Modeling transport of a pulse of radiolabeled organelles in a Drosophila unipolar motor neuron

Based on published experimental evidence, this paper develops a model for the transport of a pulse of radiolabeled organelles in a unipolar Drosophila motor neuron. In particular, since published data indicate that no microtubules (MTs) travel from the primary neurite into the dendrite, it is investigated how organelles are transported into the dendrite. Analytical solutions describing concentrations of kinesin- and dynein-driven organelles in the primary neurite, axon, and dendrite are obtained. The effects of increasing the width of the pulse and increasing the rate of organelle transition rate from the kinesin-driven to the dynein-driven state are investigated.     

Overwintering strategy of endoparasitoids in Chilo suppressalis: a perspective from the cold hardiness of a host

Although parasitoids ultimately kill their host, koinobiont parasitoids must protect not only themselves but also their hosts against extreme environments. In this study, the parasitism rate of Chilo suppressalis Walker (Lepidoptera: Pyralidae) was investigated, and the average body weights, supercooling points, and concentrations of glycerol (acting as a cryoprotectant) in the hemolymph were compared between parasitized and non‐parasitized larvae. Five species of koinobiont endoparasitoids parasitized the overwintering C. suppressalis larvae and the total parasitism rate was 47.6% (n = 1 537). Average body weight of parasitized larvae was significantly lower than that of non‐parasitized larvae, and the parasitism rate of the lighter group (20–30 mg) was highest. The supercooling point of parasitized C. suppressalis larvae (?15.7 ± 0.3 °C) was significantly lower than that of the non‐parasitized larvae (?14.3 ± 0.2 °C). In addition, supercooling points were not correlated with body weights between parasitized and non‐parasitized larvae, indicating that cold hardiness of parasitized larvae was enhanced by endoparasitoids. Furthermore, the concentration of glycerol in the hemolymph was significantly higher in parasitized larvae (205.0 ± 7.1 μmol ml^?1) than in non‐parasitized larvae (169.8 ± 14.4 μmol ml^?1), which suggests that the mechanism that decreases the supercooling point of parasitized larvae was associated with glycerol. All these results indicated that the cold hardiness of parasitized C. suppressalis larvae was enhanced by their endoparasitoids, which benefitted overwintering endoparasitoids.     

Nitrogen fertilization increases diversity and productivity of prairie communities used for bioenergy

Using prairie biomass as a renewable source of energy may constitute an important opportunity to improve the environmental sustainability of managed land. To date, assessments of the feasibility of using prairies for bioenergy production have focused on marginal areas with low yield potential. Growing prairies on more fertile soil or with moderate levels of fertilization may be an effective means of increasing yields, but increased fertility often reduces plant community diversity. At a fertile site in central Iowa with high production potential, we tested the hypothesis that nitrogen fertilization would increase aboveground biomass production but would decrease diversity of prairies sown and managed for bioenergy production. Over a 3 year period (years 2–4 after seeding), we measured aboveground biomass after plant senescence and species and functional‐group diversity in June and August for multispecies mixtures of prairie plants that received no fertilizer or 84 kg N ha^?1 year^?1. We found that nitrogen fertilization increased aboveground biomass production, but with or without fertilization, the prairies produced a substantial amount of biomass: averaging (±SE) 12.2 ± 1.3 and 9.1 ± 1.0 Mg ha^?1 in fertilized and unfertilized prairies, respectively. Unfertilized prairies had higher species diversity in June, whereas fertilized prairies had higher species diversity in August at the end of the study period. Functional‐group diversity was almost always higher in fertilized prairies. Composition of unfertilized prairies was characterized by native C₄ grasses and legumes, whereas fertilized prairies were characterized by native C₃ grasses and forbs. Although most research has found that nitrogen fertilization reduces prairie diversity, our results indicate that early‐spring nitrogen fertilization, when used with a postsenescence annual harvest, may increase prairie diversity. Managing prairies for bioenergy production, including the judicious use of fertilization, may be an effective means of increasing the amount of saleable products from managed lands while potentially increasing plant diversity.     

Identification of chloroplast genome loci suitable for high‐resolution phylogeographic studies of Colocasia esculenta (L.) Schott (Araceae) and closely related taxa

Recently, we reported the chloroplast genome‐wide association of oligonucleotide repeats, indels and nucleotide substitutions in aroid chloroplast genomes. We hypothesized that the distribution of oligonucleotide repeat sequences in a single representative genome can be used to identify mutational hotspots and loci suitable for population genetic, phylogenetic and phylogeographic studies. Using information on the location of oligonucleotide repeats in the chloroplast genome of taro (Colocasia esculenta), we designed 30 primer pairs to amplify and sequence polymorphic loci. The primers have been tested in a range of intra‐specific to intergeneric comparisons, including ten taro samples (Colocasia esculenta) from diverse geographical locations, four other Colocasia species (C. affinis, C. fallax, C. formosana, C. gigantea) and three other aroid genera (represented by Remusatia vivipara, Alocasia brisbanensis and Amorphophallus konjac). Multiple sequence alignments for the intra‐specific comparison revealed nucleotide substitutions (point mutations) at all 30 loci and microsatellite polymorphisms at 14 loci. The primer pairs reported here reveal levels of genetic variation suitable for high‐resolution phylogeographic and evolutionary studies of taro and other closely related aroids. Our results confirm that information on repeat distribution can be used to identify loci suitable for such studies, and we expect that this approach can be used in other plant groups.     

Optofluidic single‐cell absorption flow analyzer for point‐of‐care diagnosis of malaria

In this work, an optofluidic flow analyzer, which can be used to perform malaria diagnosis at the point‐of‐care is demonstrated. The presented technique is based on quantitative optical absorption measurements carried out on a single cell level for a given population of Human Red Blood Cells (RBCs). By measuring the optical absorption of each RBC, the decrease in the Hemoglobin (Hb) concentration in the cytoplasm of the cell due to the invasion of malarial parasite is detected. Cells are assessed on a single cell basis, as they pass through a microfluidic channel. The proposed technique has been implemented with inexpensive off‐the‐shelf components like laser diode, photo‐detector and a micro‐controller. The ability of the optofluidic flow analyzer to asses about 308,049 cells within 3 minutes has been demonstrated. The presented technique is capable of detecting very low parasitemia levels with high sensitivity.

     

Deriving C4 photosynthetic parameters from combined gas exchange and chlorophyll fluorescence using an Excel tool: theory and practice

The higher photosynthetic potential of C₄ plants has led to extensive research over the past 50 years, including C₄‐dominated natural biomes, crops such as maize, or for evaluating the transfer of C₄ traits into C₃ lineages. Photosynthetic gas exchange can be measured in air or in a 2% Oxygen mixture using readily available commercial gas exchange and modulated PSII fluorescence systems. Interpretation of these data, however, requires an understanding (or the development) of various modelling approaches, which limit the use by non‐specialists. In this paper we present an accessible summary of the theory behind the analysis and derivation of C₄ photosynthetic parameters, and provide a freely available Excel Fitting Tool (EFT), making rigorous C₄ data analysis accessible to a broader audience. Outputs include those defining C₄ photochemical and biochemical efficiency, the rate of photorespiration, bundle sheath conductance to CO₂ diffusion and the in vivo biochemical constants for PEP carboxylase. The EFT compares several methodological variants proposed by different investigators, allowing users to choose the level of complexity required to interpret data. We provide a complete analysis of gas exchange data on maize (as a model C₄ organism and key global crop) to illustrate the approaches, their analysis and interpretation. © 2015 John Wiley & Sons Ltd     

Molecular mechanisms underlying the emergence of bacterial pathogens: an ecological perspective

The rapid emergence of new bacterial diseases negatively affects both human health and agricultural productivity. Although the molecular mechanisms underlying these disease emergences are shared between human‐ and plant‐pathogenic bacteria, not much effort has been made to date to understand disease emergences caused by plant‐pathogenic bacteria. In particular, there is a paucity of information in the literature on the role of environmental habitats in which plant‐pathogenic bacteria evolve and on the stress factors to which these microbes are unceasingly exposed. In this microreview, we focus on three molecular mechanisms underlying pathogenicity in bacteria, namely mutations, genomic rearrangements and the acquisition of new DNA sequences through horizontal gene transfer (HGT). We briefly discuss the role of these mechanisms in bacterial disease emergence and elucidate how the environment can influence the occurrence and regulation of these molecular mechanisms by directly impacting disease emergence. The understanding of such molecular evolutionary mechanisms and their environmental drivers will represent an important step towards predicting bacterial disease emergence and developing sustainable management strategies for crops.     

Role of W181 in modulating kinetic properties of Plasmodium falciparum hypoxanthine guanine xanthine phosphoribosyltransferase

Hypoxanthine‐guanine‐xanthine phosphoribosyltransference (HGXPRT), a key enzyme in the purine salvage pathway of the malarial parasite, Plasmodium falciparum (Pf), catalyses the conversion of hypoxanthine, guanine, and xanthine to their corresponding mononucleotides; IMP, GMP, and XMP, respectively. Out of the five active site loops (I, II, III, III', and IV) in PfHGXPRT, loop III' facilitates the closure of the hood over the core domain which is the penultimate step during enzymatic catalysis. PfHGXPRT mutants were constructed wherein Trp 181 in loop III' was substituted with Ser, Thr, Tyr, and Phe. The mutants (W181S, W181Y and W181F), when examined for xanthine phosphoribosylation activity, showed an increase in K_m for PRPP by 2.1‐3.4 fold under unactivated condition and a decrease in catalytic efficiency by more than 5‐fold under activated condition as compared to that of the wild‐type enzyme. The W181T mutant showed 10‐fold reduced xanthine phosphoribosylation activity. Furthermore, molecular dynamics simulations of WT and in silico W181S/Y/F/T PfHGXPRT mutants bound to IMP.PPi.Mg²⁺ have been carried out to address the effect of the mutation of W181 on the overall dynamics of the systems and identify local changes in loop III'. Dynamic cross‐correlation analyses show a communication between loop III' and the substrate binding site. Differential cross‐correlation maps indicate altered communication among different regions in the mutants. Changes in the local contacts and hydrogen bonding between residue 181 with the nearby residues cause altered substrate affinity and catalytic efficiency of the mutant enzymes. Proteins 2016; 84:1658–1669. © 2016 Wiley Periodicals, Inc.     

Effect of surface-screening parameter of the Yukawa potential model on vapour–liquid phase coexistence and critical-point properties of confined Yukawa fluid

We report the effect of surface-screening parameter of Yukawa potential model on vapour–liquid phase coexistence and critical-point properties of slit–pore-confined Yukawa fluid, using grand canonical transition-matrix Monte Carlo along with the histogram reweighting method. The effect of surface-screening parameter on the vapour–phase coexistence density is insignificant for the studied system. On the other hand, significant effect of surface-screening parameter is observed on liquid phase coexistence density. With increasing surface-screening parameter, liquid phase coexistence density decreases. Critical-point properties have shown monotonic decreasing trends with increase in surface-screening parameter. Moreover, the effect of change of surface-screening parameter is least on critical temperature changes as compared to critical density and critical pressure changes for the studied Yukawa system in this work.     

HPV18 Utilizes Two Alternative Branch Sites for E6~*I Splicing to Produce E7 Protein

Human papillomavirus 18(HPV18) E6 and E7 oncogenes are transcribed as a single bicistronic E6 E7 pre-mRNA. The E6 ORF region in the bicistronic E6 E7 pre-mRNA contains an intron. Splicing of this intron disrupts the E6 ORF integrity and produces a spliced E6~*I RNA for efficient E7 translation. Here we report that the E6 intron has two overlapped branch point sequences(BPS) upstream of its 30 splice site, with an identical heptamer AACUA■C, for E6~*I splicing. One heptamer has a branch site adenosine(underlined) at nt 384 and the other at nt 388. E6~*I splicing efficiency correlates to the expression level of E6 and E7 proteins and depends on the selection of which branch site. In general, E6~*I splicing prefers the 30 ss-proximal branch site at nt 388 over the distal branch site at nt 384. Inactivation of the nt 388 branch site was found to activate a cryptic acceptor site at nt 636 for aberrant RNA splicing. Together, these data suggest that HPV18 modulates its production ratio of E6 and E7 proteins by alternative selection of the two mapped branch sites for the E6~*I splicing, which could be beneficial in its productive or oncogenic infection according to the host cell environment.