Genomics and expression analysis of DHHC-cysteine-rich domain S-acyl transferase protein family in apple

S-acylation is one of a group of lipid modifications that occurs on eukaryotic proteins, mediated by DHHC-CRD-containing proteins, which plays an important role in regulating the membrane association, trafficking and function of target proteins. Although genome-wide identification of PAT family has been carried out in yeast, mice, humans and Arabidopsis, little is known about apple PAT genes. In this study, a total of 33 putative apple PAT proteins, containing DHHC-CRD by domain analysis, have been identified, and were classified into three groups according to the phylogenetic analysis of PAT proteins in apple and Arabidopsis. More complex TMDs in the most MdPATs revealed the PM location of the gene family. Gene structure, gene chromosomal location and paralogs analysis of MdPAT genes within the apple genome demonstrated that tandem and segmental duplications, as well as whole genome duplications, have likely contributed to the expansion and evolution of the PAT gene family in apple. According to the microarray and expressed sequence tag (ESTs) analysis, the different expression patterns indicate that they may play different roles during fruit development and rootstock-scion interactions process. Moreover, PATs were performed expression profile analyses in different tissues, indicating that the PATs are involved in various aspects of physiological and developmental processes of apple. To our knowledge, this is the first report of a genome-wide analysis of the apple PAT gene family, and this genomic analysis of apple DHHC-CRD PAT genes provides the first step towards a functional study of this gene family in apple.     

Genome-wide comparative analysis of the codon usage patterns in plants

Codon usage analysis has been a classical area of study for decades and is important for evolution, mRNA translation, and new gene discovery. Recently, genome sequencing has made it possible to perform studies of the entire genome in plant kingdoms. The base composition of the coding sequence, codon usage pattern, codon pairs, and related indicators of relative synonymous codon usage (RSCU), including the Fop, Nc, RSCU, CAI and GC contents, were analyzed. We found that the GC content of single-celled algae is the highest, whereas dicotyledons are the lowest. Moreover, the base composition of plants is similar within the same family. In addition, the GC content of the second base of the codon is lower than the first and third base. In conclusion, the codon usage characteristics are opposite in Gramineae, single-celled algae, fern and dicotyledon, moss, and Pinaceae. Furthermore, the degree of codon usage bias is decreasing with evolution. Therefore, we hypothesize that the lower the plants, the more that they must optimize codons and that higher plants no longer need to optimize codons.     

The MIF Antagonist ISO-1 Attenuates Corticosteroid-Insensitive Inflammation and Airways Hyperresponsiveness in an Ozone-Induced Model of COPD

Introduction

Macrophage migration inhibitory factor (MIF) is an inflammatory cytokine associated with acute and chronic inflammatory disorders and corticosteroid insensitivity. Its expression in the airways of patients with chronic obstructive pulmonary disease (COPD), a relatively steroid insensitive inflammatory disease is unclear, however.

Methods

Sputum, bronchoalveolar lavage (BAL) macrophages and serum were obtained from non-smokers, smokers and COPD patients. To mimic oxidative stress-induced COPD, mice were exposed to ozone for six-weeks and treated with ISO-1, a MIF inhibitor, and/or dexamethasone before each exposure. BAL fluid and lung tissue were collected after the final exposure. Airway hyperresponsiveness (AHR) and lung function were measured using whole body plethysmography. HIF-1α binding to the Mif promoter was determined by Chromatin Immunoprecipitation assays.

Results

MIF levels in sputum and BAL macrophages from COPD patients were higher than those from non-smokers, with healthy smokers having intermediate levels. MIF expression correlated with that of HIF-1α in all patients groups and in ozone-exposed mice. BAL cell counts, cytokine mRNA and protein expression in lungs and BAL, including MIF, were elevated in ozone-exposed mice and had increased AHR. Dexamethasone had no effect on these parameters in the mouse but ISO-1 attenuated cell recruitment, cytokine release and AHR.

Conclusion

MIF and HIF-1α levels are elevated in COPD BAL macrophages and inhibition of MIF function blocks corticosteroid-insensitive lung inflammation and AHR. Inhibition of MIF may provide a novel anti-inflammatory approach in COPD.     

Turing learning: a metric-free approach to inferring behavior and its application to swarms

We propose Turing Learning, a novel system identification method for inferring the behavior of natural or artificial systems. Turing Learning simultaneously optimizes two populations of computer programs, one representing models of the behavior of the system under investigation, and the other representing classifiers. By observing the behavior of the system as well as the behaviors produced by the models, two sets of data samples are obtained. The classifiers are rewarded for discriminating between these two sets, that is, for correctly categorizing data samples as either genuine or counterfeit. Conversely, the models are rewarded for ‘tricking’ the classifiers into categorizing their data samples as genuine. Unlike other methods for system identification, Turing Learning does not require predefined metrics to quantify the difference between the system and its models. We present two case studies with swarms of simulated robots and prove that the underlying behaviors cannot be inferred by a metric-based system identification method. By contrast, Turing Learning infers the behaviors with high accuracy. It also produces a useful by-product—the classifiers—that can be used to detect abnormal behavior in the swarm. Moreover, we show that Turing Learning also successfully infers the behavior of physical robot swarms. The results show that collective behaviors can be directly inferred from motion trajectories of individuals in the swarm, which may have significant implications for the study of animal collectives. Furthermore, Turing Learning could prove useful whenever a behavior is not easily characterizable using metrics, making it suitable for a wide range of applications.     

A taxonomic revision of <Emphasis Type="Italic">Bursera</Emphasis> subgen. <Emphasis Type="Italic">Bursera</Emphasis> in the Greater Antilles and the Bahamas,including a new species from Cuba

A revision of Bursera in the Greater Antilles and the Bahamas has confirmed that Commiphora does not occur in the region and that all but one species in the region belong to Bursera subgen. Bursera. Here we describe a new species, Bursera yaterensis; B. nashii is synonymized with B. glauca and B. ovata is synonymized with B. trinitensis; and we return five species from Commiphora to Bursera. A dichotomous key is provided using mostly vegetative characters due to the frequent lack of adequate reproductive material and the relative uniformity of most floral and fruit characters.     

Scale-dependent bi-trophic interactions in a semi-arid savanna: how herbivores eliminate benefits of nutrient patchiness to plants

The scale of resource heterogeneity may influence how resources are locally partitioned between co-existing large and small organisms such as trees and grasses in savannas. Scale-related plant responses may, in turn, influence herbivore use of the vegetation. To examine these scale-dependent bi-trophic interactions, we varied fertilizer [(nitrogen (N)/phosphorus (P)/potassium (K)] applications to patches to create different scales of nutrient patchiness (patch size 2 × 2 m, 10 × 10 m, or whole-plot 50 × 50 m) in a large field experiment in intact African savanna. Within-patch fertilizer concentration and the total fertilizer load per plot were independently varied. We found that fertilization increased the leaf N and P concentrations of trees and grasses, resulting in elevated utilization by browsers and grazers. Herbivory off-take was particularly considerable at higher nutrient concentrations. Scale-dependent effects were weak. The net effect of fertilization and herbivory was that plants in fertilized areas tended to grow less and develop smaller rather than larger standing biomass compared to plants growing in areas that remained unfertilized. When all of these effects were considered together at the community (plot) level, herbivory completely eliminated the positive effects of fertilization on the plant community. While this was true for all scales of fertilization, grasses tended to profit more from coarse-grained fertilization and trees from fine-grained fertilization. We conclude that in herbivore-dominated communities, such as the African savanna, nutrient patchiness results in the herbivore community profiting rather more than the plant community, irrespective of the scale of patchiness. At the community level, the allometric scaling theory’s prediction of plant—and probably also animal—production does not hold or may even be reversed as a result of complex bi-trophic interactions.     

No need to breed for enhanced colonization by arbuscular mycorrhizal fungi to improve low-P adaptation of West African sorghums

Background and aims

Herbaspirillum seropedicae (Hs) Z67 a diazotrophic endophyte was genetically engineered for secretion of 2-keto-D-gluconic acid by heterologous expression of genes for pqq synthesis and gluconate dehydrogenase to study its beneficial effect on plants.

Methods

Two plasmids, pJNK5, containing a 5.1 Kb pqq gene cluster of Acinetobacter calcoaceticus and pJNK6, carrying in addition the Pseudomonas putida KT2440 gluconate dehydrogenase (gad) operon were constructed in pUCPM18Gm^r under Plac promoter. H. seropedicae Z67 transformants were monitored for P and K solubilization, cadmium (Cd) tolerance and rice growth promotion.

Results

Hs (pJNK5) secreted 23.5 mM gluconic acid and Hs (pJNK6) secreted 3.79 mM gluconic acid and 15.8 mM 2-ketogluconic acid respectively. Under aerobic conditions, Hs (pJNK5) and Hs (pJNK6) solubilized 239.7 μM and 457.7 μM P on HEPES rock phosphate and, 76.7 μM and 222.7 μM K on HRPF (feldspar), respectively, in minimal medium containing 50 mM glucose. Under N free minimal medium, similar effects of P and K solubilization were obtained. Hs (pJNK5) and Hs (pJNK6) inoculation increased the biomass, N, P, K content of rice plants (Gujarat – 17). These plants also accumulated 0.73 ng/g PQQ, and had improved growth and tolerance to CdCl₂.

Conclusions

Incorporation of pqq and gad gene clusters in H. seropedicae Z67 imparted additional plant growth promoting traits of P and K solubilization and ability to alleviate Cd toxicity to the host plant.