Aphids (Hemiptera,Aphididae) on ornamental plants in greenhouses in Bulgaria

Investigations on the species composition and host range of aphids on ornamental greenhouse plants in Bulgaria was conducted over a period of five years, from 2008 to 2012. Twenty greenhouses, growing ornamentals for landscaping, plant collections and other purposes were observed. They were located in the regions of Sofia, Plovdiv, Smolyan, Pavlikeni, Varna and Burgas. The total number of collected aphid samples was 279. Their composition included 33 aphid species and one subspecies from 13 genera and 5 subfamilies. Twenty-eight species were found to belong to subfamily Aphidinae. Almost 70 % of all recorded species were polyphagous. The most widespread aphid species was Myzus persicae, detected in 13 greenhouses all year round, followed by Aulacorthum solani (10 greenhouses) and Aphis gossypii (9 greenhouses). The widest host range was shown by Myzus persicae (43 hosts), Aulacorthum solani (32 hosts) and Aulacorthum circumflexum (23 hosts).The list of host plants includes 114 species from 95 genera and 58 families. The greatest variety of aphid species was detected on Hibiscus (9 species). Out of all aphid samples 12.9 % were collected on Hibiscus and 6.8 %, on Dendranthema. The greatest variety of aphid species was detected on Hibiscus (9 species).Periphyllus californiensis and Aphis (Aphis) fabae mordvilkoi are reported for the first time for Bulgaria. Furthermore, Aphis spiraecola has been found in new localities and has widened its host range in this country.     

Census-based rapid and accurate metagenome taxonomic profiling

Background

Understanding the taxonomic composition of a sample, whether from patient, food or environment, is important to several types of studies including pathogen diagnostics, epidemiological studies, biodiversity analysis and food quality regulation. With the decreasing costs of sequencing, metagenomic data is quickly becoming the preferred typed of data for such analysis.

Results

Rapidly defining the taxonomic composition (both taxonomic profile and relative frequency) in a metagenomic sequence dataset is challenging because the task of mapping millions of sequence reads from a metagenomic study to a non-redundant nucleotide database such as the NCBI non-redundant nucleotide database (nt) is a computationally intensive task. We have developed a robust subsampling-based algorithm implemented in a tool called CensuScope meant to take a ‘sneak peak’ into the population distribution and estimate taxonomic composition as if a census was taken of the metagenomic landscape. CensuScope is a rapid and accurate metagenome taxonomic profiling tool that randomly extracts a small number of reads (based on user input) and maps them to NCBI’s nt database. This process is repeated multiple times to ascertain the taxonomic composition that is found in majority of the iterations, thereby providing a robust estimate of the population and measures of the accuracy for the results.

Conclusion

CensuScope can be run on a laptop or on a high-performance computer. Based on our analysis we are able to provide some recommendations in terms of the number of sequence reads to analyze and the number of iterations to use. For example, to quantify taxonomic groups present in the sample at a level of 1% or higher a subsampling size of 250 random reads with 50 iterations yields a statistical power of >99%. Windows and UNIX versions of CensuScope are available for download at https://hive.biochemistry.gwu.edu/dna.cgi?cmd=censuscope. CensuScope is also available through the High-performance Integrated Virtual Environment (HIVE) and can be used in conjunction with other HIVE analysis and visualization tools.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-918) contains supplementary material, which is available to authorized users.     

Study on the Spatial Architecture of p53, MDM2, and p14ARF Containing Complexes

We have developed a surface plasmon resonance (SPR)-based immunocapture approach to study multimeric protein–protein complexes. A composition and spatial architecture of protein complexes that contained GST-tagged p53, p14ARF, and MDM2 was examined by the developed approach. Obtained results verified that the p53 protein possesses two binding sites for MDM2. Ternary complexes containing p14ARF, MDM2, and p53 proteins could only be formed when MDM2 protein functions as a bridging molecule. That was confirmed by immunoprecipitation and immunostaining. Andrej Savchenko and Mariya Yurchenko have contributed equally to this article.     

Paraffin-Embedded and Frozen Sections of Drosophila Adult Muscles

The molecular characterization of muscular dystrophies and myopathies in humans has revealed the complexity of muscle disease and genetic analysis of muscle specification, formation and function in model systems has provided valuable insight into muscle physiology. Therefore, identifying and characterizing molecular mechanisms that underlie muscle damage is critical. The structure of adult Drosophila multi-fiber muscles resemble vertebrate striated muscles ¹ and the genetic tractability of Drosophila has made it a great system to analyze dystrophic muscle morphology and characterize the processes affecting muscular function in ageing adult flies ². Here we present the histological technique for preparing paraffin-embedded and frozen sections of Drosophila thoracic muscles. These preparations allow for the tissue to be stained with classical histological stains and labeled with protein detecting dyes, and specifically cryosections are ideal for immunohistochemical detection of proteins in intact muscles. This allows for analysis of muscle tissue structure, identification of morphological defects, and detection of the expression pattern for muscle/neuron-specific proteins in Drosophila adult muscles. These techniques can also be slightly modified for sectioning of other body parts.     

Expression of ipt gene controlled by an ethylene and auxin responsive fragment of the LEACO1 promoter increases flower number in transgenic Nicotiana tabacum

Cytokinins play important roles in regulating plant growth and development. A new genetic construct for regulating cytokinin content in plant cells was cloned and tested. The gene coding for isopentenyl transferase (ipt) was placed under the control of a 0.821 kb fragment of the 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase gene promoter from Lycopersicon esculentum (LEACO1) and introduced into Nicotiana tabacum (cv. Havana). Some LEACO1_{0.821 kb}-ipt transgenic plant lines displayed normal shoot morphology but with a dramatic increase in the number of flower buds compared to nontransgenic plants. Other transgenic lines produced excessive lateral branch development but no change in flower bud number. Isolated leaves of transgenic tobacco plants showed a significantly prolonged retention of chlorophyll under dark incubation (25°C for 20 days). Leaves of nontransformed plants senesced gradually under the same conditions. Experiments with LEACO1_{0.821 kb}-gus transgenic tobacco plants suggested auxin and ethylene involvement in induction of LEACO1_{0.821 kb} promoter activity. Multiple copies of nucleotide base sequences associated with either ethylene or auxin response elements were identified in the LEACO1_{0.821 kb} promoter fragment. The LEACO1_{0.821 kb}-ipt fusion gene appears to have potential utility for improving certain ornamental and agricultural crop species by increasing flower bud initiation and altering branching habit.     

Enhanced cold tolerance in transgenic tobacco expressing a chloroplast ω-3 fatty acid desaturase gene under the control of a cold-inducible promoter

A new cold-inducible genetic construct was cloned using a chloroplast-specific omega-3-fatty acid desaturase gene (FAD7) under the control of a cold-inducible promoter (cor15a) from Arabidopsis thaliana. RT-PCR confirmed a marked increase in FAD7 expression, in young Nicotiana tabacum (cv. Havana) plants harboring cor15a–FAD7, after a short-term exposure to cold. When young, cold-induced tobacco seedlings were exposed to low-temperature (0.5, 2 or 3.5°C) for up to 44 days, survival within independent cor15a–FAD7 transgenic lines (40.2–96%) was far superior to the wild type (6.7–10.2%). In addition, the major trienoic fatty acid species remained stable in cold-induced cor15a–FAD7 N. tabacum plants under prolonged cold storage while the levels of hexadecatrienoic acid (16:3) and octadecatrienoic acid (18:3) declined in wild type plants under the same conditions (79 and 20.7% respectively). Electron microscopy showed that chloroplast membrane ultrastructure in cor15a–FAD7 transgenic plants was unaffected by prolonged exposure to cold temperatures. In contrast, wild type plants experienced a loss of granal stacking and disorganization of the thylakoid membrane under the same conditions. Changes in membrane integrity coincided with a precipitous decline in leaf chlorophyll concentration and low survival rates in wild type plants. Cold-induced double transgenic N. alata (cv. Domino Mix) plants, harboring both the cor15a–FAD7 cold-tolerance gene and a cor15a–IPT dark-tolerance gene, exhibited dramatically higher survival rates (89–90%) than wild type plants (2%) under prolonged cold storage under dark conditions (2°C for 50 days).     

A point mutation in the photosystem I P700 chlorophyll a apoprotein A1 gene confers variegation in Helianthus annuus L

Plant Molecular Biology - CRISPR-edited variants at the 3′-end of OsLOGL5's coding sequence (CDS), significantly increased rice grain yield under well-watered, drought, normal nitrogen,...     

ALDH1-High Ovarian Cancer Stem-Like Cells Can Be Isolated from Serous and Clear Cell Adenocarcinoma Cells,and ALDH1 High Expression Is Associated with Poor Prognosis

Cancer stem-like cells (CSCs)/cancer-initiating cells (CICs) are defined as a small population of cancer cells that have high tumorigenicity. Furthermore, CSCs/CICs are resistant to several cancer therapies, and CSCs/CICs are therefore thought to be responsible for cancer recurrence after treatment and distant metastasis. In epithelial ovarian cancer (EOC) cases, disease recurrence after chemotherapy is frequently observed, suggesting ovarian CSCs/CICs are involved. There are four major histological subtypes in EOC, and serous adenocarcinoma and clear cell adenocarcinoma are high-grade malignancies. We therefore analyzed ovarian CSCs/CICs from ovarian carcinoma cell lines (serous adenocarcinoma and clear cell adenocarcinoma) and primary ovarian cancer cells in this study. We isolated ovarian CSCs/CICs as an aldehyde dehydrogenase 1 high (ALDH1^high) population from 6 EOC cell lines (3 serous adenocarcinomas and 3 clear cell adenocarcinomas) by the ALDEFLUOR assay. ALDH1^high cells showed greater sphere-forming ability, higher tumorigenicity and greater invasive capability, indicating that ovarian CSCs/CICs are enriched in ALDH1^high cells. ALDH1^high cells could also be isolated from 8 of 11 primary ovarian carcinoma samples. Immunohistochemical staining revealed that higher ALDH1 expression levels in ovary cancer cases are related to poorer prognosis in both serous adenocarcinoma cases and clear cell adenocarcinoma cases. Taken together, the results indicate that ALDH1 is a marker for ovarian CSCs/CICs and that the expression level of ALDH1 might be a novel biomarker for prediction of poor prognosis.     

Enhanced zinc uptake by rice through phytosiderophore secretion: a modelling study

Rice (Oryza sativa L.) secretes far smaller amounts of metal-complexing phytosiderophores (PS) than other grasses. But there is increasing evidence that it relies on PS secretion for its zinc (Zn) uptake. After nitrogen, Zn deficiency is the most common nutrient disorder in rice, affecting up to 50% of lowland rice soils globally. We developed a mathematical model of PS secretion from roots and resulting solubilization and uptake of Zn, allowing for root growth, diurnal variation in secretion, decomposition of the PS in the soil, and the transport and interaction of the PS and Zn in the soil. A sensitivity analysis showed that with realistic parameter values for rice in submerged soil, the typically observed rates of PS secretion from rice are sufficient and necessary to explain observed rates of Zn uptake. There is little effect of diurnal variation in secretion on cumulative Zn uptake, irrespective of other model parameter values, indicating that the observed diurnal variation is not causally related to Zn uptake efficiency. Rooting density has a large effect on uptake per unit PS secretion as a result of overlap of the zones of influence of neighbouring roots. The effects of other complications in the rice rhizosphere are discussed.