How do soil microbes exert impact on soil respiration and its temperature sensitivity?

Understanding how soil microorganisms influence the direction and magnitude of soil carbon feedback to global warming is vital to predict future climate change. Although microbial activities are major contributors to soil respiration (R_S) and its temperature sensitivity (Q₁₀), the mechanisms underpinning microbial influence on R_S and Q₁₀ remain unclear. Coupling variation partitioning analysis (VPA), correlation analysis and multiple stepwise linear regression analysis, we illustrate that bacteria mainly affect R_S and its temperature sensitivity (Q₁₀) by shifting bacterial community composition (denoted by principal coordinates analysis). We also found that soil water content (SWC) and available nutrient (AN) were the factor key to changing bacterial community composition (P < 0.05). Co-occurrence network demonstrated that Mod 0 ecological cluster composed of copiotrophic taxa groups was significantly associated with R_S and Q₁₀ (P < 0.01, R > 0.5), including Proteobacteria, Actinobacteria, and Bacteroidetes. Illuminating the mechanisms underpinning the influence of soil microbes on R_S and Q₁₀ values is fundamental to understanding mechanistic soil-climate carbon cycles.     

Contribution of changes in translational, rotational, and vibrational degrees of freedom to the energy of complex formation of aromatic ligands with DNA

A method for calculation and analysis of the contribution of changes in translational, rotational, and vibrational degrees of freedom to the energy of complex formation of aromatic compounds with DNA duplex has been developed. The results of calculations of the thermodynamic parameters (ΔG, ΔH, ΔS) indicate that changes in the translational and rotational degrees of freedom destabilize, and changes in the vibrational degree of freedom stabilize the complexes, the energy contribution from the movements under consideration being predominantly of entropic character. It is shown that the energy components of changes in translational, rotational, and vibrational degrees of freedom are in the main comparable with the experimentally determined thermodynamic parameters, which requires consideration of these components in the energy analysis of complex formation of aromatic molecules with DNA. It has been found that the total contribution of changes in translational, rotational, and vibrational degrees of freedom to the Gibbs energy of complexing of aromatic molecules with DNA can be assumed to be on the average the same for different ligands and equal to 8.2 kcal/mol.     

The “tropical lineage” of the brown dog tick Rhipicephalus sanguineus sensu lato identified as Rhipicephalus linnaei ()

The brown dog tick (Rhipicephalus sanguineus) parasitises dogs. Over the past decade, two distinct lineages have been recognised – R. sanguineus sensu lato “temperate lineage” and R. sanguineus sensu lato “tropical lineage”. The nominal taxon R. sanguineus (Latreille, 1806) was recently associated with the “temperate lineage”. We here identify the “tropical lineage” as Rhipicephalus linnaei (Audouin, 1826) using material from Australia, where no other Rhipicephalus species parasitises dogs. Whole genome sequencing of R. linnaei from Australia, Fiji and Laos, and assembly of their complete mitochondrial DNA (~15 kb) confirms the genetic identity and distinctness from all other known species within the brown dog tick species complex. Designation of the species R. linnaei is unequivocally supported by material available through the Australian National Insect Collection, Australia. Accordingly, we are formally justified in using R. linnaei for the “tropical lineage”.     

Influence of environmental,geographic, and seasonal variations in the chemical composition of Miconia species from Cerrado

Miconia albicans (Sw.) Triana and Miconia chamissois Naudin, commonly known as “pixirica” and “pixirica-açu”, two Melastomataceae species, are commonly found in Cerrado areas. M. albicans species grows in dry and humid habitats, so it has adapted to both conditions and M. chamissois species grows in humid environment only. In this work, we have investigated the content of triterpenes, flavonols and flavanones in three different Cerrado fragments of São Paulo State, involving distinct environments (dry and humid) and seasons (dry and rainy) to comprehend the complex interactions among plants and the seasonal, environmental conditions and geographic locations. The leaves plants materials were harvest in August 2016 (dry season) and November/December 2016 (rainy season) in Pirassununga, Pedregulho and Luíz Antônio in dry and humid environments. The contents of the standards rutin (R), quercetin (Q), miconioside B (B), matteucinol 7-O-β-apiofuranosyl(1 → 6)-β-glucopyranoside (matt), ursolic acid (AU), and oleanolic acid (AO) were determined by HPLC-DAD. The data were analyzed using nonparametric tests, Pearson's linear correlation, principal component analysis and hierarchical cluster analysis. The results demonstrated similar flavanone and triterpene production during the dry period, and similar flavonol and flavanone production in the rainy season, thus confirming a seasonal variation in the content of the compounds in the evaluated specimens. Our results also demonstrated intra- and inter-population variations in compounds patterns, M. albicans contained major amounts of the flavonols R and Q; their concentrations were higher in the rainy season. B and matt were the major compounds in M. chamissois; the matt concentration decreased in the rainy season. The triterpenes AU and AO occurred in both M. albicans and M. chamissois, but their production dropped during the rainy periods. Thus corroborating the adaptation of M. albicans and M. chamissonis to the high stress and low levels of resources presented in Cerrado.     

Co-operative response of chemically excitable membrane III. Three-state model

The general three-state model is formulated first, which is the direct extension of the unified two-state model previously formulated (Kijima & Kijima, 1978). In this model, each protomer in a symmetrically interacting system (oligomers or lattices) can take three states, S, R and Q, where S and R states are the same as in the two-state model and Q state is another state either corresponding to a different open-state of ionophore from R open-state or corresponding to another closed state of ionophore. The model has no restriction on the value of Hill coefficient at the midpoint of the dose-response curves in contrast to two-state models. It is applied on GABA sensitive inhibitory synapse of crayfish muscle to account for anomalous behaviour of the membrane in I^? solution.The simplified versions of the above general three-state model are also formulated (simplified three-state model), in which it is assumed that R and Q state are equivalent in regard to the nearest neighbor interaction. By this assumption, R and Q state are collectively treated as state A and mathematical formula obtained on Ising model are applicable on this model. This model is applied on the insect sugar receptor which was shown to be incompatible with the two-state models (Kijima & Kijima, 1980). Further simplification of the above simplified model results in two convenient models: three-state KNF model and three-state MWC model, which have minimum parameters but sufficient to account for most experiments. They give plausible physico-chemical base on the “classical model” in which the existence of both inactive and active ligand-receptor complex is assumed.     

Isolation and structure elucidation of flavonoids from Amburana cearensis resin and identification of human DNA topoisomerase II-α inhibitors

Amburana cearensis, a plant in the Fabaceae family, is extensively used in folk medicine to treat grippes, coughs, bronchitis, sinusitis and external ulcers. Ultra-performance liquid chromatography coupled with diode array and quadrupole time-of-flight mass spectrometry (UPLC-DAD-QTOF-MS/MS) and combined use of data-independent acquisition (MSE) were used for profiling and structural characterization of the phenolic compounds observed in the resin of A. cearensis (16 isoflavones, 11 flavanonols, 3 chalcones, 1 isoflavonolignan and 1 isoflavoquinone). The isoflavonolignan (1”R,2”R-trans-1”-(7”-hydroxy-6”,8”-dimethoxyphenyl)-1′-(3′-hydroxy-4′-methoxyphenyl)-2”-hydroxymethyl-5-methoxy-1”,2”-dihydro-7H-1,4-dioxino[1”,2”-h]chromen-4-one) and an isoflavone (3′-hydroxy-7,8,4′-trimethoxyisoflavone) were identified as novel compounds. In this study, we isolated 15 principal phenolics and established their structures by different spectroscopic methods, including 1D and 2D NMR experiments, as well HR-ESI–MS analysis. The isolated reference compounds were used to explore fragmentation pathways. Compound identification was based on the exact mass, general fragmentation behaviors, retention times and UV absorption. The activity of the principal compounds against human DNA topoisomerase II-α was evaluated.     

Possible roles of two quinone molecules in direct and indirect proton pumps of bovine heart NADH-quinone oxidoreductase (complex I)

In many energy transducing systems which couple electron and proton transport, for example, bacterial photosynthetic reaction center, cytochrome bc₁-complex (complex III) and E. coli quinol oxidase (cytochrome bo₃ complex), two protein-associated quinone molecules are known to work together. T. Ohnishi and her collaborators reported that two distinct semiquinone species also play important roles in NADH-ubiquinone oxidoreductase (complex I). They were called SQ_Nf (fast relaxing semiquinone) and SQ_Ns (slow relaxing semiquinone). It was proposed that Q_Nf serves as a “direct” proton carrier in the semiquinone-gated proton pump (Ohnishi and Salerno, FEBS Letters 579 (2005) 4555), while Q_Ns works as a converter between one-electron and two-electron transport processes. This communication presents a revised hypothesis in which Q_Nf plays a role in a “direct” redox-driven proton pump, while Q_Ns triggers an “indirect” conformation-driven proton pump. Q_Nf and Q_Ns together serve as (1e^?/2e^?) converter, for the transfer of reducing equivalent to the Q-pool.     

Mediterranean island biogeography: Analysis of fern species distribution in the system of islets around Sicily

Abstract

The aim of this article was to test the way in which geographical factors influence island floras in the Mediterranean basin, using ferns as target organisms, and the islands surrounding Sicily as location. A matrix with presence/absence data concerning fern taxa in the 16 islands studied was compiled. Cluster analysis, principal co-ordinates analysis (PCoA), principal components analysis (PCA) and a Bayesian analysis were performed. For each island, the total number of fern taxa was regressed against three factors: island area, island elevation and isolation. All the analyses pointed to affinities between islands according to their different geological composition, independently from their geographic position. A clear positive island species/area relationship (ISAR) was shown only for the volcanic islands. The island species/(area×elevation) relationship (ISAER), on the contrary, was unsatisfactory. The main features of interest are the following: (1) the clear division of the islands into two groups, volcanic vs. sedimentary; (2) the floristic richness of the volcanic compared to sedimentary islands and (3) the uniqueness of the pteridophyte flora of Pantelleria. This seems to demonstrate that the lower number of taxa in the islands farthest away from the “mainland” (Sicily, Tunisia) is not due to isolation, but due to another factor, probably habitat availability.     

The theoretical possibility of reverse translation of proteins into genes

It is shown on a theoretical basis that the existence of a “power law” relationship between body mass M and total metabolic heat generation rate Q of the form Q = kM^α does not uniquely determine the dependence of metabolic rate on body temperature. However, it is shown that a particular assumption for this temperature dependence, successful in other problems, does predict a “power law” similar to the empirical one. At the same time it also accounts satisfactorily for the linear dependence of metabolic rate on ambient temperature.     

Fatty acids,resin acids and phenols in Pinus muricata

Acetone-soluble extractives of “blue” and “green” strain Pinus muricata D. Don were found to consist of free and “combined” fatty acids, resin acids, and phenols. The composition of the extractives from the two strains was similar though “green” strain P. muricata contained more Δ^8(9),15 isopimaric acid than “blue” strain. This difference may be used to identify these muricata strains if the age of the wood precludes a monoterpene examination.     

microRNA-mediated <Emphasis Type="Italic">R</Emphasis> gene regulation: molecular scabbards for double-edged swords

Plant resistance (R) proteins are immune receptors that recognize pathogen effectors and trigger rapid defense responses, namely effector-triggered immunity. R protein-mediated pathogen resistance is usually race specific. During plant-pathogen coevolution, plant genomes accumulated large numbers of R genes. Even though plant R genes provide important natural resources for breeding disease-resistant crops, their presence in the plant genome comes at a cost. Misregulation of R genes leads to developmental defects, such as stunted growth and reduced fertility. In the past decade, many microRNAs (miRNAs) have been identified to target various R genes in plant genomes. miRNAs reduce R gene levels under normal conditions and allow induction of R gene expression under various stresses. For these reasons, we consider R genes to be double-edged “swords” and miRNAs as molecular “scabbards”. In the present review, we summarize the contributions and potential problems of these “swords” and discuss the features and production of the “scabbards”, as well as the mechanisms used to pull the “sword” from the “scabbard” when needed.     

Biological systems of cellular organization and their computer models

The interactions of self-organizing systems possessing at least two hierarchical levels with the environment are dealt with. The dynamical deliberations taking place at the lower level Q of the organism are modelled by a finite state controlled Markov chain. The transitional probability matrix is parametrized on control variables which are related to the probabilities of “pay off” in an underlying two-agent “game” described in the paper.The environment is envisaged as another Markov chain with fixed transitional probabilities. The higher hierarchical level W plays the role of a controller which receives from the lower level Q collective properties which measure (a) the percentage of occupancy of a “homeostatic” state and (b) the cross-correlation between the dynamical processes at the level Q and the environment.The design of the controller is set up as a two-objective control problem having to do with the maximization of the long term average of an appropriately weighted sum of the conflicting terms: probability of the homeostatic state and cross-correlation with the environment.Optimal strategies are found through computing simulation which determine the efferent controls precipitated from the level W to the level Q. The relevance of the model to a number of problems related to the adaptability of hierarchical structures is discussed. Finally some extentions of the present work to do with the communication process between two multihierarchical systems are mentioned.     

Forest soil respiration reflects plant productivity across a temperature gradient in the Alps

Soil respiration (R _s) plays a key role in any consideration of ecosystem carbon (C) balance. Based on the well-known temperature response of respiration in plant tissue and microbes, R _s is often assumed to increase in a warmer climate. Yet, we assume that substrate availability (labile C input) is the dominant influence on R _s rather than temperature. We present an analysis of NPP components and concurrent R _s in temperate deciduous forests across an elevational gradient in Switzerland corresponding to a 6 K difference in mean annual temperature and a considerable difference in the length of the growing season (174 vs. 262 days). The sum of the short-lived NPP fractions (“canopy leaf litter,” “understory litter,” and “fine root litter”) did not differ across this thermal gradient (+6 % from cold to warm sites, n.s.), irrespective of the fact that estimated annual forest wood production was more than twice as high at low compared to high elevations (largely explained by the length of the growing season). Cumulative annual R _s did not differ significantly between elevations (836 ± 5 g C m^?2 a^?1 and 933 ± 40 g C m^?2 a^?1 at cold and warm sites, +12 %). Annual soil CO₂ release thus largely reflected the input of labile C and not temperature, despite the fact that R _s showed the well-known short-term temperature response within each site. However, at any given temperature, R _s was lower at the warm sites (downregulation). These results caution against assuming strong positive effects of climatic warming on R _s, but support a close substrate relatedness of R _s.     

B-Chromosomen bei der GattungLeucanthemum (Asteraceae) in der Tschechoslowakei

The taxonomic arrangement and the karyological analysis of 166 populations ofLeucanthemum demonstrates the existence of 5 taxa for Czechoslovakia; they are grouped provisionally intoL. rotundifolium (W. K.) DC. (2n = 18) and the polyploid complexL. vulgare Lam. with “subsp.vulgare” (2n = 18), “subsp.alpicola” (2n = 18), “subsp.ircutianum” (2n = ± 36) and “subsp.pannonicum” (2n = ± 54). B-chromosomes have not been traced in diploids but have turned up in great numbers in tetraploid (21%) and hexaploid populations (20%). Their presence is not apparent from external characters. Diploids and polyploids evidently are selfsterile.     

Application of microthermometry to measurement of microbial activity and inactivation process by inhibitor

A rapid and simple technique (microthermometry) was developed for the measurement of microbe's metabolic activities and its inactivation process by an inhibitor. To analyze the results and to determine the parameters for the estimation of the activity and inactivation degree, a simple model was proposed. Yeast cells (Saccharomyces cerevisiae) were used as a microbe. A differential method using two bead-type thermistors as reference and measuring probes was employed for the detection of a temperature change caused by the heat of metabolism of added carbon source (glucose) by the yeast. Experiments were conducted in a 30 °C water bath under non-growth conditions (without nitrogen source). The simple thermal response model was applied to obtain two characteristic parameters for the estimation of the yeast activities, i.e., a metabolic heat production rate, ΔQ, and a metabolic heat inhibition rate, ΔK. The proposed model was well in agreement with the experimental results, and the curve fitting gave ΔQ or ΔK. In the case of the addition of glucose to yeast as a carbon source, ΔQ was proportional to the number of live cell (CFU). The slope of CFU versus ΔQ for yeast in exponential phase was larger by about two-fold than that in the stationary phase. In the case of the addition of gultaraldehyde as an inhibitor to the above system, the logarithmic value of ΔK increased with increasing the concentration of gultaraldehyde within the range of 0.02–6.2 wt.%. It was suggested that the two model parameters, ΔQ and ΔK, can be regarded as characteristics to estimate the activities of bacteria and the degree of their inactivation by the inhibitor.     

A method of factor analysis for shape coordinates

Currently the most common reporting style for a geometric morphometric (GMM) analysis of anthropological data begins with the principal components of the shape coordinates to which the original landmark data have been converted. But this focus often frustrates the organismal biologist, mainly because principal component analysis (PCA) is not aimed at scientific interpretability of the loading patterns actually uncovered. The difficulty of making biological sense of a PCA is heightened by aspects of the shape coordinate setting that further diverge from our intuitive expectations of how morphometric measurements ought to combine. More than 50 years ago one of our sister disciplines, psychometrics, managed to build an algorithmic route from principal component analysis to scientific understanding via the toolkit generally known as factor analysis. This article introduces a modification of one standard factor‐analysis approach, Henry Kaiser's varimax rotation of 1958, that accommodates two of the major differences between the GMM context and the psychometric context for these approaches: the coexistence of “general” and “special” factors of form as adumbrated by Sewall Wright, and the typical loglinearity of partial warp variance as a function of bending energy. I briefly explain the history of principal components in biometrics and the contrast with factor analysis, introduce the modified varimax algorithm I am recommending, and work three examples that are reanalyses of previously published cranial data sets. A closing discussion emphasizes the desirability of superseding PCA by algorithms aimed at anthropological understanding rather than classification or ordination.     

A multivariate analysis of temporal change in Arikara craniometrics: A methodological approach

We have examined temporal changes in the cranial architecture of Arikara Amerindians from five archaeological sites in South Dakota which span a time period of approximately 230 years (ca. A.D. 1600–1830). We have utilized a multivariate statistical method based on a principal components analysis of the pooled within-groups correlation matrix rather than the more traditional methods of ascertaining morphological relationships, e.g., discriminant functions, Mahalanobis' D², or Penrose's Size and Shape. Our component structure, based on a regional sample and the mathematically simpler principal components analysis, is very similar to the factor structure obtained by Howells (1973) using a world-wide sample and factor analysis proper. This supports the notion of the “universality” of cranial structure. An axis of temporal variation was introduced into the component space by means of multiple regression. This analysis indicates that a substantial portion of the intergroup variation is temporal in nature and that systematic temporal changes occur along the facial height, transverse frontal flatness, and frontal profile flatness components. Earlier analyses of the same material by more conventional methods either did not detect the temporal trends at all or failed to isolate the specific nature of the temporal changes. The success of the present analysis attests to the value of examining morphological relationships by means of principal components.     

Characterization of the rumen microbiota and its relationship with residual feed intake in sheep

Feed efficiency is a highly important economic trait in sheep production and has a significant impact on the economic benefits of sheep farming. Microbial fermentation of the rumen has a vital role in the host's nutrition; the rumen microbiota might affect host feed efficiency. However, the relationship between the rumen microbiota and feed efficiency in sheep is unclear. In the present study, the microbiota of 195 Hu sheep was investigated and their residual feed intake (RFI), a commonly used measure of feed efficiency, was determined. From birth, all sheep were subjected to the same management practices. At slaughter, samples of liquid rumen contents were collected and subjected to amplicon sequencing for the 16S rDNA gene on the IonS5™XL platform. To identify the bacterial taxa differentially represented at the genus or higher taxonomy levels, we used linear discriminant analysis coupled with effect size and curve fitting. In the sheep rumen, the four most abundant phyla were Firmicutes, Bacteroidetes, Fibrobacteres, and Proteobacteria; and the dominant genera were unidentified Prevotellaceae, Fibrobacter, unidentified Lachnospiraceae, Saccharofermentans, and Succinivibrio. Pathway analysis of the 16S rDNA sequencing data from the rumen microbiota identified that carbohydrate metabolism was enriched. Using α-diversity analysis, we further identified that Observed species, ACE, Good's coverage, and Chao1 are more abundant (P < 0.01) in the low-RFI (L-RFI) group compared to the high-RFI (H-RFI) group. High-RFI sheep had a higher abundance of three bacterial taxa (Prevotellaceae, Negativicutes, and Selenomonadales), and one taxa was overrepresented in the L-RFI sheep (Succinivibrio), respectively. Furthermore, model fitting showed that Veillonellaceae, Sphaerochaeta, Negativibacillus, Saccharofermentans, and members of the Tenericutes, Kiritimatiellaeota, Deltaproteobacteria, and Campylobacterales were correlated with the sheep RFI classification and thus were indicative of a role in animal efficiency. Tax4Fun analysis revealed that metabolic pathways such as “energy metabolism,” “metabolism of cofactors and vitamins,” “poorly characterized,” and “replication recombination and repair proteins” were enriched in the rumen from H-RFI sheep, and “genetic information processing” and “lipopolysaccharide biosynthesis” were overrepresented in L-RFI sheep rumen. In addition, six Kyoto Encyclopedia of Genes and Genomes orthology pathways were identified as different between H-RFI and L-RFI groups. In conclusion, the low RFI phenotype (efficient animals) consistently (or characteristically) exhibited a more abundant and diverse microbiome in sheep.