An overview of the Phalaenopsis orchid genome through BAC end sequence analysis

<p>Abstract</p> <p>Background</p> <p><it>Phalaenopsis </it>orchids are popular floral crops, and development of new cultivars is economically important to floricultural industries worldwide. Analysis of orchid genes could facilitate orchid improvement. Bacterial artificial chromosome (BAC) end sequences (BESs) can provide the first glimpses into the sequence composition of a novel genome and can yield molecular markers for use in genetic mapping and breeding.</p> <p>Results</p> <p>We used two BAC libraries (constructed using the <it>Bam</it>HI and <it>Hin</it>dIII restriction enzymes) of <it>Phalaenopsis equestris </it>to generate pair-end sequences from 2,920 BAC clones (71.4% and 28.6% from the <it>Bam</it>HI and <it>Hin</it>dIII libraries, respectively), at a success rate of 95.7%. A total of 5,535 BESs were generated, representing 4.5 Mb, or about 0.3% of the <it>Phalaenopsis </it>genome. The trimmed sequences ranged from 123 to 1,397 base pairs (bp) in size, with an average edited read length of 821 bp. When these BESs were subjected to sequence homology searches, it was found that 641 (11.6%) were predicted to represent protein-encoding regions, whereas 1,272 (23.0%) contained repetitive DNA. Most of the repetitive DNA sequences were gypsy- and copia-like retrotransposons (41.9% and 12.8%, respectively), whereas only 10.8% were DNA transposons. Further, 950 potential simple sequence repeats (SSRs) were discovered. Dinucleotides were the most abundant repeat motifs; AT/TA dimer repeats were the most frequent SSRs, representing 253 (26.6%) of all identified SSRs. Microsynteny analysis revealed that more BESs mapped to the whole-genome sequences of poplar than to those of grape or <it>Arabidopsis</it>, and even fewer mapped to the rice genome. This work will facilitate analysis of the <it>Phalaenopsis </it>genome, and will help clarify similarities and differences in genome composition between orchids and other plant species.</p> <p>Conclusion</p> <p>Using BES analysis, we obtained an overview of the <it>Phalaenopsis </it>genome in terms of gene abundance, the presence of repetitive DNA and SSR markers, and the extent of microsynteny with other plant species. This work provides a basis for future physical mapping of the <it>Phalaenopsis </it>genome and advances our knowledge thereof.</p

Acute Diffuse Phlegmonous Esophagogastritis: A Case Report

Acute phlegmonous infection of the gastrointestinal tract is characterized by purulent inflammation of the submucosa and muscular layer with sparing of the mucosa. The authors report a rare case of acute diffuse phlegmonous esophagogastritis, which was well diagnosed based on the typical chest computed tomographic (CT) findings and was successfully treated. A 48-yr-old man presented with left chest pain and dyspnea for three days. Chest radiograph on admission showed mediastinal widening and bilateral pleural effusion. The patient became febrile and the amount of left pleural effusion is increased on follow-up chest radiograph. Left closed thoracostomy was performed with pus drainage. A CT diagnosis of acute phlegmonous esophagogastritis was suggested and a surgery was decided due to worsening of clinical condition of the patient and radiologic findings. Esophageal myotomies were performed and the submucosal layer was filled with thick, cheesy materials. The patient was successfully discharged with no postoperative complication

A Role of Canonical Transient Receptor Potential 5 Channel in Neuronal Differentiation from A2B5 Neural Progenitor Cells

Store-operated Ca2+ entry (SOCE) channels are the main pathway of Ca2+ entry in non-excitable cells such as neural progenitor cells (NPCs). However, the role of SOCE channels has not been defined in the neuronal differentiation from NPCs. Here, we show that canonical transient receptor potential channel (TRPC) as SOCE channel influences the induction of the neuronal differentiation of A2B5+ NPCs isolated from postnatal-12-day rat cerebrums. The amplitudes of SOCE were significantly higher in neural cells differentiated from proliferating A2B5+ NPCs and applications of SOCE blockers, 2-aminoethoxy-diphenylborane (2-APB), and ruthenium red (RR), inhibited their rise of SOCE. Among TRPC subtypes (TRPC1-7), marked expression of TRPC5 and TRPC6 with turned-off TRPC1 expression was observed in neuronal cells differentiated from proliferating A2B5+ NPCs. TRPC5 small interfering RNA (siRNA) blocked the neuronal differentiation from A2B5+ NPCs and reduced the rise of SOCE. In contrast, TRPC6 siRNA had no significant effect on the neuronal differentiation from A2B5+ NPCs. These results indicate that calcium regulation by TRPC5 would play a key role as a switch between proliferation and neuronal differentiation from NPCs

Post genomics era for orchid research

Among 300,000 species in angiosperms, Orchidaceae containing 30,000 species is one of the largest families. Almost every habitats on earth have orchid plants successfully colonized, and it indicates that orchids are among the plants with significant ecological and evolutionary importance. So far, four orchid genomes have been sequenced, including Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen. Here, we review the current progress and the direction of orchid research in the post genomics era. These include the orchid genome evolution, genome mapping (genome-wide association analysis, genetic map, physical map), comparative genomics (especially receptor-like kinase and terpene synthase), secondary metabolomics, and genome editing

Follicular Oocytes Better Support Development in Rabbit Cloning Than Oviductal Oocytes

This study was conducted to determine the effect of rabbit oocytes collected from ovaries or oviducts on the developmental potential of nuclear transplant embryos. Donor nuclei were obtained from adult skin fibroblasts, cumulus cells, and embryonic blastomeres. Rabbit oocytes were flushed from the oviducts (oviductal oocytes) or aspirated from the ovaries (follicular oocytes) of superovulated does at 10, 11, or 12-h post-hCG injection. The majority of collected oocytes were still attached to the sites of ovulation on the ovaries. We found that follicular oocytes had a significantly higher rate of fusion with nuclear donor cells than oviductal oocytes. There was no difference in the cleavage rate between follicular and oviductal groups, but morula and blastocyst development was significantly higher in the follicular group than in the oviductal group. Two live clones were produced in follicular group using blastomere and cumulus nuclear donors, whereas one live clone was produced in the oviductal group using a cumulus nuclear donor. These results demonstrate that cloned rabbit embryos derived from follicular oocytes have better developmental competence than those derived from oviductal oocytes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90481/1/cell-2E2011-2E0030.pd

Reduced Tomato Bacterial Wilt by Ferrous Chloride Application

Exogenous ferrous chloride (FeCl2) suppressed in vitro growth of Ralstonia pseudosolanacearum, causing bacteria for tomato bacterial wilt. More than 50 µM of FeCl2 reduced the in vitro bacterial growth in dose-dependent manners. Two to 200 µM of FeCl2 did not affect the fresh weight of detached tomato leaves at 3 and 5 days after the petiole dipping without the bacterial inoculation. The bacterial wilt of the detached tomato leaves was evaluated by inoculating two different inoculum densities of R. pseudosolanacearum (105 and 107 cfu/ml) in the presence of FeCl2. Bacterial wilt in the detached leaves by 105 cfu/ml was efficiently attenuated by 10–200 µM of FeCl2 at 3 and 5 days post-inoculation (dpi), but bacterial wilt by 107 cfu/ml was only reduced by 200 µM of FeCl2 at 3 and 5 dpi. These results suggest that iron nutrients can be included in the integrated disease management of tomato bacterial wilt

Genomic profile analysis of diffuse-type gastric cancers

Background: Stomach cancer is the third deadliest among all cancers worldwide. Although incidence of the intestinal-type gastric cancer has decreased, the incidence of diffuse-type is still increasing and its progression is notoriously aggressive. There is insufficient information on genome variations of diffuse-type gastric cancer because its cells are usually mixed with normal cells, and this low cellularity has made it difficult to analyze the genome. Results: We analyze whole genomes and corresponding exomes of diffuse-type gastric cancer, using matched tumor and normal samples from 14 diffuse-type and five intestinal-type gastric cancer patients. Somatic variations found in the diffuse-type gastric cancer are compared to those of the intestinal-type and to previously reported variants. We determine the average exonic somatic mutation rate of the two types. We find associated candidate driver genes, and identify seven novel somatic mutations in CDH1, which is a well-known gastric cancer-associated gene. Three-dimensional structure analysis of the mutated E-cadherin protein suggests that these new somatic mutations could cause significant functional perturbations of critical calcium-binding sites in the EC1-2 junction. Chromosomal instability analysis shows that the MDM2 gene is amplified. After thorough structural analysis, a novel fusion gene TSC2-RNF216 is identified, which may simultaneously disrupt tumor-suppressive pathways and activate tumorigenesis. Conclusions: We report the genomic profile of diffuse-type gastric cancers including new somatic variations, a novel fusion gene, and amplification and deletion of certain chromosomal regions that contain oncogenes and tumor suppressors.open121