Familial Infiltrative Fibromatosis (Desmoid Tumours) (MIM135290) Caused by a Recurrent 3′ APC Gene Mutation

Desmoid tumours are generally very rare but occur about 100 times more frequently in the colorectal cancer predisposition syndrome familial adenomatous polyposis (MIM 175100), being represented in about 10% of patients. In addition to desmoid disease occurring in familial adenomatous polyposis (FAP) there exist familial infiltrative fibromatosis (MIM 135290) kindreds where there is no evidence of FAP. Previously we have described a kindred with familial infiltrative fibromatosis (FIF) in which desmoid tumours were associated with nonpolyposis colorectal cancer. FAP is caused by mutations in the APC gene and various genotype-phenotype relationships have been defined including reports that colorectal polyposis is less severe with mutations 5′ to codon 157 and that the risk of desmoid tumours is high in FAP patients with APC gene mutations between codons 1444 and 1598. There is relatively little information on the phenotype of APC gene mutations 3′ to codon 1598; however, one large family has been reported with a mutation at codon 1987 which presents with a highly variable phenotype which includes desmoid disease. We screened our original FIF kindred and three further families with a similar phenotype for mutations in the APC gene. A 4 bp frameshift deletion in codon 1962 was identified in the original FIF kindred and two further apparently unrelated families. Haplotype analysis suggests a common origin for the APC mutation in all three families. Affected individuals had no evidence of congenital hypertrophy of the retinal pigment epithelium. Colorectal polyposis was variable, and most affected patients had either none or a few late onset polyps. These findings demonstrate (i) that FAP and FIF are allelic, and (ii) that APC gene mutations which truncate the APC protein distal to the beta-catenin binding domain are associated with desmoid tumours, absent CHRPE and variable but attenuated polyposis expressio

Water-soluble organic aerosol in the Los Angeles Basin and outflow regions: Airborne and ground measurements during the 2010 CalNex field campaign

A particle-into-liquid sampler coupled to a total organic carbon analyzer (PILS-TOC) quantified particulate water-soluble organic carbon (WSOC) mass concentrations during the May 2010 deployment of the Center for Interdisciplinary Remotely Piloted Aircraft Studies (CIRPAS) Twin Otter in the CalNex field study. WSOC data collected during 16 flights provide the first spatiotemporal maps of WSOC in the San Joaquin Valley, Los Angeles Basin, and outflow regions of the Basin. WSOC was consistently higher in concentration within the Los Angeles Basin, where sea breeze transport and Basin topography strongly influence the spatial distribution of WSOC. The highest WSOC levels were associated with fire plumes, highlighting the importance of both primary and secondary sources for WSOC in the region. Residual pollution layers enriched with WSOC are observed aloft up to an altitude of 3.2 km and the highest WSOC levels for each flight were typically observed above 500 m. Simultaneous ground WSOC measurements during aircraft overpasses in Pasadena and Riverside typically exhibit lower levels, especially when relative humidity (RH) was higher aloft suggestive of the influence of aerosol-phase water. This points to the underestimation of the radiative effects of WSOC when using only surface measurements. Reduced aerosol-phase water in the eastern desert outflow region likely promotes the re-partitioning of WSOC to the gas phase and suppression of processes to produce these species (partitioning, multiphase chemistry, photolytic production); as a result, WSOC is reduced relative to sulfate (but not as much as nitrate) as aerosol is advected from the Basin to the outflows

Radar-derived statistics of convective storms in southeast Queensland

The aim of this study is to examine the statistics of convective storms and their concomitant changes with thermodynamic variability. The thermodynamic variability is analyzed by performing a cluster analysis on variables derived from radiosonde releases at Brisbane Airport in Australia. Three objectively defined regimes are found: a dry, stable regime with mainly westerly surface winds, a moist northerly regime, and a moist trade wind regime. S-band radar data are analyzed and storms are identified using objective tracking software [Thunderstorm Identification, Tracking, Analysis, and Nowcasting (TITAN)]. Storm statistics are then investigated, stratified by the regime subperiods. Convective storms are found to form and maintain along elevated topography. Probability distributions of convective storm size and rain rate are found to follow lognormal distributions with differing mean and variance among the regimes. There was some evidence of trimodal storm-top heights, located at the trade inversion (1.5–2 km), freezing level (3.6–4 km), and near 6 km, but it was dependent on the presence of the trade inversion. On average, storm volume and height are smallest in the trade regime and rain rate is largest in the westerly regime. However, westerly regime storms occur less frequently and have shorter lifetimes, which were attributed to the enhanced stability and decreased humidity profiles. Furthermore, time series of diurnal rain rate exhibited early morning and midafternoon maxima for the northerly and trade regimes but were absent for the westerly regime. The observations indicate that westerly regime storms are primarily driven by large-scale forcing, whereas northerly and trade wind regime storms are more responsive to surface characteristics

Central American Trachemys revisited: New sampling questions current understanding of taxonomy and distribution (Testudines: Emydidae)

Using 3226-bp-long mtDNA sequences and five nuclear loci (Cmos, ODC, R35, Rag1, Rag2, together 3409 bp), we examine genetic differentiation and relationships of Central American slider turtles (Trachemys grayi, T. venusta). Our investigation also included samples from taxa endemic to North America (T. gaigeae, T. scripta), the Antilles (T. decorata, T. decussata, T. stejnegeri, T. terrapen), and South America (T. dorbigni, T. medemi plus the two T. venusta subspecies endemic to northern South America). Our mitochondrial phylogeny retrieves all studied species as distinct, with three well-supported clades in a polytomy: (1) the Central and South American species (T. grayi + T. venusta) + (T. dorbigni + T. medemi), (2) the Antillean species, and (3) T. gaigeae + T. scripta. Our nuclear DNA analyses also suggest three distinct but conflicting clusters: (1) T. scripta plus the Antillean species, (2) T. gaigeae, and (3) the Central and South American species T. dorbigni, T. grayi, T. medemi, and T. venusta. However, in the mitochondrial phylogeny, T. gaigeae is the little divergent sister taxon of T. scripta. This conflicting placement of T. gaigeae suggests a distinct evolutionary trajectory and old hybridization with T. scripta and mitochondrial capture. Despite prominent color pattern differences, genetic divergences within T. grayi and T. venusta are shallow and the taxonomic diversity of each species with several currently recognized subspecies could be overestimated. Finally, we provide for the first time evidence for the occurrence of T. grayi along the Caribbean versant of Costa Rica

High polygenic risk score for exceptional longevity is associated with a healthy metabolic profile

Healthy metabolic measures in humans are associated with longevity. Dysregulation leads to metabolic syndrome (MetS) and negative health outcomes. Recent exceptional longevity (EL) genome wide association studies have facilitated estimation of an individual's polygenic risk score (PRS) for EL. We tested the hypothesis that individuals with high ELPRS have a low prevalence of MetS. Participants were from five cohorts of middle-aged to older adults. The primary analyses were performed in the UK Biobank (UKBB) (n = 407,800, 40-69 years). Replication analyses were undertaken using three Australian studies: Hunter Community Study (n = 2122, 55-85 years), Older Australian Twins Study (n = 539, 65-90 years) and Sydney Memory and Ageing Study (n = 925, 70-90 years), as well as the Swedish Gothenburg H70 Birth Cohort Studies (n = 2273, 70-93 years). MetS was defined using established criteria. Regressions and meta-analyses were performed with the ELPRS and MetS and its components. Generally, MetS prevalence (22-30%) was higher in the older cohorts. In the UKBB, high EL polygenic risk was associated with lower MetS prevalence (OR = 0.94, p = 1.84 × 10-42) and its components (p < 2.30 × 10-8). Meta-analyses of the replication cohorts showed nominal associations with MetS (p = 0.028) and 3 MetS components (p < 0.05). This work suggests individuals with a high polygenic risk for EL have a healthy metabolic profile promoting longevity

High polygenic risk score for exceptional longevity is associated with a healthy metabolic profile

Healthy metabolic measures in humans are associated with longevity. Dysregulation leads to metabolic syndrome (MetS) and negative health outcomes. Recent exceptional longevity (EL) genome wide association studies have facilitated estimation of an individual’s polygenic risk score (PRS) for EL. We tested the hypothesis that individuals with high ELPRS have a low prevalence of MetS. Participants were from five cohorts of middle-aged to older adults. The primary analyses were performed in the UK Biobank (UKBB) (n = 407,800, 40–69 years). Replication analyses were undertaken using three Australian studies: Hunter Community Study (n = 2122, 55–85 years), Older Australian Twins Study (n = 539, 65–90 years) and Sydney Memory and Ageing Study (n = 925, 70–90 years), as well as the Swedish Gothenburg H70 Birth Cohort Studies (n = 2273, 70–93 years). MetS was defined using established criteria. Regressions and meta-analyses were performed with the ELPRS and MetS and its components. Generally, MetS prevalence (22–30%) was higher in the older cohorts. In the UKBB, high EL polygenic risk was associated with lower MetS prevalence (OR = 0.94, p = 1.84 × 10–42) and its components (p < 2.30 × 10–8). Meta-analyses of the replication cohorts showed nominal associations with MetS (p = 0.028) and 3 MetS components (p < 0.05). This work suggests individuals with a high polygenic risk for EL have a healthy metabolic profile promoting longevity

Multi-Messenger Gravitational Wave Searches with Pulsar Timing Arrays: Application to 3C66B Using the NANOGrav 11-year Data Set

When galaxies merge, the supermassive black holes in their centers may form binaries and, during the process of merger, emit low-frequency gravitational radiation in the process. In this paper we consider the galaxy 3C66B, which was used as the target of the first multi-messenger search for gravitational waves. Due to the observed periodicities present in the photometric and astrometric data of the source of the source, it has been theorized to contain a supermassive black hole binary. Its apparent 1.05-year orbital period would place the gravitational wave emission directly in the pulsar timing band. Since the first pulsar timing array study of 3C66B, revised models of the source have been published, and timing array sensitivities and techniques have improved dramatically. With these advances, we further constrain the chirp mass of the potential supermassive black hole binary in 3C66B to less than $(1.65\pm0.02) \times 10^9~{M_\odot}$ using data from the NANOGrav 11-year data set. This upper limit provides a factor of 1.6 improvement over previous limits, and a factor of 4.3 over the first search done. Nevertheless, the most recent orbital model for the source is still consistent with our limit from pulsar timing array data. In addition, we are able to quantify the improvement made by the inclusion of source properties gleaned from electromagnetic data to `blind' pulsar timing array searches. With these methods, it is apparent that it is not necessary to obtain exact a priori knowledge of the period of a binary to gain meaningful astrophysical inferences.Comment: 14 pages, 6 figures. Accepted by Ap

A Transcription Factor Map as Revealed by a Genome-Wide Gene Expression Analysis of Whole-Blood mRNA Transcriptome in Multiple Sclerosis

Background: Several lines of evidence suggest that transcription factors are involved in the pathogenesis of Multiple Sclerosis (MS) but complete mapping of the whole network has been elusive. One of the reasons is that there are several clinical subtypes of MS and transcription factors that may be involved in one subtype may not be in others. We investigate the possibility that this network could be mapped using microarray technologies and contemporary bioinformatics methods on a dataset derived from whole blood in 99 untreated MS patients (36 Relapse Remitting MS, 43 Primary Progressive MS, and 20 Secondary Progressive MS) and 45 age-matched healthy controls. Methodology/Principal Findings: We have used two different analytical methodologies: a non-standard differential expression analysis and a differential co-expression analysis, which have converged on a significant number of regulatory motifs that are statistically overrepresented in genes that are either differentially expressed (or differentially co-expressed) in cases and controls (e.g., V$KROX_Q6, p-value ,3.31E-6; V$CREBP1_Q2, p-value ,9.93E-6, V$YY1_02, p-value ,1.65E-5). Conclusions/Significance: Our analysis uncovered a network of transcription factors that potentially dysregulate several genes in MS or one or more of its disease subtypes. The most significant transcription factor motifs were for the Early Growth Response EGR/KROX family, ATF2, YY1 (Yin and Yang 1), E2F-1/DP-1 and E2F-4/DP-2 heterodimers, SOX5, and CREB and ATF families. These transcription factors are involved in early T-lymphocyte specification and commitment as well as in oligodendrocyte dedifferentiation and development, both pathways that have significant biological plausibility in MS causation

Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes

Northern post-glacial lakes are significant, increasing sources of atmospheric carbon through ebullition (bubbling) of microbially-produced methane (CH4) from sediments. Ebullitive CH4 flux correlates strongly with temperature, reflecting that solar radiation drives emissions. However, here we show that the slope of the temperature-CH4 flux relationship differs spatially across two post-glacial lakes in Sweden. We compared these CH4 emission patterns with sediment microbial (metagenomic and amplicon), isotopic, and geochemical data. The temperature-associated increase in CH4 emissions was greater in lake middles—where methanogens were more abundant—than edges, and sediment communities were distinct between edges and middles. Microbial abundances, including those of CH4-cycling microorganisms and syntrophs, were predictive of porewater CH4 concentrations. Results suggest that deeper lake regions, which currently emit less CH4 than shallower edges, could add substantially to CH4 emissions in a warmer Arctic and that CH4 emission predictions may be improved by accounting for spatial variations in sediment microbiota