth, Michael; Myers, Richard H; Kwak, Seung; Wheeler, Vanessa C; MacDonald, Marcy E; Gusella, James F

2017-10-01

Huntington's disease (HD) is a dominantly inherited neurodegenerative disease caused by an expanded CAG repeat in HTT. Many clinical characteristics of HD such as age at motor onset are determined largely by the size of HTT CAG repeat. However, emerging evidence strongly supports a role for other genetic factors in modifying the disease pathogenesis driven by mutant huntingtin. A recent genome-wide association analysis to discover genetic modifiers of HD onset age provided initial evidence for modifier loci on chromosomes 8 and 15 and suggestive evidence for a locus on chromosome 3. Here, genotyping of candidate single nucleotide polymorphisms in a cohort of 3,314 additional HD subjects yields independent confirmation of the former two loci and moves the third to genome-wide significance at MLH1, a locus whose mouse orthologue modifies CAG length-dependent phenotypes in a Htt-knock-in mouse model of HD. Both quantitative and dichotomous association analyses implicate a functional variant on ∼32% of chromosomes with the beneficial modifier effect that delays HD motor onset by 0.7 years/allele. Genomic DNA capture and sequencing of a modifier haplotype localize the functional variation to a 78 kb region spanning the 3'end of MLH1 and the 5'end of the neighboring LRRFIP2, and marked by an isoleucine-valine missense variant in MLH1. Analysis of expression Quantitative Trait Loci (eQTLs) provides modest support for altered regulation of MLH1 and LRRFIP2, raising the possibility that the modifier affects regulation of both genes. Finally, polygenic modification score and heritability analyses suggest the existence of additional genetic modifiers, supporting expanded, comprehensive genetic analysis of larger HD datasets. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Epigenetic silencing of MLH1 in endometrial cancers is associated with larger tumor volume, increased rate of lymph node positivity and reduced recurrence-free survival.

PubMed

Cosgrove, Casey M; Cohn, David E; Hampel, Heather; Frankel, Wendy L; Jones, Dan; McElroy, Joseph P; Suarez, Adrian A; Zhao, Weiqiang; Chen, Wei; Salani, Ritu; Copeland, Larry J; O'Malley, David M; Fowler, Jeffrey M; Yilmaz, Ahmet; Chassen, Alexis S; Pearlman, Rachel; Goodfellow, Paul J; Backes, Floor J

2017-09-01

To determine the relationship between mismatch repair (MMR) classification and clinicopathologic features including tumor volume, and explore outcomes by MMR class in a contemporary cohort. Single institution cohort evaluating MMR classification for endometrial cancers (EC). MMR immunohistochemistry (IHC)±microsatellite instability (MSI) testing and reflex MLH1 methylation testing was performed. Tumors with MMR abnormalities by IHC or MSI and MLH1 methylation were classified as epigenetic MMR deficiency while those without MLH1 methylation were classified as probable MMR mutations. Clinicopathologic characteristics were analyzed. 466 endometrial cancers were classified; 75% as MMR proficient, 20% epigenetic MMR defects, and 5% as probable MMR mutations. Epigenetic MMR defects were associated with advanced stage, higher grade, presence of lymphovascular space invasion, and older age. MMR class was significantly associated with tumor volume, an association not previously reported. The epigenetic MMR defect tumors median volume was 10,220mm 3 compared to 3321mm 3 and 2,846mm 3 , for MMR proficient and probable MMR mutations respectively (P<0.0001). Higher tumor volume was associated with lymph node involvement. Endometrioid EC cases with epigenetic MMR defects had significantly reduced recurrence-free survival (RFS). Among advanced stage (III/IV) endometrioid EC the epigenetic MMR defect group was more likely to recur compared to the MMR proficient group (47.7% vs 3.4%) despite receiving similar adjuvant therapy. In contrast, there was no difference in the number of early stage recurrences for the different MMR classes. MMR testing that includes MLH1 methylation analysis defines a subset of tumors that have worse prognostic features and reduced RFS. Copyright © 2017 Elsevier Inc. All rights reserved.

Single nucleotide polymorphisms in MLH1 predict poor prognosis of hepatocellular carcinoma in a Chinese population.

PubMed

Zhu, Xiaonian; Liu, Wei; Qiu, Xiaoqiang; Wang, Zhigang; Tan, Chao; Bei, Chunhua; Qin, Linyuan; Ren, Yuan; Tan, Shengkui

2017-10-03

Hepatocellular carcinoma (HCC) is a malignant cancer causing deleterious health effect worldwide, especially in China. So far clinical cure rate and long-term survival rate of HCC remains low. Most HCC patients after cancer resection have recurrence or metastasis within 5 years. This study aims to explore the genetic association of mutL homolog 1 ( MLH1 ) polymorphisms with HCC risk and prognosis. Four candidate MLH1 polymorphisms, rs1800734, rs10849, rs3774343 and rs1540354 were studied from a hospital-based case-control study including 1,036 cases (HCC patients) and 1,036 controls (non-HCC patients) in Guangxi, China. All these SNPs interacted with environmental risk factors, such as HBV infection, alcohol intake and smoking in the pathogenesis of HCC. However, only rs1800734 had significant difference between cases and controls. Compared to the AA genotype, patients with AG, GG and AG/GG genotype of rs1800734 had an increased risk of HCC [ORs (95% CI) = 1.217 (1.074∼1.536), 1.745 (1.301∼2.591) and 1.291 (1.126∼1.687)] and a decreased survival time [co-dominant, HR (95% CI) = 1.553 (1.257∼1.920); dominant, HR (95% CI) = 2.207 (1.572∼3.100)]. Furthermore, we found that tumor number, tumor staging, metastasis and rs1800734 were associated with the overall survival of HCC patients by multivariate COX regression analysis. No significant difference was found between the other three MLH1 polymorphisms with HCC risk and prognosis. Our study suggests MLH1 SNP, rs1800734 as a new predictor for poor prognosis of HCC patients.

Age and origin of two common MLH1 mutations predisposing to hereditary colon cancer.

PubMed

Moisio, A L; Sistonen, P; Weissenbach, J; de la Chapelle, A; Peltomäki, P

1996-12-01

Two mutations in the DNA mismatch repair gene MLH1, referred to as mutations 1 and 2, are frequent among Finnish kindreds with hereditary nonpolyposis colorectal cancer (HNPCC). In order to assess the ages and origins of these mutations, we constructed a map of 15 microsatellite markers around MLH1 and used this information in haplotype analyses of 19 kindreds with mutation 1 and 6 kindreds with mutation 2. All kindreds with mutation 1 showed a single allele for the intragenic marker D3S1611 that was not observed on any unaffected chromosome. They also shared portions of a haplotype of 4-15 markers encompassing 2.0-19.0 cM around MLH1. All kindreds with mutation 2 shared another allele for D3S1611 and a conserved haplotype of 5-14 markers spanning 2.0-15.0 cM around MLH1. The degree of haplotype conservation was used to estimate the ages of these two mutations. While some recessive disease genes have been estimated to have existed and spread for as long as thousands of generations worldwide and hundreds of generations in the Finnish population, our analyses suggest that the spread of mutation 1 started 16-43 generations (400-1,075 years) ago and that of mutation 2 some 5-21 generations (125-525 years) ago. These datings are compatible with our genealogical results identifying a common ancestor born in the 16th and 18th century, respectively. Overall, our results indicate that all Finnish kindreds studied to date showing either mutation 1 or mutation 2 are due to single ancestral founding mutations relatively recent in origin in the population. Alternatively, the mutations arose elsewhere earlier and were introduced in Finland more recently.

Gene methylation profile of gastric cancerous tissue according to tumor site in the stomach.

PubMed

Kupcinskaite-Noreikiene, Rita; Ugenskiene, Rasa; Noreika, Alius; Rudzianskas, Viktoras; Gedminaite, Jurgita; Skieceviciene, Jurgita; Juozaityte, Elona

2016-01-26

There is considerable information on the methylation of the promoter regions of different genes involved in gastric carcinogenesis. However, there is a lack of information on how this epigenetic process differs in tumors originating at different sites in the stomach. The aim of this study is to assess the methylation profiles of the MLH1, MGMT, and DAPK-1 genes in cancerous tissues from different stomach sites. Samples were acquired from 81 patients suffering stomach adenocarcinoma who underwent surgery for gastric cancer in the Lithuanian University of Health Sciences Hospital Kaunas Clinics in 2009-2012. Gene methylation was investigated with methylation-specific PCR. The study was approved by the Lithuanian Biomedical Research Ethics Committee. The frequencies of methylation in cancerous tissues from the upper, middle, and lower thirds of the stomach were 11.1, 23.1, and 45.4%, respectively, for MLH1; 22.2, 30.8, and 57.6%, respectively, for MGMT; and 44.4, 48.7, and 51.5%, respectively, for DAPK-1. MLH1 and MGMT methylation was observed more often in the lower third of the stomach than in the upper third (p < 0.05). In the middle third, DAPK-1 promoter methylation was related to more-advanced disease in the lymph nodes (N2-3 compared with N0-1 [p = 0.02]) and advanced tumor stage (stage III rather than stages I-II [p = 0.05]). MLH1 and MGMT methylation correlated inversely when the tumor was located in the lower third of the stomach (coefficient, -0.48; p = 0.01). DAPK-1 and MLH1 methylation correlated inversely in tumors in the middle-third of the stomach (coefficient, -0.41; p = 0.01). Gene promoter methylation depends on the gastric tumor location.

Clustering of Lynch syndrome malignancies with no evidence for a role of DNA Mismatch Repair

PubMed Central

Case, Ashley S.; Zighelboim, Israel; Mutch, David G.; Babb, Sheri A.; Schmidt, Amy P.; Whelan, Alison J.; Thibodeau, Stephen N.; Goodfellow, Paul J.

2010-01-01

Objectives We ascertained a large kindred with an excess of Lynch syndrome-associated cancers. Our objective was to determine if a defect in one of the DNA mismatch repair (DMMR) genes was the probable cause of cancer susceptibility as microsatellite instability (MSI) and immunohistochemical (IHC) analysis of the probands' tumors did not provide a clear indication. Methods A detailed history and review of medical records was undertaken to construct a four-generation pedigree. Blood samples were obtained for analysis of germline DNA. Polymorphic repeats from the MLH1, MSH2, MSH6, and PMS2 loci were genotyped and the co-segregation of markers and disease was assessed. DMMR gene expression for all available tumors was evaluated by IHC. Combined bisulfite restriction analysis (COBRA) of MLH1 was utilized to test for germline epimutation. Results Four gynecologic carcinomas, 3 colon carcinomas, and 13 cases of adenomatous polyps were identified. The family met Amsterdam II criteria. The mean age of cancer diagnosis in the kindred was 63 years (range 44-82). DNA marker analyses excluded linkage to MLH1, MSH2, MSH6, and PMS2. Furthermore, MSI and IHC analysis of tumors did not suggest a role for DMMR. Methylation of the MLH1 promoter was identified in the peripheral blood leukocytes (PBLs) of a family member with an early onset colon cancer. Conclusions We identified a large family with multiple Lynch malignancies and no evidence for an inherited defect in DMMR. This family represents an important but poorly understood form of autosomal dominant inherited cancer susceptibility. Aberrant MLH1 promoter methylation in normal tissues may be a marker for cancer susceptibility in families such as this. PMID:18022218

Human mismatch repair protein hMutLα is required to repair short slipped-DNAs of trinucleotide repeats.

PubMed

Panigrahi, Gagan B; Slean, Meghan M; Simard, Jodie P; Pearson, Christopher E

2012-12-07

Mismatch repair (MMR) is required for proper maintenance of the genome by protecting against mutations. The mismatch repair system has also been implicated as a driver of certain mutations, including disease-associated trinucleotide repeat instability. We recently revealed a requirement of hMutSβ in the repair of short slip-outs containing a single CTG repeat unit (1). The involvement of other MMR proteins in short trinucleotide repeat slip-out repair is unknown. Here we show that hMutLα is required for the highly efficient in vitro repair of single CTG repeat slip-outs, to the same degree as hMutSβ. HEK293T cell extracts, deficient in hMLH1, are unable to process single-repeat slip-outs, but are functional when complemented with hMutLα. The MMR-deficient hMLH1 mutant, T117M, which has a point mutation proximal to the ATP-binding domain, is defective in slip-out repair, further supporting a requirement for hMLH1 in the processing of short slip-outs and possibly the involvement of hMHL1 ATPase activity. Extracts of hPMS2-deficient HEC-1-A cells, which express hMLH1, hMLH3, and hPMS1, are only functional when complemented with hMutLα, indicating that neither hMutLβ nor hMutLγ is sufficient to repair short slip-outs. The resolution of clustered short slip-outs, which are poorly repaired, was partially dependent upon a functional hMutLα. The joint involvement of hMutSβ and hMutLα suggests that repeat instability may be the result of aberrant outcomes of repair attempts.

Prevalence of Lynch syndrome and Lynch-like syndrome among patients with colorectal cancer in a Japanese hospital-based population.

PubMed

Chika, Noriyasu; Eguchi, Hidetaka; Kumamoto, Kensuke; Suzuki, Okihide; Ishibashi, Keiichiro; Tachikawa, Tetsuhiko; Akagi, Kiwamu; Tamaru, Jun-Ichi; Okazaki, Yasushi; Ishida, Hideyuki

2017-02-09

We investigated the prevalence of Lynch syndrome and Lynch-like syndrome among Japanese colorectal cancer patients, as there have been no credible data from Japan. Immunohistochemical analyses for mismatch repair proteins (MLH1, MSH2, MSH6 and PMS2) were carried out in surgically resected, formalin-fixed paraffin-embedded specimens obtained from 1,234 newly diagnosed colorectal cancer patients between March 2005 and April 2014. The presence/absence of the BRAF V600E mutation and hypermethylation of the MLH1 promoter was analyzed where necessary. Genetic testing was finally undertaken in patients suspected as having Lynch syndrome. By the universal screening approach with immunohistochemical analysis for mismatch repair proteins followed by analyses for the BRAF V600E mutation and MLH1 promoter methylation status, 11 (0.9%) of the 1,234 patients were identified as candidates for genetic testing. Out of the 11 patients, 9 (0.7%) were finally diagnosed as having Lynch syndrome; the responsible genes included MLH1 (n = 1), MSH2 (n = 4), EPCAM (n = 1) and MSH6 (n = 3). The remaining two patients (0.2%) were regarded as having Lynch-like syndrome, since biallelic somatic deletion of the relevant mismatch repair genes was detected in the absence of germline mismatch repair alterations. None of the cases was identified as having germline MLH1 epimutation. The prevalence of Lynch syndrome among all newly diagnosed cases of colorectal cancer in Japan is in the same range as that recently reported by studies in Western population. The prevalence of Lynch-like syndrome seems to be extremely low. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Mispair-specific Recruitment of the Mlh1-Pms1 Complex Identifies Repair Substrates of the Saccharomyces cerevisiae Msh2-Msh3 Complex*

PubMed Central

Srivatsan, Anjana; Bowen, Nikki; Kolodner, Richard D.

2014-01-01

DNA mismatch repair is initiated by either the Msh2-Msh6 or the Msh2-Msh3 mispair recognition heterodimer. Here we optimized the expression and purification of Saccharomyces cerevisiae Msh2-Msh3 and performed a comparative study of Msh2-Msh3 and Msh2-Msh6 for mispair binding, sliding clamp formation, and Mlh1-Pms1 recruitment. Msh2-Msh3 formed sliding clamps and recruited Mlh1-Pms1 on +1, +2, +3, and +4 insertion/deletions and CC, AA, and possibly GG mispairs, whereas Msh2-Msh6 formed mispair-dependent sliding clamps and recruited Mlh1-Pms1 on 7 of the 8 possible base:base mispairs, the +1 insertion/deletion mispair, and to a low level on the +2 but not the +3 or +4 insertion/deletion mispairs and not on the CC mispair. The mispair specificity of sliding clamp formation and Mlh1-Pms1 recruitment but not mispair binding alone correlated best with genetic data on the mispair specificity of Msh2-Msh3- and Msh2-Msh6-dependent mismatch repair in vivo. Analysis of an Msh2-Msh6/Msh3 chimeric protein and mutant Msh2-Msh3 complexes showed that the nucleotide binding domain and communicating regions but not the mispair binding domain of Msh2-Msh3 are responsible for the extremely rapid dissociation of Msh2-Msh3 sliding clamps from DNA relative to that seen for Msh2-Msh6, and that amino acid residues predicted to stabilize Msh2-Msh3 interactions with bent, strand-separated mispair-containing DNA are more critical for the recognition of small +1 insertion/deletions than larger +4 insertion/deletions. PMID:24550389

MSH3 expression does not influence the sensitivity of colon cancer HCT116 cell line to oxaliplatin and poly(ADP-ribose) polymerase (PARP) inhibitor as monotherapy or in combination.

PubMed

Tentori, Lucio; Muzi, Alessia; Dorio, Annalisa Susanna; Dolci, Susanna; Campolo, Federica; Vernole, Patrizia; Lacal, Pedro Miguel; Praz, Françoise; Graziani, Grazia

2013-07-01

Defective expression of the mismatch repair protein MSH3 is frequently detected in colon cancer, and down-regulation of its expression was found to decrease sensitivity to platinum compounds or poly(ADP-ribose) polymerase inhibitors (PARPi) monotherapy. We have investigated whether MSH3 transfection in MSH3-deficient colon cancer cells confers resistance to oxaliplatin or PARPi and whether their combination restores chemosensitivity. MSH3-deficient/MLH1-proficient colon cancer HCT116(MLH1) cells were transfected with the MSH3 cDNA cloned into the pcDNA3.1(-) vector. MSH3/MLH1-deficient HCT116, carrying MLH1 and MSH3 mutations on chromosome 3 and 5, respectively, and HCT116 in which wild-type MLH1 (HCT116+3), MSH3 (HCT116+5) or both genes (HCT116+3+5) were introduced by chromosome transfer were also tested. Sensitivity to oxaliplatin and to PARPi was evaluated by analysis of clonogenic survival, cell proliferation, apoptosis and cell cycle. MSH3 transfection in HCT116 cells did not confer resistance to oxaliplatin or PARPi monotherapy. MSH3-proficient HCT116+5 or HCT116+3+5 cells, which were more resistant to oxaliplatin and PARPi in comparison with their MSH3-deficient counterparts, expressed higher levels of the nucleotide excision repair ERCC1 and XPF proteins, involved in the resistance to platinum compounds, and lower PARP-1 levels. In all cases, PARPi increased sensitivity to oxaliplatin. Restoring of MSH3 expression by cDNA transfection, rather than by chromosome transfer, did not affect colon cancer sensitivity to oxaliplatin or PARPi monotherapy; PARP-1 levels seemed to be more crucial for the outcome of PARPi monotherapy.

Mispair-specific recruitment of the Mlh1-Pms1 complex identifies repair substrates of the Saccharomyces cerevisiae Msh2-Msh3 complex.

PubMed

Srivatsan, Anjana; Bowen, Nikki; Kolodner, Richard D

2014-03-28

DNA mismatch repair is initiated by either the Msh2-Msh6 or the Msh2-Msh3 mispair recognition heterodimer. Here we optimized the expression and purification of Saccharomyces cerevisiae Msh2-Msh3 and performed a comparative study of Msh2-Msh3 and Msh2-Msh6 for mispair binding, sliding clamp formation, and Mlh1-Pms1 recruitment. Msh2-Msh3 formed sliding clamps and recruited Mlh1-Pms1 on +1, +2, +3, and +4 insertion/deletions and CC, AA, and possibly GG mispairs, whereas Msh2-Msh6 formed mispair-dependent sliding clamps and recruited Mlh1-Pms1 on 7 of the 8 possible base:base mispairs, the +1 insertion/deletion mispair, and to a low level on the +2 but not the +3 or +4 insertion/deletion mispairs and not on the CC mispair. The mispair specificity of sliding clamp formation and Mlh1-Pms1 recruitment but not mispair binding alone correlated best with genetic data on the mispair specificity of Msh2-Msh3- and Msh2-Msh6-dependent mismatch repair in vivo. Analysis of an Msh2-Msh6/Msh3 chimeric protein and mutant Msh2-Msh3 complexes showed that the nucleotide binding domain and communicating regions but not the mispair binding domain of Msh2-Msh3 are responsible for the extremely rapid dissociation of Msh2-Msh3 sliding clamps from DNA relative to that seen for Msh2-Msh6, and that amino acid residues predicted to stabilize Msh2-Msh3 interactions with bent, strand-separated mispair-containing DNA are more critical for the recognition of small +1 insertion/deletions than larger +4 insertion/deletions.

Inhibition of microRNA-31-5p protects human colonic epithelial cells against ionizing radiation

NASA Astrophysics Data System (ADS)

Kim, Sang Bum; Zhang, Lu; Barron, Summer; Shay, Jerry W.

2014-04-01

MicroRNAs (miRNAs), endogenous non-coding small RNAs, are sensitive to environmental changes, and their differential expression is important for adaptation to the environment. However, application of miRNAs as a clinical prognostic or diagnostic tool remains unproven. In this study we demonstrate a chronic/persistent change of miRNAs from the plasma of a colorectal cancer susceptible mouse model (CPC;Apc) about 250 days after exposure to a simulated solar particle event (SPE). Differentially expressed miRNAs were identified compared to unirradiated control mice, including miR-31-5p, which we investigated further. To address the cellular function of miR-31-5p, we transfected a miR-31-5p mimic (sense) or inhibitor (antisense) into immortalized human colonic epithelial cells followed by gamma-irradiation. A miR-31-5p mimic sensitized but a miR-31-5p inhibitor protected colonic epithelial cells against radiation induced killing. We found that the miR-31-5p mimic inhibited the induction of hMLH1 expression after irradiation, whereas the miR-31-5p inhibitor increased the basal level of hMLH1 expression. The miR-31-5p inhibitor failed to modulate radiosensitivity in an hMLH1-deficient HCT116 colon cancer cell line but protected HCT116 3-6 and DLD-1 (both hMLH1-positive) colon cancer cell lines. Our findings demonstrate that miR-31-5p has an important role in radiation responses through regulation of hMLH1 expression. Targeting this pathway could be a promising therapeutic strategy for future personalized anti-cancer radiotherapy.

Secondary mutation in a coding mononucleotide tract in MSH6 causes loss of immunoexpression of MSH6 in colorectal carcinomas with MLH1/PMS2 deficiency.

PubMed

Shia, Jinru; Zhang, Liying; Shike, Moshe; Guo, Min; Stadler, Zsofia; Xiong, Xiaoling; Tang, Laura H; Vakiani, Efsevia; Katabi, Nora; Wang, Hangjun; Bacares, Ruben; Ruggeri, Jeanine; Boland, C Richard; Ladanyi, Marc; Klimstra, David S

2013-01-01

Immunohistochemical staining for DNA mismatch repair proteins may be affected by various biological and technical factors. Staining variations that could potentially lead to erroneous interpretations have been recognized. A recently recognized staining variation is the significant reduction of staining for MSH6 in some colorectal carcinomas. The frequency and specific characteristics of this aberrant MSH6 staining pattern, however, have not been well analyzed. In this study of 420 colorectal carcinoma samples obtained from patients fulfilling the Revised Bethesda Guidelines, we detected 9 tumors (2%) showing extremely limited staining for MSH6 with positive staining present in <5% of the tumor cells. Our analyses showed that these tumors belonged to two distinct categories: (1) MLH1 and/or PMS2 protein-deficient carcinomas (n=5, including 1 with a pathogenic mutation in PMS2); and (2) MLH1, PMS2 and MSH2 normal but with chemotherapy or chemoradiation therapy before surgery (n=4). To test our hypothesis that somatic mutation in the coding region microsatellite of the MSH6 gene might be a potential underlying mechanism for such limited MSH6 staining, we evaluated frameshift mutation in a (C)(8) tract in exon 5 of the MSH6 gene in seven tumors that had sufficient DNA for analysis, and detected mutation in four; all four tumors belonged to the MLH1/PMS2-deficient group. In conclusion, our data outline the main scenarios where significant reduction of MSH6 staining is more likely to occur in colorectal carcinoma, and suggest that somatic mutations of the coding region microsatellites of the MSH6 gene is an underlying mechanism for this staining phenomenon in MLH1/PMS2-deficient carcinomas.

Remote sensing of the ionospheric F layer by use of O I 6300-A and O I 1356-A observations

NASA Technical Reports Server (NTRS)

Chandra, S.; Reed, E. I.; Meier, R. R.; Opal, C. B.; Hicks, G. T.

1975-01-01

The possibility of using airglow techniques for estimating the electron density and height of the F layer is studied on the basis of a simple relationship between the height of the F2 peak and the column emission rates of the O I 6300 A and O I 1356 A lines. The feasibility of this approach is confirmed by a numerical calculation of F2 peak heights and electron densities from simultaneous measurements of O I 6300 A and O I 1356 A obtained with earth-facing photometers carried by the Ogo 4 satellite. Good agreement is established with the F2 peak heights estimates from top-side and bottom-side ionospheric sounding.

Retrieving Smoke Aerosol Height from DSCOVR/EPIC

NASA Astrophysics Data System (ADS)

Xu, X.; Wang, J.; Wang, Y.

2017-12-01

Unlike industrial pollutant particles that are often confined within the planetary boundary layer, smoke from forest and agriculture fires can inject massive carbonaceous aerosols into the upper troposphere due to the intense pyro-convection. Sensitivity of weather and climate to absorbing carbonaceous aerosols is regulated by the altitude of those aerosol layers. However, aerosol height information remains limited from passive satellite sensors. Here we present an algorithm to estimate smoke aerosol height from radiances in the oxygen A and B bands measured by the Earth Polychromatic Imaging Camera (EPIC) from the Deep Space Climate Observatory (DSCOVR). With a suit of case studies and validation efforts, we demonstrate that smoke aerosol height can be well retrieved over both ocean and land surfaces multiple times daily.

The Effect of Backward-Facing Step Height on Instability Growth and Breakdown in Swept Wing Boundary-Layer Transition

NASA Technical Reports Server (NTRS)

Eppink, Jenna L.; Wlezien, Richard W.; King, Rudolph A.; Choudhari, Meelan

2015-01-01

A low-speed experiment was performed on a swept at plate model with an imposed pressure gradient to determine the effect of a backward-facing step on transition in a stationary-cross flow dominated flow. Detailed hot-wire boundary-layer measurements were performed for three backward-facing step heights of approximately 36, 45, and 49% of the boundary-layer thickness at the step. These step heights correspond to a subcritical, nearly-critical, and critical case. Three leading-edge roughness configurations were tested to determine the effect of stationary-cross flow amplitude on transition. The step caused a local increase in amplitude of the stationary cross flow for the two larger step height cases, but farther downstream the amplitude decreased and remained below the baseline amplitude. The smallest step caused a slight local decrease in amplitude of the primary stationary cross flow mode, but the amplitude collapsed back to the baseline case far downstream of the step. The effect of the step on the amplitude of the primary cross flow mode increased with step height, however, the stationary cross flow amplitudes remained low and thus, stationary cross flow was not solely responsible for transition. Unsteady disturbances were present downstream of the step for all three step heights, and the amplitudes increased with increasing step height. The only exception is that the lower frequency (traveling crossflow-like) disturbance was not present in the lowest step height case. Positive and negative spikes in instantaneous velocity began to occur for the two larger step height cases and then grew in number and amplitude downstream of reattachment, eventually leading to transition. The number and amplitude of spikes varied depending on the step height and cross flow amplitude. Despite the low amplitude of the disturbances in the intermediate step height case, breakdown began to occur intermittently and the flow underwent a long transition region.

Estimating the atmospheric boundary layer height over sloped, forested terrain from surface spectral analysis during BEARPEX

NASA Astrophysics Data System (ADS)

Choi, W.; Faloona, I. C.; McKay, M.; Goldstein, A. H.; Baker, B.

2010-11-01

In this study the atmospheric boundary layer (ABL) height (zi) over complex, forested terrain is estimated based on the power spectra and the integral length scale of horizontal winds obtained from a three-axis sonic anemometer during the BEARPEX (Biosphere Effects on Aerosol and Photochemistry) Experiment. The zi values estimated with this technique showed very good agreement with observations obtained from balloon tether sonde (2007) and rawinsonde (2009) measurements under unstable conditions (z/L < 0) at the coniferous forest in the California Sierra Nevada. The behavior of the nocturnal boundary layer height (h) and power spectra of lateral winds and temperature under stable conditions (z/L > 0) is also presented. The nocturnal boundary layer height is found to be fairly well predicted by a recent interpolation formula proposed by Zilitinkevich et al. (2007), although it was observed to only vary from 60-80 m during the experiment. Finally, significant directional wind shear was observed during both day and night with winds backing from the prevailing west-southwesterlies in the ABL (anabatic cross-valley circulation) to consistent southerlies in a layer ~1 km thick just above the ABL before veering to the prevailing westerlies further aloft. We show that this is consistent with the forcing of a thermal wind driven by the regional temperature gradient directed due east in the lower troposphere.

Wind-Tunnel Simulation of Weakly and Moderately Stable Atmospheric Boundary Layers

NASA Astrophysics Data System (ADS)

Hancock, Philip E.; Hayden, Paul

2018-07-01

The simulation of horizontally homogeneous boundary layers that have characteristics of weakly and moderately stable atmospheric flow is investigated, where the well-established wind engineering practice of using `flow generators' to provide a deep boundary layer is employed. Primary attention is given to the flow above the surface layer, in the absence of an overlying inversion, as assessed from first- and second-order moments of velocity and temperature. A uniform inlet temperature profile ahead of a deep layer, allowing initially neutral flow, results in the upper part of the boundary layer remaining neutral. A non-uniform inlet temperature profile is required but needs careful specification if odd characteristics are to be avoided, attributed to long-lasting effects inherent of stability, and to a reduced level of turbulent mixing. The first part of the wind-tunnel floor must not be cooled if turbulence quantities are to vary smoothly with height. Closely horizontally homogeneous flow is demonstrated, where profiles are comparable or closely comparable with atmospheric data in terms of local similarity and functions of normalized height. The ratio of boundary-layer height to surface Obukhov length, and the surface heat flux, are functions of the bulk Richardson number, independent of horizontal homogeneity. Surface heat flux rises to a maximum and then decreases.

Wind-Tunnel Simulation of Weakly and Moderately Stable Atmospheric Boundary Layers

NASA Astrophysics Data System (ADS)

Hancock, Philip E.; Hayden, Paul

2018-02-01

The simulation of horizontally homogeneous boundary layers that have characteristics of weakly and moderately stable atmospheric flow is investigated, where the well-established wind engineering practice of using `flow generators' to provide a deep boundary layer is employed. Primary attention is given to the flow above the surface layer, in the absence of an overlying inversion, as assessed from first- and second-order moments of velocity and temperature. A uniform inlet temperature profile ahead of a deep layer, allowing initially neutral flow, results in the upper part of the boundary layer remaining neutral. A non-uniform inlet temperature profile is required but needs careful specification if odd characteristics are to be avoided, attributed to long-lasting effects inherent of stability, and to a reduced level of turbulent mixing. The first part of the wind-tunnel floor must not be cooled if turbulence quantities are to vary smoothly with height. Closely horizontally homogeneous flow is demonstrated, where profiles are comparable or closely comparable with atmospheric data in terms of local similarity and functions of normalized height. The ratio of boundary-layer height to surface Obukhov length, and the surface heat flux, are functions of the bulk Richardson number, independent of horizontal homogeneity. Surface heat flux rises to a maximum and then decreases.

Mesoscopic Length Scale Controls the Rheology of Dense Suspensions

NASA Astrophysics Data System (ADS)

Bonnoit, Claire; Lanuza, Jose; Lindner, Anke; Clement, Eric

2010-09-01

From the flow properties of dense granular suspensions on an inclined plane, we identify a mesoscopic length scale strongly increasing with volume fraction. When the flowing layer height is larger than this length scale, a diverging Newtonian viscosity is determined. However, when the flowing layer height drops below this scale, we evidence a nonlocal effective viscosity, decreasing as a power law of the flow height. We establish a scaling relation between this mesoscopic length scale and the suspension viscosity. These results support recent theoretical and numerical results implying collective and clustered granular motion when the jamming point is approached from below.

Mesoscopic length scale controls the rheology of dense suspensions.

PubMed

Bonnoit, Claire; Lanuza, Jose; Lindner, Anke; Clement, Eric

2010-09-03

From the flow properties of dense granular suspensions on an inclined plane, we identify a mesoscopic length scale strongly increasing with volume fraction. When the flowing layer height is larger than this length scale, a diverging Newtonian viscosity is determined. However, when the flowing layer height drops below this scale, we evidence a nonlocal effective viscosity, decreasing as a power law of the flow height. We establish a scaling relation between this mesoscopic length scale and the suspension viscosity. These results support recent theoretical and numerical results implying collective and clustered granular motion when the jamming point is approached from below.

Utilization of O4 slant column density to derive aerosol layer height from a spaceborne UV-visible hyperspectral sensor: sensitivity and case study

NASA Astrophysics Data System (ADS)

Park, S. S.; Kim, J.; Lee, H.; Torres, O.; Lee, K.-M.; Lee, S. D.

2015-03-01

The sensitivities of oxygen-dimer (O4) slant column densities (SCDs) to changes in aerosol layer height are investigated using simulated radiances by a radiative transfer model, Linearized Discrete Ordinate Radiative Transfer (LIDORT), and Differential Optical Absorption Spectroscopy (DOAS) technique. The sensitivities of the O4 SCDs to aerosol types and optical properties are also evaluated and compared. Among the O4 absorption bands at 340, 360, 380, and 477 nm, the O4 absorption band at 477 nm is found to be the most suitable to retrieve the aerosol effective height. However, the O4 SCD at 477 nm is significantly influenced not only by the aerosol layer effective height but also by aerosol vertical profiles, optical properties including single scattering albedo (SSA), aerosol optical depth (AOD), and surface albedo. Overall, the error of the retrieved aerosol effective height is estimated to be 414 m (16.5%), 564 m (22.4%), and 1343 m (52.5%) for absorbing, dust, and non-absorbing aerosol, respectively, assuming knowledge on the aerosol vertical distribution type. Using radiance data from the Ozone Monitoring Instrument (OMI), a new algorithm is developed to derive the aerosol effective height over East Asia after the determination of the aerosol type and AOD from the MODerate resolution Imaging Spectroradiometer (MODIS). The retrieved aerosol effective heights are lower by approximately 300 m (27 %) compared to those obtained from the ground-based LIDAR measurements.

Pilot trial of a parenting and self-care intervention for HIV-positive mothers: the IMAGE program.

PubMed

Murphy, Debra A; Armistead, Lisa; Payne, Diana L; Marelich, William D; Herbeck, Diane M

2017-01-01

A pilot study was conducted to assess the effects of the IMAGE pilot intervention (Improving Mothers' parenting Abilities, Growth, and Effectiveness) on mothers living with HIV (MLH). Based on Fisher and Fisher's IMB model [1992. Changing AIDS risk behavior. Psychological Bulletin, 111, 455-474], the intervention focused on self-care and parenting behavior skills of MLH that affect maternal, child, and family outcomes. A randomized pre-test-post-test two-group design with repeated assessments was used. MLH (n = 62) and their children aged 6-14 (n = 62; total N = 124) were recruited for the trial and randomized to the theory-based skills training condition or a standard care control condition. Assessments were conducted at baseline with follow-ups at 3, 6, and 12 months. Maternal, child, and family outcomes were assessed. Results show significant effects of the intervention for improving parenting practices for mothers. The intervention also improved family outcomes, and showed improvements in the parent-child relationship. IMAGE had a positive impact on parenting behaviors, and on maternal, child, and family outcomes. Given MLH can be challenged by their illness and also live in under-resourced environments, IMAGE may be viewed as a viable way to improve quality of life and family outcomes.

Frequency of pathogenic germline mutations in cancer susceptibility genes in breast cancer patients.

PubMed

Kaur, Raman Preet; Shafi, Gowhar; Benipal, Raja Paramjeet Singh; Munshi, Anjana

2018-04-26

In this study, we evaluated the incidence of pathogenic germline mutations in 30 breast cancer susceptibility genes in breast cancer patients. Our aim was to understand the involvement of the inherited mutations in these genes in a breast cancer cohort. Two hundred ninety-six female breast cancer patients including 4.5% of familial breast cancer cases were included in the study. 200 ng of genomic DNA was used to evaluate the pathogenic mutations, detected using Global Screening Array (GSA) microchip (Illumina Inc.) according to the manufacturer's instructions. The pathogenic frameshift and nonsense mutations were observed in BRCA2 (10.9%), MLH1 (58.6%), MTHFR (50%), MSH2 (14.2%), and CYTB (52%) genes. Familial breast cancer patients (4.5%) had variations in BRCA2, MLH1, MSH2, and CYTB genes. 28% of patients with metastasis, recurrence, and death harbored mono/biallelic alterations in MSH2, MLH1, and BRCA2 genes. The results of this study can guide to develop a panel to test the breast cancer patients for pathogenic mutations, from Malwa region of Punjab. The screening of MSH2, MLH1, and BRCA2 should be carried in individuals with or without family history of breast cancer as these genes have been reported to increase the cancer risk by tenfold.

Recombination and synaptic adjustment in oocytes of mice heterozygous for a large paracentric inversion.

PubMed

Torgasheva, Anna A; Rubtsov, Nikolai B; Borodin, Pavel M

2013-03-01

Homologous chromosome synapsis in inversion heterozygotes results in the formation of inversion loops. These loops might be transformed into straight, non-homologously paired bivalents via synaptic adjustment. Synaptic adjustment was discovered 30 years ago; however, its relationship with recombination has remained unclear. We analysed this relationship in female mouse embryos heterozygous for large paracentric inversion In(1)1Rk using immunolocalisation of the synaptonemal complex (SYCP3) and mature recombination nodules (MLH1) proteins. The frequency of cells containing bivalents with inversion loops decreased from 69 % to 28 % during pachytene. If an MLH1 focus was present in the non-homologously paired inverted region of the straight bivalent, it was always located in the middle of the inversion. Most of the small, incompletely adjusted loops contained MLH1 foci near the points at which pairing partners were switched. This observation indicates that the degree of synaptic adjustment depended on the crossover position. Complete synaptic adjustment was only possible if a crossover (CO) was located exactly in the middle of the inversion. If a CO was located at any other site, this interrupted synaptic adjustment and resulted in inversion loops of different sizes with an MLH1 focus at or near the edge of the remaining loop.

Atmospheric Boundary Layer of a pasture site in Amazônia

NASA Astrophysics Data System (ADS)

Trindade de Araújo Tiburtino Neves, Theomar; Fisch, Gilberto; Raasch, Siegfried

2013-04-01

A great effort has been made by the community of micrometeorology and planetary boundary layer for a better description of the properties of the Atmospheric Boundary Layer (ABL), such as its height, thermodynamics characteristics and its time evolution. This work aims to give a review of the main characteristics of Atmospheric Boundary Layer over a pasture site in Amazonia. The measurements dataset was carried out from 3 different LBA field campaigns: RBLE 3 (during the dry season from 1993), RaCCI (during the dry-to-wet transition season from 2002) and WetAMC (during the wet season from 1999), collected with tethered balloon, radiosondes and eddy correlation method in a pasture site in the southwestern Amazonia. Different techniques and instruments were used to estimate the ABĹs properties. During the daytime, it was possible to observe that there is an abrupt growth of the Convective Boundary Layer (CBL) between 08 and 11 LT, with a stationary pattern between 14 and 17 LT. The maximum heights at late afternoon were around 1600 m during the dry season, whilst the wet season it only reached 1000 m. This is due to the lower surface turbulent sensible heat flux as the soil is wetter and the partition of energy is completely different between wet to the dry season. For the transition period (RaCCI 2002), it was possible to analyze and compare several estimates from different instruments and methods. It showed that the parcel method overestimates the heights of all measurements (mainly at 14 LT) due to the high incidence of solar radiation and superadiabatic gradients. The profile and Richardson number methods gave results very similar to estimate the height of the CBL. The onset of the Nocturnal Boundary Layer (NBL) occurs before the sunset (18 LT) and its height is reasonable stable during the night (typical values around 180-250 m). An alternative method (Vmax) which used the height of the maximum windspeed derived from a SODAR instrument during RaCCI 2002 was proposed and it showed to be satisfactory comparing with the others methods. Besides that, it has the advantage to have measurements each 30 min.

The Tall Wind project - exploring the wind profile and boundary-layer height in the atmosphere's first kilometer over flat terrain.

NASA Astrophysics Data System (ADS)

Gryning, S. E.; Batchvarova, E.; Pena, A.; Mikkelsen, T.; Brümmer, B.; Emeis, S.; Gulstad, L.; Lee, N.

2010-09-01

Predicting the wind at typical heights of present and future wind turbines is a considerable scientific challenge. Presently applied models are accurate within the surface layer. New measurements and instrument synergies are necessary as basis for developing new wind models and understanding the physical processes that form the wind profile in order to describe the wind profile above it. Analysis of the wind and turbulence profiles from a meteorological mast at heights up to 160 meters and wind lidars up to 300 meters at the National test station at Høvsøre, Denmark, shows deviations of the wind profile above 80 meters the from the profile used so far near the surface. It also reveals the importance of the boundary-layer height as a physical parameter for the description of the wind profile. In the Tall Wind project, mast and lidar measurements of wind and fluxes will be combined with monitoring of the boundary-layer height by use of an aerosol lidar. At the main project monitoring sites (Høvsøre in Denmark and Hamburg in Germany) long term monitoring programmes on tall masts (160 and 300 meters) already exists and will be intensified. As part of the project the wind profile will be measured up to 1000 meters by a wind lidar (windcube) and the boundary-layer height by an aerosol lidar. The new data sets can be used for theoretical developments and evaluation of meso-scale meteorological models. The project is an international collaboration between academia (Risoe-DTU, HU and KIT) and industry (Vestas and DONG), funded by the Danish Research Agency, the Strategic Research Council (Sagsnr. 2104-08-0025). In the paper the set-up of the Tall Wind project will be described and some first results and experience will be presented.

An investigation of methods for injecting emissions from boreal wildfires using WRF-Chem during ARCTAS

NASA Astrophysics Data System (ADS)

Sessions, W. R.; Fuelberg, H. E.; Kahn, R. A.; Winker, D. M.

2010-11-01

The Weather Research and Forecasting Model (WRF) is considered a "next generation" mesoscale meteorology model. The inclusion of a chemistry module (WRF-Chem) allows transport simulations of chemical and aerosol species such as those observed during NASA's Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) in 2008. The ARCTAS summer deployment phase during June and July coincided with large boreal wildfires in Saskatchewan and Eastern Russia. One of the most important aspects of simulating wildfire plume transport is the height at which emissions are injected. WRF-Chem contains an integrated one-dimensional plume rise model to determine the appropriate injection layer. The plume rise model accounts for thermal buoyancy associated with fires and the local atmospheric stability. This study compares results from the plume model against those of two more traditional injection methods: Injecting within the planetary boundary layer, and in a layer 3-5 km above ground level. Fire locations are satellite derived from the GOES Wildfire Automated Biomass Burning Algorithm (WF_ABBA) and the MODIS thermal hotspot detection. Two methods for preprocessing these fire data are compared: The prep_chem_sources method included with WRF-Chem, and the Naval Research Laboratory's Fire Locating and Monitoring of Burning Emissions (FLAMBE). Results from the simulations are compared with satellite-derived products from the AIRS, MISR and CALIOP sensors. Results show that the FLAMBE pre-processor produces more realistic injection heights than does prep_chem_sources. The plume rise model using FLAMBE provides the best agreement with satellite-observed injection heights. Conversely, when the planetary boundary layer or the 3-5 km AGL layer were filled with emissions, the resulting injection heights exhibit less agreement with observed plume heights. Results indicate that differences in injection heights produce different transport pathways. These differences are especially pronounced in areas of strong vertical wind shear and when the integration period is long.

An investigation of methods for injecting emissions from boreal wildfires using WRF-Chem during ARCTAS

NASA Astrophysics Data System (ADS)

Sessions, W. R.; Fuelberg, H. E.; Kahn, R. A.; Winker, D. M.

2011-06-01

The Weather Research and Forecasting Model (WRF) is considered a "next generation" mesoscale meteorology model. The inclusion of a chemistry module (WRF-Chem) allows transport simulations of chemical and aerosol species such as those observed during NASA's Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) in 2008. The ARCTAS summer deployment phase during June and July coincided with large boreal wildfires in Saskatchewan and Eastern Russia. One of the most important aspects of simulating wildfire plume transport is the height at which emissions are injected. WRF-Chem contains an integrated one-dimensional plume rise model to determine the appropriate injection layer. The plume rise model accounts for thermal buoyancy associated with fires and local atmospheric stability. This paper describes a case study of a 10 day period during the Spring phase of ARCTAS. It compares results from the plume model against those of two more traditional injection methods: Injecting within the planetary boundary layer, and in a layer 3-5 km above ground level. Fire locations are satellite derived from the GOES Wildfire Automated Biomass Burning Algorithm (WF_ABBA) and the MODIS thermal hotspot detection. Two methods for preprocessing these fire data are compared: The prep_chem_sources method included with WRF-Chem, and the Naval Research Laboratory's Fire Locating and Monitoring of Burning Emissions (FLAMBE). Results from the simulations are compared with satellite-derived products from the AIRS, MISR and CALIOP sensors. When FLAMBE provides input to the 1-D plume rise model, the resulting injection heights exhibit the best agreement with satellite-observed injection heights. The FLAMBE-derived heights are more realistic than those utilizing prep_chem_sources. Conversely, when the planetary boundary layer or the 3-5 km a.g.l. layer were filled with emissions, the resulting injection heights exhibit less agreement with observed plume heights. Results indicate that differences in injection heights produce different transport pathways. These differences are especially pronounced in area of strong vertical wind shear and when the integration period is long.

Automatic remote sensing detection of the convective boundary layer structure over flat and complex terrain using the novel PathfinderTURB algorithm

NASA Astrophysics Data System (ADS)

Poltera, Yann; Martucci, Giovanni; Hervo, Maxime; Haefele, Alexander; Emmenegger, Lukas; Brunner, Dominik; Henne, stephan

2016-04-01

We have developed, applied and validated a novel algorithm called PathfinderTURB for the automatic and real-time detection of the vertical structure of the planetary boundary layer. The algorithm has been applied to a year of data measured by the automatic LIDAR CHM15K at two sites in Switzerland: the rural site of Payerne (MeteoSwiss station, 491 m, asl), and the alpine site of Kleine Scheidegg (KSE, 2061 m, asl). PathfinderTURB is a gradient-based layer detection algorithm, which in addition makes use of the atmospheric variability to detect the turbulent transition zone that separates two low-turbulence regions, one characterized by homogeneous mixing (convective layer) and one above characterized by free tropospheric conditions. The PathfinderTURB retrieval of the vertical structure of the Local (5-10 km, horizontal scale) Convective Boundary Layer (LCBL) has been validated at Payerne using two established reference methods. The first reference consists of four independent human-expert manual detections of the LCBL height over the year 2014. The second reference consists of the values of LCBL height calculated using the bulk Richardson number method based on co-located radio sounding data for the same year 2014. Based on the excellent agreement with the two reference methods at Payerne, we decided to apply PathfinderTURB to the complex-terrain conditions at KSE during 2014. The LCBL height retrievals are obtained by tilting the CHM15K at an angle of 19 degrees with respect to the horizontal and aiming directly at the Sphinx Observatory (3580 m, asl) on the Jungfraujoch. This setup of the CHM15K and the processing of the data done by the PathfinderTURB allows to disentangle the long-transport from the local origin of gases and particles measured by the in-situ instrumentation at the Sphinx Observatory. The KSE measurements showed that the relation amongst the LCBL height, the aerosol layers above the LCBL top and the gas + particle concentration is all but trivial. Retrieving the structure of the LCBL along the line of sight connecting KSE to the Sphinx Observatory allows to monitor when the LCBL top reaches the altitude of the in-situ instrumentation at the Sphinx and to relate the measured gas + particle concentration with the locally-produced aerosols. On the other hand, when the LCBL top is lower than the Sphinx altitude, the measured concentration of gas + particle at the Sphinx is either due to long transport of aerosols (>100 km) or to the residual aerosol layer reaching the Sphinx's height or to non-local (> 5 km and <100 km) CBL aerosols advected at the Sphinx's height. Except when the aerosol layer is decoupled from the LCBL underneath, for all the other cases the CHM15K sees the probed layer as a continuous (not necessarily well-mixed) aerosol layer starting at the KSE surface. The depth of this continuous layer has been retrieved by the PathfinderTURB and related with the black carbon absorption coefficient measured at Sphinx. The result of the comparison shows clearly that the depth of the layer is well correlated with the absorption coefficient measured at the Sphinx. This is an important result that allows not only to retrieve real-time CBL heights in an automatic and trustworthy way, but also to adapt the retrievals to complex-terrain and complex-atmospheric conditions with customized tilted instrument settings.

Tunable Emission Wavelength Stacked InAs/GaAs Quantum Dots by Chemical Beam Epitaxy for Optical Coherence Tomography

PubMed Central

Ilahi, Bouraoui; Zribi, Jihene; Guillotte, Maxime; Arès, Richard; Aimez, Vincent; Morris, Denis

2016-01-01

We report on Chemical Beam Epitaxy (CBE) growth of wavelength tunable InAs/GaAs quantum dots (QD) based superluminescent diode’s active layer suitable for Optical Coherence Tomography (OCT). The In-flush technique has been employed to fabricate QD with controllable heights, from 5 nm down to 2 nm, allowing a tunable emission band over 160 nm. The emission wavelength blueshift has been ensured by reducing both dots’ height and composition. A structure containing four vertically stacked height-engineered QDs have been fabricated, showing a room temperature broad emission band centered at 1.1 µm. The buried QD layers remain insensitive to the In-flush process of the subsequent layers, testifying the reliability of the process for broadband light sources required for high axial resolution OCT imaging. PMID:28773633

Observations of the atmospheric boundary layer height over Abu Dhabi, United Arab Emirates: Investigating boundary layer climatology in arid regions

NASA Astrophysics Data System (ADS)

Marzooqi, Mohamed Al; Basha, Ghouse; Ouarda, Taha B. M. J.; Armstrong, Peter; Molini, Annalisa

2014-05-01

Strong sensible heat fluxes and deep turbulent mixing - together with marked dustiness and a low substrate water content - represent a characteristic signature in the boundary layer over hot deserts, resulting in "thicker" mixing layers and peculiar optical properties. Beside these main features however, desert ABLs present extremely complex local structures that have been scarcely addressed in the literature, and whose understanding is essential in modeling processes such as the transport of dust and pollutants, and turbulent fluxes of momentum, heat and water vapor in hyper-arid regions. In this study, we analyze a continuous record of observations of the atmospheric boundary layer (ABL) height from a single lens LiDAR ceilometer operated at Masdar Institute Field Station (24.4oN, 54.6o E, Abu Dhabi, United Arab Emirates), starting March 2013. We compare different methods for the estimation of the ABL height from Ceilometer data such as, classic variance-, gradient-, log gradient- and second derivation-methods as well as recently developed techniques such as the Bayesian Method and Wavelet covariance transform. Our goal is to select the most suited technique for describing the climatology of the ABL in desert environments. Comparison of our results with radiosonde observations collected at the nearby airport of Abu Dhabi indicate that the WCT and the Bayesian method are the most suitable tools to accurately identify the ABL height in all weather conditions. These two methods are used for the definition of diurnal and seasonal climatologies of the boundary layer conditional to different atmospheric stability classes.

Reproducibility of up-flow column percolation tests for contaminated soils

PubMed Central

Naka, Angelica; Sakanakura, Hirofumi; Kurosawa, Akihiko; Inui, Toru; Takeo, Miyuki; Inoba, Seiji; Watanabe, Yasutaka; Fujikawa, Takuro; Miura, Toshihiko; Miyaguchi, Shinji; Nakajou, Kunihide; Sumikura, Mitsuhiro; Ito, Kenichi; Tamoto, Shuichi; Tatsuhara, Takeshi; Chida, Tomoyuki; Hirata, Kei; Ohori, Ken; Someya, Masayuki; Katoh, Masahiko; Umino, Madoka; Negishi, Masanori; Ito, Keijiro; Kojima, Junichi; Ogawa, Shohei

2017-01-01

Up-flow column percolation tests are used at laboratory scale to assess the leaching behavior of hazardous substance from contaminated soils in a specific condition as a function of time. Monitoring the quality of these test results inter or within laboratory is crucial, especially if used for Environment-related legal policy or for routine testing purposes. We tested three different sandy loam type soils (Soils I, II and III) to determine the reproducibility (variability inter laboratory) of test results and to evaluate the difference in the test results within laboratory. Up-flow column percolation tests were performed following the procedure described in the ISO/TS 21268–3. This procedure consists of percolating solution (calcium chloride 1 mM) from bottom to top at a flow rate of 12 mL/h through softly compacted soil contained in a column of 5 cm diameter and 30 ± 5 cm height. Eluate samples were collected at liquid-to-solid ratio of 0.1, 0.2, 0.5, 1, 2, 5 and 10 L/kg and analyzed for quantification of the target elements (Cu, As, Se, Cl, Ca, F, Mg, DOC and B in this research). For Soil I, 17 institutions in Japan joined this validation test. The up-flow column experiments were conducted in duplicate, after 48 h of equilibration time and at a flow rate of 12 mL/h. Column percolation test results from Soils II and III were used to evaluate the difference in test results from the experiments conducted in duplicate in a single laboratory, after 16 h of equilibration time and at a flow rate of 36 mL/h. Overall results showed good reproducibility (expressed in terms of the coefficient of variation, CV, calculated by dividing the standard deviation by the mean), as the CV was lower than 30% in more than 90% of the test results associated with Soil I. Moreover, low variability (expressed in terms of difference between the two test results divided by the mean) was observed in the test results related to Soils II and III, with a variability lower than 30% in more than 88% of the cases for Soil II and in more than 96% of the cases for Soil III. We also discussed the possible factors that affect the reproducibility and variability in the test results from the up-flow column percolation tests. The low variability inter and within laboratory obtained in this research indicates that the ISO/TS 21268–3 can be successfully upgraded to a fully validated ISO standard. PMID:28582458

Remote Sensing of Cloud Top Heights Using the Research Scanning Polarimeter

NASA Technical Reports Server (NTRS)

Sinclair, Kenneth; van Diedenhoven, Bastiaan; Cairns, Brian; Yorks, John; Wasilewski, Andrzej

2015-01-01

Clouds cover roughly two thirds of the globe and act as an important regulator of Earth's radiation budget. Of these, multilayered clouds occur about half of the time and are predominantly two-layered. Changes in cloud top height (CTH) have been predicted by models to have a globally averaged positive feedback, however observational changes in CTH have shown uncertain results. Additional CTH observations are necessary to better and quantify the effect. Improved CTH observations will also allow for improved sub-grid parameterizations in large-scale models and accurate CTH information is important when studying variations in freezing point and cloud microphysics. NASA's airborne Research Scanning Polarimeter (RSP) is able to measure cloud top height using a novel multi-angular contrast approach. RSP scans along the aircraft track and obtains measurements at 152 viewing angles at any aircraft location. The approach presented here aggregates measurements from multiple scans to a single location at cloud altitude using a correlation function designed to identify the location-distinct features in each scan. During NASAs SEAC4RS air campaign, the RSP was mounted on the ER-2 aircraft along with the Cloud Physics Lidar (CPL), which made simultaneous measurements of CTH. The RSPs unique method of determining CTH is presented. The capabilities of using single and combinations of channels within the approach are investigated. A detailed comparison of RSP retrieved CTHs with those of CPL reveal the accuracy of the approach. Results indicate a strong ability for the RSP to accurately identify cloud heights. Interestingly, the analysis reveals an ability for the approach to identify multiple cloud layers in a single scene and estimate the CTH of each layer. Capabilities and limitations of identifying single and multiple cloud layers heights are explored. Special focus is given to sources of error in the method including optically thin clouds, physically thick clouds, multi-layered clouds as well as cloud phase. When determining multi-layered CTHs, limits on the upper clouds opacity are assessed.

Association of Mismatch Repair Mutation With Age at Cancer Onset in Lynch Syndrome: Implications for Stratified Surveillance Strategies.

PubMed

Ryan, Neil A J; Morris, Julie; Green, Kate; Lalloo, Fiona; Woodward, Emma R; Hill, James; Crosbie, Emma J; Evans, D Gareth

2017-12-01

Lynch syndrome is caused by dominantly inherited germline mutations that predispose individuals to colorectal, endometrial, ovarian, and other cancers through inactivation of the cellular mismatch repair system. Lynch syndrome–associated cancers are amenable to surveillance strategies that may improve survival. The age at which surveillance should start is disputed. To determine whether mutated gene and type of mutation influence age at onset of Lynch syndrome–associated cancers. A retrospective cohort study of individuals with Lynch syndrome–associated colorectal, endometrial, and/or ovarian cancers whose medical records were included in the clinical database of a large quaternary referral center for genomic medicine in the Northwest of England. Mutated gene (MLH1, MSH2, MSH6, and/or PMS2) and type of mutation (truncating, splicing, or large rearrangement). Age at cancer diagnosis. A total of 1063 individuals with proven Lynch syndrome were included, 495 male and 568 female (mean age 52 years; age range, 10-93 years [children were included in the database, but no children developed cancer]). There were 546 men and women with colorectal cancer, 162 women with endometrial cancer, and 49 women with ovarian cancer; mean follow-up was 68.2 months. Among MLH1 mutation carriers, mutations in MLH1 were associated with colorectal cancer in 249 (61%) of 409 men and women; endometrial cancer in 53 of 196 (27%) women; and ovarian cancer in 15 (8%) of 196 women. Among MSH2 mutation carriers, mutations in MSH2 (the most prevalent mutations overall) were most commonly associated with female-specific cancers: endometrial cancer in 83 (30%) of 279 women; ovarian cancer in 28 (10%) of 279 women; and colorectal cancer in 239 (50%) 479 men and women. Mutations in MSH6 were less prevalent, and MSH6 mutation carriers presented with colorectal and endometrial cancer at later ages than carriers of mutations in MSH2 or MLH1. When stratified by mutation type, women with truncating MLH1 mutations had later ages of onset of endometrial cancer than those with nontruncating mutations (median difference, 6.6 years; 95% CI, 2.7-10.4; P = .002). Carriers of truncating MLH1 mutations presented with colorectal cancer at later ages than those with other mutations, but the difference was not statistically significant. Individuals with known Lynch syndrome could be risk stratified by mutated gene and mutation type in tailored surveillance programs. Specifically, individuals with MSH6 mutations could be offered cancer surveillance from a later age. Furthermore, those with truncating MLH1 mutations could begin endometrial cancer surveillance later than those with nontruncating mutations.

Structure and seasonal variations of the nocturnal mesospheric K layer at Arecibo

NASA Astrophysics Data System (ADS)

Yue, Xianchang; Friedman, Jonathan S.; Wu, Xiongbin; Zhou, Qihou H.

2017-07-01

We present the seasonal variations of the nocturnal mesospheric potassium (K) layer at Arecibo, Puerto Rico (18.35°N, 66.75°W) from 160 nights of K Doppler lidar observations between December 2003 and January 2010, during which the solar activity is mostly low. The background temperature is also measured simultaneously by the lidar and shows a strong semiannual oscillation with maxima occurring during equinoxes at all altitudes. The annual mean K density profile is approximately Gaussian with a peak altitude of 91.7 km. The K column abundance and the centroid height have strong semiannual variations, with maxima at the solstices. Both parameters are negatively correlated to the mean background temperature with a correlation coefficient < -0.5. The root-mean-square (RMS) width has a distinct annual oscillation with the largest width occurring in May. The seasonal variation of the centroid height is similar to that of the Fe layer at the same site. The seasonal temperature variation indicates significant enhanced wave-induced downward transport for both species during spring and autumn. This explains the metal layer centroid height and column abundance variations at Arecibo and provides a general mechanism to account for the seasonal variations in the centroid height of all metal species measured at low-latitude and midlatitude sites.

Aerosol layer height from synergistic use of VIIRS and OMPS

NASA Astrophysics Data System (ADS)

Lee, J.; Hsu, N. Y. C.; Sayer, A. M.; Kim, W.; Seftor, C. J.

2017-12-01

This study presents an Aerosol Single-scattering albedo and Height Estimation (ASHE) algorithm, which retrieves the height of UV-absorbing aerosols by synergistically using the Visible Infrared Imaging Radiometer Suite (VIIRS) and the Ozone Mapping and Profiler Suite (OMPS). ASHE provides height information over a much broader area than ground-based or spaceborne lidar measurements by benefitting from the wide swaths of the two instruments used. As determination of single-scattering albedo (SSA) of the aerosol layer is the most critical part for the performance and coverage of ASHE, here we demonstrate three different strategies to constrain the SSA. First, ASHE is able to retrieve the SSA of UV-absorbing aerosols when Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) provides vertical profiles of the aerosol layer of interest. Second, Aerosol Robotic Network (AERONET) inversions can directly constrain the SSA of the aerosol layer when collocated with VIIRS or OMPS. Last, a SSA climatology from ASHE, AERONET, or other data sources can be used for large-scale, aged aerosol events, for which climatological SSA is well-known, at the cost of a slight decrease in retrieval accuracy. The same algorithm can be applied to measurements of similar type, such as those made by the Moderate Resolution Imaging Spectroradiometer (MODIS) and Ozone Monitoring Instrument (OMI), for a long-term, consistent data record.

Evaluation of helicity generation in the tropical storm Gonu

NASA Astrophysics Data System (ADS)

Farahani, Majid M.; Khansalari, Sakineh; Azadi, Majid

2017-06-01

Helicity is a valuable dynamical concept for the study of rotating flows. Consequently helicity flux, indicative of the source or sink of helicity, owns comparable importance. In this study, while reviewing the existing methods, a mathematical relation between helicity and helicity-flux is introduced, discussed and examined. The computed values of helicity and helicity fluxes in an actual case, using the classical and this proposed method are compared. The down-stream helicity flux including sources and sinks of helicity is considered for the tropical storm Gonu that occurred over the coasts of Oman and Iran on June 2-7, 2007. Results show that the buoyancy, through the upper troposphere down to a height within boundary layer, is the main source in producing helicity, and surface friction from earth surface up to a height within boundary layer, is the main dissipating element of helicity. The dominance of buoyancy forcing over the dissipative friction forcing results in generation of vortex or enhancement of it after bouncing the land. Furthermore, the increase (decrease) of helicity results in an increase (decrease) in the height of the level in which maximum helicity flux occurs. It is suggested that the maximum helicity flux occurs at the top of the turbulent boundary layer, so that the height of boundary layer could be obtained.

MISR Stereo-heights of Grassland Fire Smoke Plumes in Australia

NASA Astrophysics Data System (ADS)

Mims, S. R.; Kahn, R. A.; Moroney, C. M.; Gaitley, B. J.; Nelson, D. L.; Garay, M. J.

2008-12-01

Plume heights from wildfires are used in climate modeling to predict and understand trends in aerosol transport. This study examines whether smoke from grassland fires in the desert region of Western and central Australia ever rises above the relatively stable atmospheric boundary layer and accumulates in higher layers of relative atmospheric stability. Several methods for deriving plume heights from the Multi-angle Imaging SpectroRadiometer (MISR) instrument are examined for fire events during the summer 2000 and 2002 burning seasons. Using MISR's multi-angle stereo-imagery from its three near-nadir-viewing cameras, an automatic algorithm routinely derives the stereo-heights above the geoid of the level-of-maximum-contrast for the entire global data set, which often correspond to the heights of clouds and aerosol plumes. Most of the fires that occur in the cases studied here are small, diffuse, and difficult to detect. To increase the signal from these thin hazes, the MISR enhanced stereo product that computes stereo heights from the most steeply viewing MISR cameras is used. For some cases, a third approach to retrieving plume heights from MISR stereo imaging observations, the MISR Interactive Explorer (MINX) tool, is employed to help differentiate between smoke and cloud. To provide context and to search for correlative factors, stereo-heights are combined with data providing fire strength from the Moderate-resolution Imaging Spectroradiometer (MODIS) instrument, atmospheric structure from the NCEP/NCAR Reanalysis Project, surface cover from the Australia National Vegetation Information System, and forward and backward trajectories from the NOAA HYSPLIT model. Although most smoke plumes concentrate in the near-surface boundary layer, as expected, some appear to rise higher. These findings suggest that a closer examination of grassland fire energetics may be warranted.

Energy and macronutrient intake of a female vegan cyclist during an 8-day mountain bike stage race

PubMed Central

Kornexl, Elmar

2014-01-01

This report describes the dietary intake of a vegan mountain biker (height, 161 cm; weight, 49.6 kg; body mass index, 19.1 kg/m2; relative peak power output, 4.6 W/kg) during the Transalp Challenge 2004 (altitude climbed, 22,500 m; total distance, 662 km), illustrating an aggressive dietary strategy that allowed the cyclist to be competitive. She finished the 8-stage event in 42 hours (mixed category, rank 16; 514 minutes behind the winners of this category), cycling with an average heart rate of 79.5% of laboratory-determined maximum, spending 892 minutes and 1627 minutes at intensities below and above 80%, respectively. During racing, the consumption of energy was 69.3 MJ (1.65 MJ/h), 65.76 MJ from carbohydrates (92 g/h), which was 35% of calories and 40% of carbohydrate total intake, and the fluid ingested was 3 L/day (570 mL/h), 55% of the total fluid consumed. PMID:24381405

Energy and macronutrient intake of a female vegan cyclist during an 8-day mountain bike stage race.

PubMed

Wirnitzer, Katharina C; Kornexl, Elmar

2014-01-01

This report describes the dietary intake of a vegan mountain biker (height, 161 cm; weight, 49.6 kg; body mass index, 19.1 kg/m(2); relative peak power output, 4.6 W/kg) during the Transalp Challenge 2004 (altitude climbed, 22,500 m; total distance, 662 km), illustrating an aggressive dietary strategy that allowed the cyclist to be competitive. She finished the 8-stage event in 42 hours (mixed category, rank 16; 514 minutes behind the winners of this category), cycling with an average heart rate of 79.5% of laboratory-determined maximum, spending 892 minutes and 1627 minutes at intensities below and above 80%, respectively. During racing, the consumption of energy was 69.3 MJ (1.65 MJ/h), 65.76 MJ from carbohydrates (92 g/h), which was 35% of calories and 40% of carbohydrate total intake, and the fluid ingested was 3 L/day (570 mL/h), 55% of the total fluid consumed.

Remote Sensing of Multiple Cloud Layer Heights Using Multi-Angular Measurements

NASA Technical Reports Server (NTRS)

Sinclair, Kenneth; Van Diedenhoven, Bastiaan; Cairns, Brian; Yorks, John; Wasilewski, Andrzej; Mcgill, Matthew

2017-01-01

Cloud top height (CTH) affects the radiative properties of clouds. Improved CTH observations will allow for improved parameterizations in large-scale models and accurate information on CTH is also important when studying variations in freezing point and cloud microphysics. NASAs airborne Research Scanning Polarimeter (RSP) is able to measure cloud top height using a novel multi-angular contrast approach. For the determination of CTH, a set of consecutive nadir reflectances is selected and the cross-correlations between this set and co-located sets at other viewing angles are calculated for a range of assumed cloud top heights, yielding a correlation profile. Under the assumption that cloud reflectances are isotropic, local peaks in the correlation profile indicate cloud layers. This technique can be applied to every RSP footprint and we demonstrate that detection of multiple peaks in the correlation profile allow retrieval of heights of multiple cloud layers within single RSP footprints. This paper provides an in-depth description of the architecture and performance of the RSPs CTH retrieval technique using data obtained during the Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC(exp. 4)RS) campaign. RSP retrieved cloud heights are evaluated using collocated data from the Cloud Physics Lidar (CPL). The method's accuracy associated with the magnitude of correlation, optical thickness, cloud thickness and cloud height are explored. The technique is applied to measurements at a wavelength of 670 nm and 1880 nm and their combination. The 1880-nm band is virtually insensitive to the lower troposphere due to strong water vapor absorption.

Mixed Layer Heights Derived from the NASA Langley Research Center Airborne High Spectral Resolution Lidar

NASA Technical Reports Server (NTRS)

Scarino, Amy J.; Burton, Sharon P.; Ferrare, Rich A.; Hostetler, Chris A.; Hair, Johnathan W.; Obland, Michael D.; Rogers, Raymond R.; Cook, Anthony L.; Harper, David B.; Fast, Jerome;

Immunohistochemistry for PMS2 and MSH6 alone can replace a four antibody panel for mismatch repair deficiency screening in colorectal adenocarcinoma.

PubMed

Hall, Geoffrey; Clarkson, Adele; Shi, Amanda; Langford, Eileen; Leung, Helen; Eckstein, Robert P; Gill, Anthony J

2010-01-01

Currently, testing for mismatch repair deficiency in colorectal cancers is initiated by performing immunohistochemistry with four antibodies (MLH1, PMS2, MSH2 and MSH6). If any one of these stains is negative the tumour is considered microsatellite unstable and, if clinical circumstances warrant it, the patient is offered genetic testing for Lynch's syndrome. Due to the binding properties of the mismatch repair heterodimer complexes, gene mutation and loss of MLH1 and MSH2 invariably result in the degradation of PMS2 and MSH6, respectively, but the converse is not true. We propose that staining for PMS2 and MSH6 alone will be sufficient to detect all cases of mismatch repair deficiency and should replace routine screening with all four antibodies. The electronic database of the department of Anatomical Pathology, Royal North Shore Hospital, Sydney, Australia, was searched for all colorectal carcinomas on which a four panel immunohistochemical microsatellite instability screen was performed. An audit of the slides for concordant loss of MLH1-PMS2 and MSH2-MSH6 was then undertaken. Unusual or discordant cases were reviewed and, in some cases, re-stained to confirm the staining pattern. Of 344 cases of colorectal cancer which underwent four antibody immunohistochemistry, 104 displayed loss of at least one mismatch repair protein. Of these, 100 showed concordant mismatch repair loss (i.e., loss of MLH1 and PMS2 or loss of MSH2 and MSH6). The four discordant cases comprised two single negative cases (1 MSH6 negative/MSH2 positive case, 1 PMS2 negative/MLH1 positive) and two triple negative (both MLH1/PMS2/MSH6 negative). The microsatellite instability (MSI) group showed a relatively high median age (69.3 years) due to the departmental policy of testing all cases with possible MSI morphology regardless of age. The sensitivity and specificity of a two panel test comprised of PMS2 and MSH6, compared to a four panel test, is 100%. No false negatives or positives were identified. We conclude that the two panel test should replace a four panel protocol for immunohistochemical screening for mismatch repair deficiency.

Quantifying the relationship between PM2.5 concentration, visibility and planetary boundary layer height for long-lasting haze and fog-haze mixed events in Beijing

NASA Astrophysics Data System (ADS)

Luan, Tian; Guo, Xueliang; Guo, Lijun; Zhang, Tianhang

2018-01-01

Air quality and visibility are strongly influenced by aerosol loading, which is driven by meteorological conditions. The quantification of their relationships is critical to understanding the physical and chemical processes and forecasting of the polluted events. We investigated and quantified the relationship between PM2.5 (particulate matter with aerodynamic diameter is 2.5 µm and less) mass concentration, visibility and planetary boundary layer (PBL) height in this study based on the data obtained from four long-lasting haze events and seven fog-haze mixed events from January 2014 to March 2015 in Beijing. The statistical results show that there was a negative exponential function between the visibility and the PM2.5 mass concentration for both haze and fog-haze mixed events (with the same R2 of 0.80). However, the fog-haze events caused a more obvious decrease of visibility than that for haze events due to the formation of fog droplets that could induce higher light extinction. The PM2.5 concentration had an inversely linear correlation with PBL height for haze events and a negative exponential correlation for fog-haze mixed events, indicating that the PM2.5 concentration is more sensitive to PBL height in fog-haze mixed events. The visibility had positively linear correlation with the PBL height with an R2 of 0.35 in haze events and positive exponential correlation with an R2 of 0.56 in fog-haze mixed events. We also investigated the physical mechanism responsible for these relationships between visibility, PM2.5 concentration and PBL height through typical haze and fog-haze mixed event and found that a double inversion layer formed in both typical events and played critical roles in maintaining and enhancing the long-lasting polluted events. The variations of the double inversion layers were closely associated with the processes of long-wave radiation cooling in the nighttime and short-wave solar radiation reduction in the daytime. The upper-level stable inversion layer was formed by the persistent warm and humid southwestern airflow, while the low-level inversion layer was initially produced by the surface long-wave radiation cooling in the nighttime and maintained by the reduction of surface solar radiation in the daytime. The obvious descending process of the upper-level inversion layer induced by the radiation process could be responsible for the enhancement of the low-level inversion layer and the lowering PBL height, as well as high aerosol loading for these polluted events. The reduction of surface solar radiation in the daytime could be around 35 % for the haze event and 94 % for the fog-haze mixed event. Therefore, the formation and subsequent descending processes of the upper-level inversion layer should be an important factor in maintaining and strengthening the long-lasting severe polluted events, which has not been revealed in previous publications. The interactions and feedbacks between PM2.5 concentration and PBL height linked by radiation process caused a more significant and long-lasting deterioration of air quality and visibility in fog-haze mixed events. The interactions and feedbacks of all processes were particularly strong when the PM2.5 mass concentration was larger than 150-200 µg m-3.

Cloud Height Estimation with a Single Digital Camera and Artificial Neural Networks

NASA Astrophysics Data System (ADS)

Carretas, Filipe; Janeiro, Fernando M.

2014-05-01

Clouds influence the local weather, the global climate and are an important parameter in the weather prediction models. Clouds are also an essential component of airplane safety when visual flight rules (VFR) are enforced, such as in most small aerodromes where it is not economically viable to install instruments for assisted flying. Therefore it is important to develop low cost and robust systems that can be easily deployed in the field, enabling large scale acquisition of cloud parameters. Recently, the authors developed a low-cost system for the measurement of cloud base height using stereo-vision and digital photography. However, due to the stereo nature of the system, some challenges were presented. In particular, the relative camera orientation requires calibration and the two cameras need to be synchronized so that the photos from both cameras are acquired simultaneously. In this work we present a new system that estimates the cloud height between 1000 and 5000 meters. This prototype is composed by one digital camera controlled by a Raspberry Pi and is installed at Centro de Geofísica de Évora (CGE) in Évora, Portugal. The camera is periodically triggered to acquire images of the overhead sky and the photos are downloaded to the Raspberry Pi which forwards them to a central computer that processes the images and estimates the cloud height in real time. To estimate the cloud height using just one image requires a computer model that is able to learn from previous experiences and execute pattern recognition. The model proposed in this work is an Artificial Neural Network (ANN) that was previously trained with cloud features at different heights. The chosen Artificial Neural Network is a three-layer network, with six parameters in the input layer, 12 neurons in the hidden intermediate layer, and an output layer with only one output. The six input parameters are the average intensity values and the intensity standard deviation of each RGB channel. The output parameter in the output layer is the cloud height estimated by the ANN. The training procedure was performed, using the back-propagation method, in a set of 260 different clouds with heights in the range [1000, 5000] m. The training of the ANN has resulted in a correlation ratio of 0.74. This trained ANN can therefore be used to estimate the cloud height. The previously described system can also measure the wind speed and direction at cloud height by measuring the displacement, in pixels, of a cloud feature between consecutively acquired photos. Also, the geographical north direction can be estimated using this setup through sequential night images with high exposure times. A further advantage of this single camera system is that no camera calibration or synchronization is needed. This significantly reduces the cost and complexity of field deployment of cloud height measurement systems based on digital photography.

Real-time reconstruction of topside ionosphere scale height from coordinated GPS-TEC and ionosonde observations

NASA Astrophysics Data System (ADS)

Gulyaeva, Tamara; Poustovalova, Ljubov

The International Reference Ionosphere model extended to the plasmasphere, IRI-Plas, has been recently updated for assimilation of total electron content, TEC, derived from observations with Global Navigation Satellite System, GNSS. The ionosonde products of the F2 layer peak density (NmF2) and height (hmF2) ensure true electron density maximum at the F2 peak. The daily solar and magnetic indices used by IRI-Plas code are compiled in data files including the 3-hour ap and kp magnetic index from 1958 onward, 12-monthly smoothed sunspot number R12 and Global Electron Content GEC12, daily solar radio flux F10.7 and daily sunspot number Ri. The 3-h ap-index is available in Real Time, RT, mode from GFZ, Potsdam, Germany, daily update of F10.7 is provided by Space Weather Canada service, and daily estimated international sunspot number Ri is provided by Solar Influences Data Analysis Center, SIDC, Belgium. For IRI-Plas-RT operation in regime of the daily update and prediction of the F2 layer peak parameters, the proxy kp and ap forecast for 3 to 24 hours ahead based on data for preceding 12 hours is applied online at http://www.izmiran.ru/services/iweather/. The topside electron density profile of IRI-Plas code is expressed with complementary half-peak density anchor height above hmF2 which corresponds to transition O+/H+ height. The present investigation is focused on reconstruction of topside ionosphere scale height using vertical total electron content (TEC) data derived from the Global Positioning System GPS observations and the ionosonde derived F2 layer peak parameters from 25 observatories ingested into IRI-Plas model. GPS-TEC and ionosonde measurements at solar maximum (September, 2002, and October, 2003) for quiet, positively disturbed, and negatively disturbed days of the month are used to obtain the topside scale height, Htop, representing the range of altitudes from hmF2 to the height where NmF2 decay by e times occurs. Mapping of the F2 layer peak parameters and TEC allows interpolate these parameters at coordinated grid sites from independent GPS receivers and ionosondes data. Exponential scale height Htop exceeds scale height HT of the α-Chapman layer by 3 times - the latter refers to a narrow altitude range from hmF2 to the height of 1.2 times decay of NmF2. While typical quiet daytime value of the topside scale height is around 200 km, it can be enhanced by 2-3 times during the negative phase of the ionospheric storm as it is captured by IRI-Plas-RT model ingesting the F2 peak and TEC data. This study is supported by the joint grant of RFBR 13-02-91370-CT_a and TUBITAK 112E568.

Hereditary cancer genes are highly susceptible to splicing mutations

PubMed Central

Soemedi, Rachel; Maguire, Samantha; Murray, Michael F.; Monaghan, Sean F.

2018-01-01

Substitutions that disrupt pre-mRNA splicing are a common cause of genetic disease. On average, 13.4% of all hereditary disease alleles are classified as splicing mutations mapping to the canonical 5′ and 3′ splice sites. However, splicing mutations present in exons and deeper intronic positions are vastly underreported. A recent re-analysis of coding mutations in exon 10 of the Lynch Syndrome gene, MLH1, revealed an extremely high rate (77%) of mutations that lead to defective splicing. This finding is confirmed by extending the sampling to five other exons in the MLH1 gene. Further analysis suggests a more general phenomenon of defective splicing driving Lynch Syndrome. Of the 36 mutations tested, 11 disrupted splicing. Furthermore, analyzing past reports suggest that MLH1 mutations in canonical splice sites also occupy a much higher fraction (36%) of total mutations than expected. When performing a comprehensive analysis of splicing mutations in human disease genes, we found that three main causal genes of Lynch Syndrome, MLH1, MSH2, and PMS2, belonged to a class of 86 disease genes which are enriched for splicing mutations. Other cancer genes were also enriched in the 86 susceptible genes. The enrichment of splicing mutations in hereditary cancers strongly argues for additional priority in interpreting clinical sequencing data in relation to cancer and splicing. PMID:29505604

C-Terminal Fluorescent Labeling Impairs Functionality of DNA Mismatch Repair Proteins

PubMed Central

Brieger, Angela; Plotz, Guido; Hinrichsen, Inga; Passmann, Sandra; Adam, Ronja; Zeuzem, Stefan

2012-01-01

The human DNA mismatch repair (MMR) process is crucial to maintain the integrity of the genome and requires many different proteins which interact perfectly and coordinated. Germline mutations in MMR genes are responsible for the development of the hereditary form of colorectal cancer called Lynch syndrome. Various mutations mainly in two MMR proteins, MLH1 and MSH2, have been identified so far, whereas 55% are detected within MLH1, the essential component of the heterodimer MutLα (MLH1 and PMS2). Most of those MLH1 variants are pathogenic but the relevance of missense mutations often remains unclear. Many different recombinant systems are applied to filter out disease-associated proteins whereby fluorescent tagged proteins are frequently used. However, dye labeling might have deleterious effects on MutLα's functionality. Therefore, we analyzed the consequences of N- and C-terminal fluorescent labeling on expression level, cellular localization and MMR activity of MutLα. Besides significant influence of GFP- or Red-fusion on protein expression we detected incorrect shuttling of single expressed C-terminal GFP-tagged PMS2 into the nucleus and found that C-terminal dye labeling impaired MMR function of MutLα. In contrast, N-terminal tagged MutLαs retained correct functionality and can be recommended both for the analysis of cellular localization and MMR efficiency. PMID:22348133

Inventory of File naefs_geavg.t12z.pgrb2a_anvf06

Science.gov Websites

Records: 19 Number Level/Layer Parameter Forecast Valid Description 001 1000 mb HGT 6 hour fcst Geopotential Height [gpm] ens-mean 002 700 mb HGT 6 hour fcst Geopotential Height [gpm] ens-mean 003 500 mb HGT 6 hour fcst Geopotential Height [gpm] ens-mean 004 250 mb HGT 6 hour fcst Geopotential Height [gpm

Monsoon dependent ecosystems: Implications of the vertical distribution of soil moisture on land surface-atmosphere interactions

NASA Astrophysics Data System (ADS)

Sanchez-Mejia, Zulia M.

Uncertainty of predicted change in precipitation frequency and intensity motivates the scientific community to better understand, quantify, and model the possible outcome of dryland ecosystems. In pulse dependent ecosystems (i.e. monsoon driven) soil moisture is tightly linked to atmospheric processes. Here, I analyze three overarching questions; Q1) How does soil moisture presence or absence in a shallow or deep layer influence the surface energy budget and planetary boundary layer characteristics?, Q2) What is the role of vegetation on ecosystem albedo in the presence or absence of deep soil moisture?, Q3) Can we develop empirical relationships between soil moisture and the planetary boundary layer height to help evaluate the role of future precipitation changes in land surface atmosphere interactions? . To address these questions I use a conceptual framework based on the presence or absence of soil moisture in a shallow or deep layer. I define these layers by using root profiles and establish soil moisture thresholds for each layer using four years of observations from the Santa Rita Creosote Ameriflux site. Soil moisture drydown curves were used to establish the shallow layer threshold in the shallow layer, while NEE (Net Ecosystem Exchange of carbon dioxide) was used to define the deep soil moisture threshold. Four cases were generated using these thresholds: Case 1, dry shallow layer and dry deep layer; Case 2, wet shallow layer and dry deep layer; Case 3, wet shallow layer and wet deep layer, and Case 4 dry shallow and wet deep layer. Using this framework, I related data from the Ameriflux site SRC (Santa Rita Creosote) from 2008 to 2012 and from atmospheric soundings from the nearby Tucson Airport; conducted field campaigns during 2011 and 2012 to measure albedo from individual bare and canopy patches that were then evaluated in a grid to estimate the influence of deep moisture on albedo via vegetation cover change; and evaluated the potential of using a two-layer bucket model and empirical relationships to evaluate the link between deep soil moisture and the planetary boundary layer height under changing precipitation regime. My results indicate that (1) the presence or absence of water in two layers plays a role in surface energy dynamics, (2) soil moisture presence in the deep layer is linked with decreased ecosystem albedo and planetary boundary layer height, (3) deep moisture sustains vegetation greenness and decreases albedo, and (4) empirical relationships are useful in modeling planetary boundary layer height from dryland ecosystems. Based on these results we argue that deep soil moisture plays an important role in land surface-atmosphere interactions.

RenalGuard system in high-risk patients for contrast-induced acute kidney injury.

PubMed

Briguori, Carlo; Visconti, Gabriella; Donahue, Michael; De Micco, Francesca; Focaccio, Amelia; Golia, Bruno; Signoriello, Giuseppe; Ciardiello, Carmine; Donnarumma, Elvira; Condorelli, Gerolama

2016-03-01

High urine flow rate (UFR) has been suggested as a target for effective prevention of contrast-induced acute kidney injury (CI-AKI). The RenalGuard therapy (saline infusion plus furosemide controlled by the RenalGuard system) facilitates the achievement of this target. Four hundred consecutive patients with an estimated glomerular filtration rate ≤30 mL/min per 1.73 m(2) and/or a high predicted risk (according to the Mehran score ≥11 and/or the Gurm score >7%) treated by the RenalGuard therapy were analyzed. The primary end points were (1) the relationship between CI-AKI and UFR during preprocedural, intraprocedural, and postprocedural phases of the RenalGuard therapy and (2) the rate of acute pulmonary edema and impairment in electrolytes balance. Urine flow rate was significantly lower in the patients with CI-AKI in the preprocedural phase (208 ± 117 vs 283 ± 160 mL/h, P < .001) and in the intraprocedural phase (389 ± 198 vs 483 ± 225 mL/h, P = .009). The best threshold for CI-AKI prevention was a mean intraprocedural phase UFR ≥450 mL/h (area under curve 0.62, P = .009, sensitivity 80%, specificity 46%). Performance of percutaneous coronary intervention (hazard ratio [HR] 4.13, 95% CI 1.81-9.10, P < .001), the intraprocedural phase UFR <450 mL/h (HR 2.27, 95% CI 1.05-2.01, P = .012), and total furosemide dose >0.32 mg/kg (HR 5.03, 95% CI 2.33-10.87, P < .001) were independent predictors of CI-AKI. Pulmonary edema occurred in 4 patients (1%). Potassium replacement was required in 16 patients (4%). No patients developed severe hypomagnesemia, hyponatremia, or hypernatremia. RenalGuard therapy is safe and effective in reaching high UFR. Mean intraprocedural UFR ≥450 mL/h should be the target for optimal CI-AKI prevention. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Clouds above the Martin Limb: Viking observations

NASA Technical Reports Server (NTRS)

Martin, L. J.; Baum, W. A.; Wasserman, L. H.; Kreidl, T. J.

1984-01-01

Whenever Viking Orbiter images included the limb of Mars, they recorded one or more layers of clouds above the limb. The height above the limb and the brightness (reflectivity) of these clouds were determined in a selected group of these images. Normalized individual brightness profiles of three separate traverses across the limb of each image are shown. The most notable finding is that some of these clouds can be very high. Many reach heights of over 60 km, and several are over 70 km above the limb. Statistically, the reflectivity of the clouds increases with phase angle. Reflectivity and height both appear to vary with season, but the selected images spanned only one Martian year, so the role of seasons cannot be isolated. Limb clouds in red-filter images tend to be brighter than violet-filter images, but both season and phase appear to be more dominant factors. Due to the limited sample available, the possible influences of latitude and longitude are less clear. The layering of these clouds ranges from a single layer to five or more layers. Reflectivity gradients range from smooth and gentle to steep and irregular.

Developments in the Aerosol Layer Height Retrieval Algorithm for the Copernicus Sentinel-4/UVN Instrument

NASA Astrophysics Data System (ADS)

Nanda, Swadhin; Sanders, Abram; Veefkind, Pepijn

2016-04-01

The Sentinel-4 mission is a part of the European Commission's Copernicus programme, the goal of which is to provide geo-information to manage environmental assets, and to observe, understand and mitigate the effects of the changing climate. The Sentinel-4/UVN instrument design is motivated by the need to monitor trace gas concentrations and aerosols in the atmosphere from a geostationary orbit. The on-board instrument is a high resolution UV-VIS-NIR (UVN) spectrometer system that provides hourly radiance measurements over Europe and northern Africa with a spatial sampling of 8 km. The main application area of Sentinel-4/UVN is air quality. One of the data products that is being developed for Sentinel-4/UVN is the Aerosol Layer Height (ALH). The goal is to determine the height of aerosol plumes with a resolution of better than 0.5 - 1 km. The ALH product thus targets aerosol layers in the free troposphere, such as desert dust, volcanic ash and biomass during plumes. KNMI is assigned with the development of the Aerosol Layer Height (ALH) algorithm. Its heritage is the ALH algorithm developed by Sanders and De Haan (ATBD, 2016) for the TROPOMI instrument on board the Sentinel-5 Precursor mission that is to be launched in June or July 2016 (tentative date). The retrieval algorithm designed so far for the aerosol height product is based on the absorption characteristics of the oxygen-A band (759-770 nm). The algorithm has heritage to the ALH algorithm developed for TROPOMI on the Sentinel 5 precursor satellite. New aspects for Sentinel-4/UVN include the higher resolution (0.116 nm compared to 0.4 for TROPOMI) and hourly observation from the geostationary orbit. The algorithm uses optimal estimation to obtain a spectral fit of the reflectance across absorption band, while assuming a single uniform layer with fixed width to represent the aerosol vertical distribution. The state vector includes amongst other elements the height of this layer and its aerosol optical thickness. We will present the development work around the ALH retrieval algorithm in the framework of the Sentinel-4/UVN instrument. The main challenges are highlighted and retrieval simulation results are provided. Also, an outlook towards application of the S4 bread board algorithm to Sentinel-5 Precursor data later this year will be discussed.

A model for capillary rise in micro-tube restrained by a sticky layer

NASA Astrophysics Data System (ADS)

Shen, Anqi; Xu, Yun; Liu, Yikun; Cai, Bo; Liang, Shuang; Wang, Fengjiao

2018-06-01

Fluid transport in a microscopic capillary under the effects of a sticky layer was theoretically investigated. A model based on the classical Lucas-Washburn (LW) model is proposed for the meniscus rise with the sticky layer present. The sticky layer consists of two parts: a fixed (located at the wall) and a movable part (located on the inside of the capillary), affecting the micro-capillary flow in different ways. Within our model, the movable layer is defined by the capillary radius and pressure gradient. From the model it follows that the fixed sticky layer leads to a decrease of capillary radius, while the movable sticky layer increases flow resistance. The movable layer thickness varies with the pressure gradient, which in turn varies with the rising of the meniscus. The results of our theoretical calculation also prove that the capillary radius has a greater effect on the meniscus height, rather than the additional resistance caused by the movable layer. Moreover, the fixed sticky layer, which affects the capillary radius, has a greater influence than the movable sticky layer. We conclude that the sticky layer causes a lower imbibition height than the LW model predicts.

Laboratory simulations of the atmospheric mixed-layer in flow over complex topography

EPA Science Inventory

A laboratory study of the influence of complex terrain on the interface between a well-mixed boundary layer and an elevated stratified layer was conducted in the towing-tank facility of the U.S. Environmental Protection Agency. The height of the mixed layer in the daytime boundar...

The Fanconi Anemia BRCA Pathway as a Predictor of Benefit from Bevacizumab in a Large Phase-3 Clinical Trial in Ovarian Cancer

DTIC Science & Technology

2014-10-01

FAM175A (3), PMS2 (2), and MLH1 (1). Consistent with their role as ovarian cancer susceptibility genes, BRIP1, RAD51C, and RAD51D were significantly...ATM (11), RAD51C (10), NBN (9), TP53 (6), BARD1 (4), MSH6 (4), FAM175A (3), PMS2 (2), and MLH1 (1). Consistent with their role as ovarian cancer

Vertical profiles of selected mean and turbulent characteristics of the boundary layer within and above a large banana screenhouse

NASA Astrophysics Data System (ADS)

Tanny, Josef; Lukyanov, Victor; Neiman, Michael; Cohen, Shabtai; Teitel, Meir

2017-04-01

The area of agricultural crops covered by screens is constantly increasing worldwide. While irrigation requirements for open canopies are well documented, corresponding information for covered crops is scarce. Therefore much effort in recent years has focused on measuring and modeling evapotranspiration of screen-covered crops. One model that can be utilized for such estimations is the mixing length model. As a first step towards future application of this model, selected mean and turbulent properties of the boundary layer above and below a shading screen were measured and analyzed. Experiments were carried out in a large banana plantation, covered by a light-weight horizontal shading screen deployed 5.5 m high. During the measurement period, plant height increased from 2.5 to 4.1 m. A 3D ultrasonic anemometer and temperature and humidity sensors were mounted on a lifting tower with a manual crank that could measure between 2.8 and 10.2 m height, i.e., both below and above the screen. In each profile, the sensors measured at different heights during consecutive time intervals of about 15 min each. Vertical profiles were measured around noon when external meteorological conditions were relatively stable. An additional stationary tower installed within the screenhouse about 20 m to the north of the lifting tower, continuously measured corresponding reference values at 4.5 m height. Footprint analysis shows that out of the 62 measured time intervals, only in 4 cases the 90% flux contribution originated from outside the screenhouse. Both horizontal air velocity, Uh, and normalized horizontal air velocity increased with height. Air temperature generally decreased with height, indicating that the boundary layer was statically unstable. Specific humidity decreased with height, as is typical for a well irrigated crop. Friction velocity, u∗, was higher above than below the screen, illustrating the role of the screen as a momentum sink. The mean ratio between friction velocity below and above the screen was 0.55. Vertical profiles of the surface drag coefficientCd = (u∗/U h)2 showed a consistent decease of √Cd-with height, mainly above the screen. This result is expected since, with a constant flux layer, the surface drag is bound to decrease with height. The energy spectrum of each velocity component, both below and above the screen, was calculated separately and their sum, the 3D spectrum (Tennekes and Lumely, 1972), was plotted as a function of frequency. Slopes of linear fits to the spectra ranged between -1.42 and -1.68, with a mean value of -1.59±0.04. These slopes are close to -5/3 (-1.67), the value typical of the inertial subrange in steady state turbulent boundary layers (Stull, 1988).

Sensitivity of turbine-height wind speeds to parameters in planetary boundary-layer and surface-layer schemes in the weather research and forecasting model

DOE PAGES

Yang, Ben; Qian, Yun; Berg, Larry K.; ...

2016-07-21

We evaluate the sensitivity of simulated turbine-height wind speeds to 26 parameters within the Mellor–Yamada–Nakanishi–Niino (MYNN) planetary boundary-layer scheme and MM5 surface-layer scheme of the Weather Research and Forecasting model over an area of complex terrain. An efficient sampling algorithm and generalized linear model are used to explore the multiple-dimensional parameter space and quantify the parametric sensitivity of simulated turbine-height wind speeds. The results indicate that most of the variability in the ensemble simulations is due to parameters related to the dissipation of turbulent kinetic energy (TKE), Prandtl number, turbulent length scales, surface roughness, and the von Kármán constant. Themore » parameter associated with the TKE dissipation rate is found to be most important, and a larger dissipation rate produces larger hub-height wind speeds. A larger Prandtl number results in smaller nighttime wind speeds. Increasing surface roughness reduces the frequencies of both extremely weak and strong airflows, implying a reduction in the variability of wind speed. All of the above parameters significantly affect the vertical profiles of wind speed and the magnitude of wind shear. Lastly, the relative contributions of individual parameters are found to be dependent on both the terrain slope and atmospheric stability.« less

The Budget of Turbulent Kinetic Energy in the Urban Roughness Sublayer

NASA Astrophysics Data System (ADS)

Christen, Andreas; Rotach, Mathias W.; Vogt, Roland

2009-05-01

Full-scale observations from two urban sites in Basel, Switzerland were analysed to identify the magnitude of different processes that create, relocate, and dissipate turbulent kinetic energy (TKE) in the urban atmosphere. Two towers equipped with a profile of six ultrasonic anemometers each sampled the flow in the urban roughness sublayer, i.e. from street canyon base up to roughly 2.5 times the mean building height. This observational study suggests a conceptual division of the urban roughness sublayer into three layers: (1) the layer above the highest roofs, where local buoyancy production and local shear production of TKE are counterbalanced by local viscous dissipation rate and scaled turbulence statistics are close to to surface-layer values; (2) the layer around mean building height with a distinct inflexional mean wind profile, a strong shear and wake production of TKE, a more efficient turbulent exchange of momentum, and a notable export of TKE by transport processes; (3) the lower street canyon with imported TKE by transport processes and negligible local production. Averaged integral velocity variances vary significantly with height in the urban roughness sublayer and reflect the driving processes that create or relocate TKE at a particular height. The observed profiles of the terms of the TKE budget and the velocity variances show many similarities to observations within and above vegetation canopies.

Sensitivity of turbine-height wind speeds to parameters in planetary boundary-layer and surface-layer schemes in the weather research and forecasting model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Ben; Qian, Yun; Berg, Larry K.

We evaluate the sensitivity of simulated turbine-height wind speeds to 26 parameters within the Mellor–Yamada–Nakanishi–Niino (MYNN) planetary boundary-layer scheme and MM5 surface-layer scheme of the Weather Research and Forecasting model over an area of complex terrain. An efficient sampling algorithm and generalized linear model are used to explore the multiple-dimensional parameter space and quantify the parametric sensitivity of simulated turbine-height wind speeds. The results indicate that most of the variability in the ensemble simulations is due to parameters related to the dissipation of turbulent kinetic energy (TKE), Prandtl number, turbulent length scales, surface roughness, and the von Kármán constant. Themore » parameter associated with the TKE dissipation rate is found to be most important, and a larger dissipation rate produces larger hub-height wind speeds. A larger Prandtl number results in smaller nighttime wind speeds. Increasing surface roughness reduces the frequencies of both extremely weak and strong airflows, implying a reduction in the variability of wind speed. All of the above parameters significantly affect the vertical profiles of wind speed and the magnitude of wind shear. Lastly, the relative contributions of individual parameters are found to be dependent on both the terrain slope and atmospheric stability.« less

Application and Limitations of GPS Radio Occultation (GPS-RO) Data for Atmospheric Boundary Layer Height Detection over the Arctic.

NASA Astrophysics Data System (ADS)

Ganeshan, M.; Wu, D. L.

2014-12-01

Due to recent changes in the Arctic environment, it is important to monitor the atmospheric boundary layer (ABL) properties over the Arctic Ocean, especially to explore the variability in ABL clouds (such as sensitivity and feedback to sea ice loss). For example, radiosonde and satellite observations of the Arctic ABL height (and low-cloud cover) have recently suggested a positive response to sea ice loss during October that may not occur during the melt season (June-September). Owing to its high vertical and spatiotemporal resolution, an independent ABL height detection algorithm using GPS Radio Occultation (GPS-RO) refractivity in the Arctic is explored. Similar GPS-RO algorithms developed previously typically define the level of the most negative moisture gradient as the ABL height. This definition is favorable for subtropical oceans where a stratocumulus-topped ABL is often capped by a layer of sharp moisture lapse rate (coincident with the temperature inversion). The Arctic Ocean is also characterized by stratocumulus cloud cover, however, the specific humidity does not frequently decrease in the ABL capping inversion. The use of GPS-RO refractivity for ABL height retrieval therefore becomes more complex. During winter months (December-February), when the total precipitable water in the troposphere is a minimum, a fairly straightforward algorithm for ABL height retrieval is developed. The applicability and limitations of this method for other seasons (Spring, Summer, Fall) is determined. The seasonal, interannual and spatial variability in the GPS-derived ABL height over the Arctic Ocean, as well as its relation to the underlying surface (ice vs. water), is investigated. The GPS-RO profiles are also explored for the evidence of low-level moisture transport in the cold Arctic environment.

Chemical analysis of aerosol in the Venusian cloud layer by reaction gas chromatography on board the Vega landers

NASA Technical Reports Server (NTRS)

Gelman, B. G.; Drozdov, Y. V.; Melnikov, V. V.; Rotin, V. A.; Khokhlov, V. N.; Bondarev, V. B.; Dolnikov, G. G.; Dyachkov, A. V.; Nenarokov, D. F.; Mukhin, L. M.

1986-01-01

The experiment on sulfuric acid aerosol determination in the Venusian cloud layer on board the Vega landers is described. An average content of sulfuric acid of approximately 1 mg/cu m was found for the samples taken from the atmosphere at heights from 63 to 48 km and analyzed with the SIGMA-3 chromatograph. Sulfur dioxide (SO2) was revealed in the gaseous sample at the height of 48 km. From the experimental results and blank run measurements, a suggestion is made that the Venusian cloud layer aerosol consists of more complicated particles than the sulfuric acid water solution does.

Simulating Carbon cycle and phenology in complex forests using a multi-layer process based ecosystem model; evaluation and use of 3D-CMCC-Forest Ecosystem Model in a deciduous and an evergreen neighboring forests, within the area of Brasschaat (Be)

NASA Astrophysics Data System (ADS)

Marconi, S.; Collalti, A.; Santini, M.; Valentini, R.

2013-12-01

3D-CMCC-Forest Ecosystem Model is a process based model formerly developed for complex forest ecosystems to estimate growth, water and carbon cycles, phenology and competition processes on a daily/monthly time scale. The Model integrates some characteristics of the functional-structural tree models with the robustness of the light use efficiency approach. It treats different heights, ages and species as discrete classes, in competition for light (vertical structure) and space (horizontal structure). The present work evaluates the results of the recently developed daily version of 3D-CMCC-FEM for two neighboring different even aged and mono specific study cases. The former is a heterogeneous Pedunculate oak forest (Quercus robur L. ), the latter a more homogeneous Scot pine forest (Pinus sylvestris L.). The multi-layer approach has been evaluated against a series of simplified versions to determine whether the improved model complexity in canopy structure definition increases its predictive ability. Results show that a more complex structure (three height layers) should be preferable to simulate heterogeneous scenarios (Pedunculate oak stand), where heights distribution within the canopy justify the distinction in dominant, dominated and sub-dominated layers. On the contrary, it seems that using a multi-layer approach for more homogeneous stands (Scot pine stand) may be disadvantageous. Forcing the structure of an homogeneous stand to a multi-layer approach may in fact increase sources of uncertainty. On the other hand forcing complex forests to a mono layer simplified model, may cause an increase in mortality and a reduction in average DBH and Height. Compared with measured CO2 flux data, model results show good ability in estimating carbon sequestration trends, on both a monthly/seasonal and daily time scales. Moreover the model simulates quite well leaf phenology and the combined effects of the two different forest stands on CO2 fluxes.

Negative post sunset height rise of F layer: Causes and implications

NASA Astrophysics Data System (ADS)

Joshi, Lalit Mohan; Patra, Amit

Post sunset height rise (PSHR) of the F layer is a manifestation of the pre reversal enhancement (PRE) of zonal electric field in the equatorial and low latitude ionosphere. Ionosonde observations, made during the equinox period from Sriharikota (13.7 degree North, 80.1 degree East, 6.7 degree North magnetic latitude), a low latitude station in India, have been utilized to study the PSHR of the F layer. Normally, the height of the F layer increases during the early post sunset period (positive PSHR) whose magnitude has a direct bearing on the equatorial spread F (ESF). However, observations revealed that on a few nights (about 3% nights) the height of the F layer descended in the early post sunset period itself, indicating the absence of PRE of zonal field. Such events have been termed as negative PSHR events. Such events never preceded ESF. Detailed investigations revealed that the negative PSHR events were accompanied by an enhancement of low latitude sporadic E (Es) activity with increase in the Es blanketing (fbEs) and top (ftEs) frequencies, during the post sunset period. Numerical simulations have been carried out to evaluate the effectiveness of the westward Pedersen and Hall conductivity gradients that exists in the low latitude E region during the evening hours, in causing the PRE of zonal field and the PSHR of the F layer. Model simulation reveals that the dominant cause of PRE of zonal field is the divergence of Hall current in the low latitude E region. When the zonal conductivity gradient of the low latitude E region was assumed to be either zero or slightly eastward, owing to the intensification of Es, model computation resulted in the negative PSHR of the F layer. Thus, the observational and computational results highlight the important role of the low latitude Es in the PRE of the zonal electric field.

Cloud layer thicknesses from a combination of surface and upper-air observations

NASA Technical Reports Server (NTRS)

Poore, Kirk D.; Wang, Junhong; Rossow, William B.

1995-01-01

Cloud layer thicknesses are derived from base and top altitudes by combining 14 years (1975-1988) of surface and upper-air observations at 63 sites in the Northern Hemisphere. Rawinsonde observations are employed to determine the locations of cloud-layer top and base by testing for dewpoint temperature depressions below some threshold value. Surface observations serve as quality checks on the rawinsonde-determined cloud properties and provide cloud amount and cloud-type information. The dataset provides layer-cloud amount, cloud type, high, middle, or low height classes, cloud-top heights, base heights and layer thicknesses, covering a range of latitudes from 0 deg to 80 deg N. All data comes from land sites: 34 are located in continental interiors, 14 are near coasts, and 15 are on islands. The uncertainties in the derived cloud properties are discussed. For clouds classified by low-, mid-, and high-top altitudes, there are strong latitudinal and seasonal variations in the layer thickness only for high clouds. High-cloud layer thickness increases with latitude and exhibits different seasonal variations in different latitude zones: in summer, high-cloud layer thickness is a maximum in the Tropics but a minimum at high latitudes. For clouds classified into three types by base altitude or into six standard morphological types, latitudinal and seasonal variations in layer thickness are very small. The thickness of the clear surface layer decreases with latitude and reaches a summer minimum in the Tropics and summer maximum at higher latitudes over land, but does not vary much over the ocean. Tropical clouds occur in three base-altitude groups and the layer thickness of each group increases linearly with top altitude. Extratropical clouds exhibit two groups, one with layer thickness proportional to their cloud-top altitude and one with small (less than or equal to 1000 m) layer thickness independent of cloud-top altitude.

Temperature dependent current-voltage characteristics of Au/n-Si Schottky barrier diodes and the effect of transition metal oxides as an interface layer

NASA Astrophysics Data System (ADS)

Mahato, Somnath; Puigdollers, Joaquim

2018-02-01

Temperature dependent current-voltage (I‒V) characteristics of Au/n-type silicon (n-Si) Schottky barrier diodes have been investigated. Three transition metal oxides (TMO) are used as an interface layer between gold and silicon. The basic Schottky diode parameters such as ideality factor (n), barrier height (ϕb 0) and series resistance (Rs) are calculated and successfully explained by the thermionic emission (TE) theory. It has been found that ideality factor decreased and barrier height increased with increased of temperature. The conventional Richardson plot of ln(I0/T2) vs. 1000/T is determined the activation energy (Ea) and Richardson constant (A*). Whereas value of 'A*' is much smaller than the known theoretical value of n-type Si. The temperature dependent I-V characteristics obtained the mean value of barrier height (ϕb 0 bar) and standard deviation (σs) from the linear plot of ϕap vs. 1000/T. From the modified Richardson plot of ln(I0/T2) ˗ (qσ)2/2(kT)2 vs. 1000/T gives Richardson constant and homogeneous barrier height of Schottky diodes. Main observation in this present work is the barrier height and ideality factor shows a considerable change but the series resistance value exhibits negligible change due to TMO as an interface layer.

Transition in a Supersonic Boundary-Layer Due to Roughness and Acoustic Disturbances

NASA Technical Reports Server (NTRS)

Balakumar, P.

2003-01-01

The transition process induced by the interaction of an isolated roughness with acoustic disturbances in the free stream is numerically investigated for a boundary layer over a flat plate with a blunted leading edge at a free stream Mach number of 3.5. The roughness is assumed to be of Gaussian shape and the acoustic disturbances are introduced as boundary condition at the outer field. The governing equations are solved using the 5'h-rder accurate weighted essentially non-oscillatory (WENO) scheme for space discretization and using third- order total-variation-diminishing (TVD) Runge- Kutta scheme for time integration. The steady field induced by the two and three-dimensional roughness is also computed. The flow field induced by two-dimensional roughness exhibits different characteristics depending on the roughness heights. At small roughness heights the flow passes smoothly over the roughness, at moderate heights the flow separates downstream of the roughness and at larger roughness heights the flow separates upstream and downstream of the roughness. Computations also show that disturbances inside the boundary layer is due to the direct interaction of the acoustic waves and isolated roughness plays a minor role in generating instability waves.

Cytosine-based nucleoside analogs are selectively lethal to DNA mismatch repair-deficient tumour cells by enhancing levels of intracellular oxidative stress

PubMed Central

Hewish, M; Martin, S A; Elliott, R; Cunningham, D; Lord, C J; Ashworth, A

2013-01-01

Background: DNA mismatch repair deficiency is present in a significant proportion of a number of solid tumours and is associated with distinct clinical behaviour. Methods: To identify the therapeutic agents that might show selectivity for mismatch repair-deficient tumour cells, we screened a pair of isogenic MLH1-deficient and MLH1-proficient tumour cell lines with a library of clinically used drugs. To test the generality of hits in the screen, selective agents were retested in cells deficient in the MSH2 mismatch repair gene. Results: We identified cytarabine and other related cytosine-based nucleoside analogues as being selectively toxic to MLH1 and MSH2-deficient tumour cells. The selective cytotoxicity we observed was likely caused by increased levels of cellular oxidative stress, as it could be abrogated by antioxidants. Conclusion: We propose that cytarabine-based chemotherapy regimens may represent a tumour-selective treatment strategy for mismatch repair-deficient cancers. PMID:23361057

[How much water is lost during breathing?].

PubMed

Zieliński, Jakub; Przybylski, Jacek

2012-01-01

Arising from the Antoine equation and the ideal gas law, the volume of exhaled water has been calculated. Air temperature, humidity and minute ventilation has been taken into account. During physical exercise amount of exhaled H(2)O is linear, but not proportional to heart rate. And so at the heart rate of 140 bpm amount of exhaled water is approximately four times higher than during the rest and equals about 60-70 ml/h. The effect of external temperature and humidity on water lost via lungs was assessed as well. When temperature of inspired air and its humidity is 35°C an 75% respectively loss of water is 7 ml/h. Whereas when above parameters are changed to minus 10°C and 25% lung excretion of H(2)O increases up to 20 ml/h. The obtained results may become the basis for the assessment of osmolarity changes on the surface of the lower airways. The increase of which is recently considered as one of the factors responsible for exercise induced bronchospasm.

Recombination Proteins Mediate Meiotic Spatial Chromosome Organization and Pairing

PubMed Central

Storlazzi, Aurora; Gargano, Silvana; Ruprich-Robert, Gwenael; Falque, Matthieu; David, Michelle; Kleckner, Nancy; Zickler, Denise

2010-01-01

SUMMARY Meiotic chromosome pairing involves not only recognition of homology but also juxtaposition of entire chromosomes in a topologically regular way. Analysis of filamentous fungus Sordaria macrospora reveals that recombination proteins Mer3, Msh4 and Mlh1 play direct roles in all of these aspects, in advance of their known roles in recombination. Absence of Mer3 helicase results in interwoven chromosomes, thereby revealing the existence of features that specifically ensure “entanglement avoidance”. Entanglements that remain at zygotene, i.e. “interlockings”, require Mlh1 for resolution, likely to eliminate constraining recombinational connections. Patterns of Mer3 and Msh4 foci along aligned chromosomes show that the double-strand breaks mediating homologous alignment have spatially separated ends, one localized to each partner axis, and that pairing involves interference among developing interhomolog interactions. We propose that Mer3, Msh4 and Mlh1 execute all of these roles during pairing by modulating the state of nascent double-strand break/partner DNA contacts within axis-associated recombination complexes. PMID:20371348

MIE Lidar proposed for the German Space Shuttle Mission D2

NASA Technical Reports Server (NTRS)

Renger, W.; Endemann, M.; Quenzel, H.; Werner, C.

1986-01-01

Firm plans for a second German Spacelab mission (D2-mission), originally scheduled for late 1988 is basically a zero-g mission, but will also include earth observation experiments. On board the D2-facility will allow performance of a number of different measurements with the goal to obtain performance data (cloud top heights, height of the planetary boundary layer, optical thickness, and cloud base height of thin and medium thick clouds, ice/water phase discriminatin for clouds, tropopause height, tropaspheric height, tropospheric aerosols, and stratospheric aerosols.

The influence of the atmospheric boundary layer on nocturnal layers of noctuids and other moths migrating over southern Britain.

PubMed

Wood, Curtis R; Chapman, Jason W; Reynolds, Donald R; Barlow, Janet F; Smith, Alan D; Woiwod, Ian P

2006-03-01

Insects migrating at high altitude over southern Britain have been continuously monitored by automatically operating, vertical-looking radars over a period of several years. During some occasions in the summer months, the migrants were observed to form well-defined layer concentrations, typically at heights of 200-400 m, in the stable night-time atmosphere. Under these conditions, insects are likely to have control over their vertical movements and are selecting flight heights that are favourable for long-range migration. We therefore investigated the factors influencing the formation of these insect layers by comparing radar measurements of the vertical distribution of insect density with meteorological profiles generated by the UK Meteorological Office's (UKMO) Unified Model (UM). Radar-derived measurements of mass and displacement speed, along with data from Rothamsted Insect Survey light traps, provided information on the identity of the migrants. We present here three case studies where noctuid and pyralid moths contributed substantially to the observed layers. The major meteorological factors influencing the layer concentrations appeared to be: (a) the altitude of the warmest air, (b) heights corresponding to temperature preferences or thresholds for sustained migration and (c) on nights when air temperatures are relatively high, wind-speed maxima associated with the nocturnal jet. Back-trajectories indicated that layer duration may have been determined by the distance to the coast. Overall, the unique combination of meteorological data from the UM and insect data from entomological radar described here show considerable promise for systematic studies of high-altitude insect layering.

All-sky photogrammetry techniques to georeference a cloud field

NASA Astrophysics Data System (ADS)

Crispel, Pierre; Roberts, Gregory

2018-01-01

In this study, we present a novel method of identifying and geolocalizing cloud field elements from a portable all-sky camera stereo network based on the ground and oriented towards zenith. The methodology is mainly based on stereophotogrammetry which is a 3-D reconstruction technique based on triangulation from corresponding stereo pixels in rectified images. In cases where clouds are horizontally separated, identifying individual positions is performed with segmentation techniques based on hue filtering and contour detection algorithms. Macroscopic cloud field characteristics such as cloud layer base heights and velocity fields are also deduced. In addition, the methodology is fitted to the context of measurement campaigns which impose simplicity of implementation, auto-calibration, and portability. Camera internal geometry models are achieved a priori in the laboratory and validated to ensure a certain accuracy in the peripheral parts of the all-sky image. Then, stereophotogrammetry with dense 3-D reconstruction is applied with cameras spaced 150 m apart for two validation cases. The first validation case is carried out with cumulus clouds having a cloud base height at 1500 m a.g.l. The second validation case is carried out with two cloud layers: a cumulus fractus layer with a base height at 1000 m a.g.l. and an altocumulus stratiformis layer with a base height of 2300 m a.g.l. Velocity fields at cloud base are computed by tracking image rectangular patterns through successive shots. The height uncertainty is estimated by comparison with a Vaisala CL31 ceilometer located on the site. The uncertainty on the horizontal coordinates and on the velocity field are theoretically quantified by using the experimental uncertainties of the cloud base height and camera orientation. In the first cumulus case, segmentation of the image is performed to identify individuals clouds in the cloud field and determine the horizontal positions of the cloud centers.

Nonlinear Excitation of Inviscid Stationary Vortex in a Boundary-Layer Flow

NASA Technical Reports Server (NTRS)

Choudhari, Meelan; Duck, Peter W.

1996-01-01

We examine the excitation of inviscid stationary crossflow instabilities near an isolated surface hump (or indentation) underneath a three-dimensional boundary layer. As the hump height (or indentation depth) is increased from zero, the receptivity process becomes nonlinear even before the stability characteristics of the boundary layer are modified to a significant extent. This behavior contrasts sharply with earlier findings on the excitation of the lower branch Tollmien-Schlichting modes and is attributed to the inviscid nature of the crossflow modes, which leads to a decoupling between the regions of receptivity and stability. As a result of this decoupling, similarity transformations exist that allow the nonlinear receptivity of a general three-dimensional boundary layer to be studied with a set of canonical solutions to the viscous sublayer equations. The parametric study suggests that the receptivity is likely to become nonlinear even before the hump height becomes large enough for flow reversal to occur in the canonical solution. We also find that the receptivity to surface humps increases more rapidly as the hump height increases than is predicted by linear theory. On the other hand, receptivity near surface indentations is generally smaller in comparison with the linear approximation. Extension of the work to crossflow receptivity in compressible boundary layers and to Gortler vortex excitation is also discussed.

Effects of Elongation on Stochastic Layer and Magnetic Footprint in Divertor Tokamaks

NASA Astrophysics Data System (ADS)

Wadi, Hasina; Jones, Morgin; Ali, Halima; Punjabi, Alkesh

2007-11-01

An area-preserving map is constructed to calculate effects of elongation on the stochastic layer and magnetic footprint in divertor tokamaks. The generating function for the map is S(x,y) = -(1/2)α^2y^2 (1-y^2/2a^2)+(1/2)β^2x^2. Method of maps developed by Punjabi and Boozer [1,2] is used to construct the map and to calculate the stochastic layer and the magnetic footprints. The poloidal magnetic flux inside the ideal separatrix and the safety factor profile are held constant, and elongation is varied by (1) varying the width of separatrix surface in the midplane keeping the height fixed, and (2) varying the height keeping the width of separatrix surface fixed. As the width is increased, the stochastic layer and the footprint become narrower. As the height is increased, the width of stochastic layer and the footprint become narrower. Detailed results of this study will be presented. This work is supported by US DOE OFES DE-FG02-01ER54624 and DE-FG02-04ER54793. [1] A. Punjabi, A. Verma, and A. Boozer, Phys Rev Lett, 69, 3322-3325 (1992). [2] A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys Lett A 364 140--145 (2007).

Immunohistochemical null-phenotype for mismatch repair proteins in colonic carcinoma associated with concurrent MLH1 hypermethylation and MSH2 somatic mutations.

PubMed

Wang, Tao; Stadler, Zsofia K; Zhang, Liying; Weiser, Martin R; Basturk, Olca; Hechtman, Jaclyn F; Vakiani, Efsevia; Saltz, Lenard B; Klimstra, David S; Shia, Jinru

2018-04-01

Microsatellite instability, a well-established driver pathway in colorectal carcinogenesis, can develop in both sporadic and hereditary conditions via different molecular alterations in the DNA mismatch repair (MMR) genes. MMR protein immunohistochemistry (IHC) is currently widely used for the detection of MMR deficiency in solid tumors. The IHC test, however, can show varied staining patterns, posing challenges in the interpretation of the staining results in some cases. Here we report a case of an 80-year-old female with a colonic adenocarcinoma that exhibited an unusual "null" IHC staining pattern with complete loss of all four MMR proteins (MLH1, MSH2, MSH6, and PMS2). This led to subsequent MLH1 methylation testing and next generation sequencing which demonstrated that the loss of all MMR proteins was associated with concurrent promoter hypermethylation of MLH1 and double somatic truncating mutations in MSH2. These molecular findings, in conjunction with the patient's age being 80 years and the fact that the patient had no personal or family cancer history, indicated that the MMR deficiency was highly likely sporadic in nature. Thus, the stringent Lynch syndrome type surveillance programs were not recommended to the patient and her family members. This case illustrates a rare but important scenario where a null IHC phenotype signifies complex underlying molecular alternations that bear clinical management implications, highlighting the need for recognition and awareness of such unusual IHC staining patterns.

Mismatch repair genes on chromosomes 2p and 3p account for a major share of hereditary nonpolyposis colorectal cancer families evaluable by linkage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nystroem-Lahti, M.; Pylkkaenen, L.; Aaltonen, L.A.

1994-10-01

Two susceptibility loci for hereditary nonpolyposis colorectal cancer (HNPCC) have been identified, and each contains a mismatch repair gene: MSH2 on chromosome 2p and MLH1 on chromosome 3p. We studied the involvement of these loci in 13 large HNPCC kindreds originating from three different continents. Six families showed close linkage to the 2p locus, and a heritable mutation of the MSH2 gene was subsequently found in four. The 2p-linked kindreds included a family characterized by the lack of extracolonic manifestations (Lynch I syndrome), as well as two families with cutaneous manifestations typical of the Muir-Torre syndrome. Four families showed evidencemore » for linkage to the 3p locus, and a heritable mutation of the MLH1 gene was later detected in three. One 3p-linked kindred was of Amerindian origin. Of the remaining three families studied for linkage, one showed lod scores compatible with exclusion of both MSH2 and MLH1, while lod scores obtained in the other two families suggested exclusion of one HNPCC locus (MSH2 or MLH1) but were uninformative for markers flanking the other locus. Our results suggest that mismatch repair genes on 2p and 3p account for a major share of HNPCC in kindreds that can be evaluated by linkage analysis. 36 refs., 2 figs., 3 tabs.« less

Evaluation of markers for CpG island methylator phenotype (CIMP) in colorectal cancer by a large population-based sample.

PubMed

Ogino, Shuji; Kawasaki, Takako; Kirkner, Gregory J; Kraft, Peter; Loda, Massimo; Fuchs, Charles S

2007-07-01

The CpG island methylator phenotype (CIMP or CIMP-high) with extensive promoter methylation is a distinct phenotype in colorectal cancer. However, a choice of markers for CIMP has been controversial. A recent extensive investigation has selected five methylation markers (CACNA1G, IGF2, NEUROG1, RUNX3, and SOCS1) as surrogate markers for epigenomic aberrations in tumor. The use of these markers as a CIMP-specific panel needs to be validated by an independent, large dataset. Using MethyLight assays on 920 colorectal cancers from two large prospective cohort studies, we quantified DNA methylation in eight CIMP-specific markers [the above five plus CDKN2A (p16), CRABP1, and MLH1]. A CIMP-high cutoff was set at > or = 6/8 or > or = 5/8 methylated promoters, based on tumor distribution and BRAF/KRAS mutation frequencies. All but two very specific markers [MLH1 (98% specific) and SOCS1 (93% specific)] demonstrated > or = 85% sensitivity and > or = 80% specificity, indicating overall good concordance in methylation patterns and good performance of these markers. Based on sensitivity, specificity, and false positives and negatives, the eight markers were ranked in order as: RUNX3, CACNA1G, IGF2, MLH1, NEUROG1, CRABP1, SOCS1, and CDKN2A. In conclusion, a panel of markers including at least RUNX3, CACNA1G, IGF2, and MLH1 can serve as a sensitive and specific marker panel for CIMP-high.

Overexpression of MutL homolog 1 and MutS homolog 2 proteins have reversed prognostic implications for stage I-II colon cancer patients.

PubMed

Huang, Shih-Chiang; Huang, Shiu-Feng; Chen, Ya-Ting; Chang, Yu; Chiu, Yu-Ting; Chang, Il-Chi; Wu, Hong-Dar Isaac; Chen, Jinn-Shiun

2017-02-01

The outcome of colon cancer patients without lymph node metastasis is heterogeneous. Searching for new prognostic markers is warranted. One hundred twenty stage I-II colon cancer patients who received complete surgical excision during 1995-2004 were selected for this biomarker study. Immunohistochemical method was used to assess p53, epidermal growth factor receptor, MLH1, and MSH2 status. KRAS mutation was examined by direct sequencing. Thirty three patients (27.5%) developed metachronous metastasis during follow up. By multivariate analysis, only female gender (p = 0.03), high serum carcinoembryonic antigen (CEA) level (≧5 ng/ml) (p = 0.04), and MLH1 overexpression (p = 0.003) were associated with the metastasis group. The 5-year-survival rate were also significantly lower for female gender (71.7% versus 88.9%, p = 0.025), high CEA level (64.9% versus 92.4%, p < 0.001), and MLH1 overexpression (77.5% versus 94.4%, p = 0.039). In contrast, MSH2 overexpression was associated with better survival, 95.1% versus 75.5% (p = 0.024). The reversed prognostic implications in the overexpression of MLH1 and MSH2 for stage I-II colon cancer patients is a novel finding and worthy of further confirmation. Copyright © 2017 Chang Gung University. Published by Elsevier B.V. All rights reserved.

Microsatellite instability and the clinicopathological features of sporadic colorectal cancer

PubMed Central

Ward, R; Meagher, A; Tomlinson, I; O'Connor, T; Norrie, M; Wu, R; Hawkins, N

2001-01-01

BACKGROUND AND AIMS—In this study, we prospectively examined the clinical significance of the microsatellite instability (MSI) phenotype in sporadic colorectal cancer, and investigated methods for effective identification of these tumours in routine pathology practice.
METHODS—DNA was extracted from 310 tumours collected from 302 consecutive individuals undergoing curative surgery for sporadic colorectal cancer. Microsatellite status was determined by polymerase chain reaction amplification using standard markers, while immunostaining was used to examine expression of MLH1, MSH2, and p53.
RESULTS—Eleven per cent of tumours showed high level instability (MSI-H), 6.8% had low level instability (MSI-L), and the remainder were stable. MSI-H tumours were significantly more likely to be of high histopathological grade, have a mucinous phenotype, and to harbour increased numbers of intraepithelial lymphocytes. They were also more likely to be right sided, occur in women, and be associated with improved overall survival. In total, 25 (8%) tumours showed loss of staining for MLH1 and a further three tumours showed absence of staining for MSH2. The positive and negative predictive value of immunohistochemistry in the detection of MSI-H tumours was greater than 95%.
CONCLUSIONS—We conclude that the MSI-H phenotype constitutes a pathologically and clinically distinct subtype of sporadic colorectal cancer. Immunohistochemical staining for MLH1 and MSH2 represents an inexpensive and accurate means of identifying such tumours.


Keywords: colorectal carcinoma; microsatellite instability; survival; MLH1; MSH2; immunohistochemistry PMID:11358903

Expression of the hMLH1 and hMSH2 proteins in normal tissues: relationship to cancer predisposition in hereditary non-polyposis colon cancer.

PubMed

Plevová, Pavlína; Sedláková, Eva; Zapletalová, Jana; Krepelová, Anna; Skýpalová, Petra; Kolár, Zdenek

2005-02-01

The majority of tumours in patients with hereditary non-polyposis colon cancer (HNPCC) occur in large intestine and endometrium; also, other tissues are at increased risk. We studied expression of hMLH1 and hMSH2 proteins in 148 normal samples of various tissues from non-HNPCC patients and in 14 normal colon tissues from HNPCC patients. Immunohistochemical technique was used. Intensity of nuclear staining, percentage of stained cells and H-scores were calculated. Tissues were divided into groups. Groups A, B and C included tissues with increased risk of cancer in HNPCC A) stomach, small and large bowel; (B) endometrium; (C) ovary, ureter, urinary bladder, kidney and liver. Group D tissues were without increased risk. Expression of the proteins was significantly higher in groups A, B and C compared with group D (P<0.0001, P=0.0004 for hMSH2 in C versus D). The expression was highest in testis. In colons of HNPCC patients, expression of the mutated gene product was significantly lower than in non-HNPCC patients. In conclusion, hMLH1/hMSH2 protein expression is constitutively higher in certain cell types of certain tissues, including the majority of tissues that are at increased risk of cancer in HNPCC. However, association of strong hMLH1/hMSH2 expression with cancer risk is not strictly valid.

Feasibility study of a layer-oriented wavefront sensor for solar telescopes.

PubMed

Marino, Jose; Wöger, Friedrich

2014-02-01

Solar multiconjugate adaptive optics systems rely on several wavefront sensors, which measure the incoming turbulent phase along several field directions to produce a tomographic reconstruction of the turbulent phase. In this paper, we explore an alternative wavefront sensing approach that attempts to directly measure the turbulent phase present at a particular height in the atmosphere: a layer-oriented cross-correlating Shack-Hartmann wavefront sensor (SHWFS). In an experiment at the Dunn Solar Telescope, we built a prototype layer-oriented cross-correlating SHWFS system conjugated to two separate atmospheric heights. We present the data obtained in the observations and complement these with ray-tracing computations to achieve a better understanding of the instrument's performance and limitations. The results obtained in this study strongly indicate that a layer-oriented cross-correlating SHWFS is not a practical design to measure the wavefront at a high layer in the atmosphere.

Interfacial elastic relaxation during the ejection of bi-layered tablets.

PubMed

Anuar, M S; Briscoe, B J

2010-03-15

The predilection of a bi-layered tablet to fail in the interface region after its initial formation in the compaction process reduces its practicality as a choice for controlled release solid drug delivery system. Hence, a fundamental appreciation of the governing mechanism that causes the weakening of the interfacial bonds within the bi-layered tablet is crucial in order to improve the overall bi-layered tablet mechanical integrity. This work has shown that the occurrence of the elastic relaxation in the interface region during the ejection stage of the compaction process decreases with the increase in the bi-layered tablet interface strength. This is believed to be due to the increase in the plastic bonding in the interface region. The tablet diametrical elastic relaxation affects the tablet height elastic relaxation, where the impediment of the tablet height expansion is observed when the interface region experiences a diametrical expansion. 2009 Elsevier B.V. All rights reserved.

Identification of atmospheric boundary layer thickness using doppler radar datas and WRF - ARW model in Merauke

NASA Astrophysics Data System (ADS)

Putri, R. J. A.; Setyawan, T.

2017-01-01

In the synoptic scale, one of the important meteorological parameter is the atmospheric boundary layer. Aside from being a supporter of the parameters in weather and climate models, knowing the thickness of the layer of the atmosphere can help identify aerosols and the strength of the vertical mixing of pollutants in it. The vertical wind profile data from C-band Doppler radar Mopah-Merauke which is operated by BMKG through Mopah-Merauke Meteorological Station can be used to identify the peak of Atmospheric Boundaryu Layer (ABL). ABL peak marked by increasing wind shear over the layer blending. Samples in January 2015 as a representative in the wet and in July 2015 as the representation of a dry month, shows that ABL heights using WRF models show that in July (sunny weather) ABL height values higher than in January (cloudy)

Temperature-dependent layer breathing modes in two-dimensional materials

NASA Astrophysics Data System (ADS)

Maity, Indrajit; Maiti, Prabal K.; Jain, Manish

2018-04-01

Relative out-of-plane displacements of the constituent layers of two-dimensional materials give rise to unique low-frequency breathing modes. By computing the height-height correlation functions from molecular dynamics simulations, we show that the layer breathing modes (LBMs) can be mapped consistently to vibrations of a simple linear chain model. Our calculated thickness dependence of LBM frequencies for few-layer (FL) graphene and molybdenum disulfide (MoS2) are in excellent agreement with available experiments. Our results show a redshift of LBM frequency with an increase in temperature, which is a direct consequence of anharmonicities present in the interlayer interaction. We also predict the thickness and temperature dependence of LBM frequencies for FL hexagonal boron nitride. Our Rapid Communication provides a simple and efficient way to probe the interlayer interaction for layered materials and their heterostructures with the inclusion of anharmonic effects.

Planetary Boundary Layer Dynamics over Reno, Nevada in Summer

NASA Astrophysics Data System (ADS)

Liming, A.; Sumlin, B.; Loria Salazar, S. M.; Holmes, H.; Arnott, W. P.

2014-12-01

Quantifying the height of the planetary boundary layer (PBL) is important to understand the transport behavior, mixing, and surface concentrations of air pollutants. In Reno, NV, located in complex, mountainous terrain with high desert climate, the daytime boundary layer can rise to an estimated 3km or more on a summer day due to surface heating and convection. The nocturnal boundary layer, conversely, tends to be much lower and highly stable due to radiative cooling from the surface at night and downslope flow of cool air from nearby mountains. With limited availability of radiosonde data, current estimates of the PBL height at any given time or location are potentially over or underestimated. To better quantify the height and characterize the PBL physics, we developed portable, lightweight sensors that measure CO2 concentrations, temperature, pressure, and humidity every 5 seconds. Four of these sensors are used on a tethered balloon system to monitor CO2 concentrations from the surface up to 300m. We will combine this data with Radio Acoustic Sounding System (RASS) data that measures vertical profiles of wind speed, temperature, and humidity from 40m to 400m. This experiment will characterize the diurnal evolution of CO2 concentrations at multiple heights in the PBL, provide insight into PBL physics during stability transition periods at sunrise and sunset, and estimate the nighttime PBL depth during August in Reno. Further, we expect to gain a better understanding of the impact of mixing volume changes (i.e., PBL height) on air quality and pollution concentrations in Reno. The custom portable sensor design will also be presented. It is expected that these instruments can be used for indoor or outdoor air quality studies, where lightness, small size, and battery operation can be of benefit.

On Displacement Height, from Classical to Practical Formulation: Stress, Turbulent Transport and Vorticity Considerations

NASA Astrophysics Data System (ADS)

Sogachev, Andrey; Kelly, Mark

2016-03-01

Displacement height ( d) is an important parameter in the simple modelling of wind speed and vertical fluxes above vegetative canopies, such as forests. Here we show that, aside from implicit definition through a (displaced) logarithmic profile, accepted formulations for d do not consistently predict flow properties above a forest. Turbulent transport can affect the displacement height, and is an integral part of what is called the roughness sublayer. We develop a more general approach for estimation of d, through production of turbulent kinetic energy and turbulent transport, and show how previous stress-based formulations for displacement height can be seen as simplified cases of a more general definition including turbulent transport. Further, we also give a simplified and practical form for d that is in agreement with the general approach, exploiting the concept of vortex thickness scale from mixing-layer theory. We assess the new and previous displacement height formulations by using flow statistics derived from the atmospheric boundary-layer Reynolds-averaged Navier-Stokes model SCADIS as well as from wind-tunnel observations, for different vegetation types and flow regimes in neutral conditions. The new formulations tend to produce smaller d than stress-based forms, falling closer to the classic logarithmically-defined displacement height. The new, more generally defined, displacement height appears to be more compatible with profiles of components of the turbulent kinetic energy budget, accounting for the combined effects of turbulent transport and shear production. The Coriolis force also plays a role, introducing wind-speed dependence into the behaviour of the roughness sublayer; this affects the turbulent transport, shear production, stress, and wind speed, as well as the displacement height, depending on the character of the forest. We further show how our practical (`mixing-layer') form for d matches the new turbulence-based relation, as well as correspondence to previous (stress-based) formulations.

Modeling large wind farms in conventionally neutral atmospheric boundary layers under varying initial conditions

NASA Astrophysics Data System (ADS)

Allaerts, Dries; Meyers, Johan

2014-05-01

Atmospheric boundary layers (ABL) are frequently capped by an inversion layer limiting the entrainment rate and boundary layer growth. Commonly used analytical models state that the entrainment rate is inversely proportional to the inversion strength. The height of the inversion turns out to be a second important parameter. Conventionally neutral atmospheric boundary layers (CNBL) are ABLs with zero surface heat flux developing against a stratified free atmosphere. In this regime the inversion-filling process is merely driven by the downward heat flux at the inversion base. As a result, CNBLs are strongly dependent on the heating history of the boundary layer and strong inversions will fail to erode during the course of the day. In case of large wind farms, the power output of the farm inside a CNBL will depend on the height and strength of the inversion above the boundary layer. On the other hand, increased turbulence levels induced by wind farms may partially undermine the rigid lid effect of the capping inversion, enhance vertical entrainment of air into the farm, and increase boundary layer growth. A suite of large eddy simulations (LES) is performed to investigate the effect of the capping inversion on the conventionally neutral atmospheric boundary layer and on the wind farm performance under varying initial conditions. For these simulations our in-house pseudo-spectral LES code SP-Wind is used. The wind turbines are modelled using a non-rotating actuator disk method. In the absence of wind farms, we find that a decrease in inversion strength corresponds to a decrease in the geostrophic angle and an increase in entrainment rate and geostrophic drag. Placing the initial inversion base at higher altitudes further reduces the effect of the capping inversion on the boundary layer. The inversion can be fully neglected once it is situated above the equilibrium height that a truly neutral boundary layer would attain under the same external conditions such as geostrophic wind speed and surface roughness. Wind farm simulations show the expected increase in boundary layer height and growth rate with respect to the case without wind farms. Raising the initial strength of the capping inversion in these simulations dampens the turbulent growth of the boundary layer above the farm, decreasing the farms energy extraction. The authors acknowledge support from the European Research Council (FP7-Ideas, grant no. 306471). Simulations were performed on the computing infrastructure of the VSC Flemish Supercomputer Center, funded by the Hercules Foundation and the Flemish Government.

Correlation of film morphology and defect content with the charge-carrier transport in thin-film transistors based on ZnO nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polster, S.; Jank, M. P. M.; Frey, L.

2016-01-14

The correlation of defect content and film morphology with the charge-carrier transport in field-effect devices based on zinc oxide nanoparticles was investigated. Changes in the defect content and the morphology were realized by annealing and sintering of the nanoparticle thin films. Temperature-dependent electrical measurements reveal that the carrier transport is thermally activated for both the unsintered and sintered thin films. Reduced energetic barrier heights between the particles have been determined after sintering. Additionally, the energetic barrier heights between the particles can be reduced by increasing the drain-to-source voltage and the gate-to-source voltage. The changes in the barrier height are discussedmore » with respect to information obtained by scanning electron microscopy and photoluminescence measurements. It is found that a reduction of surface states and a lower roughness at the interface between the particle layer and the gate dielectric lead to lower barrier heights. Both surface termination and layer morphology at the interface affect the barrier height and thus are the main criteria for mobility improvement and device optimization.« less

Identification of Variants in Breast Cancer Susceptibility Genes and Determination of Functional and Clinical Significance of Novel Mutations

DTIC Science & Technology

2014-10-01

to cause other cancer susceptibility (CDKN2A, MLH1, MSH2, MSH6, PMS2 ); 3) genes known or postulated to be moderate penetrance cancer susceptibility...susceptibility (CDKN2A, MLH1, MSH2, MSH6, PMS2 ); 3) genes known or postulated to be moderate penetrance cancer susceptibility genes (ATM, BARD1, BRIP1...AK, Lindor NM, Jenkins MA. Risk of breast cancer in Lynch syndrome : a systematic review. Breast Cancer Res 2013;15:R27. 55. Brunet J, Gutierrez

Current Status of Aerosol Retrievals from TOMS

NASA Technical Reports Server (NTRS)

Torres, O.; Herman, J. R.; Bhartia, P. K.; Ginoux, P.

1999-01-01

Properties of atmospheric aerosols over all land and water surfaces are retrieved from TOMS measurements of backscattered radiances. The TOMS technique, uses observations at two wavelengths. In the near ultraviolet (330-380 nm) range, where the effects of gaseous absorption are negligible. The retrieved properties are optical depth and a measure of aerosol absorptivity, generally expressed as single scattering albedo. The main sources of error of the TOMS aerosol products are sub-pixel cloud contamination and uncertainty on the height above the surface of UV-absorbing aerosol layers. The first error source is related to the large footprint (50 x 50 km at nadir) of the sensor, and the lack of detection capability of sub-pixel size clouds. The uncertainty associated with the height of the absorbing aerosol layers, on the other hand, is related to the pressure dependence of the molecular scattering process, which is the basis of the near-UV method of absorbing aerosol detection. The detection of non-absorbing aerosols is not sensitive to aerosol layer height. We will report on the ongoing work to overcome both of these difficulties. Coincident measurements of high spatial resolution thermal infrared radiances are used to address the cloud contamination issue. Mostly clear scenes for aerosol retrieval are selected by examining the spatial homogeneity of the IR radiance measurements within a TOMS pixel. The approach to reduce the uncertainty associated with the height of the aerosol layer by making use of a chemical transport model will also be discussed.

Observation of layered antiferromagnetism in self-assembled parallel NiSi nanowire arrays on Si(110) by spin-polarized scanning tunneling spectromicroscopy

NASA Astrophysics Data System (ADS)

Hong, Ie-Hong; Hsu, Hsin-Zan

2018-03-01

The layered antiferromagnetism of parallel nanowire (NW) arrays self-assembled on Si(110) have been observed at room temperature by direct imaging of both the topographies and magnetic domains using spin-polarized scanning tunneling microscopy/spectroscopy (SP-STM/STS). The topographic STM images reveal that the self-assembled unidirectional and parallel NiSi NWs grow into the Si(110) substrate along the [\\bar{1}10] direction (i.e. the endotaxial growth) and exhibit multiple-layer growth. The spatially-resolved SP-STS maps show that these parallel NiSi NWs of different heights produce two opposite magnetic domains, depending on the heights of either even or odd layers in the layer stack of the NiSi NWs. This layer-wise antiferromagnetic structure can be attributed to an antiferromagnetic interlayer exchange coupling between the adjacent layers in the multiple-layer NiSi NW with a B2 (CsCl-type) crystal structure. Such an endotaxial heterostructure of parallel magnetic NiSi NW arrays with a layered antiferromagnetic ordering in Si(110) provides a new and important perspective for the development of novel Si-based spintronic nanodevices.

Artificial plasma cusp generated by upper hybrid instabilities in HF heating experiments at HAARP

NASA Astrophysics Data System (ADS)

Kuo, Spencer; Snyder, Arnold

2013-05-01

High Frequency Active Auroral Research Program digisonde was operated in a fast mode to record ionospheric modifications by the HF heating wave. With the O mode heater of 3.2 MHz turned on for 2 min, significant virtual height spread was observed in the heater off ionograms, acquired beginning the moment the heater turned off. Moreover, there is a noticeable bump in the virtual height spread of the ionogram trace that appears next to the plasma frequency (~ 2.88 MHz) of the upper hybrid resonance layer of the HF heating wave. The enhanced spread and the bump disappear in the subsequent heater off ionograms recorded 1 min later. The height distribution of the ionosphere in the spread situation indicates that both electron density and temperature increases exceed 10% over a large altitude region (> 30 km) from below to above the upper hybrid resonance layer. This "mini cusp" (bump) is similar to the cusp occurring in daytime ionograms at the F1-F2 layer transition, indicating that there is a small ledge in the density profile reminiscent of F1-F2 layer transitions. Two parametric processes exciting upper hybrid waves as the sidebands by the HF heating waves are studied. Field-aligned purely growing mode and lower hybrid wave are the respective decay modes. The excited upper hybrid and lower hybrid waves introduce the anomalous electron heating which results in the ionization enhancement and localized density ledge. The large-scale density irregularities formed in the heat flow, together with the density irregularities formed through the parametric instability, give rise to the enhanced virtual height spread. The results of upper hybrid instability analysis are also applied to explain the descending feature in the development of the artificial ionization layers observed in electron cyclotron harmonic resonance heating experiments.

Cirrus Cloud Retrieval Using Infrared Sounding Data: Multilevel Cloud Errors.

NASA Astrophysics Data System (ADS)

Baum, Bryan A.; Wielicki, Bruce A.

1994-01-01

In this study we perform an error analysis for cloud-top pressure retrieval using the High-Resolution Infrared Radiometric Sounder (HIRS/2) 15-µm CO2 channels for the two-layer case of transmissive cirrus overlying an overcast, opaque stratiform cloud. This analysis includes standard deviation and bias error due to instrument noise and the presence of two cloud layers, the lower of which is opaque. Instantaneous cloud pressure retrieval errors are determined for a range of cloud amounts (0.1 1.0) and cloud-top pressures (850250 mb). Large cloud-top pressure retrieval errors are found to occur when a lower opaque layer is present underneath an upper transmissive cloud layer in the satellite field of view (FOV). Errors tend to increase with decreasing upper-cloud elective cloud amount and with decreasing cloud height (increasing pressure). Errors in retrieved upper-cloud pressure result in corresponding errors in derived effective cloud amount. For the case in which a HIRS FOV has two distinct cloud layers, the difference between the retrieved and actual cloud-top pressure is positive in all casts, meaning that the retrieved upper-cloud height is lower than the actual upper-cloud height. In addition, errors in retrieved cloud pressure are found to depend upon the lapse rate between the low-level cloud top and the surface. We examined which sounder channel combinations would minimize the total errors in derived cirrus cloud height caused by instrument noise and by the presence of a lower-level cloud. We find that while the sounding channels that peak between 700 and 1000 mb minimize random errors, the sounding channels that peak at 300—500 mb minimize bias errors. For a cloud climatology, the bias errors are most critical.

Boundary Layer Control for Hypersonic Airbreathing Vehicles

NASA Technical Reports Server (NTRS)

Berry, Scott A.; Nowak, Robert J.; Horvath, Thomas J.

2004-01-01

Active and passive methods for tripping hypersonic boundary layers have been examined in NASA Langley Research Center wind tunnels using a Hyper-X model. This investigation assessed several concepts for forcing transition, including passive discrete roughness elements and active mass addition (or blowing), in the 20-Inch Mach 6 Air and the 31-Inch Mach 10 Air Tunnels. Heat transfer distributions obtained via phosphor thermography, shock system details, and surface streamline patterns were measured on a 0.333-scale model of the Hyper-X forebody. The comparisons between the active and passive methods for boundary layer control were conducted at test conditions that nearly match the Hyper-X nominal Mach 7 flight test-point of an angle-of-attack of 2-deg and length Reynolds number of 5.6 million. For passive roughness, the primary parametric variation was a range of trip heights within the calculated boundary layer thickness for several trip concepts. The passive roughness study resulted in a swept ramp configuration, scaled to be roughly 0.6 of the calculated boundary layer thickness, being selected for the Mach 7 flight vehicle. For the active blowing study, the manifold pressure was systematically varied (while monitoring the mass flow) for each configuration to determine the jet penetration height, with schlieren, and transition movement, with the phosphor system, for comparison to the passive results. All the blowing concepts tested, which included various rows of sonic orifices (holes), two- and three-dimensional slots, and random porosity, provided transition onset near the trip location with manifold stagnation pressures on the order of 40 times the model surface static pressure, which is adequate to ensure sonic jets. The present results indicate that the jet penetration height for blowing was roughly half the height required with passive roughness elements for an equivalent amount of transition movement.

Large Eddy Simulations of a Bottom Boundary Layer Under a Shallow Geostrophic Front

NASA Astrophysics Data System (ADS)

Bateman, S. P.; Simeonov, J.; Calantoni, J.

2017-12-01

The unstratified surf zone and the stratified shelf waters are often separated by dynamic fronts that can strongly impact the character of the Ekman bottom boundary layer. Here, we use large eddy simulations to study the turbulent bottom boundary layer associated with a geostrophic current on a stratified shelf of uniform depth. The simulations are initialized with a spatially uniform vertical shear that is in geostrophic balance with a pressure gradient due to a linear horizontal temperature variation. Superposed on the temperature front is a stable vertical temperature gradient. As turbulence develops near the bottom, the turbulence-induced mixing gradually erodes the initial uniform temperature stratification and a well-mixed layer grows in height until the turbulence becomes fully developed. The simulations provide the spatial distribution of the turbulent dissipation and the Reynolds stresses in the fully developed boundary layer. We vary the initial linear stratification and investigate its effect on the height of the bottom boundary layer and the turbulence statistics. The results are compared to previous models and simulations of stratified bottom Ekman layers.

Dual polarization micropulse lidar observations of the diurnal evolution of atmospheric boundary layer over a tropical coastal station

NASA Astrophysics Data System (ADS)

Rajeev, K.; Mishra, Manoj K.; Sunilkumar, S. V.; Sijikumar, S.

2016-05-01

High-resolution dual polarized micropulse lidar (MPL) observations have been used to investigate the diurnal evolution of atmospheric boundary layer (ABL) during winter (2008-2011) over Thiruvananthapuram (8.5°N, 77°E), a tropical coastal station located at southwest Peninsular India, adjoining the Arabian Sea. The lidar observations are compared with the boundary layer characteristics derived from concurrent balloon-borne radiosonde observations. This study shows that the mixed layer height over this coastal station generally increases from <300 m in the morning to 1500 m by the afternoon. Growth rate of the mixed layer height is rapid ( 350 m/hr) during 09-11 IST and slows down with time to <150 m/hr during 11-14 IST and <90 m/hr during 14-16 IST. Thermal internal boundary layer during the afternoon, caused by sea breeze circulation, extends up to 500 m altitude and is characterized by highly spherical aerosols, while a distinctly non-spherical aerosol layer appear above this altitude, in the return flow arising from the landmass.

Modeling the effect of dune sorting on the river long profile

NASA Astrophysics Data System (ADS)

Blom, A.

2012-12-01

River dunes, which occur in low slope sand bed and sand-gravel bed rivers, generally show a downward coarsening pattern due to grain flows down their avalanche lee faces. These grain flows cause coarse particles to preferentially deposit at lower elevations of the lee face, while fines show a preference for its upper elevations. Before considering the effect of this dune sorting mechanism on the river long profile, let us first have a look at some general trends along the river profile. Tributaries increasing the river's water discharge in streamwise direction also cause a streamwise increase in flow depth. As under subcritical conditions mean dune height generally increases with increasing flow depth, the dune height shows a streamwise increase, as well. This means that also the standard deviation of bedform height increases in streamwise direction, as in earlier work it was found that the standard deviation of bedform height linearly increases with an increasing mean value of bedform height. As a result of this streamwise increase in standard deviation of dune height, the above-mentioned dune sorting then results in a loss of coarse particles to the lower elevations of the bed that are less and even rarely exposed to the flow. This loss of coarse particles to lower elevations thus increases the rate of fining in streamwise direction. As finer material is more easily transported downstream than coarser material, a smaller bed slope is required to transport the same amount of sediment downstream. This means that dune sorting adds to river profile concavity, compared to the combined effect of abrasion, selective transport and tributaries. A Hirano-type mass conservation model is presented that deals with dune sorting. The model includes two active layers: a bedform layer representing the sediment in the bedforms and a coarse layer representing the coarse and less mobile sediment underneath migrating bedforms. The exposure of the coarse layer is governed by the rate of sediment supply from upstream. By definition the sum of the exposure of both layers equals unity. The model accounts for vertical sediment fluxes due to grain flows down the bedform lee face and the formation of a less mobile coarse layer. The model with its vertical sediment fluxes is validated against earlier flume experiments. It deals well with the transition between a plane bed and a bedform-dominated bed. Applying the model to field scale confirms that dune sorting increases river profile concavity.

Air Modeling - Observational Meteorological Data

EPA Pesticide Factsheets

Observed meteorological data for use in air quality modeling consist of physical parameters that are measured directly by instrumentation, and include temperature, dew point, wind direction, wind speed, cloud cover, cloud layer(s), ceiling height,

Thin layer drying of cassava starch using continuous vibrated fluidized bed dryer

NASA Astrophysics Data System (ADS)

Suherman, Trisnaningtyas, Rona

2015-12-01

This paper present the experimental work and thin layer modelling of cassava starch drying in continuous vibrated fluidized bed dryer. The experimental data was used to validate nine thin layer models of drying curve. Cassava starch with 0.21 initial moisture content was dried in different air drying temperature (50°C, 55°C, 60°C, 65°C, 70°C), different weir height in bed (0 and 1 cm), and different solid feed flow (10 and 30 gr.minute-1). The result showed air dryer temperature has a significant effect on drying curve, while the weir height and solid flow rate are slightly. Based on value of R2, χ2, and RMSE, Page Model is the most accurate simulation for thin layer drying model of cassava starch.

Turbulent Flow Over Large Roughness Elements: Effect of Frontal and Plan Solidity on Turbulence Statistics and Structure

NASA Astrophysics Data System (ADS)

Placidi, M.; Ganapathisubramani, B.

2018-04-01

Wind-tunnel experiments were carried out on fully-rough boundary layers with large roughness (δ /h ≈ 10, where h is the height of the roughness elements and δ is the boundary-layer thickness). Twelve different surface conditions were created by using LEGO™ bricks of uniform height. Six cases are tested for a fixed plan solidity (λ _P) with variations in frontal density (λ _F), while the other six cases have varying λ _P for fixed λ _F. Particle image velocimetry and floating-element drag-balance measurements were performed. The current results complement those contained in Placidi and Ganapathisubramani (J Fluid Mech 782:541-566, 2015), extending the previous analysis to the turbulence statistics and spatial structure. Results indicate that mean velocity profiles in defect form agree with Townsend's similarity hypothesis with varying λ _F, however, the agreement is worse for cases with varying λ _P. The streamwise and wall-normal turbulent stresses, as well as the Reynolds shear stresses, show a lack of similarity across most examined cases. This suggests that the critical height of the roughness for which outer-layer similarity holds depends not only on the height of the roughness, but also on the local wall morphology. A new criterion based on shelter solidity, defined as the sheltered plan area per unit wall-parallel area, which is similar to the `effective shelter area' in Raupach and Shaw (Boundary-Layer Meteorol 22:79-90, 1982), is found to capture the departure of the turbulence statistics from outer-layer similarity. Despite this lack of similarity reported in the turbulence statistics, proper orthogonal decomposition analysis, as well as two-point spatial correlations, show that some form of universal flow structure is present, as all cases exhibit virtually identical proper orthogonal decomposition mode shapes and correlation fields. Finally, reduced models based on proper orthogonal decomposition reveal that the small scales of the turbulence play a significant role in assessing outer-layer similarity.

An Examination of the Effect of Boundary Layer Ingestion on Turboelectric Distributed Propulsion Systems

NASA Technical Reports Server (NTRS)

Felder, James L.; Kim, Huyn Dae; Brown, Gerald V.; Chu, Julio

2011-01-01

A Turboelectric Distributed Propulsion (TeDP) system differs from other propulsion systems by the use of electrical power to transmit power from the turbine to the fan. Electrical power can be efficiently transmitted over longer distances and with complex topologies. Also the use of power inverters allows the generator and motors speeds to be independent of one another. This decoupling allows the aircraft designer to place the core engines and the fans in locations most advantageous for each. The result can be very different installation environments for the different devices. Thus the installation effects on this system can be quite different than conventional turbofans where the fan and core both see the same installed environments. This paper examines a propulsion system consisting of two superconducting generators, each driven by a turboshaft engine located so that their inlets ingest freestream air, superconducting electrical transmission lines, and an array of superconducting motor driven fan positioned across the upper/rear fuselage area of a hybrid wing body aircraft in a continuous nacelle that ingests all of the upper fuselage boundary layer. The effect of ingesting the boundary layer on the design of the system with a range of design pressure ratios is examined. Also the impact of ingesting the boundary layer on off-design performance is examined. The results show that when examining different design fan pressure ratios it is important to recalculate of the boundary layer mass-average Pt and MN up the height for each inlet height during convergence of the design point for each fan design pressure ratio examined. Correct estimation of off-design performance is dependent on the height of the column of air measured from the aircraft surface immediately prior to any external diffusion that will flow through the fan propulsors. The mass-averaged Pt and MN calculated for this column of air determine the Pt and MN seen by the propulsor inlet. Since the height of this column will change as the amount of air passing through the fans change as the propulsion system is throttled, and since the mass-average Pt and MN varies by height, this capture height must be recalculated as the airflow through the propulsor is varied as the off-design performance point is converged.

Application of Lidar remote sensing to the estimation of forest canopy and stand structure

NASA Astrophysics Data System (ADS)

Lefsky, Michael Andrew

A new remote sensing instrument, SLICER (Scanning Lidar Imager of Canopies by Echo Recovery), has been applied to the problem of remote sensing the canopy and stand structure of two groups of deciduous forests, Tulip Poplar-Oak stands in the vicinity of Annapolis, MD. and bottomland hardwood stands near Williamston, NC. The ability of the SLICER instrument to remotely sense the vertical distribution of canopy structure (Canopy Height Profile), bulk canopy transmittance, and several indices of canopy height has been successfully validated using twelve stands with coincident field and SLICER estimates of canopy structure. Principal components analysis has been applied to canopy height profiles from both field sites, and three significant factors were identified, each closely related to the amount of foliage in a recognizable layer of the forest, either understory, midstory, or overstory. The distribution of canopy structure to these layers is significantly correlated with the size and number of stems supporting them. The same layered structure was shown to apply to both field and SLICER remotely sensed canopy height profiles, and to apply to SLICER remotely sensed canopy profiles from both the bottomland hardwood stands in the coastal plain of North Carolina, and to mesic Tulip-Poplars stands in the upland coastal plain of Maryland. Linear regressions have demonstrated that canopy and stand structure are correlated to both a statistically significant and useful degree. Stand age and stem density is more highly correlated to stand height, while stand basal area and aboveground biomass are more closely related to a new measure of canopy structure, the quadratic mean canopy height. A geometric model of canopy structure has been shown to explain the differing relationships between canopy structure and stand basal area for stands of Eastern Deciduous Forest and Douglas Fir Forest.

Convective boundary layer heights over mountainous terrain - A review of concepts -

NASA Astrophysics Data System (ADS)

De Wekker, Stephan; Kossmann, Meinolf

2015-12-01

Mountainous terrain exerts an important influence on the Earth's atmosphere and affects atmospheric transport and mixing at a wide range of temporal and spatial scales. The vertical scale of this transport and mixing is determined by the height of the atmospheric boundary layer, which is therefore an important parameter in air pollution studies, weather forecasting, climate modeling, and many other applications. It is recognized that the spatio-temporal structure of the daytime convective boundary layer (CBL) height is strongly modified and more complex in hilly and mountainous terrain compared to flat terrain. While the CBL over flat terrain is mostly dominated by turbulent convection, advection from multi-scale thermally driven flows plays an important role for the CBL evolution over mountainous terrain. However, detailed observations of the CBL structure and understanding of the underlying processes are still limited. Characteristics of CBL heights in mountainous terrain are reviewed for dry, convective conditions. CBLs in valleys and basins, where hazardous accumulation of pollutants is of particular concern, are relatively well-understood compared to CBLs over slopes, ridges, or mountain peaks. Interests in the initiation of shallow and deep convection, and of budgets and long-range transport of air pollutants and trace gases, have triggered some recent studies on terrain induced exchange processes between the CBL and the overlying atmosphere. These studies have helped to gain more insight into CBL structure over complex mountainous terrain, but also show that the universal definition of CBL height over mountains remains an unresolved issue. The review summarizes the progress that has been made in documenting and understanding spatio-temporal behavior of CBL heights in mountainous terrain and concludes with a discussion of open research questions and opportunities for future research.

Cloud and boundary layer structure over San Nicolas Island during FIRE

NASA Technical Reports Server (NTRS)

Albrecht, Bruce A.; Fairall, Christopher W.; Syrett, William J.; Schubert, Wayne H.; Snider, Jack B.

1990-01-01

The temporal evolution of the structure of the marine boundary layer and of the associated low-level clouds observed in the vicinity of the San Nicolas Island (SNI) is defined from data collected during the First ISCCP Regional Experiment (FIRE) Marine Stratocumulus Intense Field Observations (IFO) (July 1 to 19). Surface, radiosonde, and remote-sensing measurements are used for this analysis. Sounding from the Island and from the ship Point Sur, which was located approximately 100 km northwest of SNI, are used to define variations in the thermodynamic structure of the lower-troposphere on time scales of 12 hours and longer. Time-height sections of potential temperature and equivalent potential temperature clearly define large-scale variations in the height and the strength of the inversion and periods where the conditions for cloud-top entrainment instability (CTEI) are met. Well defined variations in the height and the strength of the inversion were associated with a Cataline Eddy that was present at various times during the experiment and with the passage of the remnants of a tropical cyclone on July 18. The large-scale variations in the mean thermodynamic structure at SNI correlate well with those observed from the Point Sur. Cloud characteristics are defined for 19 days of the experiment using data from a microwave radiometer, a cloud ceilometer, a sodar, and longwave and shortwave radiometers. The depth of the cloud layer is estimated by defining inversion heights from the sodar reflectivity and cloud-base heights from a laser ceilometer. The integrated liquid water obtained from NOAA's microwave radiometer is compared with the adiabatic liquid water content that is calculated by lifting a parcel adiabatically from cloud base. In addition, the cloud structure is characterized by the variability in cloud-base height and in the integrated liquid water.

Flight-measured pressure characteristics of aft-facing steps in high Reynolds number flow at Mach numbers of 2.20, 2.50, and 2.80 and comparison with other data

NASA Technical Reports Server (NTRS)

Powers, S. G.

1978-01-01

The YF-12 airplane was studied to determine the pressure characteristics associated with an aft-facing step in high Reynolds number flow for nominal Mach numbers of 2.20, 2.50, and 2.80. Base pressure coefficients were obtained for three step heights. The surface static pressures ahead of and behind the step were measured for the no-step condition and for each of the step heights. A boundary layer rake was used to determine the local boundary layer conditions. The Reynolds number based on the length of flow ahead of the step was approximately 10 to the 8th power and the ratios of momentum thickness to step height ranged from 0.2 to 1.0. Base pressure coefficients were compared with other available data at similar Mach numbers and at ratios of momentum thickness to step height near 1.0. In addition, the data were compared with base pressure coefficients calculated by a semiempirical prediction method. The base pressure ratios are shown to be a function of Reynolds number based on momentum thickness. Profiles of the surface pressures ahead of and behind the step and the local boundary layer conditions are also presented.

Observations of stratospheric aerosols associated with the El Chichon eruption

NASA Technical Reports Server (NTRS)

Thomas, L.; Vaughan, G.; Jenkins, D. B.; Wareing, D.; Farrington, M.

1986-01-01

Lidar observations of aerosols were carried out at Aberystwyth between Nov. 1982 and Dec. 1985 using a frequency doubled and frequency tripled Nd/Yag laser and a receiver incorporating a 1 m diameter in a Newtonian telescope configuration. In analyses of the experimental data attention is paid to the magnitude of the coefficient relating extinction and backscatter, the choice being related to the possible presence of aerosols in the upper troposphere and the atmospheric densities employed in the normalisation procedure. The aerosol loading showed marked day to day changes in early months and an overall decay was apparent only after April 1983, this decay being consistent with an e sup -1 time of about 7 months. The general decay was accompanied by a lowering of the layer but layers of aerosols were shown intermittently at heights above the main layer in winter months. The height variations of photon counts corrected for range, or of aerosol backscatter ratio, showed clear signatures of the tropopause. A strong correlation was found between the heights of the tropopause identified from the lidar measurements and from radiosonde-borne temperature measurements. A notable feature of the observations is the appearance of very sharp height gradients of backscatter ratio which seem to be produced by differential advection.

Comparison between a disposable and an electronic PCA device for labor epidural analgesia.

PubMed

Sumikura, Hiroyuki; van de Velde, Marc; Tateda, Takeshi

2004-01-01

The aims of the present study were (1) to investigate if a disposable patient-controlled analgesia (PCA) device can be used for labor analgesia and (2) to evaluate the device by midwives and parturients. Forty healthy parturients were divided into two groups and received combined spinal epidural analgesia for labor pain relief. Following intrathecal administration of 3 mg ropivacaine and 1.5 microg sufentanil, either a disposable PCA device (Coopdech Syrinjector; Daiken Medical, Osaka, Japan) or an electronic PCA device (IVAC PCAM PCA Syringe Pump; Alaris, Basingstoke, UK) was connected to the epidural catheter, and 0.15% ropivacaine with sufentanil 0.75 microg/ml was used for continuous infusion and PCA. For an electronic PCA device, continuous infusion rate, bolus dose, lockout time, and hourly limit were set at 4 ml/h, 3 ml, 15 min, and 16 ml, respectively. For a disposable PCA device, continuous infusion rate, bolus dose, and an hourly limit were set at 4 ml/h, 3 ml, and 16 ml, respectively, but lockout function was not available. No differences were observed between the groups concerning demographic data, obstetric data, and outcome of labor. Anesthetic requirements (disposable, 9.7 +/- 4.7 ml/h; electronic, 8.2 +/- 4.0 ml/h) and VAS score during the delivery (disposable, 26 +/- 25; electronic, 21 +/- 22) were similar between the groups. Midwives praised the disposable PCA device as well as the electronic one. The present results imply that the disposable PCA device can be an alternative to the electronic PCA device for labor analgesia.

Warthin tumors do not have microsatellite instability and express normal DNA mismatch repair proteins.

PubMed

Hunt, Jennifer L

2006-01-01

Warthin tumors are controversial entities with a poorly understood etiology. Although some investigators have suggested a neoplastic origin, others have supported a developmental anomaly. A recent study described the absence of staining for hMLH1 and hMSH2 proteins in the epithelial component of Warthin tumors, suggesting that they arise secondary to defects in the DNA mismatch repair system. To determine if Warthin tumors exhibit evidence of DNA mismatch repair defects. Immunostains for hMLH1 and hMSH2 were performed using a standard approach. Microdissection of the epithelial component was followed by DNA extraction from the tissue fragments. Polymerase chain reaction and capillary electrophoresis analyses were performed for the following 5 National Cancer Institute-recommended microsatellites: D2s123, D5s346, D17s250, BAT25, and BAT26. Twelve patients with Warthin tumors were included. The immunostains for hMLH1 and hMSH2 showed preserved expression in the nuclei of the epithelial component of all Warthin tumors. No microsatellite instability was detected, and no loss of heterozygosity was seen. These results are not concordant with previously reported results showing loss of expression of the hMLH1 and hMSH2 DNA mismatch repair enzymes in the epithelial component of Warthin tumors. Furthermore, no microsatellite instability was detected in the 5 loci tested for each tumor in this series. These data demonstrate that Warthin tumors do not have evidence of DNA mismatch repair defects at the genomic or protein expression level.

Outcome and status of microsatellite stability in Japanese atomic bomb survivors with early gastric carcinoma.

PubMed

Yamamoto, Manabu; Taguchi, Kenichi; Yamanaka, Takeharu; Matsuyama, Ayumi; Yoshinaga, Keiji; Tsutsui, Shinichi; Ishida, Teruyoshi

2013-03-01

In the decade after the 1945 atomic bombing of Hiroshima, a high incidence of leukemia was observed among atomic bomb survivors. However, the incidence of other cancers gradually increased, while that of leukemia decreased after this period. We evaluated the clinical outcome of early gastric cancer and microsatellite stability over a long-term period in atomic bomb survivors. The results of surgical treatment for early gastric cancer were reviewed for 117 atomic bomb survivors and 394 control patients between 1995 and 2006. In addition, immunohistochemical staining for hMSH2 and hMLH1 expression was performed to evaluate the status of microsatellite stability in 57 atomic bomb survivors and 82 control patients. The long-term survival rate for early gastric cancer in atomic bomb survivors was significantly lower than that in control patients (p < 0.01). Multivariable analysis revealed that age and sex were significant and independent prognostic factors for early gastric cancer. Defective hMSH2 and/or hMLH1 expression was also significantly higher in survivors than in control patients (p < 0.001). Logistic regression analysis revealed that atomic bomb survivorship was related to defective hMSH2 and/or hMLH1 expression. The prognosis of early gastric cancer in atomic bomb survivors was poor and was related to age and sex, rather than to being an atomic bomb survivor. Furthermore, a higher rate of defective hMSH2 and/or hMLH1 expression was observed in the survivors.

Estimating the planetary boundary layer height from radiosonde and doppler lidar measurements in the city of São Paulo - Brazil

NASA Astrophysics Data System (ADS)

Marques, Márcia T. A.; Moreira, Gregori de A.; Pinero, Maciel; Oliveira, Amauri P.; Landulfo, Eduardo

2018-04-01

This study aims to compare the planetary boundary layer height (PBLH) values estimated by radiosonde data through the bulk Richardson number (BRN) method and by Doppler lidar measurements through the Carrier to Noise Ratio (CNR) method, which corresponds to the maximum of the variance of CNR profile. The measurement campaign was carried during the summer of 2015/2016 in the city of São Paulo. Despite the conceptual difference between these methods, the results show great agreement between them.

Improvements to the OMI Near-uv Aerosol Algorithm Using A-train CALIOP and AIRS Observations

NASA Technical Reports Server (NTRS)

Torres, O.; Ahn, C.; Zhong, C.

2014-01-01

The height of desert dust and carbonaceous aerosols layers and, to a lesser extent, the difficulty in assessing the predominant size mode of these absorbing aerosol types, are sources of uncertainty in the retrieval of aerosol properties from near UV satellite observations. The availability of independent, near-simultaneous measurements of aerosol layer height, and aerosol-type related parameters derived from observations by other A-train sensors, makes possible the direct use of these parameters as input to the OMI (Ozone Monitoring Instrument) near UV retrieval algorithm. A monthly climatology of aerosol layer height derived from observations by the CALIOP (Cloud-Aerosol Lidar with Orthogonal Polarization) sensor, and real-time AIRS (Atmospheric Infrared Sounder) CO observations are used in an upgraded version of the OMI near UV aerosol algorithm. AIRS CO measurements are used as a reliable tracer of carbonaceous aerosols, which allows the identification of smoke layers in areas and times of the year where the dust-smoke differentiation is difficult in the near-UV. The use of CO measurements also enables the identification of elevated levels of boundary layer pollution undetectable by near UV observations alone. In this paper we discuss the combined use of OMI, CALIOP and AIRS observations for the characterization of aerosol properties, and show a significant improvement in OMI aerosol retrieval capabilities.

Inventory of File nam.t00z.smartpr00.tm00.grib2

Science.gov Websites

layer WDIR analysis Wind Direction (from which blowing) [degtrue] 016 planetary boundary layer WIND analysis Wind Speed [m/s] 017 planetary boundary layer RH analysis Relative Humidity [%] 018 planetary boundary layer DIST analysis Geometric Height [m] 019 surface 4LFTX analysis Best (4 layer) Lifted Index [K

Inventory of File nam.t00z.smartak00.tm00.grib2

Science.gov Websites

layer WDIR analysis Wind Direction (from which blowing) [degtrue] 016 planetary boundary layer WIND analysis Wind Speed [m/s] 017 planetary boundary layer RH analysis Relative Humidity [%] 018 planetary boundary layer DIST analysis Geometric Height [m] 019 surface 4LFTX analysis Best (4 layer) Lifted Index [K

Inventory of File gfs.t06z.smartguam00.tm00.grib2

Science.gov Websites

boundary layer WDIR analysis Wind Direction (from which blowing) [degtrue] 013 planetary boundary layer WIND analysis Wind Speed [m/s] 014 planetary boundary layer RH analysis Relative Humidity [%] 015 planetary boundary layer DIST analysis Geometric Height [m] 016 surface 4LFTX analysis Best (4 layer) Lifted

Inventory of File nam.t00z.smarthi00.tm00.grib2

Science.gov Websites

layer WDIR analysis Wind Direction (from which blowing) [degtrue] 016 planetary boundary layer WIND analysis Wind Speed [m/s] 017 planetary boundary layer RH analysis Relative Humidity [%] 018 planetary boundary layer DIST analysis Geometric Height [m] 019 surface 4LFTX analysis Best (4 layer) Lifted Index [K

Airborne Lidar measurements of aerosols, mixed layer heights, and ozone during the 1980 PEPE/NEROS summer field experiment

NASA Technical Reports Server (NTRS)

Browell, E. V.; Shipley, S. T.; Butler, C. F.; Ismail, S.

1985-01-01

A detailed summary of the NASA Ultraviolet Differential Absorption Lidar (UV DIAL) data archive obtained during the EPA Persistent Elevated Pollution Episode/Northeast Regional Oxidant Study (PEPE/NEROS) Summer Field Experiment Program (July through August 1980) is presented. The UV dial data set consists of remote measurements of mixed layer heights, aerosol backscatter cross sections, and sequential ozone profiles taken during 14 long-range flights onboard the NASA Wallops Flight Center Electra aircraft. These data are presented in graphic and tabular form, and they have been submitted to the PEPE/NEROS data archive on digital magnetic tape. The derivation of mixing heights and ozone profiles from UV Dial signals is discussed, and detailed intercomparisons with measurements obtained by in situ sensors are presented.

Pairing and recombination features during meiosis in Cebus paraguayanus (Primates: Platyrrhini)

PubMed Central

Garcia-Cruz, Raquel; Robles, Pedro; Steinberg, Eliana R; Camats, Nuria; Brieño, Miguel A; Garcia-Caldés, Montserrat; Mudry, Marta D

2009-01-01

Background Among neotropical Primates, the Cai monkey Cebus paraguayanus (CPA) presents long, conserved chromosome syntenies with the human karyotype (HSA) as well as numerous C+ blocks in different chromosome pairs. In this study, immunofluorescence (IF) against two proteins of the Synaptonemal Complex (SC), namely REC8 and SYCP1, two recombination protein markers (RPA and MLH1), and one protein involved in the pachytene checkpoint machinery (BRCA1) was performed in CPA spermatocytes in order to analyze chromosome meiotic behavior in detail. Results Although in the vast majority of pachytene cells all autosomes were paired and synapsed, in a small number of nuclei the heterochromatic C-positive terminal region of bivalent 11 remained unpaired. The analysis of 75 CPA cells at pachytene revealed a mean of 43.22 MLH1 foci per nucleus and 1.07 MLH1 foci in each CPA bivalent 11, always positioned in the region homologous to HSA chromosome 21. Conclusion Our results suggest that C blocks undergo delayed pairing and synapsis, although they do not interfere with the general progress of pairing and synapsis. PMID:19500368

The Vertical Error Characteristics of GOES-derived Winds: Description and Impact on Numerical Weather Prediction

NASA Technical Reports Server (NTRS)

Rao, P. Anil; Velden, Christopher S.; Braun, Scott A.; Einaudi, Franco (Technical Monitor)

2001-01-01

Errors in the height assignment of some satellite-derived winds exist because the satellites sense radiation emitted from a finite layer of the atmosphere rather than a specific level. Potential problems in data assimilation may arise because the motion of a measured layer is often represented by a single-level value. In this research, cloud and water vapor motion winds that are derived from the Geostationary Operational Environmental Satellites (GOES winds) are compared to collocated rawinsonde observations (RAOBs). An important aspect of this work is that in addition to comparisons at each assigned height, the GOES winds are compared to the entire profile of the collocated RAOB data to determine the vertical error characteristics of the GOES winds. The impact of these results on numerical weather prediction is then investigated. The comparisons at individual vector height assignments indicate that the error of the GOES winds range from approx. 3 to 10 m/s and generally increase with height. However, if taken as a percentage of the total wind speed, accuracy is better at upper levels. As expected, comparisons with the entire profile of the collocated RAOBs indicate that clear-air water vapor winds represent deeper layers than do either infrared or water vapor cloud-tracked winds. This is because in cloud-free regions the signal from water vapor features may result from emittance over a thicker layer. To further investigate characteristics of the clear-air water vapor winds, they are stratified into two categories that are dependent on the depth of the layer represented by the vector. It is found that if the vertical gradient of moisture is smooth and uniform from near the height assignment upwards, the clear-air water vapor wind tends to represent a relatively deep layer. The information from the comparisons is then used in numerical model simulations of two separate events to determine the forecast impacts. Four simulations are performed for each case: 1) A control simulation that assimilates no satellite wind data, 2) assimilation of all GOES winds according to their assigned single level height, 3) assimilation of all GOES winds spread over multiple levels, and 4) assimilation of all GOES winds spread over multiple levels, but with variations in the vertical influence of clear-air water vapor winds based on the moisture profile in the model. In the first case, a strong mid-latitude cyclone is present and the use of the satellite data results in improved storm tracks during the initial approx. 36 h forecast period. This is because the satellite data improves the analysis of the environment into which the storm progresses. Statistics for mean wind vector and height differences show that, with the exception of the height field at later times in the first case, the use of GOES winds improves the simulation with time. The simulation results suggest that it is beneficial to spread the GOES wind information over multiple levels, particularly when the moisture profile is used to define the vertical influence.

A unified view of convective transports by stratocumulus clouds, shallow cumulus clouds, and deep convection

NASA Technical Reports Server (NTRS)

Randall, David A.

1990-01-01

A bulk planetary boundary layer (PBL) model was developed with a simple internal vertical structure and a simple second-order closure, designed for use as a PBL parameterization in a large-scale model. The model allows the mean fields to vary with height within the PBL, and so must address the vertical profiles of the turbulent fluxes, going beyond the usual mixed-layer assumption that the fluxes of conservative variables are linear with height. This is accomplished using the same convective mass flux approach that has also been used in cumulus parameterizations. The purpose is to show that such a mass flux model can include, in a single framework, the compensating subsidence concept, downgradient mixing, and well-mixed layers.

Lidar observations of vertically organized convection in the planetary boundary layer over the ocean

NASA Technical Reports Server (NTRS)

Melfi, S. H.; Spinhirne, J. D.; Chou, S.-H.; Palm, S. P.

1985-01-01

Observations of a convective planetary boundary layer (PBL) were made with an airborne, downward-looking lidar system over the Atlantic Ocean during a cold air outbreak. The lidar data revealed well-organized, regularly spaced cellular convection with dominant spacial scales between two and four times the height of the boundary layer. It is demonstrated that the lidar can accurately measure the structure of the PBL with high vertical and horizontal resolution. Parameters important for PBL modeling such as entrainment zone thickness, entrainment rate, PBL height and relative heat flux can be inferred from the lidar data. It is suggested that wind shear at the PBL top may influence both entrainment and convective cell size.

Direct numerical simulation of a compressible boundary-layer flow past an isolated three-dimensional hump in a high-speed subsonic regime

NASA Astrophysics Data System (ADS)

De Grazia, D.; Moxey, D.; Sherwin, S. J.; Kravtsova, M. A.; Ruban, A. I.

2018-02-01

In this paper we study the boundary-layer separation produced in a high-speed subsonic boundary layer by a small wall roughness. Specifically, we present a direct numerical simulation (DNS) of a two-dimensional boundary-layer flow over a flat plate encountering a three-dimensional Gaussian-shaped hump. This work was motivated by the lack of DNS data of boundary-layer flows past roughness elements in a similar regime which is typical of civil aviation. The Mach and Reynolds numbers are chosen to be relevant for aeronautical applications when considering small imperfections at the leading edge of wings. We analyze different heights of the hump: The smaller heights result in a weakly nonlinear regime, while the larger result in a fully nonlinear regime with an increasing laminar separation bubble arising downstream of the roughness element and the formation of a pair of streamwise counterrotating vortices which appear to support themselves.

High Reynolds number rough wall turbulent boundary layer experiments using Braille surfaces

NASA Astrophysics Data System (ADS)

Harris, Michael; Monty, Jason; Nova, Todd; Allen, James; Chong, Min

2007-11-01

This paper details smooth, transitional and fully rough turbulent boundary layer experiments in the New Mexico State high Reynolds number rough wall wind tunnel. The initial surface tested was generated with a Braille printer and consisted of an uniform array of Braille points. The average point height being 0.5mm, the spacing between the points in the span was 0.5mm and the surface consisted of span wise rows separated by 4mm. The wavelength to peak ratio was 8:1. The boundary layer thickness at the measurement location was 190mm giving a large separation of roughness height to layer thickness. The maximum friction velocity was uτ=1.5m/s at Rex=3.8 x10^7. Results for the skin friction co-efficient show that this surface follows a Nikuradse type inflectional curve and that Townsends outer layer similarity hypothesis is valid for rough wall flows with a large separation of scales. Mean flow and turbulence statistics will be presented.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, B.; Lu, S. X.; Li, C. H.

In an atrium measured 120 m by 180 m by 36.5 m high, fire tests were conducted under 'natural filling' and 'mechanical exhaust' conditions by hot smoke test method. The fire size was 8 MW released by an ethanol pool of 3.6 m in diameter. The distribution of vertical temperature profiles above the fire source and the gas layer temperatures were measured. From these measurements, it was shown that the fans successfully exhausted hot smoke to control descending of hot smoke layer and temperature rising rate. The hot smoke layer can be maintained at about 30 m which was almostmore » 2 times of hot layer height in 'natural filling' condition. The temperature risings in both conditions were too low to cause thermal damage to the structure, only 18.6 K and 12 K. The centerline temperature above the fire source and the height of hot smoke layer were calculated using the plume models. The calculated results agreed well with the conclusions obtained from the experiment results.« less

Airborne LIDAR Measurements of Aerosol and Ozone Above the Alberta Oil Sands Region

NASA Astrophysics Data System (ADS)

Aggarwal, M.; Whiteway, J. A.; Seabrook, J.; Gray, L. H.

2014-12-01

Lidar measurements of ozone and aerosol were conducted from a Twin Otter aircraft above the oil sands region of northern Alberta. The field campaign was carried out with a total of five flights out of Fort McMurray, Alberta during the period between August 22 and August 26, 2013. Significant amounts of aerosol were observed within the boundary layer, up to a height of 1.6 km, but the ozone concentration remained at or below background levels. On August 24th the lidar observed a separated layer of aerosol above the boundary layer, at a height of 1.8 km, in which the ozone mixing ratio increased to 70 ppbv. Backward trajectory calculations revealed that the air containing this separated aerosol layer had passed over an area of forest fires. Directly below the layer of forest fire smoke, in the pollution from the oil sands industry, the measured ozone mixing ratio was lower than the background levels (≤35 ppbv).

Comparison between reflectivity statistics at heights of 3 and 6 km and rain rate statistics at ground level

NASA Technical Reports Server (NTRS)

Crane, R. K.

1975-01-01

An experiment was conducted to study the relations between the empirical distribution functions of reflectivity at specified locations above the surface and the corresponding functions at the surface. A bistatic radar system was used to measure continuously the scattering cross section per unit volume at heights of 3 and 6 km. A frequency of 3.7 GHz was used in the tests. It was found that the distribution functions for reflectivity may significantly change with height at heights below the level of the melting layer.

Microsatellites in the Eukaryotic DNA Mismatch Repair Genes as Modulators of Evolutionary Mutation Rate

NASA Technical Reports Server (NTRS)

Chang, Dong Kyung; Metzgar, David; Wills, Christopher; Boland, C. Richard

2003-01-01

All "minor" components of the human DNA mismatch repair (MMR) system-MSH3, MSH6, PMS2, and the recently discovered MLH3-contain mononucleotide microsatellites in their coding sequences. This intriguing finding contrasts with the situation found in the major components of the DNA MMR system-MSH2 and MLH1-and, in fact, most human genes. Although eukaryotic genomes are rich in microsatellites, non-triplet microsatellites are rare in coding regions. The recurring presence of exonal mononucleotide repeat sequences within a single family of human genes would therefore be considered exceptional.

Novel lidar algorithms for atmospheric slantrange visibility, planetary boundary layer height, meteorogical phenomena and atmospheric layering measurements

NASA Astrophysics Data System (ADS)

Pantazis, Alexandros; Papayannis, Alexandros; Georgoussis, Georgios

2018-04-01

In this paper we present a development of novel algorithms and techniques implemented within the Laser Remote Sensing Laboratory (LRSL) of the National Technical University of Athens (NTUA), in collaboration with Raymetrics S.A., in order to incorporate them into a 3-Dimensional (3D) lidar. The lidar is transmitting at 355 nm in the eye safe region and the measurements then are transposed to the visual range at 550 nm, according to the World Meteorological Organization (WMO) and the International Civil Aviation Organization (ICAO) rules of daytime visibility. These algorithms are able to provide horizontal, slant and vertical visibility for tower aircraft controllers, meteorologists, but also from pilot's point of view. Other algorithms are also provided for detection of atmospheric layering in any given direction and vertical angle, along with the detection of the Planetary Boundary Layer Height (PBLH).

Black Walnut Growth Better on Deep, Well-Drained BottomLand Soils

Treesearch

Craig K. Losche

1973-01-01

Site requirements of 25-year-old plantation-grown black walnut on floodplains in southern Illinois were studied. Depth to a gravel layer was the only soil factor that significantly influenced height growth. There was a relationship between internal soil drainage and height growth.

Characteristics of haze and the atmospheric boundary layer height during the periods with different category of haze over Suzhou observed by Micro-Pulse Lidar

NASA Astrophysics Data System (ADS)

Huijuan, L.

2015-12-01

Based on the observed hourly meterological data, atmospheric composition data, and the Micro-Pulse Lidar (MPL) detecting data over Suzhou during 2010 to 2014, this study concentrates on revealing the characteristics of haze weather and the atmospheric boundary layer height during the periods with different category of haze over Suzhou. The main results are shown as follows: The haze frequency over Suzhou is 30.9% with the frequency of 18% for the slight haze, 7.8% for the light haze, 3.1% for the moderate haze and 2.0% for the heavy haze. The haze frequency shows an obvious diurnal variation with a peak (valley) value at the local solar time around 08:00~09:00 am (14:00~16:00pm).The haze happens much more frequent in nighttime than in daytime. The atmospheric boundary layer height (ABLH) associated with haze also shows a clear diurnal variation. The mean ABLH over Suzhou during the period of haze is more (less) than 1000m (500m) in daytime (nighttime). Meanwhile, the ABLH during the period of haze is higher in summer than in winter. In addition, the mean ABLH during the period without (with) haze is around 700m (500m) in winter. The diurnal variation of the ABLH during the period of moderate to heavy haze in winter ranges from 350m to 500m, which is less than the winter mean ABLH by 50~150m. KEY WORDS: Micro-Pulse Lidar; haze frequency; moderate and heavy haze；atmospheric boundary layer height

Sensitivity of Turbine-Height Wind Speeds to Parameters in Planetary Boundary-Layer and Surface-Layer Schemes in the Weather Research and Forecasting Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Ben; Qian, Yun; Berg, Larry K.

We evaluate the sensitivity of simulated turbine-height winds to 26 parameters applied in a planetary boundary layer (PBL) scheme and a surface layer scheme of the Weather Research and Forecasting (WRF) model over an area of complex terrain during the Columbia Basin Wind Energy Study. An efficient sampling algorithm and a generalized linear model are used to explore the multiple-dimensional parameter space and quantify the parametric sensitivity of modeled turbine-height winds. The results indicate that most of the variability in the ensemble simulations is contributed by parameters related to the dissipation of the turbulence kinetic energy (TKE), Prandtl number, turbulencemore » length scales, surface roughness, and the von Kármán constant. The relative contributions of individual parameters are found to be dependent on both the terrain slope and atmospheric stability. The parameter associated with the TKE dissipation rate is found to be the most important one, and a larger dissipation rate can produce larger hub-height winds. A larger Prandtl number results in weaker nighttime winds. Increasing surface roughness reduces the frequencies of both extremely weak and strong winds, implying a reduction in the variability of the wind speed. All of the above parameters can significantly affect the vertical profiles of wind speed, the altitude of the low-level jet and the magnitude of the wind shear strength. The wind direction is found to be modulated by the same subset of influential parameters. Remainder of abstract is in attachment.« less

Evaluation of retrieval methods of daytime convective boundary layer height based on lidar data

NASA Astrophysics Data System (ADS)

Li, Hong; Yang, Yi; Hu, Xiao-Ming; Huang, Zhongwei; Wang, Guoyin; Zhang, Beidou; Zhang, Tiejun

2017-04-01

The atmospheric boundary layer height is a basic parameter in describing the structure of the lower atmosphere. Because of their high temporal resolution, ground-based lidar data are widely used to determine the daytime convective boundary layer height (CBLH), but the currently available retrieval methods have their advantages and drawbacks. In this paper, four methods of retrieving the CBLH (i.e., the gradient method, the idealized backscatter method, and two forms of the wavelet covariance transform method) from lidar normalized relative backscatter are evaluated, using two artificial cases (an idealized profile and a case similar to real profile), to test their stability and accuracy. The results show that the gradient method is suitable for high signal-to-noise ratio conditions. The idealized backscatter method is less sensitive to the first estimate of the CBLH; however, it is computationally expensive. The results obtained from the two forms of the wavelet covariance transform method are influenced by the selection of the initial input value of the wavelet amplitude. Further sensitivity analysis using real profiles under different orders of magnitude of background counts show that when different initial input values are set, the idealized backscatter method always obtains consistent CBLH. For two wavelet methods, the different CBLH are always obtained with the increase in the wavelet amplitude when noise is significant. Finally, the CBLHs as measured by three lidar-based methods are evaluated by as measured from L-band soundings. The boundary layer heights from two instruments coincide with ±200 m in most situations.

Fabrication of Crack-Free Barium Titanate Thin Film with High Dielectric Constant Using Sub-Micrometric Scale Layer-by-Layer E-Jet Deposition.

PubMed

Liang, Junsheng; Li, Pengfei; Wang, Dazhi; Fang, Xu; Ding, Jiahong; Wu, Junxiong; Tang, Chang

2016-01-19

Dense and crack-free barium titanate (BaTiO₃, BTO) thin films with a thickness of less than 4 μm were prepared by using sub-micrometric scale, layer-by-layer electrohydrodynamic jet (E-jet) deposition of the suspension ink which is composed of BTO nanopowder and BTO sol. Impacts of the jet height and line-to-line pitch of the deposition on the micro-structure of BTO thin films were investigated. Results show that crack-free BTO thin films can be prepared with 4 mm jet height and 300 μm line-to-line pitch in this work. Dielectric constant of the prepared BTO thin film was recorded as high as 2940 at 1 kHz at room temperature. Meanwhile, low dissipation factor of the BTO thin film of about 8.6% at 1 kHz was also obtained. The layer-by-layer E-jet deposition technique developed in this work has been proved to be a cost-effective, flexible and easy to control approach for the preparation of high-quality solid thin film.

Observations of marine decoupled boundary layer during the ICOS campaign at the GAW Mace Head station, Ireland.

NASA Astrophysics Data System (ADS)

Milroy, Conor; Martucci, Giovanni; O'Dowd, Colin

2010-05-01

The planetary boundary layer (PBL) top height detections have been retrieved by two ceilometers (Vaisala CL31 and Jenoptik CHM15K) and a microwave radiometer (RPG-HATPRO) based at the Mace Head Research station, Ireland, from the 8th to the 28th of June 2009 during the ICOS Mace Head campaign. Characteristic of this region, with warm waters, the marine boundary layer is typically 2-layered with a surface mixed layer (SML) and a decoupled residual or convective layer (DRCL), above which is the free troposphere (Kunz et al. 2002). The PBL data have been analyzed using a newly developed Temporal Height-Tracking (THT) algorithm (Martucci et al., 2010) for automatic detection of the independent SML and DRCL tops. Daily and weekly averages of the PBL data have been performed to smooth out the short term variability and assess the dependence of the PBL depth on different air masses advected over the Mace Head station. Moreover, a qualitative comparison between the ceilometer and radiometer PBL top detected values has been done to assess their consistency.

Wind Tunnel Experiments to Study Chaparral Crown Fires.

PubMed

Cobian-Iñiguez, Jeanette; Aminfar, AmirHessam; Chong, Joey; Burke, Gloria; Zuniga, Albertina; Weise, David R; Princevac, Marko

2017-11-14

The present protocol presents a laboratory technique designed to study chaparral crown fire ignition and spread. Experiments were conducted in a low velocity fire wind tunnel where two distinct layers of fuel were constructed to represent surface and crown fuels in chaparral. Chamise, a common chaparral shrub, comprised the live crown layer. The dead fuel surface layer was constructed with excelsior (shredded wood). We developed a methodology to measure mass loss, temperature, and flame height for both fuel layers. Thermocouples placed in each layer estimated temperature. A video camera captured the visible flame. Post-processing of digital imagery yielded flame characteristics including height and flame tilt. A custom crown mass loss instrument developed in-house measured the evolution of the mass of the crown layer during the burn. Mass loss and temperature trends obtained using the technique matched theory and other empirical studies. In this study, we present detailed experimental procedures and information about the instrumentation used. The representative results for the fuel mass loss rate and temperature filed within the fuel bed are also included and discussed.

Inventory of File nam.t00z.smartconus00.tm00.grib2

Science.gov Websites

(Eta model reduction) [Pa] 014 planetary boundary layer WDIR analysis Wind Direction (from which blowing) [degtrue] 015 planetary boundary layer WIND analysis Wind Speed [m/s] 016 planetary boundary layer RH analysis Relative Humidity [%] 017 planetary boundary layer DIST analysis Geometric Height [m

Vorticity and Vertical Motions Diagnosed from Satellite Deep-Layer Temperatures. Revised

NASA Technical Reports Server (NTRS)

Spencer, Roy W.; Lapenta, William M.; Robertson, Franklin R.

1994-01-01

Spatial fields of satellite-measured deep-layer temperatures are examined in the context of quasigeostrophic theory. It is found that midtropospheric geostrophic vorticity and quasigeostrophic vertical motions can be diagnosed from microwave temperature measurements of only two deep layers. The lower- ( 1000-400 hPa) and upper- (400-50 hPa) layer temperatures are estimated from limb-corrected TIROS-N Microwave Sounding Units (MSU) channel 2 and 3 data, spatial fields of which can be used to estimate the midtropospheric thermal wind and geostrophic vorticity fields. Together with Trenberth's simplification of the quasigeostrophic omega equation, these two quantities can be then used to estimate the geostrophic vorticity advection by the thermal wind, which is related to the quasigeostrophic vertical velocity in the midtroposphere. Critical to the technique is the observation that geostrophic vorticity fields calculated from the channel 3 temperature features are very similar to those calculated from traditional, 'bottom-up' integrated height fields from radiosonde data. This suggests a lack of cyclone-scale height features near the top of the channel 3 weighting function, making the channel 3 cyclone-scale 'thickness' features approximately the same as height features near the bottom of the weighting function. Thus, the MSU data provide observational validation of the LID (level of insignificant dynamics) assumption of Hirshberg and Fritsch.

Core-Sheath Paraffin-Wax-Loaded Nanofibers by Electrospinning for Heat Storage.

PubMed

Lu, Yuan; Xiao, Xiudi; Zhan, Yongjun; Huan, Changmeng; Qi, Shuai; Cheng, Haoliang; Xu, Gang

2018-04-18

Paraffin wax (PW) is widely used for smart thermoregulation materials due to its good thermal performance. However, the leakage and low thermal conductivity of PW hinder its application in the heat storage field. Accordingly, developing effective methods to address these issues is of great importance. In this study, we explored a facile approach to obtain PW-loaded core-sheath structured flexible nanofibers films via coaxial electrospinning technique. The PW as the core layer was successfully encapsulated by the sheath-layer poly(methyl methacrylate). The diameter of the fiber core increased from 395 to 848 nm as the core solution speed rate increased from 0.1 to 0.5 mL/h. In addition, it can be seen that higher core solution speed rate could lead to higher PW encapsulation efficiency according to the transmission electron microscopy results. The core-sheath nanofiber films, moreover, possessed the highest latent heat of 58.25 J/g and solidifying enthalpy of -56.49 J/g. In addition, we found that after 200 thermal cycles, there was little change in latent heat, which demonstrated that it is beneficial for the PW-loaded core-sheath structure to overcome the leakage issue and enhance thermal stability properties for the thermoregulation film.

Investigating the interaction between positions and signals of height-channel loudspeakers in reproducing immersive 3d sound

NASA Astrophysics Data System (ADS)

Karampourniotis, Antonios

Since transmission capacities have significantly increased over the past few years, researchers are now able to transmit a larger amount of data, namely multichannel audio content, in the consumer applications. What has not been investigated in a systematic way yet is how to deliver the multichannel content. Specifically, researchers' attention is focused on the quest of a standardized immersive reproduction format that incorporates height loudspeakers coupled with the new high-resolution and three-dimensional (3D) media content for a comprehensive 3D experience. To better understand and utilize the immersive audio reproduction, this research focused on the (1) interaction between the positioning of height loudspeakers and the signals fed to the loudspeakers, (2) investigation of the perceptual characteristics associated with the height ambiences, and (3) the influence of inverse filtering on perceived sound quality for the realistic 3D sound reproduction. The experiment utilized the existence of two layers of loudspeakers: horizontal layer following the ITU-R BS.775 five-channel loudspeaker configuration and height layer locating a total of twelve loudspeakers at the azimuth of +/-30°, +/-50°, +/-70°, +/-90°, +/-110° and +/-130° and elevation of 30°. Eight configurations were formed, each of which selected four height-loudspeakers from twelve. In the subjective evaluation, listeners compared, ranked and described the eight randomly presented configurations of 4-channel height ambiences. The stimuli for the experiment were four nine-channel (5 channels for the horizontal and 4 for the height loudspeakers) multichannel music. Moreover, an approach of Finite Impulse Response (FIR) inverse filtering was attempted, in order to remove the particular room's acoustic influence. Another set of trained professionals was informally asked to use descriptors to characterize the newly presented multichannel music with height ambiences rendered with inverse filtering. The experimental results indicate the significance of the positioning of the loudspeakers with respect to the signals being fed to those loudspeakers in delivering a 3D sound field. Furthermore, it has been revealed that the perceptual characteristics that listeners linked for multichannel music with height ambiences include envelopment, elevatedness and fullness. Last but not least, after applying the inverse filtering the subjective preference was not affected significantly. This allows for the author to believe that, in fact, the room's influence with respect to the subjective evaluation is not as important as the appropriate loudspeaker-positioning for the multichannel-reproduced music with height ambiences.

Absolute calibration of the Jenoptik CHM15k-x ceilometer and its applicability for quantitative aerosol monitoring

NASA Astrophysics Data System (ADS)

Geiß, Alexander; Wiegner, Matthias

2014-05-01

The knowledge of the spatiotemporal distribution of atmospheric aerosols and its optical characterization is essential for the understanding of the radiation budget, air quality, and climate. For this purpose, lidar is an excellent system as it is an active remote sensing technique. As multi-wavelength research lidars with depolarization channels are quite complex and cost-expensive, increasing attention is paid to so-called ceilometers. They are simple one-wavelength backscatter lidars with low pulse energy for eye-safe operation. As maintenance costs are low and continuous and unattended measurements can be performed, they are suitable for long-term aerosol monitoring in a network. However, the signal-to-noise ratio is low, and the signals are not calibrated. The only optical property that can be derived from a ceilometer is the particle backscatter coefficient, but even this quantity requires a calibration of the signals. With four years of measurements from a Jenoptik ceilometer CHM15k-x, we developed two methods for an absolute calibration on this system. This advantage of our approach is that only a few days with favorable meteorological conditions are required where Rayleigh-calibration and comparison with our research lidar is possible to estimate the lidar constant. This method enables us to derive the particle backscatter coefficient at 1064 nm, and we retrieved for the first time profiles in near real-time within an accuracy of 10 %. If an appropriate lidar ratio is assumed the aerosol optical depth of e.g. the mixing layer can be determined with an accuracy depending on the accuracy of the lidar ratio estimate. Even for 'simple' applications, e.g. assessment of the mixing layer height, cloud detection, detection of elevated aerosol layers, the particle backscatter coefficient has significant advantages over the measured (uncalibrated) attenuated backscatter. The possibility of continuous operation under nearly any meteorological condition with temporal resolution in the order of 30 seconds makes it also possible to apply time-height-tracking methods for detecting mixing layer heights. The combination of methods for edge detection (e.g. wavelet covariance transform, gradient method, variance method) and edge tracking techniques is used to increase the reliability of the layer detection and attribution. Thus, a feature mask of aerosols and clouds can be derived. Four years of measurements constitute an excellent basis for a climatology including a homogeneous time series of mixing layer heights, aerosol layers and cloud base heights of the troposphere. With a low overlap region of 180 m of the Jenoptik CHM15k-x even very narrow mixing layers, typical for winter conditions, can be considered.

An Online 3D Database System for Endangered Architectural and Archaeological Heritage in the South-Eastern Mediterranean

NASA Astrophysics Data System (ADS)

Abate, D.; Avgousti, A.; Faka, M.; Hermon, S.; Bakirtzis, N.; Christofi, P.

2017-10-01

This study compares performance of aerial image based point clouds (IPCs) and light detection and ranging (LiDAR) based point clouds in detection of thinnings and clear cuts in forests. IPCs are an appealing method to update forest resource data, because of their accuracy in forest height estimation and cost-efficiency of aerial image acquisition. We predicted forest changes over a period of three years by creating difference layers that displayed the difference in height or volume between the initial and subsequent time points. Both IPCs and LiDAR data were used in this process. The IPCs were constructed with the Semi-Global Matching (SGM) algorithm. Difference layers were constructed by calculating differences in fitted height or volume models or in canopy height models (CHMs) from both time points. The LiDAR-derived digital terrain model (DTM) was used to scale heights to above ground level. The study area was classified in logistic regression into the categories ClearCut, Thinning or NoChange with the values from the difference layers. We compared the predicted changes with the true changes verified in the field, and obtained at best a classification accuracy for clear cuts 93.1 % with IPCs and 91.7 % with LiDAR data. However, a classification accuracy for thinnings was only 8.0 % with IPCs. With LiDAR data 41.4 % of thinnings were detected. In conclusion, the LiDAR data proved to be more accurate method to predict the minor changes in forests than IPCs, but both methods are useful in detection of major changes.

Altered expression of HER-2 and the mismatch repair genes MLH1 and MSH2 predicts the outcome of T1 high-grade bladder cancer.

PubMed

Sanguedolce, Francesca; Cormio, Antonella; Massenio, Paolo; Pedicillo, Maria C; Cagiano, Simona; Fortunato, Francesca; Calò, Beppe; Di Fino, Giuseppe; Carrieri, Giuseppe; Bufo, Pantaleo; Cormio, Luigi

2018-04-01

The identification of factors predicting the outcome of stage T1 high-grade bladder cancer (BC) is a major clinical issue. We performed immunohistochemistry to assess the role of human epidermal growth factor receptor-2 (HER-2) and microsatellite instability (MSI) factors MutL homologue 1 (MLH1) and MutS homologue 2 (MSH2) in predicting recurrence and progression of T1 high-grade BCs having undergone transurethral resection of bladder tumor (TURBT) alone or TURBT + intravesical instillations of bacillus Calmette-Guerin (BCG). HER-2 overexpression was a significant predictor of disease-free survival (DFS) in the overall as well as in the two patients' population; as for progression-free survival (PFS), it was significant in the overall but not in the two patients' population. MLH1 was an independent predictor of PFS only in patients treated with BCG and MSH2 failed to predict DFS and PFS in all populations. Most importantly, the higher the number of altered markers the lowers the DFS and PFS. In multivariate Cox proportional-hazards regression analysis, the number of altered molecular markers and BCG treatment were significant predictors (p = 0.0004 and 0.0283, respectively) of DFS, whereas the number of altered molecular markers was the only significant predictor (p = 0.0054) of PFS. Altered expression of the proto-oncogene HER-2 and the two molecular markers of genetic instability MLH1 and MSH2 predicted T1 high-grade BC outcome with the higher the number of altered markers the lower the DFS and PFS. These findings provide grounds for further testing them in predicting the outcome of this challenging disease.

DNA Mismatch Repair Deficiency Promotes Genomic Instability in a Subset of Papillary Thyroid Cancers.

PubMed

Javid, Mahsa; Sasanakietkul, Thanyawat; Nicolson, Norman G; Gibson, Courtney E; Callender, Glenda G; Korah, Reju; Carling, Tobias

2018-02-01

Efficient DNA damage repair by MutL-homolog DNA mismatch repair (MMR) enzymes, MLH1, MLH3, PMS1 and PMS2, are required to maintain thyrocyte genomic integrity. We hypothesized that persistent oxidative stress and consequent transcriptional dysregulation observed in thyroid follicles will lead to MMR deficiency and potentiate papillary thyroid tumorigenesis. MMR gene expression was analyzed by targeted microarray in 18 papillary thyroid cancer (PTC), 9 paracarcinoma normal thyroid (PCNT) and 10 normal thyroid (NT) samples. The findings were validated by qRT-PCR, and in follicular thyroid cancers (FTC) and follicular thyroid adenomas (FTA) for comparison. FOXO transcription factor expression was also analyzed. Protein expression was assessed by immunohistochemistry. Genomic integrity was evaluated by whole-exome sequencing-derived read-depth analysis and Mann-Whitney U test. Clinical correlations were assessed using Fisher's exact and t tests. Microarray and qRT-PCR revealed reduced expression of all four MMR genes in PTC compared with PCNT and of PMS2 compared with NT. FTC and FTA showed upregulation in MLH1, MLH3 and PMS2. PMS2 protein expression correlated with the mRNA expression pattern. FOXO1 showed lower expression in PMS2-deficient PTCs (log2-fold change -1.72 vs. -0.55, U = 11, p < 0.05 two-tailed). Rate of LOH, a measure of genomic instability, was higher in PMS2-deficient PTCs (median 3 and 1, respectively; U = 26, p < 0.05 two-tailed). No correlation was noted between MMR deficiency and clinical characteristics. MMR deficiency, potentially promoted by FOXO1 suppression, may explain the etiology for PTC development in some patients. FTC and FTA retain MMR activity and are likely caused by a different tumorigenic pathway.

Whole Gene Capture Analysis of 15 CRC Susceptibility Genes in Suspected Lynch Syndrome Patients.

PubMed

Jansen, Anne M L; Geilenkirchen, Marije A; van Wezel, Tom; Jagmohan-Changur, Shantie C; Ruano, Dina; van der Klift, Heleen M; van den Akker, Brendy E W M; Laros, Jeroen F J; van Galen, Michiel; Wagner, Anja; Letteboer, Tom G W; Gómez-García, Encarna B; Tops, Carli M J; Vasen, Hans F; Devilee, Peter; Hes, Frederik J; Morreau, Hans; Wijnen, Juul T

2016-01-01

Lynch Syndrome (LS) is caused by pathogenic germline variants in one of the mismatch repair (MMR) genes. However, up to 60% of MMR-deficient colorectal cancer cases are categorized as suspected Lynch Syndrome (sLS) because no pathogenic MMR germline variant can be identified, which leads to difficulties in clinical management. We therefore analyzed the genomic regions of 15 CRC susceptibility genes in leukocyte DNA of 34 unrelated sLS patients and 11 patients with MLH1 hypermethylated tumors with a clear family history. Using targeted next-generation sequencing, we analyzed the entire non-repetitive genomic sequence, including intronic and regulatory sequences, of 15 CRC susceptibility genes. In addition, tumor DNA from 28 sLS patients was analyzed for somatic MMR variants. Of 1979 germline variants found in the leukocyte DNA of 34 sLS patients, one was a pathogenic variant (MLH1 c.1667+1delG). Leukocyte DNA of 11 patients with MLH1 hypermethylated tumors was negative for pathogenic germline variants in the tested CRC susceptibility genes and for germline MLH1 hypermethylation. Somatic DNA analysis of 28 sLS tumors identified eight (29%) cases with two pathogenic somatic variants, one with a VUS predicted to pathogenic and LOH, and nine cases (32%) with one pathogenic somatic variant (n = 8) or one VUS predicted to be pathogenic (n = 1). This is the first study in sLS patients to include the entire genomic sequence of CRC susceptibility genes. An underlying somatic or germline MMR gene defect was identified in ten of 34 sLS patients (29%). In the remaining sLS patients, the underlying genetic defect explaining the MMRdeficiency in their tumors might be found outside the genomic regions harboring the MMR and other known CRC susceptibility genes.

Missense variants in hMLH1 identified in patients from the German HNPCC consortium and functional studies.

PubMed

Hardt, Karin; Heick, Sven Boris; Betz, Beate; Goecke, Timm; Yazdanparast, Haniyeh; Küppers, Robin; Servan, Kati; Steinke, Verena; Rahner, Nils; Morak, Monika; Holinski-Feder, Elke; Engel, Christoph; Möslein, Gabriela; Schackert, Hans-Konrad; von Knebel Doeberitz, Magnus; Pox, Christian; Hegemann, Johannes H; Royer-Pokora, Brigitte

2011-06-01

Missense mutations of the DNA mismatch repair gene MLH1 are found in a significant fraction of patients with Lynch syndrome (hereditary nonpolyposis colorectal cancer, HNPCC) and their pathogenicity often remains unclear. We report here all 88 MLH1 missense variants identified in families from the German HNPCC consortium with clinical details of these patients/families. We investigated 23 MLH1 missense variants by two functional in vivo assays in yeast; seven map to the ATPase and 16 to the protein interaction domain. In the yeast-2-hybrid (Y2H) assay three variants in the ATPase and twelve variants in the interaction domain showed no or a reduced interaction with PMS2; seven showed a normal and one a significantly higher interaction. Using the Lys2A (14) reporter system to study the dominant negative mutator effect (DNE), 16 variants showed no or a low mutator effect, suggesting that these are nonfunctional, three were intermediate and four wild type in this assay. The DNE and Y2H results were concordant for all variants in the interaction domain, whereas slightly divergent results were obtained for variants in the ATPase domain. Analysis of the stability of the missense proteins in yeast and human embryonic kidney cells (293T) revealed a very low expression for seven of the variants in yeast and for nine in human cells. In total 15 variants were classified as deleterious, five were classified as variants of unclassified significance (VUS) and three were basically normal in the functional assays, P603R, K618R, Q689R, suggesting that these are neutral.

Systematic immunohistochemical screening for Lynch syndrome in colorectal cancer: a single centre experience of 486 patients.

PubMed

Zumstein, Valentin; Vinzens, Fabrizio; Zettl, Andreas; Heinimann, Karl; Koeberle, Dieter; von Flüe, Markus; Bolli, Martin

2016-01-01

Germline mutations in DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2 cause autosomal dominantly inherited Lynch syndrome. Lynch syndrome patients and their families benefit from life-saving intensive cancer surveillance. Approximately one in 30 colorectal cancers arises in the setting of Lynch syndrome. The aim of this study was to assess the detection rate of Lynch syndrome at our institution after introduction of systematic immunohistochemical screening for MMR deficiency in colorectal cancers from 2011 to 2015. Following the recommendations by the Evaluation of Genomic Applications in Practice and Prevention working group all colorectal cancers were immunohistochemically stained for the presence of MMR proteins MLH1, PMS2, MSH2 and MSH6, independent of clinical criteria. In the case of loss of MLH1, the somatic BRAF mutation V600E was assessed with molecular testing and/or immunohistochemistry. Clinical follow-up of potential Lynch syndrome carriers (patients with tumours showing loss of MLH1 expression with absence of BRAFV600E, loss of PMS2, MSH2 or MSH6) was evaluated. Of all patients (n = 486), loss of MMR protein expression was found in 73 (15.0%) tumours. Twenty-eight (6.0%) were classified as potential Lynch syndrome carriers. Of the genetically tested potential Lynch syndrome carriers (10 out of 28 patients), 40% were first diagnosed with Lynch syndrome. Implementation of systematic immunohistochemistry screening for Lynch syndrome showed that 6% of colorectal cancers were potentially Lynch-syndrome related. Tumour board protocols should systematically contain information on MMR status of all colorectal cancers and, in MMR deficient cases, include clear recommendations for genetic counselling for all potential Lynch syndrome patients.

Combined Microsatellite Instability, MLH1 Methylation Analysis, and Immunohistochemistry for Lynch Syndrome Screening in Endometrial Cancers From GOG210: An NRG Oncology and Gynecologic Oncology Group Study.

PubMed

Goodfellow, Paul J; Billingsley, Caroline C; Lankes, Heather A; Ali, Shamshad; Cohn, David E; Broaddus, Russell J; Ramirez, Nilsa; Pritchard, Colin C; Hampel, Heather; Chassen, Alexis S; Simmons, Luke V; Schmidt, Amy P; Gao, Feng; Brinton, Louise A; Backes, Floor; Landrum, Lisa M; Geller, Melissa A; DiSilvestro, Paul A; Pearl, Michael L; Lele, Shashikant B; Powell, Matthew A; Zaino, Richard J; Mutch, David

2015-12-20

The best screening practice for Lynch syndrome (LS) in endometrial cancer (EC) remains unknown. We sought to determine whether tumor microsatellite instability (MSI) typing along with immunohistochemistry (IHC) and MLH1 methylation analysis can help identify women with LS. ECs from GOG210 patients were assessed for MSI, MLH1 methylation, and mismatch repair (MMR) protein expression. Each tumor was classified as having normal MMR, defective MMR associated with MLH1 methylation, or probable MMR mutation (ie, defective MMR but no methylation). Cancer family history and demographic and clinical features were compared for the three groups. Lynch mutation testing was performed for a subset of women. Analysis of 1,002 ECs suggested possible MMR mutation in 11.8% of tumors. The number of patients with a family history suggestive of LS was highest among women whose tumors were classified as probable MMR mutation (P = .001). Lynch mutations were identified in 41% of patient cases classified as probable mutation (21 of 51 tested). One of the MSH6 Lynch mutations was identified in a patient whose tumor had intact MSH6 expression. Age at diagnosis was younger for mutation carriers than noncarriers (54.3 v 62.3 years; P < .01), with five carriers diagnosed at age > 60 years. Combined MSI, methylation, and IHC analysis may prove useful in Lynch screening in EC. Twenty-four percent of mutation carriers presented with ECs at age > 60 years, and one carrier had an MSI-positive tumor with no IHC defect. Restricting Lynch testing to women diagnosed at age < 60 years or to women with IHC defects could result in missing a substantial fraction of genetic disease. © 2015 by American Society of Clinical Oncology.

Combined Microsatellite Instability, MLH1 Methylation Analysis, and Immunohistochemistry for Lynch Syndrome Screening in Endometrial Cancers From GOG210: An NRG Oncology and Gynecologic Oncology Group Study

PubMed Central

Goodfellow, Paul J.; Billingsley, Caroline C.; Lankes, Heather A.; Ali, Shamshad; Cohn, David E.; Broaddus, Russell J.; Ramirez, Nilsa; Pritchard, Colin C.; Hampel, Heather; Chassen, Alexis S.; Simmons, Luke V.; Schmidt, Amy P.; Gao, Feng; Brinton, Louise A.; Backes, Floor; Landrum, Lisa M.; Geller, Melissa A.; DiSilvestro, Paul A.; Pearl, Michael L.; Lele, Shashikant B.; Powell, Matthew A.; Zaino, Richard J.; Mutch, David

2015-01-01

Purpose The best screening practice for Lynch syndrome (LS) in endometrial cancer (EC) remains unknown. We sought to determine whether tumor microsatellite instability (MSI) typing along with immunohistochemistry (IHC) and MLH1 methylation analysis can help identify women with LS. Patients and Methods ECs from GOG210 patients were assessed for MSI, MLH1 methylation, and mismatch repair (MMR) protein expression. Each tumor was classified as having normal MMR, defective MMR associated with MLH1 methylation, or probable MMR mutation (ie, defective MMR but no methylation). Cancer family history and demographic and clinical features were compared for the three groups. Lynch mutation testing was performed for a subset of women. Results Analysis of 1,002 ECs suggested possible MMR mutation in 11.8% of tumors. The number of patients with a family history suggestive of LS was highest among women whose tumors were classified as probable MMR mutation (P = .001). Lynch mutations were identified in 41% of patient cases classified as probable mutation (21 of 51 tested). One of the MSH6 Lynch mutations was identified in a patient whose tumor had intact MSH6 expression. Age at diagnosis was younger for mutation carriers than noncarriers (54.3 v 62.3 years; P < .01), with five carriers diagnosed at age > 60 years. Conclusion Combined MSI, methylation, and IHC analysis may prove useful in Lynch screening in EC. Twenty-four percent of mutation carriers presented with ECs at age > 60 years, and one carrier had an MSI-positive tumor with no IHC defect. Restricting Lynch testing to women diagnosed at age < 60 years or to women with IHC defects could result in missing a substantial fraction of genetic disease. PMID:26552419

Relationship between PTEN, DNA mismatch repair, and tumor histotype in endometrial carcinoma: retained positive expression of PTEN preferentially identifies sporadic non-endometrioid carcinomas.

PubMed

Djordjevic, Bojana; Barkoh, Bedia A; Luthra, Rajyalakshmi; Broaddus, Russell R

2013-10-01

Loss of PTEN (phosphatase and tensin homolog) expression and microsatellite instability are two of the more common molecular alterations in endometrial carcinoma. From the published literature, it is controversial as to whether there is a relationship between these different molecular mechanisms. Therefore, a cohort of 187 pure endometrioid and non-endometrioid endometrial carcinomas, carefully characterized as to clinical and pathological features, was examined for PTEN sequence abnormalities and the immunohistochemical expression of PTEN and the DNA mismatch repair proteins MLH1, MSH2, MSH6, and PMS2. MLH1 methylation analysis was performed when tumors had loss of MLH1 protein. Mismatch repair protein loss was more frequent in endometrioid carcinomas compared with non-endometrioid carcinomas, a difference primarily attributable to the presence of MLH1 methylation in a greater proportion of endometrioid tumors. Among the non-endometrioid group, mixed endometrioid/non-endometrioid carcinomas were the histotype that most commonly had loss of a mismatch repair protein. In endometrioid tumors, the frequency of PTEN loss measured by immunohistochemistry and mutation did not differ significantly between the mismatch repair protein intact or mismatch repair protein loss groups, suggesting that PTEN loss is independent of mismatch protein repair status in this group. However, in non-endometrioid carcinomas, both intact positive PTEN immunohistochemical expression and PTEN wild type were highly associated with retained positive expression of mismatch repair proteins in the tumor. Relevant to screening endometrial cancers for Lynch Syndrome, an initial PTEN immunohistochemistry determination may be able to replace the use of four mismatch repair immunohistochemical markers in 63% of patients with non-endometrioid endometrial carcinoma. Therefore, PTEN immunohistochemistry, in combination with tumor histotype, is a useful adjunct in the clinical evaluation of endometrial carcinomas for Lynch Syndrome.

Peritumoral granulomatous reaction in endometrial carcinoma: association with DNA mismatch repair protein deficiency, particularly loss of PMS2 expression.

PubMed

Stewart, Colin J R; Pearn, Amy; Pachter, Nicholas; Tan, Adeline

2018-04-30

The observation of peritumoral granulomatous reactions (PGRs) in two endometrial carcinomas (ECs) with a PMS2-deficient/MLH1-intact expression pattern led us to investigate whether PGRs in EC were specifically associated with DNA mismatch repair (MMR) protein deficiency, particularly PMS2 loss. Hysterectomy specimens from 22 MMR protein-intact and 54 MMR protein-deficient ECs were reviewed with specific attention to the presence of a PGR and a tumour-associated lymphoid reaction [including tumour-infiltrating lymphocytes (TILs) and stromal lymphoid infiltrates]. The MMR protein-deficient ECs included 22 cases with combined MLH1/PMS2 loss, 11 with combined MSH2/MSH6 loss, 11 with isolated MSH6 loss, and 10 with PMS2 loss but intact MLH1 staining (including the two 'index' cases). Overall, PGRs were identified in seven of 54 (13%) MMR protein-deficient ECs, five of which showed a PMS2-deficient/MLH1-intact immunophenotype; three of these patients had germline PMS2 mutations and one additional patient had a germline MSH6 mutation. None of the MMR protein-intact tumours showed a PGR. Although five of the seven PGR-positive ECs had a high-grade histological component, six were stage I. Most ECs with PGRs also showed TILs and stromal lymphoid reactions, similarly to MMR protein-deficient ECs in general. MMR protein-deficient ECs, particularly those with PMS2 loss, occasionally show PGRs in addition to stromal lymphoid infiltrates and TILs. Therefore, PGRs could be considered to constitute a histological prompt for consideration of Lynch syndrome. The potential prognostic significance of PGRs in EC requires further study. © 2018 John Wiley & Sons Ltd.

A Sensitivity Analysis of the Nocturnal Boundary-Layer Properties to Atmospheric Emissivity Formulations

NASA Astrophysics Data System (ADS)

Siqueira, Mario B.; Katul, Gabriel G.

2010-02-01

A one-dimensional model for the mean potential temperature within the nocturnal boundary layer (NBL) was used to assess the sensitivity of three NBL properties (height, thermal stratification strength, and near-surface cooling) to three widely used atmospheric emissivity formulations. The calculations revealed that the NBL height is robust to the choice of the emissivity function, though this is not the case for NBL Richardson number and near-surface cooling rate. Rather than endorse one formulation, our analysis highlights the importance of atmospheric emissivity in modelling the radiative properties of the NBL especially for clear-sky conditions.

Comparison of mixed layer heights from airborne high spectral resolution lidar, ground-based measurements, and the WRF-Chem model during CalNex and CARES

NASA Astrophysics Data System (ADS)

Scarino, A. J.; Obland, M. D.; Fast, J. D.; Burton, S. P.; Ferrare, R. A.; Hostetler, C. A.; Berg, L. K.; Lefer, B.; Haman, C.; Hair, J. W.; Rogers, R. R.; Butler, C.; Cook, A. L.; Harper, D. B.

2013-05-01

The California Research at the Nexus of Air Quality and Climate Change (CalNex) and Carbonaceous Aerosol and Radiative Effects Study (CARES) field campaigns during May and June 2010 provided a data set appropriate for studying characteristics of the planetary boundary layer (PBL). The NASA Langley Research Center (LaRC) airborne High Spectral Resolution Lidar (HSRL) was deployed to California onboard the NASA LaRC B-200 aircraft to aid in characterizing aerosol properties during these two field campaigns. Measurements of aerosol extinction (532 nm), backscatter (532 and 1064 nm), and depolarization (532 and 1064 nm) profiles during 31 flights, many in coordination with other research aircraft and ground sites, constitute a diverse data set for use in characterizing the spatial and temporal distribution of aerosols, as well as the depth and variability of the daytime mixed layer (ML), which is a subset within the PBL. This work illustrates the temporal and spatial variability of the ML in the vicinity of Los Angeles and Sacramento, CA. ML heights derived from HSRL measurements are compared to PBL heights derived from radiosonde profiles, ML heights measured from ceilometers, and simulated PBL heights from the Weather Research and Forecasting Chemistry (WRF-Chem) community model. Comparisons between the HSRL ML heights and the radiosonde profiles in Sacramento result in a correlation coefficient value (R) of 0.93 (root-mean-square (RMS) difference of 157 m and bias difference (HSRL - radiosonde) of 57 m). HSRL ML heights compare well with those from the ceilometer in the LA Basin with an R of 0.89 (RMS difference of 108 m and bias difference (HSRL - Ceilometer) of -9.7 m) for distances of up to 30 km between the B-200 flight track and the ceilometer site. Simulated PBL heights from WRF-Chem were compared with those obtained from all flights for each campaign, producing an R of 0.58 (RMS difference of 604 m and a bias difference (WRF-Chem - HSRL) of -157 m) for CalNex and 0.59 (RMS difference of 689 m and a bias difference (WRF-Chem - HSRL) of 220 m) for CARES. Aerosol backscatter simulations are also available from WRF-Chem and are compared to those from HSRL to examine differences among the methods used to derive ML heights.

Impact of rockfalls on protection measures: an experimental approach

NASA Astrophysics Data System (ADS)

Yuan, J.; Li, Y.; Huang, R.; Pei, X.

2015-01-01

The determination of rockfall impact force is crucial in designing the protection measures. In the present study, laboratory tests are carried out by taking the weight and shape of the falling rock fragments, drop height, incident angle, platform on the slideway and cushion layer on the protection measures as factors to investigate their influences on the impact force. The test results indicate that the impact force is positively exponential to the weight of rockfall and the instantaneous impact velocity of the rockfall approaching the protection measures. The impact velocity is found to be dominated not only by the drop height but also by the shape of rockfall as well as the length of the platform on the slideway. A great drop height and/or a short platform produce a fast impact velocity. Spherical rockfalls experience a reater impact velocity than cubic and cylindrical ones. A layer of cushion on the protection measures may reduce the impact force to a greater extent. The reduction effects are dominated by the cushion material and the thickness of the cushion layer. The thicker the cushion layer, the greater the reduction effect and the less the impact force. The stiffer the buffer material, the less the buffering effect and the greater the impact force. The present study indicates that the current standard in China for designing protection measures may overestimate the impact force by taking no consideration for the rockfall shape, platform and cushion layer.

Microfluidic channel fabrication method

DOEpatents

Arnold, Don W.; Schoeniger, Joseph S.; Cardinale, Gregory F.

2001-01-01

A new channel structure for microfluidic systems and process for fabricating this structure. In contrast to the conventional practice of fabricating fluid channels as trenches or grooves in a substrate, fluid channels are fabricated as thin walled raised structures on a substrate. Microfluidic devices produced in accordance with the invention are a hybrid assembly generally consisting of three layers: 1) a substrate that can or cannot be an electrical insulator; 2) a middle layer, that is an electrically conducting material and preferably silicon, forms the channel walls whose height defines the channel height, joined to and extending from the substrate; and 3) a top layer, joined to the top of the channels, that forms a cover for the channels. The channels can be defined by photolithographic techniques and are produced by etching away the material around the channel walls.

Capacitance-voltage characterization of Al/Al2O3/PVA-PbSe MIS diode

NASA Astrophysics Data System (ADS)

Gawri, Isha; Sharma, Mamta; Jindal, Silky; Singh, Harpreet; Tripathi, S. K.

2018-05-01

The present paper reports the capacitance-voltage characterization of Al/Al2O3/PVA-PbSe MIS diode using chemical bath deposition method. Here anodic alumina layer prepared using electrolytic deposition method on Al substrate is used as insulating material. Using the capacitance-voltage variation at a fixed frequency, the different parameters such as Depletion layer width, Barrier height, Built-in voltage and Carrier concentration has been calculated at room temperature as well as at temperature range from 123 K to 323 K. With the increase in temperature the barrier height and depletion layer width follow a decreasing trend. Therefore, the capacitance-voltage characterization at different temperatures characterization provides strong evidence that the properties of MIS diode are primarily affected by diode parameters.

Correlations between In Situ Conductivity and Uniform-Height Epitaxial Morphology in Pb / Si ( 1 1 1 ) ₋ ( 7 × 7 )

DOE PAGES

Jałochowski, M.; Zdyb, R.; Tringides, M. C.

2016-02-23

The growth of Pb on Si(111)-7x7 at temperatures from 72 K to 201 K has been investigated using in situ electrical resistivity measurements and Scanning Tunneling Microscopy (STM). For temperatures T>140 K the specific resistivity ρ(θ) vs coverage θ shows an unusual "hump", instead of the expected monotonic decrease with θ. This novel result correlates well with the formation of uniform height 8-layer Pb islands and the superdiffusive motion of the wetting layer, despite the low temperatures. A model of the film resistivity as two resistors in series, the amorphous wetting layer and the crystalline islands, explains quantitatively the resistivitymore » dependence on θ.« less

46 CFR 164.009-15 - Test procedure.

Code of Federal Regulations, 2010 CFR

2010-10-01

... material, is less than 47 mm, the specimens prepared consist of layers of the sample. (3) If the sample is a composite material and has a height that is not 50 ±3mm, the layers of the specimen prepared are proportional in thickness to the layers of the sample. (4) The top and bottom faces of each specimen prepared...

Development and applications of the LANDFIRE forest structure layers

Treesearch

Chris Toney; Birgit Peterson; Don Long; Russ Parsons; Greg Cohn

2012-01-01

The LANDFIRE program is developing 2010 maps of vegetation and wildland fuel attributes for the United States at 30-meter resolution. Currently available vegetation layers include ca. 2001 and 2008 forest canopy cover and canopy height derived from Landsat and Forest Inventory and Analysis (FIA) plot measurements. The LANDFIRE canopy cover layer for the conterminous...

Investigation of sacrificial layer and building block for layered nanofabrication (LNF)

NASA Astrophysics Data System (ADS)

Shih, Ting-Yu

Layered Nanoscale Fabrication (LNF) is a "bottom-up" procedure that uses multiple layers to build 3-dimensional nanoscale structures. Here, in this dissertation, several candidates for sacrificial layers were explored, The thermal stability of gold nanoparticles and simple patterns are also reported. In order to obtain information on layer thickness and film quality; the samples were characterized using atomic force microscopy (AFM) and ellipsometry. Octadecyltrichlorosilane (OTS) was first investigated for use as a sacrificial layer and we studied filth growth by targeted self-replication of silane multilayers with and without the presence of thiolated gold nanoparticles on silicon oxide substrates. The particles adhered to the substrate during layer grafting. The film grew selectively on the substrate, without covering the particles. AFM was used to investigate the growth mechanism and the process of embedding the nanoparticles. OTS multilayer films up to 9 layers were grown in a linear, bilayer-by bilayer mode, free of islands and defects. We also report on studies of monolayer and multilayer formation of Methyl-11-dimethylmonochlorosilyl-undecanoate films. Flat multilayers up to 3-layers thick were grown. AFM was used to measure the height of an observable "edge" of the multilayer film and this provides and independent determination of the MOSUD layer height of 1.5 nm: However, the particles detached from the surface when we attempted to grow multilayer. One strategy of linking the particles to form 2D arrays, thermal activation in ambient air, was investigated. The morphological properties of flaked nanoparticles and structures on silicon oxide substrates before and after heating were characterized by using AFM. For widely separated 5 nm gold nanoparticles height decreased over 50% at 600 °C. Further heating to 630 °C caused most particles to completely disappear, with small amount of particle residue left on the surface. Particles positioned near to other particles first formed a neck-like structure at 570 °C and then deformed into one wide particle with tail-shape residue at 650 °C. Clusters of Au nanoparticles rearranged and became one large collide with particles residues left on the surface at 630 °C.

The Parameterization of PBL height with Helicity and preliminary Application in Tropical Cyclone Prediction

NASA Astrophysics Data System (ADS)

Ma, Leiming

2015-04-01

Planetary Boundary Layer (PBL) plays an important role in transferring the energy and moisture from ocean to tropical cyclone (TC). Thus, the accuracy of PBL parameterization determines the performance of numerical model on TC prediction to a large extent. Among various components of PBL parameterization, the definition on the height of PBL is the first should be concerned, which determines the vertical scale of PBL and the associated processes of turbulence in different scales. However, up to now, there is lacked consensus on how to define the height of PBL in the TC research community. The PBL heights represented by current numerical models usually exhibits significant difference with TC observation (e.g., Zhang et al., 2011; Storm et al., 2008), leading to the rapid growth of error in TC prediction. In an effort to narrow the gap between PBL parameterization and reality, this study presents a new parameterization scheme for the definition of PBL height. Instead of using traditional definition for PBL height with Richardson number, which has been verified not appropriate for the strongly sheared structure of TC PBL in recent observation studies, the new scheme employs a dynamical definition based on the conception of helicity. In this sense the spiral structures associated with inflow layer and rolls are expected to be represented in PBL parameterization. By defining the PBL height at each grid point, the new scheme also avoids to assume the symmetric inflow layer that is usually implemented in observational studies. The new scheme is applied to the Yonsei University (YSU) scheme in the Weather Research and Forecasting (WRF) model of US National Center for Atmospheric Research (NCAR) and verified with numerical experiments on TC Morakot (2009), which brought torrential rainfall and disaster to Taiwan and China mainland during landfall. The Morakot case is selected in this study to examine the performance of the new scheme in representing various structures of PBL over land and ocean. The results of simulations show that, in addition to enhancing the PBL height in the situation of intensive convection, the new scheme also significantly reduces the PBL height and 2m-temperature over land during the night time, a well-known problem for YSU scheme according to previous studies. The activity of PBL processes are modulated due to the improved PBL height, which ultimately leads to the improvement of prediction on TC Morakot. Key Words: PBL; Parameterization; Numerical Prediction; Tropical Cyclone Acknowledgements. This study was jointly supported by the Chinese National 973 Project (No. 2013CB430300, and No. 2009CB421500) and grant from the National Natural Science Foundation (No. 41475059). References Zhang, J. A., R. F. Rogers, D. S. Nolan, and F. D. Marks Jr., 2011: On the characteristic height scales of the hurricane boundary layer, Mon. Weather Rev., 139, 2523-2535. Storm B., J. Dudhia, S. Basu, et al., 2008: Evaluation of the Weather Research and Forecasting Model on forecasting Low-level Jets: Implications for Wind Energy. Wind Energ., DOI: 10.1002/we.

Evaluation of urban surface parameterizations in the WRF model using measurements during the Texas Air Quality Study 2006 field campaign

NASA Astrophysics Data System (ADS)

Lee, S.-H.; Kim, S.-W.; Angevine, W. M.; Bianco, L.; McKeen, S. A.; Senff, C. J.; Trainer, M.; Tucker, S. C.; Zamora, R. J.

2010-10-01

The impact of urban surface parameterizations in the WRF (Weather Research and Forecasting) model on the simulation of local meteorological fields is investigated. The Noah land surface model (LSM), a modified LSM, and a single-layer urban canopy model (UCM) have been compared, focusing on urban patches. The model simulations were performed for 6 days from 12 August to 17 August during the Texas Air Quality Study 2006 field campaign. Analysis was focused on the Houston-Galveston metropolitan area. The model simulated temperature, wind, and atmospheric boundary layer (ABL) height were compared with observations from surface meteorological stations (Continuous Ambient Monitoring Stations, CAMS), wind profilers, the NOAA Twin Otter aircraft, and the NOAA Research Vessel Ronald H. Brown. The UCM simulation showed better results in the comparison of ABL height and surface temperature than the LSM simulations, whereas the original LSM overestimated both the surface temperature and ABL height significantly in urban areas. The modified LSM, which activates hydrological processes associated with urban vegetation mainly through transpiration, slightly reduced warm and high biases in surface temperature and ABL height. A comparison of surface energy balance fluxes in an urban area indicated the UCM reproduces a realistic partitioning of sensible heat and latent heat fluxes, consequently improving the simulation of urban boundary layer. However, the LSMs have a higher Bowen ratio than the observation due to significant suppression of latent heat flux. The comparison results suggest that the subgrid heterogeneity by urban vegetation and urban morphological characteristics should be taken into account along with the associated physical parameterizations for accurate simulation of urban boundary layer if the region of interest has a large fraction of vegetation within the urban patch. Model showed significant discrepancies in the specific meteorological conditions when nocturnal low-level jets exist and a thermal internal boundary layer over water forms.

Understanding the Effects of a High Surface Area Nanostructured Indium Tin Oxide Electrode on Organic Solar Cell Performance.

PubMed

Cao, Bing; He, Xiaoming; Sorge, Jason B; Lalany, Abeed; Ahadi, Kaveh; Afshar, Amir; Olsen, Brian C; Hauger, Tate C; Mobarok, Md Hosnay; Li, Peng; Cadien, Kenneth C; Brett, Michael J; Luber, Erik J; Buriak, Jillian M

2017-11-08

Organic solar cells (OSCs) are a complex assembly of disparate materials, each with a precise function within the device. Typically, the electrodes are flat, and the device is fabricated through a layering approach of the interfacial layers and photoactive materials. This work explores the integration of high surface area transparent electrodes to investigate the possible role(s) a three-dimensional electrode could take within an OSC, with a BHJ composed of a donor-acceptor combination with a high degree of electron and hole mobility mismatch. Nanotree indium tin oxide (ITO) electrodes were prepared via glancing angle deposition, structures that were previously demonstrated to be single-crystalline. A thin layer of zinc oxide was deposited on the ITO nanotrees via atomic layer deposition, followed by a self-assembled monolayer of C 60 -based molecules that was bound to the zinc oxide surface through a carboxylic acid group. Infiltration of these functionalized ITO nanotrees with the photoactive layer, the bulk heterojunction comprising PC 71 BM and a high hole mobility low band gap polymer (PDPPTT-T-TT), led to families of devices that were analyzed for the effect of nanotree height. When the height was varied from 0 to 50, 75, 100, and 120 nm, statistically significant differences in device performance were noted with the maximum device efficiencies observed with a nanotree height of 75 nm. From analysis of these results, it was found that the intrinsic mobility mismatch between the donor and acceptor phases could be compensated for when the electron collection length was reduced relative to the hole collection length, resulting in more balanced charge extraction and reduced recombination, leading to improved efficiencies. However, as the ITO nanotrees increased in height and branching, the decrease in electron collection length was offset by an increase in hole collection length and potential deleterious electric field redistribution effects, resulting in decreased efficiency.

Microsatellite instability and MLH1 promoter hypermethylation in colorectal cancer

PubMed Central

Niv, Yaron

2007-01-01

Colorectal cancer (CRC) is caused by a series of genetic or epigenetic changes, and in the last decade there has been an increased awareness that there are multiple forms of colorectal cancer that develop through different pathways. Microsatellite instability is involved in the genesis of about 15% of sporadic colorectal cancers and most of hereditary nonpolyposis cancers. Tumors with a high frequency of microsatellite instability tend to be diploid, to possess a mucinous histology, and to have a surrounding lymphoid reaction. They are more prevalent in the proximal colon and have a fast pass from polyp to cancer. Nevertheless, they are associated with longer survival than stage-matched tumors with microsatellite stability. Resistance of colorectal cancers with a high frequency of microsatellite instability to 5-fluorouracil-based chemotherapy is well established. Silencing the MLH1 gene expression by its promoter methylation stops the formation of MLH1 protein, and prevents the normal activation of the DNA repair gene. This is an important cause for genomic instability and cell proliferation to the point of colorectal cancer formation. Better knowledge of this process will have a huge impact on colorectal cancer management, prevention, treatment and prognosis. PMID:17465465

Customized three-dimensional printed optical phantoms with user defined absorption and scattering

NASA Astrophysics Data System (ADS)

Pannem, Sanjana; Sweer, Jordan; Diep, Phuong; Lo, Justine; Snyder, Michael; Stueber, Gabriella; Zhao, Yanyu; Tabassum, Syeda; Istfan, Raeef; Wu, Junjie; Erramilli, Shyamsunder; Roblyer, Darren M.

2016-03-01

The use of reliable tissue-simulating phantoms spans multiple applications in spectroscopic imaging including device calibration and testing of new imaging procedures. Three-dimensional (3D) printing allows for the possibility of optical phantoms with arbitrary geometries and spatially varying optical properties. We recently demonstrated the ability to 3D print tissue-simulating phantoms with customized absorption (μa) and reduced scattering (μs`) by incorporating nigrosin, an absorbing dye, and titanium dioxide (TiO2), a scattering agent, to acrylonitrile butadiene styrene (ABS) during filament extrusion. A physiologically relevant range of μa and μs` was demonstrated with high repeatability. We expand our prior work here by evaluating the effect of two important 3D-printing parameters, percent infill and layer height, on both μa and μs`. 2 cm3 cubes were printed with percent infill ranging from 10% to 100% and layer height ranging from 0.15 to 0.40 mm. The range in μa and μs` was 27.3% and 19.5% respectively for different percent infills at 471 nm. For varying layer height, the range in μa and μs` was 27.8% and 15.4% respectively at 471 nm. These results indicate that percent infill and layer height substantially alter optical properties and should be carefully controlled during phantom fabrication. Through the use of inexpensive hobby-level printers, the fabrication of optical phantoms may advance the complexity and availability of fully customizable phantoms over multiple spatial scales. This technique exhibits a wider range of adaptability than other common methods of fabricating optical phantoms and may lead to improved instrument characterization and calibration.

Error sources in the retrieval of aerosol information over bright surfaces from satellite measurements in the oxygen A band

NASA Astrophysics Data System (ADS)

Nanda, Swadhin; de Graaf, Martin; Sneep, Maarten; de Haan, Johan F.; Stammes, Piet; Sanders, Abram F. J.; Tuinder, Olaf; Pepijn Veefkind, J.; Levelt, Pieternel F.

2018-01-01

Retrieving aerosol optical thickness and aerosol layer height over a bright surface from measured top-of-atmosphere reflectance spectrum in the oxygen A band is known to be challenging, often resulting in large errors. In certain atmospheric conditions and viewing geometries, a loss of sensitivity to aerosol optical thickness has been reported in the literature. This loss of sensitivity has been attributed to a phenomenon known as critical surface albedo regime, which is a range of surface albedos for which the top-of-atmosphere reflectance has minimal sensitivity to aerosol optical thickness. This paper extends the concept of critical surface albedo for aerosol layer height retrievals in the oxygen A band, and discusses its implications. The underlying physics are introduced by analysing the top-of-atmosphere reflectance spectrum as a sum of atmospheric path contribution and surface contribution, obtained using a radiative transfer model. Furthermore, error analysis of an aerosol layer height retrieval algorithm is conducted over dark and bright surfaces to show the dependence on surface reflectance. The analysis shows that the derivative with respect to aerosol layer height of the atmospheric path contribution to the top-of-atmosphere reflectance is opposite in sign to that of the surface contribution - an increase in surface brightness results in a decrease in information content. In the case of aerosol optical thickness, these derivatives are anti-correlated, leading to large retrieval errors in high surface albedo regimes. The consequence of this anti-correlation is demonstrated with measured spectra in the oxygen A band from the GOME-2 instrument on board the Metop-A satellite over the 2010 Russian wildfires incident.

Radiative Effects of African Dust and Smoke Observed from CERES and CALIOP Data

NASA Technical Reports Server (NTRS)

Yorks, John E.; McGill, Matt; Rodier, Sharon; Vaughan, Mark; Xu, Yongxiang; Hlavka, Dennis

2009-01-01

Cloud and aerosol effects have a significant impact on the atmospheric radiation budget in the Tropical Atlantic because of the spatial and temporal extent of desert dust and smoke from biomass burning in the atmosphere. The influences of African dust and smoke aerosols on cloud radiative properties over the Tropical Atlantic Ocean were analyzed for the month of July for three years (2006-2008) using collocated data collected by the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) and Clouds and the Earth s Radiant Energy System (CERES) instruments on the CALIPSO and Aqua satellites. Aerosol layer height and type can be more accurately determined using CALIOP data, through parameters such as cloud and aerosol layer height, optical depth and depolarization ratio, than data from atmospheric imagers used in previous cloud-aerosol interaction studies. On average, clouds below 5 km had a daytime instantaneous shortwave (SW) radiative flux of 270.2 +/- 16.9 W/sq m and thin cirrus clouds had a SW radiative flux of 208.0 +/- 12.7 W/sq m. When dust aerosols interacted with clouds below 5 km, as determined from CALIPSO, the SW radiative flux decreased to 205.4 +/- 13.0 W/sq m. Similarly, smoke aerosols decreased the SW radiative flux of low clouds to a value of 240.0 +/- 16.6 W/sq m. These decreases in SW radiative flux were likely attributed to the aerosol layer height and changes in cloud microphysics. CALIOP lidar observations, which more accurately identify aerosol layer height than passive instruments, appear essential for better understanding of cloud-aerosol interactions, a major uncertainty in predicting the climate system.

Determination of smoke plume and layer heights using scanning lidar data

Treesearch

Vladimir A. Kovalev; Alexander Petkov; Cyle Wold; Shawn Urbanski; Wei Min Hao

2009-01-01

The methodology of using mobile scanning lidar data for investigation of smoke plume rise and high-resolution smoke dispersion is considered. The methodology is based on the lidar-signal transformation proposed recently [Appl. Opt. 48, 2559 (2009)]. In this study, similar methodology is used to create the atmospheric heterogeneity height indicator (HHI...

Electrode Plate For An Eletrlchemical Cell And Having A Metal Foam Type Support, And A Method Of Obtaining Such An Electrode

DOEpatents

Verhoog, Roelof; Precigout, Claude; Stewart, Donald

1996-05-21

The electrode plate includes an active portion that is pasted with active material, and a plate head that is made up of three layers of compressed metal foam comprising: a non-pasted portion of height G of the support of the electrode plate; and two strips of non-pasted metal foam of height R on either side of the non-pasted portion of height G of the support and also extending for an overlap height h.sub.2 over the pasted portion of the support. The plate head includes a zone of reduced thickness including a portion that is maximally compressed, and a transitional portion between said maximally compressed portion and the remainder of the electrode which is of thickness e.sub.2. A portion of said plate head forms a connection tab. The method of obtaining the electrode consists in simultaneously rolling all three layers of metal foam in the plate head, and then in cutting matter away from the plates so as to obtain respective connection tabs.

Geomagnetic Storm Effects at F1 Layer Altitudes in Various Periods of Solar Activity (Irkutsk Station)

NASA Astrophysics Data System (ADS)

Kushnarenko, G. P.; Yakovleva, O. E.; Kuznetsova, G. M.

2018-03-01

The influence of geomagnetic disturbances on electron density Ne at F1 layer altitudes in different conditions of solar activity during the autumnal and vernal seasons of 2003-2015, according to the data from the Irkutsk digital ionospheric station (52° N, 104° E) is examined. Variations of Ne at heights of 150-190 km during the periods of twenty medium-scale and strong geomagnetic storms have been analyzed. At these specified heights, a vernal-autumn asymmetry of geomagnetic storm effects is discovered in all periods of solar activity of 2003-2015: a considerable Ne decrease at a height of 190 km and a weaker effect at lower levels during the autumnal storms. During vernal storms, no significant Ne decrease as compared with quiet conditions was registered over the entire analyzed interval of 150-190 km.

Computation of turbulent flow in a thin liquid layer of fluid involving a hydraulic jump

NASA Technical Reports Server (NTRS)

Rahman, M. M.; Faghri, A.; Hankey, W. L.

1991-01-01

Numerically computed flow fields and free surface height distributions are presented for the flow of a thin layer of liquid adjacent to a solid horizontal surface that encounters a hydraulic jump. Two kinds of flow configurations are considered: two-dimensional plane flow and axisymmetric radial flow. The computations used a boundary-fitted moving grid method with a k-epsilon model for the closure of turbulence. The free surface height was determined by an optimization procedure which minimized the error in the pressure distribution on the free surface. It was also checked against an approximate procedure involving integration of the governing equations and use of the MacCormack predictor-corrector method. The computed film height also compared reasonably well with previous experiments. A region of recirculating flow was found to be present adjacent to the solid boundary near the location of the jump, which was caused by a rapid deceleration of the flow.

Online Chapmann Layer Calculator for Simulating the Ionosphere with Undergraduate and Graduate Students

NASA Astrophysics Data System (ADS)

Gross, N. A.; Withers, P.; Sojka, J. J.

2014-12-01

The Chapman Layer Model is a "textbook" model of the ionosphere (for example, "Theory of Planetary Atmospheres" by Chamberlain and Hunten, Academic Press (1978)). The model use fundamental assumptions about the neutral atmosphere, the flux of ionizing radiation, and the recombination rate to calculation the ionization rate, and ion/electron density for a single species atmosphere. We have developed a "Chapman Layer Calculator" application that is deployed on the web using Java. It allows the user to see how various parameters control ion density, peak height, and profile of the ionospheric layer. Users can adjust parameters relevant to thermosphere scale height (temperature, gravitational acceleration, molecular weight, neutral atmosphere density) and to Extreme Ultraviolet solar flux (reference EUV, distance from the Sun, and solar Zenith Angle) and then see how the layer changes. This allows the user to simulate the ionosphere on other planets, by adjusting to the appropriate parameters. This simulation has been used as an exploratory activity for the NASA/LWS - Heliophysics Summer School 2014 and has an accompanying activity guide.

Experiments on Hypersonic Roughness Induced Transition by Means of Infrared Thermography

NASA Astrophysics Data System (ADS)

Schrijer, F. F. J.; Scarano, F.; van Oudheusden, B. W.; Bannink, W. J.

2005-02-01

Roughness induced boundary layer transition is experimentally investigated in the hypersonic flow regime at M = 9. The primary interest is the possible effect of stepwise geometry imperfections (2D isolated roughness) on (boundary layer) transition which may be caused on the EXPERT vehicle by the difference in thermal expansion due to the different materials used in the vehicle-nose construction. Also 3D isolated and 3D distributed roughness configurations were studied. Quantitative Infra-Red Thermography (QIRT) is used as primary diagnostic technique to measure the surface convective heat transfer and to detect boundary layer laminar-to-turbulent transition. The investigation shows that for a given height of the roughness element, the boundary layer is least sensitive to a step-like disturbance, whereas distributed 3D roughness was found to be effective in triggering transition. The experimental results have been compared to existing hypersonic transition correlations (PANT and Shuttle). Finally a transition criterion is evaluated which is based on the critical roughness height Reynolds number. Usage of this criterion enables a straightforward extrapolation to flight. Key words: hypersonic flow, boundary layer transition.

Dryline on 22 May 2002 During IHOP: Convective Scale Measurements at the Profiling Site

NASA Technical Reports Server (NTRS)

Demoz, Belay; Flamant, Cyrille; Miller, David; Evans, Keith; Fabry, Federic; DiGirolamo, Paolo; Whiteman, David; Geerts, Bart; Weckwerth, Tammy; Brown, William

2004-01-01

A unique set of measurements of wind, water vapor mixing ratio and boundary layer height variability was observed during the first MOP dryline mission of 22 May 2002. Water vapor mixing ratio from the Scanning Raman Lidar (SRL), high-resolution profiles of aerosol backscatter from the HARLIE and wind profiles from the GLOW are combined with the vertical velocity derived from the NCAR/ISS/MAPR and the high-resolution FMCW radar to reveal the convective variability of the cumulus cloud-topped boundary layer. A combined analysis of the in-situ and remote sensing data from aircraft, radiosonde, lidars, and radars reveals moisture variability within boundary layer updraft and downdraft regions as well as characterizes the boundary layer height variability in the dry and moist sides of the dryline. The profiler site measurements will be tied to aircraft data to reveal the relative intensity and location of these updrafts to the dry line. This study provides unprecedented high temporal and spatial resolution measurements of wind, moisture and backscatter within a dryline and the associated convective boundary layer.

Estimation of the marine boundary layer height over the central North Pacific using GPS radio occultation

NASA Astrophysics Data System (ADS)

Winning, Thomas E.; Chen, Yi-Leng; Xie, Feiqin

2017-01-01

Global positioning system radio occultation (GPS RO) refractivity data obtained from the first Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC) for the years 2007 to 2012 were used to estimate an overall climatology for the height of the marine boundary layer (MBL) over the central North Pacific Ocean including the Hawaiian Island region (10°N-45°N; 125°W-175°W). The trade wind days are identified based on the six-year National Centers for Environmental Prediction (NCEP) global analysis for the same period. About 87% of the RO soundings in summer (June-July-August, JJA) and 47% in winter (December-January-February, DJF) are under trade wind conditions. The MBL height climatology under trade wind conditions is derived and compared to the overall climatology. In general, MBL heights are lowest adjacent to the southern coast of California and gradually increase to the south and west. During the summer (JJA) when the northeasterly trade winds are the dominant surface flow, the median MBL height decreases from 2.0 km over Kauai to 1.9 km over the Big Island with an approximate 2 km maximum that progresses from southwest to northeast throughout the year. If the surface flow is restricted to trade winds only, the maximum MBL heights are located over the same areas, but they increase to a median height of 1.8 km during DJF and 2.1 km during JJA. For the first time, the GPS RO technique allows the depiction of the spatial variations of the MBL height climatology over the central North Pacific.

Herbaceious layer and soil response to experimental acidification in a central Appalachian hardwood forest

Treesearch

Frank S. Gilliam; Nicole L. Turrill; Staci D. Aulick; Dan K. Evans; Mary Beth Adams

1994-01-01

The herbaceous layer (vascular plants ≤1 m in height) is an important component of forest ecosystems and a potentially sensitive vegetation stratum in response to acid deposition. This study tested several hypotheses concerning soil and herbaceous layer response to experimental acidification at the Fernow Experimental Forest in north-central West Virginia. Fifteen...

Inventory of File gfs.t06z.smartguam24.tm00.grib2

Science.gov Websites

boundary layer WDIR 24 hour fcst Wind Direction (from which blowing) [degtrue] 016 planetary boundary layer WIND 24 hour fcst Wind Speed [m/s] 017 planetary boundary layer RH 24 hour fcst Relative Humidity [%] 018 planetary boundary layer DIST 24 hour fcst Geometric Height [m] 019 surface 4LFTX 24 hour fcst

A fast wind-farm boundary-layer model to investigate gravity wave effects and upstream flow deceleration

NASA Astrophysics Data System (ADS)

Allaerts, Dries; Meyers, Johan

2017-11-01

Wind farm design and control often relies on fast analytical wake models to predict turbine wake interactions and associated power losses. Essential input to these models are the inflow velocity and turbulent intensity at hub height, which come from prior measurement campaigns or wind-atlas data. Recent LES studies showed that in some situations large wind farms excite atmospheric gravity waves, which in turn affect the upstream wind conditions. In the current study, we develop a fast boundary-layer model that computes the excitation of gravity waves and the perturbation of the boundary-layer flow in response to an applied force. The core of the model is constituted by height-averaged, linearised Navier-Stokes equations for the inner and outer layer, and the effect of atmospheric gravity waves (excited by the boundary-layer displacement) is included via the pressure gradient. Coupling with analytical wake models allows us to study wind-farm wakes and upstream flow deceleration in various atmospheric conditions. Comparison with wind-farm LES results shows excellent agreement in terms of pressure and boundary-layer displacement levels. The authors acknowledge support from the European Research Council (FP7-Ideas, Grant No. 306471).

Improved Modeling of Surface Layer Parameters in a AGCM Using Refined Vertical Resolution in the Surface Layer

NASA Astrophysics Data System (ADS)

Shin, H. H.; Zhao, M.; Ming, Y.; Chen, X.; Lin, S. J.

2017-12-01

Surface layer (SL) parameters in atmospheric models - such as 2-m air temperature (T2), 10-m wind speed (U10), and surface turbulent fluxes - are computed by applying the Monin-Obukhov Similarity Theory (MOST) to the lowest model level height (LMH) in the models. The underlying assumption is that LMH is within surface layer height (SLH), but most AGCMs hardly meet the condition in stable boundary layers (SBLs) over land. To assess the errors in modeled SL parameters caused by this, offline computations of the MOST are performed with different LMHs from 1 to 100 m, for an idealized SBL case with prescribed surface parameters (surface temperature, roughness length and Obukhov length), and vertical profiles of temperature and winds. The results show that when LMH is higher than SLH, T2 and U10 are underestimated by O(1 K) and O(1 m/s), respectively, and the biases increase as LMH increases. Based on this, the refined vertical resolution with an additional layer in the SL is applied to the GFDL AGCM, and it reduces the systematic cold biases in T2 and the systematic underestimation of U10.

Simulations of thermal Rayleigh-Marangoni convection in a three-layer liquid-metal-battery model

NASA Astrophysics Data System (ADS)

Köllner, Thomas; Boeck, Thomas; Schumacher, Jörg

2017-11-01

Operating a liquid-metal battery produces Ohmic losses in the electrolyte layer that separates both metal electrodes. As a consequence, temperature gradients establish which potentially cause thermal convection since density and interfacial tension depend on the local temperature. In our numerical investigations, we considered three plane, immiscible layers governed by the Navier-Stokes-Boussinesq equations held at a constant temperature of 500°C at the bottom and top. A homogeneous current is applied that leads to a preferential heating of the mid electrolyte layer. We chose a typical material combination of Li separated by LiCl-KCl (a molten salt) from Pb-Bi for which we analyzed the linear stability of pure thermal conduction and performed three-dimensional direct-numerical simulations by a pseudospectral method probing different: electrolyte layer heights, overall heights, and current densities. Four instability mechanisms are identified, which are partly coupled to each other: buoyant convection in the upper electrode, buoyant convection in the molten salt layer, and Marangoni convection at both interfaces between molten salt and electrode. The global turbulent heat transfer follows scaling predictions for internally heated buoyant convection. Financial support by the Deutsche Forschungsgemeinschaft under Grant No. KO 5515/1-1 is gratefully acknowledged.

Fabrication of Crack-Free Barium Titanate Thin Film with High Dielectric Constant Using Sub-Micrometric Scale Layer-by-Layer E-Jet Deposition

PubMed Central

Liang, Junsheng; Li, Pengfei; Wang, Dazhi; Fang, Xu; Ding, Jiahong; Wu, Junxiong; Tang, Chang

2016-01-01

Dense and crack-free barium titanate (BaTiO3, BTO) thin films with a thickness of less than 4 μm were prepared by using sub-micrometric scale, layer-by-layer electrohydrodynamic jet (E-jet) deposition of the suspension ink which is composed of BTO nanopowder and BTO sol. Impacts of the jet height and line-to-line pitch of the deposition on the micro-structure of BTO thin films were investigated. Results show that crack-free BTO thin films can be prepared with 4 mm jet height and 300 μm line-to-line pitch in this work. Dielectric constant of the prepared BTO thin film was recorded as high as 2940 at 1 kHz at room temperature. Meanwhile, low dissipation factor of the BTO thin film of about 8.6% at 1 kHz was also obtained. The layer-by-layer E-jet deposition technique developed in this work has been proved to be a cost-effective, flexible and easy to control approach for the preparation of high-quality solid thin film. PMID:28787860

Relationship between boundary layer heights and growth rates with ground-level ozone in Houston, Texas

NASA Astrophysics Data System (ADS)

Haman, C. L.; Couzo, E.; Flynn, J. H.; Vizuete, W.; Heffron, B.; Lefer, B. L.

2014-05-01

Measurements and predictions of ambient ozone (O3), planetary boundary layer (PBL) height, the surface energy budget, wind speed, and other meteorological parameters were made near downtown Houston, Texas, and were used to investigate meteorological controls on elevated levels of ground-level O3. Days during the study period (1 April 2009 to 31 December 2010 for measurements and 15 April 2009 to 17 October 2009 for modeled) were classified into low (LO3) and high ozone (HO3) days. The majority of observed high HO3 days occurred in a postfrontal environment. Observations showed there is not a significant difference in daily maximum PBL heights on HO3 and LO3 days. Modeling results showed large differences between maximum PBL heights on HO3 and LO3 days. Nighttime and early morning observed and modeled PBL heights are consistently lower on HO3 days than on LO3 days. The observed spring LO3 days had the most rapid early morning PBL growth (~350 m h-1) while the fall HO3 group had the slowest (~200 m h-1). The predicted maximum average hourly morning PBL growth rates were greater on HO3 (624 m h-1) days than LO3 days (361 m h-1). Observed turbulent mixing parameters were up to 2-3 times weaker on HO3 days, which indicate large-scale subsidence associated with high-pressure systems (leading to clear skies and weak winds) substantially suppresses mixing. Lower surface layer ventilation coefficients were present in the morning on HO3 days in the spring and fall, which promotes the accumulation of O3 precursors near the surface.

Deep Convective Cloud Top Heights and Their Thermodynamic Control During CRYSTAL-FACE

NASA Technical Reports Server (NTRS)

Sherwood, Steven C.; Minnis, Patrick; McGill, Matthew

2004-01-01

Infrared (11 micron) radiances from GOES-8 and local radiosonde profiles, collected during the Cirrus Regional Study of Tropical Anvils and Cirrus Layers-Florida Area Cirrus Experiment (CRYSTAL-FACE) in July 2002, are used to assess the vertical distribution of Florida-area deep convective cloud top height and test predictions as to its variation based on parcel theory. The highest infrared tops (Z(sub 11)) reached approximately to the cold point, though there is at least a 1-km uncertainty due to unknown cloud-environment temperature differences. Since lidar shows that visible 'tops' are 1 km or more above Z(sub 11), visible cloud tops frequently penetrated the lapse-rate tropopause (approx. 15 km). Further, since lofted ice content may be present up to approx. 1 km above the visible tops, lofting of moisture through the mean cold point (15.4 km) was probably common. Morning clouds, and those near Key West, rarely penetrated the tropopause. Non-entraining parcel theory (i.e., CAPE) does not successfully explain either of these results, but can explain some of the day-to-day variations in cloud top height over the peninsula. Further, moisture variations above the boundary layer account for most of the day-today variability not explained by CAPE, especially over the oceans. In all locations, a 20% increase in mean mixing ratio between 750 and 500 hPa was associated with about 1 km deeper maximum cloud penetration relative to the neutral level. These results suggest that parcel theory may be useful for predicting changes in cumulus cloud height over time, but that parcel entrainment must be taken into account even for the tallest clouds. Accordingly, relative humidity above the boundary layer may exert some control on the height of the tropical troposphere.

Importance of Thickness in Human Cardiomyocyte Network for Effective Electrophysiological Stimulation Using On-Chip Extracellular Microelectrodes

NASA Astrophysics Data System (ADS)

Hamada, Tomoyo; Nomura, Fumimasa; Kaneko, Tomoyuki; Yasuda, Kenji

2012-06-01

We have developed a three-dimensionally controlled in vitro human cardiomyocyte network assay for the measurements of drug-induced conductivity changes and the appearance of fatal arrhythmia such as ventricular tachycardia/fibrillation for more precise in vitro predictive cardiotoxicity. To construct an artificial conductance propagation model of a human cardiomyocyte network, first, we examined the cell concentration dependence of the cell network heights and found the existence of a height limit of cell networks, which was double-layer height, whereas the cardiomyocytes were effectively and homogeneously cultivated within the microchamber maintaining their spatial distribution constant and their electrophysiological conductance and propagation were successfully recorded using a microelectrode array set on the bottom of the microchamber. The pacing ability of a cardiomyocyte's electrophysiological response has been evaluated using microelectrode extracellular stimulation, and the stimulation for pacing also successfully regulated the beating frequencies of two-layered cardiomyocyte networks, whereas monolayered cardiomyocyte networks were hardly stimulated by the external electrodes using the two-layered cardiomyocyte stimulation condition. The stability of the lined-up shape of human cardiomyocytes within the rectangularly arranged agarose microchambers was limited for a two-layered cardiomyocyte network because their stronger force generation shrunk those cells after peeling off the substrate. The results indicate the importance of fabrication technology of thickness control of cellular networks for effective extracellular stimulation and the potential concerning thick cardiomyocyte networks for long-term cultivation.

Status of the Topside Vary-Chap Ionospheric Model

NASA Astrophysics Data System (ADS)

Reinisch, Bodo; Nsumei, Patrick; Huang, Xueqin; Bilitza, Dieter

Status of the Topside Vary-Chap Ionospheric Model The general alpha-Chapman function for a multi-constituent gas which includes a continuously varying scale height and was therefore dubbed the Vary-Chap function, can present the topside electron density profiles in analytical form. The Vary-Chap profile is defined by the scale height function H(h) and the height and density of the F2 layer peak. By expressing 80,000 ISIS-2 measured topside density profiles as Vary-Chap functions we derived 80,000 scale height functions, which form the basis for the topside density profile modeling. The normalized scale height profiles Hn = H(h)/Hm were grouped according to season, MLAT, and MLT for each 50 km height bin from 200 km to 1400 km, and the median, lower, and upper quartiles for each bin were calculated. Hm is the scale height at the F2 layer peak. The resulting Hn functions are modeled in terms of hyperbolic tangent functions using 5 parameters that are determined by multivariate least squares, including the transition height hT where the scale height gradient has a maximum. These normalized scale height functions, representing the model of the topside electron density profiles from hmF2 to 1,400 km altitude, are independent of hmF2 and NmF2 and can therefore be directly used for the topside Ne profile in IRI. Similarly, this model can extend measured bottomside profiles to the topside, replacing the simple alpha-Chapman function with constant scale height that is currently used for construction of the topside profile in the Digisondes / ARTIST of the Global Ionospheric Radio Observatory (GIRO). It turns out that Hm(top) calculated from the topside profiles is generally several times larger than Hm(bot) derived from the bottomside profiles. This follows necessarily from the difference in the definition of the scale height functions for the topside and bottomside profiles. The diurnal variations of the ratio Hm(top) / Hm(bot) has been determined for different latitudes which makes it now possible to specify the topside profile for any given bottomside profile.

The Impact of the Afternoon Planetary Boundary-Layer Height on the Diurnal Cycle of CO and CO2 Mixing Ratios at a Low-Altitude Mountaintop

NASA Astrophysics Data System (ADS)

Lee, Temple R.; De Wekker, Stephan F. J.; Pal, Sandip

2018-02-01

Mountaintop trace-gas mixing ratios are often assumed to represent free atmospheric values, but are affected by valley planetary boundary-layer (PBL) air at certain times. We hypothesize that the afternoon valley-PBL height relative to the ridgetop is important in the diurnal cycle of mountaintop trace-gas mixing ratios. To investigate this, we use, (1) 4-years (1 January 2009-31 December 2012) of CO and CO2 mixing-ratio measurements and supporting meteorological observations from Pinnacles (38.61°N , 78.35°W , 1017 m a.s.l.), which is a monitoring site in the Appalachian Mountains, (2) regional O3 mixing-ratio measurements, and (3) PBL heights determined from a nearby sounding station. Results reveal that the amplitudes of the diurnal cycles of CO and CO2 mixing ratios vary as a function of the daytime maximum valley-PBL height relative to the ridgetop. The mean diurnal cycle for the subset of days when the afternoon valley-PBL height is at least 400 m below the ridgetop shows a daytime CO mixing-ratio increase, implying the transport of PBL air from the valley to the mountaintop. During the daytime, on days when the PBL heights exceed the mountaintop, PBL dilution and entrainment cause CO mixing ratios to decrease. This decrease in CO mixing ratio, especially on days when PBL heights are at least 400 m above the ridgetop, suggests that measurements from these days can be used as with afternoon measurements from flat terrain in applications requiring regionally-representative measurements.