Smoke-water effect on the germination of Amazonian tree species

Smoke stimulates seed germination of a range of species from ecosystems that may or may not be fire prone. We evaluated the effects of smoke-water on germination of ten tree species of economic value in the Amazon region. Two materials were burnt to produce smoke-water: germination paper and the wood of Cecropia palmata Willd. Seven dilutions of the solutions were tested. Seeds of nine forest trees were germinated under controlled laboratory conditions (25 °C. ± 2 °C) in the laboratory. Bertholletia excelsa Humb. & Bonpl., was tested in the nursery (approximately 25-36. °C) because of its large seeds. Irrespective of the material burned, smoke-water significantly increased seed germination of three species: Cordia goeldiana Hub., Ochroma pyramidale (Cav. ex Lam.) Urb. and Jacaranda copaia (Aubl.) D. Don. and there was a significant inhibitory effect on Swietenia macrophylla King. Germination was accelerated by smoke in J. copaia, B. excelsa and Bellucia grossularioides (L.) Triana. The most pronounced effect was observed in B. excelsa, as the mean germination time of 108. d (control) was reduced to 76. d with smoke-water made from germination paper (dilution of 1:25) and to 61. d with the one from Cecropia wood (dilution of 1:250). For five of the ten species studied, smoke-water either increased or accelerated seed germination, irrespective of the materials used for its production. Seeds with low vigour and prolonged germination time seemed to be more receptive to smoke. © 2013 South African Association of Botanists

Determination of the physicochemical and microbiological quality of carcass, bone and blood meal

The pH value and the moisture, fat and protein content of abattoir by products which are commercially available in the Republic of South Africa were examined, and the total bacterial count and the extent of Salmonella, Escherichia coli, Bacillus, yeast and fungus contamination were determined. The extremes and reasonably attainable quality standards were deduced from the highest frequency and mean values of these figures. The total bacterial count was not statistically predictable from variables such as pH, moisture, protein and fat, but was found to be related to the combined effect of all 4 independent variables.The articles have been scanned in colour with a HP Scanjet 5590; 300dpi. Adobe Acrobat XI Pro was used to OCR the text and also for the merging and conversion to the final presentation PDF-format

A dual laser scanning confocal and transmission electron microscopy analysis of the intracellular localization, aggregation and particle formation of African horse sickness virus major core protein VP7

The bulk of African horse sickness virus (AHSV) major core protein VP7 self-assembles into flat, hexagonal crystalline particles in a process appearing unrelated to viral replication. Why this unique characteristic of AHSV VP7 is genetically conserved, and whether VP7 aggregation and particle formation have an effect on cellular biology or the viral life cycle, is unknown. Here we investigated how different small peptide and enhanced green fluorescent protein (eGFP) insertions into the VP7 top domain affected VP7 localisation, aggregation and particle formation. This was done using a dual laser scanning confocal and transmission electron microscopy approach in conjunction with analyses of the solubility, aggregation and fluorescence profiles of the proteins. VP7 top domain modifications did not prevent trimerisation, or intracellular trafficking to one or two discrete sites in the cell. However, modifications that resulted in a misfolded and insoluble VP7-eGFP component blocked trafficking, and precluded protein accumulation at a single cellular site, perhaps by interfering with normal trimer-trimer interactions. Furthermore, the modifications disrupted the stable layering of the trimers into characteristic AHSV VP7 crystalline particles. It was concluded that VP7 trafficking is driven by a balance between VP7 solubility, trimer forming ability and trimer-trimer interactions.http://journals.cambridge.org/action/displayJournal?jid=MAM2017-06-30hb2017Genetic

African horse sickness virus NS4 protein is an important virulence factor and interferes with JAK-STAT signaling during viral infection

African horse sickness virus (AHSV) non-structural protein NS4 is a nucleocytoplasmic protein that is expressed in the heart, lung, and spleen of infected horses, binds dsDNA, and colocalizes with promyelocytic leukemia nuclear bodies (PML-NBs). The aim of this study was to investigate the role of AHSV NS4 in viral replication, virulence and the host immune response. Using a reverse genetics-derived virulent strain of AHSV-5 and NS4 deletion mutants, we showed that knockdown of NS4 expression has no impact in cell culture, but results in virus attenuation in infected horses. RNA sequencing (RNA-seq) was used to investigate the transcriptional response in these horses, to see how the lack of NS4 mediates the transition of the virus from virulent to attenuated. The presence of NS4 was shown to result in a 24 hour (h) delay in the transcriptional activation of several immune system processes compared to when the protein was absent. Included in these processes were the RIG-I-like, Toll-like receptor, and JAK-STAT signaling pathways, which are key pathways involved in innate immunity and the antiviral response. Thus, it was shown that AHSV NS4 suppresses the host innate immune transcriptional response in the early stages of the infection cycle. We investigated whether AHSV NS4 affects the innate immune response by impacting the JAK-STAT signaling pathway specifically. Using confocal laser scanning microscopy (CLSM) we showed that AHSV NS4 disrupts JAK-STAT signaling by interfering with the phosphorylation and/or translocation of STAT1 and pSTAT1 into the nucleus. Overall, these results showed that AHSV NS4 is a key virulence factor in horses and allows AHSV to overcome host antiviral responses in order to promote viral replication and spread.SUPPLEMENTARY MATERIAL: Supplementary table 1: Full list of differentially expressed genes in the transcriptome analysis. The genes were sorted according to log2Fold change values and then grouped according to up- or down-regulated genes. Days 1, 2 and 4 are presented for the horse inoculated with rAHSV-5 (NS4) and days 1 and 2 for the horses inoculated with rAHSV-5minNS4 (minNS4). The log2FC is indicated in bold for genes differentially expressed on the same day in both NS4 and minNS4. aRanks of up- or down-regulated genes in each comparison. *Involved in innate immunity according to InnateDB.Supplementary table 2: Full list of KEGG pathways enriched by the differentially expressed genes in the transcriptome analysis. The data is displayed per day and includes the up- and down- regulated genes enriching each pathway. Pathways were sorted based on corrected P-value. Days 1, 2 and 4 are presented for the horse inoculated with rAHSV-5 (NS4) and days 1 and 2 for the horses inoculated with rAHSV-5minNS4 (minNS4).Supplementary Figure 1: Images obtained from post-mortem examination of horses inoculated with rAHSV-5. Classical lesions of disease such as frothing from the nostrils (a), interstitial and subpleural lung edema (b, e), alveolar edema (c, f) and hydropericardium (d, g) were observed.Deltamune (Pty) Ltd, the University of Pretoria Institutional Research Themes, the Poliomyelitis Research Foundation, South Africa and the Genomics Research Institute, University of Pretoria. Postgraduate support was received from the Poliomyelitis Research Foundation, South Africa, the National Research Foundation, South Africa and the University of Pretoria, South Africa.http://www.elsevier.com/locate/virusreshj2022BiochemistryGeneticsMicrobiology and Plant Patholog

Revival of the magnetar PSR J1622-4950: observations with MeerKAT, Parkes, XMM-Newton, Swift, Chandra, and NuSTAR

New radio (MeerKAT and Parkes) and X-ray (XMM-Newton, Swift, Chandra, and NuSTAR) observations of PSR J1622-4950 indicate that the magnetar, in a quiescent state since at least early 2015, reactivated between 2017 March 19 and April 5. The radio flux density, while variable, is approximately 100x larger than during its dormant state. The X-ray flux one month after reactivation was at least 800x larger than during quiescence, and has been decaying exponentially on a 111+/-19 day timescale. This high-flux state, together with a radio-derived rotational ephemeris, enabled for the first time the detection of X-ray pulsations for this magnetar. At 5%, the 0.3-6 keV pulsed fraction is comparable to the smallest observed for magnetars. The overall pulsar geometry inferred from polarized radio emission appears to be broadly consistent with that determined 6-8 years earlier. However, rotating vector model fits suggest that we are now seeing radio emission from a different location in the magnetosphere than previously. This indicates a novel way in which radio emission from magnetars can differ from that of ordinary pulsars. The torque on the neutron star is varying rapidly and unsteadily, as is common for magnetars following outburst, having changed by a factor of 7 within six months of reactivation.Comment: Published in ApJ (2018 April 5); 13 pages, 4 figure

Inferring Binding Energies from Selected Binding Sites

We employ a biophysical model that accounts for the non-linear relationship between binding energy and the statistics of selected binding sites. The model includes the chemical potential of the transcription factor, non-specific binding affinity of the protein for DNA, as well as sequence-specific parameters that may include non-independent contributions of bases to the interaction. We obtain maximum likelihood estimates for all of the parameters and compare the results to standard probabilistic methods of parameter estimation. On simulated data, where the true energy model is known and samples are generated with a variety of parameter values, we show that our method returns much more accurate estimates of the true parameters and much better predictions of the selected binding site distributions. We also introduce a new high-throughput SELEX (HT-SELEX) procedure to determine the binding specificity of a transcription factor in which the initial randomized library and the selected sites are sequenced with next generation methods that return hundreds of thousands of sites. We show that after a single round of selection our method can estimate binding parameters that give very good fits to the selected site distributions, much better than standard motif identification algorithms

Identification of Hyaloperonospora arabidopsidis Transcript Sequences Expressed during Infection Reveals Isolate-Specific Effectors

Biotrophic plant pathogens secrete effector proteins that are important for infection of the host. The aim of this study was to identify effectors of the downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa) that are expressed during infection of its natural host Arabidopsis thaliana. Infection-related transcripts were identified from Expressed Sequence Tags (ESTs) derived from leaves of the susceptible Arabidopsis Ws eds1-1 mutant inoculated with the highly virulent Hpa isolate Waco9. Assembly of 6364 ESTs yielded 3729 unigenes, of which 2164 were Hpa-derived. From the translated Hpa unigenes, 198 predicted secreted proteins were identified. Of these, 75 were found to be Hpa-specific and six isolate Waco9-specific. Among 42 putative effectors identified there were three Elicitin-like proteins, 16 Cysteine-rich proteins and 18 host-translocated RXLR effectors. Sequencing of alleles in different Hpa isolates revealed that five RXLR genes show signatures of diversifying selection. Thus, EST analysis of Hpa-infected Arabidopsis is proving to be a powerful method for identifying pathogen effector candidates expressed during infection. Delivery of the Waco9-specific protein RXLR29 in planta revealed that this effector can suppress PAMP-triggered immunity and enhance disease susceptibility. We propose that differences in host colonization can be conditioned by isolate-specific effectors

Rate accelerations in nuclear 18S rDNA of mycoheterotrophic and parasitic angiosperms

Rate variation in genes from all three genomes has been observed frequently in plant lineages with a parasitic and mycoheterotrophic mode of life. While the loss of photosynthetic ability leads to a relaxation of evolutionary constraints in genes involved in the photosynthetic apparatus, it remains to be determined how prevalent increased substitution rates are in nuclear DNA of non-photosynthetic angiosperms. In this study we infer rates of molecular evolution of 18S rDNA of all parasitic and mycoheterotorphic plant families (except Lauraceae and Polygalaceae) using relative rate tests. In several holoparasitic and mycoheterotrophic plant lineages extremely high substitution rates are observed compared to other photosynthetic angiosperms. The position and frequency of these substitutions have been identified to understand the mutation dynamics of 18S rRNA in achlorophyllous plants. Despite the presence of significantly elevated substitution rates, very few mutations occur in major functional and structural regions of the small ribosomal molecule, providing evidence that the efficiency of the translational apparatus in non-photosynthetic plants has not been affected

Interaction of plant growth regulators and reactive oxygen species to regulate petal senescence in wallflowers (Erysimum linifolium)

Background In many species floral senescence is coordinated by ethylene. Endogenous levels rise, and exogenous application accelerates senescence. Furthermore, floral senescence is often associated with increased reactive oxygen species, and is delayed by exogenously applied cytokinin. However, how these processes are linked remains largely unresolved. Erysimum linifolium (wallflower) provides an excellent model for understanding these interactions due to its easily staged flowers and close taxonomic relationship to Arabidopsis. This has facilitated microarray analysis of gene expression during petal senescence and provided gene markers for following the effects of treatments on different regulatory pathways. Results In detached Erysimum linifolium (wallflower) flowers ethylene production peaks in open flowers. Furthermore senescence is delayed by treatments with the ethylene signalling inhibitor silver thiosulphate, and accelerated with ethylene released by 2-chloroethylphosphonic acid. Both treatments with exogenous cytokinin, or 6-methyl purine (which is an inhibitor of cytokinin oxidase), delay petal senescence. However, treatment with cytokinin also increases ethylene biosynthesis. Despite the similar effects on senescence, transcript abundance of gene markers is affected differentially by the treatments. A significant rise in transcript abundance of WLS73 (a putative aminocyclopropanecarboxylate oxidase) was abolished by cytokinin or 6-methyl purine treatments. In contrast, WFSAG12 transcript (a senescence marker) continued to accumulate significantly, albeit at a reduced rate. Silver thiosulphate suppressed the increase in transcript abundance both of WFSAG12 and WLS73. Activity of reactive oxygen species scavenging enzymes changed during senescence. Treatments that increased cytokinin levels, or inhibited ethylene action, reduced accumulation of hydrogen peroxide. Furthermore, although auxin levels rose with senescence, treatments that delayed early senescence did not affect transcript abundance of WPS46, an auxin-induced gene. Conclusions A model for the interaction between cytokinins, ethylene, reactive oxygen species and auxin in the regulation of floral senescence in wallflowers is proposed. The combined increase in ethylene and reduction in cytokinin triggers the initiation of senescence and these two plant growth regulators directly or indirectly result in increased reactive oxygen species levels. A fall in conjugated auxin and/or the total auxin pool eventually triggers abscission