Trypanosoma brucei RRM1 is a nuclear RNA-binding protein and modulator of chromatin structure

TbRRM1 of Trypanosoma brucei is a nucleoprotein that was previously identified in a search for splicing factors in T. brucei. We show that TbRRM1 associates with mRNAs and with the auxiliary splicing factor polypyrimidine tract-binding protein 2, but not with components of the core spliceosome. TbRRM1 also interacts with several retrotransposon hot spot (RHS) proteins and histones. RNA immunoprecipitation of a tagged form of TbRRM1 from procyclic (insect) form trypanosomes identified ca. 1,500 transcripts that were enriched and 3,000 transcripts that were underrepresented compared to cellular mRNA. Enriched transcripts encoded RNA-binding proteins, including TbRRM1 itself, several RHS transcripts, mRNAs with long coding regions, and a high proportion of stage-regulated mRNAs that are more highly expressed in bloodstream forms. Transcripts encoding ribosomal proteins, other factors involved in translation, and procyclic-specific transcripts were underrepresented. Knockdown of TbRRM1 by RNA interference caused widespread changes in mRNA abundance, but these changes did not correlate with the binding of the protein to transcripts, and most splice sites were unchanged, negating a general role for TbRRM1 in splice site selection. When changes in mRNA abundance were mapped across the genome, regions with many downregulated mRNAs were identified. Two regions were analyzed by chromatin immunoprecipitation, both of which exhibited increases in nucleosome occupancy upon TbRRM1 depletion. In addition, subjecting cells to heat shock resulted in translocation of TbRRM1 to the cytoplasm and compaction of chromatin, consistent with a second role for TbRRM1 in modulating chromatin structure. IMPORTANCE: Trypanosoma brucei, the parasite that causes human sleeping sickness, is transmitted by tsetse flies. The parasite progresses through different life cycle stages in its two hosts, altering its pattern of gene expression in the process. In trypanosomes, protein-coding genes are organized as polycistronic units that are processed into monocistronic mRNAs. Since genes in the same unit can be regulated independently of each other, it is believed that gene regulation is essentially posttranscriptional. In this study, we investigated the role of a nuclear RNA-binding protein, TbRRM1, in the insect stage of the parasite. We found that TbRRM1 binds nuclear mRNAs and also affects chromatin status. Reduction of nuclear TbRRM1 by RNA interference or heat shock resulted in chromatin compaction. We propose that TbRRM1 regulates RNA polymerase II-driven gene expression both cotranscriptionally, by facilitating transcription and efficient splicing, and posttranscriptionally, via its interaction with nuclear mRNAs.

Red deer as maintenance host for bovine tuberculosis, Alpine region.

To estimate the prevalence of bovine tuberculosis in the Alpine region, we studied the epidemiology of Mycobacterium caprae in wildlife during the 2009-2012 hunting seasons. Free-ranging red deer (Cervus elaphus) were a maintenance host in a hot-spot area, mainly located in Austria.

Genetic epidemiologic methods in risk determination in Li-Fraumeni syndrome

Li-Fraumeni syndrome (LFS) is characterized by a variety of neoplasms occurring at a young age with an apparent autosomal dominant transmission. Individuals in pedigrees with LFS have high incidence of second malignancies. Recently LFS has been found to be associated with germline mutations of a tumor-suppressor gene, p53. Because LFS is rare and indeed not a clear-cut disease, it is not known whether all cases of LFS are attributable to p53 germline mutations and how p53 plays in cancer occurrence in such cancer syndrome families. In the present study, DNAs from constitutive cells of two-hundred and thirty-three family members from ten extended pedigrees were screened for p53 mutations. Six out of the ten LFS families had germline mutations at the p53 locus, including point and deletion mutations. In these six families, 55 out of 146 members were carriers of p53 mutations. Except one, all mutations occurred in exons 5 to 8 (i.e., the "hot spot" region) of the p53 gene. The age-specific penetrance of cancer was estimated after the genotype for each family member at risk was determined. The penetrance was 0.15, 0.29, 0.35, 0.77, and 0.91 by 20, 30, 40, 50 and 60 year-old, respectively, in male carriers; 0.19, 0.44, 0.76, and 0.90 by 20, 30, 40, and 50 year-old, respectively, in female carriers. These results indicated that one cannot escape from tumorigenesis if one inherits a p53 mutant allele; at least ninety percent of p53 carriers will develop cancer by the age of 60. To evaluate the possible bias due to the unexamined blood-relatives in LFS families, I performed a simulation analysis in which a p53 genotype was assigned to each unexamined person based on his cancer status and liability to cancer. The results showed that the penetrance estimates were not biased by the unexamined relatives. I also determined the sex, site, and age-specific penetrance of breast cancer in female carriers and lung cancer in male carriers. The penetrance of breast cancer in female carriers was 0.81 by age 45; the penetrance of lung cancer in male carriers was 0.78 by age 60, indicating that p53 play a key role for tumorigenesis in common cancers. ^

Spatial analysis of pertussis cases in Harris County from 2005-2010

Objective: This study examined the recent trends and characteristics of reported pertussis in Harris County from 2005-2010. ^ Methods: The study population included surveillance data from all reported pertussis cases from January 1, 2005 to December 31, 2010 to Harris County Public Health and Environmental Services (HCPHES). We calculated incidence and attack rates for varying age groups, race/ethnicity, and gender. Spatial analyses were conducted of hot spot and cluster of incident cases in Harris County census tracts. Maps were constructed using geographic information system. ^ Results: Age-specific incidence rates of reported cases of pertussis were highest among infants under a year of age and lowest among adults age 20 and older. Hispanics represented the most cases reported compared to any other race or ethnic group (42% of 483 cases). Age-adjusted rates were highest in 2009 at 9.81 cases per 100,000 population. Only 31.2% of people received at least four of the recommended five doses of vaccine. Spatial analyses revealed statistically significant clusters within the northeast region of Harris County. ^ Conclusions: Hispanic infants are the most at risk group for pertussis. Although 70% of cases had a history of immunization, 41.8% of infants were appropriately vaccinated for their age. Increased vaccination coverage may decrease the incidence of pertussis.^

Burden of invasive pneumococcal disease in Harris County, Texas (2003--2010) and the implication for enhanced public health surveillance of isolates

Invasive pneumococcal disease (IPD) causes significant health burden in the US, is responsible for the majority of bacterial meningitis, and causes more deaths than any other vaccine preventable bacterial disease in the US. The estimated National IPD rate is 14.3 cases per 100,000 population with a case-fatality rate of 1.5 cases per 100,000 population. Although cases of IPD are routinely reported to the local health department in Harris County Texas, the incidence (IR) and case-fatality (CFR) rates have not been reported. Additionally, it is important to know which serotypes of S. pneumoniae are circulating in Harris County Texas and to determine if ‘replacement disease’ is occurring. ^ This study reported incidence and case-fatality rates from 2003 to 2009, and described the trends in IPD, including the IPD serotypes circulating in Harris County Texas during the study period, particularly in 2008 and 2010. Annual incidence rates were calculated and reported for 2003 to 2009, using complete surveillance-year data. ^ Geographic information system (GIS) software was used to create a series of maps of the data reported during the study period. Cluster and outlier analysis and hot spot analysis were conducted using both case counts by census tract and disease rate by census tract. ^ IPD age- and race-adjusted IR for Harris County Texas and their 95% confidence intervals (CIs) were 1.40 (95% CI 1.0, 1.8), 1.71 (95% CI 1.24, 2.17), 3.13 (95% CI 2.48, 3.78), 3.08 (95% CI 2.43, 3.74), 5.61 (95% CI 4.79, 6.43), 8.11 (95% CI 7.11, 9.1), and 7.65 (95% CI 6.69, 8.61) for the years 2003 to 2009, respectively (rates were age- and race-adjusted to each year's midyear US population estimates). A Poisson regression model demonstrated a statistically significant increasing trend of about 32 percent per year in the IPD rates over the course of the study period. IPD age- and race-adjusted case-fatality rates (CFR) for Harris County Texas were also calculated and reported. A Poisson regression model demonstrated a statistically significant increasing trend of about 26 percent per year in the IPD case-fatality rates from 2003 through 2009. A logistic regression model associated the risk of dying from IPD to alcohol abuse (OR 4.69, 95% CI 2.57, 8.56) and to meningitis (OR 2.42, 95% CI 1.46, 4.03). ^ The prevalence of non-vaccine serotypes (NVT) among IPD cases with serotyped isolates was 98.2 percent. In 2008, the year with the sample more geographically representative of all areas of Harris County Texas, the prevalence was 96 percent. Given these findings, it is reasonable to conclude that ‘replacement disease’ is occurring in Harris County Texas, meaning that, the majority of IPD is caused by serotypes not included in the PCV7 vaccine. Also in conclusion, IPD rates increased during the study period in Harris County Texas.^

Altered tumorigenic phenotype in mice with a hypomorphic p53 mutant allele

Mutations in the p53 tumor suppressor gene are found in over 50% of human tumors and in the germline of Li-Fraumeni syndrome families. About 80% of these mutations are missense in nature. In order to study how p53 missense mutations affect tumorigenesis in vivo, we focused on the murine p53 arg-to-his mutation at amino acid 172, which corresponds to the human hot spot mutation at amino acid 175. The double replacement procedure was employed to introduce the p53 R172H mutation into the p53 locus of ES cells and mice were generated. An additional 1bp deletion in the intron 2 splice acceptor site was detected in the same allele in mice. We named this allele p53R172HΔg. This allele makes a small amount of full length p53 mutant protein. ^ Spontaneous tumor formation and survival were studied in these mice. Mice heterozygous for the p53R172HΔg allele showed 50% survival at 17 months of age, similar to the p53+/− mice. Moreover, the p53R172HΔg/+ mice showed a distinct tumor spectrum: 55% sarcomas, including osteosarcoms, fibrosarcomas and angiosarcomas; 27% carcinomas, including lung adenocarcinomas, squamous cell carcinomas, hepatocellular carcinomas and islet cell carcinomas; and 18% lymphomas. Compared to the p53+/− mice, there was a clear increase in the frequency of carcinoma development and a decrease in lymphoma incidence. Among the sarcomas that developed, fibrosarcomas in the skin were also more frequently observed. More importantly, osteosarcomas and carinomas that developed in the p53R172HΔg/+ mice metastasized at very high frequency (64% and 67%, respectively) compared with less than 10% in the p53+/− mice. The metastatic lesions were usually found in lung and liver, and less frequently in other tissues. The altered tumor spectrum in the mice and increased metastatic potential of the tumors suggested that the p53R172H mutation represents a gain-of-function. ^ Mouse embryonic fibroblasts (MEFs) from the mice homozygous and heterozygous for the p53R172HΔg allele were studied for growth characteristics, immortalization potential and genomic instability. All of the p53R172HΔg /+ MEF lines are immortalized under a 3T3 protocol while under the same protocol p53+/− MEFs are not immortalized. Karyotype analysis showed a persistent appearance of chromosome end-to-end fusion in the MEFs both homozygous and heterozygous for the p53R172HΔg allele. These observations suggest that increased genomic instability in the cells may cause the altered tumor phenotypes. ^

(Table 1) Bulk geochemistry of some lavas at DSDP Hole 55-433C

According to Wilson's (1963a, b) hypothesis, the volcanoes of the Hawaiian-Emperor Chain are formed as the Pacific lithospheric plate moves over a source of magma in the mantle. Morgan (1971, 1972) proposed that these "hot spots" resulted from "mantle plumes" that rise vertically from the core/mantle boundary and that are fixed about the deep mantle and rotating globe poles. The age of volcanoes increases with distance away from the recent "hot spot" beneath Kilauea volcano. The Hawaiian-Emperor bend indicates that the direction of motion of the Pacific plate changed about 40 m.y. ago.

Geochemistry at DSDP Leg 82 Holes

DSDP Leg 82 drilled nine sites to the southwest of the Azores Islands on the west flank of the Mid-Atlantic Ridge (MAR) in an attempt to determine the temporal and spatial evolution of the Azores "hot-spot" activity. The chemistry of the basalts recovered during Leg 82 is extremely varied: in Holes 558 and 561, both enriched (E-type: CeN/YbN = 1.5 to 2.7; Zr/Nb = 4.5 to 9.6) and depleted (or normal-N-type: CeN/YbN = 0.6 to 0.8; Zr/Nb > 20) mid-ocean ridge basalts (MORB) occur as intercalated lava flows. To the north of the Hayes Fracture Zone, there is little apparent systematic relationship between basalt chemistry and geographic position. However, to the south of the Hayes Fracture Zone, the chemical character of the basalts (N-type MORB) is more uniform. The coexistence of both E-type and N-type MORB in one hole may be explicable in terms of either complex melting/ fractionation processes during basalt genesis or chemically heterogeneous mantle sources. Significant variation in the ratios of strongly incompatible trace elements (e.g., La/Ta; Th/Ta) in the basalts of Holes 558 and 561 are not easily explicable by processes such as dynamic partial melting or open system crystal fractionation. Rather, the trace element data require that the basalts are ultimately derived from at least two chemically distinct mantle sources. The results from Leg 82 are equivocal in terms of the evolution of the Azores "hot spot," but would appear not to be compatible with a simple model of E-type MORB magmatism associated with upwelling mantle "blobs." Models that invoke a locally chemically heterogeneous mantle are best able to account for the small-scale variation in basalt chemistry.

Composition and age of rocks from the King's Trough and Palmer Ridge

This paper presents results of studies of rocks sampled during Cruise 19 of R/V Akademik Mstislav Keldysh with the Mir submersibles in the Atlantic Ocean (slopes of the King's Trough and Palmer Ridge). Based on these materials and published data two stages of magmatism and evolution in the region are distinguished: 1) formation of a mid-ocean ridge in the rift zone (68-32 Ma); 2) development of intraplate volcanism during movement of the plate over a "hot spot" (32-0 Ma).

Underway CH4 measurements during POSEIDON cruises POS320/1 and POS348

Coastal upwelling regions have been identified as sites of enhanced CH4 emissions to the atmosphere. The coastal upwelling area off Mauritania (NW Africa) is one of the most biologically productive regions of the world's ocean but its CH4 emissions have not been quantified so far. More than 1000 measurements of atmospheric and dissolved CH4 in the surface layer in the upwelling area off Mauritania were performed as part of the German SOPRAN (Surface Ocean Processes in the Anthropocene) study during two cruises in March/April 2005 (P320/1) and February 2007 (P348). During P348 enhanced CH4 saturations of up to 200% were found close to the coast and were associated with upwelling of South Atlantic Central Water. An area-weighted, seasonally adjusted estimate yielded overall annual CH4 emissions in the range from 1.6 to 2.9 Gg CH4. Thus the upwelling area off Mauritania represents a regional hot spot of CH4 emissions but seems to be of minor importance for the global oceanic CH4 emissions.

Geochemistry at DSDP Leg 82 Holes

The nine holes (556-564) drilled during DSDP Leg 82 in a region west and southwest of the Azores Platform (Fig. 1) exhibit a wide variety of chemical compositions that indicate a complex petrogenetic history involving crystal fractionation, magma mixing, complex melting, and mantle heterogeneity. The major element chemistry of each hole except Hole 557 is typical of mid-ocean ridge basalts (MORBs), whereas the trace element and rare earth element (REE) abundances and ratios are more variable, and show that both depleted Type I and enriched Type II basalts have been erupted in the region. Hole 556 (30-34 Ma), located near a flow line through the Azores Triple Junction, contains typically depleted basalts, whereas Hole 557 (18 Ma), located near the same flow line but closer to the Azores Platform, is a highly enriched FeTi basalt, indicating that the Azores hot-spot anomaly has existed in its present configuration for at least 18 Ma, but less than 30-34 Ma. Hole 558 (34-37 Ma), located near a flow line through the FAMOUS and Leg 37 sites, includes both Type I and II basalts. Although the differences in Zr/Nb and light REE/heavy REE ratios imply different mantle sources, the (La/Ce)ch (>1) and Nd isotopic ratios are almost the same, suggesting that the complex melting and pervasive, small-scale mantle heterogeneity may account for the variations in trace element and REE ratios observed in Hole 558 (and FAMOUS sites). Farther south, Hole 559 (34-37 Ma), contains enriched Type II basalts, whereas Hole 561 (14-17 Ma), located further east near the same flow line, contains Type I and II basalts. In this case, the (La/Ce)ch and Nd isotopic ratios are different, indicating two distinct mantle sources. Again, the existence along the same flow line of two holes exhibiting such different chemistry suggests that mantle heterogeneity may exist on a more pervasive and transient smaller scale. (Hole 560 was not sampled for this study because the single basalt clast recovered was used for shipboard analysis.) All of the remaining three holes (562, 563, 564), located along a flow line about 100 km south of the Hayes Fracture Zone (33°N), contain only depleted Type I basalts. The contrast in chemical compositions suggests that the Hayes Fracture Zone may act as a "domain" boundary between an area of fairly homogeneous, depleted Type I basalts to the south (Holes 562-564) and a region of complex, highly variable basalts to the north near the Azores hot-spot anomaly (Holes 556-561).

Geochemistry of basalts from ODP Hole 113-690C

Basalts from Maud Rise, Weddell Sea, are vesicular and olivine-phyric. Major, trace, and rare earth element concentrations are similar to those of alkali basalts from ocean islands and seamounts. The rocks are low in MgO, Cr, Ni, and Sc, and high in TiO2, K2O, P2O5, Zr, and LREE contents. The abundance of "primary" biotite and apatite in the matrix indicates the melting of a hydrous mantle. Prevalence of olivine and absence of plagioclase in the rocks suggests that the volatile in the melt was an H2O-CO2 mixture, where H2O was <0.5. Mantle derived xenocrysts in the basalt include corroded orthopyroxene, chromite, apatite, and olivine. Olivine (Fo90) is too magnesian to be in equilibrium with the basalts, as they contain only 5-6 wt% MgO. Based on the presence of mantle xenocrysts, the high concentration of incompatible elements, the spatial and chemical affinity with other ocean island basalts from the area, and the relative age of the basalt (overlain by late Campanian sediments), it is suggested that Maud Rise was probably generated by hot-spot activity, possible during a ridge crest jump prior to 84 Ma (anomaly 34 time). Iddingsite, a complex intergrowth of montmorillonite and goethite, is the major alteration product of second generation olivine. It is suggested that iddingsite crystallized at low temperatures (<200°C) from an oxidized fluid during deuteric alteration. Vesicles are commonly filled by zeolites which have been replaced by K-feldspars.