Cryptic diversity and diversification processes in three cis-Andean Rhamdia species (Siluriformes: Heptapteridae) revealed by DNA barcoding

The wide distribution of the Neotropical freshwater catfish Rhamdia offers an excellent opportunity to investigate the historical processes responsible for modeling South America’s hydrogeological structure. We used sequences from cis-Andean and Mesoamerican Rhamdia species to reconstruct and estimate divergence times among cis-Andean lineages, correlating the results with known geological events. Species delimitation methods based on distance (DNA barcoding and BIN) and coalescence (GMYC) approaches identified nine well-supported lineages from the cis-Andean region from sequences available in the BOLD dataset. The cis-Andean Rhamdia lineages diversification process began in Eocene and represented the split between cis-Andean and Mesoamerican clades. The cis-Andean clade contains two principal groups: Northwest clade (MOTUs from Amazon, Essequibo, Paraguay, and Itapecuru basins) and Southeast clade (Eastern Brazilian shield basins (Paraná, Uruguay, Iguaçu, and São Francisco) plus eastern coastal basins). The diversification of the cis-Andean Rhamdia lineages results from vicariance and geodispersion events, which played a key role in the current intricate distribution pattern of the Rhamdia lineages. The wide geographical distribution and large size of the specimens make it attractive to cultivate in different countries of the Neotropical region. The lineages delimitation minimizes identification mistakes, unintentional crossings by aquaculture, and reduces natural stocks contamination.     

Sources of Blood Meals of Sylvatic Triatoma guasayana near Zurima,Bolivia, Assayed with qPCR and 12S Cloning

Background

In this study we compared the utility of two molecular biology techniques, cloning of the mitochondrial 12S ribosomal RNA gene and hydrolysis probe-based qPCR, to identify blood meal sources of sylvatic Chagas disease insect vectors collected with live-bait mouse traps (also known as Noireau traps). Fourteen T. guasayana were collected from six georeferenced trap locations in the Andean highlands of the department of Chuquisaca, Bolivia.

Methodology/Principal Findings

We detected four blood meals sources with the cloning assay: seven samples were positive for human (Homo sapiens), five for chicken (Gallus gallus) and unicolored blackbird (Agelasticus cyanopus), and one for opossum (Monodelphis domestica). Using the qPCR assay we detected chicken (13 vectors), and human (14 vectors) blood meals as well as an additional blood meal source, Canis sp. (4 vectors).

Conclusions/Significance

We show that cloning of 12S PCR products, which avoids bias associated with developing primers based on a priori knowledge, detected blood meal sources not previously considered and that species-specific qPCR is more sensitive. All samples identified as positive for a specific blood meal source by the cloning assay were also positive by qPCR. However, not all samples positive by qPCR were positive by cloning. We show the power of combining the cloning assay with the highly sensitive hydrolysis probe-based qPCR assay provides a more complete picture of blood meal sources for insect disease vectors.     

Lipid rafts-protein association and the regulation of protein activity

Lipid rafts are membrane microdomains enriched in saturated phospholipids, sphingolipids, and cholesterol. They have a varied but distinct protein composition and have been implicated in diverse cellular processes including polarized traffic, signal transduction, endo- and exo-cytoses, entrance of obligate intracellular pathogens, and generation of pathological forms of proteins associated with Alzheimer's and prion diseases. Raft proteins can be permanently or temporarily associated to lipid rafts. Here, we review recent advances on the biochemical and cell biological characterization of rafts, and on the emerging concept of the temporary residency of proteins in rafts as a regulatory mechanism of their biological activity.     

(T2AG3)n Telomeric Sequence Hybridization Suggestive of Centric Fusion in Karyotype Marsupials Evolution

It has been suggested that the karyotype of the marsupials derived from a low diploid number (2n = 14) which originated, through fissions of biarmed chromosomes, the karyotypes with a higher 2n. The telomeric sequence (T₂AG₃)_nwas in situhybridized to the chromosomes of Gracilinanus microtarsusand G. emiliae, Micoureus demeraraeand Marmosa murina, species with 2n = 14, in Monodelphissp., M. domestica, M. kunsiand M. brevicaudatawith 2n = 18, and in Lutreolina crassicaudata, Didelphis albiventris, Chironectes minimus, Philander opossumand P. frenata, all of them with 2n = 22. The probe hybridization occurred in the telomeric regions of both arms, short and long, of all chromosomes of the complement of all individuals of all species analysed. However, in some pairs of the karyotypes of Gracilinanus microtarsusand Micoureus demerarae(with 2n = 14), and in Monodelphissp., M. domestica, M. kunsiand M. brevicaudata(2n = 18) ectopic signs of hybridization were detected proximal to the centromeres, suggesting the retention of this telomeric sequence in the centromeric regions of some chromosomes of these species. Based on these results, it is proposed that the karyotype of marsupials evolved from a 2n = 22 to a 2n = 14, by means of chromosomal fusions. This revised version was published online in July 2006 with corrections to the Cover Date.     

Camponotus ants mine sand for vertebrate urine to extract nitrogen

The ability of some ant species (including Camponotus spp.) to forage on vertebrate urine to extract urea may extend their niche in competitive and strongly nitrogen‐limited environments. We examined the preference of Camponotus terebrans, a sand‐dwelling ant widespread in southern Australia, for baits including urine, and the duration of their foraging on those baits. We baited ants with liquid stains of urine (human and kangaroo), urea in water (2.5%. 3.5%, 7.0%, 10.0%) and sucrose in water (20% and 40%) poured directly on the ground, as well as hard baits in plots drawn on sandy soil (Kangaroo Island, South Australia). We counted individuals of this mostly nocturnal species to determine their attraction to different baits for one month. We checked plant growth on the plots after nine and 13 months. Ants collected insects and meat; they foraged for at least 29 days on stains. Ants were most numerous on 10% urea, followed by 7% urea, 3.5% urea, urine (which contains ~2.5% urea) and 2.5% urea, 40% sucrose and 20% sucrose; sucrose was less attractive to them than equimolar urea bait. Ants were attracted to human, kangaroo, and unidentified urines, and they collected bird guano. Baits and ant foraging did not affect plant recruitment in plots. We observed incidentally Camponotus consobrinus foraging on urine, which may be a common resource for this genus at the site. The remarkable ability of C. terebrans to extract nitrogen from dry sand over weeks explains partly its success on sandy soils. Foraging on urine may be an important strategy to address nitrogen limitation on sandy soils and exploit commensally niches in which hosts are kangaroos, wallabies and other vertebrates. The understanding of plant–vertebrate interactions must factor in the role of ants as commensal organisms. Such ants could also reduce greenhouse gas emissions from urine.     

The geometry and genetics of hybridization

When divergent populations form hybrids, hybrid fitness can vary with genome composition, current environmental conditions, and the divergence history of the populations. We develop analytical predictions for hybrid fitness, which incorporate all three factors. The predictions are based on Fisher's geometric model, and apply to a wide range of population genetic parameter regimes and divergence conditions, including allopatry and parapatry, local adaptation, and drift. Results show that hybrid fitness can be decomposed into intrinsic effects of admixture and heterozygosity, and extrinsic effects of the (local) adaptedness of the parental lines. Effect sizes are determined by a handful of geometric distances, which have a simple biological interpretation. These distances also reflect the mode and amount of divergence, such that there is convergence toward a characteristic pattern of intrinsic isolation. We next connect our results to the quantitative genetics of line crosses in variable or patchy environments. This means that the geometrical distances can be estimated from cross data, and provides a simple interpretation of the “composite effects.” Finally, we develop extensions to the model, involving selectively induced disequilibria, and variable phenotypic dominance. The geometry of fitness landscapes provides a unifying framework for understanding speciation, and wider patterns of hybrid fitness.     

Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536

The genome of uropathogenic Escherichia coli isolate 536 contains five well-characterized pathogenicity islands (PAIs) encoding key virulence factors of this strain. Except PAI IV(536), the four other PAIs of strain 536 are flanked by direct repeats (DRs), carry intact integrase genes and are able to excise site-specifically from the chromosome. Genome screening of strain 536 identified a sixth putative asnW-associated PAI. Despite the presence of DRs and an intact integrase gene, excision of this island was not detected. To investigate the role of PAI-encoded integrases for the recombination process the int genes of each unstable island of strain 536 were inactivated. For PAI I(536) and PAI II(536), their respective P4-like integrase was required for their excision. PAI III(536) carries two integrase genes, intA, encoding an SfX-like integrase, and intB, coding for an integrase with weak similarity to P4-like integrases. Only intB was required for site-specific excision of this island. For PAI V(536), excision could not be abolished after deleting its P4-like integrase gene but additional deletion of the PAI II(536)-specific integrase gene was required. Therefore, although all mediated by P4-like integrases, the activity of the PAI excision machinery is most often restricted to its cognate island. This work also demonstrates for the first time the existence of a cross-talk between integrases of different PAIs and shows that this cross-talk is unidirectional.     

Assessing spatial patterns and density of a dolphin population through signature whistles

Some dolphin species produce signature whistles, which may allow the identification of individual dolphins using passive acoustic monitoring (PAM). Identifying individuals by their sounds may enhance the opportunities for monitoring and addressing biological and ecological questions about these species. Here, we explored the potential of signature whistles to investigate ecological aspects of a resident bottlenose dolphin population. Using a limited data set, with few individuals recognized by signature whistles, combined with spatial capture-recapture (SCR) methods, we investigated how effective such approach is describing spatial use patterns and estimating density for this population. The data were collected using 4–6 stationary bottom-moored recorders. Since only eight signature whistles were identified, our density estimate may represent a subset of the entire population. However, even with only a few signature whistles identified, our results confirmed the center of the core area used by these dolphins as the area with the highest encounter probability. In addition, our results provided evidence that these dolphins have the same spatial use pattern at night as during the day. This study shows that SCR analysis of signature whistle data can improve our ecological knowledge and understanding of dolphin populations.     

Studies on stimulus-response coupling in human neutrophils. II. Relationships between the effects of changes of external ionic composition on the properties of N-formylmethionylleucylphenylalanine receptors and on the respiratory and secretory responses

Studies were carried out on the mechanism responsible for the enhancement of the respiratory and secretory responses to N-formylmethionylleucylphenylalanine (fMet-Leu-Phe) exhibited by human neutrophils suspended in Na+-free, high-K+ buffered solution. The results demonstrate that: (a) the variation of Na+ concentration in the suspending solution induces in human neutrophils a marked modification of the recognition apparatus for the chemotactic peptide fMet-Leu-Phe, the lack of or low concentration of this ion increasing the number of the receptors and their specific affinity for the ligand; (b) the greater respiratory burst and secretion induced by fMet-Leu-Phe in human neutrophils suspended in Na+-free, high-K+ medium are due to the increased formation of receptor-ligand complexes at the cell membrane; (c) the greater respiratory response is partially due also to a higher efficiency of these receptor-ligand complexes. The molecular mechanism by which Na+ exerts a regulative role on the properties of the recognition apparatus for the chemotactic peptide and its possible significance are discussed.