Phenotypic population divergence in terrestrial vertebrates at macro scales

Phenotypic divergence between populations, i.e. how much phenotypes within a species vary geographically, is critical to many aspects of ecology and evolution, including eco-geographical trends, speciation and coexistence. Yet, the variation of divergence across species with different ecologies and distributions and the relative role of adaptive causes remains little understood. We predict that genetic control vs. phenotypic plasticity of traits, geographical distance and (assuming adaptation) environmental differences should explain much of the phenotypic variability between populations. We tested these predictions with body sizes of 1447 populations in 98 terrestrial vertebrate species. Population phenotypic variability differs strongly across species, and divergence increases with increasing levels of clade-typical phenotypic plasticity, the area covered by populations and body size. Geographical distance and environmental dissimilarity are similarly important predictors of divergence within species, highlighting a potential role for biotic and environmental conditions. Increased availability of phylogeographical and ecological data should facilitate further understanding of population divergence drivers at broad scales.     

Evidence for the adaptive significance of circadian rhythms

Circadian (∼24 h) clock regulated biological rhythms have been identified in a wide range of organisms from prokaryotic unicellular cyanobacteria to higher mammals. These rhythms regulate an enormous variety of processes including gene expression, metabolic processes, activity and reproduction. Given the widespread occurrence of circadian systems it is not surprising that extensive efforts have been directed at understanding the adaptive significance of circadian rhythms. In this review we discuss the approaches and findings that have resulted. In studies on organisms in their natural environments, some species show adaptations in their circadian systems that correlate with living at different latitudes, such as clines in circadian clock properties. Additionally, some species show plasticity in their circadian systems suggested to match the demands of their physical and social environment. A number of experiments, both in the field and in the laboratory, have examined the effects of having a circadian system that does not resonate with the organism's environment. We conclude that the results of these studies suggest that having a circadian system that matches the oscillating environment is adaptive.     

A review on data mining and continuous optimization applications in computational biology and medicine

An emerging research area in computational biology and biotechnology is devoted to mathematical modeling and prediction of gene‐expression patterns; it nowadays requests mathematics to deeply understand its foundations. This article surveys data mining and machine learning methods for an analysis of complex systems in computational biology. It mathematically deepens recent advances in modeling and prediction by rigorously introducing the environment and aspects of errors and uncertainty into the genetic context within the framework of matrix and interval arithmetics. Given the data from DNA microarray experiments and environmental measurements, we extract nonlinear ordinary differential equations which contain parameters that are to be determined. This is done by a generalized Chebychev approximation and generalized semi‐infinite optimization. Then, time‐discretized dynamical systems are studied. By a combinatorial algorithm which constructs and follows polyhedra sequences, the region of parametric stability is detected. In addition, we analyze the topological landscape of gene‐environment networks in terms of structural stability. As a second strategy, we will review recent model selection and kernel learning methods for binary classification which can be used to classify microarray data for cancerous cells or for discrimination of other kind of diseases. This review is practically motivated and theoretically elaborated; it is devoted to a contribution to better health care, progress in medicine, a better education, and more healthy living conditions. Birth Defects Research (Part C) 87:165–181, 2009. © 2009 Wiley‐Liss, Inc.     

Studies on water-vapor flux characteristic and the relationship with environmental factors over a planted coniferous forest in Qianyanzhou Station

Water-vapor flux over a planted coniferous forest ecosystem near Qianyanzhou, Jiangxi Province, China, was continuously measured with the eddy covariance technique for 2004. How environmental variables, including net radiation, air temperature, and soil moisture, affected water-vapor flux variation was studied in detail. Results showed that winter had the lowest monthly water-vapor flux value, whereas summer had the highest. The diurnal variation of water-vapor flux showed different patterns for clear and cloudy days. The annual total evapotranspiration was 736.1 mm. Regression analysis showed that daily water-vapor flux was significantly correlated with net radiation, air temperature, soil temperature, and soil heat flux on both clear and cloudy days, all in quadratic relationships. Stepwise regression analysis demonstrated that a different set of environmental factors controlled water-vapor flux on days with different weather conditions. From this study, it was clear that these environmental variables, especially net radiation and soil temperature, regulated water-vapor flux over the planted coniferous ecosystem.     

Does Lake Balaton affected by pollution? Assessment through surface water quality monitoring by using different assessment methods

In order to maintain a good environmental status of surface waters, an assessment of water quality carried out at specific intervals to monitor the changes of water quality in function of time. Human knowledge and experience are currently focused on using assessment methods, especially the integration of multiple constraining factors and considering them in conjugation with the correct decision-making process concerning the environment. When surface water is highly exposed to human activities, either from recreational or economic activity, the degree of vulnerability is high, and the quality of surface water is highly compromised. In case of Lake Balaton, there are many activities that can disrupt water dynamics. The first goal of this study is to determine the location of the least and most polluted sites around Lake Balaton. The processing of data was carried out by using multi-criteria decision techniques and environmental impact assessment method based on physical–chemical parameters in comparison with the limiting parameters. Based on the results of those methods water quality needs to be improved in western parts of the lake by using several geoengineering treatment techniques. This work covers a novel approach to comparing methods based on sum of ranking differences, whereas many method comparison studies suffer from ambiguity or from comparisons not being quite fair. This problem can be avoided if there are differences between ideal and actual rankings.     

Coalescent approximation for structured populations in a stationary random environment

We establish convergence to the Kingman coalescent for the genealogy of a geographically-or otherwise-structured version of the Wright-Fisher population model with fast migration. The new feature is that migration probabilities may change in a random fashion. This brings a novel formula for the coalescent effective population size (EPS). We call it a quenched EPS to emphasize the key feature of our model — random environment. The quenched EPS is compared with an annealed (mean-field) EPS which describes the case of constant migration probabilities obtained by averaging the random migration probabilities over possible environments.     

Characterization of the abiotic drivers of abundance of nearshore Arctic fishes

Fish are critical ecologically and socioeconomically for subsistence economies in the Arctic, an ecosystem undergoing unprecedented environmental change. Our understanding of the responses of nearshore Arctic fishes to environmental change is inadequate because of limited research on the physicochemical drivers of abundance occurring at a fine scale. Here, high‐frequency in situ measurements of pH, temperature, salinity, and dissolved oxygen were paired with daily fish catches in nearshore Alaskan waters of the Beaufort Sea. Due to the threat that climate change poses to high‐latitude marine ecosystems, our main objective was to characterize the abiotic drivers of abundance and elucidate how nearshore fish communities may change in the future. We used generalized additive models (GAMs) to describe responses to the nearshore environment for 18 fish species. Relationships between abundance and the physicochemical environment were variable between species and reflected life history. Each abiotic covariate was significant in at least one GAM, exhibiting both nonlinear and linear associations with abundance. Temperature was the most important predictor of abundance and was significant in GAMs for 11 species. Notably, pH was a significant predictor of abundance for six species: Arctic cod (Boreogadus saida), broad whitefish (Coregonus nasus), Dolly Varden (Salvelinus malma), ninespine stickleback (Pungitius pungitius), saffron cod (Eleginus gracilis), and whitespotted greenling (Hexagrammos stelleri). Broad whitefish and whitespotted greenling abundance was positively associated with pH, while Arctic cod and saffron cod abundance was negatively associated with pH. These results may be a bellwether for future nearshore Arctic fish community change by providing a foundational characterization of the relationships between abundance and the abiotic environment, particularly in regard to pH, and demonstrate the importance of including a wider range of physicochemical habitat covariates in future research.     

Disease-toxicant screen reveals a neuroprotective interaction between Huntington's disease and manganese exposure

Recognizing the similarities between Huntington's disease (HD) pathophysiology and the neurotoxicology of various metals, we hypothesized that they may exhibit disease-toxicant interactions revealing cellular pathways underlying neurodegeneration. Here, we utilize metals and the ST Hdh mouse striatal cell line model of HD to perform a gene–environment interaction screen. We report that striatal cells expressing mutant Huntingtin exhibit elevated sensitivity to cadmium toxicity and resistance to manganese toxicity. This neuroprotective gene–environment interaction with manganese is highly specific, as it does not occur with iron, copper, zinc, cobalt, cadmium, lead, or nickel ions. Analysis of the Akt cell stress signaling pathway showed diminished activation with manganese exposure and elevated activation after cadmium exposure in the mutant cells. Direct examination of intracellular manganese levels found that mutant cells have a significant impairment in manganese accumulation. Furthermore, YAC128Q mice, a HD model, showed decreased total striatal manganese levels following manganese exposure relative to wild-type mice. Thus, this disease-toxicant interaction screen has revealed that expression of mutant Huntingtin results in heightened sensitivity to cadmium neurotoxicity and a selective impairment of manganese accumulation.     

Investigation of critical inter‐related factors affecting the efficacy of pulsed light for inactivating clinically relevant bacterial pathogens

Aims: To investigate critical electrical and biological factors governing the efficacy of pulsed light (PL) for the in vitro inactivation of bacteria isolated from the clinical environment. Development of this alternative PL decontamination approach is timely, as the incidence of health care–related infections remains unacceptably high. Methods and Results: Predetermined cell numbers of clinically relevant Gram‐positive and Gram‐negative bacteria were inoculated separately on agar plates and were flashed with ≤60 pulses of broad‐spectrum light under varying operating conditions, and their inactivation measured. Significant differences in inactivation largely occurred depending on the level of the applied lamp discharge energy (range 3·2–20 J per pulse), the amount of pulsing applied (range 0–60 pulses) and the distance between light source and treatment surface (range 8–20 cm) used. Greater decontamination levels were achieved using a combination of higher lamp discharge energies, increased number of pulses and shorter distances between treatment surface and the xenon light source. Levels of microbial sensitivity also varied depending on the population type, size and age of cultures treated. Production of pigment pyocynanin and alginate slime in mucoid strains of Pseudomonas aeruginosa afforded some protection against lethal action of PL; however, this was evident only by using a combination of reduced amount of pulsing at the lower lamp discharge energies tested. A clear pattern was observed where Gram‐positive bacterial pathogens were more resistant to cidal effects of PL compared to Gram negatives. While negligible photoreactivation of PL‐treated bacterial strains occurred after full pulsing regimes at the different lamp discharge energies tested, some repair was evident when using a combination of reduced pulsing at the lower lamp discharge energies. Strains harbouring genes for multiple resistances to antibiotics were not significantly more resistant to PL treatments. Slight temperature rises (≤4·2°C) were measured on agar surfaces after extended pulsing at higher lamp discharge energies. Presence of organic matter on treatment surface did not significantly affect PL decontamination efficacy, nor did growth of PL‐treated bacteria on selective agar diminish survival compared to similarly treated bacteria inoculated and enumerated on nonselective agar plates. Conclusions: Critical inter‐related factors affecting the effective and repeatable in vitro decontamination performance of PL were identified during this study that will aid further development of this athermal process technology for applications in health care and in industry. Very rapid reductions (c. 7 log₁₀ CFU cm^?2 within ≤10 pulses) occurred using discharge energy of 20 J for all tested clinically relevant bacteria under study when treated at 8 cm distance from xenon light source. While no resistant flora is expected to develop for treatment of microbial pathogens on two‐dimensional surfaces, careful consideration of scale up factors such as design and operational usage of this PL technique will be required to assure operator safety. Significance and Impact of the Study: Findings and conclusions derived from this study will enable further development and optimization of this decontamination technique in health care and in food preparation settings, and will advance the field of nonthermal processing technologies.     

Use of bioluminescence imaging to monitor Campylobacter survival in chicken litter

Aim: The aim of this study was to develop a novel approach for characterizing the growth and persistence of Campylobacter in different poultry‐rearing environments. Specifically, we constructed bioluminescent Campylobacter strains and used them to monitor the survival of these pathogens in litter (bedding) material. Methods and Results: We inserted shuttle plasmids carrying the luminescence genes (luxCDABE) into C. jejuni and C. coli to construct bioluminescent strains of these pathogens. The strains were spiked into microcosms containing samples of litter‐washings and dry litter collected from different enclosures that housed broiler chickens. Our results show that C. jejuni and C. coli survived for at least 20 days in reused (old) litter while the growth of these pathogens was inhibited in clean (new) litter. Furthermore, our results suggest that the availability of nutrients and the condition of the litter (reused vs new) are important factors in the persistence of these pathogens. Conclusions: Reused litter can potentially predispose chickens to Campylobacter contamination and maintaining clean litter might reduce the incidences of colonization with these pathogens. Significance and Impact of the Study: Bioluminescence provided a simple, sensitive, and rapid approach for analysing the growth dynamics of Campylobacter. Using this technology, we highlighted the potential role of litter material in maintaining these pathogens in the chicken environment.