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Phylogeography of the Small Indian Civet and Origin of Introductions to Western Indian Ocean Islands
(2016)
The biogeographic dynamics affecting the Indian subcontinent, East and Southeast Asia during the Plio-Pleistocene has generated complex biodiversity patterns. We assessed the molecular biogeography of the small Indian civet (Viverricula indica) through mitogenome and cytochrome b + control region sequencing of 89 historical and modern samples to (1) establish a time-calibrated phylogeography across the species’ native range and (2) test introduction scenarios to western Indian Ocean islands. Bayesian phylogenetic analyses identified 3 geographic lineages (East Asia, sister-group to Southeast Asia and the Indian subcontinent + northern Indochina) diverging 3.2–2.3 million years ago (Mya), with no clear signature of past demographic expansion. Within Southeast Asia, Balinese populations separated from the rest 2.6–1.3 Mya. Western Indian Ocean populations were assigned to the Indian subcontinent + northern Indochina lineage and had the lowest mitochondrial diversity. Approximate Bayesian computation did not distinguish between single versus multiple introduction scenarios. The early diversification of the small Indian civet was likely shaped by humid periods in the Late Pliocene–Early Pleistocene that created evergreen rainforest barriers, generating areas of intra-specific endemism in the Indian subcontinent, East, and Southeast Asia. Later, Pleistocene dispersals through drier conditions in South and Southeast Asia were likely, giving rise to the species’ current natural distribution. Our molecular data supported the delineation of only 4 subspecies in V. indica, including an endemic Balinese lineage. Our study also highlighted the influence of prefirst millennium AD introductions to western Indian Ocean islands, with Indian and/or Arab traders probably introducing the species for its civet oil.
Engineered nanogels are of high value for a targeted and controlled transport of compounds due to the ability to change their chemical properties by external stimuli. As it has been indicated that nanogels possess a high ability to penetrate the stratum corneum, it cannot be excluded that nanogels interact with dermal dendritic cells, especially in diseased skin. In this study the potential crosstalk of the thermore-sponsive nanogels (tNGs) with the dendritic cells of the skin was investigated with the aim to determine the immunotoxicological properties of the nanogels. The investigated tNGs were made of dendritic polyglycerol (dPG) and poly(glycidyl methyl ether-co-ethyl glycidyl ether) (p(GME-co-EGE)), as polymer conferring thermoresponsive properties. Although the tNGs were taken up, they displayed neither cytotoxic and genotoxic effects nor any induction of reactive oxygen species in the tested cells. Interestingly, specific uptake mechanisms of the tNGs by the dendritic cells were depending on the nanogels cloud point temperature (Tcp), which determines the phase transition of the nanoparticle. The study points to caveolae-mediated endocytosis as being the major tNGs uptake mechanism at 37 degrees C, which is above the Tcp of the tNGs. Remarkably, an additional uptake mechanism, beside caveolae-mediated endocytosis, was observed at 29 degrees C, which is the Tcp of the tNGs. At this temperature, which is characterized by two different states of the tNGs, macropinocytosis was involved as well. In summary, our study highlights the impact of thermoresponsivity on the cellular uptake mechanisms which has to be taken into account if the tNGs are used as a drug delivery system.
Aims Plants directly and indirectly interact with many abiotic and biotic soil components. Research so far mostly focused on direct, individual abiotic or biotic effects on plant growth, but only few studies tested the indirect effects of abiotic soil factors on plant growth. Therefore, we investigated how abiotic soil conditions affect plant performance, via changes induced by soil biota. Methods In a full-factorial experiment, we grew the widespread grass Dactylis glomerata either with or without soil biota and investigated the impact of soil temperature, fertility and moisture on the soil biota effects on plant growth. We measured biomass production, root traits and colonization by arbuscular mycorrhizal fungi as well as microbial respiration. Important Findings We found significant interaction effects between abiotic soil conditions and soil biota on plant growth for fertility, but especially for soil temperature, as an increase of 10 degrees C significantly changed the soil biota effects on plant growth from positive to neutral. However, if tested individually, an increase in soil temperature and fertility per se positively affected plant biomass production, whereas soil biota per se did not affect overall plant growth, but both influenced root architecture. By affecting soil microbial activity and root architecture, soil temperature might influence both mutualistic and pathogenic interactions between plants and soil biota. Such soil temperature effects should be considered in soil feedback studies to ensure greater transferability of results from artificial and experimental conditions to natural environmental conditions.
Fruits exhibit a vast array of different 3D shapes, from simple spheres and cylinders to more complex curved forms; however, the mechanism by which growth is oriented and coordinated to generate this diversity of forms is unclear. Here, we compare the growth patterns and orientations for two very different fruit shapes in the Brassicaceae: the heart-shaped Capsella rubella silicle and the near-cylindrical Arabidopsis thaliana silique. We show, through a combination of clonal and morphological analyses, that the different shapes involve different patterns of anisotropic growth during three phases. These experimental data can be accounted for by a tissue level model in which specified growth rates vary in space and time and are oriented by a proximodistal polarity field. The resulting tissue conflicts lead to deformation of the tissue as it grows. The model allows us to identify tissue-specific and temporally specific activities required to obtain the individual shapes. One such activity may be provided by the valve-identity gene FRUITFULL, which we show through comparative mutant analysis to modulate fruit shape during post-fertilisation growth of both species. Simple modulations of the model presented here can also broadly account for the variety of shapes in other Brassicaceae species, thus providing a simplified framework for fruit development and shape diversity.
The abandonment of military areas leads to succession processes affecting valuable open-land habitats and is considered to be a major threat for European butterflies. We assessed the ability of hyper spectral remote sensing data to spatially predict the occurrence of one of the most endangered butterfly species (Hipparchia statilinus) in Brandenburg (Germany) on the basis of habitat characteristics at a former military training area. Presence-absence data were sampled on a total area of 36 km(2), and N = 65 adult individuals of Hipparchia statilinus could be detected. The floristic composition within the study area was modeled in a three-dimensional ordination space. Occurrence probabilities for the target species were predicted as niches between ordinated floristic gradients by using Regression Kriging of Indicators. Habitat variance could be explained by up to 81 % with spectral variables at a spatial resolution of 2 x 2 m by transferring PLSR models to imagery. Ordinated ecological niche of Hipparchia statilinus was tested against environmental predictor variables. N = 6 variables could be detected to be significantly correlated with habitat preferences of Hipparchia statilinus. They show that Hipparchia statilinus can serve as a valuable indicator for the evaluation of the conservation status of Natura 2000 habitat type 2330 (inland dunes with open Corynephorus and Agrostis grasslands) protected by the Habitat Directive (Council Directive 92/43/EEC). The authors of this approach, conducted in August 2013 at Doberitzer Heide Germany, aim to increase the value of remote sensing as an important tool for questions of biodiversity research and conservation.
Warming and eutrophication are two of the most important global change stressors for natural ecosystems, but their interaction is poorly understood. We used a dynamic model of complex, size-structured food webs to assess interactive effects on diversity and network structure. We found antagonistic impacts: Warming increases diversity in eutrophic systems and decreases it in oligotrophic systems. These effects interact with the community size structure: Communities of similarly sized species such as parasitoid-host systems are stabilized by warming and destabilized by eutrophication, whereas the diversity of size-structured predator-prey networks decreases strongly with warming, but decreases only weakly with eutrophication. Nonrandom extinction risks for generalists and specialists lead to higher connectance in networks without size structure and lower connectance in size-structured communities. Overall, our results unravel interactive impacts of warming and eutrophication and suggest that size structure may serve as an important proxy for predicting the community sensitivity to these global change stressors.
1. Plant-plant interactions may critically modify the impact of climate change on plant communities. However, the magnitude and even direction of potential future interactions remains highly debated, especially for water-limited ecosystems. Predictions range from increasing facilitation to increasing competition with future aridification. 2. The different methodologies used for assessing plant-plant interactions under changing environmental conditions may affect the outcome but they are not equally represented in the literature. Mechanistic experimental manipulations are rare compared with correlative approaches that infer future patterns from current observations along spatial climatic gradients. 3. Here, we utilize a unique climatic gradient in combination with a large-scale, long-term experiment to test whether predictions about plant-plant interactions yield similar results when using experimental manipulations, spatial gradients or temporal variation. We assessed shrub-annual interactions in three different sites along a natural rainfall gradient (spatial) during 9 years of varying rainfall (temporal) and 8 years of dry and wet manipulations of ambient rainfall (experimental) that closely mimicked regional climate scenarios. 4. The results were fundamentally different among all three approaches. Experimental water manipulations hardly altered shrub effects on annual plant communities for the assessed fitness parameters biomass and survival. Along the spatial gradient, shrub effects shifted from clearly negative to mildly facilitative towards drier sites, whereas temporal variation showed the opposite trend: more negative shrub effects in drier years. 5. Based on our experimental approach, we conclude that shrub-annual interaction will remain similar under climate change. In contrast, the commonly applied space-for-time approach based on spatial gradients would have suggested increasing facilitative effects with climate change. We discuss potential mechanisms governing the differences among the three approaches. 6. Our study highlights the critical importance of long-term experimental manipulations for evaluating climate change impacts. Correlative approaches, for example along spatial or temporal gradients, may be misleading and overestimate the response of plant-plant interactions to climate change.
In nature, plants often encounter chronic or recurring stressful conditions. Recent results indicate that plants can remember a past exposure to stress to be better prepared for a future stress incident. However, the molecular basis of this is poorly understood. Here, we report the involvement of chromatin modifications in the maintenance of acquired thermotolerance (heat stress [HS] memory). HS memory is associated with the accumulation of histone H3 lysine 4 di- and trimethylation at memory-related loci. This accumulation outlasts their transcriptional activity and marks them as recently transcriptionally active. High accumulation of H3K4 methylation is associated with hyper-induction of gene expression upon a recurring HS. This transcriptional memory and the sustained accumulation of H3K4 methylation depend on HSFA2, a transcription factor that is required for HS memory, but not initial heat responses. Interestingly, HSFA2 associates with memory-related loci transiently during the early stages following HS. In summary, we show that transcriptional memory after HS is associated with sustained H3K4 hyper-methylation and depends on a hit-and-run transcription factor, thus providing a molecular framework for HS memory.
Mediated bioelectrochemical system for biosensing the cell viability of Staphylococcus aureus
(2016)
Staphylococcus aureus is one of the most dangerous human pathogens and is the cause of numerous illnesses ranging from moderate skin infections to life-threatening diseases. Despite advances made in identifying microorganisms, rapid detection methods for the viability of bacteria are still missing. Here, we report a rapid electrochemical assay for cell viability combining the use of double redox mediators and multiwall carbon nanotubes-screen printed electrodes (MWCNTs-SPE), ferricyanide (FCN) and 2,6-dichlorophenolindophenol (DCIP), which served as electron shuttle to enable the bacterial-electrode communications. The current originating from the metabolically active cells was recorded for probing the activity of the intracellular redox centers. Blocking of the respiratory chain pathways with electron transfer inhibitors demonstrated the involvement of the electron transport chain in the reaction. A good correlation between the number of the metabolically active cells and the current was obtained. The proposed assay has been exploited for monitoring cell proliferation of S. aureus during the growth. The sensitivity of the detection method reached 0.1 OD600. Therefore, the technique described is promising for estimating the cell number, measuring the cell viability, and probing intracellular redox center(s).
Polychlorinated biphenyls (PCBs) can cause endocrine disruption, cancer, immunosuppression, or reproductive failure in animals. We used an individual-based model to explore whether and how PCB-associated reproductive failure could affect the dynamics of a hypothetical polar bear (Ursus maritimus) population exposed to PCBs to the same degree as the East Greenland subpopulation. Dose-response data from experimental studies on a surrogate species, the mink (Mustela vision), were used in the absence of similar data for polar bears. Two alternative types of reproductive failure in relation to maternal sum-PCB concentrations were considered: increased abortion rate and increased cub mortality. We found that the quantitative impact of PCB-induced reproductive failure on population growth rate depended largely on the actual type of reproductive failure involved. Critical potencies of the dose-response relationship for decreasing the population growth rate were established for both modeled types of reproductive failure. Comparing the model predictions of the age-dependent trend of sum-PCBs concentrations in females with actual field measurements from East Greenland indicated that it was unlikely that PCB exposure caused a high incidence of abortions in the subpopulation. However, on the basis of this analysis, it could not be excluded that PCB exposure contributes to higher cub mortality. Our results highlight the necessity for further research on the possible influence of PCBs on polar bear reproduction regarding their physiological pathway. This includes determining the exact cause of reproductive failure, i.e., in utero exposure versus lactational exposure of offspring; the timing of offspring death; and establishing the most relevant reference metrics for the dose-response relationship.
Objectives: To reanalyze the between-population variance in height, weight, and body mass index (BMI), and to provide a globally applicable technique for generating synthetic growth reference charts. Methods: Using a baseline set of 196 female and 197 male growth studies published since 1831, common factors of height, weight, and BMI are extracted via Principal Components separately for height, weight, and BMI. Combining information from single growth studies and the common factors using in principle a Bayesian rationale allows for provision of completed reference charts. Results: The suggested approach can be used for generating synthetic growth reference charts with LMS values for height, weight, and BMI, from birth to maturity, from any limited set of height and weight measurements of a given population. Conclusion: Generating synthetic growth reference charts by incorporating information from a large set of reference growth studies seems suitable for populations with no autochthonous references at hand yet. (C) 2015 Wiley Periodicals, Inc.
Abstract
By combining high-throughput sequencing with target enrichment (‘hybridization capture’), researchers are able to obtain molecular data from genomic regions of interest for projects that are otherwise constrained by sample quality (e.g. degraded and contamination-rich samples) or a lack of a priori sequence information (e.g. studies on nonmodel species). Despite the use of hybridization capture in various fields of research for many years, the impact of enrichment conditions on capture success is not yet thoroughly understood. We evaluated the impact of a key parameter – hybridization temperature – on the capture success of mitochondrial genomes across the carnivoran family Felidae. Capture was carried out for a range of sample types (fresh, archival, ancient) with varying levels of sequence divergence between bait and target (i.e. across a range of species) using pools of individually indexed libraries on Agilent SureSelect™ arrays. Our results suggest that hybridization capture protocols require specific optimization for the sample type that is being investigated. Hybridization temperature affected the proportion of on-target sequences following capture: for degraded samples, we obtained the best results with a hybridization temperature of 65 °C, while a touchdown approach (65 °C down to 50 °C) yielded the best results for fresh samples. Evaluation of capture performance at a regional scale (sliding window approach) revealed no significant improvement in the recovery of DNA fragments with high sequence divergence from the bait at any of the tested hybridization temperatures, suggesting that hybridization temperature may not be the critical parameter for the enrichment of divergent fragments.
Synthetic promoters are important for temporal and spatial gene expression in transgenic plants. To identify novel microbe-associated molecular pattern (MAMP)-responsive cis-regulatory sequences for synthetic promoter design, a combination of bioinformatics and experimental approaches was employed. One cis-sequence was identified which confers strong MAMP-responsive reporter gene activity with low background activity. The 35-bp-long cis-sequence was identified in the promoter of the Arabidopsis thaliana DJ1E gene, a homologue of the human oncogene DJ1. In this study, this cis-sequence is shown to be a tripartite cis-regulatory module (CRM). A synthetic promoter with four copies of the CRM linked to a minimal promoter increases MAMP-responsive reporter gene expression compared to the wild-type DJ1E promoter. The CRM consists of two WT-boxes (GGACTTTT and GGACTTTG) and a variant of the GCC-box (GCCACC), all required for MAMP and salicylic acid (SA) responsivity. Yeast one-hybrid screenings using a transcription factor (TF)-only prey library identified two AP2/ERFs, ORA59 and ERF10, interacting antagonistically with the CRM. ORA59 activates reporter gene activity and requires the consensus core sequence GCCNCC for gene expression activation. ERF10 down-regulates MAMP-responsive gene expression. No TFs interacting with the WT-boxes GGACTTTT and GGACTTTG were selected in yeast onehybrid screenings with the TF-only prey library. In transgenic Arabidopsis, the synthetic promoter confers strong and specific reporter gene activity in response to biotrophs and necrotrophs as well as SA.
Arf-like proteins (ARLs) are ubiquitously expressed small G proteins of the RAS superfamily. In photoreceptors, ARL2 and ARL3 participate in the trafficking of lipidated membrane-associated proteins and colocalize in the inner segment with UNC119A and PDE delta. UNC119A and PDE delta are acyl-and prenyl-binding proteins, respectively, involved in trafficking of acylated (transducin-alpha subunit, nephrocystin NPHP3) and prenylated proteins (GRK1, PDE6). Germline Arl3 knockout mice do not survive beyond postnatal day 21 and display ciliary defects in multiple organs (kidney, liver and pancreas) as well as retinal degeneration. Conditional knockouts will be necessary to delineate mechanisms of protein transport in retina disease.
Flower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana. In A. lyrata, we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon.
Herein we present an efficient synthesis of a biomimetic probe with modular construction that can be specifically bound by the mannose binding FimH protein - a surface adhesion protein of E. coli bacteria. The synthesis combines the new and interesting DBD dye with the carbohydrate ligand mannose via a Click reaction. We demonstrate the binding to E. coli bacteria over a large concentration range and also present some special characteristics of those molecules that are of particular interest for the application as a biosensor. In particular, the mix-and-measure ability and the very good photo-stability should be highlighted here.
The importance of ciliates as herbivores and in biogeochemical cycles is increasingly recognized. An opportunity to observe the potential consequences of zooplankton dominated by ciliates arose when winter fish kills resulted in strong suppression of crustaceans by young planktivorous fish in two shallow lakes. On an annual average, ciliates made up 38-76% of the total zooplankton biomass in both lakes during two subsequent years. Consequently, ciliate biomass and their estimated grazing potential were extremely high compared with other lakes of various trophic states and depths. Grazing estimates based on abundance and size suggest that ciliates should have cleared the water column of small (<5 mu m) and intermediate (5-50 mu m) sized phytoplankton more than once a day. Especially, small feeders within the ciliates were important, likely exerting a strong top-down control on small phytoplankton. Particle-attached bacteria were presumably strongly suppressed by intermediate-sized ciliate feeders. In contrast to other lakes, large phytoplankton was proportionately very abundant. The phytoplankton community had a high evenness, which may be attributed to the feeding by numerous fast growing and selective ciliate species. Our study highlights ciliates as an important trophic link and adds to the growing awareness of the role of winter processes for plankton dynamics.
Molybdoenzymes are widespread in eukaryotic and prokaryotic organisms where they play crucial functions in detoxification reactions in the metabolism of humans and bacteria, in nitrate assimilation in plants and in anaerobic respiration in bacteria. To be fully active, these enzymes require complex molybdenum-containing cofactors, which are inserted into the apoenzymes after folding. For almost all the bacterial molybdoenzymes, molybdenum cofactor insertion requires the involvement of specific chaperones. In this review, an overview on the molybdenum cofactor biosynthetic pathway is given together with the role of specific chaperones dedicated for molybdenum cofactor insertion and maturation. Many bacteria are involved in geochemical cycles on earth and therefore have an environmental impact. The roles of molybdoenzymes in bioremediation and for environmental applications are presented.This review gives an overview of the diverse mechanisms leading to the insertion of the different forms of the molybdenum cofactor into the respective target enzymes and summarizes the roles of different molybdoenzymes in the environment.This review gives an overview of the diverse mechanisms leading to the insertion of the different forms of the molybdenum cofactor into the respective target enzymes and summarizes the roles of different molybdoenzymes in the environment.
Animal-associated microbial communities can play major roles in the physiology, development, ecology, and evolution of their hosts, but the study of their diversity has yet focused on a limited number of host species. In this study, we used high-throughput sequencing of partial sequences of the bacterial 16S rRNA gene to assess the diversity of the gut-inhabiting bacterial communities of 212 specimens of tropical anuran amphibians from Brazil and Madagascar. The core gut-associated bacterial communities among tadpoles from two different continents strongly overlapped, with eight highly represented operational taxonomic units (OTUs) in common. In contrast, the core communities of adults and tadpoles from Brazil were less similar with only one shared OTU. This suggests a community turnover at metamorphosis. Bacterial diversity was higher in tadpoles compared to adults. Distinct differences in composition and diversity occurred among gut bacterial communities of conspecific tadpoles from different water bodies and after experimental fasting for 8 days, demonstrating the influence of both environmental factors and food on the community structure. Communities from syntopic tadpoles clustered by host species both in Madagascar and Brazil, and the Malagasy tadpoles also had species-specific isotope signatures. We recommend future studies to analyze the turnover of anuran gut bacterial communities at metamorphosis, compare the tadpole core communities with those of other aquatic organisms, and assess the possible function of the gut microbiota as a reservoir for protective bacteria on the amphibian skin.
Body height is associated with environmental conditions. It has been suggested that under poor conditions when inequality within a population increases, also the variability in height tends to increase. We studied the association of body height, within-country variability in height and geographic and historic origin in 767 growth studies carried out in 80 countries, published between 1794 and 2013, with data on N = 78,184 infants age 2 years, and N = 2,130,729 juveniles age 7 years. The studies represent almost the whole spectrum of economic diversity in human societies since the end-18 th century. 207 studies contained data for both infants and juveniles with 50,819 subjects (age 2), and 123,078 subjects (age 7). Multiple linear regressions showed significant interactions between height, sex, historic year of the study, geographic origin, and within-study standard deviation for height with multiple R-squared = 0.527, p < 0.001, at age 2, and multiple R-squared = 0.436, p < 0.001, at age 7. Yet, the two age groups differed in respect to within-study standard deviation for height. We found a significant association between body height and within-study standard deviation for height only at age 2: tall infant populations are less variable in height (r = –0.27, p < 0.01). There was no such association in children aged 7 years. Tall children from affluent and short children from less affluent countries do not differ in the variability of body height. The data suggest that the 'environmental adversity' hypothesis for variation in growth: small mean values for height go along with large standard deviations for height, does not apply for children at age 7.