Multiplexed miRNA northern blots via hybridization chain reaction

Northern blots enable detection of a target RNA of interest in a biological sample using standard benchtop equipment. miRNAs are the most challenging targets as they must be detected with a single short nucleic acid probe. With existing approaches, it is cumbersome to perform multiplexed blots in which several RNAs are detected simultaneously, impeding the study of interacting regulatory elements. Here, we address this shortcoming by demonstrating multiplexed northern blotting based on the mechanism of hybridization chain reaction (HCR). With this approach, nucleic acid probes complementary to RNA targets trigger chain reactions in which fluorophore-labeled DNA hairpins self-assemble into tethered fluorescent amplification polymers. The programmability of HCR allows multiple amplifiers to operate simultaneously and independently within a blot, enabling straightforward multiplexing. We demonstrate simultaneous detection of three endogenous miRNAs in total RNA extracted from 293T and HeLa cells. For a given target, HCR signal scales linearly with target abundance, enabling relative and absolute quantitation. Using non-radioactive HCR, sensitive and selective miRNA detection is achieved using 2′OMe-RNA probes. The HCR northern blot protocol takes ∼1.5 days independent of the number of target RNAs.     

Functional morphology of scale hinges used to transport water: convergent drinking adaptations in desert lizards (<Emphasis Type="Italic">Moloch horridus</Emphasis> and <Emphasis Type="Italic">Phrynosoma cornutum</Emphasis>)

The Australian thorny devil, Moloch horridus Gray, 1841, and the Texas horned lizard, Phrynosoma cornutum Harlan, 1825, have the remarkable ability to rapidly move water through interscalar spaces on their skin’s surface to their mouth for drinking. The morphology of these scale hinges has not been studied. We used histological and SEM techniques to examine and compare the scale hinges of both species. Additional taxa in their respective lineages were examined in order to evaluate the potential that convergent evolution has occurred. In the two species that transport water, each scale hinge has a basally expanded and semi-enclosed channel formed by the hinge joint that is interconnected with all scale hinges on the body. We hypothesize that it is within this semi-tubular channel system of hinge joints, where the β-layer keratin of the integument is very thin, that water is transported. Hinge joint walls are covered by a complex topography of fractured surfaces that greatly expand the channel’s surface area and probably enhance capillary transport of water. In addition, we note differing morphology of scale surfaces at the rear of the jaws of both species. We hypothesize that capillary forces fill the scale-hinge system and additional forces, generated within the mouth by observed motions during drinking, depress local water-pressure to pull water through the channels of the hinge-joint system. We conclude that the combined features in the two species, semi-tubular hinge-joint channels with convoluted walls and a jaw-buccal cavity pumping-mechanism, have convergently evolved for capture, transport, and drinking of water from sporadic rainfall.     

Formation and Degradation Pathways of Intermediate Products Formed during the Hydropyrolysis of Glucose as a Model Substance for Wet Biomass in a Tubular Reactor

In this study, glucose as a model substance for cellulose is pyrolyzed in supercritical water. The experiments are conducted in a continuously operated tubular reactor. From the usage of model substances, key information on the degradation pathway of biomass in supercritical water can be obtained. With this knowledge, it is tried to optimize a new method for gasification of wet biomass considering high yields of hydrogen and methane and also the suppressing of tar and char formation. The gaseous products mainly contain hydrogen, carbon dioxide, methane and a small amount of carbon monoxide. The effect of experimental conditions, such as pressure, temperature and reaction time, on the degradation of glucose is investigated in the experiments. The qualitative and quantitative composition of the gas and liquid phases formed are determined. The results show that only the amount of phenols increases with increasing temperature in the liquid phase. No complete gasification of glucose is achieved in the studied temperature range between 400 °C and 500 °C. The addition of alkali salts leads to a higher gas generation and to a decrease in carbon monoxide concentration via water‐gas‐shift reaction. A lower furfural concentration is obtained in the presence of KHCO₃. Furthermore, this study shows that there is a wide conformity between the results of real and model biomass. A simplified scheme for glucose degradation is also presented with the help of the results found.     

Field and tree distribution of Capnodis tenebrionis (Linnaeus, 1767) (Col., Buprestidae) adults in an apricot orchard in Italy

A study was conducted into the spatio–temporal distribution of adult Capnodis tenebrionis (Linnaeus, 1767) in an apricot orchard in Sicily (Italy) using inverse distance squared weighting (IDW), a spatial interpolation technique to create a distribution map of adults in the orchard. The study was conducted throughout the period of presence of the adult in the field and it investigated distribution on individual plants with regard to the observed height on the crown and exposure to the sun’s rays. The variation is gradual in the distribution of the buprestid in the field and the areas with the greatest exposition to the sun (south‐east) were marked by the highest densities. The presence of the pest was also found to be higher in those parts of the crown most exposed to the sun; moreover, the position in relation to the ground varied constantly and was increasingly linked to time and temperature. The data obtained confirmed the distinct thermal demands of the species and provided useful information on both sampling and control.     

Assessing the value of acoustic indices to distinguish species and quantify activity: A case study using frogs

1. Soundscapes can provide information about a wide range of habitats and species through the recording of vocalisations over long temporal scales. Because of the large volumes of data collected, computational approaches, such as the application of acoustic indices, are required to extract useful information from long-duration recordings.
2. Acoustic indices summarise various soundscape features into frequency ranges over defined time intervals and can aid in the visual exploration, detection, and analysis of species vocalisation patterns. Here, we examine the performance of combinations of three acoustic indices commonly used in visual exploration, the acoustic complexity index, the temporal entropy spectrum index, and the event spectrum index, and assess their ability to distinguish species and describe acoustic features commonly used to detect species and analyse activity. Our case study focuses on three frog species with distinct call structures from Bickerton Island, Northern Territory, Australia. Call structure was categorised based on the number of pulses and harmonics.
3. We summarised acoustic activity by calculating acoustic indices in 256 equal-sized bins over the entire the frequency spectrum, for 30-s intervals, and found that acoustic index values could be used to distinguish species and describe acoustic features. The acoustic complexity index was the most effective index for distinguishing species. To describe acoustic features, we examined correlations between acoustic index values and summarised acoustic features, including call rate, total duration, loudness and signal-to-noise ratio. In single-pulsed species with no harmonics, we found spectral index values were significantly and sometimes strongly correlated with acoustic features. In comparison, species with harmonics were found to be weakly and less frequently correlated with acoustic features even if sampled calls were loud and have high signal-to-noise ratio. We suggest that acoustic indices have the potential to describe acoustic features in single-pulsed species but are limited in those with harmonics.
4. We conclude that acoustic indices can be a useful tool to distinguish some anuran species and to broadly understand specific acoustic features used to analyse calling activity over long periods of time.
5. Further research is required to better understand the relationships between acoustic indices and acoustic features to determine the general utility of indices to detect and distinguish audible species and to identify other acoustic features of various taxa.

     

Population growth lags in introduced species

When introduced to new ecosystems, species'' populations often grow immediately postrelease. Some introduced species, however, maintain a low population size for years or decades before sudden, rapid population growth is observed. Because exponential population growth always starts slowly, it can be difficult to distinguish species experiencing the early phases of slow exponential population growth (inherent lags) from those with actively delayed growth rates (prolonged lags). Introduced ungulates provide an excellent system in which to examine lags, because some introduced ungulate populations have demonstrated rapid population growth immediately postintroduction, while others have not. Using studies from the literature, we investigated which exotic ungulate species and populations (n = 36) showed prolonged population growth lags by comparing the doubling time of real ungulate populations to those predicted from exponential growth models for theoretical populations. Having identified the specific populations that displayed prolonged lags, we examined the impacts of several environmental and biological variables likely to influence the length of lag period. We found that seventeen populations (47%) showed significant prolonged population growth lags. We could not, however, determine the specific factors that contributed to the length of these lag phases, suggesting that these ungulate populations'' growth is idiosyncratic and difficult to predict. Introduced species that exhibit delayed growth should be closely monitored by managers, who must be proactive in controlling their growth to minimize the impact such populations may have on their environment.     

Effects of emerging infectious diseases on host population genetics: a review

Emerging infectious diseases threaten the survival of many species and populations by causing large declines and altering life history traits and population demographics. Therefore, it is imperative to understand how diseases impact wildlife populations so that effective management strategies can be planned. Many studies have focused on understanding the ecology of host/pathogen interactions, but it is equally important to understand the effects on host population genetic structure. In this review, we examined the literature on how infectious diseases influence host population genetic makeup, with a particular focus on whether or not they alter gene flow patterns, reduce genetic variability, and drive selection. Although the results were mixed, there was evidence for all of these outcomes. Diseases often fragmented populations into small, genetically distinct units with limited gene flow among them. In some cases, these isolated populations showed the genetic hallmarks of bottlenecks and inbreeding, but in other populations, there was sufficient gene flow or enough survivors to prevent genetic drift and inbreeding. Direct evidence of diseases acting as selective pressures in wild populations is somewhat limited, but there are several clear examples of it occurring. Also, several studies found that gene flow can impact the evolution of small populations either beneficially, by providing them with variation, or detrimentally, by swamping them with alleles that are not locally adaptive. Thus, differences in gene flow levels may explain why some species adapt while others do not. There are also intermediate cases, whereby some species may adapt to disease, but not at a rate that is meaningful for conservation purposes.     

Nonlinear variation in clinging performance with surface roughness in geckos

Understanding the challenges faced by organisms moving within their environment is essential to comprehending the evolution of locomotor morphology and habitat use. Geckos have developed adhesive toe pads that enable exploitation of a wide range of microhabitats. These toe pads, and their adhesive mechanisms, have typically been studied using a range of artificial substrates, usually significantly smoother than those available in nature. Although these studies have been fundamental in understanding the mechanisms of attachment in geckos, it is unclear whether gecko attachment simply gradually declines with increased roughness as some researchers have suggested, or whether the interaction between the gekkotan adhesive system and surface roughness produces nonlinear relationships. To understand ecological challenges faced in their natural habitats, it is essential to use test surfaces that are more like surfaces used by geckos in nature. We tested gecko shear force (i.e., frictional force) generation as a measure of clinging performance on three artificial substrates. We selected substrates that exhibit microtopographies with peak‐to‐valley heights similar to those of substrates used in nature, to investigate performance on a range of smooth surfaces (glass), and fine‐grained (fine sandpaper) to rough (coarse sandpaper). We found that shear force did not decline monotonically with roughness, but varied nonlinearly among substrates. Clinging performance was greater on glass and coarse sandpaper than on fine sandpaper, and clinging performance was not significantly different between glass and coarse sandpaper. Our results demonstrate that performance on different substrates varies, probably depending on the underlying mechanisms of the adhesive apparatus in geckos.