Using lognormal distributions and lognormal probability plots in probabilistic risk assessments

Lognormal distributions play a central role in human and ecological risk assessment, so every risk assessor needs to understand and exploit their basic properties. Similarly, Lognormal probability plots are invaluable because they provide a powerful way to visualize measured data or simulated results.     

Microbiological methods for the cleanup of soil and ground water contaminated with halogenated organic compounds

Abstract There is growing interest in the enhancement of microbial degradative activities as a means of bringing about the in situ cleanup of contaminated soils and ground water. The halogenated organic compounds are likely to be prime targets for such biotechnological processes because of their widespread utilisation and the biodegradability of many of the most commonly used compounds. The aim of this review is to consider the potential for microbiological cleanup of haloorganic-contaminated sites. The technologies available involve the provision of suitable environmental conditions to facilitate maximum biodegradation rates either in the subsurface or in on-site bioreactors. Methodologies include the supply of inorganic nutrients, the supply of oxygen gas, the addition of degradative microbial inocula and the introduction of co-metabolic substrates. The potential efficiencies and limitations of the methods are critically discussed from a microbiological viewpoint with respect to substrate degradability and population responses to supplementation.     

Microbiological methods for the cleanup of soil and ground water contaminated with halogenated organic compounds

There is growing interest in the enhancement of microbial degradative activities as a means of bringing about the in situ cleanup of contaminated soils and ground water. The halogenated organic compounds are likely to be prime targets for such biotechnological processes because of their widespread utilisation and the biodegradability of many of the most commonly used compounds. The aim of this review is to consider the potential for microbiological cleanup of haloorganic-contaminated sites. The technologies available involve the provision of suitable environmental conditions to facilitate maximum biodegradation rates either in the subsurface or in on-site bioreactors. Methodologies include the supply of inorganic nutrients, the supply of oxygen gas, the addition of degradative microbial inocula and the introduction of co-metabolic substrates. The potential efficiencies and limitations of the methods are critically discussed from a microbiological viewpoint with respect to substrate degradability and population responses to supplementation.     

The discovery and validation of new drug targets in cancer

Advances in our understanding of the signal transduction pathways involved in cellular growth control have provided several new strategies for cancer therapy. Recent advances now make it possible to develop selective inhibitors targeting genomic instability, the growth, survival, and invasion of the tumor, and its nourishment through the growth of new blood vessels.     

From cancer metabolism to new biomarkers and drug targets

Great interest is presently given to the analysis of metabolic changes that take place specifically in cancer cells. In this review we summarize the alterations in glycolysis, glutamine utilization, fatty acid synthesis and mitochondrial function that have been reported to occur in cancer cells and in human tumors. We then propose considering cancer as a system-level disease and argue how two hallmarks of cancer, enhanced cell proliferation and evasion from apoptosis, may be evaluated as system-level properties, and how this perspective is going to modify drug discovery. Given the relevance of the analysis of metabolism both for studies on the molecular basis of cancer cell phenotype and for clinical applications, the more relevant technologies for this purpose, from metabolome and metabolic flux analysis in cells by Nuclear Magnetic Resonance and Mass Spectrometry technologies to positron emission tomography on patients, are analyzed. The perspectives offered by specific changes in metabolism for a new drug discovery strategy for cancer are discussed and a survey of the industrial activity already going on in the field is reported.     

MiRNA genes constitute new targets for microsatellite instability in colorectal cancer

Mismatch repair-deficient colorectal cancers (CRC) display widespread instability at DNA microsatellite sequences (MSI). Although MSI has been reported to commonly occur at coding repeats, leading to alterations in the function of a number of genes encoding cancer-related proteins, nothing is known about the putative impact of this process on non-coding microRNAs. In miRbase V15, we identified very few human microRNA genes with mono- or di-nucleotide repeats (n = 27). A mutational analysis of these sequences in a large series of MSI CRC cell lines and primary tumors underscored instability in 15 of the 24 microRNA genes successfully studied at variable frequencies ranging from 2.5% to 100%. Following a maximum likelihood statistical method, microRNA genes were separated into two groups that differed significantly in their mutation frequencies and in their tendency to represent mutations that may or may not be under selective pressures during MSI tumoral progression. The first group included 21 genes that displayed no or few mutations in CRC. The second group contained three genes, i.e., hsa-mir-1273c, hsa-mir-1303 and hsa-mir-567, with frequent (≥ 80%) and sometimes bi-allelic mutations in MSI tumors. For the only one expressed in colonic tissues, hsa-mir-1303, no direct link was found between the presence or not of mono- or bi-allelic alterations and the levels of mature miR expression in MSI cell lines, as determined by sequencing and quantitative PCR respectively. Overall, our results provide evidence that DNA repeats contained in human miRNA genes are relatively rare and preserved from mutations due to MSI in MMR-deficient cancer cells. Functional studies are now required to conclude whether mutated miRNAs, and especially the miR-1303, might have a role in MSI tumorigenesis.     

Including species interactions in risk assessments for global change

Most ecological risk assessments for global change are restricted to the effects of trends in climate or atmospheric carbon dioxide. In order to move beyond investigation of the effects of climate alone, the climex ^™ model was extended to investigate the effects of species interactions, in the same or different trophic levels, along environmental gradients on a geographical scale. Specific needs that were revealed during the investigations include: better treatment of the effects of temporal and spatial climatic variation; elucidation of the nature of boundaries of species ranges; data to quantify the role of species traits in interspecies interactions; integrated observational, experimental, and modelling studies on mechanisms of species interactions along environmental gradients; and high‐resolution global environmental datasets. Greater acknowledgement of the shared limitations of simplified models and experimental studies is also needed. Above all, use of the scientific method to understand representative species ranges is essential. This requires the use of mechanistic approaches capable of progressive enhancement.     

Quick start guide to soil methods for ecologists

Increasingly biologists and ecologists are becoming aware of the vital importance of soil to processes observed aboveground and are incorporating soil analyses into their research. Because of the dynamic and heterogeneous nature of soil, proper incorporation of soil analysis into ecological studies requires knowledge and planning. Unfortunately, many ecologists may not be current (or trained at all) in soil science. We provide this review, based on our cumulative >60 years of work in soil science, to help familiarize researchers with essential information to appropriately incorporate soil analyses into ecological studies. Specifically, we provide a brief introduction into soils and then discuss issues related to soil sterilization, choosing a soil for a greenhouse project, sampling soils, and soil analyses.     

Valid historical data for probabilistic risk analysis in natural disasters

With the changes in the nature and the society, risks will inevitably change. It implies that, with the passage of time, some historical data would be invalid for probabilistic risk analysis. In this paper, a model to acquire the valid data is suggested, which is based on the Mann- Kendall test to detect abrupt change-point on time series data. What's more, the typhoon risk analysis in Guangdong Province, China is used as a case study to show how to apply the model. The valid data of the intensities of typhoons and the related losses in the province for the probabilistic risk analysis is obtained from the data during the time from 1984 to 2012. Comparing with the results based on the set of invalid data and the set of all collected data, the assessed risk based on the valid data is more reliable, which could reflect the dynamics of the typhoon risk.     

An improved understanding of soil Cd risk to humans and low cost methods to phytoextract Cd from contaminated soils to prevent soil Cd risks

We believe greater consideration should be given the agronomic and nutritional/bioavailability factors that influence risk from Cd-contaminated soils. We have argued that the ability of rice to accumulate soil Cd in grain while excluding Fe, Zn and Ca (even though the soil contains 100-times more Zn than Cd) was important in adverse effects of soil Cd is farm families in Asia. Further, polished rice grain is deficient in Fe, Zn and Ca for humans, which promotes Cd absorption into duodenal cells. New kinetic studies clarified that dietary Cd is absorbed into duodenum enterocytes; 109Cd from a single meal remained in the duodenum for up to 16 days; part of the turnover pool 109Cd moved to the liver and kidneys by the end of the 64-day 'chase' period. Thus malnutrition induced by subsistence rice diets caused a higher absorption of dietary Cd and much higher potential risk from soil Cd than other crops. Because rice-induced Fe-Zn-Ca-malnutrition is so important in soil Cd risk, it seems evident that providing nutritional supplements to populations of exposed subsistence rice farmers could protect them against soil Cd during a period of soil remediation. In the long term, high Cd rice soils need to be remediated. Remediation by removal and replacement of contaminated soil is very expensive (on the order of $3 million/ha); while phytoextraction using the high Cd accumulating ecotypes of the Zn-Cd hyperaccumulator, Thlaspi caerulescens, should provide low cost soil Cd remediation.     

Splicing dysregulation in cancer: from mechanistic understanding to a new class of therapeutic targets

RNA splicing dysregulation is widespread in cancer. Accumulating evidence demonstrates that splicing defects resulting from splicing dysregulation play critical roles in cancer pathogenesis and can serve as new biomarkers and therapeutic targets for cancer intervention. These findings have greatly deepened the mechanistic understandings of the regulation of alternative splicing in cancer cells, leading to rapidly growing interests in targeting cancer-related splicing defects as new therapies. Here we summarize the current research progress on splicing dysregulation in cancer and highlight the strategies available or under development for targeting RNA splicing defects in cancer.     

Mechanisms for stalled replication fork stabilization: new targets for synthetic lethality strategies in cancer treatments

Timely and faithful duplication of the entire genome depends on completion of replication. Replication forks frequently encounter obstacles that may cause genotoxic fork stalling. Nevertheless, failure to complete replication rarely occurs under normal conditions, which is attributed to an intricate network of proteins that serves to stabilize, repair and restart stalled forks. Indeed, many of the components in this network are encoded by tumour suppressor genes, and their loss of function by mutation or deletion generates genomic instability, a hallmark of cancer. Paradoxically, the same fork‐protective network also confers resistance of cancer cells to chemotherapeutic drugs that induce high‐level replication stress. Here, we review the mechanisms and major pathways rescuing stalled replication forks, with a focus on fork stabilization preventing fork collapse. A coherent understanding of how cells protect their replication forks will not only provide insight into how cells maintain genome stability, but also unravel potential therapeutic targets for cancers refractory to conventional chemotherapies.     

转Bt基因作物对土壤节肢动物的生态风险性

土壤节肢动物在土壤生态系统物质循环中起着非常重要的作用,因此人们越来越关心转基因作物对土壤节肢动物的生态安全性。本文在介绍转基因作物对土壤节肢动物影响机制的基础上,重点论述了土壤跳虫、螨类、甲虫、水生昆虫等节肢动物对不同转基因作物响应的研究进展,旨在为科学全面的开展转基因作物土壤生态风险评价提供参考。