The kinetics of oligonucleotide replacements

The formation of a duplex between two nucleic acid strands is restricted if one of the strands forms an intra- or intermolecular secondary structure. The formation of the new duplex requires the dissociation and replacement of the initial structure. To understand the mechanism of this type of kinetics we studied the replacement of a labeled DNA oligonucleotide probe bound to a complementary DNA target with an unlabeled probe of the same sequence. The replacement kinetics were measured using a gel-shift assay for 12, 14 and 16-nucleotide probes as a function of temperature and concentration of the unlabeled probe. The results demonstrate that the overall replacement rate is a combination of two kinetic pathways: dissociative and sequential displacement. The dissociative pathway occurs by the spontaneous dissociation of the initial duplex followed by association of the target and unlabeled probe. The sequential displacement pathway requires only the partial melting of the initial duplex to allow for the formation of a branched nucleation complex with the unlabeled probe, followed by the complete displacement of the labeled probe by migration of the branch point. The contribution from the dissociative pathway is predominant at temperatures close to the melting point of the labeled probe, whereas the contribution from the displacement pathway prevails at lower temperatures and when the concentration of the replacing unlabeled probe is high. The results show that at physiological conditions, duplex formation between a single-stranded oligonucleotide probe and a structured region of a target molecule occurs mainly by the sequential-displacement mechanism.     

Delay-Dependent Response in Weakly Electric Fish under Closed-Loop Pulse Stimulation

In this paper, we apply a real time activity-dependent protocol to study how freely swimming weakly electric fish produce and process the timing of their own electric signals. Specifically, we address this study in the elephant fish, Gnathonemus petersii, an animal that uses weak discharges to locate obstacles or food while navigating, as well as for electro-communication with conspecifics. To investigate how the inter pulse intervals vary in response to external stimuli, we compare the response to a simple closed-loop stimulation protocol and the signals generated without electrical stimulation. The activity-dependent stimulation protocol explores different stimulus delivery delays relative to the fish’s own electric discharges. We show that there is a critical time delay in this closed-loop interaction, as the largest changes in inter pulse intervals occur when the stimulation delay is below 100 ms. We also discuss the implications of these findings in the context of information processing in weakly electric fish.     

New Chinchillid Rodents (Hystricognathi: Caviomorpha) from Northern Chile and Bolivia Fill a 17-Million-Year Gap in the Pan-Chinchilline Fossil Record

Journal of Mammalian Evolution - The fossil record of chinchillid rodents (Hystricomorpha: Caviomorpha) begins in the early Miocene. However, nearly all remains have thus far been limited to the...     

Spatial and temporal variability of pCO2 and CO2 efflux in seven Amazonian Rivers

Current estimates of CO₂ outgassing from Amazonian rivers and streams have considerable uncertainty since they are based on limited-time surveys of pCO₂ measurements along the Amazon mainstem and mouths of major tributaries, using conservative estimates of gas exchange velocities. In order to refine basin-scale CO₂ efflux estimates from Amazonian rivers, we present a long time (5-year) dataset of direct measurements of CO₂ fluxes, gas transfer velocities and pCO₂ measurements in seven representative rivers of the lowland Amazon basin fluvial network, six non-tidal (Negro, Solimões, Teles Pires, Cristalino, Araguaia and Javaés) and one tidal river (Caxiuanã), with sizes ranging from 4th to 9th order. Surveys were conducted from January 2006 to December 2010, in a total of 389 campaigns covering all stages of their hydrographs. CO₂ fluxes and gas transfer velocities (k) were measured using floating chambers and pCO₂ was measured simultaneously by headspace extraction followed by gas chromatography analysis. Results show high CO₂ flux rate variability among rivers and hydrograph stages, ranging from ?0.8 to 15.3 μmol CO₂ m^?2 s^?1, with unexpected negative fluxes in clear-water rivers during low waters. Non-tidal rivers showed marked seasonal CO₂ flux patterns, with significantly higher exchange during high waters. Seasonality was modulated by pCO₂, which was positive and strongly correlated with discharge. In these rivers k was well correlated with wind speed, which allowed the use of wind data to model k. We estimate a release of 360 ± 60 Tg C year^?1 from Amazonian rivers and streams within a 1.47 million km² quadrant in the central lowland Amazon. Extrapolating these values to the basin upstream of Óbidos, results in an outgassing of 0.8 Pg C to the atmosphere each year. Our results are a step forward in achieving more accurate gas emission values for Amazonian rivers and their role in the annual carbon budget of the Amazon basin.     

Intra and interannual variability in the Madeira River water chemistry and sediment load

Concentrations of cations (Na⁺, Ca²⁺, Mg²⁺, K⁺, NH₄ ⁺), anions (HCO₃ ^?, Cl^?,?NO₃ ^?, SO₄ ^2?, PO₄ ^3?) and suspended sediments in the Madeira River water were?determined near the city of Porto Velho (RO), in order to assess variation in?water chemistry from 2004 to 2007. Calcium and bicarbonate were the dominant?cation and anion, respectively. Significant seasonal differences were found,?with highest concentrations occurring during the dry season, as expected from?the drainage of Andean carbonate-rich substratum. Interannual variations were?also observed, but became significant only when annual average discharge was?25% less than normal. Under this atypical discharge condition, bicarbonate was?replaced by sulfate, and higher suspended sediment concentrations and loads?were also observed. Compared to previously published studies, it appears that?no significant changes in water chemistry have occurred during the last 20?C30?years, although differences in approaches and sampling designs among this and previous studies may not allow detection of modest changes.?The calculated suspended sediment load reported here is close to the values presented elsewhere, reinforcing the relative importance of this river as a?sediment supplier for the Amazon Basin. Seasonality has a significant control?on the chemistry of Madeira River waters, and severe decrease in discharge due?to anthropogenic changes, such as construction of reservoirs or the occurrence?of drier years??a plausible consequence of global climate change??may lead?to modification in the chemical composition as well in the sediment deliver to?the Amazon River.     

The spatial scale of homogenisation and differentiation in Chihuahuan Desert fish assemblages

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Automatic Realistic Real Time Stimulation/Recording in Weakly Electric Fish: Long Time Behavior Characterization in Freely Swimming Fish and Stimuli Discrimination

Weakly electric fish are unique model systems in neuroethology, that allow experimentalists to non-invasively, access, central nervous system generated spatio-temporal electric patterns of pulses with roles in at least 2 complex and incompletely understood abilities: electrocommunication and electrolocation. Pulse-type electric fish alter their inter pulse intervals (IPIs) according to different behavioral contexts as aggression, hiding and mating. Nevertheless, only a few behavioral studies comparing the influence of different stimuli IPIs in the fish electric response have been conducted. We developed an apparatus that allows real time automatic realistic stimulation and simultaneous recording of electric pulses in freely moving Gymnotus carapo for several days. We detected and recorded pulse timestamps independently of the fish’s position for days. A stimulus fish was mimicked by a dipole electrode that reproduced the voltage time series of real conspecific according to previously recorded timestamp sequences. We characterized fish behavior and the eletrocommunication in 2 conditions: stimulated by IPIs pre-recorded from other fish and random IPI ones. All stimuli pulses had the exact Gymontus carapo waveform. All fish presented a surprisingly long transient exploratory behavior (more than 8 h) when exposed to a new environment in the absence of electrical stimuli. Further, we also show that fish are able to discriminate between real and random stimuli distributions by changing several characteristics of their IPI distribution.     

Non-woody life-form contribution to vascular plant species richness in a tropical American forest

We provide total vascular plant species counts for three 1-ha plots in deciduous, semi-deciduous and evergreen forests in central Bolivia. Species richness ranged from 297 species and 22,360 individuals/ha in the dry deciduous forest to 382 species and 31,670 individuals/ha in the evergreen forest. Orchidaceae, Pteridophyta and Leguminosae were among the most species-rich major plant groups in each plot, and Peperomia (Piperaceae), Pleurothallis (Orchidaceae) and Tillandsia (Bromeliaceae), all epiphytes, were the most species-rich genera. This dominance of a few but very diverse and/or widespread taxa contrasted with the low compositional similarity between plots. In a neotropical context, these Central Bolivian forest plots are similar in total species richness to other dry deciduous and humid montane forests, but less rich than most Amazonian forests. Nevertheless, lianas, terrestrial herbs and especially epiphytes proved to be of equal or higher species richness than most other neotropical forest inventories from which data are available. We therefore highlight the importance of non-woody life-forms (especially epiphytes and terrestrial herbs) in Andean foothill forest ecosystems in terms of species richness and numbers of individuals, representing in some cases nearly 50% of the species and more than 75% of the individuals. These figures stress the need for an increased inventory effort on non-woody plant groups in order to accurately direct conservation actions. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Human immunodeficiency virus type-1 subtypes of infected patients in Espírito Santo, Brazil

Genetic variability of human immunodeficiency virus type-1(HIV-1) is a potential threat for both diagnosis and treatment of HIV/AIDS, as well as the development of effective vaccines. Up to now, HIV subtypes circulating among HIV-positive patients in the state of Espírito Santo were not known. In the present study, blood samples from 100 therapy-na?ve HIV-1 infected patients were collected and the HIV subtype was determined through the Heteroduplex Mobility Assay (HMA). Ninety-seven out of 100 studied samples were subtyped by HMA, 73 samples (75.2%) were from subtype B, 9 (9.3%) from subtype F, 3 (3.1%) from subtype C, 6 (6.2%) Benv/Fgag, and another 6 (6.2%) Fenv/Bgag, what suggests that recombinant viruses were present in the studied samples. Twenty-eight percent of the subtype B samples were represented by the Brazilian B" subtype, which were identified by RFLP with Fok I. Data presented here demonstrate that the epidemiological characteristics of the HIV epidemic in the state of Espírito Santo are similar to those from the other Southeastern states and helped to better understand the genetic polymorphism of HIV in Brazil.