Capturing open ocean biodiversity: Comparing environmental DNA metabarcoding to the continuous plankton recorder.

Environmental DNA (eDNA) metabarcoding is emerging as a novel, objective tool for monitoring marine metazoan biodiversity. Zooplankton biodiversity in the vast open ocean is currently monitored through continuous plankton recorder (CPR) surveys, using ship-based bulk plankton sampling and morphological identification. We assessed whether eDNA metabarcoding (2 L filtered seawater) could capture similar Southern Ocean zooplankton biodiversity as conventional CPR bulk sampling (~1,500 L filtered seawater per CPR sample). We directly compared eDNA metabarcoding with (a) conventional morphological CPR sampling and (b) bulk DNA metabarcoding of CPR collected plankton (two transects for each comparison, 40 and 44 paired samples, respectively). A metazoan-targeted cytochrome c oxidase I (COI) marker was used to characterize species-level diversity. In the 2 L seawater eDNA samples, this marker amplified large amounts of non-metazoan picoplanktonic algae, but eDNA metabarcoding still detected up to 1.6 times more zooplankton species than morphologically analysed bulk CPR samples. COI metabarcoding of bulk DNA samples mostly avoided nonmetazoan amplifications and recovered more zooplankton species than eDNA metabarcoding. However, eDNA metabarcoding detected roughly two thirds of metazoan species and identified similar taxa contributing to community differentiation across the subtropical front separating transects. We observed a diurnal pattern in eDNA data for copepods which perform diel vertical migrations, indicating a surprisingly short temporal eDNA signal. Compared to COI, a eukaryote-targeted 18S ribosomal RNA marker detected a higher proportion, but lower diversity, of metazoans in eDNA. With refinement and standardization of methodology, eDNA metabarcoding could become an efficient tool for monitoring open ocean biodiversity.

Clinical features, treatment, and survival of patients with colorectal cancer with or without inflammatory bowel disease.

BACKGROUND & AIMS: Inflammatory bowel disease (IBD) increases the risk of colorectal cancer (CRC), indicating that inflammation might alter tumor characteristics and potentially affect treatment and survival. Published data on this topic are inconclusive, so we conducted a population-based study in Ireland to address it. METHODS: We used the National Cancer Registry to collect data on all patients diagnosed with CRC in Ireland from 1994 to 2005 (n = 22,335) and identified those who also had IBD (n = 170). The clinical characteristics, treatment, and survival of patients with IBD and CRC were compared with those of patients with CRC without IBD. RESULTS: Patients with CRC and IBD were, on average, 7.7 years younger than those without IBD at diagnosis of CRC (P = .001), and were less likely to smoke (P = .002). Fewer CRCs in patients with IBD were stage 4 at diagnosis (12% vs 22% in non-IBD patients; P < .001). There was no significant difference in CRC treatment modalities between patients with or without IBD (P = .57). The median survival time of CRC patients with IBD was about 3 years longer than that of patients without IBD (P < .001). However, Cox proportional hazards analysis revealed that IBD was not a significant prognostic factor for CRC (P = .97). However, older age, male sex, smoking, and advanced grade and stage all were associated independently with shorter survival time. When propensity score matching was used to analyze outcomes, the survival times of CRC patients with and without IBD did not differ significantly. CONCLUSIONS: The features of patients with CRC and IBD differ significantly from those of CRC patients without IBD, but each group of patients receive similar treatment and have similar patterns of disease progression after diagnosis.

Regulation of NF-kappaB responses by epigenetic suppression of IkappaBalpha expression in HCT116 intestinal epithelial cells.

Intestinal epithelial cells play critical roles in regulating mucosal immunity. Since epigenetic factors such as DNA methylation and histone modifications are implicated in aging, carcinogenesis, and immunity, we set out to assess any role for epigenetic factors in the regulation of intestinal epithelial cell immune responses. Experiments were conducted using the HCT116 cell line, and a subclone was genetically engineered to lack DNA methyltransferases (DNMT). The induction of the chemokine interleukin-8 and the antiapoptotic protein cFLIP by tumor necrosis factor-alpha were markedly less in HCT116 cells lacking DNMT than in parental cells. These effects were accompanied by lower monocyte chemotaxis and higher caspase signaling in HCT116 cells lacking DNMT than parental cells. Tumor necrosis factor-alpha-induced NF-kappaB activation was blocked and IkappaBalpha expression was higher in HCT116 cells lacking DNMT than in parental cells. A CpG island in the IkappaBalpha gene promoter region was found to contain variable levels of methylation in parental HCT116 cells. Chromatin immunoprecipitation analysis of histone proteins bound to the IkappaBalpha gene promoter revealed that higher levels of IkappaBalpha expression in HCT116 cells lacking DNMT compared with parental cells were accompanied by more chromatin marks permissive to gene transcription. These findings show that epigenetic factors influence the NF-kappaB system in intestinal epithelial cells, resulting in a previously unrecognized mechanism of innate immune regulation.

In Situ Vibrational Probes of Epoxy Gelation.

This paper presents an efficient way to measure the curing kinetics and gel point, αgel, in epoxy resins from one single experiment. The epoxy curing reaction is herein monitored using in situ and time-resolved near-infrared absorption spectroscopy (NIR). The curing profiles over different isothermal conditions are in good agreement with DSC. Furthermore, the increase of the NIR absorption bands of aromatic rings (unreactive throughout curing) probe the cure shrinkage, as more and more aromatic rings are localized within the fixed sample volume. Therefore, the gel point is determined using the onset of the aromatic absorption increase. The results are in good agreement with the theoretical gel point, as well as DMA results. This innovative approach enables gelation measurements on epoxy neat resins and film composites with an easy-to-perform, accurate, robust, and versatile method.

Diurnally Fluctuating pCO2 Modifies the Physiological Responses of Coral Recruits Under Ocean Acidification.

Diurnal pCO2 fluctuations have the potential to modulate the biological impact of ocean acidification (OA) on reef calcifiers, yet little is known about the physiological and biochemical responses of scleractinian corals to fluctuating carbonate chemistry under OA. Here, we exposed newly settled Pocillopora damicornis for 7 days to ambient pCO2, steady and elevated pCO2 (stable OA) and diurnally fluctuating pCO2 under future OA scenario (fluctuating OA). We measured the photo-physiology, growth (lateral growth, budding and calcification), oxidative stress and activities of carbonic anhydrase (CA), Ca-ATPase and Mg-ATPase. Results showed that while OA enhanced the photochemical performance of in hospite symbionts, it also increased catalase activity and lipid peroxidation. Furthermore, both OA treatments altered the activities of host and symbiont CA, suggesting functional changes in the uptake of dissolved inorganic carbon (DIC) for photosynthesis and calcification. Most importantly, only the fluctuating OA treatment resulted in a slight drop in calcification with concurrent up-regulation of Ca-ATPase and Mg-ATPase, implying increased energy expenditure on calcification. Consequently, asexual budding rates decreased by 50% under fluctuating OA. These results suggest that diel pCO2 oscillations could modify the physiological responses and potentially alter the energy budget of coral recruits under future OA, and that fluctuating OA is more energetically expensive for the maintenance of coral recruits than stable OA.

A new model to monitor the virological efficacy of antiretroviral treatment in resource-poor countries.

Monitoring the efficacy of antiretroviral treatment in developing countries is difficult because these countries have few laboratory facilities to test viral load and drug resistance. Those that exist are faced with a shortage of trained staff, unreliable electricity supply, and costly reagents. Not only that, but most HIV patients in resource-poor countries do not have access to such testing. We propose a new model for monitoring antiretroviral treatment in resource-limited settings that uses patients' clinical and treatment history, adherence to treatment, and laboratory indices such as haemoglobin level and total lymphocyte count to identify virological treatment failure, and offers patients future treatment options. We believe that this model can make an accurate diagnosis of treatment failure in most patients. However, operational research is needed to assess whether this strategy works in practice.

First-line antiretroviral therapy in Africa--how evidence-base are our recommendations?

According to the World Health Organization guidelines, a non-nucleoside reverse transcriptase inhibitor (NNRTI) along with two nucleoside reverse transcriptase inhibitors (NRTI) is the treatment of choice as first-line antiretroviral therapy. The results of the 2NN and different cohort studies performed in developed countries do not provide sufficient evidence by which to select between nevirapine and efavirenz as the first-line NNRTI for antiretroviral therapy in Africa. The current first-line NNRTI-containing antiretroviral therapy regimens used in Africa are certainly not ideal. Nevirapine interacts with rifampicin and therefore is not indicated in patients with tuberculosis. On the other hand, efavirenz should not be given to pregnant women. NNRTI-containing regimens may be less effective in women who received nevirapine monotherapy at delivery. Stavudine, used in the nucleoside backbone, may lead to lipoatrophy, lactic acidosis and polyneuritis. Zidovudine may cause serious anemia. Mainly because of cost considerations, the generic fixed-drug combination of nevirapine plus two NRTI seems at the moment to be the best choice. It is clear, however, that antiretroviral programs should not rely only on this combination for initial antiretroviral treatment. Most importantly, more HIV clinical trials need to be conducted in Africa, and African cohorts of patients on antiretroviral therapy need to be established in order to develop recommendations that are evidence based.

Effect of genetic deletion or pharmacological antagonism of tumor necrosis factor alpha on colitis-associated carcinogenesis in mice.

BACKGROUND: Intestinal inflammation in inflammatory bowel diseases is driven by abnormal levels of proinflammatory cytokines, where tumor necrosis factor (TNF)-α seems to be particularly important. Chronic inflammatory signaling in the colon increases the risk of colorectal cancer, so we sought to evaluate the role of TNF-α in a mouse model of this condition. METHODS: TNF mice were treated with azoxymethane/dextran sulfate sodium to induce inflammation and tumorigenesis. Etanercept was used to produce pharmacological ablation of TNF-α in wild-type mice. Subsequent activation of procarcinogenic transcription factor NF-κB and relevant proinflammatory cytokines of the TNF superfamily were measured through immunohistochemistry and quantitative polymerase chain reaction methods. RESULTS: Results showed that the severity of colitis, as assessed by mortality, histological scoring, and cytokine expression levels, was similar or slightly higher in mice lacking TNF-α than in control mice. Activation levels of NF-κB were not influenced by the presence of TNF-α. We also observed upregulated expression of TNF family member TNF-ß, TNF receptors 1 and 2 and a variety of other proinflammatory factors in colitis-associated tumors of TNF mice, compared with levels in tumors of control mice. Neither genetic ablation of TNF-α nor pharmacological inhibition of the TNF family using etanercept reduced tumor number. CONCLUSIONS: Our results reveal a redundant role for TNF-α in a mouse model of colitis-associated tumorigenesis, indicating a high degree of redundancy in proinflammatory cytokine networks in this model.

Ozone and natural systems: understanding exposure, response, and risk.

Research aimed at understanding the response of plants to ozone has been conducted for over four decades but little of it has addressed intact natural systems. Even so, there is sufficient scientific information at this time to support air quality standards that will protect natural terrestrial ecosystems from ozone. What is unknown is the risk associated with continued exposure of natural systems, including both above- and below-ground components, in combination with other stresses including changing temperature and precipitation, elevated carbon dioxide, pests and pathogens, invasive species, and other activities that may fragment the landscape. Research to support an assessment of the ecological risk associated with ozone as it exists, in a milieu of stresses, must include endpoints beyond those addressed in the past, primarily productivity and species composition. To estimate the risk to society of ozone impacts on natural systems, endpoints such as the integrity of soil food webs, the quantity and quality of water supplied from terrestrial ecosystems, wildlife and recreational values, and the transfer and fate of carbon, nutrients, and water within the systems must be quantified. Not only will this research provide the basis for a sound estimate of risk, but also it will improve our understanding of fundamental ecosystem processes.

How to manage the risk of colorectal cancer in ulcerative colitis.

There is a strong association between chronic inflammation and cancer formation. This correlation has been well observed in patients with long standing inflammatory bowel disease (IBD) who are at high risk of colorectal cancer (CRC). At present, there is a lack of good markers for predicting the progression from normal to neoplastic mucosa in patients with IBD. IBD patients who are 'at-risk' of CRC should be identified, evaluated and should also be enrolled in surveillance program, regardless of their disease activity. Early identification of dysplasia and its appropriate management using endoscopic techniques or surgery are essential in patients with long-standing IBD, to minimize CRC morbidity and mortality. Gastroenterologists should work along with experienced, specialised gastrointestinal pathologists, surgeons and with fully informed and compliant IBD patients' to ensure the success of surveillance programme in early detection of CRC.

Stricter ozone ambient air quality standard has beneficial effect on ponderosa pine in California.

Ambient air quality standards and control strategies are implemented to protect humans and vegetation from adverse effects. We used a process-based tree-growth model (TREGRO) to show that over the past 37 years, changes in O(3) exposure, with accompanying variation in climate, are reflected in changes in the growth of Pinus ponderosa Dougl. ex Laws. in the San Bernardino Mountains near Los Angeles, California, USA. Despite variation in temperature and precipitation over the study period (1963-1999), O(3) exposure consistently reduced simulated tree growth. Simulated growth reductions increased concurrent with increasing O(3) exposure. The maximum growth reduction occurred in 1979. As O(3) exposures decreased during the 1980s and 1990s, effects on growth also decreased. This implies that emission control strategies taken to reduce exposures to attain O(3) standards benefited P. ponderosa growth in the San Bernardino Mountains. This modeling approach provides a powerful tool for solving the difficult problem of evaluating regulatory effectiveness by simulating plant response using long-term climate and air pollution exposure records for a given region.