Variable effects of the conserved RNA hairpin element upon 3' end processing of histone pre-mRNA in vitro.

We have studied the requirements for efficient histone-specific RNA 3' processing in nuclear extract from mammalian tissue culture cells. Processing is strongly impaired by mutations in the pre-mRNA spacer element that reduce the base-pairing potential with U7 RNA. Moreover, by exchanging the hairpin and spacer elements of two differently processed H4 genes, we find that this difference is exclusively due to the spacer element. Finally, processing is inhibited by the addition of competitor RNAs, if these contain a wild-type spacer sequence, but not if their spacer element is mutated. Conversely, the importance of the hairpin for histone RNA 3' processing is highly variable: A hairpin mutant of the H4-12 gene is processed with almost wild-type efficiency in extract from K21 mouse mastocytoma cells but is strongly affected in HeLa cell extract, whereas an identical hairpin mutant of the H4-1 gene is affected in both extracts. The hairpin defect of H4-12-specific RNA in HeLa cells can be overcome by a compensatory mutation that increases the base complementarity to U7 snRNA. Very similar results were also obtained in RNA competition experiments: processing of H4-12-specific RNA can be competed by RNA carrying a wild-type hairpin element in extract from HeLa, but not K21 cells, whereas processing of H4-1-specific RNA can be competed in both extracts. With two additional histone genes we obtained results that were in one case intermediate and in the other similar to those obtained with H4-1. These results suggest that hairpin binding factor(s) can cooperatively support the ability of U7 snRNPs to form an active processing complex, but is(are) not directly involved in the processing mechanism.

Correlation of blood type with thrombosis in pancreatic cancer patients

Objective: The study aimed to identify the risk factors involved in initiating thromboembolism (TE) in pancreatic cancer (PC) patients, with focus on ABO blood type. ^ Methods and Patients: There were 35.7% confirmed cases of TE and 64.3% cases remained free of TE (n=687). There were 12.7% only Pulmonary embolism (PE), 9% only Deep vein thrombosis (DVT), 53.5% only other sites, 3.3% combined PE and DVT, 8.6% combined PE and other sites, 9.8% combined DVT and other sites, and 3.3% all three combined cases. ^ Results: The risk factors for thrombosis identified by multivariate logistic regression were: history of previous anti-thrombotic treatment, tumor site in pancreatic body or tail, large tumor size, maximum glucose category more than 126 and 200 mg/dL. ^ The factors with worse overall survival by multivariate Cox regression and Kaplan Meier analyses were: locally advanced or metastatic stage, worsening performance status, high CA 19-9 levels, and HbA1C levels more than 6 %, at diagnosis. ^ There were 29.1% and 39.1% of the patients with thrombosis in the O and non-O blood type groups respectively. Both Non-O blood type (P=0.02) and the A, B and AB blood types (P= 0.007) were associated with thrombosis as compared to O type. The odds of thrombosis were nearly half in O blood type patients as compared to non-O blood type [OR-0.54 (95% C.I.- 0.37-0.79), P<0.001]. ^ Conclusion: A better understanding of the TE and PC relationship and involved risk factors may provide insights on tumor biology and patient response to prophylactic anticoagulation therapy.^

Rhenium and platinum-group element concentrations and Os isotope data for Philippine Sea Plate basalts from DSDP Legs 31, 58, and 59

Platinum-group elements (PGE), rhenium and osmium isotope data are reported for basalts from Deep Sea Drilling Project cores in the Philippine Sea Plate (PSP). Lithophile trace element and isotopic characteristics indicate a range of source components including DMM, EMII and subduction-enriched mantle. MORB-like basalts possess smooth, inclined chondrite-normalised PGE patterns with high palladium-PGE/iridium-PGE ratios, consistent with previously published data for MORB, and with the inferred compatibility of PGE. In contrast, while basalts with EMII-type lithophile element chemistry possess high Pt/Ir ratios, many have much lower Pd/Ir and unusually high Ru/Ir of >10. Similarly, back-arc samples from the Shikoku and Parece-Vela basins have very high Ru/Ir ratios (>30) and Pd/Ir as low as 1.1. Such extreme Pd/Ir and Ru/Ir ratios have not been previously reported in mafic volcanic suites and cannot be easily explained by variable degrees of melting, fractional crystallisation or by a shallow-level process such as alteration or degassing. The data appear most consistent with sampling of at least two mantle components with distinct PGE compositions. Peridotites with the required PGE characteristics (i.e. low Pd, but relatively high Ru and Re) have not been documented in oceanic mantle, but have been found in sub-continental mantle lithosphere and are the result of considerable melt depletion and selective metasomatic enrichment (mainly Re). The long-term presence of subduction zones surrounding the Philippine Sea Plate makes this a prime location for metasomatic enrichment of mantle, either through fluid enrichment or infiltration by small melt fractions. The Re-Os isotope data are difficult to interpret with confidence due to low Os concentrations in most samples and the uncertainty in sample age. Data for Site 444A (Shikoku Basin) give an age of 17.7+/-1.3 Ma (MSWD = 14), consistent with the proposed age of basement at the site and thus provides the first robust radiometric age for these samples. The initial 187Os/188Os of 0.1298+/-0.0069 is consistent with global MORB, and precludes significant metasomatic enrichment of Os by radiogenic slab fluids. Re-Os data for Sites 446A (two suites, Daito Basin) and 450 (Parece-Vela Basin) indicate ages of 73, 68 and 43 Ma, which are respectively, 30, 17 and >12 Ma older than previously proposed ages. The alkalic and tholeiitic suites from Site 446A define regression lines with different 187Os/188Osinitial (0.170+/-0.033 and 0.112+/-0.024, respectively) which could perhaps be explained by preferential sampling of interstitial, metasomatic sulphides (with higher time-integrated Re/Os ratios) by smaller percentage alkalic melts. One sample, with lithophile elements indistinguishable from MORB, is Os-rich (146 pg/g) and has an initial 187Os/188Os of 0.1594, which is at the upper limit of the accepted OIB range. Given the Os-rich nature of this sample and the lack of evidence for subduction or recycled crust inputs, this osmium isotope ratio likely reflects heterogeneity in the DMM. The dataset as a whole is a striking indication of the possible PGE and Os isotope variability within a region of mantle that has experienced a complex tectonic history.

Pollen analysis, particle size analysis, end-member modelling and x-ray fluorescence measurements from sediment cores off Cape Ghir, Morocco

Understanding past human-climate-environment interactions is essential for assessing the vulnerability of landscapes and ecosystems to future climate change. This is particularly important in southern Morocco where the current vegetation is impacted by pastoralism, and the region is highly sensitive to climate variability. Here, we present a 2000-year record of vegetation, sedimentation rate, XRF chemical element intensities, and particle size from two decadal-resolved, marine sediment cores, raised from offshore Cape Ghir, southern Morocco. The results show that between 650 and 850 AD the sedimentation rate increased dramatically from 100 cm/1000 years to 300 cm/1000 years, and the Fe/Ca and pollen flux doubled, together indicating higher inputs of terrestrial sediment. Particle size measurements and end-member modelling suggest increased fluvial transport of the sediment. Beginning at 650 AD pollen levels from Cichorioideae species show a sharp rise from 10% to 20%. Pollen from Atemisia and Plantago, also increase from this time. Deciduous oak pollen percentages show a decline, whereas those of evergreen oak barely change. The abrupt increase in terrestrial/fluvial input from 650 to 850 AD occurs, within the age uncertainty, of the arrival of Islam (Islamisation) in Morocco at around 700 AD. Historical evidence suggests Islamisation led to population increase and development of southern Morocco, including expanded pastoralism, deforestation and agriculture. Livestock pressure may have changed the vegetation structure, accounting for the increase in pollen from Cichorioideae, Plantago, and Artemisia, which include many weedy species. Goats in particular may have played a dominant role as agents of erosion, and intense browsing may have led to the decline in deciduous oak; evergreen oak is more likely to survive as it re-sprouts more vigorously after browsing. From 850 AD to present sedimentation rates, Fe/Ca ratios and fluvial discharge remain stable, whereas pollen results suggest continued degradation. Pollen results from the past 150 years suggest expanded cultivation of olives and the native argan tree, and the introduction of Australian eucalyptus trees. The rapidly increasing population in southern Morocco is causing continued pressure to expand pastoralism and agriculture. The history of land degradation presented here suggests that the vegetation in southern Morocco may have been degraded for a longer period than previously thought and may be particularly sensitive to further land use changes. These results should be included in land management strategies for southern Morocco.

Cloning and Characterization of peter pan, a Novel Drosophila Gene Required for Larval Growth

We identified a new Drosophila gene, peter pan (ppan), in a screen for larval growth–defective mutants. ppan mutant larvae do not grow and show minimal DNA replication but can survive until well after their heterozygotic siblings have pupariated. We cloned the ppan gene by P-element plasmid rescue. ppan belongs to a highly conserved gene family that includes Saccharomyces cerevisiae SSF1 and SSF2, as well as Schizosaccharomyces pombe, Arabidopsis, Caenorhabditis elegans, mouse, and human homologues. Deletion of both SSF1 and SSF2 in yeast is lethal, and depletion of the gene products causes cell division arrest. Mosaic analysis of ppan mutant clones in Drosophila imaginal disks and ovaries demonstrates that ppan is cell autonomous and required for normal mitotic growth but is not absolutely required for general biosynthesis or DNA replication. Overexpression of the wild-type gene causes cell death and disrupts the normal development of adult structures. The ppan gene family appears to have an essential and evolutionarily conserved role in cell growth.

Probing of tertiary interactions in RNA: 2'-hydroxyl-base contacts between the RNase P RNA and pre-tRNA.

A general method has been developed to analyze all 2' hydroxyl groups involved in tertiary interactions in RNA in a single experiment. This method involves comparing the activity of populations of circularly permuted RNAs that contain or lack potential hydrogen-bond donors at each position. The 2' hydroxyls of the pre-tRNA substrate identified as potential hydrogen bond donors in intermolecular interactions with the ribozyme from eubacterial RNase P (P RNA) are located in the T stem and T loop, acceptor stem, and 3' CCA regions. To locate the hydrogen-bond acceptors for one of those 2' hydroxyls in the P RNA, a phylogenetically conserved adenosine was mutated to a guanosine. When this mutant P RNA was used, increased cleavage activity of a single circularly permuted substrate within the population was observed. The cleavage efficiency (kcat/Km) of a singly 2'-deoxy-substituted substrate at this position in the T stem was also determined. For the wild-type P RNA, the catalytic efficiency was significantly decreased compared with that of the all-ribo substrate, consistent with the notion that this 2' hydroxyl plays an important role. For the P RNA mutant, no additional effect was found upon 2'-deoxy substitution. We propose that this particular 2' hydroxyl in the pre-tRNA interacts specifically with this adenosine in the P RNA. This method should be useful in examining the role of 2' hydroxyl groups in other RNA-RNA and RNA-protein complexes.

Gene disruptions using P transposable elements: an integral component of the Drosophila genome project.

Biologists require genetic as well as molecular tools to decipher genomic information and ultimately to understand gene function. The Berkeley Drosophila Genome Project is addressing these needs with a massive gene disruption project that uses individual, genetically engineered P transposable elements to target open reading frames throughout the Drosophila genome. DNA flanking the insertions is sequenced, thereby placing an extensive series of genetic markers on the physical genomic map and associating insertions with specific open reading frames and genes. Insertions from the collection now lie within or near most Drosophila genes, greatly reducing the time required to identify new mutations and analyze gene functions. Information revealed from these studies about P element site specificity is being used to target the remaining open reading frames.

Distortional buckling of I-beams by finite element method

Distortional buckling, unlike the usual lateral-torsional buckling in which the cross-section remains rigid in its own plane, involves distortion of web in the cross-section. This type of buckling typically occurs in beams with slender web and stocky flanges. Most of the published studies assume the web to deform with a cubic shape function. As this assumption may limit the accuracy of the results, a fifth order polynomial is chosen here for the web displacements. The general line-type finite element model used here has two nodes and a maximum of twelve degrees of freedom per node. The model not only can predict the correct coupled mode but also is capable of handling the local buckling of the web.

Photoelastic Analysis Of Fixed Partial Prosthesis Crown Height And Implant Length On Distribution Of Stress In Two Dental Implant Systems.

The aim of this study was to evaluate by photoelastic analysis stress distribution on short and long implants of two dental implant systems with 2-unit implant-supported fixed partial prostheses of 8 mm and 13 mm heights. Sixteen photoelastic models were divided into 4 groups: I: long implant (5 × 11 mm) (Neodent), II: long implant (5 × 11 mm) (Bicon), III: short implant (5 × 6 mm) (Neodent), and IV: short implants (5 × 6 mm) (Bicon). The models were positioned in a circular polariscope associated with a cell load and static axial (0.5 Kgf) and nonaxial load (15°, 0.5 Kgf) were applied to each group for both prosthetic crown heights. Three-way ANOVA was used to compare the factors implant length, crown height, and implant system (α = 0.05). The results showed that implant length was a statistically significant factor for both axial and nonaxial loading. The 13 mm prosthetic crown did not result in statistically significant differences in stress distribution between the implant systems and implant lengths studied, regardless of load type (P > 0.05). It can be concluded that short implants showed higher stress levels than long implants. Implant system and length was not relevant factors when prosthetic crown height were increased.

Identification and partial characterization of a Carica papaya-infecting isolate of Alfalfa mosaic virus in Brazil

A Carica papaya plant with severe yellow leaf mosaic, leaf distortion, and systemic necrosis was found in the municipality of Piracicaba, state of So Paulo, Brazil. Transmission electron microscopy (TEM) analysis revealed the presence of potyvirus-like particles and bacilliform particles similar to those of the Alfamovirus genus. The potyvirus was identified as Papaya ringspot virus-type P (PRSV-P). Biological, serological, and molecular studies confirmed the bacilliform virus as an isolate of Alfalfa mosaic virus (AMV). Partial nucleotide and amino acid sequences of the coat protein gene of this AMV isolate shared 97-98% identity with the AMV isolates in the GenBank database. This report is the first of the natural infection of papaya plants by AMV.

Predictive factors for local recurrence and incomplete resection of early gastric cancer treated by endoscopic resection: A Western experience

BACKGROUND: Early gastric cancer (EGC) is defined as adenocarcinoma limited to the mucosa or submucosa regardless of lymph node involvement. Local EGC recurrence rates have been described ill Lip to 6% of cases. OBJECTIVES: To evaluate predictive factors for incomplete resection and local recurrence of EGC treated by endoscopic mucosal resection (EMR) that was followed up for at least one year. METHODS: From June 1994 to December 2005, 46 patients with EGC underwent EMR. Possible predictive factors for incomplete endoscopic resection and local recurrence were identified by medical chart analysis. Demographic, endoscopic and histopathological data were retrospectively evaluated. EMR was considered complete or incomplete. Patients from the complete resection group were divided into subgroups (with and without local EGC recurrence). RESULTS: Complete resection was possible in 36 cases (76.6%). Predictive factors for incomplete resection were turnout location (P=0.035), histological type (P=0.021), lesion size (P=0.022) and number of resected fragments (P=0.013). On multivariate analysis, undifferentiated histological type (OR 0.8; 95% Cl 0.036 to 0.897) and number of resected fragments (OR 7.34; 95% Cl 1.266 to 42.629) were independent predictive factors for incomplete resection. In the complete resection group, a larger lesion size was associated with a higher the number of resected fragments (P=0.018). Local recurrence occurred in nine cases (25%). Use of the cap technique was the only predictive factor for local recurrence in five of seven cases (71.4%) (P=0.006). CONCLUSIONS: A larger lesion size was associated with a higher number of resected fragments. Undifferentiated adenocarcinoma and piecemeal resection were predictive factors for incomplete resection. Technique type was a predictive factor for local EGC recurrence.

Lymph Node Involvement and Not the Histophatologic Subtype Is Correlated with Outcome After Resection of Adenocarcinoma of the Ampulla of Vater

Background Intestinal and pancreaticobiliary types of Vater`s ampulla adenocarcinoma have been considered as having different biologic behavior and prognosis. The aim of the present study was to determine the best immunohistochemical panel for tumor classification and to analyze the survival of patients having these histological types of adenocarcinoma. Method Ninety-seven resected ampullary adenocarcinomas were histologically classified, and the prognosis factors were analyzed. The expression of MUC1, MUC2, MUC5AC, MUC6, CK7, CK17, CK20, CD10, and CDX2 was evaluated by using immunohistochemistry. Results Forty-three Vater`s ampulla carcinomas were histologically classified as intestinal type, 47 as pancreaticobiliary, and seven as other types. The intestinal type had a significantly higher expression of MUC2 (74.4% vs. 23.4%), CK20 (76.7% vs. 29.8%), CDX2 (86% vs. 21.3%), and CD10 (81.4% vs. 51.1%), while MUC1 (53.5% vs. 82.9%) and CK7 (79.1% vs. 95.7%) were higher in pancreatobiliary adenocarcinomas. The most accurate markers for immunohistochemical classification were CDX2, MUC1, and MUC2. Survival was significantly affected by pancreaticobiliary type (p=0.021), but only lymph node metastasis, lymphatic invasion, and stage were independent risk factors for survival in a multivariate analysis. Conclusion The immunohistochemical expression of CDX2, MUC1, and MUC2 allows a reproducible classification of ampullary carcinomas. Although carcinomas of the intestinal type showed better survival in the univariate analysis, neither histological classification nor immunohistochemistry were independent predictors of poor prognosis.

Dental caries status and salivary properties of asthmatic children and adolescents

Aims. This study aimed to investigate the dental caries status and salivary properties in 3- to 15-year-old children/adolescents. Methods. The sample was split in two groups: asthma group (AG), composed of 65 patients who attended Public Health Service; asthma-free group (AFG), composed of 65 nonasthmatic children/adolescents recruited in two public schools. Stimulated salivary samples were collected for 3 min. Buffering capacity and pH were ascertained in each salivary sample. A single trained and calibrated examiner (kappa = 0.98) performed the dental caries examination according to WHO criteria. Results. The AFG showed salivary flow rate (1.10 +/- 0.63 mL/min) higher (P = 0.002) than AG (0.80 +/- 0.50 mL/min). An inverse relationship was observed between asthma severity and salivary flow rate (Phi coefficient, r phi: 0.79, P = 0.0001). Children with moderate or severe asthma showed an increased risk for reduced salivary flow rate (OR: 17.15, P < 0.001). No association was observed between drug use frequency (P > 0.05) and drug type (P > 0.05) with salivary flow rate. Buffering capacity was similar in both groups. No significant differences were encountered in dental caries experience between AFG and AG groups. Conclusions. Although asthma can cause reduction in flow rate, the illness did not seem to influence dental caries experience in children with access to proper dental care.