Conducting metagenomic studies in microbiology and clinical research

Owing to the increased cost-effectiveness of high-throughput technologies, the number of studies focusing on the human microbiome and its connections to human health and disease has recently surged. However, best practices in microbiology and clinical research have yet to be clearly established. Here, we present an overview of the challenges and opportunities involved in conducting a metagenomic study, with a particular focus on data processing and analytical methods.

     

The endothelin/sarafotoxin-induced increase of the proliferation of undifferentiated and DMSO-differentiated GEM-81 goldfish erythrophoroma cells is mediated by ETB receptors

Endothelins (ETs) and sarafotoxins (SRTXs) have been reported to exert ET(B)-mediated effects on vertebrate pigment cells. GEM-81 cell line, a red pigment cell-derived cutaneous tumor of the teleost Carassius auratus, expresses ET(B) receptors and can be differentiated with 1.5% DMSO treatment, thus constituting an useful model to investigate ET and SRTX effects on cultured fish pigment cells. Our aim was to characterize the pharmacology and biological effects mediated by ET receptors in DMSO-differentiated and undifferentiated cells. ET subtype receptors and their respective Ki values in both cell types were determined by competitive binding assays using (125)I ET-1 and BQ-485 (an ET(A) antagonist) or BQ-788 (an ET(B) antagonist). BQ-788, but not BQ-485, significantly reduced (125)I-ET-1 binding in both cell types, with similar low (Ki > nM) affinities. To determine the proliferation effects of ETs/SRTXs, cells were treated for 72 h with the hormones, and counted in a hemocytometer. The proliferation assays were repeated for SRTX S6c in the presence or absence of BQ-788. The results demonstrated that, with the exception of ET-1 (biphasic effect) and ET-3 (no significant effect) in undifferentiated GEM-81 cells, all the tested hormones induced increases in the proliferation of both types of cells. The hormones were equipotent in DMSO-differentiated cells, which exhibited increased sensitivity to ETs, but not to SRTXs, as compared with undifferentiated cells. The BQ-788 antagonistic effect was also exerted on the proliferation responses to SRTX S6c. These results corroborate the long and important evolutionary history of the ET/SRTX receptor system in vertebrate pigment cells.     

Future hotspots of terrestrial mammal loss

Current levels of endangerment and historical trends of species and habitats are the main criteria used to direct conservation efforts globally. Estimates of future declines, which might indicate different priorities than past declines, have been limited by the lack of appropriate data and models. Given that much of conservation is about anticipating and responding to future threats, our inability to look forward at a global scale has been a major constraint on effective action. Here, we assess the geography and extent of projected future changes in suitable habitat for terrestrial mammals within their present ranges. We used a global earth-system model, IMAGE, coupled with fine-scale habitat suitability models and parametrized according to four global scenarios of human development. We identified the most affected countries by 2050 for each scenario, assuming that no additional conservation actions other than those described in the scenarios take place. We found that, with some exceptions, most of the countries with the largest predicted losses of suitable habitat for mammals are in Africa and the Americas. African and North American countries were also predicted to host the most species with large proportional global declines. Most of the countries we identified as future hotspots of terrestrial mammal loss have little or no overlap with the present global conservation priorities, thus confirming the need for forward-looking analyses in conservation priority setting. The expected growth in human populations and consumption in hotspots of future mammal loss mean that local conservation actions such as protected areas might not be sufficient to mitigate losses. Other policies, directed towards the root causes of biodiversity loss, are required, both in Africa and other parts of the world.     

Contrasting changes in the abundance and diversity of North American bird assemblages from 1971 to 2010

Although it is generally recognized that global biodiversity is declining, few studies have examined long‐term changes in multiple biodiversity dimensions simultaneously. In this study, we quantified and compared temporal changes in the abundance, taxonomic diversity, functional diversity, and phylogenetic diversity of bird assemblages, using roadside monitoring data of the North American Breeding Bird Survey from 1971 to 2010. We calculated 12 abundance and diversity metrics based on 5‐year average abundances of 519 species for each of 768 monitoring routes. We did this for all bird species together as well as for four subgroups based on breeding habitat affinity (grassland, woodland, wetland, and shrubland breeders). The majority of the biodiversity metrics increased or remained constant over the study period, whereas the overall abundance of birds showed a pronounced decrease, primarily driven by declines of the most abundant species. These results highlight how stable or even increasing metrics of taxonomic, functional, or phylogenetic diversity may occur in parallel with substantial losses of individuals. We further found that patterns of change differed among the species subgroups, with both abundance and diversity increasing for woodland birds and decreasing for grassland breeders. The contrasting changes between abundance and diversity and among the breeding habitat groups underscore the relevance of a multifaceted approach to measuring biodiversity change. Our findings further stress the importance of monitoring the overall abundance of individuals in addition to metrics of taxonomic, functional, or phylogenetic diversity, thus confirming the importance of population abundance as an essential biodiversity variable.     

Human intestinal parasites in Subsaharan Africa. I. Eastern Boè and Canhabaque Island (Guinea-Bissau)

A coprological survey was carried out in 1982-1983 in East Boè and in Canhabaque Island, (Bijagòs Islands), where 289 and 288 specimens of stools, respectively, have been collected. The samples were taken from apparently healthy subjects, of both sexes and of different age groups. The tests were made according to the modified Ritchie technique. The following results were obtained: A) East Boè: 1) Protozoa: E. coli 68.9%, E. nana 24.6%, G. intestinalis 8.7%, I. buetschlii 5.9%, E. histolytica 1.7%, E. hartmanni 0.7%, T. intestinalis 0.7%. b) Helminths: Ancylostomatidae 69.2%, T. trichiura 38.4%, S. stercoralis 6.2%, Taenia sp. 1.7%, H. nana 0.7%, S. haematobium 0.7%, S. mansoni 0.7%, S. fuelleborni 0.7%. B) Canhabaque: a) Protozoa: E. coli 85.1%, I. buetschlii 14.9%, E. nana 12.5%, G. intestinalis 8.3%, C. mesnili 7.3%, E. hartmanni 1.4%, E. histolytica 1.0%, T. intestinalis 0.4%. b) Helminths: Ancylostomatidae 87.9%, T. trichiura 9.4%, S. stercoralis 7.9%, S. fuelleborni 2.8%, Trichostrongylus sp. 1.4%, A. lumbricoides 0.7%, H. nana 0.4%. Eggs of Capillaria sp. probably pseudoparasites, were found in 8.7% of samples. The high prevalence of Ancylostomatidae infections appears to be related to the heavy fecal pollution all over the examined territory. The utilization of antihelminthic drug of popular medicine, which has a specific action on A. lumbricoides, could explain the lack and the low prevalence, respectively, of A. lumbricoides infections in both examined areas. In the past, other authors emphasized the low prevalence of this parasite for other Guinea Bissau regions which have a different geomorfological constitution. The cases of S. fuelleborni and H. nana are the first reported for Guinea Bissau.     

A framework for the identification of hotspots of climate change risk for mammals

As rates of global warming increase rapidly, identifying species at risk of decline due to climate impacts and the factors affecting this risk have become key challenges in ecology and conservation biology. Here, we present a framework for assessing three components of climate‐related risk for species: vulnerability, exposure and hazard. We used the relationship between the observed response of species to climate change and a set of intrinsic traits (e.g. weaning age) and extrinsic factors (e.g. precipitation seasonality within a species geographic range) to predict, respectively, the vulnerability and exposure of all data‐sufficient terrestrial non‐volant mammals (3,953 species). Combining this information with hazard (the magnitude of projected climate change within a species geographic range), we identified global hotspots of species at risk from climate change that includes the western Amazon basin, south‐western Kenya, north‐eastern Tanzania, north‐eastern South Africa, Yunnan province in China, and mountain chains in Papua‐New Guinea. Our framework identifies priority areas for monitoring climate change effects on species and directing climate mitigation actions for biodiversity.     

Signalling pathways evoked by alpha1-adrenoceptors in human melanoma cells

The biological effects of catecholamines in mammalian pigment cells are poorly understood, but in poikilothermic vertebrates they regulate the translocation of pigment granules. We have previously demonstrated in SK-Mel 23-human melanoma cells the presence of low affinity alpha(1)-adrenoceptors, which mediate a decrease in cell proliferation and increase in tyrosinase activity, with no change of tyrosinase expression. In this report, we investigated the signalling pathways involved in these responses. Calcium mobilization in response to phenylephrine (PHE), an alpha(1)-adrenergic agonist, was investigated by confocal microscopy, and no change of fluorescence during the treatment was observed, suggesting that calcium is not involved in the signalling pathway activated by alpha(1)-adrenoceptors in SK-Mel 23 cells. cAMP levels, determined by enzyme-immunoassay, were significantly increased by PHE (10(-5)-10(-4)M), that could be blocked by the alpha(1)-adrenergic antagonist benoxathian (10(-5)-10(-4)M). Several biological assays were then performed with PHE, for 72 h, in the absence or presence of various signalling pathway inhibitors, in an attempt to determine the intracellular messengers involved in the responses of proliferation and tyrosinase activity. Our results suggest the participation of p38 and ERKs in PHE-induced decrease of proliferation, and possibly also of cAMP and protein kinase A. Regarding PHE-induced increase of tyrosinase activity, it is suggested that the following signalling components are involved: cAMP/PKA, PKC, PI3K, p38 and ERKs.     

Socio-economic and ecological impacts of global protected area expansion plans

Several global strategies for protected area (PA) expansion have been proposed to achieve the Convention on Biological Diversity''s Aichi target 11 as a means to stem biodiversity loss, as required by the Aichi target 12. However, habitat loss outside PAs will continue to affect habitats and species, and PAs may displace human activities into areas that might be even more important for species persistence. Here we measure the expected contribution of PA expansion strategies to Aichi target 12 by estimating the extent of suitable habitat available for all terrestrial mammals, with and without additional protection (the latter giving the counterfactual outcome), under different socio-economic scenarios and consequent land-use change to 2020. We found that expanding PAs to achieve representation targets for ecoregions under a Business-as-usual socio-economic scenario will result in a worse prognosis than doing nothing for more than 50% of the world''s terrestrial mammals. By contrast, targeting protection towards threatened species can increase the suitable habitat available to over 60% of terrestrial mammals. Even in the absence of additional protection, an alternative socio-economic scenario, adopting progressive changes in human consumption, leads to positive outcomes for mammals globally and to the largest improvements for wide-ranging species.     

Ion Permeabilities in Mouse Sperm Reveal an External Trigger for SLO3-Dependent Hyperpolarization

Unlike most cells of the body which function in an ionic environment controlled within narrow limits, spermatozoa must function in a less controlled external environment. In order to better understand how sperm control their membrane potential in different ionic conditions, we measured mouse sperm membrane potentials under a variety of conditions and at different external K⁺ concentrations, both before and after capacitation. Experiments were undertaken using both wild-type, and mutant mouse sperm from the knock-out strain of the sperm-specific, pH-sensitive, SLO3 K⁺ channel. Membrane voltage data were fit to the Goldman-Hodgkin-Katz equation. Our study revealed a significant membrane permeability to both K⁺ and Cl⁻ before capacitation, as well as Na⁺. The permeability to both K⁺ and Cl⁻ has the effect of preventing large changes in membrane potential when the extracellular concentration of either ion is changed. Such a mechanism may protect against undesired shifts in membrane potential in changing ionic environments. We found that a significant portion of resting membrane potassium permeability in wild-type sperm was contributed by SLO3 K⁺ channels. We also found that further activation of SLO3 channels was the essential mechanism producing membrane hyperpolarization under two separate conditions, 1) elevation of external pH prior to capacitation and 2) capacitating conditions. Both conditions produced a significant membrane hyperpolarization in wild-type which was absent in SLO3 mutant sperm. Hyperpolarization in both conditions may result from activation of SLO3 channels by raising intracellular pH; however, demonstrating that SLO3-dependent hyperpolarization is achieved by an alkaline environment alone shows that SLO3 channel activation might occur independently of other events associated with capacitation. For example sperm may undergo stages of membrane hyperpolarization when reaching alkaline regions of the female genital tract. Significantly, other events associated with sperm capacitation, occur in SLO3 mutant sperm and thus proceed independently of hyperpolarization.     

Continuous ethanol fermentation in a tower reactor with flocculating yeast recycle: scale-up effects on process performance, kinetic parameters and model predictions

An unsegregated and unstructured model developed for a small-scale process of ethanol production in a tower reactor with cell recycle was applied to describe the experimental data obtained in a large-scale process. The model was developed considering the following points: reactor hydrodynamic behavior analogous to that of ideal CSTR, substrate limitation, inhibition phenomena linked both to ethanol and to biomass, absence of fermentation in the settler, and no loss of cell viability. The scale-up criterion consisted in maintaining an identical relation settler volume/fermentor volume on the two scales. All large-scale experiments were carried out using a flocculating yeast strain IR-2, isolated from fermented food, and identified as Saccharomyces cerevisiae. Sugarcane juice was used as the substrate source with sugar concentrations of 150?g/l. Different values of dilution rate and recycle ratio were employed (D?=?0.11–0.33?h^?1, α?=?5.4–18.0) and the temperature was of 32?°C. The kinetic parameters were similar on both scales and the model predictions agreed well with the large-scale experimental data.