Molecular evolution of chloroplast DNA sequences

Comparative data on the evolution of chloroplast genes are reviewed. The chloroplast genome has maintained a similar structural organization over most plant taxa so far examined. Comparisons of nucleotide sequence divergence among chloroplast genes reveals marked similarity across the plant kingdom and beyond to the cyanobacteria (blue-green algae). Estimates of rates of nucleotide substitution indicate a synonymous rate of 1.1 x 10(-9) substitutions per site per year. Noncoding regions also appear to be constrained in their evolution, although addition/deletion events are common. There have also been evolutionary changes in the distribution of introns in chloroplast encoded genes. Relative to mammalian mitochondrial DNA, the chloroplast genome evolves at a conservative rate.      

Novel p19-related protein in Rous-associated virus type 61: implications for avian gag gene order

Virions of Rous-associated virus type 61 contain a previously unrecognized p19-related protein, called p19f, which comigrates with gag protein p12 during electrophoresis in sodium dodecyl sulfate-polyacrylamide gels but can be separated by gel filtration chromatography in 6 M guanidine hydrochloride. It is shown that the existence of p19f accounts for the earlier inability to order p27 and p12 by the pactamycin mapping procedure. Remapping with pactamycin by using methods which take this new protein into account yielded a gag gene order of NH2-p219-p27-p12-p15-COOH. It also confirmed earlier positions for the env and pol genes and placed unclassified protein p10 near a translational initiation site. The pactamycin-derived mapping position of p12 differs from reports based on tryptic analysis. An analysis of procedural shortcomings emphasizes the need for more definitive determinations of the avian gag gene order.     

SEGMENTATION APPROACHES THAT DIFFERENTIATE CONSUMPTION FREQUENCY FROM SENSORY PREFERENCE1

People can eat a food without having a strong preference for it, and people can prefer a food without eating it. Given this seeming disconnect between attitude and behavior, which type of measure or segment can best be used to profile or identify loyal consumer segments of a food, such as soy? This research compares a usage‐based method (heavy‐light‐nonusers) with a new attitude‐based method (seeker‐neutral‐avoider), and finds that the attitude‐based method differentiates purchase‐related intentions better than the usage‐based method. Implications for profiling consumer taste patterns and consumer segments are provided.     

Clubroot resistance QTL are modulated by nitrogen input in <Emphasis Type="Italic">Brassica napus</Emphasis>

Key message

Nitrogen levels can modulate the effectiveness of clubroot resistance in an isolate- and host-specific manner. While the same QTL were detected under high and low nitrogen, their effects were altered.

Abstract

Clubroot, caused by Plasmodiophora brassicae, is one of the most damaging diseases of oilseed rape and is known to be affected by nitrogen fertilization. However, the genetic factors involved in clubroot resistance have not been characterized under nitrogen-limiting conditions. This study aimed to assess the variability of clubroot resistance under different nitrogen levels and to characterize the impact of nitrogen supply on genetic resistance factors. Linkage analyses and a genome-wide association study were conducted to detect QTL for clubroot resistance and evaluate their sensitivity to nitrogen. The clubroot response of a set of 92 diverse oilseed rape accessions and 108 lines derived from a cross between ‘Darmor-bzh’ (resistant) and ‘Yudal’ (susceptible) was studied in the greenhouse under high- and low-nitrogen conditions, following inoculation with the P. brassicae isolates eH and K92-16. Resistance to each isolate was controlled by a major QTL and a few small-effects QTL. While the same QTL were detected under both high and low nitrogen, their effects were altered. Clubroot resistance to isolate eH, but not K92-16, was greater under a low-N supply versus a high-N supply. New sources of resistance were found among the oilseed rape accessions under both low and high-N conditions. The results are discussed relative to the literature and from a crop improvement perspective.

     

An approach to rapid processing of camera trap images with minimal human input

1. Camera traps have become an extensively utilized tool in ecological research, but the manual processing of images created by a network of camera traps rapidly becomes an overwhelming task, even for small camera trap studies.
2. We used transfer learning to create convolutional neural network (CNN) models for identification and classification. By utilizing a small dataset with an average of 275 labeled images per species class, the model was able to distinguish between species and remove false triggers.
3. We trained the model to detect 17 object classes with individual species identification, reaching an accuracy up to 92% and an average F1 score of 85%. Previous studies have suggested the need for thousands of images of each object class to reach results comparable to those achieved by human observers; however, we show that such accuracy can be achieved with fewer images.
4. With transfer learning and an ongoing camera trap study, a deep learning model can be successfully created by a small camera trap study. A generalizable model produced from an unbalanced class set can be utilized to extract trap events that can later be confirmed by human processors.

     

Alkane composition diversity among populations of dwarf forms of Juniperus communis L.: comparison between western Europe and northern American populations

The cuticular wax composition of leaves has been analysed in three western European populations (Corsica, central Pyrenees, northern Alps) of Juniperus communis var. saxatilis Pall. (=  J. nana Willd., nom illeg.) and in one population of J. communis L. var. depressa Pursh. from North America (Sierra Nevada). Gas chromatography shows the presence of 13 alkanes in all samples ranging from C₂₃ to C₃₅ with important intraspecific polymorphism in alkane content. The dominant alkanes range from C₃₃ to C₃₅. Alkanes C₂₁ and C₂₂ were found only in Corsica and Sierra Nevada populations. Canonical discriminant analysis separated the J. communis L. var. depressa Pursh. of the population of Sierra Nevada from other populations of J. communis var. saxatilis Pall. on the basis of their higher C₃₁ content and the constant presence of C₂₁ and C₂₂ alkanes. J. communis var. saxatilis Pall. populations from the Pyrenees are close to northern Alps populations characterized by high concentrations of C₃₃, C₃₄ and C₃₅ alkanes. This paper confirms the existence of Juniperus var. saxatilis Pall. in the Pyrenees (France).  © The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 165–168.     

<i>Trichoderma</i> spp. fostering growth on <i>Capsicum chinense</i> Jacq. seedlings and antagonistic against <i>Meloidogyne incognita</i>

Fourteen native strains of Trichoderma spp. from wildand agricultural pathosystems in the state of Yucatan, Mexico, with growth-promoting ability of Capsicum chinense Jacq. seedlings were evaluated and antagonistic effect of their filtrate against second-stage juveniles (J2) of Meloidogyne incognita. The strains Th05-02 and Th27-08 showed the best significant effects on plant hight variable increments 55.57 and 47.62%, theTh07-04 with 29.48% more root length, theTh02-01 and Th07-04 isolates increased from 48.71 to 84.61% in volume radical and 53.40% of total dry biomass. Statistical analysis (p≤0.001) of Th43 and Th43-13-14 filtrates caused 100% mortality at 24 and 48h. In the test of reversibility to 24 h after replacing the filtrates Th43-13, Th43-14, TH09-06 and TH20-07 by sterile distilled water, the J2 did not recover their viability, so they were considered as the best potential strains of Trichoderma spp. with antagonistic capacity in J2 of M.incognita.     

A new ant genus from the Greater Antilles and Central America,Zatania (Hymenoptera: Formicidae), exemplifies the utility of male and molecular character systems

The ant genus Prenolepis (Hymenoptera: Formicidae) is the nominal member of the recently established Prenolepis genus‐group within the subfamily Formicinae. Our molecular phylogenetic analyses using fragments from five nuclear genes (arginine kinase, carbomoylphosphate synthase, elongation factor 1‐alpha F1, elongation factor 1‐alpha F2, wingless) and one mitochondrial gene (cytochrome oxidase I) indicate that this genus is polyphyletic. Although the majority of Prenolepis species was found to belong to the same monophyletic group (Prenolepis sensu stricto), a smaller subset of Prenolepis species, all found in either Central America or the Greater Antilles, was robustly inferred to comprise a distinct lineage that is sister to the Old World genus Paraparatrechina. Here we describe this newly discovered lineage within the larger Prenolepis genus‐group clade. The genus Zatania, gen.n. is composed of five extant species (Zatania albimaculata, Zatania cisipa, Zatania gibberosa, Zatania gloriosa, sp.n. and Zatania karstica) and one Dominican amber fossil species (Zatania electra^?, sp.n. ). These are medium‐sized ants (generally between 2.5 and 3 mm in total length) that are characterized by having long scapes and legs, and elongated mesosomata. A reliance on worker‐based taxonomy has previously prevented the discovery of this new lineage because of worker convergence consisting of various combinations of elongated mesosomata, long scapes and legs, and a constriction immediately behind the pronotum, observed in several distinct lineages within the Prenolepis genus‐group. However, we did find that male morphology complements our molecular results in revealing important diagnostic and potentially phylogenetically informative characters. Our study highlights the value for ant systematics to expand beyond its traditional foundation of worker‐based morphology and embrace character systems from other castes and molecular data.     

Heterologous expression of bacteriocin E-760 in Chlamydomonas reinhardtii and functional analysis

The use of antimicrobial peptides (AMPs) synthesized by bacteria (bacteriocins) is an alternative for combating multidrug resistant bacterial strains and their production by recombinant route is a viable option for their mass production. The bacteriocin E-760 isolated from the genus Enterococcus sp. has been shown to possess inhibitory activity against Gram-negative and Gram-positive bacteria. In this study, the expression of a chimeric protein coding for E-760 in the nucleus of C. reinhardtii was evaluated, as well as, its antibacterial activity. The synthetic gene E-760S was inserted into the genome of C. reinhardtii using Agrobacterium tumefaciens. A transgenic line was identified in TAP medium with hygromycin and also by PCR. The increment in the culture medium temperature of the transgenic strain at 35 °C for 10 minutes, increased the production level of the recombinant protein from 0.14 (Noninduced culture, NIC) to 0.36% (Induced culture, IC) of total soluble proteins (TSP); this was quantified by an ELISA assay. Recombinant E-760 possesses activity against Staphylococcus aureus in 0.34 U log, Streptococcus agalactiae in 0.48 U log, Enterococcus faecium in 0.36 U log, Pseudomonas aeruginosa in 2 U log and for Klebsiella pneumoniae, the activity was 0.07 U log. These results demonstrate that the nucleus transformation of C. reinhardtii can function as a stable expression platform for the production of the synthetic gene E-760 and it can potentially be used as an antibacterial agent.