The North American Plums (<em>Prunus</em> Spp.): A Review of the Taxonomic and Phylogenetic Relationships

North America is a center of diversity for Prunus species. Tree architecture, chilling requirement, heat requirement, fruit development period, fruit size, fruit texture, disease resistance, and adaptive changes to multiple environmental conditions are a few examples of the traits of which tremendous genetic variability is available in the native plum species. Wild native Prunus species constitute an important potential source of genetic diversity for stone fruit breeding and selection. A review of the North American plum taxonomic treatment and phylogenetic studies is described. Various studies have been done with three major groups being identified: Americana series, Chickasaw series, and Beach series

Molecular analysis of capsid protein of Homalodisca coagulata Virus-1, a new leafhopper-infecting virus from the glassy-winged sharpshooter, Homalodisca coagulata

A new virus that infects and causes increased mortality in leafhoppers was isolated from the glassy-winged sharpshooter, Homalodisca coagulata (Say) (Hemiptera: Cicadellidae). The virus, named Homalodisca coagulata virus -1, HoCV-1, was associated with increased mortality of cultured 5th instar H. coagulata. To identify the presence of H. coagulata viral pathogens, cDNA expression libraries were made from adult and nymphs. Analysis using reverse transcriptase PCR demonstrated that the virus was present in midgut tissues. As the viral capsid proteins are commonly used in classification of newly discovered viruses, the capsid proteins (CP) of the virus discovered in H. coagulata was examined. The order of the polyprotein subunits of HoCV-1 capsid proteins was determined to be CP2, CP4, CP3, and CP1. The CP4/CP3 (AFGL/GKPK) cleavage boundary site was clearly identified when the sequences were aligned. The putative CP3/CP1 (ADVQ/SAFA) cleavage site and the putative CP2/CP4 (VTMQ/EQSA) cleavage site of HoCV-1, respectively, were located in the same region as that of the other viruses. After alignment, the CP3/CP1 cleavage sites and CP2/CP4 cleavage sites of the viruses analyzed fell within 50 amino acids of one another. As with the cricket paralysis virus, HoCV-1 was found to be mainly comprised of β-sandwiches in CP1-3 with a jelly roll topological motif. CP4 of HoCV-1 appeared to be mainly α-helical in structure. CP1-4 domains are most homologous to insect picorna-like virus coat proteins as was demonstrated by the results of the BLASTP and PSI-BLAST tests, and is strongly supported by the structural modeling. While sequence homology between the cricket paralysis virus and HoCV-1 was low, the global structure of the proteins was conserved. Sequence identities were analyzed by in silico comparison to known genes in the public database, NCBI. Phylogenetic analysis performed using the optimized protein alignment generated a phylogram containing 5 clades. Clade 1 consisted of Drosophila C virus, Clade 2 consisted of cricket paralysis virus, Clade 3 of Triatoma virus, Plautia stali intestine virus, Himetobi P virus, black queen cell virus, and HoCV-1. Clade 4 encompassed acute bee paralysis virus and Kashmir bee virus, and Clade 5 consisted of Rhopalosiphum padi virus. Analysis of the capsid protein of this new leafhopper virus provided significant evidence that it is related to other ssRNA insect viruses within the Family, Dicistroviridae. The HoCV-1, capsid protein sequence has been deposited in GenBank, Accession number: DQ308403

The zygotic origin of hybrids from Thompson Seedless grape, Vitis vinifera L.

Seedlings from open pollination and controlled crosses of Thompson Seedless were different from the parent in either fruit color, seed size, flavor or isozyme pattern. These results confirm that plants produced by in ovulo embryo culture of Thompson Seedless are usually zygotic in origin. This is a useful tool for producing hybrid plants from stenospermic seedless genotypes, allowing the hybridization of seedless by seedless and permitting many crosses previously unattainable.Die zygotische Herkunft von Hybriden der Rebsorte Thompson Seedless (Vitis vinifera L.)Um die zygotische Herkunft von Nachkommen der stenospermokarpen Sorte Thompson Seedless abzusichern, wurden aus in vitro kultivierten Samenanlagen Pflanzen herangezogen und eine Reihe von Merkmalen analysiert. Die Sämlinge aus unkontrollierter Bestäubung oder aus gezielter Kreuzung von Thompson Seedless unterschieden sich von der Muttersorte entweder in Beerenfarbe, Samengröße, Aroma oder Isoenzymmuster. Diese Befunde bestätigen, daß die durch in vitro-Kultur der Samenanlagen von Thompson Seedless erzeugten Pflanzen in der Regel zygotischen Ursprungs sind. Die Embryokultur aus Samenanlagen ist eine wertvolle Technik zur Erzeugung von Hybriden aus stenospermokarpen Genotypen; sie erlaubt die Kreuzung mit anderen kernlosen Sorten und ermöglicht viele bisher nicht realisierbare Kreuzungskombinationen

Aphid biology: Expressed genes from alate Toxoptera citricida, the brown citrus aphid

The brown citrus aphid, Toxoptera citricida (Kirkaldy), is considered the primary vector of citrus tristeza virus, a severe pathogen which causes losses to citrus industries worldwide. The alate (winged) form of this aphid can readily fly long distances with the wind, thus spreading citrus tristeza virus in citrus growing regions. To better understand the biology of the brown citrus aphid and the emergence of genes expressed during wing development, we undertook a large-scale 5′ end sequencing project of cDNA clones from alate aphids. Similar large-scale expressed sequence tag (EST) sequencing projects from other insects have provided a vehicle for answering biological questions relating to development and physiology. Although there is a growing database in GenBank of ESTs from insects, most are from Drosophila melanogaster and Anopheles gambiae, with relatively few specifically derived from aphids. However, important morphogenetic processes are exclusively associated with piercing-sucking insect development and sap feeding insect metabolism. In this paper, we describe the first public data set of ESTs from the brown citrus aphid, T. citricida. The cDNA library was derived from alate adults due to their significance in spreading viruses (e.g., citrus tristeza virus). Over 5180 cDNA clones were sequenced, resulting in 4263 high-quality ESTs. Contig alignment of these ESTs resulted in 2124 total assembled sequences, including both contiguous sequences and singlets. Approximately 33% of the ESTs currently have no significant match in either the non-redundant protein or nucleic acid databases. Sequences returning matches with an E-value of ≤ −10 using BLASTX, BLASTN, or TBLASTX were annotated based on their putative molecular function and biological process using the Gene Ontology classification system. These data will aid research efforts in the identification of important genes within insects, specifically aphids and other sap feeding insects within the Order Hemiptera. The sequence data described in this paper have been submitted to Genbank's dbEST under the following accession numbers.: CB814527-CB814982, CB832665-CB833296, CB854878-CB855147, CB909714-CB910020, CB936196-CB936346, CD449954-CD450759. Abbreviation: / EST: expressed sequence ta

Visual Similarity Perception of Directed Acyclic Graphs: A Study on Influencing Factors

While visual comparison of directed acyclic graphs (DAGs) is commonly encountered in various disciplines (e.g., finance, biology), knowledge about humans' perception of graph similarity is currently quite limited. By graph similarity perception we mean how humans perceive commonalities and differences in graphs and herewith come to a similarity judgment. As a step toward filling this gap the study reported in this paper strives to identify factors which influence the similarity perception of DAGs. In particular, we conducted a card-sorting study employing a qualitative and quantitative analysis approach to identify 1) groups of DAGs that are perceived as similar by the participants and 2) the reasons behind their choice of groups. Our results suggest that similarity is mainly influenced by the number of levels, the number of nodes on a level, and the overall shape of the graph.Comment: Graph Drawing 2017 - arXiv Version; Keywords: Graphs, Perception, Similarity, Comparison, Visualizatio

Dislocation-induced spatial ordering of InAs quantum dots: Effects on optical properties

Misfit dislocations were used to modify the surface morphology and to attain spatial ordering of quantum dots (QDs) by molecular beam epitaxy. Effects of anneal time and temperature on strain-relaxed InxGa1-xAs/GaAs layers and subsequent spatial ordering of InAs QDs were investigated. Photoluminescence (PL) and time-resolved PL was used to study the effects of increased QD positional ordering, increased QD uniformity, and their proximity to dislocation arrays on their optical properties. Narrower inhomogeneous PL broadening from the QDs ordered on dislocation arrays were observed, and differences in PL dynamics were found. (C) 2002 American Institute of Physics

Correlation Between Anti-TNF Serum Levels and Endoscopic Inflammation in Inflammatory Bowel Disease Patients

Objectives: (a) To evaluate the diagnostic accuracy of anti-TNF trough levels to predict mucosal healing in inflammatory bowel disease (IBD); (b) to determine the best cut-off point to predict mucosal healing in IBD patients treated with anti-TNF. Methods: This is a multicenter, prospective study. IBD patients under anti-TNF treatment for at least 6 months that had to undergo an endoscopy were included. Mucosal healing was defined as: Simple endoscopic score for Crohn’s Disease < 3 for Crohn’s disease (CD), Rutgeerts score < i2 for CD in postoperative setting, or Mayo endoscopic score = 1 for ulcerative colitis (UC). Anti-TNF concentrations were measured using SMART ELISAs at trough. Results: A total of 182 patients were included. Anti-TNF trough levels were significantly higher among patients that had mucosal healing than among those who did not. The area under the curve of infliximab for mucosal healing was 0.63 (best cutoff value 3.4 µg/mL), and for adalimumab 0.60 (best cutoff value 7.2 µg/mL). In the multivariate analysis, having anti-TNF drug levels above the cutoff values [odds ratio (OR) 3.1]) and having UC instead of CD (OR 4) were associated with a higher probability of having mucosal healing. Additionally, the need for an escalated dosage (OR 0.2) and current smoking habit (OR 0.2) were also associated with a lower probability of mucosal healing. Conclusions: There was an association between anti-TNF trough levels and mucosal healing in IBD patients; however, the accuracy of the determination of infliximab and adalimumab concentrations able to predict mucosal healing was suboptimal