New insights into molecular evolution: prospects from the Barcode of Life Initiative (BOLI)

Geographic and temporal patterns of morphological and behavioral diversifications among species stimulated Darwin to propose a mechanism for evolutionary change through natural selection. Scientific developments have revealed an even more fundamental level of biological complexity: sequence variation in DNA. While genome projects yield spectacular insights into molecular evolution, they have targeted only a few species. In contrast, the Barcode of Life Initiative (BOLI) proposes a horizontal approach to genomics, examining short, standardized genome segments across the sweep of eukaryotic life, all 10 million species. BOLI will extend our understanding of evolution and speciation in varied ways. It will facilitate quantification of biological diversity by disclosing cryptic species and enabling a rapid survey of taxon diversity in groups that have hitherto received scant morphological examination. It will facilitate assignment of life history stages to known species and provide a first estimate of species ages. It will also reveal key features of the mitochondrial genome, because the evolutionary properties of barcodes relate to those in the mitochondrial genome as a whole, acting to flag taxonomic groups or species with unusual nucleotide composition or evolutionary rates. The growing volume of barcode records has revealed that sequence variability within species is generally much lower than divergence among species (barcoding gap), a pattern that occurs in diverse lineages, suggesting a pervasive evolutionary process. Low variability may reflect recurrent selective sweeps of favored mitochondrial variants propagating as single linkage units across species. If this hypothesis is substantiated, the implications are significant, particularly for our understanding of molecular evolution of mitochondrial DNA and its relationship with species delineation.     

<Emphasis Type="Italic">α</Emphasis>-Amylase inhibitor-1 gene from <Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> expressed in <Emphasis Type="Italic">Coffea arabica</Emphasis>plants inhibits α-amylases from the coffee berry borer pest

Background  

Coffee is an important crop and is crucial to the economy of many developing countries, generating around US70 billion per year. There are 115 species in the < i > Coffea < /i > genus, but only two, < i > C. arabica < /i > and < i > C. canephora < /i > , are commercially cultivated. Coffee plants are attacked by many pathogens and insect-pests, which affect not only the production of coffee but also its grain quality, reducing the commercial value of the product. The main insect-pest, the coffee berry borer ( < i > Hypotheneumus hampei < /i > ), is responsible for worldwide annual losses of around US70 billion per year. There are 115 species in the Coffea genus, but only two, C. arabica and C. canephora, are commercially cultivated. Coffee plants are attacked by many pathogens and insect-pests, which affect not only the production of coffee but also its grain quality, reducing the commercial value of the product. The main insect-pest, the coffee berry borer (Hypotheneumus hampei), is responsible for worldwide annual losses of around US500 million. The coffee berry borer exclusively damages the coffee berries, and it is mainly controlled by organochlorine insecticides that are both toxic and carcinogenic. Unfortunately, natural resistance in the genus Coffea to H. hampei has not been documented. To overcome these problems, biotechnological strategies can be used to introduce an α-amylase inhibitor gene (α-AI1), which confers resistance against the coffee berry borer insect-pest, into C. arabica plants.     

Up- and down-modulation of liver cytochrome P450 activities and associated events in two murine malaria models

Background

The mechanisms by which malaria up and down-regulates CYP activities are not understood yet. It is also unclear whether CYP activities are modulated during non-lethal malaria infections. This study was undertaken to evaluate the time course of CYP alterations in lethal (Plasmodium berghei ANKA) and non-lethal (Plasmodium chabaudi chabaudi) murine malaria. Additionally, hypotheses on the association of CYP depression with enhanced nitric oxide (NO) production, and of CYP2a5 induction with endoplasmic reticulum dysfunction, enhanced haem metabolism and oxidative stress were examined as well.

Methods

Female DBA-2 and C57BL/6 mice were infected with P.berghei ANKA or P. chabaudi and killed at different post-infection days. Infection was monitored by parasitaemia rates and clinical signs. NO levels were measured in the serum. Activities of CYP1a (ethoxyresorufin-O-deethylase), 2b (benzyloxyresorufin-O-debenzylase), 2a5 (coumarin-7-hydroxylase) and uridine-diphosphoglucuronyl-transferase (UGT) were determined in liver microsomes. Glutathione-S-transferase (GST) activity and concentrations of gluthatione (GSH) and thiobarbituric acid-reactive substances (TBARS) were determined in the liver. Levels of glucose-regulated protein 78 (GRP78) were evaluated by immunoblotting, while mRNAs of haemoxygenase-1 (HO-1) and inducible nitric oxide synthase (iNOS) were determined by quantitative RT-PCR.

Results

Plasmodium berghei depressed CYP1a and 2b and induced 2a5 in DBA-2 mice. In P.berghei-infected C57BL/6 mice CYP activities remained unaltered. In both strains, GST and UGT were not affected by P.berghei. Plasmodium c. chabaudi depressed CYP1a and 2b and induced 2a5 activities on the day of peak parasitaemia or near this day. CYP2a5 induction was associated with over-expression of HO-1 and enhanced oxidative stress, but it was not associated with GRP78 induction, a marker of endoplasmic reticulum stress. Plasmodium chabaudi increased serum NO on days near the parasitaemia peak in both strains. Although not elevating serum NO, P.berghei enhanced iNOS mRNA expression in the liver.

Conclusion

Down-regulation of CYP1a and 2b and induction of 2a5 occurred in lethal and non-lethal infections when parasitaemia rates were high. A contribution of NO for depression of CYP2b cannot be ruled out. Results were consistent with the view that CYP2a5 and HO-1 are concurrently up-regulated and suggested that CYP2a5 induction may occur in the absence of enhanced endoplasmic reticulum stress.     

Effects of the microcystin profile of a cyanobacterial bloom on growth and toxin accumulation in common carp Cyprinus carpio larvae

A 12 day growth trial was conducted to compare the effect of the variation in microcystins (MC) composition of two bloom samples of Microcystis aeruginosa on the growth performance and microcystin accumulation in common carp Cyprinus carpio larvae. Two M. aeruginosa natural bloom samples with different MC profiles were collected and larvae were exposed to cyanobacterial cells through their diet. Three diets, a basal control diet and two diets prepared from the basal diet plus the same toxins content (60 ng MC g^?1 diet) of each cyanobacterial bloom, were given at the same ration level to three groups of larvae during the experimental period. Larval mass and standard length from day 9 were significantly different between cyanobacterial treatments and in both cases lower than that of the control. The MC accumulation by larvae, inversely correlated with the growth performance, was also significantly different between cyanobacterial treatments (26·96 v. 17·32 ng g^?1 at the end of the experimental period). These results indicate that MC variants profile may have effects on the toxin uptake and toxicity. To date, this is the first laboratory study to show that fish accumulate MC depending on the toxin profile of the cyanobacterial bloom.     

<Emphasis Type="BoldItalic">In vitro</Emphasis> propagation of the ornamental bromeliad <Emphasis Type="BoldItalic">Acanthostachys strobilacea</Emphasis> (Schult. f.) Klotzsch via nodal segments

Acanthostachys strobilacea (Schult. f.) Klotzsch is an ornamental species of Bromeliaceae that may show an elongated stem when cultivated in vitro. This work reports a micropropagation protocol for A. strobilacea using nodal segments. Seeds were placed in Murashige and Skoog’s medium with macronutrients diluted to 1/5. Nodal segments isolated from the stems of in vitro elongated plants were subcultured in the same medium and kept in different light intensities (14, 41, and 50 μmol m⁻² s⁻¹) or continuous darkness. Another group of nodes was subcultured according to the position in the mother seedling. The plants that showed the most stem elongation were those that were cultured in 14 μmol m⁻² s⁻¹ or that came from isolated nodal segments in the median and basal regions of the mother plant. After 2 mo, all of the plants originating from the development of lateral buds were transferred to a greenhouse. Only those that were not elongated survived ex vitro and flowered after 1 yr.     

Quantification of five putative periodontal pathogens in female patients with and without chronic periodontitis by real-time polymerase chain reaction

Chronic periodontitis is a highly prevalent endogenous polymicrobial disease. To better understand the etiology of the disease a quantitative approach is mandatory and real-time PCR is the molecular technique currently preferred to achieve this purpose. Taking into account that such a kind of study is still scarce, we aimed to evaluate the association between periodontal microbiota and chronic periodontitis. A total of 60 low-income age-matched female adults, 30 with chronic periodontitis and 30 without periodontal disease, were enrolled. DNA obtained from subgingival specimens was used for quantification of Aggregatibacter actinomycetemcomitans, Eikenella corrodens, Fusobacterium nucleatum, Porphyromonas gingivalis, and Prevotella intermedia by real-time PCR. A. actinomycetemcomitans, E. corrodens, and F. nucleatum were detected in all subjects, P. gingivalis was observed in 70.0% and 46.6% and P. intermedia in 90.0% and 80.0% of chronic periodontitis patients and periodontally healthy subjects, respectively. P. gingivalis mean count was significantly higher in patients with chronic periodontitis than in periodontally healthy individuals. Accurate detection and quantification of five putative periodontal pathogens was feasible using a simple and fast real-time PCR protocol. Although P. gingivalis and P. intermedia have been found more commonly in chronic periodontitis patients, no statistical difference was observed between periodontally diseased and healthy groups. Quantitative data indicated association between P. gingivalis and chronic periodontitis. However, because of its uneven distribution, it should not be solely taken as a marker of periodontal status.     

Effects of galactose on direct and indirect pathway estimates of hepatic glycogen synthesis

Hepatic glycogen is formed by direct and indirect pathways whose activities reflect altered nutrition or disease. Direct/indirect pathway measurements often involve test meals where ～10% of carbohydrate is galactose, but its effects on direct/indirect pathway estimates are unknown. Therefore, direct/indirect pathway contributions in 24-h fasted rats given 2 g/kg 100% glucose (GLU, n=6) or 90% glucose–10% galactose (GLU+GAL, n=6) were measured by [U-¹³C]glucose dilution and by position-5/position-2 glycogen enrichment (H5/H2) from 2H₂O. For GLU+GAL, galactose glycogenesis was independently measured with [1-¹³C]galactose. Glycogenesis was equivalent in both groups but for GLU+GAL, 23±4% of glycogen was derived from galactose. [U-¹³C]glucose reported a 30±3% direct pathway contribution to glycogenesis for GLU but only 20±3% for GLU+GAL (p=0.012 vs. GLU). H5/H2 yielded identical direct pathway estimates (32±3% GLU, 29±6% GLU+GAL). Thus, galactose glycogenesis was undetected by H5/H2 while [U-¹³C]glucose reported a reduced direct/indirect pathway ratio. With [1-¹³C]galactose also present, correct glycogenic source contributions were obtained.     

Monitoring fermentation parameters during phytase production in column-type bioreactor using a new data acquisition system

Fermentation parameters for phytase production in column-type bioreactor were monitored using a new data acquisition system. There are a number of studies reporting phytase production in flasks, but a lack of data about microorganism respiration behaviour during phytase production using column bioreactor. The objectives of this work were the monitoration of fermentation parameters during phytase production and its relation with fungal growth and forced air. Phytase production by A. niger FS3 increased with forced air. The O₂ consumption and CO₂ production during solid-state fermentation were monitored by sensors (in the bottom and top of the columns) linked to controllers, recorded by acquisition software and processed by Fersol2^® software tool. Phytase synthesis was associated with fungal growth. Therefore, phytase could be used to estimate FS3 biomass formed in citric pulp degradation.     

Quaternary β-carboline alkaloids from Psychotria prunifolia (Kunth) Steyerm.

Two new quaternary alkaloids, compound 1 and the 14-oxo derivative 2, were isolated along with the known alkaloid strictosamide (3) from the leaves of Psychotria prunifolia (Kunth) Steyerm. (Rubiaceae, Psychotriae). Their structures were elucidated using spectroscopic methods (1D and 2D NMR, IR, and HRMS).