Revisiting the Waxy Locus and the Capsicum annuum L. Complex

Waxy locus introns from 35 accessions of the species comprising the Cap­sicum annuum complex [C. annuum (7), C. frutescens (10), and C. chinense (11)1, C. baccatum (5), C. chacoense (1) and C. pubescens (1) were cloned and sequenced. These data were combined with existing GenBank waxy intron data on these same species, C. tovarii, C. ciliatum, Lycianthes heteroclita, L. lenta, and L. glandulosa in order to examine the phyloge­netic relationships within this group of plant materials, and to re-examine the strength of the delimitation of the members of the C. annuum complex provided previously by analysis of indel and transition/transversion poly­morphisms at this locus. Included in the subject materials analyzed were genotypes of C. annuum, C. chinense, and C. frutescens that possessed characteristics that were atypical for these respective species. PAUP analy­sis revealed strong support of Capsicum at the genus level. Capsicum ciliatum was the sister species to C. tovarii which was the sister species to a clade containing the five cultivated taxa and C. chacoense. The separation of C. pubescens from other cultivated Capsicum spp. was well supported. The separation of C. annuum from C. chinense and C. frutescens was less strongly supported based on bootstrap values. In contrast, no clear separa­tion of Capsicum chinense from Capsicum frutescens was observed

A Deep learning based food recognition system for lifelog images

In this paper, we propose a deep learning based system for food recognition from personal life archive im- ages. The system first identifies the eating moments based on multi-modal information, then tries to focus and enhance the food images available in these moments, and finally, exploits GoogleNet as the core of the learning process to recognise the food category of the images. Preliminary results, experimenting on the food recognition module of the proposed system, show that the proposed system achieves 95.97% classification accuracy on the food images taken from the personal life archive from several lifeloggers, which potentially can be extended and applied in broader scenarios and for different types of food categories

Phase Structure of Bose - Einstein Condensate in Ultra - Cold Bose Gases

The Bose - Einstein condensation of ultra - cold Bose gases is studied by means of the Cornwall - Jackiw - Tomboulis effective potential approach in the improved double - bubble approximation which preserves the Goldstone theorem. The phase structure of Bose - Einstein condensate associating with two different types of phase transition is systematically investigated. Its main feature is that the symmetry which was broken at zero temperature gets restore at higher temperature

Peanut (Arachis hypogaea) Expressed Sequence Tag Project: Progress and Application

Many plant ESTs have been sequenced as an alternative to whole genome sequences, including peanut because of the genome size and complexity. The US peanut research community had the historic 2004 Atlanta Genomics Workshop and named the EST project as a main priority. As of August 2011, the peanut research community had deposited 252,832 ESTs in the public NCBI EST database, and this resource has been providing the community valuable tools and core foundations for various genome-scale experiments before the whole genome sequencing project. These EST resources have been used for marker development, gene cloning, microarray gene expression and genetic map construction. Certainly, the peanut EST sequence resources have been shown to have a wide range of applications and accomplished its essential role at the time of need. Then the EST project contributes to the second historic event, the Peanut Genome Project 2010 Inaugural Meeting also held in Atlanta where it was decided to sequence the entire peanut genome. After the completion of peanut whole genome sequencing, ESTs or transcriptome will continue to play an important role to fill in knowledge gaps, to identify particular genes and to explore gene function

Characterization of small RNA populations in non-transgenic andaflatoxin-reducing-transformed peanut

Aflatoxin contamination is a major constraint in food production worldwide. In peanut (Arachis hypogaea L.), these toxic and carcinogenic aflatoxins are mainly produced by Aspergillus flavus Link and A. parasiticus Speare. The use of RNA interference (RNAi) is a promising method to reduce or prevent the accumula-tion of aflatoxin in peanut seed. In this study, we performed high-throughput sequencing of small RNApopulations in a control line and in two transformed peanut lines that expressed an inverted repeattargeting five genes involved in the aflatoxin-biosynthesis pathway and that showed up to 100% less aflatoxin B1 than the controls. The objective was to determine the putative involvement of the smallRNA populations in aflatoxin reduction. In total, 41 known microRNA (miRNA) families and many novel miRNAs were identified. Among those, 89 known and 10 novel miRNAs were differentially expressed in the transformed lines. We furthermore found two small interfering RNAs derived from the inverted repeat, and 39 sRNAs that mapped without mismatches to the genome of A. flavus and were present only in the transformed lines. This information will increase our understanding of the effectiveness of RNAi and enable the possible improvement of the RNAi technology for the control of aflatoxins

Peanut gene expression profiling in developing seeds at different reproduction stages during Aspergillus parasiticus infection

<p>Abstract</p> <p>Background</p> <p>Peanut (<it>Arachis hypogaea </it>L.) is an important crop economically and nutritionally, and is one of the most susceptible host crops to colonization of <it>Aspergillus parasiticus </it>and subsequent aflatoxin contamination. Knowledge from molecular genetic studies could help to devise strategies in alleviating this problem; however, few peanut DNA sequences are available in the public database. In order to understand the molecular basis of host resistance to aflatoxin contamination, a large-scale project was conducted to generate expressed sequence tags (ESTs) from developing seeds to identify resistance-related genes involved in defense response against <it>Aspergillus </it>infection and subsequent aflatoxin contamination.</p> <p>Results</p> <p>We constructed six different cDNA libraries derived from developing peanut seeds at three reproduction stages (R5, R6 and R7) from a resistant and a susceptible cultivated peanut genotypes, 'Tifrunner' (susceptible to <it>Aspergillus </it>infection with higher aflatoxin contamination and resistant to TSWV) and 'GT-C20' (resistant to <it>Aspergillus </it>with reduced aflatoxin contamination and susceptible to TSWV). The developing peanut seed tissues were challenged by <it>A. parasiticus </it>and drought stress in the field. A total of 24,192 randomly selected cDNA clones from six libraries were sequenced. After removing vector sequences and quality trimming, 21,777 high-quality EST sequences were generated. Sequence clustering and assembling resulted in 8,689 unique EST sequences with 1,741 tentative consensus EST sequences (TCs) and 6,948 singleton ESTs. Functional classification was performed according to MIPS functional catalogue criteria. The unique EST sequences were divided into twenty-two categories. A similarity search against the non-redundant protein database available from NCBI indicated that 84.78% of total ESTs showed significant similarity to known proteins, of which 165 genes had been previously reported in peanuts. There were differences in overall expression patterns in different libraries and genotypes. A number of sequences were expressed throughout all of the libraries, representing constitutive expressed sequences. In order to identify resistance-related genes with significantly differential expression, a statistical analysis to estimate the relative abundance (<it>R</it>) was used to compare the relative abundance of each gene transcripts in each cDNA library. Thirty six and forty seven unique EST sequences with threshold of <it>R </it>> 4 from libraries of 'GT-C20' and 'Tifrunner', respectively, were selected for examination of temporal gene expression patterns according to EST frequencies. Nine and eight resistance-related genes with significant up-regulation were obtained in 'GT-C20' and 'Tifrunner' libraries, respectively. Among them, three genes were common in both genotypes. Furthermore, a comparison of our EST sequences with other plant sequences in the TIGR Gene Indices libraries showed that the percentage of peanut EST matched to <it>Arabidopsis thaliana</it>, maize (<it>Zea mays</it>), <it>Medicago truncatula</it>, rapeseed (<it>Brassica napus</it>), rice (<it>Oryza sativa</it>), soybean (<it>Glycine max</it>) and wheat (<it>Triticum aestivum</it>) ESTs ranged from 33.84% to 79.46% with the sequence identity ≥ 80%. These results revealed that peanut ESTs are more closely related to legume species than to cereal crops, and more homologous to dicot than to monocot plant species.</p> <p>Conclusion</p> <p>The developed ESTs can be used to discover novel sequences or genes, to identify resistance-related genes and to detect the differences among alleles or markers between these resistant and susceptible peanut genotypes. Additionally, this large collection of cultivated peanut EST sequences will make it possible to construct microarrays for gene expression studies and for further characterization of host resistance mechanisms. It will be a valuable genomic resource for the peanut community. The 21,777 ESTs have been deposited to the NCBI GenBank database with accession numbers <ext-link ext-link-type="gen" ext-link-id="ES702769">ES702769</ext-link> to <ext-link ext-link-type="gen" ext-link-id="ES724546">ES724546</ext-link>.</p

Development of trinucleotide (GGC)n SSR markers in peanut ( Arachis hypogaea L.)

Cultivated peanut ( Arachis hypogaea L.) is an oilseed crop of economic importance. It is native to South America, and it is grown extensively in the semi-arid tropics of Asia, Africa, and Latin America. Given an extremely narrow genetic base, efforts are being made to develop simple sequence repeat (SSR) markers to provide useful genetic and genomic tools for the peanut research community. A SSR-enriched library to isolate trinucleotide (GGC)n SSRs in peanut was constructed. A total of 143 unique sequences containing (GGC)n repeats were identified. One hundred thirty eight primer pairs were successfully designed at the flanking regions of SSRs. A suitable polymerase was chosen to amplify these GC-rich sequences. Although a low level of polymorphism was observed in cultivated peanut by these new developed SSRs, a high level of transferability to wild species would be beneficial to increasing the number of SSRs in wild species

Synthesis of Gold Nanobipyramids by Seed-mediated Method and Santibacterial Activities

Metallic nanoparticles as antibacterial agents have been studied for several years. The most used antibacterial nanoparticles are silver nanoparticles. The mechanisms and  antibacterial properties of silver nanoparticles are well known, but the effects of gold nanoparticles, especially gold Nano bipyramids, are not considered. In this research, we synthesized gold nanobipyramids (NBPs) by seed mediated method using surfactant cetyltrimethylammonium bromide (CTAB). After preparing, gold nanobipyramids is removed CTAB and modified the surface using polyethylene glycol, polyvinyl alcohol and chitosan as the stabilizers. Besides, antibacterial effects of gold nanobipyramids on both Escherichia coli (Gram negative) and Staphylococcus aureus (Gram positive) are investigated in this paper. The results show that gold nanobipyramids have good antibacterial activities even at low concentration. The optimal concentration of stabilizers and gold nanobipyramids in antibacterial activities are also studied in this paper

Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera)

Aphids are the leading pests in agricultural crops. A large-scale sequencing of 40,904 ESTs from the pea aphid Acyrthosiphon pisum was carried out to define a catalog of 12,082 unique transcripts. A strong AT bias was found, indicating a compositional shift between Drosophila melanogaster and A. pisum. An in silico profiling analysis characterized 135 transcripts specific to pea-aphid tissues (relating to bacteriocytes and parthenogenetic embryos). This project is the first to address the genetics of the Hemiptera and of a hemimetabolous insect.Beatriz Sabater-Muñoz... et al