Seasonal use by birds of stream-side riparian habitat in coniferous forest of northcentral British Columbia

To determine use of riparian habitats by birds in the northern coniferous forest of British Columbia, we censused birds and vegetation along 500 m transects placed parallel and perpendicular to three second-order streams. Censuses were conducted during spring, summer, autumn, and winter to investigate how use of riparian habitat changed seasonally. Stream-side riparian zones were characterized by a dense understorey of deciduous vegetation not found in the upslope forest. Nine bird species preferred the riparian understorey for breeding, six preferred it only during migration. Neotropical migrants (16 of 46 species) were more closely associated with stream-sides than year-round residents (11 species). Some breeding birds (five species) were significantly negatively associated with riparian habitats. The density of riparian birds declined with distance upstream but did not decline up to 250 m away from the stream. The more extensive riparian areas downstream supported a greater density of birds in all seasons compared to upstream areas, but more species only in spring and autumn. Species that nested in non-riparian areas in summer used riparian habitat in autumn, making riparian corridors in the northern coniferous forest important during migration. Maintaining both riparian and upslope habitats is necessary to preserve species diversity al the landscape level.     

ATG genes involved in non-selective autophagy are conserved from yeast to man, but the selective Cvt and pexophagy pathways also require organism-specific genes

ATG genes encode proteins that are required for macroautophagy, the Cvt pathway and/or pexophagy. Using the published Atg protein sequences, we have screened protein and DNA databases to identify putative functional homologs (orthologs) in 21 fungal species (yeast and filamentous fungi) of which the genome sequences were available. For comparison with Atg proteins in higher eukaryotes, also an analysis of Arabidopsis thaliana and Homo sapiens databases was included. This analysis demonstrated that Atg proteins required for non-selective macroautophagy are conserved from yeast to man, stressing the importance of this process in cell survival and viability. The A. thaliana and human genomes encode multiple proteins highly similar to specific fungal Atg proteins (paralogs), possibly representing cell type-specific isoforms. The Atg proteins specifically involved in the Cvt pathway and/or pexophagy showed poor conservation, and were generally not present in A. thaliana and man. Furthermore, Atg19, the receptor of Cvt cargo, was only detected in Saccharomyces cerevisiae. Nevertheless, Atg11, a protein that links receptor-bound cargo (peroxisomes, the Cvt complex) to the autophagic machinery was identified in all yeast species and filamentous fungi under study. This suggests that in fungi an organism-specific form of selective autophagy may occur, for which specialized Atg proteins have evolved.     

Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets

Marine protists have traditionally been assumed to be lowly diverse and cosmopolitan. Yet, several recent studies have shown that many protist species actually consist of cryptic complexes of species whose members are often restricted to particular biogeographic regions. Nonetheless, detection of cryptic species is usually hampered by sampling coverage and application of methods (e.g. phylogenetic trees) that are not well suited to identify relatively recent divergence and ongoing gene flow. In this paper, we show how these issues can be overcome by inferring phylogenetic haplotype networks from global metabarcoding datasets. We use the Chaetoceros curvisetus (Bacillariophyta) species complex as study case. Using two complementary metabarcoding datasets (Ocean Sampling Day and Tara Oceans), we equally resolve the cryptic complex in terms of number of inferred species. We detect new hypothetical species in both datasets. Gene flow between most of species is absent, but no barcoding gap exists. Some species have restricted distribution patterns whereas others are widely distributed. Closely related taxa occupy contrasting biogeographic regions, suggesting that geographic and ecological differentiation drive speciation. In conclusion, we show the potential of the analysis of metabarcoding data with evolutionary approaches for systematic and phylogeographic studies of marine protists.Subject terms: Population genetics, Biodiversity, Biogeography, Next-generation sequencing     

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)     

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.     

Necropsy findings in American alligator late-stage embryos and hatchlings from northcentral Florida lakes contaminated with organochlorine pesticides

Increased American alligator (Alligator mississippiensis) embryo and neonatal mortality has been reported from several northcentral Florida lakes contaminated with old-use organochlorine pesticides (OCPs). However, a clear relationship among these contaminants and egg viability has not been established, suggesting the involvement of additional factors in these mortalities. Thus, the main objective of this study was to determine the ultimate cause of mortality of American alligator late-stage embryos and hatchlings through the conduction of detailed pathological examinations, and to evaluate better the role of OCPs in these mortalities. Between 2000 and 2001, 236 dead alligators were necropsied at or near hatching (after approximately 65 days of artificial incubation and up to 1 mo of age posthatch). Dead animals were collected from 18 clutches ranging in viability from 0% to 95%. Total OCP concentrations in yolk ranged from approximately 100 to 52,000 microg/kg, wet weight. The most common gross findings were generalized edema (34%) and organ hyperemia (29%), followed by severe emaciation (14%) and gross deformities (3%). Histopathologic examination revealed lesions in 35% of the animals, with over half of the cases being pneumonia, pulmonary edema, and atelectasis. Within and across clutches, dead embryos and hatchlings compared with their live cohorts were significantly smaller and lighter. Although alterations in growth and development were not related to yolk OCPs, there was an increase in prevalence of histologic lesions in clutches with high OCPs. Overall, these results indicate that general growth retardation and respiratory abnormalities were a major contributing factor in observed mortalities and that contaminants may increase the susceptibility of animals to developing certain pathologic conditions.     

Analysis of steroid metabolites produced by theca cells from the adult domestic hen

In a previous study on steroid metabolism by hen ovarian cells we reported on the production of 17-hydroxyprogesterone (17OH), androstenedione (A), testosterone (T), and oestrogens from [3H]progesterone (P) by theca cells. The present study examines further the metabolism of P by theca cells from the preovulatory follicles of the hen. The results show that the major metabolite of P is 20 beta-hydroxy-4-pregnen-3-one (20 beta-DHP), representing up to 40% of the recovered radioactivity. In addition, 3 alpha-hydroxy-4-pregnen-20-one (3 alpha-DHP) and 17 alpha,20 beta-dihydroxy-4-pregnen-3-one (17,20 beta) were identified as metabolites of P, comprising 1 and 3% of the recovered radioactivity, respectively. This is the first evidence that the allylic steroid, 3 alpha-DHP, can be produced by avian ovaries.     

Progesterone as a predictor of cyclicity in Bolivian squirrel monkeys during the breeding season

In a squirrel monkey breeding colony, two distinct groups of females were observed during the breeding season, December through March. One had low and the other had high estradiol (E2) and progesterone (P) concentrations. The conception rate in females with high E2 and P values was 74%. However, only 25% of monkeys with low steroid concentrations became pregnant during the breeding season. This study showed that all mature females in a colony may not be cycling concurrently and that two serum P measurements obtained at four-day intervals may be utilized to detect noncycling monkeys during the breeding season.