Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach

Background

Continuous efforts to estimate actual diversity and to trace the species distribution and ranges in the natural environments have gone in equal pace with advancements of the technologies in the study of microbial species diversity from microscopic observations to DNA-based barcoding. DNA metabarcoding based on Next Generation Sequencing (NGS) constitutes the latest advancement in these efforts. Here we use NGS data from different sites to investigate the geographic range of six species of the diatom family Leptocylindraceae and to identify possible new taxa within the family.

Methodology/Principal Findings

We analysed the V4 and V9 regions of the nuclear-encoded SSU rDNA gene region in the NGS database of the European ERA-Biodiversa project BioMarKs, collected in plankton and sediments at six coastal sites in European coastal waters, as well as environmental sequences from the NCBI database. All species known in the family Leptocylindraceae were detected in both datasets, but the much larger Illumina V9 dataset showed a higher species coverage at the various sites than the 454 V4 dataset. Sequences identical or similar to the references of Leptocylindrus aporus, L. convexus, L. danicus/hargravesii and Tenuicylindrus belgicus were found in the Mediterranean Sea, North Atlantic Ocean and Black Sea as well as at locations outside Europe. Instead, sequences identical or close to that of L. minimus were found in the North Atlantic Ocean and the Black Sea but not in the Mediterranean Sea, while sequences belonging to a yet undescribed taxon were encountered only in Oslo Fjord and Baffin Bay.

Conclusions/Significance

Identification of Leptocylindraceae species in NGS datasets has expanded our knowledge of the species biogeographic distribution and of the overall diversity of this diatom family. Individual species appear to be widespread, but not all of them are found everywhere. Despite the sequencing depth allowed by NGS and the wide geographic area covered by this study, the diversity of this ancient diatom family appears to be low, at least at the level of the marker used in this study.     

Salinity as a regulator of DMSP degradation in Ruegeria pomeroyi DSS-3

Dimethylsulfoniopropionate (DMSP) is an important carbon and sulfur source to marine bacterial communities and the main precursor of dimethylsulfide (DMS), a gas that influences atmospheric chemistry and potentially the global climate. In nature, bacterial DMSP catabolism can yield different proportions of DMS and methanethiol (MeSH), but relatively little is known about the factors controlling the pathways of bacterial degradation that select between their formation (cleavage vs. demethiolation). In this study, we carried out experiments to evaluate the influence of salinity on the routes of DMSP catabolism in Ruegeria pomeroyi DSS-3. We monitored DMS and MeSH accumulation in cell suspensions grown in a range of salinities (10, 20, 30 ppt) and with different DMSP amendments (0, 50, 500 µM). Significantly higher concentrations of DMS accumulated in low salinity treatments (10 ppt; P < 0.001), in both Marine Basal Medium (MBM) and half-strength Yeast Tryptone Sea Salts (1/2 YTSS) media. Results showed a 47.1% and 87.5% decrease of DMS accumulation, from salinity 10 to 20 ppt, in MBM and 1/2 YTSS media, respectively. On the other hand, MeSH showed enhanced accumulations at higher salinities (20, 30 ppt), with a 90.6% increase of MeSH accumulation from the 20 ppt to the 30 ppt salinity treatments. Our results with R. pomeroyi DSS-3 in culture are in agreement with previous results from estuarine sediments and demonstrate that salinity can modulate selection of the DMSP enzymatic degradation routes, with a consequent potential impact on DMS and MeSH liberation into the atmosphere.     

Systematic Review of the Risk of Adverse Outcomes Associated with Vascular Endothelial Growth Factor Inhibitors for the Treatment of Cancer

Background

Anti-angiogenic therapy targeted at vascular endothelial growth factor (VEGF) is now used to treat several types of cancer. We did a systematic review of randomized controlled trials (RCTs) to summarize the adverse effects of vascular endothelial growth factor inhibitors (VEGFi), focusing on those with vascular pathogenesis.

Methods and Findings

We searched MEDLINE, EMBASE and Cochrane Library until April 19, 2012 to identify parallel RCTs comparing a VEGFi with a control among adults with any cancer. We pooled the risk of mortality, vascular events (myocardial infarction, stroke, heart failure, and thromboembolism), hypertension and new proteinuria using random-effects models and calculated unadjusted relative risk (RR). We also did meta-regression and assessed publication bias. We retrieved 83 comparisons from 72 studies (n = 38,078) on 11 different VEGFi from 7901 identified citations. The risk of mortality was significantly lower among VEGFi recipients than controls (pooled RR 0.96, 95% confidence interval [CI] 0.94 to 0.98, I² = 0%, tau2 = 0; risk difference 2%). Compared to controls, VEGFi recipients had significantly higher risk of myocardial infarction (MI) (RR 3.54, 95% CI 1.61 to 7.80, I² = 0%, tau2 = 0), arterial thrombotic events (RR 1.80, 95% CI 1.24 to 2.59, I² = 0%, tau2 = 0); hypertension (RR 3.46, 95% CI 2.89 to 4.15, I² = 58%, tau2 = 0.16), and new proteinuria (RR 2.51, 95% CI 1.60 to 3.94, I² = 87%, tau2 = 0.65). The absolute risk difference was 0.8% for MI, 1% for arterial thrombotic events, 15% for hypertension and 12% for new proteinuria. Meta-regression did not suggest any statistically significant modifiers of the association between VEGFi treatment and any of the vascular events. Limitations include heterogeneity across the trials.

Conclusions

VEGFi increases the risk of MI, hypertension, arterial thromboembolism and proteinuria. The absolute magnitude of the excess risk appears clinically relevant, as the number needed to harm ranges from 7 to 125. These adverse events must be weighed against the lower mortality associated with VEGFi treatment.     

Expression of Integrin ��v��6 and TGF-�� in Scarless vs Scar-forming Wound Healing

Oral mucosal wounds heal with reduced scar formation compared with skin. The epithelial integrin αvβ6 is induced during wound healing, and it can activate fibrogenic transforming growth factor β1 (TGF-β1) and anti-fibrogenic TGF-β3 that play key roles in scar formation. In this study, expression of β6 integrin and members of the TGF-β pathway were studied in experimental wounds of human gingiva and both gingiva and skin of red Duroc pigs using real-time PCR, gene microarrays, and immunostaining. Similar to human wounds, the expression of β6 integrin was induced in the pig wounds 7 days after wounding and remained upregulated >49 days. The αvβ6 integrin was colocalized with both TGF-β isoforms in the wound epithelium. Significantly higher expression levels of β6 integrin and TGF-β1 were observed in the pig gingival wounds compared with skin. Early gingival wounds also expressed higher levels of TGF-β3 compared with skin. The spatio-temporal colocalization of αvβ6 integrin with TGF-β1 and TGF-β3 in the wound epithelium suggests that αvβ6 integrin may activate both isoforms during wound healing. Prolonged expression of αvβ6 integrin along with TGF-β3 in the gingival wound epithelium may be important in protection of gingiva from scar formation. (J Histochem Cytochem 57:543–557, 2009)     

Contact angle anomalies indicate that surface-active eluates from silicone coatings inhibit the adhesive mechanisms of fouling organisms

Silicone coatings with critical surface tensions (CST) between 20 and 30 mN m-1 more easily release diverse types of biofouling than do materials of higher and lower CST. Oils added to these coatings selectively further diminish the attachment strengths of different marine fouling organisms, without significantly modifying the initial CST. In a search for the mechanisms of this improved biofouling resistance, the interfacial instabilities of four silicone coatings were characterised by comprehensive contact angle analyses, using up to 12 different diagnostic fluids selected to mimic the side chain chemistries of the common amino acids of bioadhesive proteins. The surfaces of painted steel test panels were characterised both before and after exposure to freshwater, brackish water, and seawater over periods ranging from 9 months to nearly 4 years. Contact angle measurements demonstrated significant surface activity of the oil-amended coatings both before and after long-term underwater exposure. The surface activity of the control (coating without oil) increased as a result of underwater exposure, consistent with mild surface chain scission and hydrolysis imparting a self-surfactancy to the coating and providing a weak boundary layer promoting continuing easy release of attaching foulants. Coatings with additives that most effectively reduced biofouling showed both initial and persistent contact angle anomalies for the test liquid, thiodiglycol, suggesting lower-shear biofouling release mechanisms based upon diminished bioadhesive crosslinking by interfering with hydrogen- and sulfhydryl bonds. Swelling of the silicone elastomeric coatings by hydrocarbon fluids was observed for all four coatings, before and after immersion.     

Interspecific variation in patterns of adhesion of marine fouling to silicone surfaces

The adhesion of six fouling organisms: the barnacle Balanus eburneus, the gastropod mollusc Crepidulafornicata, the bivalve molluscs Crassostrea virginica and Ostrea/Dendrostrea spp., and the serpulid tubeworms Hydroides dianthus and H. elegans, to 12 silicone fouling-release surfaces was examined. Removal stress (adhesion strength) varied among the fouling species and among the surfaces. Principal component analysis of the removal stress data revealed that the fouling species fell into two distinct groups, one comprising the bivalve molluscs and tubeworms, and the other the barnacle and the gastropod mollusc. None of the silicone materials generated a minimum in removal stress for all the organisms tested, although several surfaces produced low adhesion strengths for both groups of species. These results suggest that fouling-release materials do not rank (in terms of adhesion strength) identically for all fouling organisms, and thus development of a globally-effective hull coating will continue to require testing against a diversity of encrusting species.     

Benefits and harms of erythropoiesis-stimulating agents for anemia related to cancer: a meta-analysis

Background

Erythropoiesis-stimulating agents are used to treat anemia in patients with cancer. However, their safety and effectiveness is controversial. We did a systematic review of the clinical efficacy and harms of these agents in adults with anemia related to cancer or chemotherapy.

Methods

We conducted a systematic review of published and unpublished randomized controlled trials (RCTs) using accepted methods for literature searches, article selection, data extraction and quality assessment. We included RCTs involving anemic adults with cancer. We compared the use of erythropoiesis-stimulating agents with nonuse and assessed clinical outcomes (all-cause mortality, cardiovascular events and hypertension, health-related quality of life, blood transfusions and tumour response) and harms (serious adverse events) between groups.

Results

We identified 52 trials (n = 12 006) that met our selection criteria. The pooled all-cause mortality during treatment was significantly higher in the group receiving erythropoiesis-stimulating therapy than in the control group (relative risk [RR] 1.15, 95% confidence interval [CI] 1.03 to 1.29). Compared with no treatment, use of erythropoiesis-stimulating agents led to clinically detectable improvements in disease-specific measures of quality of life. It also reduced the use of blood transfusions (RR 0.64, 95% CI 0.56 to 0.73). However, it led to an increased risk of thrombotic events (RR 1.69, 95% CI 1.27 to 2.24) and serious adverse events (RR 1.16, 95% CI 1.08 to 1.25).

Interpretation

Use of erythropoiesis-stimulating agents in patients with cancer-related anemia improved some disease-specific measures of quality of life and decreased the use of blood transfusions. However, it increased the risk of death and serious adverse events. Our findings suggest that such therapy not be used routinely as an alternative to blood transfusion in patients with anemia related to cancer.Anemia related to cancer may be due to the cancer itself or it may be a complication of chemotherapy. Because anemia is associated with adverse clinical outcomes in people with cancer, including impaired quality of life¹ and decreased survival,² treatment with erythropoiesis-stimulating agents has been widely used. These agents are costly, and reimbursement policies for their use in patients with cancer-related anemia vary across Canadian jurisdictions. Recent studies suggest that their use in such patients may be associated with an increased risk of adverse events such as thromboembolism.³ Potential adverse effects have also been identified in patients with chronic kidney disease.^4,5Therefore, an assessment of the efficacy and harms of erythropoiesis-stimulating agents in patients with cancer-related anemia would be useful to clinicians, and to jurisdictions that seek to develop an evidence-based reimbursement policy for these drugs. We conducted a systematic review based on work done for the Canadian Agency for Drugs and Technologies in Health⁶ to summarize the clinical efficacy and harms of these agents in adults with anemia related to cancer.     

Peroxisomes Are Required for Efficient Penicillin Biosynthesis in Penicillium chrysogenum

In the fungus Penicillium chrysogenum, penicillin (PEN) production is compartmentalized in the cytosol and in peroxisomes. Here we show that intact peroxisomes that contain the two final enzymes of PEN biosynthesis, acyl coenzyme A (CoA):6-amino penicillanic acid acyltransferase (AT) as well as the side-chain precursor activation enzyme phenylacetyl CoA ligase (PCL), are crucial for efficient PEN synthesis. Moreover, increasing PEN titers are associated with increasing peroxisome numbers. However, not all conditions that result in enhanced peroxisome numbers simultaneously stimulate PEN production. We find that conditions that lead to peroxisome proliferation but simultaneously interfere with the normal physiology of the cell may be detrimental to antibiotic production. We furthermore show that peroxisomes develop in germinating conidiospores from reticule-like structures. During subsequent hyphal growth, peroxisome proliferation occurs at the tip of the growing hyphae, after which the organelles are distributed over newly formed subapical cells. We observed that the organelle proliferation machinery requires the dynamin-like protein Dnm1.Penicillins (PENs) belong to the group of β-lactam antibiotics that are produced as secondary metabolites by specific actinomycetous bacteria and fungal species (26). For the industrial production of PEN, the filamentous fungus Penicillium chrysogenum is used. The biosynthesis of penicillin G (PenG) has been characterized in detail at the genetic and biochemical levels using P. chrysogenum and a related fungus, Aspergillus nidulans, as model organisms (7, 28). Starting from three amino acids, α-amino adipic acid, cysteine, and valine, PenG is formed in three unique enzymatic conversions (Fig. ​(Fig.1).1). These amino acids are first condensed to a tripeptide mediated by the function of a nonribosomal peptide synthetase, δ-(l-α-aminoadipyl)-l-cysteinyl-d-valine (ACV) synthetase (ACVS). The resulting tripeptide, ACV, is cyclized by isopenicillin N synthase (IPNS) to form a β-lactam, isopenicillin N (IPN). As a final step, the enzyme acyl coenzyme A (CoA):6-amino penicillanic acid acyltransferase (AT) replaces the α-aminoadipyl side chain of IPN with a more hydrophobic one. In industrial fermentations, phenylacetic acid (PAA) or phenoxyacetic acid (POA) is applied to produce PenG or penicillin V (PenV), respectively.Open in a separate windowFIG. 1.Schematic overview of the penicillin biosynthetic pathway. ACVS, δ-(l-α-aminoadipyl)-l-cysteinyl-d-valine synthetase; IPNS, isopenicillin N synthase; AT, acyl-CoA:6-amino penicillanic acid acyltransferase; PCL, phenylacetyl CoA ligase; PAA, phenylacetic acid.In filamentous fungi, the PEN biosynthetic machinery is compartmentalized (Fig. ​(Fig.1).1). The first two enzymes, ACVS and IPNS, are both located in the cytosol (19, 32). As the pH of the cytosol in filamentous fungi is between 6.5 and 7.0 (9, 31), these enzymes are in their optimal physiological surroundings. The AT and phenylacetyl CoA ligase (PCL) enzymes have specific targeting sequences that sort these enzymes to the lumen of their target compartment, the peroxisome (18, 19). The pH of this organelle was shown to be 7.5, which is close to the pH optima of both AT and PCL (31). Apparently, the compartmentalization of these enzymes creates defined microenvironments and enables the generation of favorable substrate and cofactor concentrations for enzyme function.Peroxisomes (belonging to the family of microbodies) are ubiquitously present in eukaryotic cells. They typically consist of a protein-rich matrix surrounded by a single membrane and are 0.1 to 1 μm in size. Although their function is often species and cell type specific, two widely distributed functions can be distinguished, namely, H₂O₂ metabolism and β-oxidation of fatty acids (for reviews, see references 25, 29, and 30). Muller et al. (18, 19) demonstrated the role of peroxisomes in PEN biosynthesis for the first time. Subsequently, it was speculated that a correlation may exist between the volume fraction of these organelles and PEN production rates (18, 27). This speculation was reinforced by Kiel and colleagues (13), who showed that the artificial proliferation of peroxisomes via the overexpression of the pex11 gene was associated with a 2- to 3-fold increase in PEN production rates. Here we further elaborate on these studies and show that peroxisomes de facto are required for efficient PEN biosynthesis in P. chrysogenum. In addition, we present details on the origin and subsequent partitioning of the organelles over newly formed subapical cells during hyphal development.