Rhizodeposition shapes rhizosphere microbial community structure in organic soil

The aims of the study were to determine group specificity in microbial utilization of root-exudate compounds and whole rhizodeposition; quantify the proportions of carbon acquired by microbial groups from soil organic matter and rhizodeposition, respectively; and assess the importance of root-derived C as a driver of soil microbial community structure. Additions of 13C-labelled root-exudate compounds to organic soil and steady-state labelling of Lolium perenne, coupled to compound-specific isotope ratio mass spectrometry, were used to quantify group-specific microbial utilization of rhizodeposition. Microbial utilization of glucose and fumaric acid was widespread through the microbial community, but glycine was utilized by a narrower range of populations, as indicated by the enrichment of phospholipid fatty acid (PLFA) analysis fractions. In L. perenne rhizospheres, high rates of rhizodeposit utilization by microbial groups showed good correspondence with increased abundance of these groups in the rhizosphere. Although rhizodeposition was not the quantitatively dominant C source for microbes in L. perenne rhizospheres, relative utilization of this C source was an important driver of microbial group abundance in organic soil.     

Statistical optimisation of growth conditions and diesel degradation by the Antarctic bacterium,Rhodococcus sp. strain AQ5‒07

Petroleum pollution is a major concern in Antarctica due to the persistent nature of its hydrocarbon components coupled with the region’s extreme environmental conditions, which means that bioremediation approaches are largely inapplicable at present. The current study assessed the ability of the psychrotolerant phenol-degrader, Rhodococcus sp. strain AQ5-07, to assimilate diesel fuel as the sole carbon source. Factors expected to influence the efficiency of diesel degradation, including the initial hydrocarbon concentration, nitrogen source concentration and type, temperature, pH and salinity were studied. Strain AQ5-07 displayed optimal cell growth and biodegradation activity at 1% v/v initial diesel concentration, 1 g/L NH₄Cl concentration, pH 7 and 1% NaCl during one-factor-at-a-time (OFAT) analyses. Strain AQ5-07 was psychrotolerant based on its optimum growth temperature being near 20 °C. In conventionally optimised media, strain AQ5-07 showed total petroleum hydrocarbons (TPH) mineralisation of 75.83%. However, the optimised condition for TPH mineralisation predicted through statistical response surface methodology (RSM) enhanced the reduction to 90.39% within a 2 days incubation. Our preliminary data support strain AQ5-07 being a potential candidate for real-field soil bioremediation by specifically adopting sludge-phase bioreactor system in chronically cold environments such as Antarctica. The study also confirmed the utility of RSM in medium optimisation.

     

Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales)

Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using "early but risky" fossil constraints in addition to "safe but late" constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of divergence times. For example, our estimates for the crown group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical reassessment of their phylogenetic position.     

Lithium Polyacrylate (LiPAA) as an Advanced Binder and a Passivating Agent for High‐Voltage Li‐Ion Batteries

Intensive studies of an advanced energy material are reported and lithium polyacrylate (LiPAA) is proven to be a surprisingly unique, multifunctional binder for high‐voltage Li‐ion batteries. The absence of effective passivation at the interface of high‐voltage cathodes in Li‐ion batteries may negatively affect their electrochemical performance, due to detrimental phenomena such as electrolyte solution oxidation and dissolution of transition metal cations. A strategy is introduced to build a stable cathode–electrolyte solution interphase for LiNi_0.5Mn_1.5O₄ (LNMO) spinel high‐voltage cathodes during the electrode fabrication process by simply using LiPAA as the cathode binder. LiPAA is a superb binder due to unique adhesion, cohesion, and wetting properties. It forms a uniform thin passivating film on LNMO and conducting carbon particles in composite cathodes and also compensates Li‐ion loss in full Li‐ion batteries by acting as an extra Li source. It is shown that these positive roles of LiPAA lead to a significant improvement in the electrochemical performance (e.g., cycle life, cell impedance, and rate capability) of LNMO/graphite battery prototypes, compared with that obtained using traditional polyvinylidene fluoride (PVdF) binder for LNMO cathodes. In addition, replacing PVdF with LiPAA binder for LNMO cathodes offers better adhesion, lower cost, and clear environmental advantages.     

Identification and characterization of protein interactions in the mammalian mRNA processing body using a novel two-hybrid assay

Components of the mRNA processing body (P-body) regulate critical steps in mRNA storage, transport, translation and degradation. At the core of the P-body is the decapping complex, which removes the 5′ cap from de-adenylated mRNAs and mediates an irreversible step in mRNA degradation. The assembly of P-bodies in Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster has been previously described. Less is known about the assembly of mammalian P-bodies. To investigate the interactions that occur between components of mammalian P-bodies, we developed a fluorescence-based, two-hybrid assay system. The assay depends on the ability of one P-body component, fused to an exogenous nuclear localization sequence (NLS), to recruit other P-body components to the nucleus. The assay was used to investigate interactions between P-body components Ge-1, DCP2, DCP1, EDC3, RAP55, and RCK. The results of this study show that the modified two-hybrid assay can be used to identify protein interactions that occur in a macromolecular complex. The assay can also be used to efficiently detect protein interaction domains. The results provide important insights into mammalian P-body assembly and demonstrate similarities, and critical differences, between P-body assembly in mammalian cells compared with that of other species.     

Biochemical Conservation and Evolution of Germacrene A Oxidase in Asteraceae

Sesquiterpene lactones are characteristic natural products in Asteraceae, which constitutes ∼8% of all plant species. Despite their physiological and pharmaceutical importance, the biochemistry and evolution of sesquiterpene lactones remain unexplored. Here we show that germacrene A oxidase (GAO), evolutionarily conserved in all major subfamilies of Asteraceae, catalyzes three consecutive oxidations of germacrene A to yield germacrene A acid. Furthermore, it is also capable of oxidizing non-natural substrate amorphadiene. Co-expression of lettuce GAO with germacrene synthase in engineered yeast synthesized aberrant products, costic acids and ilicic acid, in an acidic condition. However, cultivation in a neutral condition allowed the de novo synthesis of a single novel compound that was identified as germacrene A acid by gas and liquid chromatography and NMR analyses. To trace the evolutionary lineage of GAO in Asteraceae, homologous genes were further isolated from the representative species of three major subfamilies of Asteraceae (sunflower, chicory, and costus from Asteroideae, Cichorioideae, and Carduoideae, respectively) and also from the phylogenetically basal species, Barnadesia spinosa, from Barnadesioideae. The recombinant GAOs from these genes clearly showed germacrene A oxidase activities, suggesting that GAO activity is widely conserved in Asteraceae including the basal lineage. All GAOs could catalyze the three-step oxidation of non-natural substrate amorphadiene to artemisinic acid, whereas amorphadiene oxidase diverged from GAO displayed negligible activity for germacrene A oxidation. The observed amorphadiene oxidase activity in GAOs suggests that the catalytic plasticity is embedded in ancestral GAO enzymes that may contribute to the chemical and catalytic diversity in nature.     

Neighbourhood Factors and Depression among Adolescents in Four Caribbean Countries

Background

Past research suggests that perceived neighbourhood conditions may influence adolescents'' emotional health. Relatively little research has been conducted examining the association of perceived neighbourhood conditions with depressive symptoms among Caribbean adolescents. This project examines the association of perceived neighbourhood conditions with levels of depressive symptoms among adolescents in Jamaica, the Bahamas, St. Kitts and Nevis, and St. Vincent.

Methods

Adolescents attending grade ten of the academic year 2006/2007 in Jamaica, the Bahamas, St. Vincent, and St. Kitts and Nevis were administered the Neighbourhood Characteristics Questionnaire along with the BDI-II. Social cohesion, attachment to the neighbourhood, neighbourhood quality, neighbourhood crime, and neighbourhood disorder scales were created by summing the relevant subscales of the Neighbourhood Characteristics Questionnaire. Multiple regression analyses were used to examine the relationships of perceived neighbourhood conditions to depressive symptoms.

Results

A wide cross-section of tenth grade students in each nation was sampled (n = 1955; 278 from Jamaica, 217 from the Bahamas, 737 St. Kitts and Nevis, 716 from St. Vincent; 52.1% females, 45.6% males and 2.3% no gender reported; 12 to 19 years, mean = 15.3 yrs, sd = .95 yr). Nearly half (52.1%) of all adolescents reported mild to severe symptoms of depression with 29.1% reporting moderate to severe symptoms of depression. Overall, Jamaican adolescents perceived their neighbourhoods in a more positive manner than those in the Bahamas, St. Vincent and St. Kitts and Nevis. Results of a series of hierarchical multiple regression analyses suggested that a different pattern of neighbourhood factors for each island were associated with depressive symptoms. However, neighbourhood factors were more highly associated with depressive symptoms for Jamaican students than for students in the other three islands.

Conclusions

Neighbourhood factors appear to be partially associated with adolescents'' self-reports of depressive symptoms. However, other factors may mitigate this relationship.     

The genome sequence of a reassortant bluetongue virus serotype 3 from India

All 10 genome segments (Seg-1 to 10-a total of 19,188 bp) were sequenced from a strain of bluetongue virus serotype 3 (BTV-3) from India (strain IND2003/08). Sequence comparisons showed that nine of the genome segments from this virus group with other eastern topotype strains. Genome Seg-2 and Seg-6 group with eastern BTV-3 strains from Japan. However, Seg-5 (the NS1 gene) from IND2003/08 belongs to a western lineage, demonstrating that IND2003/08 is a reassortant between eastern and western topotype bluetongue viruses. This confirms that western BTV strains have been imported and are circulating within the subcontinent.     

Technical Note: Calcium and carbon stable isotope ratios as paleodietary indicators

Calcium stable isotope ratios are hypothesized to vary as a function of trophic level. This premise raises the possibility of using calcium stable isotope ratios to study the dietary behaviors of fossil taxa and to test competing hypotheses on the adaptive origins of euprimates. To explore this concept, we measured the stable isotope composition of contemporary mammals in northern Borneo and northwestern Costa Rica, two communities with functional or phylogenetic relevance to primate origins. We found that bone collagen δ¹³C and δ¹⁵N values could differentiate trophic levels in each assemblage, a result that justifies the use of these systems to test the predicted inverse relationship between bioapatite δ¹³C and δ⁴⁴Ca values. As expected, taxonomic carnivores (felids) showed a combination of high δ¹³C and low δ⁴⁴Ca values; however, the δ⁴⁴Ca values of other faunivores were indistinguishable from those of primary consumers. We suggest that the trophic insensitivity of most bioapatite δ⁴⁴Ca values is attributable to the negligible calcium content of arthropod prey. Although the present results are inconclusive, the tandem analysis of δ⁴⁴Ca and δ¹³C values in fossils continues to hold promise for informing paleodietary studies and we highlight this potential by drawing attention to the stable isotope composition of the Early Eocene primate Cantius. Am J Phys Anthropol 154:633–643, 2014. © 2014 Wiley Periodicals, Inc.