dD values of C31 n-alkane (dD wax) from sediment core GeoB9501-4 offshore the Northwest African Sahel

Various studies have demonstrated that the stable hydrogen isotopic composition (dD) of terrestrial leaf waxes tracks that of precipitation (dDprecip) both spatially across climate gradients and over a range of different timescales. Yet, reconstructed estimates of dDprecip and corresponding rainfall typically remain largely qualitative, due mainly to uncertainties in plant ecosystem net fractionation, relative humidity, and the stability of the amount effect through time. Here we present dD values of the C31n-alkane (dDwax) from a marine sediment core offshore the Northwest (NW) African Sahel covering the past 100 years and overlapping with the instrumental record of rainfall. We use this record to investigate whether accurate, quantitative estimates of past rainfall can be derived from our dDwax time series. We infer the composition of vegetation (C3/C4) within the continental catchment area by analysis of the stable carbon isotopic composition of the same compounds (d13Cwax), calculated a net ecosystem fractionation factor, and corrected the dDwax time series accordingly to derive dDprecip. Using the present-day relationship between dDprecip and the amount of precipitation in the tropics, we derive quantitative estimates of past precipitation amounts. Our data show that (a) vegetation composition can be inferred from d13Cwax, (b) the calculated net ecosystem fractionation represents a reasonable estimate, and (c) estimated total amounts of rainfall based on dDwax correspond to instrumental records of rainfall. Our study has important implications for future studies aiming to reconstruct rainfall based on dDwax; the combined data presented here demonstrate that it is feasible to infer absolute rainfall amounts from sedimentary dDwax in tandem with d13Cwax in specific depositional settings.

Efeito da oxigenação hiperbárica no reparo ósseo de ratos diabéticos

The chronic state of hyperglycemia due to diabetes mellitus affects multiples organs impairing life quality. In bone, diabetes alters strength and mineral density and also suppresses the osteoblast activity, leading to an unbalanced bone healing process. Hyperbaric oxygen therapy (HBO) is suggested as an adjuvant treatment to accelerate bone repair. This study evaluated the effects of HBO in the number of mast cells and in new bone formation at the initial stage of bone repair in normoglycemic and diabetic rats. It was hypothesized that HBO treatment may improve bone repair in diabetic bone. The rats were equally divided in four groups: Control (C); Control + HBO (CH); Diabetes (D) and Diabetes + HBO (DH). Diabetes was induced by streptozotocin (65mg/kg) and femoral bone defects were created thirty days after diabetes induction in all groups. HBO initiated immediately after surgery procedure and was performed daily, for 7 days, in the CH e DH groups. Seven days after surgery, all animals were euthanized. The femur diaphyses were removed, fixated, decalcified and processed for paraffin embedding. The semi-serial histological sections obtained were stained with Hematoxylin-Eosin (HE), Mallory Trichrome and Toluidine Blue. The qualitative analysis was conducted in the histology slides stained with HE, where it was evaluated the morphological aspects of bone repair in the lesion area, observing the presence of clot, inflammatory cells, granulation tissue, type of bone tissue, morphology of bone cells, and thickness and organization of bone trabeculae. In the slides stained with Mallory Trichrome and Toluidine Blue were evaluated the percentage of new bone formation and number of mast cells, respectively. The qualitative analysis showed that the CH group presented a more advanced stage of bone repair compared to the C group, showing thicker trabeculae and greater bone filling of the lesion area. In D and DH group, the lesion area was partially filled with new bone formation tissue and presented thinner trabeculae and fewer areas associated to osteoclasts compared to control group. The histomorphometric analysis showed a significant improvement in new bone formation (p<0.001) comparing CH (38.08 ± 4.05) and C (32.05 ± 5.51); C and D (24.62 ± 2.28 and CH and DH (27.14 ± 4.21) groups. In the normoglycemic rats there was a significant increasing in the number of mast cells (p<0.05) comparing C (8.06 ± 5.15) and CH (21.06 ± 4.91) groups. In conclusion, this study showed that diabetes impaired bone repair and HBO was only able to increase new bone formation and the number of mast cells in the normoglycemic animals.

Análise da expressão dos receptores HER-2 e sua correlação clínica em pacientes com neoplasia gástrica do setor de Oncologia do Hospital de Clínicas da Universidade Federal de Uberlândia-UFU

Introduction: Gastric cancer is currently the fourth higher cancer mortality rate among men in the world and the fifth among women, despite the progressive advances in oncology. The identification of tumor receptors and the development of target-drugs to block them has contributed to increased survival and quality of life of patients, but it becomes important to know the tumor profile of the population being treated, avoiding burdening treatment with examinations and treatments that are not cost-effective. Objective: To evaluate the profile of the population with gastric cancer treated in five years at the Clinical Hospital of the Federal University of Uberlândia and verify the correlation between overexpression of HER-2 receptor with an unfavorable prognosis. Methods: 203 records with gastric cancer were selected through the system database, attending a five-year period, of which 117 paraffin blocks were available for immunohistochemical assessment of HER2 receptor. Results: 2.6% of tumors showed overexpression of HER2, considering for this study two crosses as positive. There was no statistically significant difference in correlation between expression of the HER2 receptor with age, gender, tumor grade, local involvement, Lauren classification, Borrmann classification or staging. Conclusion: For this studied population, we can conclude that there is no need to employ HER2 blockers with high cost as a target-therapy in patients with gastric cancer, since no clinical benefit probably will be obtained due to a low percentage of these patients that demonstrated superexpression of this receptor or even there is no patients with gastric cancer with superexpression of HER2 with more than three crosses of positivity in immunochemistry

Accumulation rates of plant-wax-derived long-chain C25 to C35 odd-numbered n-alkanes and d13C values of the n-C31 alkane of ODP Hole 175-1077B

The dominant forcing factors for past large-scale changes in vegetation are widely debated. Changes in the distribution of C4 plants-adapted to warm, dry conditions and low atmospheric CO2 concentrations (Collatz et al., 1998, doi:10.1007/s004420050468) -have been attributed to marked changes in environmental conditions, but the relative impacts of changes in aridity, temperature (Pagani et al., 1999, doi:10.1126/science.285.5429.876; Huang et al., 2001, doi:10.1126/science.1060143) and CO2 concentration (Cerling et al., 1993, doi:10.1038/361344a0; Kuypers et al., 1999, doi:10.1038/20659) are not well understood. Here, we present a record of African C4 plant abundance between 1.2 and 0.45 million years ago, derived from compound-specific carbon isotope analyses of wind-transported terrigenous plant waxes. We find that large-scale changes in African vegetation are linked closely to sea surface temperatures in the tropical Atlantic Ocean. We conclude that, in the mid-Pleistocene, changes in atmospheric moisture content - driven by tropical sea surface temperature changes and the strength of the African monsoon - controlled aridity on the African continent, and hence large-scale vegetation changes.

Stable oxygen and carbon isotopes ratios of sediment core GeoB9528-3

The carbon isotopic composition of individual plant leaf waxes (a proxy for C3 vs. C4 vegetation) in a marine sediment core collected from beneath the plume of Sahara-derived dust in northwest Africa reveals three periods during the past 192,000 years when the central Sahara/Sahel contained C3 plants (likely trees), indicating substantially wetter conditions than at present. Our data suggest that variability in the strength of Atlantic meridional overturning circulation (AMOC) is a main control on vegetation distribution in central North Africa, and we note expansions of C3 vegetation during the African Humid Period (early Holocene) and within Marine Isotope Stage (MIS) 3 (approx. 50-45 ka) and MIS 5 (approx. 120-110 ka). The wet periods within MIS 3 and 5 coincide with major human migration events out of sub-Saharan Africa. Our results thus suggest that changes in AMOC influenced North African climate and, at times, contributed to amenable conditions in the central Sahara/Sahel, allowing humans to cross this otherwise inhospitable region.

n-alkane carbon isotope ratios in plants and recent lake sediments from Cameroon

Trees and shrubs in tropical Africa use the C3 cycle as a carbon fixation pathway during photosynthesis, while grasses and sedges mostly use the C4 cycle. Leaf-wax lipids from sedimentary archives such as the long-chain n-alkanes (e.g., n-C27 to n-C33) inherit carbon isotope ratios that are representative of the carbon fixation pathway. Therefore, n-alkane d13C values are often used to reconstruct past C3/C4 composition of vegetation, assuming that the relative proportions of C3 and C4 leaf waxes reflect the relative proportions of C3 and C4 plants. We have compared the d13C values of n-alkanes from modern C3 and C4 plants with previously published values from recent lake sediments and provide a framework for estimating the fractional contribution (areal-based) of C3 vegetation cover (fC3) represented by these sedimentary archives. Samples were collected in Cameroon, across a latitudinal transect that accommodates a wide range of climate zones and vegetation types, as reflected in the progressive northward replacement of C3-dominated rain forest by C4-dominated savanna. The C3 plants analysed were characterised by substantially higher abundances of n-C29 alkanes and by substantially lower abundances of n-C33 alkanes than the C4 plants. Furthermore, the sedimentary d13C values of n-C29 and n-C31 alkanes from recent lake sediments in Cameroon (-37.4 per mil to -26.5 per mil) were generally within the range of d13C values for C3 plants, even when from sites where C4 plants dominated the catchment vegetation. In such cases simple linear mixing models fail to accurately reconstruct the relative proportions of C3 and C4 vegetation cover when using the d13C values of sedimentary n-alkanes, overestimating the proportion of C3 vegetation, likely as a consequence of the differences in plant wax production, preservation, transport, and/or deposition between C3 and C4 plants. We therefore tested a set of non-linear binary mixing models using d13C values from both C3 and C4 vegetation as end-members. The non-linear models included a sigmoid function (sine-squared) that describes small variations in the fC3 values as the minimum and maximum d13C values are approached, and a hyperbolic function that takes into account the differences between C3 and C4 plants discussed above. Model fitting and the estimation of uncertainties were completed using the Monte Carlo algorithm and can be improved by future data addition. Models that provided the best fit with the observed d13C values of sedimentary n-alkanes were either hyperbolic functions or a combination of hyperbolic and sine-squared functions. Such non-linear models may be used to convert d13C measurements on sedimentary n-alkanes directly into reconstructions of C3 vegetation cover.

Younger Dryas-Holocene sedimentary plant-wax hydrogen isotopes from the southern European Alps

We present a Younger Dryas-Holocene record of the hydrogen isotopic composition of sedimentary plant waxes (dDwax) from the southern European Alps (Lake Ghirla, N-Italy) to investigate its sensitivity to climatic forcing variations in this mid-latitude region (45°N). A modern altitudinal transect of dD values of river water and leaf waxes in the Lake Ghirla catchment is used to test present-day climate sensitivity of dDwax. While we find that altitudinal effects on dDwax are minor at our study site, temperature, precipitation amount, and evapotranspiration all appear to influence dDwax to varying extents. In the lake-sediment record, dDwax values vary between -134 and -180 per mil over the past 13 kyr. The long-term Holocene pattern of dDwax parallels the trend of decreasing temperature and is thus likely forced by the decline of northern hemisphere summer insolation. Shorter-term fluctuations, in contrast, may reflect both temperature and moisture-source changes. During the cool Younger Dryas and Little Ice Age (LIA) periods we observe unexpectedly high dDwax values relative to those before and after. We suggest that a change towards a more D-enriched moisture source is required during these intervals. In fact, a shift from northern N-Atlantic to southern N-Atlantic/western Mediterranean Sea sources would be consistent with a southward migration of the Westerlies with climate cooling. Prominent dDwax fluctuations in the early and middle Holocene are negative and potentially associated with temperature declines. In the late Holocene (<4 kyr BP), excursions are partly positive (as for the LIA) suggesting a stronger influence of moisture-source changes on dDwax variation. In addition to isotopic fractionations of the hydrological cycle, changes in vegetation composition, in the length of the growing season, and in snowfall amount provide additional potential sources of variability, although we cannot yet quantitatively assess these in the paleo-record. We conclude that while our dDwax record from the Alps does contain climatic information, it is a complicated record that would require additional constraints to be robustly interpreted. This also has important implications for other water-isotope-based proxy records of precipitation and hydro-climate from this region, such as cave speleothems.

Association Between Results of a Gene Expression Signature Assay and Recurrence-Free Interval in Patients With Stage II Colon Cancer in Cancer and Leukemia Group B 9581 (Alliance)

PURPOSE: Conventional staging methods are inadequate to identify patients with stage II colon cancer (CC) who are at high risk of recurrence after surgery with curative intent. ColDx is a gene expression, microarray-based assay shown to be independently prognostic for recurrence-free interval (RFI) and overall survival in CC. The objective of this study was to further validate ColDx using formalin-fixed, paraffin-embedded specimens collected as part of the Alliance phase III trial, C9581.

PATIENTS AND METHODS: C9581 evaluated edrecolomab versus observation in patients with stage II CC and reported no survival benefit. Under an initial case-cohort sampling design, a randomly selected subcohort (RS) comprised 514 patients from 901 eligible patients with available tissue. Forty-nine additional patients with recurrence events were included in the analysis. Final analysis comprised 393 patients: 360 RS (58 events) and 33 non-RS events. Risk status was determined for each patient by ColDx. The Self-Prentice method was used to test the association between the resulting ColDx risk score and RFI adjusting for standard prognostic variables.

RESULTS: Fifty-five percent of patients (216 of 393) were classified as high risk. After adjustment for prognostic variables that included mismatch repair (MMR) deficiency, ColDx high-risk patients exhibited significantly worse RFI (multivariable hazard ratio, 2.13; 95% CI, 1.3 to 3.5; P < .01). Age and MMR status were marginally significant. RFI at 5 years for patients classified as high risk was 82% (95% CI, 79% to 85%), compared with 91% (95% CI, 89% to 93%) for patients classified as low risk.

CONCLUSION: ColDx is associated with RFI in the C9581 subsample in the presence of other prognostic factors, including MMR deficiency. ColDx could be incorporated with the traditional clinical markers of risk to refine patient prognosis.

Prognostic role of the LCS6 KRAS variant in locally advanced rectal cancer: results of the EXPERT-C trial.

Background: Lethal-7 (let-7) is a tumour suppressor miRNA which acts by down-regulating several oncogenes including KRAS. A single-nucleotide polymorphism (rs61764370, T > G base substitution) in the let-7 complementary site 6 (LCS-6) of KRAS mRNA has been shown to predict prognosis in early-stage colorectal cancer (CRC) and benefit from anti-epidermal growth factor receptor monoclonal antibodies in metastatic CRC. Patients and methods: We analysed rs61764370 in EXPERT-C, a randomised phase II trial of neoadjuvant CAPOX followed by chemoradiotherapy, surgery and adjuvant CAPOX plus or minus cetuximab in locally advanced rectal cancer. DNA was isolated from formalin-fixed paraffin-embedded tumour tissue and genotyped using a PCR-based commercially available assay. Kaplan–Meier method and Cox regression analysis were used to calculate survival estimates and compare treatment arms. Results: A total of 155/164 (94.5%) patients were successfully analysed, of whom 123 (79.4%) and 32 (20.6%) had the LCS-6 TT and LCS-6 TG genotype, respectively. Carriers of the G allele were found to have a statistically significantly higher rate of complete response (CR) after neoadjuvant therapy (28.1% versus 10.6%; P = 0.020) and a trend for better 5-year progression-free survival (PFS) [77.4% versus 64.5%: hazard ratio (HR) 0.56; P = 0.152] and overall survival (OS) rates (80.3% versus 71.9%: HR 0.59; P = 0.234). Both CR and survival outcomes were independent of the use of cetuximab. The negative prognostic effect associated with KRAS mutation appeared to be stronger in patients with the LCS-6 TT genotype (HR PFS 1.70, P = 0.078; HR OS 1.79, P = 0.082) compared with those with the LCS-6 TG genotype (HR PFS 1.33, P = 0.713; HR OS 1.01, P = 0.995). Conclusion: This analysis suggests that rs61764370 may be a biomarker of response to neoadjuvant treatment and an indicator of favourable outcome in locally advanced rectal cancer possibly by mitigating the poor prognosis of KRAS mutation. In this setting, however, this polymorphism does not appear to predict cetuximab benefit.

Efficient Genotyping of KRAS Mutant Non-Small Cell Lung Cancer Using a Multiplexed Droplet Digital PCR Approach.

Droplet digital PCR (ddPCR) can be used to detect low frequency mutations in oncogene-driven lung cancer. The range of KRAS point mutations observed in NSCLC necessitates a multiplex approach to efficient mutation detection in circulating DNA. Here we report the design and optimisation of three discriminatory ddPCR multiplex assays investigating nine different KRAS mutations using PrimePCR™ ddPCR™ Mutation Assays and the Bio-Rad QX100 system. Together these mutations account for 95% of the nucleotide changes found in KRAS in human cancer. Multiplex reactions were optimised on genomic DNA extracted from KRAS mutant cell lines and tested on DNA extracted from fixed tumour tissue from a cohort of lung cancer patients without prior knowledge of the specific KRAS genotype. The multiplex ddPCR assays had a limit of detection of better than 1 mutant KRAS molecule in 2,000 wild-type KRAS molecules, which compared favourably with a limit of detection of 1 in 50 for next generation sequencing and 1 in 10 for Sanger sequencing. Multiplex ddPCR assays thus provide a highly efficient methodology to identify KRAS mutations in lung adenocarcinoma.

Focused molecular analysis of small cell lung cancer: feasibility in routine clinical practice.

Background: There is an urgent need to identify molecular signatures in small cell lung cancer (SCLC) that may select patients who are likely to respond to molecularly targeted therapies. In this study, we investigate the feasibility of undertaking focused molecular analyses on routine diagnostic biopsies in patients with SCLC.

Methods: A series of histopathologically confirmed formalin-fixed, paraffin-embedded SCLC specimens were analysed for epidermal growth factor receptors (EGFR), KRAS, NRAS and BRAF mutations, ALK gene rearrangements and MET amplification. EGFR and KRAS mutation testing was evaluated using real time polymerase chain reaction (RT-PCR cobas®), BRAF and NRAS mutations using multiplex PCR and capillary electrophoresis-single strand conformation analysis, and ALK and MET aberrations with fluorescent in situ hybridization. All genetic aberrations detected were validated independently.

Results: A total of 105 patients diagnosed with SCLC between July 1990 and September 2006 were included. 60 (57 %) patients had suitable tumour tissue for molecular testing. 25 patients were successfully evaluated for all six pre-defined molecular aberrations. Eleven patients failed all molecular analysis. No mutations in EGFR, KRAS and NRAS were detected, and no ALK gene rearrangements or MET gene amplifications were identified. A V600E substitution in BRAF was detected in a Caucasian male smoker diagnosed with SCLC with squamoid and glandular features.

Conclusion: The paucity of patients with sufficient tumour tissue, quality of DNA extracted and low frequency of aberrations detected indicate that alternative molecular characterisation approaches are necessary, such as the use of circulating plasma DNA in patients with SCLC.

Variation in pre-PCR processing of FFPE samples leads to discrepancies in BRAF and EGFR mutation detection: a diagnostic RING trial.

AIMS: Mutation detection accuracy has been described extensively; however, it is surprising that pre-PCR processing of formalin-fixed paraffin-embedded (FFPE) samples has not been systematically assessed in clinical context. We designed a RING trial to (i) investigate pre-PCR variability, (ii) correlate pre-PCR variation with EGFR/BRAF mutation testing accuracy and (iii) investigate causes for observed variation. METHODS: 13 molecular pathology laboratories were recruited. 104 blinded FFPE curls including engineered FFPE curls, cell-negative FFPE curls and control FFPE tissue samples were distributed to participants for pre-PCR processing and mutation detection. Follow-up analysis was performed to assess sample purity, DNA integrity and DNA quantitation. RESULTS: Rate of mutation detection failure was 11.9%. Of these failures, 80% were attributed to pre-PCR error. Significant differences in DNA yields across all samples were seen using analysis of variance (p

A new generation of companion diagnostics: cobas BRAF, KRAS and EGFR mutation detection tests

The cobas® (Roche) portfolio of companion diagnostics in oncology currently has three assays CE-marked for in vitro diagnostics. Two of these (EGFR and BRAF) are also US FDA-approved. These assays detect clinically relevant mutations that are correlated with response (BRAF, EGFR) or lack of response (KRAS) to targeted therapies such as selective mutant BRAF inhibitors in malignant melanoma, tyrosine kinases inhibitor in non-small cell lung cancer and anti-EGFR monoclonal antibodies in colorectal cancer, respectively. All these assays are run on a single platform using DNA extracted from a single 5 µm section of a formalin-fixed paraffin-embedded tissue block. The assays provide an ‘end-to-end’ solution from extraction of DNA to automated analysis and report on the cobas z 480. The cobas tests have shown robust and reproducible performance, with high sensitivity and specificity and low limit of detection, making them suitable as companion diagnostics for clinical use.