Dye-conjugated complementary lipophilic nucleosides as useful probes to study association processes by fluorescence resonance energy transfer.

Modern supramolecular chemistry relies on the combination of diverse analytical techniques that can provide complementary information on complex self-assembly landscapes. Among them, resonance energy transfer, monitored by fluorescence emission spectroscopy, arises as a sensitive and convenient phenomenon to report binding intermolecular interactions. The use of molecular probes labelled with suitable complementary energy-transfer pairs can provide valuable information about the thermodynamics, kinetics and self-sorting characteristics of a particular self-assembled system. The objective of this work is to generate a set of nucleoside FRET probes that can be reliably employed to prove and analyse quantitatively H-bonding interactions between complementary Watson-Crick pairs. We first describe the preparation of a set of lipophilic nucleosides that are linked to a π-conjugated functional fragment. The bases include guanosine and 2-aminoadenosine as purine heterocycles, and cytidine and uridine as complementary pyrimidine bases. The π-conjugated moiety comprises either a short phenylene-ethynylene oligomer, a bithiophene, or a BODIPY dye. We then demonstrate that the last two chromophores constitute an energy donor-acceptor couple and that donor emission quenching can be related to the ratio of molecules bound to the complementary acceptor pair. Hence, fluorescence spectroscopy in combination with resonance energy transfer, is shown here to be a useful tool to study and quantify the association and self-sorting events between complementary and non-complementary nucleosides in apolar aromatic solvents, where the binding strength is considerably high, and sensitive techniques that employ low concentrations are demanded.

Bevacizumab plus preoperative chemotherapy in operable HER2 negative breast cancer: biomarkers and pathologic response.

PURPOSE: The primary aim of this trial was to assess the rate of pathologic complete responses (pCR) of doxorubicin/cyclophosphamide (AC) followed by bevacizumab/docetaxel (BT), as neoadjuvant therapy for breast cancer (BC). Furthermore, the association between biomarkers and the pCR was explored. METHODS: Patients with HER-negative operable stage II-III BC ≥ 2 cm were enrolled. Four cycles of AC (A 60 mg/m(2) and C 600 mg/m(2), every 3 weeks) followed by 4 cycles of BT (B 15 mg/kg and T 75 mg/m(2), every 3 weeks), were planned. A core-biopsy was performed for biological markers assessment. RESULTS: Seventy-two women were included. Forty-three (63 %) patients were hormone receptor-positive. Sixty-four (89 %) completed the planned treatment, and 66 evaluable patients underwent surgery (92 %): a pCR was achieved in 16 of them (24, 95 % CI 15-36 %). pCR was significantly higher in tumors hormone receptor-negative, and in those with Angiotensin II type 1 receptor (AGTR1) protein overexpression. The overall clinical response rate was 86 % (95 % CI 76-93 %), including 42 complete responses. No unexpected toxicities or treatment-related deaths were observed. CONCLUSION: This regimen showed a remarkable clinical and pathological activity: the suggested relation between pCR and AGTR1 overexpression should be confirmed in larger trials.

Molecular basis of colorrectal cancer: towards an individualized management?

Colorectal cancer (CRC) has become a highly relevant condition nowadays. In this respect, advances in the understanding of its molecular basis are key for an adequate management. From the time when the adenoma-carcinoma sequence was formulated as a carcinogenesis model to this day, when -among other things- three major carcinogenic pathways have been identified, the CRC concept has evolved from that of a single disease to the notion that each CRC is a differentiated condition in itself. The suppressor or chromosome instability pathway, the mutator or microsatellite instability pathway, and the methylator or CpG island methylation pathway allow various phenotypes to be identified within CRC. Similarly, the presence of different changes in certain genes confers several behaviors on CRC from both the prognostic and responsive standpoints to specific therapies. However, this apparent complexity does help develop the clinical management of this disease through the identification of novel, more specific therapy targets, and also markers for various behaviors within the condition, which will most likely lead us to an individualized management for these patients.

Surgical management of hereditary colorectal cancer: surgery based on molecular analysis and family history.

The importance of colorectal cancer (CRC) is increasing. A proportion show a hereditary component, as in Lynch syndrome and Familial Adenomatous Polyposis, and a recently defined entity as well, namely, Familial Colorectal Cancer type X. The high probability to develop CRC in these groups may, at the time of recognition, change surgical management, including its timing or even the surgical technique. In some cases prophylactic surgery can play an important role. The possibility of using tools that allow recognition of the aforementioned syndromes, including microsatellite instability, immunohistochemistry for DNA mismatch repair system proteins, and especially their mutations, is on the basis of therapeutic strategies that differ from those employed in sporadic CRC cases.

Global responses of terrestrial productivity to contemporary climatic oscillations.

The terrestrial biosphere is subjected to a wide range of natural climatic oscillations. Best known is the El Niño-southern oscillation (ENSO) that exerts globally extensive impacts on crops and natural vegetation. A 50-year time series of ENSO events has been analysed to determine those geographical areas that are reliably impacted by ENSO events. Most areas are impacted by changes in precipitation; however, the Pacific Northwest is warmed by El Niño events. Vegetation gross primary production (GPP) has been simulated for these areas, and tests well against independent satellite observations of the normalized difference vegetation index. Analyses of selected geographical areas indicate that changes in GPP often lead to significant changes in ecosystem structure and dynamics. The Pacific decadal oscillation (PDO) is another climatic oscillation that originates from the Pacific and exerts global impacts that are rather similar to ENSO events. However, the longer period of the PDO provided two phases in the time series with a cool phase from 1951 to 1976 and a warm phase from 1977 to 2002. It was notable that the cool phase of the PDO acted additively with cool ENSO phases to exacerbate drought in the earlier period for the southwest USA. By contrast in India, the cool phase of the PDO appears to reduce the negative impacts of warm ENSO events on crop production.

Phase-II study of weekly schedule of trastuzumab, paclitaxel, and carboplatin followed by a week off every 28 days for HER2+ metastatic breast cancer.

BACKGROUND: Addition of carboplatin (C) to trastuzumab (T) and paclitaxel (P) improves the efficacy in HER2+ metastatic breast cancer (MBC). The aim of this phase-II study was to evaluate the efficacy and safety of this combination given weekly (3x) followed by a week off. The primary endpoint was: objective response rate (ORR), and secondary endpoints were: time to progression (TTP), overall survival (OS), and toxicity profile. METHODS: HER2+ MBC patients were included in the study. Treatment was as follows: T (loading dose:4 mg/kg per week and 2 mg/kg per day thereafter), P (80 mg/m(2)) and C (AUC 2) given weekly 3x, followed by 1 week off until disease progression or unacceptable toxicity. RESULTS: Forty-one patients (pts) were enrolled-median age: 54.5 years (range 29-75); 87.8% PS 0 or 1; 39 (97.5%) had received prior adjuvant or neoadjuvant treatment; 11 (27%) had received one prior CT line for metastatic disease; disease sites: liver (40%), bone (32.5%), lymph nodes (32.5%) and lung (20%); 19 (47.5%) had > or =2 lesions and 97.5% had measurable disease. A total of 37 pts were evaluated for response: 11(26.8%) CR; 12 (29.3%) PR; 9 (22%) SD; 5 (12.2%) PD and 4 NE, resulting in an ORR of 56.1% (95% CI 39.7-71.5%) and tumor growth control rate (RR + SD) of 78% (95% CI 62.4-89.4%). With a median follow up of 39.4 months, 26 (70.3%) patients have progressed. The median time to progression was 12.3 months (95% CI 8.2-15.5). At the time of this report, ten patients have died. Forty patients received 202 cycles (median five cycles). Grades 3-4 toxicities/pts: 3 (7.5%) anemia, 2 (5%) leucopenia, 10 (25%) neutropenia, 1 (2.5%) febrile neutropenia,1 (2.5%) thrombopenia, 2 (5%) asthenia, 2 (5%) diarrhea, 3 (7.5%) nausea, 2 (5%) vomiting, and 3 (7.5%) mucositis. CONCLUSIONS: The schedule showed an interesting activity, taking into account that 27% of patients had received previous treatment for MBC. One week of rest may benefit not only the patient but may also improve tolerability and efficacy of the combination.

Docetaxel and mitomycin as second-line treatment in advanced non-small cell lung cancer.

PURPOSE: To evaluate the feasibility, toxicity and efficacy of the combination of docetaxel and mitomycin C as second-line chemotherapy in patients with advanced non-small cell lung cancer (NSCLC). PATIENTS AND METHODS: Thirty-eight patients with histologically confirmed, locally advanced or metastatic NSCLC were included in this phase II trial. All patients had been previously treated with a platinum-based regimen. Treatment consisted of docetaxel (75 mg/m2) followed by mitomycin C (8 mg/m2) on day 1, every 21 days. Patients received a minimum of three courses unless progressive disease was detected. RESULTS: A total of 190 courses of docetaxel-mitomycin C were administered (median five courses per patient). This combination was well tolerated with grade 3-4 toxicity experienced with the following frequency: neutropenia in five patients (13%), fatigue in four (11%), anaemia, thrombocytopenia, nausea/vomiting and peripheral neuropathy in one each (3%). Three of 38 patients had a partial response (8%, 95% confidence interval 2.6-21.6%), 14 patients (37%) experienced stabilization of disease and 21 (55%) had disease progression. Median time to progression was 3.6 months. Overall median survival was 10.4 months, with the 1-year actuarial survival rate being 35%. CONCLUSIONS: The addition of mitomycin C to docetaxel as second-line therapy in NSCLC is well tolerated but does not seem to improve the response rate.

Fixed dose-rate infusion of gemcitabine in combination with cisplatin and UFT in advanced carcinoma of the pancreas.

BACKGROUND: Gemcitabine is currently considered the standard treatment for advanced pancreatic cancer (APC). Cisplatin and a fluoropyrimidine have some activity in the treatment of this cancer. The aim of this trial is to evaluate the efficacy and toxicity of a fixed dose-rate infusion of gemcitabine associated with cisplatin and UFT in patients with APC. PATIENTS AND METHODS: Forty-six chemotherapy-naïve patients with APC that was either unresectable or metastatic were included in this phase II study. All of them had Karnofsky performance status > or =50 and unidimensionally measurable disease. Treatment consisted of gemcitabine 1,200 mg/m2 given as a 120-min infusion weekly for three consecutive weeks, cisplatin 50 mg/m2 on day 1 and oral UFT 400 mg/m2/day (in two to three daily doses) on days 1 to 21; cycles of treatment were given every 28 days. RESULTS: A total of 208 cycles of chemotherapy were given with a median of 4 per patient. Fourteen patients (30%) achieved partial responses (95% CI 19-48%) and 17 (37%) had stable disease. The median time to progression was 5 months, and the median overall survival 9 months. Nineteen patients (49%; 95% CI 32-64%) had a clinical benefit response. Grade 3-4 WHO toxicities were as follows: neutropaenia in 26 patients (57%), with 5 cases of febrile neutropaenia (11%), thrombocytopaenia in 15 (33%), anaemia in six (13%), diarrhoea in 5 (11%), asthenia in 2 (4%) and mucositis in 1 (2%). Seven patients required hospitalisation for treatment-related complications. CONCLUSION: A fixed dose-rate infusion of gemcitabine associated with cisplatin and UFT is active in patients with APC, though at the cost of considerable toxicity.

Constraining the Sheffield dynamic global vegetation model using stream-flow measurements in the United Kingdom.

The biospheric water and carbon cycles are intimately coupled, so simulating carbon fluxes by vegetation also requires modelling of the water fluxes, with each component influencing the other. Observations of river streamflow integrate information at the catchment scale and are widely available over a long period; they therefore provide an important source of information for validating or calibrating vegetation models. In this paper, we analyse the performance of the Sheffield dynamic global vegetation model (SDGVM) for predicting river streamflow and quantifying how this information helps to constrain carbon flux predictions. The SDGVM is run for 29 large catchments in the United Kingdom. Annual streamflow estimates are compared with long time-series observations. In 23 out of the 29 catchments, the bias between model and observations is less than 50 mm, equivalent to less than 10% of precipitation. In the remaining catchments, larger errors are because of combinations of unpredictable causes, in particular various human activities and measurement issues and, in two cases, unidentified causes. In one of the catchments, we assess to what extent a knowledge of annual streamflow can constrain model parameters and in turn constrain estimates of gross primary production (GPP). For this purpose, we assume the model parameters are uncertain and constrain them by the streamflow observations using the generalized likelihood uncertainty estimation method. Comparing the probability density function of GPP with and without constraint shows that streamflow effectively constrains GPP, mainly by setting a low probability to GPP values below about 1100 g C-1 m2 yr-1 . In other words, streamflow observations allow the rejection of low values of GPP, so that the potential range of possible GPP values is almost halved.

Global climate and the distribution of plant biomes.

Biomes are areas of vegetation that are characterized by the same life-form. Traditional definitions of biomes have also included either geographical or climatic descriptors. This approach describes a wide range of biomes that can be correlated with characteristic climatic conditions, or climatic envelopes. The application of remote sensing technology to the frequent observation of biomes has led to a move away from the often subjective definition of biomes to one that is objective. Carefully characterized observations of life-form, by satellite, have been used to reconsider biome classification and their climatic envelopes. Five major tree biomes can be recognized by satellites based on leaf longevity and morphology: needleleaf evergreen, broadleaf evergreen, needleleaf deciduous, broadleaf cold deciduous and broadleaf drought deciduous. Observations indicate that broadleaf drought deciduous vegetation grades substantially into broadleaf evergreen vegetation. The needleleaf deciduous biome occurs in the world's coldest climates, where summer drought and therefore a drought deciduous biome are absent. Traditional biome definitions are quite static, implying no change in their life-form composition with time, within their particular climatic envelopes. However, this is not the case where there has been global ingress of grasslands and croplands into forested vegetation. The global spread of grasses, a new super-biome, was probably initiated 30-45 Myr ago by an increase in global aridity, and was driven by the natural spread of the disturbances of fire and animal grazing. These disturbances have been further extended over the Holocene era by human activities that have increased the land areas available for domestic animal grazing and for growing crops. The current situation is that grasses now occur in most, if not all biomes, and in many areas they dominate and define the biome. Croplands are also increasing, defining a new and relatively recent component to the grassland super-biome. In the case of both grassland and croplands, various forms of disturbance, particularly frequent disturbance, lead to continued range extensions of the biomes.

Phase II study of UFT and oxaliplatin in first-line treatment of advanced colorectal cancer.

The purpose of this study was to evaluate the efficacy, assessed as response rate, and toxicity of UFT (Tegafur-Uracil) in combination with oxaliplatin as first-line treatment of advanced colorectal cancer (CRC). In all, 84 patients with recurrent or metastatic CRC with measurable disease were included. Treatment consisted of oxaliplatin 85 mg m(-2) in 120-min intravenous (i.v.) infusion on days 1 and 15; i.v. l,leucovorin (l,LV) 250 mg m(-2) given in 2 h on day 1, followed by oral UFT 390 mg m(-2) on days 1-14, and oral l,LV 7.5 mg/12 h on days 2-14. Cycles were repeated every 28 days. A total of 492 cycles of chemotherapy were delivered with a median of six per patient (range 1-12). There was one complete response (1%) and 28 partial responses (34%) for an overall response rate of 35% (95% confidence interval (CI): 24-46%). A total of 36 patients (44%) had stable disease, whereas 17 (21%) had a progression. The median time to progression was 7.3 months and the median overall survival was 16.8 months. A prescheduled preliminary analysis was performed after inclusion of 16 patients who detected a high gastrointestinal toxicity, which led to a reduction of the UFT dose to 300 mg m(-2). With this new dosage, grade 3-4 diarrhoea and grade 3-4 nausea/vomiting dropped to 21 and 14% of patients, respectively. Other grade 3-4 toxicities were stomatitis in one (1%), anaemia in three (5%), neutropenia in two (3%), thrombocytopenia in one(1%), fatigue in six (9%), peripheral sensory neuropathy in nine (14%) and laryngopharyngeal dysesthesia in two patients (2%). The combination of oxaliplatin and UFT-l,LV is an active, easy-to-administer regimen with moderate toxicity. Hence, this regimen is worthy of further investigation.

Vegetation dynamics--simulating responses to climatic change.

A modelling approach to simulating vegetation dynamics is described, incorporating critical processes of carbon sequestration, growth, mortality and distribution. The model has been developed to investigate the responses of vegetation to environmental change, at time scales from days to centuries and from the local to the global scale. The model is outlined and subsequent tests, against independent data sources, are relatively successful, from the small scale to the global scale. Tests against eddy covariance observations of carbon exchange by vegetation indicated significant differences between measured and simulated net ecosystem production (NEP). NEP is the net of large fluxes due to gross primary production and respiration, which are not directly measured and so there is some uncertainty in explaining differences between observations and simulations. In addition it was noted that closer agreement of fluxes was achieved for natural, or long-lived managed vegetation than for recently managed vegetation. The discrepancies appear to be most closely related to respiratory carbon losses from the soil, but this area needs further exploration. The differences do not scale up to the global scale, where simulated and measured global net biome production were similar, indicating that fluxes measured at the managed observed sites are not typical globally. The model (the Sheffield Dynamic Global Vegetation Model, SDGVM) has been applied to contemporary vegetation dynamics and indicates a significant CO2 fertilisation effect on the sequestration of atmospheric CO2. The terrestrial carbon sink for the 20th century is simulated to be widespread between latitudes 40 degrees S and 65 degrees N, but is greatest between 10 degrees S and 6 degrees N, excluding the effects of human deforestation. The mean maximum sink capacity over the 20th century is small, at 25 gC m(-2) year(-1), or approximately 1% of gross primary production. Simulations of vegetation dynamics under a scenario of future global warming indicate a gradual decline in the terrestrial carbon sink, with the capacity to absorb human emissions of CO2 being reduced from 20% in 2000 to approximately 2% between 2075 and 2100. The responses of carbon sequestration and vegetation structure and distribution to stabilisation of climate and CO2 may extend for up to 50 years after stabilisation has occurred.

Phase I clinical trial of a human idiotypic p53 vaccine in patients with advanced malignancy.

BACKGROUND: The purpose of this study was to induce immunity to p53 by using an idiotypic vaccine, composed of a pool of eight peptides derived from the complimentarity determining regions (CDRs) of human anti-p53 antibodies. PATIENTS AND METHODS: Subjects with advanced malignancy received up to four, monthly intradermal injections of pooled peptides (500 microg of each) admixed with granulocyte-macrophage colony-stimulating factor (GM-CSF; 100 microg). In addition, two sheep and two rabbits were also vaccinated with the pooled peptides. RESULTS: Fourteen subjects were enrolled into the study and six of these completed the vaccination schedule. The vaccine was well tolerated by all subjects and no major adverse events were attributable to the vaccine. All subjects mounted in vivo delayed type hypersensitivity (DTH) responses to two or more of the individual vaccine peptides. Vaccine-induced antibodies specific for peptides 2, 5 or 8 were detected in four of six subjects, and two of these had vaccine-specific, cell-mediated responses. Increasing titers of p53-specific antibodies were found in one patient. No T-cell response to p53 was observed in any of the subjects. All animals developed humoral immunity to the peptides and one of the sheep developed rising serum titers of anti-p53 antibodies. CONCLUSIONS: Vaccination with human antibody CDR regions represents a novel method for inducing human antibodies, which may in turn serve as immunological mimics of p53.

Gemcitabine/vinorelbine in metastatic breast cancer patients previously treated with anthracyclines: results of a phase II trial.

This phase II study was designed to evaluate the response rate (RR) and toxicity of gemcitabine/vinorelbine in patients with metastatic breast cancer. All patients had previously received anthracyclines. Treatment consisted of gemcitabine 1200 mg/m2 and vinorelbine 30 mg/m2 on days 1 and 8, every 3 weeks. Twenty-five patients were enrolled. Median age was 59 years (range, 33-73 years). Ten patients had received only adjuvant therapy with anthracyclines. The remaining 15 patients had received chemotherapy for metastatic disease, including taxanes in 11 cases. Four patients could not be evaluated for response. By intent-to-treat analysis, the overall RR was 44% (95% CI, 24.4%-65%). Median duration of response and median time to treatment failure were 21 and 17 weeks, respectively. The main toxicity was hematologic, with grade 3/4 neutropenia occurring in 13 patients and 1 patient developing febrile neutropenia. Two deaths from pneumonia occurred. These results reveal an encouraging activity with a reasonable toxicity profile in a patient population with an unfavorable prognosis. Our group is conducting a randomized study to compare this combination with vinorelbine alone in patients with metastatic breast cancer after failure to respond to anthracyclines and taxanes

The activation of fibroblast growth factors by heparin: synthesis, structure, and biological activity of heparin-like oligosaccharides.

An effective strategy has been designed for the synthesis of oligosaccharides of different sizes structurally related to the regular region of heparin; this is illustrated by the preparation of hexasaccharide 1 and octasaccharide 2. This synthetic strategy provides the oligosaccharide sequence containing a D-glucosamine unit at the nonreducing end that is not available either by enzymatic or chemical degradation of heparin. It may permit, after slight modifications, the preparation of oligosaccharide fragments with different charge distribution as well. NMR spectroscopy and molecular dynamics simulations have shown that the overall structure of 1 in solution is a stable right-hand helix with four residues per turn. Hexasaccharide 1 and, most likely, octasaccharide 2 are, therefore, chemically well-defined structural models of naturally occurring heparin-like oligosaccharides for use in binding and biological activity studies. Both compounds 1 and 2 induce the mitogenic activity of acid fibroblast growth factor (FGF1), with the half-maximum activating concentration of 2 being equivalent to that of heparin. Sedimentation equilibrium analysis with compound 2 suggests that heparin-induced FGF1 dimerization is not an absolute requirement for biological activity.