Social environment and genetics underlie body site‐specific microbiomes of Yellowstone National Park gray wolves (Canis lupus)

The host‐associated microbiome is an important player in the ecology and evolution of species. Despite growing interest in the medical, veterinary, and conservation communities, there remain numerous questions about the primary factors underlying microbiota, particularly in wildlife. We bridged this knowledge gap by leveraging microbial, genetic, and observational data collected in a wild, pedigreed population of gray wolves (Canis lupus) inhabiting Yellowstone National Park. We characterized body site‐specific microbes across six haired and mucosal body sites (and two fecal samples) using 16S rRNA amplicon sequencing. At the phylum level, we found that the microbiome of gray wolves primarily consists of Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria, consistent with previous studies within Mammalia and Canidae. At the genus level, we documented body site‐specific microbiota with functions relevant to microenvironment and local physiological processes. We additionally employed observational and RAD sequencing data to examine genetic, demographic, and environmental correlates of skin and gut microbiota. We surveyed individuals across several levels of pedigree relationships, generations, and social groups, and found that social environment (i.e., pack) and genetic relatedness were two primary factors associated with microbial community composition to differing degrees between body sites. We additionally reported body condition and coat color as secondary factors underlying gut and skin microbiomes, respectively. We concluded that gray wolf microbiota resemble similar host species, differ between body sites, and are shaped by numerous endogenous and exogenous factors. These results provide baseline information for this long‐term study population and yield important insights into the evolutionary history, ecology, and conservation of wild wolves and their associated microbes.     

Molecular insight into substrate recognition by human cytosolic sialidase NEU2

Sialidases or neuramidases are glycoside hydrolases removing terminal sialic acid residues from sialo-glycoproteins and sialo-glycolipids. Viral neuraminidases (NAs) have been extensively characterized and represent an excellent target for antiviral therapy through the synthesis of a series of competitive inhibitors that block the release of newly formed viral particles from infected cells. The human cytosolic sialidase NEU2 is the only mammalian enzyme structurally characterized and represents a valuable model to study the specificity of novel NA inhibitory drugs. Moreover, the availability of NEU2 3D structure represents a pivotal step toward the characterization of the molecular basis of natural substrates recognition by the enzyme. In this perspective, we have carried out a study of molecular docking of NEU2 active site using natural substrates of increasing complexity. Moreover, selective mutations of the residues putatively involved into substrate(s) interaction/recognition have been performed, and the resulting mutant enzymes have been preliminary tested for their catalytic activity and substrate specificity. We found that Q270 is involved in the binding of the disaccharide α(2,3) sialyl-galactose, whereas K45 and Q112 bind the distal glucose of the trisaccharide α(2,3) sialyl-lactose, corresponding to the oligosaccharide moiety of GM3 ganglioside. In addition, E218, beside D46, is proved to be a key catalytic residue, being, together with Y334, the second member of the nucleophile pair required for the catalysis. Overall, our results point out the existence of a dynamic network of interactions that are possibly involved in the recognition of the glycans bearing sialic acid.     

Promoting RRI and active citizenship in an inquiry-based controversial socio-scientific issue: the case of cholesterol regulation with statins

ABSTRACT

Science education is an important dimension of the European Commission’s Responsible Research and Innovation (RRI) objectives; however, RRI is not an explicit focus of biology teaching and few biology teachers have experience in integrating RRI in classroom practice. This study examines the impact of a three 80-minute RRI and active citizenship module on 11th grade biology students, based on the SSIBL pedagogical framework. A representative national sample of 11th grade biology students in Cyprus (n = 398) participated. A pre-post research design examined impact in relation to students’ conceptual understanding regarding cholesterol and its regulation, their understanding of the controversy about cholesterol regulation, awareness of RRI components, feeling of responsibility and willingness to act. Analyses indicated statistically significant gains in conceptual understanding and the understanding of the controversy about cholesterol regulation and awareness of RRI components, as well as in students’ socio-scientific accountability (feeling of responsibility and willingness to act). Conceptual understanding showed increased correlations with Controversy understanding and RRI understanding forming the three of them the cognitive elements of individuals understanding. All of the examined variables are deemed, as of great importance for the design, implementation and evaluation of innovative biology RRI and active citizenship modules.     

An activated sludge modeling framework for xenobiotic trace chemicals (ASM-X): Assessment of diclofenac and carbamazepine

Conventional models for predicting the fate of xenobiotic organic trace chemicals, identified, and calibrated using data obtained in batch experiments spiked with reference substances, can be limited in predicting xenobiotic removal in wastewater treatment plants (WWTPs). At stake is the level of model complexity required to adequately describe a general theory of xenobiotic removal in WWTPs. In this article, we assess the factors that influence the removal of diclofenac and carbamazepine in activated sludge, and evaluate the complexity required for the model to effectively predict their removal. The results are generalized to previously published cases. Batch experimental results, obtained under anoxic and aerobic conditions, were used to identify extensions to, and to estimate parameter values of the activated sludge modeling framework for Xenobiotic trace chemicals (ASM‐X). Measurement and simulation results obtained in the batch experiments, spiked with the diclofenac and carbamazepine content of preclarified municipal wastewater shows comparably high biotransformation rates in the presence of growth substrates. Forward dynamic simulations were performed using full‐scale data obtained from Bekkelaget WWTP (Oslo, Norway) to evaluate the model and to estimate the level of re‐transformable xenobiotics present in the influent. The results obtained in this study demonstrate that xenobiotic loading conditions can significantly influence the removal capacity of WWTPs. We show that the trace chemical retransformation in upstream sewer pipes can introduce considerable error in assessing the removal efficiency of a WWTP, based only on parent compound concentration measurements. The combination of our data with those from the literature shows that solids retention time (SRT) can enhance the biotransformation of diclofenac, which was not the case for carbamazepine. Model approximation of the xenobiotic concentration, detected in the solid phase, suggest that between approximately 1% and 16% of the total solid carbamazepine and diclofenac concentrations, respectively, is due to sorption—the remainder being non‐bioavailable and sequestered. We demonstrate the effectiveness of the model's predictive power over conventional tools in a statistical analysis, performed at four levels of structural complexity. To assess WWTP retrofitting needs to remove xenobiotic trace chemicals, we suggest using mechanistic models, e.g., ASM‐X, in regional risk assessments. For preliminary evaluations, we present operating charts that can be used to estimate average xenobiotic removal rates in WWTPs as a function of SRT and the xenobiotics mass loads normalised to design treatment capacity. Biotechnol. Bioeng. 2012; 109: 2757–2769. © 2012 Wiley Periodicals, Inc.     

Mechanism of zinc-mediated inhibition of caspase-9

Zinc-mediated inhibition is implicated in global caspase regulation, with relief of zinc-mediated inhibition central to both small-molecule and natively induced caspase activation. As an initiator, caspase-9 regulates the upstream stages of the apoptotic caspase cascade, making it a critical control point. Here we identify two distinct zinc-binding sites on caspase-9. The first site, composed of H237, C239, and C287, includes the active site dyad and is primarily responsible for zinc-mediated inhibition. The second binding site at C272 is distal from the active site. Given the amino-acid conservation in both regions, these sites appear to be present across the caspase family underscoring the importance of zinc-mediated regulation of this class of enzymes.     

Rapid,in situ detection of Agrobacterium tumefaciens attachment to leaf tissue

Attachment of the plant pathogen Agrobacterium tumefaciens to host plant cells is an early and necessary step in plant transformation and agroinfiltration processes. However, bacterial attachment behavior is not well understood in complex plant tissues. Here we developed an imaging‐based method to observe and quantify A. tumefaciens attached to leaf tissue in situ. Fluorescent labeling of bacteria with nucleic acid, protein, and vital dyes was investigated as a rapid alternative to generating recombinant strains expressing fluorescent proteins. Syto 16 green fluorescent nucleic acid stain was found to yield the greatest signal intensity in stained bacteria without affecting viability or infectivity. Stained bacteria retained the stain and were detectable over 72 h. To demonstrate in situ detection of attached bacteria, confocal fluorescent microscopy was used to image A. tumefaciens in sections of lettuce leaf tissue following vacuum‐infiltration with labeled bacteria. Bacterial signals were associated with plant cell surfaces, suggesting detection of bacteria attached to plant cells. Bacterial attachment to specific leaf tissues was in agreement with known leaf tissue competencies for transformation with Agrobacterium. Levels of bacteria attached to leaf cells were quantified over time post‐infiltration. Signals from stained bacteria were stable over the first 24 h following infiltration but decreased in intensity as bacteria multiplied in planta. Nucleic acid staining of A. tumefaciens followed by confocal microscopy of infected leaf tissue offers a rapid, in situ method for evaluating attachment of A. tumefaciens' to plant expression hosts and a tool to facilitate management of transient expression processes via agroinfiltration. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

The Michaelis–Menten kinetics of soil extracellular enzymes in response to temperature: a cross‐latitudinal study

Decomposition of soil organic matter (SOM) is mediated by microbial extracellular hydrolytic enzymes (EHEs). Thus, given the large amount of carbon (C) stored as SOM, it is imperative to understand how microbial EHEs will respond to global change (and warming in particular) to better predict the links between SOM and the global C cycle. Here, we measured the Michaelis–Menten kinetics [maximal rate of velocity (V_max) and half‐saturation constant (K_m)] of five hydrolytic enzymes involved in SOM degradation (cellobiohydrolase, β‐glucosidase, β‐xylosidase, α‐glucosidase, and N‐acetyl‐β‐d ‐glucosaminidase) in five sites spanning a boreal forest to a tropical rainforest. We tested the specific hypothesis that enzymes from higher latitudes would show greater temperature sensitivities than those from lower latitudes. We then used our data to parameterize a mathematical model to test the relative roles of V_max and K_m temperature sensitivities in SOM decomposition. We found that both V_max and K_m were temperature sensitive, with Q₁₀ values ranging from 1.53 to 2.27 for V_max and 0.90 to 1.57 for K_m. The Q₁₀ values for the K_m of the cellulose‐degrading enzyme β‐glucosidase showed a significant (P = 0.004) negative relationship with mean annual temperature, indicating that enzymes from cooler climates can indeed be more sensitive to temperature. Our model showed that K_m temperature sensitivity can offset SOM losses due to V_max temperature sensitivity, but the offset depends on the size of the SOM pool and the magnitude of V_max. Overall, our results suggest that there is a local adaptation of microbial EHE kinetics to temperature and that this should be taken into account when making predictions about the responses of C cycling to global change.     

典型岩溶区域主要土壤类型分布特征与表层土壤保有量估算

在我国西南岩溶区域,土壤受地质和地形条件的影响程度较深,表现出强烈的非均一性;且在不同地质地形条件下,缺乏具体的量化参照系数,致使对土壤元素库容等方面的估算存在较大偏差。据此,本研究基于对贵阳市乌当区实地考察结果,归纳确立土壤在不同地质与地形下的分布特征,修正了现有的土壤图。利用地形图提取区域的坡度信息,再与土壤图和地质图进行叠加,乘以相应类型条件下土壤的经验系数,估算区域主要土壤类型表层(≤1m)土壤的保有量。结果表明,乌当区境内坡度>35°的碳酸盐岩地区无黄壤分布;石灰土的覆盖率和土壤剖面深度随坡度的增加,呈下降趋势,但连续性石灰岩分布区的石灰土变异程度较大;该区表层土壤(≤1m)保有量约为65656万t,主要集中分布在0°～15°碳酸盐岩分布区,且黄壤占50%以上。     

Multi‐Length‐Scale Morphologies in PCPDTBT/PCBM Bulk‐Heterojunction Solar Cells

Additives are known to improve the performance of organic photovoltaic devices based on mixtures of a low bandgap polymer, poly[2,6‐(4,4‐bis(2‐ethylhexyl)‐4H‐cyclopenta[2,1‐b;3,4‐b′]‐dithiophene)‐alt‐4,7‐(2,1,3‐benzothiadiazole)] (PCPDTBT) and [6,6]‐phenyl C61‐butyric acid methyl ester (PCBM). The evolution of the morphology during the evaporation of the mixed solvent, which comprises additive and chlorobenzene (CB), is investigated by in‐situ grazing incidence X‐ray scattering, providing insight into the key role the additive plays in developing a multi‐length‐scale morphology. Provided the additive has a higher vapor pressure and a selective solubility for PCBM, as the host solvent (CB) evaporates, the mixture of the primary solvent and additive becomes less favorable for the PCPDTBT, while completely solubilizing the PCBM. During this process, the PCPDTBT first crystallizes into fibrils and then the PCBM, along with the remaining PCPDTBT, is deposited, forming a phase‐separated morphology comprising domains of pure, crystalline PCPDTBT fibrils and another domain that is a PCBM‐rich mixture with amorphous PCPDTBT. X‐ray/neutron scattering and diffraction methods, in combination with UV–vis absorption spectroscopy and transmission electron microscopy, are used to determine the crystallinity and phase separation of the resultant PCPDTBT/PCBM thin films processed with or without additives. Additional thermal annealing is carried out and found to change the packing of the PCPDTBT. The two factors, degree of crystallinity and degree of phase separation, control the multi‐length‐scale morphology of the thin films and significantly influence device performance.     

Materials Challenges for High Performance Magnetocaloric Refrigeration Devices

Magnetocaloric materials with a Curie temperature near room temperature have attracted significant interest for some time due to their possible application for high‐efficiency refrigeration devices. This review focuses on a number of key issues of relevance for the characterization, performance and implementation of such materials in actual devices. The phenomenology and fundamental thermodynamics of magnetocaloric materials is discussed, as well as the hysteresis behavior often found in first‐order materials. A number of theoretical and experimental approaches and their implications are reviewed. The question of how to evaluate the suitability of a given material for use in a magnetocaloric device is covered in some detail, including a critical assessment of a number of common performance metrics. Of particular interest is which non‐magnetocaloric properties need to be considered in this connection. An overview of several important materials classes is given before considering the performance of materials in actual devices. Finally, an outlook on further developments is presented.