Ecology in the age of DNA barcoding: the resource,the promise and the challenges ahead

Ten years after DNA barcoding was initially suggested as a tool to identify species, millions of barcode sequences from more than 1100 species are available in public databases. While several studies have reviewed the methods and potential applications of DNA barcoding, most have focused on species identification and discovery, and relatively few have addressed applications of DNA barcoding data to ecology. These data, and the associated information on the evolutionary histories of taxa that they can provide, offer great opportunities for ecologists to investigate questions that were previously difficult or impossible to address. We present an overview of potential uses of DNA barcoding relevant in the age of ecoinformatics, including applications in community ecology, species invasion, macroevolution, trait evolution, food webs and trophic interactions, metacommunities, and spatial ecology. We also outline some of the challenges and potential advances in DNA barcoding that lie ahead.     

Structure-Activity Relationship of Benzophenanthridine Alkaloids from Zanthoxylum rhoifolium Having Antimicrobial Activity

Zanthoxylum rhoifolium (Rutaceae) is a plant alkaloid that grows in South America and has been used in Brazilian traditional medicine for the treatment of different health problems. The present study was designed to evaluate the antimicrobial activity of the steam bark crude methanol extract, fractions, and pure alkaloids of Z. rhoifolium. Its stem bark extracts exhibited a broad spectrum of antimicrobial activity, ranging from 12.5 to 100 µg/mL using bioautography method, and from 125 to 500 µg/mL in the microdilution bioassay. From the dichloromethane basic fraction, three furoquinoline alkaloids (1–3), and nine benzophenanthridine alkaloids (4–12) were isolated and the antimicrobial activity of the benzophenanthridine alkaloids is discussed in terms of structure-activity relationships. The alkaloid with the widest spectrum of activity was chelerythrine (10), followed by avicine (12) and dihydrochelerythrine (4). The minimal inhibitory concentrations of chelerythrine, of 1.50 µg/mL for all bacteria tested, and between 3.12 and 6.25 µg/mL for the yeast tested, show this compound to be a more powerful antimicrobial agent when compared with the other active alkaloids isolated from Z. rhoifolium. To verify the potential importance of the methylenedioxy group (ring A) of these alkaloids, chelerythrine was selected to represent the remainder of the benzophenanthridine alkaloids isolated in this work and was subjected to a demethylation reaction giving derivative 14. Compared to chelerythrine, the derivative (14) was less active against the tested bacteria and fungi. Kinetic measurements of the bacteriolytic activities of chelerythrine against the bacteria Bacillus subtilis (Gram-positive) and Escherichia coli (Gram-negative) were determined by optical density based on real time assay, suggesting that its mechanism of action is not bacteriolytic. The present study did not detect hemolytic effects of chelerythrine on erythrocytes and found a protective effect considering the decrease in TBARS and AOPP (advanced oxidized protein products) levels when compared to the control group.     

Avian Influenza Virus (H11N9) in Migratory Shorebirds Wintering in the Amazon Region,Brazil

Aquatic birds are the natural reservoir for avian influenza viruses (AIV). Habitats in Brazil provide stopover and wintering sites for water birds that migrate between North and South America. The current study was conducted to elucidate the possibility of the transport of influenza A viruses by birds that migrate annually between the Northern and Southern Hemispheres. In total, 556 orotracheal/cloacal swab samples were collected for influenza A virus screening using real-time RT-PCR (rRT-PCR). The influenza A virus-positive samples were subjected to viral isolation. Four samples were positive for the influenza A matrix gene by rRT-PCR. From these samples, three viruses were isolated, sequenced and characterized. All positive samples originated from a single bird species, the ruddy turnstone (Arenaria interpres), that was caught in the Amazon region at Caeté Bay, Northeast Pará, at Ilha de Canelas. To our knowledge, this is the first isolation of H11N9 in the ruddy turnstone in South America.     

In vitro organogenesis from root culture segments of Bixa orellana L. (Bixaceae)

The organogenic potential of root explants derived from cultured seedlings of Bixa orellana L. (annatto) was investigated in response to different incubation conditions and either 4.44 μM 6-benzyladenine, 4.54 μM Thidiazuron, or 4.56 μM Zeatin. Explants cultured in liquid media with agitation generally showed better development of adventitious buds versus explants cultured on semi-solid media. The most adventitious buds developed from explants cultured in liquid media under a 16-h photoperiod. Use of Zeatin and Thidiazuron promoted the development of more adventitious buds than 6-benzyladenine but morphological abnormalities among regenerating shoots and plants were observed. Fewer adventitious buds developed from explants cultured in liquid media supplemented with 6-benzyladenine, but the buds gave rise to the highest percentage of morphologically normal regenerated plants. Histological analyses showed that adventitious buds originated from cell proliferation within the pericycle, opposite the protoxylem poles of the explant. Seedling root tissue is useful for in vitro propagation of B. orellana.     

Neurolysin Knockout Mice Generation and Initial Phenotype Characterization

The oligopeptidase neurolysin (EC 3.4.24.16; Nln) was first identified in rat brain synaptic membranes and shown to ubiquitously participate in the catabolism of bioactive peptides such as neurotensin and bradykinin. Recently, it was suggested that Nln reduction could improve insulin sensitivity. Here, we have shown that Nln KO mice have increased glucose tolerance, insulin sensitivity, and gluconeogenesis. KO mice have increased liver mRNA for several genes related to gluconeogenesis. Isotopic label semiquantitative peptidomic analysis suggests an increase in specific intracellular peptides in gastrocnemius and epididymal adipose tissue, which likely is involved with the increased glucose tolerance and insulin sensitivity in the KO mice. These results suggest the exciting new possibility that Nln is a key enzyme for energy metabolism and could be a novel therapeutic target to improve glucose uptake and insulin sensitivity.     

Distantiae Transmission of Trypanosoma cruzi: A New Epidemiological Feature of Acute Chagas Disease in Brazil

Background

The new epidemiological scenario of orally transmitted Chagas disease that has emerged in Brazil, and mainly in the Amazon region, needs to be addressed with a new and systematic focus. Belém, the capital of Pará state, reports the highest number of acute Chagas disease (ACD) cases associated with the consumption of açaí juice.

Methodology/Principal Findings

The wild and domestic enzootic transmission cycles of Trypanosoma cruzi were evaluated in the two locations (Jurunas and Val-de Cães) that report the majority of the autochthonous cases of ACD in Belém city. Moreover, we evaluated the enzootic cycle on the three islands that provide most of the açaí fruit that is consumed in these localities. We employed parasitological and serological tests throughout to evaluate infectivity competence and exposure to T. cruzi. In Val-de-Cães, no wild mammal presented positive parasitological tests, and 56% seroprevalence was observed, with low serological titers. Three of 14 triatomines were found to be infected (TcI). This unexpected epidemiological picture does not explain the high number of autochthonous ACD cases. In Jurunas, the cases of ACD could not be autochthonous because of the absence of any enzootic cycle of T. cruzi. In contrast, in the 3 island areas from which the açaí fruit originates, 66.7% of wild mammals and two dogs displayed positive hemocultures, and 15.6% of triatomines were found to be infected by T. cruzi. Genotyping by mini-exon gene and PCR-RFLP (1f8/Akw21I) targeting revealed that the mammals and triatomines from the islands harbored TcI and Trypanosoma rangeli in single and mixed infections.

Conclusion/Significance

These findings show that cases of Chagas disease in the urban area of Belém may be derived from infected triatomines coming together with the açaí fruits from distant islands. We term this new epidemiological feature of Chagas disease as “Distantiae transmission”.     

Titi monkeys (Callicebus spp., Atelidae: Platyrrhini) in the Brazilian state of Rondônia

Five species of titi monkey (Callicebus brunneus, Callicebus caligatus Callicebus cinerascens, Callicebus donacophilus, andCallicebus moloch) were recorded in surveys of primate populations at 26 sites throughout the Brazilian state of Rondônia. The distribution of the two species,C. cinerascens andC. donacophilus (recorded in the state for the first time), appeared to be related to that of non-forest ecosystems, the former in thecerrado woodlands, and the latter in gallery forests of the Guaporé grasslands. The results of the surveys also indicate thatC. brunneus has a more restricted distribution in southern Rondônia than was previously thought, whereasC. moloch is more widespread. However, the ecological factors that determine species distribution in the south of the state remain unclear on the basis of the available data. All species were observed in small social groups of no more than five individuals, which are typical of the genus, generally in the middle and lower forest strate.     

Ichnology and sedimentology of a tide‐influenced delta in the Ordovician from the northeastern Alborz range of Iran (Kopet Dagh region)

The Middle–Late Ordovician Ghelli Formation in the Kopet Dagh region northeastern Alborz range of Iran is composed of siliciclastic rocks deposited in a variety of turbidite to marginal marine environments (deep marine clastic fan and related environments and prodelta, distal delta front, proximal delta front and distributary channels). The ichnology of the middle member of the Ghelli Formation is here reported. Combined sedimentological and ichnological analysis allows recognition of a tide‐influenced deltaic succession in the middle member of the Ghelli Formation consisting of three main facies associations: lower distributary channels, delta front and prodelta facies. Twenty‐two ichnogenera have been identified in this marginal marine succession: Arenicolites, Arthrophycus, Bergaueria, Chondrites, Conichnus, Cruziana, Cylindrichnus, Didymaulichnus, Diplichnites, Diplocraterion, Helminthopsis, Gyrochorte, Lockeia, Macaronichnus, Monomorphichnus, Palaeophycus, Planolites, Rosselia, Rusophcus, Skolithos, Teichichnus and ?Scolicia. Their distribution is clearly linked with lithofacies and depositional palaeoenvironments. The ichnological analysis reveals that the trace fossil suites developed in these environments indicate low diversity and low to moderate abundance of burrows, poor development of tiering and sporadic distribution. Low ichnodiversity and low bioturbation intensities with higher bioturbation clusters consist of facies‐crossing ichnogenera, and the impoverishment of suspension‐feeding trophic types indicates ‘stressed’, non‐archetypal expression of the Cruziana ichnofacies. The periodic higher intensities of bioturbation due to variations in hydrodynamic regimes of tidal currents reflect the archetypal of the Cruziana ichnofacies (and rare Skolithos ichnofacies).     

Homogeneous Canine Chest Phantom Construction: A Tool for Image Quality Optimization

Digital radiographic imaging is increasing in veterinary practice. The use of radiation demands responsibility to maintain high image quality. Low doses are necessary because workers are requested to restrain the animal. Optimizing digital systems is necessary to avoid unnecessary exposure, causing the phenomenon known as dose creep. Homogeneous phantoms are widely used to optimize image quality and dose. We developed an automatic computational methodology to classify and quantify tissues (i.e., lung tissue, adipose tissue, muscle tissue, and bone) in canine chest computed tomography exams. The thickness of each tissue was converted to simulator materials (i.e., Lucite, aluminum, and air). Dogs were separated into groups of 20 animals each according to weight. Mean weights were 6.5 ± 2.0 kg, 15.0 ± 5.0 kg, 32.0 ± 5.5 kg, and 50.0 ± 12.0 kg, for the small, medium, large, and giant groups, respectively. The one-way analysis of variance revealed significant differences in all simulator material thicknesses (p < 0.05) quantified between groups. As a result, four phantoms were constructed for dorsoventral and lateral views. In conclusion, the present methodology allows the development of phantoms of the canine chest and possibly other body regions and/or animals. The proposed phantom is a practical tool that may be employed in future work to optimize veterinary X-ray procedures.