Optimal window period for mapping Parthenium weed in South Africa,using high temporal resolution imagery and the ExtraTrees classifier

Parthenium weed (Parthenium hysterophorus) is one of the most noxious herbaceous weeds in the world with adverse impacts on among others animal and human health, crop production, the environment, local as well as national economies. To optimize Parthenium mitigation, it is necessary to accurately monitor its spread using earth observation data. However, one of the challenges of mapping Parthenium weed is that its spectral response is similar to that of surrounding herbaceous plant species, resulting in low classification accuracies. Due to variability in its phenological characteristics and associated species, determining differences within the growing season may optimize the discrimination and subsequent mapping of the Parthenium weed. However, determination of the window(s) with the most prominent variability has been overlooked in past studies. Furthermore, no specific algorithm has been determined to be efficient in finding such window(s). ExtraTrees (EXT), an underused classifier in earth observation studies, possess interesting properties for satellite image processing such as high speed and performance. In this regard, this study attempted to (1) determine the optimal window period for discriminating Parthenium weed from coexisting plant species and (2) to compare the performance of EXT and the random forest (RF) algorithms. Results showed that the beginning of February was the optimal period for mapping Parthenium weed, with overall accuracy of 88.1%. EXT outperformed RF for most of the dates. This study lays the foundation for optimizing earth observation data derived models for characterizing invasive species, leveraging on the high temporal resolution of the new generation sensors.

     

Analysis of plastid DNA-like sequences within the nuclear genomes of higher plants

A wide-ranging examination of plastid (pt)DNA sequence homologies within higher plant nuclear genomes (promiscuous DNA) was undertaken. Digestion with methylation-sensitive restriction enzymes and Southern analysis was used to distinguish plastid and nuclear DNA in order to assess the extent of variability of promiscuous sequences within and between plant species. Some species, such as Gossypium hirsutum (cotton), Nicotiana tabacum (tobacco), and Chenopodium quinoa, showed homogenity of these sequences, while intraspecific sequence variation was observed among different cultivars of Pisum sativum (pea), Hordeum vulgare (barley), and Triticum aestivum (wheat). Hypervariability of plastid sequence homologies was identified in the nuclear genomes of Spinacea oleracea (spinach) and Beta vulgaris (beet), in which individual plants were shown to possess a unique spectrum of nuclear sequences with ptDNA homology. This hypervariability apparently extended to somatic variation in B. vulgaris. No sequences with ptDNA homology were identified by this method in the nuclear genome of Arabidopsis thaliana.      

Phylogeny of Greya (Lepidoptera: Prodoxidae), based on nucleotide sequence variation in mitochondrial cytochrome oxidase I and II: congruence with morphological data

The phylogeny of Greya Busck (Lepidoptera: Prodoxidae) was inferred from nucleotide sequence variation across a 765-bp region in the cytochrome oxidase I and II genes of the mitochondrial genome. Most parsimonious relationships of 25 haplotypes from 16 Greya species and two outgroup genera (Tetragma and Prodoxus) showed substantial congruence with the species relationships indicated by morphological variation. Differences between mitochondrial and morphological trees were found primarily in the positions of two species, G. variabilis and G. pectinifera, and in the branching order of the three major species groups in the genus. Conflicts between the data sets were examined by comparing levels of homoplasy in characters supporting alternative hypotheses. The phylogeny of Greya species suggests that host-plant association at the family level and larval feeding mode are conservative characters. Transition/transversion ratios estimated by reconstruction of nucleotide substitutions on the phylogeny had a range of 2.0-9.3, when different subsets of the phylogeny were used. The decline of this ratio with the increase in maximum sequence divergence among taxa indicates that transitions are masked by transversions along deeper internodes or long branches of the phylogeny. Among transitions, substitutions of A-->G and T-->C outnumbered their reciprocal substitutions by 2-6 times, presumably because of the approximately 4:1 (77%) A+T-bias in nucleotide base composition. Of all transversions, 73%-80% were A<-->T substitutions, 85% of which occurred at third positions of codons; these estimates did not decrease with an increase in maximum sequence divergence of taxa included in the analysis. The high frequency of A<-->T substitutions is either a reflection or an explanation of the 92% A+T bias at third codon positions.      

Explaining grass-nutrient patterns in a savanna rangeland of southern Africa

Aim The search for possible factors influencing the spatial variation of grass quality is an important step towards understanding the distribution of herbivores, as well as a step towards identifying crucial areas for conservation and restoration. A number of studies have shown that grass quality at a regional scale is influenced by climatic variables. At a local scale, site factors and their interaction are considered important. In this study, we aimed at examining environmental correlates of grass quality at a local scale. The study also sought to establish if biotic factors interact significantly with abiotic factors in influencing a variation in grass quality. Location The study area is located in the Kruger National Park of South Africa. The study area stretches from west (22°49′ S and 31°01′ E) to east, (22°44′ S and 31°22′ E) covering an area of about 25 × 6 km in the far northern region of the Kruger National Park. Methods We collected environmental data such as soil texture, percentage grass cover and biomass as well as grass samples for chemical analysis from specific locations in the study area. In addition, a digital elevation model (DEM) with a resolution of 5 m was used to derive elevation, slope and aspect using a geographic information system (GIS), which were related to grass quality. We used correlation analysis and anova to relate environmental variables to grass quality. Multivariate analysis techniques were used to simultaneously analyse and explore the complex interactions between variables. Results and conclusions Our results indicate that there is a significant relationship between grass quality parameters and site‐specific factors such as slope, altitude, percentage grass cover, aspect and soil texture. Relatively, percentage grass cover and soil texture were more critical in explaining a variation in grass quality. Plant characteristics such as species type interact significantly with slope, altitude and geology in influencing nutrient distribution. The results of this study may give a better insight on foliar nutrient distribution patterns at a landscape scale in savanna rangelands. Furthermore, the results of this study may help in the selection of ancillary information, which could be used in conjunction with other data such as remotely sensed data to map grass quality – an important step towards understanding the distribution and feeding patterns of wildlife. However, we acknowledge that this study is based on one seasonal snapshot, therefore some slightly different findings may be obtained during other times of the year. Nevertheless, the study has revealed that under the conditions experienced during the study period, nutrient distribution varies with varying biotic and abiotic factors.     

Late immature mortality is the major influence on reproductive success of African black beetle, Heteronychus arator (Fabricius) (Coleoptera: Scarabaeidae), in a Mediterranean-climate region of Australia

In field and laboratory studies, mortality of African black beetle, Heteronychus arator, in the winter-rainfall, Mediterranean-type climate region of south-western Australia was higher in the late immature stages during summer than in the early immature stages that occur during spring, a contrast to summer-rainfall climatic regions. Greatest mortality occurred around the pupal stage in contrasting soil types, despite drying differences in summer and supplementary watering in some plots. Sampling of natural populations confirmed experimental results that mortality in late immature stages is the major factor limiting H. arator populations under a Mediterranean-type climate. Inter-generation increase in H. arator abundance was uncommon, explaining the consistent abundance typically observed between years in south-western Australia. Random dispersal of newly emerged adults in autumn was inferred to restore uniformity in adult abundance between areas of varying favourability for immature survival.     

Multispectral and hyperspectral remote sensing for identification and mapping of wetland vegetation: a review

Wetland vegetation plays a key role in the ecological functions of wetland environments. Remote sensing techniques offer timely, up-to-date, and relatively accurate information for sustainable and effective management of wetland vegetation. This article provides an overview on the status of remote sensing applications in discriminating and mapping wetland vegetation, and estimating some of the biochemical and biophysical parameters of wetland vegetation. Research needs for successful applications of remote sensing in wetland vegetation mapping and the major challenges are also discussed. The review focuses on providing fundamental information relating to the spectral characteristics of wetland vegetation, discriminating wetland vegetation using broad- and narrow-bands, as well as estimating water content, biomass, and leaf area index. It can be concluded that the remote sensing of wetland vegetation has some particular challenges that require careful consideration in order to obtain successful results. These include an in-depth understanding of the factors affecting the interaction between electromagnetic radiation and wetland vegetation in a particular environment, selecting appropriate spatial and spectral resolution as well as suitable processing techniques for extracting spectral information of wetland vegetation.     

BRCT domains: Easy as one,two, three

BRCA1 C-terminal (BRCT) domains are integral signaling modules in the DNA damage response (DDR). Aside from their established roles as phospho-peptide binding modules, BRCT domains have been implicated in phosphorylation-independent protein interactions, DNA binding and poly(ADP-ribose) (PAR) binding. These numerous functions can be attributed to the diversity in BRCT domain structure and architecture, where domains can exist as isolated single domains or assemble into higher order homo- or hetero-domain complexes. In this review, we incorporate recent structural and biochemical studies to demonstrate how structural features allow single and tandem BRCT domains to attain a high degree of functional diversity.Key words: BRCT domain, DNA repair, phosphorylation, phospho-peptide interaction, protein interaction, DNA binding, DNA damage response     

Metabolic footprint of epiphytic bacteria on Arabidopsis thaliana leaves

The phyllosphere, which is defined as the parts of terrestrial plants above the ground, is a large habitat for different microorganisms that show a high extent of adaption to their environment. A number of hypotheses were generated by culture-independent functional genomics studies to explain the competitiveness of specialized bacteria in the phyllosphere. In contrast, in situ data at the metabolome level as a function of bacterial colonization are lacking. Here, we aimed to obtain new insights into the metabolic interplay between host and epiphytes upon colonization of Arabidopsis thaliana leaves in a controlled laboratory setting using environmental metabolomics approaches. Quantitative nuclear magnetic resonance (NMR) and imaging high-resolution mass spectrometry (IMS) methods were used to identify Arabidopsis leaf surface compounds and their possible involvement in the epiphytic lifestyle by relative changes in compound pools. The dominant carbohydrates on the leaf surfaces were sucrose, fructose and glucose. These sugars were significantly and specifically altered after epiphytic leaf colonization by the organoheterotroph Sphingomonas melonis or the phytopathogen Pseudomonas syringae pv. tomato, but only to a minor extent by the methylotroph Methylobacterium extorquens. In addition to carbohydrates, IMS revealed surprising alterations in arginine metabolism and phytoalexin biosynthesis that were dependent on the presence of bacteria, which might reflect the consequences of bacterial activity and the recognition of not only pathogens but also commensals by the plant. These results highlight the power of environmental metabolomics to aid in elucidating the molecular basis underlying plant–epiphyte interactions in situ.     

Identification of genes differentially expressed in dorsal and ventral chick midbrain during early Development

Background  

During the development of the central nervous system (CNS), patterning processes along the dorsoventral (DV) axis of the neural tube generate different neuronal subtypes. As development progresses these neurons are arranged into functional units with varying cytoarchitecture, such as laminae or nuclei for efficient relaying of information. Early in development ventral and dorsal regions are similar in size and structure. Different proliferation rates and cell migration patterns are likely to result in the formation of laminae or nuclei, eventually. However, the underlying molecular mechanisms that establish these different structural arrangements are not well understood.