Characterization of bacterial communities in anode microbial fuel cells fed with glucose,propyl alcohol and methanol

Bacterial communities in anode microbial fuel cells (MFC) obtained from anaerobic digester sludge in a municipal wastewater treatment plant (Nanjing, China) were investigated. Glucose, propyl alcohol and methanol were used as sole carbon source in two-chamber MFC. The results showed that a reproducible cycle of power production can be formed in MFC fed with 3 substrates and glucose-fed MFC had the highest peak power density of 1499 ± 33 mW/m³, followed by methanol- (1264 ± 47 mW/m³) and propyl alcohol-fed MFC (1192 ± 36 mW/m³). Firmicutes, Bacteroidetes, Verrucomicrobia, Proteobacteria, Synergistetes and Armatimonadetes were dominant phyla in 3 MFC. Firmicutes was the most dominant phylum in glucose-fed MFC samples and Bacteroidetes prevailed in methanol- and propyl alcohol-fed MFC. These data indicate that propyl alcohol and methanol along with glucose can be used as substrates of MFC.     

Intrapopulation heterogeneity of the fluorescence parameters of the marine plankton alga <Emphasis Type="Italic">Thalassiosira weissflogii</Emphasis> at various nitrogen levels

Fluorescence of the marine alga Thalassiosira weissflogii (Grunow) Fryxell et Hasle with open (F _o ) and closed (F _m ) reaction centers of photosystem 2 (PS 2) and its relative variable fluorescence (F _v/F _m ) were measured at various levels of inorganic nitrogen. A significant heterogeneity of the population in terms of these parameters was revealed. Some cells within the population were more sensitive to nitrogen deficiency, and their photosynthetic apparatus was disrupted to a greater extent. The cells within a population also differed in terms of their ability to recover after incubation at low nitrogen levels. Enhancement of nitrogen deficiency resulted in an increase in the variability of the F _o and F _v/F _m values of the cells. Fluorescence variability decreased at a less pronounced deficiency. Fluorescence variability should be taken into consideration in the studies concerning responses of algae to changes in nutrient contents.     

A framework for space-efficient read clustering in metagenomic samples

Background

A metagenomic sample is a set of DNA fragments, randomly extracted from multiple cells in an environment, belonging to distinct, often unknown species. Unsupervised metagenomic clustering aims at partitioning a metagenomic sample into sets that approximate taxonomic units, without using reference genomes. Since samples are large and steadily growing, space-efficient clustering algorithms are strongly needed.

Results

We design and implement a space-efficient algorithmic framework that solves a number of core primitives in unsupervised metagenomic clustering using just the bidirectional Burrows-Wheeler index and a union-find data structure on the set of reads. When run on a sample of total length n, with m reads of maximum length ? each, on an alphabet of total size σ, our algorithms take O(n(t+logσ)) time and just 2n+o(n)+O(max{? σlogn,K logm}) bits of space in addition to the index and to the union-find data structure, where K is a measure of the redundancy of the sample and t is the query time of the union-find data structure.

Conclusions

Our experimental results show that our algorithms are practical, they can exploit multiple cores by a parallel traversal of the suffix-link tree, and they are competitive both in space and in time with the state of the art.

     

Length of meristematic and fully elongated root cells related to haploid DNA content

The lengths of meristematic (l_m) and fully-elongated cells (l_e) were measured in the roots of 118 monocot and dicot species of herbaceous plants from 20 angiosperm families. The results were analyzed using the data on haploid DNA content (C_val) for the same species from the website (http://data.kew.org/cvalues). The distribution range of l_m, l_e, and C_val was wider in monocot plants compared to dicots. Values of l_m and l_e in monocot and l_m in dicot species correlated positively with C_val. Dependence of l_m and l_e on C_val was similar in diploid and polyploid species, both monocots and dicots. The average length of root cells differed less than the root length.     

Chaotic Dynamics of Neuromuscular System Parameters and the Problems of the Evolution of Complexity

The evolution rate v(t) varies among diverse biosystems, but a general theory can be formulated when the dynamics of the biosystem stater x = x(t) = (x₁, x₂, x _m ) ^T is considered in the m-dimensional space of states. A mathematical approach is proposed for evaluating such processes and describes the processes in terms of particular chaos of the statistical distribution functions f(x). In the case of complex multicomponent systems with a high dimension number m (m ?1) of the phase space of states, we propose using pairwise comparison matrices of samples x(t) when homeostasis is constant and calculating the parameters of quasiattractors. The Glensdorff–Prigogine thermodynamic approach to estimating evolution is inefficient in assessing the third-type systems, while it is applicable and the Prigogine theorem works at the level of molecular systems. Alterations in the state of the human neuromuscular system were found to lead to chaotic changes in the statistical functions f(x) in tremor recording samples, while quasiattractor parameters demonstrate a certain regularity.     

Evolution of protein transport to the chloroplast envelope membranes

Comparing with other angiosperms, most members within the family Orchidaceae have lower photosynthetic capacities. However, the underlying mechanisms remain unclear. Cypripedium and Paphiopedilum are closely related phylogenetically in Orchidaceae, but their photosynthetic performances are different. We explored the roles of internal anatomy and diffusional conductance in determining photosynthesis in three Cypripedium and three Paphiopedilum species, and quantitatively analyzed their diffusional and biochemical limitations to photosynthesis. Paphiopedilum species showed lower light-saturated photosynthetic rate (A _N), stomatal conductance (g _s), and mesophyll conductance (g _m) than Cypripedium species. A _N was positively correlated with g _s and g _m. And yet, in both species A _N was more strongly limited by g _m than by biochemical factors or g _s. The greater g _s of Cypripedium was mainly affected by larger stomatal apparatus area and smaller pore depth, while the less g _m of Paphiopedilum was determined by the reduced surface area of mesophyll cells and chloroplasts exposed to intercellular airspace per unit of leaf area, and much thicker cell wall thickness. These results suggest that leaf anatomical structure is the key factor affecting g _m, which is largely responsible for the difference in photosynthetic capacity between those two genera. Our findings provide new insight into the photosynthetic physiology and functional diversification of orchids.     

Interspecific variation in extracellular polysaccharide content and colony formation of <Emphasis Type="Italic">Microcystis</Emphasis> spp. cultured under different light intensities and temperatures

Single cells of five different Microcystis species (M. ichthyoblabe, M. viridis, M. flos-aquae, M. wesenbergii, and M. aeruginosa) were batch-cultured at different temperatures and light intensities: (a) 25 °C and 50 μmol photons m^?2 s^?1 (control culture); (b) 25 °C and 10 μmol photons m^?2 s^?1; and (c) 15 °C and 50 μmol photons m^?2 s^?1. The extracellular polysaccharide content was significantly higher in treatments b and c than in the control treatment. All Microcystis species existed as single cells under the control treatment but formed colonies in treatments b and c. All of the colonies were irregular with indistinct margins. M. ichthyoblabe, M. viridis, M. flos-aquae, and M. wesenbergii formed colonies with similar morphologies and their cells were loosely aggregated. In contrast, M. aeruginosa formed denser colonies with no distinct holes. The colony morphologies differed from the classic morphology of M. ichthyoblabe field-grown colonies but resembled that of small colonies found in Lake Taihu (Yangtze Delta Plain, China) during early spring. This indicates that field- and laboratory-grown colonies are governed by similar formation processes. We suggest that in laboratory and field environments, M. ichthyoblabe (or M. flos-aquae) colonies are representative of small colonies formed from single Microcystis cells, whereas the morphology of older colonies evolves to resemble M. wesenbergii and M. aeruginosa colonies.     

The eurythermal adaptivity and temperature tolerance of a newly isolated psychrotolerant Arctic <Emphasis Type="Italic">Chlorella</Emphasis> sp.

A new strain of Chlorella sp. (Chlorella-Arc), isolated from Arctic glacier melt water, was found to have high specific growth rates (μ) between 3 and 27 °C, with a maximum specific growth rate of 0.85 day^?1 at 15 °C, indicating that this strain was a eurythermal strain with a broad temperature tolerance range. To understand its acclimation strategies to low and high temperatures, the physiological and biochemical responses of the Chlorella-Arc to temperature were studied and compared with those of a temperate Chlorella pyrenoidosa strain (Chlorella-Temp). As indicated by declining F _v/F _m, photoinhibition occurred in Chlorella-Arc at low temperature. However, Chlorella-Arc reduced the size of the light-harvesting complex (LHC) to alleviate photoinhibition, as indicated by an increasing Chl a/b ratio with decreasing temperatures. Interestingly, Chlorella-Arc tended to secrete soluble sugar into the culture medium with increasing temperature, while its intracellular soluble sugar content did not vary with temperature changes, indicating that the algal cells might suffer from osmotic stress at high temperature, which could be adjusted by excretion of soluble sugar. Chlorella-Arc accumulated protein and lipids under lower temperatures (<15 °C), and its metabolism switched to synthesis of soluble sugar as temperatures rose. This reflects a flexible ability of Chlorella-Arc to regulate carbon and energy distribution when exposed to wide temperature shifts. More saturated fatty acids (SFA) in Chlorella-Arc than Chlorella-Temp also might serve as the energy source for growth in the cold and contribute to its cold tolerance.     

Antibiotic-Resistant Genes and Pathogens Shed by Wild Deer Correlate with Land Application of Residuals

The purpose of this study was to investigate genetic biomarkers of zoonotic enteric pathogens and antibiotic-resistant genes (ARGs) in the feces of white-tailed deer (Odocoileus virginianus) as related to proximity of deer to land that receives livestock manure or human waste biosolid fertilizers. Deer feces were collected in the St. Lawrence River Valley and Adirondack State Park of New York. Campylobacter spp. 16S rDNA was detected in 12 of 232 fecal samples (8 of 33 sites). Salmonellae were cultivated from 2 of 182 fecal samples (2 of 29 sites). Genetic virulence markers for Shiga-like toxin I (stx₁) and enterohemolysin (hylA) were each detected in one isolate of Escherichia coli; E. coli O157 was not detected in any of 295 fecal samples. ARGs detected in deer feces included ermB (erythromycin-resistant gene; 9 of 295 fecal samples, 5 of 38 sites), vanA (vancomycin-resistant gene; 93 of 284 samples, 33 of 38 sites), tetQ (tetracycline-resistant gene; 93 of 295 samples, 25 of 38 sites), and sul(I) (sulfonamide-resistant gene; 113 of 292 samples, 28 of 38 sites). Genetic markers of pathogens and ARGs in deer feces were spatially associated with collection near concentrated animal feeding operations (CAFOs; Campylobacter spp., tetQ, and ermB) and land-applied biosolids (tetQ). These results indicate that contact with human waste biosolids or animal manure may be an important method of pathogen and ARG transmission and that deer in proximity to land-applied manure and human waste biosolids pose increased risk to nearby produce and water quality.     

A novel approach for metabolic pathway optimization: Oligo-linker mediated assembly (OLMA) method

Background

Imbalances in gene expression of a metabolic pathway can result in less-yield of the desired products. Several targets were intensively investigated to balance the gene expression, such as promoter, ribosome binding site (RBS), the order of genes, as well as the species of the enzymes. However, the capability of simultaneous manipulation of multiple targets still needs to be explored.

Results

We reported a new DNA assembling method to vary all the above types of regulatory targets simultaneously, named oligo-linker mediated assembly (OLMA) method, which can incorporate up to 8 targets in a single assembly step. Two experimental cases were used to demonstrate the capability of the method: (1) assembly of multiple pieces of lacZ expression cassette; (2) optimization of four enzymes in lycopene biosynthetic pathway. Our results indicated that the OLMA method not only exploited larger combinatorial space, but also reduced the inefficient mutants.

Conclusions

The unique feature of oligo-linker mediated assembly (OLMA) method is inclusion of a set of chemically synthetic double-stranded DNA oligo library, which can be designed as promoters and RBSs, or designed with different overhang to bridge the genes in different orders. The inclusion of the oligos resulted in a PCR-free and zipcode-free DNA assembly reaction for OLMA.

     

Plans for Liquid Metal Divertor in Tokamak Compass

The COMPASS tokamak (R = 0.56 m, a = 0.2 m, B_T = 1.3 T, I_p ~ 300 kA, pulse duration 0.4 s) operates in ITER-like plasma shape in H-mode with Type-I ELMs. In 2019, we plan to install into the divertor a test target based on capillary porous system filled with liquid lithium/tin. This single target will be inclined toroidally in order to be exposed to ITER-relevant surface heat flux (20 MW/m²). Based on precisely measured actual heat fluxes, our simulations predict (for 45° inclination, without accounting for the lithium vapor shielding) the surface temperature rises up to 700°C within 120 ms of the standard ELMy H-mode heat flux with ELM filaments reaching hundreds MW/m². Significant lithium vaporization is expected. The target surface will be observed by spectroscopy, fast visible and infrared cameras. The scientific program will be focused on operational issues (redeposition of the evaporated metal, ejection of droplets, if any) as well as on the effect on the plasma physics (improvement of plasma confinement, L–H power threshold, Z_eff, etc.). After 2024, a closed liquid divertor may be installed into the planned COMPASS Upgrade tokamak (R = 0.84 m, a = 0.3 m, B_T = 5 T, I_p = 2 MA, P_in = 8 MW, pulse duration ~2 s) with ITER-relevant heat fluxes loading the entire toroidal divertor.     

Mesophyll conductance to CO<Subscript>2</Subscript> in leaves of Siebold’s beech (<Emphasis Type="Italic">Fagus crenata</Emphasis>) seedlings under elevated ozone

Ozone is an air pollutant that negatively affects photosynthesis in woody plants. Previous studies suggested that ozone-induced reduction in photosynthetic rates is mainly attributable to a decrease of maximum carboxylation rate (V_cmax) and/or maximum electron transport rate (J_max) estimated from response of net photosynthetic rate (A) to intercellular CO₂ concentration (C_i) (A/C_i curve) assuming that mesophyll conductance for CO₂ diffusion (g_m) is infinite. Although it is known that C_i-based V_cmax and J_max are potentially influenced by g_m, its contribution to ozone responses in C_i-based V_cmax and J_max is still unclear. In the present study, therefore, we analysed photosynthetic processes including g_m in leaves of Siebold’s beech (Fagus crenata) seedlings grown under three levels of ozone (charcoal-filtered air or ozone at 1.0- or 1.5-times ambient concentration) for two growing seasons in 2016–2017. Leaf gas exchange and chlorophyll fluorescence were simultaneously measured in July and September of the second growing season. We determined the A, stomatal conductance to water vapor and g_m, and analysed A/C_i curve and A/C_c curve (C_c: chloroplast CO₂ concentration). We also determined the Rubisco and chlorophyll contents in leaves. In September, ozone significantly decreased C_i-based V_cmax. At the same time, ozone decreased g_m, whereas there was no significant effect of ozone on C_c-based V_cmax or the contents of Rubisco and chlorophyll in leaves. These results suggest that ozone-induced reduction in C_i-based V_cmax is a result of the decrease in g_m rather than in carboxylation capacity. The decrease in g_m by elevated ozone was offset by an increase in C_i, and C_c did not differ depending on ozone treatment. Since C_c-based V_cmax was also similar, A was not changed by elevated ozone. We conclude that g_m is an important factor for reduction in C_i-based V_cmax of Siebold’s beech under elevated ozone.     

Change of Mendelian ratios and meiotic recombination parameters in F<Subscript>1</Subscript> hybrid tomatoes under the influence of γ-irradiation

The effect of γ-irradiation treatment of seeds of intra- and interspecific F₁ hybrid tomatoes on distortion of Mendelian monohybrid segregation, crossover variability, and recombination frequency of unlinked marker genes of chromosomes 2 and 6 was studied. It was found that more significant distortion effect on the segregation of marker loci of studied chromosomes was detected for seed treatment with 130 Gy. The significant direct relationship between Mendelian segregation for m-2 gene and a rf _m-2c vaue for 60 Gy and for aw and m-2 genes and rf _{aw c} , _{aw m-2} values for 60 and 130 Gy treatment in combination Mo500 × var. cerasiforme was revealed. The latter corresponds to the effect of “quasirepulsion.”     

Properties of Surface Plasmon Polaritons Excited by Radially Polarized Sinh Gaussian Beams

Properties of surface plasmon polaritons (SPPs) excited by radially polarized sinh Gaussian beams with high-numerical-aperture system is investigated theoretically based on vector diffraction theory. It is observed that by properly tuning the beam waist size (w ₀ ) and beam order (m) of the incident sinh Gaussian beam, one can achieve higher confinement in axial and lateral size of the generated plasmonic focal spot. We observed that sinh Gaussian beam of larger w ₀ and m results in generation of highly confined plasmonic focal spot.     

Electronic fine structure calculation of metal complexes with three-open-shell <Emphasis Type="Italic">s</Emphasis>, <Emphasis Type="Italic">d,and p</Emphasis> configurations

The ligand field density functional theory (LFDFT) algorithm is extended to treat the electronic structure and properties of systems with three-open-shell electron configurations, exemplified in this work by the calculation of the core and semi-core 1s, 2s, and 3s one-electron excitations in compounds containing transition metal ions. The work presents a model to non-empirically resolve the multiplet energy levels arising from the three-open-shell systems of non-equivalent ns, 3d, and 4p electrons and to calculate the oscillator strengths corresponding to the electric-dipole 3d ^m  → ns ¹3d ^m 4p ¹ transitions, with n = 1, 2, 3 and m = 0, 1, 2, …, 10 involved in the s electron excitation process. Using the concept of ligand field, the Slater-Condon integrals, the spin-orbit coupling constants, and the parameters of the ligand field potential are determined from density functional theory (DFT). Therefore, a theoretical procedure using LFDFT is established illustrating the spectroscopic details at the atomic scale that can be valuable in the analysis and characterization of the electronic spectra obtained from X-ray absorption fine structure or electron energy loss spectroscopies.     

Combinatorics of Contacts in Protein Contact Maps

Contacts play a fundamental role in the study of protein structure and folding problems. The contact map of a protein can be represented by arranging its amino acids on a horizontal line and drawing an arc between two residues if they form a contact. In this paper, we are mainly concerned with the combinatorial enumeration of the arcs in m-regular linear stack, an elementary structure of the protein contact map, which was introduced by Chen et al. (J Comput Biol 21(12):915–935, 2014). We modify the generating function for m-regular linear stacks by introducing a new variable y regarding to the number of arcs and obtain an equation satisfied by the generating function for m-regular linear stacks with n vertices and k arcs. Consequently, we also derive an equation satisfied by the generating function of the overall number of arcs in m-regular linear stacks with n vertices.     

Congruence and the Biomonitoring of Aquatic Ecosystems: Are Odonate Larvae or Adults the Most Effective for the Evaluation of Impacts

Odonata have been widely used as indicators for the biomonitoring of terrestrial and aquatic habitats due to their sensitivity to environmental impacts. We aimed to determine whether the larval or adult phases of these insects were the best predictors of variation in habitat parameters and the loss of environmental integrity. Specimens were collected during three seasons (dry, rainy, and ebb) from 12 points in the Suiá-missu River basin, at the headwaters of the Xingu River in Mato Grosso, Brazil. The Protest analysis indicated a high degree of congruence between the assemblages of larvae and adults in streams with varying degrees of habitat integrity (R = 0.832, p < 0.001, m ² = 0.307). When the congruence with environmental factors was analyzed, a significant association was found only for the larval phase (R = 0.318, p = 0.03, m ² = 0.888). When the suborders were analyzed separately, congruence was confirmed for anisopteran adults (R = 0.338, p = 0.031, m ² = 0.885) and larvae (R = 0.417, p = 0.003, m ² = 0.826) and for the zygopteran adults (R = 0.345, p = 0.027, m ² = 0.881) and larvae (R = 0.405, p = 0.011, m ² = 0.836). These results indicate that both larvae and adults respond systematically to environmental impacts. We suggest that either life phase can be used for biomonitoring, given their effectiveness for the interpretation of disturbance in terrestrial and aquatic habitats. These findings further reinforce the effectiveness of this insect order for the detection of modifications to the environment, showing that they are good indicators of environmental conditions.     

Bioactive effect of the preparation biostyl on the reproductive function of different genotypes of American mink

The different role of coat color mutations in the American mink on the per os effect of the biologically active preparation Biostyl was shown. The number of kits per female was the same in all control genotypes, including Standard (+/+ +/+), sapphire (a/a p/p), and lavender (a/a m/m): 4.4 ± 0.4, 4.4 ± 0.5, and 4.3 ± 0.5, respectively. Experimental groups of these genotypes have shown a great contrast among each other: stimulation of the reproductive function was 5.2 ± 0.3 in Standard minks, while suppression of the reproductive function was 3.8 ± 0.6, and 2.3 ± 0.5 in the double recessive mutants sapphire and lavender, respectively. The differentiation in body mass between experimental and control newborn Standard kits was not revealed. A significant decrease in the body mass of newborn experimental sapphire kits as compared to control group in a sex-specific manner was registered.     

Conspecific tolerance and heterospecific competition as mechanisms for overcoming resistance to invasion by an intertidal crab

The success of the invasive Asian shore crab, Hemigrapsus sanguineus, stems partly from its ability to exclude established crab species from preferred rocky and cobble intertidal habitat. Here, we assessed preference and competition for habitat types (cobble vs. sand) for H. sanguineus and two competitor species; the previous invasive green crab, Carcinus maenas, and the native rock crab, Cancer irroratus, in New England. In simple laboratory experiments, we paired similarly sized heterospecifics and conspecifics from each species, and also grouped combinations of C. maenas and H. sanguineus in a series of four-individual sets in order to dissect the outcome of intra- and inter-specific competition at different densities. Individually, all three species preferred cobble substrate. With paired conspecifics, H. sanguineus individuals would cohabitate in cobble, whereas C. maenas and C. irroratus individuals each excluded conspecifics from cobble. In heterospecific pairs, H. sanguineus excluded both C. maenas and C. irroratus from cobble. C. maenas and C. irroratus, were equally likely to exclude the other species, but rarely excluded H. sanguineus. In larger assemblages, H. sanguineus preferentially grouped under cobble, whereas C. maenas were more evenly distributed among habitat types. These observations demonstrate that conspecific tolerance and heterospecific competition can be effective, complementary mechanisms for overcoming invasion resistance. Such mechanisms help explain the well-studied success of H. sanguineus following its introduction into New England coastal habitats, and the resulting exclusion of preexisting crab species.     

Physics of Root Growth

THE elongation of a plant cell involves the yielding of the cell wall under the action of tensile stresses in the wall¹. The rate of elongation, R, can be expressed simply as R=mW, where m is the extensibility of thé cell wall material and W is the wall pressure. Changes in either m or W have been used to explain the effect of biochemical factors on the growth rate of plant cells^2,3. Cell growth is also affected by the physical environment and this becomes particularly important in the case of plant roots where soil water potential and the mechanical resistance of the soil to deformation can become rate controlling. Working with 3-5 day old radicles of Pisum sativum, growing in soil cores, we have obtained values of wall pressure in terms of these two properties and we find that the rate of root elongation can be described by a simple extensibility equation.