CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms

Summary: Accurate estimation of DNA copy numbers from arraycomparative genomic hybridization (CGH) data is important forcharacterizing the cancer genome. An important part of thisprocess is the segmentation of the log-ratios between the sampleand control DNA along the chromosome into regions of differentcopy numbers. However, multiple algorithms are available inthe literature for this procedure and the results can vary substantiallyamong these. Thus, a visualization tool that can display thesegmented profiles from a number of methods can be helpful tothe biologist or the clinician to ascertain that a feature ofinterest did not arise as an artifact of the algorithm. Sucha tool also allows the methodologist to easily contrast hismethod against others. We developed a web-based tool that applies a number of popularalgorithms to a single array CGH profile entered by the user.It generates a heatmap panel of the segmented profiles for eachmethod as well as a consensus profile. The clickable heatmapcan be moved along the chromosome and zoomed in or out. It alsodisplays the time that each algorithm took and provides numericalvalues of the segmented profiles for download. The web interfacecalls algorithms written in the statistical language R. We encouragedevelopers of new algorithms to submit their routines to beincorporated into the website. Availability: http://compbio.med.harvard.edu/CGHweb Contact: peter_park{at}harvard.edu Associate Editor: Keith Crandall     

Pot experiment to study the uptake of Cd and Pb by three Indian mustards (Brassica juncea) grown in artificially contaminated soils

Most of the metals-contaminated and fallow lands in Taiwan are a result of irrigation with illegal effluent of factories. Phytoextraction methods can be applied to reach the target of fallow-lands reuse and earn more incomes for farmers. In many studies, Indian mustards (Brassica juncea) were planted in the metal-contaminated soils to study their suitability in phytoextraction. However, the total removal of metals by plants was quite different between accessions. In this pot study, three accessions of B. juncea (cv. 182921, cv. 211000, and cv. 426308) were planted in artificially Cd- or Pb-contaminated soils to investigate the differences between them. EDTA was applied to study its effect in increasing the bioavailability of Cd and Pb and their uptake by these Indian mustards. Experimental result showed that three accessions of Indian mustard can accumulate a high concentration of Cd and Pb when growing in the artificially Cd- and Pb-contaminated soils. Their shoot Cd or Pb concentrations were significantly enhanced, resulting from the application of EDTA. Among the three accessions, B. juncea cv. 211000 accumulated the highest concentrations of Cd and Pb in their shoots compared with B. juncea cv. 182921 and cv. 426308, but its total removal was the lowest due to its lower biomass.     

Antitumor activity of rapamycin in a Phase I trial for patients with recurrent PTEN-deficient glioblastoma

Background

There is much discussion in the cancer drug development community about how to incorporate molecular tools into early-stage clinical trials to assess target modulation, measure anti-tumor activity, and enrich the clinical trial population for patients who are more likely to benefit. Small, molecularly focused clinical studies offer the promise of the early definition of optimal biologic dose and patient population.

Methods and Findings

Based on preclinical evidence that phosphatase and tensin homolog deleted on Chromosome 10 (PTEN) loss sensitizes tumors to the inhibition of mammalian target of rapamycin (mTOR), we conducted a proof-of-concept Phase I neoadjuvant trial of rapamycin in patients with recurrent glioblastoma, whose tumors lacked expression of the tumor suppressor PTEN. We aimed to assess the safety profile of daily rapamycin in patients with glioma, define the dose of rapamycin required for mTOR inhibition in tumor tissue, and evaluate the antiproliferative activity of rapamycin in PTEN-deficient glioblastoma. Although intratumoral rapamycin concentrations that were sufficient to inhibit mTOR in vitro were achieved in all patients, the magnitude of mTOR inhibition in tumor cells (measured by reduced ribosomal S6 protein phosphorylation) varied substantially. Tumor cell proliferation (measured by Ki-67 staining) was dramatically reduced in seven of 14 patients after 1 wk of rapamycin treatment and was associated with the magnitude of mTOR inhibition (p = 0.0047, Fisher exact test) but not the intratumoral rapamycin concentration. Tumor cells harvested from the Ki-67 nonresponders retained sensitivity to rapamycin ex vivo, indicating that clinical resistance to biochemical mTOR inhibition was not cell-intrinsic. Rapamycin treatment led to Akt activation in seven patients, presumably due to loss of negative feedback, and this activation was associated with shorter time-to-progression during post-surgical maintenance rapamycin therapy (p < 0.05, Logrank test).

Conclusions

Rapamycin has anticancer activity in PTEN-deficient glioblastoma and warrants further clinical study alone or in combination with PI3K pathway inhibitors. The short-term treatment endpoints used in this neoadjuvant trial design identified the importance of monitoring target inhibition and negative feedback to guide future clinical development.Trial registration: http://www.ClinicalTrials.gov (#{"type":"clinical-trial","attrs":{"text":"NCT00047073","term_id":"NCT00047073"}}NCT00047073).     

Inhibition of migration and invasion of colorectal cancer cells via deletion of Rac1 with RNA interference

Nucleotides and nucleosides represent an important and ubiquitous class of molecules that interact with specific receptors, regulate a variety of activities within the liver, and play a role in the pathogenesis of hepatic fibrosis. Ecto-nucleotide pyrophosphatase/phosphodiesterases (E-NPPs) are ecto-enzymes that are located on the cell surface. NPP1, NPP2, and NPP3 (abbreviated as NPP1–3 hereafter) have been implicated in the hydrolysis of nucleotides; together with other ecto-nucleotidases, they control the events induced by extracellular nucleotides. We have identified and compared the expression of E-NPP family members in two different phenotypes of the mouse hepatic stellate cell line (GRX). In quiescent-like hepatic stellate cells (HSCs), E-NPP activity was significantly higher, NPP2 mRNA expression decreased and NPP3 mRNA increased. The differential NPP activity and expression in two phenotypes of GRX cells suggests that they are involved in the regulation of extracellular nucleotide metabolism in HSCs. However, the role of E-NPPs in the liver remains to be clarified.     

How to make siRNA lipoplexes efficient? Add a DNA cargo

Background

We recently reported an efficient formulation of siRNA targeting TNF-α, that was able to restore immunological balance in a mouse arthritis model following intravenous injection.

Method

Since this efficient formulation included the pre association of siRNA with a DNA cargo, we decided to extensively characterise siRNA lipoplexes with or without DNA cargo, in order to better understand the DNA cargo enhancing effect.

Results

We showed that addition of DNA cargo to siRNA lipoplexes led to specific gene extinction in vitro, using reduced siRNA concentration. This procedure is also applicable to other lipid vectors, like Lipofectamine or DMRIE-C. No structural modification could be observed in siRNA lipoplexes upon addition of DNA cargo using dynamic light scattering or transmission electronic microscopy. Nevertheless, we observed some slight differences, in the amount of lipid required to obtain neutrality of the complex and in stability of the complex towards incubation with heparan sulfate.

Conclusions

These results suggest that the addition of DNA cargo to siRNA complexes is an easy procedure that leads to more efficient complexes to transfer siRNA at low concentration and in the presence of serum.     

Stratigraphy and palaeoenvironmental implications of Pleistocene and Holocene aeolian sediments in the Lhasa area,southern Tibet (China)

Along the middle and lower reaches of the Kyichu River and its tributaries (Lhasa area, southern Tibet), a multidisciplinary study was carried out in order to investigate the areal distribution, sedimentological properties, ages and palaeoenvironmental implications of aeolian deposits including intercalated palaeosols. This research was initiated to investigate to what extent southern Tibet is influenced by past human activity, as even recent evaluations perceive the present treeless desertic environment as natural. Fifteen profiles were recorded at an altitude of 3540–4580 m a.s.l. with subsequent sedimentological, geochronological (OSL, AMS ¹⁴C) and palaeobotanical (charcoal) analyses. Sediment properties of both loesses and aeolian sands reveal an origin from aeolian sorting of nearby fluvial deposits. The calculated ages are the oldest obtained thus far on aeolian sediments from southern and interior Tibet, revealing natural aeolian sedimentation before and around the Last Glacial Maximum (c. 20 ka). However, a distinct portion of Late Holocene sandy aeolian sediments also occurs. Both the evidence for the aeolian dynamics (widespread Pleistocene loess and aeolian sand deposition, local Late Holocene aeolian sand deposition, modern reactivation of widespread Pleistocene aeolian sands) and the palaeobotanical findings (Late Holocene vegetation change from a tree-bearing to a widely treeless landscape) provide evidence that the Lhasa area was strongly influenced by human activity since at least the Late Neolithic (c. 4200 cal yrs BP). Thus the present-day desertic environment might not primarily be a result of the semiarid climate or the high-altitude conditions, but rather of activities of the humans and their collateral effects. However, once established, this semi-natural ecosystem persisted, controlled by strong grazing, firewood extraction, erosion and harsh edaphic conditions, preventing the recovery of trees.     

Carbon balance of anaerobic granulation process: carbon credit

The concept of carbon credit arose out of increasing awareness of the need to reduce emissions of greenhouse gases to combat global warming which was formalized in the Kyoto protocol. In addition to contribution to sustainable development with energy recovery in the form of methane, carbon credits can be claimed by application of advanced anaerobic processes in wastewater treatment for reducing emissions of greenhouse gases. As anaerobic granular systems are capable of handling high organic loadings concomitant with high strength wastewater and short hydraulic retention time, they could render much more carbon credits than other conventional anaerobic systems. This study investigated the potential carbon credit derived from laboratory-scale upflow anaerobic sludge blanket (UASB) reactors based on a carbon balance analysis. Methane emission reduction could be calculated by calculating the difference of UASB reactors and open lagoon treatment systems. Based on the 2.5l bench-scale reactor, the total CH(4) emissions reduction was calculated as 29 kg CO(2)/year. On scaling up to a typical full-scale anaerobic digester, the total CH(4) emissions reduction could achieve 46,420 tons CO(2) reduction/year. The estimated carbon credits would amount to 278,500 US$ per year by assuming a carbon price of 6 US$ per metric ton CO(2) reduction. The analysis postulated that it is financially viable to invest in advanced anaerobic granular treatment system from the revenue generated from carbon credits.     

Discovery of diarylpyridine derivatives as novel non-nucleoside HIV-1 reverse transcriptase inhibitors

Two series (4 and 5) of diarylpyridine derivatives were designed, synthesized, and evaluated for anti-HIV-1 activity. The most promising compound, 5e, inhibited HIV-1 IIIB, NL4-3, and RTMDR1 with low nanomolar EC₅₀ values and selectivity indexes of >10,000. The results of this study indicate that diarylpyridine can be used as a novel scaffold to derive a new class of potent NNRTIs, active against both wild-type and drug-resistant HIV-1 strains.