Panax ginseng C. A. Meyer is one of the most widely used medicinal plants. Complete genome information for this species remains unavailable due to its large genome size. At present, analysis of expressed sequence tags is still the most powerful tool for large-scale gene discovery. The global expressed sequence tags from P. ginseng tissues, especially those isolated from stems, leaves and flowers, are still limited, hindering in-depth study of P. ginseng.P. ginseng roots, stems, leaves and flowers. The high-quality reads from each of the tissues were independently assembled into separate and shared contigs. In the separately assembled database, 45,849, 6,172, 4,041 and 3,273 unigenes were only found in the roots, stems, leaves and flowers database, respectively. In the jointly assembled database, 178,145 unigenes were observed, including 86,609 contigs and 91,536 singletons. Among the 178,145 unigenes, 105,522 were identified for the first time, of which 65.6% were identified in the stem, leaf or flower cDNA libraries of P. ginseng. After annotation, we discovered 223 unigenes involved in ginsenoside backbone biosynthesis. Additionally, a total of 326 potential cytochrome P450 and 129 potential UDP-glycosyltransferase sequences were predicted based on the annotation results, some of which may encode enzymes responsible for ginsenoside backbone modification. A BLAST search of the obtained high-quality reads identified 14 potential microRNAs in P. ginseng, which were estimated to target 100 protein-coding genes, including transcription factors, transporters and DNA binding proteins, among others. In addition, a total of 13,044 simple sequence repeats were identified from the 178,145 unigenes.Two 454 pyrosequencing runs generated a total of 2,423,076 reads from P. ginseng, which will contribute significantly to further genome-wide research and analyses in this species. The novel unigenes identified here enlarge the available P. ginseng gene pool and will facilitate gene discovery. In addition, the identification of microRNAs and the prediction of targets from this study will provide information on gene transcriptional regulation in P. ginseng. Finally, the analysis of simple sequence repeats will provide genetic makers for molecular breeding and genetic applications in this species.This study provides global expressed sequence tags for  Panax ginseng C. A. Meyer is a widely used medicinal plant with multiple clinical and pharmacological effects related to cancer, diabetes and cardiovascular disease. It also promotes immune and central nervous system function as well as relieving stress [P. ginseng are the ginsenosides, a group of dammarane- and oleanane-type triterpenoid saponins. The total ginsenoside content is highest in the flower, followed by the root, leaf and stem [P. ginseng genome, which is reportedly tetraploid and ~3.2 Gb in size [P. ginseng by employing expressed sequence tags (ESTs), which are considered an efficient tool for gene discovery, especially in plants lacking an assembled genome [P. ginseng roots, rhizomes, seeds and leaves using the Sanger method [P. ginseng roots via 454 sequencing [P. ginseng.g stress . The majand stem . The lard genome . Previour method -8. Howevr method ,10. For quencing . Given tP. ginseng.ESTs are considered to represent a reliable source of data for predicting microRNAs (miRNAs) and their targets, especially in species without complete genome information . miRNAs P. ginseng[Simple sequence repeats (SSRs), also termed microsatellites, are nucleotide motifs consisting of tandem repeats of two to six base pairs. It is more likely for SSRs from ESTs (EST-SSRs) to be tightly linked to specific gene functions and perhaps even play a direct role in controlling important agronomic traits . To date. ginseng.P. ginseng plants. Novel and tissue-specific P. ginseng unigenes were obtained. Furthermore, our database includes all of the genes encoding enzymes involved in ginsenoside backbone biosynthesis and modification. Based on the obtained unigenes, we also identified 14 potential P. ginseng miRNAs and 100 of their potential target genes. Moreover, a total of 13,044 EST-SSRs were identified from the P. ginseng unigene dataset, which will facilitate marker-assisted breeding of P. ginseng.In the present study, we globally sequenced the transcriptomes of the roots, stems, leaves and flowers of 4-year-old P. ginseng and generate expression profiles, we sequenced cDNA samples from four P. ginseng tissues  using a Roche/454 GS-FLX (Titanium) pyrosequencing machine. One half run was performed for each sample, yielding approximately 2.42 million raw reads, ultimately totaling ~1.01 billion base pairs (bp). Of these ESTs, 70.2% were over 400 bp in length. The size distributions of the raw reads from the four samples are shown in Additional file de novo assembly using GS De NovoAssembler software, v2.6, both for each tissue individually and for all tissues as a group. The size distributions of the contigs from each tissue are presented in Additional file To characterize the transcriptome of P. ginseng EST library found in the TSA database contains 15,357 ESTs from 11-year-old root tissue [P. ginseng root transcriptome examined in the present study. Furthermore, 82,666 novel P. ginseng root unigenes were discovered in this study, some of which may be specifically expressed in 4-year-old roots. Whereas there are 32,441 ESTs in the NCBI database that were obtained via 454 and Sanger sequencing, 72,623 homologous genes and 105,522 novel unigenes were discovered in the present study. The large quantity of novel unique sequences identified in this study constitutes a powerful resource for P. ginseng researchers.The current P. ginseng-specific genes or homologous genes with unknown functions in other species.To obtain the most informative and complete annotation, all of the contigs from roots, stems, leaves and flowers were annotated separately. The numbers and percentages of the annotated unique sequences are presented in Additional file Based on the annotation results, transcripts encoding all of the known enzymes involved in ginsenoside biosynthesis and modification were identified in our dataset Figure . In mostP. ginseng roots and discovered many genes involved in ginsenoside biosynthesis. However, several genes encoding key enzymes involved in ginsenoside skeleton biosynthesis were absent, such as mevalonate kinase (MVK), geranylgeranyl pyrophosphate synthase (GPS), amyrin synthase (AS) and dammarendiol synthase (DS). From the global tissue transcriptome analysis, we obtained higher coverage genetic information and more candidate genes for further analysis. MVK, GPS and DS were found in our 4-year-old root cDNA library  unigenes were found in the P. ginseng transcriptome, of which 6 showed a high sequence similarity to the candidate glucosidase genes identified in P. quinquefolius by Sun et al. [P. ginseng UGTs included contig89150, contig89599, contig48582, contig18298, contig76094 and contig72547 from the database derived from assembling all tissues simultaneously. The roles of these candidate UGT unigenes in ginsenoside biosynthesis need to be further characterized.Specific CYP450s catalyze the conversion of dammarenediol-II or β-amyrin to various ginsenosides. Han et al. identified the involvement of CYP716A47 in the hydroxylation of the C-12 position to yield protopanaxadiol . In thisn et al. . These pP. ginseng four tissues were compared with each other and was shown by a Venn diagram  is widely used to standardize the representation of genes across species and to provide a controlled vocabulary of terms for describing gene products . The conP. ginseng-specific proteins.The abundance of particular transcripts within a specific tissue provides clues about the biological processes occurring there. The most highly expressed genes observed in each cDNA library are listed in Table In the stem-derived cDNA library, the most highly expressed gene encoded phloem protein 2 (PP2)-like protein. PP2 is involved in the assimilate stream and has the capacity to interact with the mesophyll plasmodesmata to increase their size exclusion limit as well as cell-to-cell trafficking . The secThe most highly expressed genes in the leaf-derived cDNA library encoded proteins including ribulose bisphosphate carboxylase, photosystem II 10 kDa polypeptide and the chlorophyll a-b binding protein, as well as some proteins with an undefined function. Ribulose biphosphate carboxylase was also the most abundant transcript in the flower-derived libraries. Ribulose bisphosphate carboxylase catalyzes the initial step in the photosynthetic fixation of carbon dioxide .Histone H4, aquaporin and a photosystem II 10 kDa polypeptide represented the three dominant transcripts in the flower-derived cDNA library. Histone H4 acetylation within euchromatic and heterochromatic domains plays a key role in DNA replication . In highP. ginseng growth and development. Some housekeeping genes exhibit high expression levels in specific tissues, as observed for transport-related genes in the stem and photosynthesis-related genes in the leaf. This phenomenon can be explained by the fact that the proteins encoded by these genes are responsible for the characteristic functions of the corresponding tissues.All of the predominantly expressed transcripts in each of these four tissue-derived cDNA libraries belong to the group of 50,957 genes shared by the four tissues. These genes are normally associated with housekeeping functions and play key roles in P. ginseng until now. Because only mature miRNA sequences (rather than precursor sequences) are conserved among plant species, mature miRNA sequences were used as queries for BLAST searches against the high-quality P. ginseng reads derived from our experiments. This process yielded 8,375 reads that were found to significantly match at least one mature miRNA sequence with no more than two mismatches and that could be related to either a target or an miRNA precursor sequence. A total of 3,707 noncoding reads were obtained after removing repeat and protein-coding sequences. Ultimately, we identified 14 candidate P. ginseng miRNAs with a proper miRNA precursor secondary structure and a minimal folding free energy index (MFEI) of at least 0.85  in length that have been shown to regulate gene expression at the post-transcriptional level by targeting mRNAs for degradation or inhibiting protein translation . There aP. ginseng miRNAs, 4 were found to be located on the 5′ arm of the stem-loop hairpin structure, while 10 resided on the 3′ arm. The length of the putative P. ginseng miRNAs varied from 20 to 22 nt, with an average of 21 ± 0.5 nt. The majority  of the miRNAs were 21 nt in length. The length of the P. ginseng pre-miRNAs varied from 68 to 294 nt, averaging 143 ± 67 nt. The length distribution of the miRNAs and their precursor sequences was similar to the distributions described in previous reports in other plant species [Mature miRNA sequences can be located on either arm of the secondary stem-loop hairpin structure of the potential miRNA precursor (pre-miRNA). Of the 14 identified  species ,31.P. ginseng miRNAs was −54.78 ± 21.82 kcal/mol, with a range of −21.9 to −99.2 kcal/mol. The minimal folding free energy index (MFEI) is a criterion for distinguishing miRNAs from other RNAs. Previous studies have shown that a sequence is more likely to be a potential miRNA if it presents an MFEI value greater than 0.85 [P. ginseng miRNAs, the average MFEI was 1.04 ± 0.17, with a range of 0.85 to 1.55. The secondary structures of the putative P. ginseng miRNA precursors are reported in Additional file The minimal folding free energy (MFE) is important for the formation of RNA secondary structures. Generally, the lower the MFE, the more stable the secondary structure of a given RNA sequences. The average MFE value obtained in the present study for the han 0.85 . For theIdentification of miRNA target genes, in addition to constituting indirect existence evidence of miRNAs, is a fundamental step for the determination of biological function for miRNAs. Evolutionarily conserved targets have been shown to be useful in testing the effectiveness of miRNA target detection. A perfect, or near perfect, complementarity between an miRNA and its target mRNA, which is a peculiar feature of plant miRNAs, provides a powerful tool for the identification of target genes through BLAST analysis of mature miRNA sequences against EST sequences. After carefully considering the alignment results, we predicted at least one target for 7 miRNAs and a total of 100 potential targets for 14 miRNAs , which plays an important role in the control of the flowering time and floral morphology. miR172 has also been shown to target AP2 in tobacco, the opium poppy and Brassica oleracea[Arabidopsis[P. ginseng. Previous studies have also shown that MYB proteins may be targeted by miR5021 in B. oleracea[Arabidopsis[Several studies have demonstrated that miRNAs can target transcription factors that control plant growth and development ,31. In t oleracea-36. Aukeabidopsis. In addi oleracea. Zinc fiabidopsis. Other mP. ginseng unigenes containing at least two SSRs. The observed frequency of unigenes was 7.3%, and the distribution density was 172.5 per Mb. As is shown in Table SSRs are one of the most powerful types of molecular marker because of their relative abundance and ease of generation, and they have been widely applied for molecular-assisted selection (MAS) in plant breeding programs . SSR marP. ginseng. The obtained EST dataset provides a comprehensive resource for gene discovery and genetic analyses in P. ginseng. The genes identified in this study will help to decipher the molecular mechanisms of secondary metabolism in P. ginseng. Moreover, this study identified putative miRNAs from P. ginseng and their targets, thus representing a foundation for further research into transcriptional regulation. Finally, the large set of SSRs identified in this work provides abundant genetic markers for molecular breeding and genetic applications in this species.In this study, a large-scale EST investigation was performed in root, stem, leaf and flower tissues from P. ginseng C. A. Meyer) was harvested from a field plot in Kuandian County, Liaoning Province, China, on June 27, 2011. At that time, the temperature ranged from 14.3 ~ 24.7°C, averaging 19.4°C. The four seasons in Kuandian County are distinct. A majority of the annual rainfall occurs in July and August. The monthly 24-hour average temperatures range from −11.5°C in January to 22.5°C in July, while the annual mean is 6.5°C. The average relative humidity is 70%, and the frost-free period is 140 days. Main roots, stems, leaves and flower buds were collected separately from a single plant and cut into small pieces followed immediately by storage in liquid nitrogen until further processing.Actively growing 4-year-old ginseng . Quality control was performed in the samples using RNA 6000 Nano LabChips with Bioanalyzer 2100 , and the obtained concentrations were assessed using a NanoDrop ND-1000 spectrophotometer  before processing. The RNA samples were treated with TURBO DNase  at a concentration of 1.5 units/μg of total RNA prior to cDNA synthesis.P. ginseng. First-strand cDNA was produced from 2 μg of total RNA extracted from each of the P. ginseng tissues using the SMART cDNA synthesis kit  according to the manufacturer’s instructions, with slight modifications, as described in a previous report [BsgI  overnight and recovered using the QIAquick PCR Purification Kit .Four cDNA libraries were constructed from the roots, stems, leaves and flowers of s report . For douNext, 500 ng of ds cDNA from each tissue was used for shotgun cDNA library construction according to the manual of the GS FLX Titanium Rapid Library Preparation Kit . The DNA was nebulized for 1 minute and then end-repaired using T4 DNA polymerase and T4 polynucleotide kinase. Adaptors were blunt-end ligated to the fragment ends using T4 DNA ligase. AMPure beads  were employed to remove small DNA fragments and to collect DNA fragments between 600 bp and 900 bp in length.Using emulsion PCR, the DNA molecules in the shotgun library were amplified with the GS FLX Titanium LV emPCR package , according to the manufacturer’s recommendations. After amplification, the beads bound to amplified molecules were collected, and the emulsion oil was removed via washing, according to the manufacturer’s protocol. Beads bound to a sufficient number of copies of the clonally amplified library fragments were selected using a specified enrichment procedure and were subsequently counted with a Multisizer 3 Coulter Counter  prior to sequencing.Following emulsion PCR enrichment, the selected beads were loaded into the wells of a Titanium Series PicoTiterPlate device via centrifugation. Then, 454 sequencing was performed according to the manufacturer’s instruction manual . Image analysis, signal processing, and base calling were conducted using Newbler 2.3 software .E-value ≤ 1e-5. The functional categories of these unique sequences were further analyzed according to GO terms based on InterPro GO slim provided by InterPro [The raw 454 reads were screened and trimmed for weak signals using GS FLX pyrosequencing software to yield high-quality reads. The primer and adapter sequences were trimmed from the high-quality sequences to obtain clean ESTs. Then, sequences shorter than 50 bp were removed. Finally, the data from the 454 reads was assembled into unigenes (containing contigs and singletons) using GS De NovoAssembler software, v2.6 . Functional annotation was carried out against a series of nucleotide and protein databases, including the Swiss-Prot , InterPrInterPro .P. ginseng was carried out using previously reported methods [A set of known miRNAs was downloaded from miRBase , comprising a total of 4,743 mature miRNA sequences from 51 plant species . A homol methods ,31. SubsP. ginseng, we performed SSR analysis of the obtained unigenes using the microsatellite identification tool MISA [To detect SSRs in ool MISA . The parool MISA . Primer3ool MISA . The maiool MISA .Panax ginseng C. A. Meyer; NGS: Next-generation sequencing; BLAST: Basic local alignment search tool; Nt: Nucleotide; Bp: Base pair; cDNA: Complementary DNA; AACT: Acetyl-CoA acetyltransferase; HMGS: HMG-CoA synthase; HMGR: HMG-CoA reductase; MVK: Mevalonate kinase; PMK: Phosphomevalonate kinase; MVD: Mevalonate diphosphate decarboxylase; GPS: Geranylgeranyl pyrophosphate synthase; IDI: Isopentenyl diphosphate isomerase; FPS: Farnesyl diphosphate synthase; SS: Squalene synthase; SE: Squalene epoxidase; AS: Amyrin synthase; DS: Dammarendiol synthase; UGT: UDP glycosyltransferase; CYP450: Cytochrome P450; EST: Expressed sequence tag; GO: Gene ontology; Nt: NCBI non-redundant nucleotide; Nr: NCBI non-redundant protein; KEGG: Kyoto encyclopedia of genes and genomes; NCBI: National center for biotechnology information; MFE: Minimal folding free energy; MFEI: Minimal folding free energy index; miRNA: microRNA; pre-miRNA: miRNA precursor; AP2: APETALA2.P. ginseng: The authors declare that they have no competing interests.CFL conceived the study, built the cDNA libraries, performed 454 sequencing, participated in the data analysis and drafted the manuscript. YJZ performed most of the data analysis. XG participated in 454 sequencing. CS contributed to designing the study. HML and JYS helped to conceive the study. YL participated in the data analysis. LZW participated in cDNA library construction and 454 sequencing. JQ performed the SSR analysis. SLC initiated the project, designed the study and participated in study coordination. All authors read and approved the final manuscript.Length distributions of reads. TIFF document for the length distributions of P. ginseng four tissues reads.Click here for fileLength distributions of contigs. TIFF document for the length distributions of P. ginseng four tissues contigs.Click here for fileSummary of the 454 sequencing and assembly for P. ginseng four tissues. DOCX document for the summary of 454 sequencing and assembly data.Click here for fileSummary of annotation statistics against public databases for P. ginseng four tissues. DOCX document for the summary of annotation results.Click here for fileTranscripts involved in ginsenoside skeleton biosynthesis in P. ginseng four tissues. DOCX document for the number of ginsenoside skeleton biosynthesis genes in P. ginseng each tissue and four tissues.Click here for fileSecondary structures of the putative miRNA precursors. DOCX document for the predicted secondary structures of the putative miRNA precursors.Click here for filemiRNA potential target genes. DOCX document for the predicted miRNA target genes.Click here for fileOccurrence of SSRs in P. ginseng unigenes. DOCX document for the summary of occurrence of SSRs in P. ginseng unigenes.Click here for filePrimer pairs for each SSR. XLSX document for the primer pairs for each SSR.Click here for file


Bartonella henselae, usually benign and self-limited. However, various clinical manifestations and no pathognomonic histopathologic features can lead to misinterpretations and diagnostic disputes. We report a case of cat scratch disease in a 39-yr-old male patient with fever and left axillary lymphadenitis. He had a history of cat bite on the left hand dorsum. On excision, the lymph node showed follicular hyperplasia, stellate microabscesses with a rim of granulomatous inflammation. Warthin-Starry silver staining showed many clumps of silver-stained bacilli within the necrotic foci. Serological tests were negative. Diagnosis was established by PCR analysis.Cat scratch disease, necrotizing granulomatous lymphadenitis caused by http://www.diagnosticpathology.diagnomx.eu/vs/1877499238123059The virtual slides for this article can be found here:  Bartonella henselae [Cat scratch disease (CSD) is caused by henselae -3. The phenselae -3. HistoA 39-year-old male patient was admitted with painful swelling in the left axilla and elbow and fever for 3 weeks. He had a history of cat bite on the left hand dorsum 3 weeks before admission. His temperature was 39.3°C. A rash was noted on the left hand dorsum. Two tender palpable lymph nodes were present at the left axillary and epitrochlear regions. Laboratory results were unremarkable. Liver enzymes were normal. Blood cultures and viral serologic tests results were all negative.Bartonella (B.) quintana and B. henselae gave negative results . Serologic tests for Tularemia and Toxoplasmosis were also negative. Although the fever subsided after 3 days of antibiotics, the axillary lymphadenopathy didn’t resolve and an excisional biopsy of the affected lymph nodes was performed.An indirect fluorescence assay  against pap31 gene, according to the previous description by Zeaiter et al. , prolonged fever/fever of unknown origin and hepatosplenic disease, and less common various manifestations [As Florin et al. summarized, clinical manifestations of stations .B. henselae antibodies [Culture is not reliable for the diagnosis of CSD, as the organism is slow-growing and difficult to culture ,16. Moretibodies ,19. One Bartonella organisms; however, organisms are variably detectable, and these stains are technically challenging [Tissue biopsy is one useful way to diagnose CSD and to exclude other etiologies, despite its invasive nature ,9. Silvellenging .Bartonella, and molecular studies might be required to distinguish between the two.The histologic differential diagnosis of CSD lymphadenitis primarily includes Kikuchi necrotizing lymphadenitis (KNL), Kawasaki disease and other infectious processes, such as tularemia, mycobacterial infection, brucellosis, fungal infection, lymphogranuloma venereum (LGV) and lymphadenitis associated with idiopathic granulomatous mastitis  ,3,20. LGIn our case, histopathologically, the lesion showed suppurative granulomatous inflammation, and the WS stain detected clumps of bacilli, highly suggestive of CSD but not definitive ,22. ChonIn our case, the serology for tularemia was negative. No microorganism was found by a Brown-Brenn Gram stain. No fungal species were detected by the PAS stain.KNL can be histologically similar to CSD, however, KNL lacks neutrophils or epithelioid cells with granulomatous arrangements .B. infection (three of 4 of the following): 1. cat or flea contact regardless of presence of inoculation site, 2. negative serology for other causes of adenopathy, sterile pus aspirated from a node, a positive PCR assay, and/or liver/spleen lesions seen on CT scan, 3. positive enzyme immunoassay or IFA assay with a titer ratio of ≥1:64, and 4. biopsy showing granulomatous inflammation consistent with CSD or a positive WS stain [Ultimately, no single criterion can be considered the diagnostic gold standard . In 2000WS stain ,25.We report a case of CSD, sero-negative but confirmed by PCR, with histopathologic features. Characteristic histopathologic findings combined with the WS stain, may contribute to the diagnosis.Written informed consent was obtained from the patient for publication of this Case Report and accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.CSD: Cat scratch disease; KNL: Kikuchi necrotizing lymphadenitis; IFA: Indirect fluorescence assay; PCR: Polymerase chain reaction; LGV: Lymphogranuloma venereum.The authors declare that they have no competing interests.YRK, THB and TSL collected the clinical data. ORS made the final diagnosis of this disease. SYK performed serologic tests. THH performed PCR test. KJS and ORS drafted the manuscript. All authors have read and approved the final manuscript.


Phyllanthus niruri (Aq.E.PN) against doxorubicin (Dox)-induced myocardial toxicity in rats.To investigate the effect of the aqueous extract of Cardiotoxicity was produced by Dox administration (15 mg/kg for 2 weeks). Aq.E PN  was administered as pretreatment for 2 weeks alternated with Dox for the next 2 weeks. The general observations, mortality, histopathology, biomarker enzymes like lactate dehydrogenase (LDH), creatinine phosphokinase (CPK) and alkaline phosphatase, diagnostic enzyme markers like aspartate aminotransferase (AST) and alanine aminotransferase (ALT), and antioxidants such as glutathione (GSH), superoxide dismutase (SOD), catalase (CAT) and malondialdehyde (MDA) were monitored after 3 weeks of the last dose.P < 0.01) protected the myocardium from the toxic effects of Dox by reducing the elevated level of biomarker and diagnostic enzymes like LDH, CPK, AST and ALT to the normal levels. Aq.E PN increased the GSH, SOD and CAT levels and decreased the MDA levels in cardiac tissue. Administration of Dox caused cardiomyopathy associated with an antioxidant deficiency.Pretreatment with the Aq.E.PN significantly (P. niruri due to its antioxidant properties.These results suggest a cardioprotective effect of  However, the clinical use is restricted by an unusual and often irreversible dose-dependent cardiomyopathy. The Dox-hosphate.Phyllanthus niruri (Linn.), also known as Phyllanthus amarus, is a traditional herbaceous plant distributed all over India. It has been reported to have hypotensive,[P. niruri, the aim of this study was to evaluate the antioxidant and cardioprotective properties of the aqueous extract of P. niruri on Dox-induced cardiotoxicity.The species otensive, antiulceotensive, antitumootensive, antioxidotensive, wound heotensive, and antiotensive, propertiotensive, ConsiderP. niruri Linn. was collected from Hubli and its surrounding areas, Karnataka, India. The plant was identified and authenticated by the Botany Department of H.S.K. Science Institute, Hubli. The plant material was dried at room temperature and subjected to coarse powder of desired particle size.The whole plant of Weighed quantity of powdered plant material (25 g) was soaked in boiling water (250 ml) for 15 min, allowed to cool and filtered using Whatman filter paper. The obtained residues were further extracted twice and then concentrated using a rotary evaporator. The concentrated extract was then taken in a china dish and evaporated on a thermostat-controlled water bath till it formed a thick paste.ad libitum. The study was approved by the institutional animal ethics committee (KLESCOPH / IAEC. Clear / 2007-08).Healthy albino Wistar rats of either sex weighing between 150 and 200 g of 10–12 weeks of age were used. Animals were housed individually in polypropylene cages, maintained under standard conditions , fed with standard rat pellet diet,  and water Dox was procured from Dr. R. B. Patil Cancer Research Hospital, Hubli, India. Other chemicals used were of analytical grade and were procured locally. Analyzing kits were obtained from ERBA Diagnostics, Daman, India.P. niruri.The acute oral toxicity study was carried out as per the revised guidelines by Organization for Economic Co-Operation and Development (OECD) and Committee for the Purpose of Control and Supervision of Experiments on Animals (CPCSEA). Acute toxicity studies were performed on albino mice weighing between 20 and 30 g using the up and down method employed prior to evaluating the cardioprotective activity of After 1 week of acclimatization, the animals were randomly divided into four groups of six animals each. Group 1 served as normal control and received normal saline 5 ml/kg body weight (i.p.). Group 2 was treated with Dox (2.5 mg/kg body weight i.p.) in six equal injections alternatively for 2 weeks to make a total cumulative dose of 15 mg/kg body weight. Group 3 received Aq.E. PN (200 mg/kg body weight p.o.) for 2 weeks and then alternatively with vehicle for the next 2 weeks. Group 4 was pretreated with Aq.E. PN 200 mg/kg body weight p.o. for 2 weeks followed by Dox administration as in group 2.Thirty-six hours after the last treatment, orbital blood samples were obtained under light ether anesthesia using heparinized microcapillaries for the estimation of biomarkers lactate dehydrogenase (LDH), creatiniThe results were expressed as the mean ± SEM and analyzed using one-way ANOVA followed by Dunnett’s multiple comparison tests. Data were computed for statistical analysis using the Graph Pad Prism Software.thof the maximum tolerated dose, 200 mg/kg b.w., was chosen for further studies.Chronic administration of Dox induced cardiac toxicity and effect of Aq.E PN was established by measuring cardiac biomarker enzymes, endogenous antioxidants and heart tissue histopathology. Acute toxicity studies observed that a maximum dose of 2000 mg/kg b.w. was safe in animals. However, few changes in the behavioral response, like alertness, touch and restlessness, were noted. Therefore, 1/10P < 0.01) increased compared with normal rats in group 2, and significantly (P < 0.01) decreased in group 4 as compared with the Dox-treated group [The heart weight, body weight and ratio of heart to body weight was significantly (ed group .P < 0.01) increase in the level of LDH and CPK as compared with the rats in group 1 [Animals treated with Dox produced a significant ( group 1 . PretreaP < 0.01) increase in the level of AST, ALT and ALP as compared with group 1 [Animals treated with Dox produced a significant ( group 1 . PretreaP < 00.01) decreased in the Dox-treated group as compared with normal animals [The MDA level was increased whereas the GSH, SOD and CAT levels were significantly ( animals . Group 4The histology of the heart tissue from the control and the Aq.E. PN treated animals showed normal morphological appearances Figures  and 3, w2+ influx induced by toxic agents. Oral administration of the Aq.E. PN extract along with Dox maintained the concentration of GSH at near-normal levels, which prevents cell disruption probably by decreasing the Ca2+influx.The existing experimental evidence suggests that Dox oxidative stress is due to the generation of free radicals in the heart tissue. Heart tiThe present study has shown that Dox induces lipid peroxidation and decreases the levels of protective enzymes in the heart tissues. Pretreatment with Aq.E. PN significantly reduced the lipid peroxidation and increased the levels of SOD, CAT and GSH. These results indicate the protective effect of Aq.E. PN on Dox-induced cardiotoxicity by scavenging of free radicals.P. urinaria and P. emblica reduced the oxidative damage in Dox-induced cardiotoxicity[P. niruri may have different functional properties, such as scavenging of reactive oxygen species, inhibition of generation of free radicals and chain-breaking activity. This may act as hydrogen-donating radical scavenger by scavenging lipid alkoxyl and peroxyl radical and protect the myocardium from Dox-induced injury.The antioxidant effects of plant species in the genus Phyllanthus have been reported. For example, otoxicity and ischotoxicity respectiet al.[P. niruri pretreated group attenuates the Dox-induced loss of myofibrils, vacuolization of the cytoplasm and swelling of mitochondria. Phyllanthin, hypophyllanthin, triterpenoids, niruriflavone and phenolic compounds present in P. niruri may be responsible for reducing the oxidative damage.A deficiency of oxygen supply or glucose may damage the myocardial cells and the cell membrane becomes permeable or ruptures, resulting in leakage of enzymes. We observed an increase in the activities of LDH, CPK, AST and ALT in Dox-treated rats. Pretreatment with Aq.E. PN decreased the enzyme activities in serum and increased the same in the heart. Similar results have been observed by Koti et al. This couP. niruri prevents the Dox-induced myocardial toxicity by boosting the endogenous antioxidant activity. Further studies are needed to elucidate the exact mechanism of action of P. niruri and its clinical application.In conclusion, the present results suggest that


Staphylococcus aureus and Staphylococcus epidermidis are notable for their propensity to form biofilms on implanted medical devices. Staphylococcal biofilm infections are typified by their recalcitrance to antibiotics and ability to circumvent host immune-mediated clearance, resulting in the establishment of chronic infections that are often recurrent in nature. Indeed, the immunomodulatory lifestyle of biofilms seemingly shapes the host immune response to ensure biofilm engraftment and persistence in an immune competent host. Here, we provide a brief review of the mechanisms whereby S. aureus and S. epidermidis biofilms manipulate host–pathogen interactions and discuss the concept of microenvironment maintenance in infectious outcomes, as well as speculate how these findings pertain to the challenges of staphylococcal vaccine development. Staphylococcus aureus and Staphylococcus epidermidis are highly opportunistic pathogens and a major cause of nosocomial and community-associated infections  –29. NeutS. aureus biofilms both in vitro and in vivo have decreased inducible nitric oxide synthase (iNOS) concomitant with increased Arg1 expression, as well as attenuated cytokine and chemokine production  alter biofilm gene expression profiles . Transcr periods . This da periods , 68, 69.S. aureus to survive intracellularly in neutrophils    and phenin (Hla) –77. Inteexposure , 74. Not in vivo . Likewisbiofilms . Collect release –80. WhilS. aureus, in particular, utilizes numerous hemolysins (N-Acyl homoserine lactones (AHL)  , 89. TheS. aureus turns the immune response against itself (S. aureus PSM expression is induced following neutrophil phagocytosis, resulting in neutrophil lysis and bacterial escape (Besides virulence factors, staphylococci also secrete molecules for nutrient procurement and cell signaling. For example, siderophores are critical for iron acquisition , while st itself . In addil escape , 76, 93.l escape –99. Indel escape .However, secreted factors are not the only means whereby staphylococcal biofilms could regulate the host response in an exogenous manner. While bacteria have a plethora of environmental sensory mechanisms at their disposal, host immune cells are also very sensitive to their surrounding environment –103. BecS. epidermidis.Most implanted medical devices are at risk for biofilm colonization , 11, 15.S. aureus biofilms promote their growth and expansion by manipulating the host immune response (S. aureus biofilm infection (in vivo (Our laboratory has reported that response , 44, 111response , 44, 48.nfection , 43, 44.(in vivo , 43, 44.S. aureus biofilms in vivo and in vitro typified by Arg1 concomitant with minimal iNOS expression (S. aureus biofilm infections, whereas another group reported Th2/Treg involvement in biofilm clearance (S. aureus strains tested. Impaired adaptive immunity or memory responses could compromise the success of vaccine strategies against staphylococcal biofilms.Besides dampening the local inflammatory environment, numerous mechanisms likely exist to explain the chronicity of staphylococcal biofilm infections in an immune competent host. For example, we have demonstrated the preferential accumulation of M2-activated macrophages in pression , 43, 44.pression –116. Indlearance , 55. TheS. aureus to circumvent immune-mediated clearance has complicated staphylococcal vaccine development. Indeed, previous studies have shown that S. aureus infection alone is not sufficient to induce protective immunity (in vivo (S. aureus clonal complex groups (As ongoing staphylococcal biofilm research elucidates mechanisms contributing to the persistence and virulence of these infections, it is becoming clear that novel strategies are needed to combat the complex biofilm lifestyle. The inherent ability of immunity . Moreove(in vivo –120. Anox groups .S. aureus strains (in vivo (Recent staphylococcal vaccine efforts have utilized new approaches to increase efficacy. Vaccination with attenuated  strains  has led  strains , 124. In strains , and bio strains , 127 mod(in vivo , 128. Fu(in vivo , 130. Whin vivo interactions. Additional insights into staphylococcal biofilm metabolism, in particular, how the biofilm metabolome changes once immune cells are encountered, may be beneficial as it could facilitate the identification of virulence determinants for vaccine development. A recent analogy is the use of metabolic stimuli to induce aminoglycoside susceptibility in otherwise recalcitrant S. aureus cell populations, such as biofilms (In this context, a successful staphylococcal vaccine may be facilitated by a more comprehensive understanding of the staphylococcal biofilm transcriptome and secretome, particularly in response to relevant host phagocytes, which will be an important next step toward replicating complex biofilms . Also, cThe authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Helicobacter pylori (H. pylori) is a risk factor for distal stomach cancer, and a few small studies have suggested that H. pylori may be a potential risk factor for lung cancer. To test this hypothesis, we conducted a study of 350 lung adenocarcinoma cases, 350 squamous cell carcinoma cases, and 700 controls nested within the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study (ATBC) cohort of male Finnish smokers. Controls were one-to-one matched by age and date of baseline serum draw. Using enzyme-linked immunosorbent assays to detect immunoglobulin G antibodies against H. pylori whole-cell and cytotoxin-associated gene (CagA) antigens, we calculated odds ratios (ORs) and 95% confidence intervals (95% CIs) for associations between H. pylori seropositivity and lung cancer risk using conditional logistic regression. H. pylori seropositivity was detected in 79.7% of cases and 78.5% of controls. After adjusting for pack-years and cigarettes smoked per day, H. pylori seropositivity was not associated with either adenocarcinoma  or squamous cell carcinoma . Results were similar for CagA-negative and CagA-positive H. pylori seropositivity. Despite earlier small studies suggesting that H. pylori may contribute to lung carcinogenesis, H. pylori seropositivity does not appear to be associated with lung cancer.Lung cancer is the leading cause of cancer mortality worldwide.  Lung cancer kills more people worldwide (over 1 million each year) than any other cancer Helicobacter pylori (H. pylori) H. pylori is a key etiologic agent in the development of distal stomach cancer H. pylori colonizes the gastric mucosa, inducing local inflammation and a systemic immune response H. pylori has been classified as a group 1 carcinogen for stomach cancer by the International Agency for Research on Cancer H. pylori can be broadly categorized into two groups: type I strains, which express the cytotoxin-associated gene (cagA), and type II strains, which do not CagA-positive strains affect gastric epithelial cell signal transduction, which can affect the cytoskeleton, inflammatory cascades, and mitogenic pathways One microbe postulated to play a role in lung cancer is H. pylori could potentially affect the lungs in several ways. Lipopolysaccharide is the major component of the cell wall of gram-negative bacteria like H. pylori. Lipopolysaccharide stimulates the production of pro-inflammatory cytokines including IL-1, IL-6, and tumor necrosis factor (TNF)-alpha. This local inflammation can have systemic effects H. pylori persistence leads to chronic inflammation and immune stimulation, which could contribute to carcinogenesis or conditions associated with lung cancer, such as chronic bronchitis H. pylori in the stomach might promote cellular proliferation in the lungs as well H. pylori colonization could decrease the risk of lung cancer. H. pylori prevalence has declined over the last 70 years, accompanied by a marked decrease in noncardia gastric cancer and an increase in esophageal adenocarcinoma H. pylori and esophageal adenocarcinoma in Western countries and the lack of association with esophageal squamous cell carcinoma, an inverse association between H. pylori and lung adenocarcinoma but no association with lung squamous cell carcinoma also could be hypothesized.It is also possible that gastric H. pylori and lung cancer has been limited, with fewer than 75 cases in each of five case-control studies H. pylori seropositivity data from previous studies in the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study (ATBC) cohort of male Finnish smokers H. pylori with lung adenocarcinoma, but not squamous cell carcinoma (see Methods section). Based on these intriguing preliminary data and the lack of well-powered, high-quality studies, we designed the first prospective study of H. pylori seropositivity and lung cancer in ATBC.Prior assessment of the association between The ATBC Study, a randomized, double-blind, placebo-controlled, primary prevention trial, was designed to test the hypothesis that daily supplementation with alpha-tocopherol, beta-carotene, or both would reduce the incidence of lung or other cancers among male smokers. Details of this study have been published H. pylori seropositivity data from previous studies in ATBC H. pylori and lung cancer. Enzyme-linked immunosorbent assay (ELISA) measurements of H. pylori seropositivity were available from 98 lung cancer cases (11 with documented adenocarcinoma and 33 with squamous cell carcinoma) and over 1500 subjects without lung cancer. The preliminary data revealed no apparent association between H. pylori seropositivity and lung cancer overall . However, we observed a trend toward an inverse association with adenocarcinoma , which was stronger for CagA-positive H. pylori strains .We used existing th Revision (ICD-9) nd edition (ICD-O-2), and 3rd edition (ICD-O-3). Squamous cell carcinoma included malignant ICD-O codes of 8070. Adenocarcinoma included malignant ICD-O codes of 8140 (adenocarcinoma), 8250 , and 8260 (papillary carcinoma). Cases were selected from among all first primary lung squamous cell carcinoma or adenocarcinoma cases diagnosed at least 1 year after the baseline draw date through 30 July 2007. We randomly selected 350 from 927 eligible squamous cell carcinoma cases and 350 from 392 eligible adenocarcinoma cases  compared to seronegativity for both whole-cell and CagA antigens. Second, we split H. pylori seropositivity into whole-cell and CagA seropositivity. Twelve individuals were classified as seropositive for CagA and seronegative for antibodies against the whole-cell antigen. A previous study comparing serology with gastric biopsy culture found that individuals who are negative for H. pylori whole-cell antibodies but positive for CagA antibodies had CagA-positive H. pylori organisms present in their stomach by culture H. pylori negative, individuals seropositive for whole-cell but seronegative for CagA as H. pylori-seropositive/CagA seronegative (CagA-negative strains), and individuals seropositive for CagA, regardless of whole-cell serostatus, as CagA seropositive (CagA-positive strains).We tested fasting serum specimens collected at baseline and stored in aliquots at −70°C for immunoglobulin G antibodies against In addition to the 1389 samples from lung cancer cases and controls, 3 quality control serum samples aliquoted from a single large pool were equally distributed among 37 different batches. All samples were assayed in duplicate in the same batch by experienced technicians blinded to case-control status. In the case of indeterminate results , a repeat analysis was conducted on the residual of the original aliquot and averaged across all results, excluding obvious outliers. 95.9% of the samples were resolved with two runs in the whole-cell ELISA, and 94.9% of the samples were resolved with two runs in the CagA ELISA. More than 99% of samples were resolved with two or three runs (99.5% for whole-cell and 99.4% for CagA). The remainders were resolved with four runs.H. pylori seropositivity in a prior ATBC study with a prevalence of 45% among controls H. pylori exposure prevalence of 75% among the controls, the minimal detectable ORs at 90% power were 0.68 or 1.53 for all lung cases compared to controls. We calculated within-batch coefficients of variation (CV) for the whole-cell and CagA antigen assays based on continuous optical density values from the 111 pooled QC samples (three within each batch). The within batch CVs were 12.9% for the whole-cell assay and 25.5% for the CagA assay, similar to the CVs of 15% and 20%, respectively, in a previous study of H. pylori and gastric cancer in ATBC using the same laboratory Based on the observed prevalence of H. pylori seropositivity, using the categories described above. Results for adenocarcinoma and squamous cell carcinoma were similar according to the Wald test for homogeneity We used conditional logistic regression to calculate separate ORs and 95% CIs for the association of lung adenocarcinoma and squamous cell carcinoma with H. pylori seropositivity).Potential confounders included ATBC treatment group , age at randomization (continuous), baseline pack-years (continuous), baseline number of cigarettes per day (continuous), tooth loss (continuous), dentures (yes/no), obesity , asthma (yes/no), emphysema (yes/no), bronchitis (yes/no), and education . We evaluated the importance of these variables by removing each covariate from the model one by one through backwards modeling and determining whether the ORs for CagA-negative strains and CagA-positive strains changed by at least 10% in comparison with the full model. No covariate met this criterion. However, we included pack-years and smoking amount (cigarettes per day) in all final models to adjust for smoking exposure, in accord with several recent studies H. pylori seropositivity in Finland found that antibody levels remain relatively stable over time in this population H. pylori and gastric cancer was similar when stratified by time to diagnosis H. pylori antibody levels over time, we stratified by median time since blood draw. Since microbe-related cancers often occur at younger ages than those not related to infection H. pylori seropositivity and lung cancer varied by age at diagnosis  using the likelihood ratio test (LRT) for interaction terms A previous study of H. pylori and lung cancer, as described in the Methods section. Among the 696 cases and 693 controls with sufficient sample available, 555 cases (79.7%) and 544 controls (78.5%) had antibodies against either H. pylori whole-cell or CagA antigens  and 44.2% of controls (N = 306) were seropositive for CagA-positive strains. Of the 603 CagA-positive individuals, 591 [289 out of 297 cases (97.3%) and 302 out of 306 controls (98.7%)] also were positive for antibodies against the whole-cell antigens.The case and control series were similar with regard to age, median cigarettes per day, and other characteristics . As expeantigens . Thirty-H. pylori seropositivity was not associated with lung cancer in ATBC . The ORs did not vary by histology . In addition, there was no notable variability in the associations for CagA-negative or CagA-positive H. pylori seropositivity . in ATBC . The OR sitivity . ResultsH. pylori seropositivity over time may weaken the association between H. pylori seropositivity and cancer risk, associations were similar by median time between baseline serum draw and diagnosis in this study (H. pylori seropositivity and lung cancer by median age at diagnosis (age 68). For example, the ORs for any H. pylori seropositivity and any lung cancer were 1.1 (95% CI: 0.73–1.6) for cases diagnosed at or before age 68 compared to their matched controls and 1.2 (95% CI: 0.79–1.8) for cases diagnosed after age 68 . Similarly, the ORs for CagA-negative H. pylori seropositivity and CagA-positive H. pylori were 1.0 (95% CI: 0.68–1.6) and 1.1 (95% CI: 0.72–1.7), respectively, for cases diagnosed at or before age 68 and 1.3 (95% CI: 0.83–2.0) and 1.1 (95% CI: 0.69–1.7) for cases diagnosed after age 68 . Results were similar for adenocarcinoma and squamous cell carcinoma separately.Despite concerns that changes in is study . ORs tenH. pylori seropositivity and lung adenocarcinoma on the one hand, and previous published studies supporting a positive association on the other, we carefully designed a large nested case-control study to thoroughly address the hypothesis that H. pylori is associated with lung cancer. In this well-powered nested case-control study, we found no evidence of an association between H. pylori and lung cancer. Neither overall H. pylori seropositivity nor CagA-specific H. pylori seropositivity were associated with lung cancer. Results were equally null for lung adenocarcinoma and squamous cell carcinoma. Sensitivity analyses by time since diagnosis and age had little effect.Given our preliminary evidence from existing data in ATBC supporting an inverse association between H. pylori seropositivity and lung cancer have been mixed. Of the five previous small case-control studies, three found moderate to strong increased risk of lung cancer associated with H. pylori seropositivity H. pylori seropositivity by lung histology; the association in that study did not vary by lung histology H. pylori seropositivity and lung cancer. Given this lack of adjustment for potential confounders and the fact that small studies are more likely to be affected by chance The results of previous studies of H. pylori seropositivity and subsequent risk of lung cancer. With 700 lung cancer cases, this study is nearly 10 times larger than the next largest study and is well powered to assess differences by histology (adenocarcinoma and squamous cell carcinoma). In addition, all participants were smokers at baseline, so there is less variation in smoking habits and therefore less potential for confounding by smoking. As a well-characterized epidemiologic cohort, ATBC has extensive information about potential confounders, which allowed us to carefully control for cumulative smoking exposure and thoroughly assess other potential confounders. Finally, the association between H. pylori and gastric cancer has already been established in this population using these same assays, demonstrating the adequacy of these assays.This study improves on previous studies in a number of ways. First, as a case-control study nested within the ATBC cohort, this study provides the only prospective data on H. pylori seropositivity and subsequent risk of lung cancer in women. In addition, never smokers may have a different risk of lung cancer associated with H. pylori seropositivity than ever smokers. Although unlikely, it is possible that the potential biologic mechanisms described in the H. pylori infection) may be gender specific or may only be evident in never smokers.Although the inclusion of only Finish male smokers is beneficial in limiting the potential for confounding, it also limits the generalizability of these findings. This study could not address the association between H. pylori seropositivity and lung cancer to date. In this population of Finish male smokers, H. pylori seropositivity was not associated with lung cancer. Although these findings are not entirely generalizable to other populations , it seems unlikely that H. pylori is involved in lung carcinogenesis.This study provides the most definitive findings for


Microscopic polyangiitis is characterized by pauci-immune, necrotizing small-vessel vasculitis and an anti-neutrophil cytoplasmic antibody-associated vasculitis. Although gastrointestinal involvement in microscopic polyangiitis is not rare, endoscopic observation of it is extremely rare. To the best of our knowledge, this is the first case report of small intestinal involvement in microscopic polyangiitis detected and followed up by double-balloon endoscopy.A 70-year-old Japanese woman was transferred to our hospital for close examination of suspected small intestinal lymphoma. Retrograde double-balloon endoscopy revealed various forms of ulcers with redness and edema in the ileum. Histological findings suggested ischemic changes. Because mononeuritis multiplex and a fever spike appeared later, vasculitis was suspected. The perinuclear anti-neutrophil cytoplasmic antibody titer was elevated. Nerve biopsy results suggested vasculitis. From these findings, microscopic polyangiitis was diagnosed. It was suggested that microscopic polyangiitis caused the intestinal involvement. Intravenous pulse cyclophosphamide and oral predonisolone were started. After treatment, perinuclear anti-neutrophil cytoplasmic antibodies decreased to the normal range. Retrograde double-balloon endoscopy after treatment showed ulcer scars and no ulcer.The cause of gastrointestinal involvement in microscopic polyangiitis is ischemia due to vasculitis. It is difficult to diagnose small-vessel vasculitis by endoscopic biopsy. Although histological evidence of microscopic polyangiitis is important, the treatment should not be delayed by repeating the biopsy, because such delay can result in adverse sequela.This case report shows that microscopic polyangiitis should be considered as a differential diagnosis when small intestinal changes like those in the present case are observed by endoscopy. Microscopic polyangiitis (MPA) is pauci-immune, necrotizing vasculitis of small vessels without necrotizing granuloma. MPA is one of several systemic anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitides, along with granulomatosis with polyangiitis and allergic granulomatous angiitis. The term MPA was advocated at the Chapel Hill International Consensus Conference in 1994 , MPA typ4/μl , hemoglobin, 8.2 g/dl , and hematocrit, 26.0% ). Her white blood cell count was 12600/μl  with 1% eosinophils . She demonstrated hypoproteinemia at 6.0 g/dl  and hypoalbuminemia at 2.3 g/dl . The C-reactive protein level was 6.07 mg/dl . Blood urea nitrogen and creatinine levels were in the normal range. Slight proteinuria (1+) was observed. Hematuria was not observed. Chest and abdominal CT scans showed honeycomb changes and ground-glass opacities in the lung and dilatation and wall thickening of the small intestine  scan showed widespread thickening of the small intestinal wall and ascites. The soluble interleukin-2 receptor level was increased to 2930 U/ml . She was transferred to our hospital for close examination of the small intestine because intestinal malignant lymphoma was suspected. Her blood pressure and pulse were normal. Her body temperature was 37.4°C. Her weight decreased from 54 to 41 kg in 1.5 years. She had a 2-year history of lower-extremity paresthesia, and lumbar spinal canal stenosis was diagnosed at another hospital. A physical examination revealed signs of anemia. Superficial lymph nodes were not palpable. Livedo reticularis appeared occasionally on the extremities. She was not taking any non-steroidal anti-inflammatory drugs or antibiotics. Peripheral blood analysis showed normocytic normochromic anemia . Anti-proteinase 3 ANCA, IgG, IgA, IgM, and IgE were within their normal ranges. Sural nerve biopsy was carried out. It did not reveal necrotizing vasculitis; however, it suggested small-vessel vasculitis , anaphylactoid purpura, and so on. We strongly suspected ANCA-associated vasculitides based on the nerve biopsy findings, clinical symptoms, and blood test results. Signs and symptoms of upper airway involvement, granulomatous formation, asthma, and eosinophilia did not exist. Therefore, MPA was diagnosed with Watts’ algorithm.In this case, DBE showed multiple irregular ulcerations with redness and edema in the ileum. Ulcer formation was variable. Gastrointestinal involvement of MPA is caused by ischemia due to vasculitis. Endoscopically observed small intestinal involvement in ANCA-associated vasculitides is extremely rare, and only three previous reports of this disorder as observed by endoscopy have been documented -11. AmonWritten informed consent was obtained from the patient for publication of this case report and any accompanying images. A copy of the written consent is available for review by the Series Editor of this journal.MPA: Microscopic polyangiitis; ANCA: Anti-neutrophil cytoplasmic antibody; DBE: Double-balloon endoscopy; CT: Computed tomographyThe authors declare that they have no competing interests.MF designed and drafted the manuscript. MF and SI carried out double-balloon endoscopy. SI and TI revised and supervised the manuscript. YO treated the patient. YT and HY carried out neurological examination and nerve biopsy. YI supervised the pathological interpretation. All authors read and approved the final version of the manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-230X/13/42/prepub


Monanema joopi n. sp. is described from blood drawn from the heart of the murid Acomys (Acomys) spinosissimus in South Africa. It is characterised by a non-bulbous cephalic extremity, shared with only one of its five congeners, and a cylindrical tail with caudal alae and a spicular ratio of 2.7 in the male. As is typical for the genus, microfilariae are skin-dwelling. They are 185 to 215 micrometres long and have no refractory granules beneath their sheath. A key to the species of Monanema is presented and an amended generic description, based on the six currently known species, is proposed. Species of Monanema are primarily lymphatic and the low intensity of infection with M. joopi n. sp. in blood from the heart, might suggest that not all adults settle in the heart cavities. One might also consider that other, more susceptible rodents serve as hosts for this parasite as well. To date, the geographic range of Monanema includes North America, Africa and Australia, each with representatives of a different lineage. Given the present hypotheses on the evolutionary origin and subsequent migrations of rodents, we expect the origin of Monanema to be in the Palearctic-Oriental region. Acomys (Acomys) spinosissimus . They represented a new species of Monanema Anteson, 1968 (Onchocercidae), a genus parasitic in rodents of which the microfilariae are not in the blood, but in the skin . In this paper, we give a morphological description of the new species and provide a synthetic analysis of the morphology and biology of all currently known species of Monanema. As a result, the definition of the genus was amended, and a hypothesis on its evolution proposed.During an on-going ecological study investigating the ectoparasite and helminth assemblages of murids in South Africa, tiny filarial worms were collected from blood taken from the heart of the Spiny mouse Acomys (A.) spinosissimus was recovered from Goro Game Reserve  in the Limpopo Province in South Africa. Filarial worms were fixed in 70 % ethanol. For morphological studies, worms were cleared in lactophenol and examined under a Wild compound light microscope equipped with a drawing tube. Caudal papillae are tentatively numbered following Monanema indicated that the ear lobes are a predilection site for its skindwelling microfilariae , ear snips were taken from the frozen carcasses of all infected animals and teased apart in lactophenol to check for microfilariae. Specimens have been deposited in the collection of the Muséum National d’Histoire Naturelle (MNHN), Paris, France (accession numbers 340 – 347 YU). Nomenclature of small mammals follows A. (A.) spinosissimus. The liver, lungs and wall of the caecum-colon of five, two and four of these ten hosts, respectively, did not contain any filariae. Microfilariae were found in ear snips of two of the hosts harbouring adult worms.One to two filarial worms were present in blood drawn from the heart of ten of 139 Large parts of the specimens’ body were covered with patches of red blood cells. Slender worms, offwhite in colour. Body of both sexes tapering at ends but anterior extremity nearly cylindrical. Head not bulbous. Oesophagus not divided into muscular and glandular part, of nearly uniform diameter, posterior extremity slightly flattened at junction with intestine. Mouth opening tiny, round . Buccal Female  posteriovagina vera, transverse, with flattened lumen; vagina uterina well-developed, directed posteriorly, with a chamber terminating in a sphincter, composed of epithelial cells  spinosissimus Peters, 1852 (Muridae).Type host: Type locality: Goro Game Reserve , Limpopo Province, South Africa. Collection date: 20.02.2008.Site of infection: blood drawn from cardiac cavities. Prevalence and intensity: prevalence was 7.2 %. Five hosts harboured a single worm, five hosts yielded two worms eachType material: 346 YU; holotype female. Deposited in the MNHN collection.Additional material: Collected from January to August 2008. All specimens deposited in the MNHN collection. 340 YU; entire female. 342 YU; entire female. 343 YU; two entire females, both burst posteriorly. 344 YU; entire female, anterior fragment  and posterior fragment of female. 345YU; entire female. 347YU; two entire females. 341YU; entire male, broken into anterior and posterior part during preparation of drawing.Etymology: the new species is named after Prof. Joop Boomker in recognition of his vast contribution to our knowledge of the helminth fauna of South African wildlife.Monanema (Monanema marmotae (Ackertia marmotaeMarmota (Mar- mota) monax canadensis  [= Marmota monax canadensis ] in Canada and the remaining four from murid hosts. Monanema globulosa  in Kenya, Monanema nilotica El Arvicanthis niloticus  [= A. niloticus testicularis ] in Sudan, Monanema martiniA. niloticus in Mali, and Monanema australeMelomys cervinipes  in Australia ; male tail conical in ventral view, without caudal alae; area rugosa extending to tail; left spicule approximately two to three times longer (411–599 vs 190), spicular ratio about twice as high (5.5–6.7 vs 2.7); microfilariae shorter (117–142 vs 185–215) (185–215) .Monanema australe: head bulbous; tip of female tail not bulbous; male tail twice shorter, conical in ventral view, with prominent paracloacal alae ornamented with small rugosities at base and with three pairs of adcloacal, pedunculate, laterally directed papillae; left spicule longer (231–238 vs 190), right spicule shorter (47–52 vs 68), resulting in higher spicular ratio (4.6–4.9 vs 2.7); microfilariae shorter (125) (er (125) .Monanema globulosa: head bulbous [we noted discrepancies between the scale bar, illustration and text concerning vs 24.5–30.8 mm), with two pairs of small appendages on tail; male tail conical in ventral view, without caudal alae; caudal papillae more symmetrically arranged, with three regular pairs of precloacal papillae; left and right spicules shorter , right spicule without hook; microfilariae shorter (135–150 vs 185–215), 10–11 refractory granules beneath sheath , tip of tail with several conical projections; caudal papillae grossly symmetrical; area rugosa extending to mid-tail; both left and right spicule shorter , right spicule with double hook; microfilariae larger (235–263 vs 185–215), 11–26 refractory granules beneath sheath ; male tail conical in ventral view, without caudal alae; all caudal papillae paired and symmetrically arranged; two precloacal pairs; spicular ratio higher (3.6 vs 2.7); microfilariae larger (203–235 vs 185–215), 13–34 refractory granules beneath sheath (El 1-(4) Cephalic extremity not bulbous.2-(3) Male tail conical in ventral view, caudal alae absent. Spicular ratio 3.6. 17–34 refractory granules beneath sheath of microfilariae. Microfilariae 203–235 long.M. nilotica El Bihari, Hussein & Muller, 19773-(2) Male tail cylindrical in ventral view, caudal alae present. Spicular ratio 2.7. No refractory granules beneath sheath of microfilariae. Microfilariae 185–215 long.M. joopi n. sp.4-(1) Cephalic extremity bulbous.5-(8) Female tail with appendages or projections. Spicular ratio 2.6–2.9. Filamentous part of lamina of left spicule not longer than membranous part. Refractory granules beneath sheath of microfilariae.6-(7) Female tail with several conical projections. Male tail cylindrical, narrow caudal alae present. Right spicule with double hook. 11–26 refractory granules beneath sheath of microfilariae. Microfilariae 235–288 long.M. martiniBain, Bartlett & Petit, 19867-(6) Female tail with two pairs of small appendages. Male tail conical, caudal alae absent. Right spicule without hook. 10–11 refractory granules beneath sheath of microfilariae. Microfilariae 135–150 long.M. globulosaMuller & Nelson, 19758-(5) Female tail without appendages or projections. Spicular ratio > 4.6.Filamentous part of lamina of left spicule longer than membranous part. No refractory granules beneath sheath of microfilariae.Area rugosa anterior and posterior tocloaca. Spicular ratio 5.5–6.7. Membranous part of lamina of left spicule reduced. Right spicule with simple hook. Microfilariae 117–142 long.9-(10) Male tail conical in ventral view, caudal alaeabsent. M. marmotaeWebster, 1967Area rugosa anterior to cloaca, but cuticular rugosities at base of paracloacal alae. Spicular ratio 4.6–4.9. Right spicule with pair of keel-like structures. Microfilariae 125 long.10-(9) Male tail conical in ventral view, paracloacalalae prominent with three pairs of laterallydirected adcloacal pedunculate papillae. M. australeSpratt, 2008Monanema was created by Anteson , Monanema listed by these authors, the undivided oesophagus and caudal papillae on the tail were consistent, but other characters  changed, to accommodate the increasing number of species described. Taking into account the characteristics of the six presently described species, we propose the following amended generic definition for Mona- nema: buccal capsule small ; oesophagus not divided into muscular and glandular part; vulva on level of posterior half of oesophagus; vagina large with chamber and sphincter; absence of caudal appendages on tip of male tail; 7–10 pairs of caudal papillae  and M. martini  spinosissimus examined during the current study, Rhipicephalus simus Koch, 1844 and Rhipicephalus follis Donitz, 1910. While they are likely vectors, their role in the life cycle of M. joopi n. sp. remains to be confirmed.The life cycles of three of six species have been elucidated. The intermediate hosts are ixodid ticks for marmotae , M. globMonanema are diverse, including the lungs, heart cavities, lymphatics of liver and caecum-colon. For a given species, as for example M. martini, filariae can settle in different places, the lymphatics and, less commonly, in the pulmonary arteries . This also suggests that other, more permissive murids might contribute to the maintenance of M. joopi n. sp. in nature.Sites of infection for the species of Monanema has few representatives but a wide geographic distribution ; in South Africa, M. joopi n. sp.; in East Africa, M. nilotica . In Australia, M. australe represents a third evolutionary lineage  and Cercopithifilaria spp. (Monanema in which only six species have been described in over 40 years, although their current geographical and host distribution suggests a much higher diversity.Filariae with dermal microfilariae are rarely detected. Even in animals as well-studied as dogs and rodents, several new species have been reported in the past ten years, for example


AbstractRhynostelis Moure & Urban is a monotypic cleptoparasitic neotropical anthidiine genus currently known from two females. Herein, we describe and illustrate for the first time the male and its genitalia and it is confirmed that Rhynostelis parasitizes nests of Eufriesea. An identification key to the genera of cleptoparasitic anthidiine from the Neotropical region is also presented. Anthidiini and presumably evolved multiple times within the tribe . Austrostelis was recorded by Epanthidium tigrinum ; Hoplostelis is known to parasitize the orchid bee Euglossa cordata   Robertson, 1901  ; Dolichoon, 1901 ; Stelis er, 1806 ; Heteroser, 1804 .Rhynostelis consists of a single species, Rhynostelis multiplicata , which is known from two female specimens collected on the State of Amazonas, Brazil. Herein, we present an updated diagnosis of Rhynostelis, describe and illustrate the male of Rhynostelis multiplicata and, based on two specimens collected from a trap-nest, we record the orchid bee Eufriesea laniventris  as its host. A key to all neotropical cleptoparasitic anthidiine genera is also provide.PageBreakMorphological terminology follows Moure & Urban, 1995http://species-id.net/wiki/RhynostelisRhynostelis Moure & Urban, 1995: 297.HoplostelisRhynostelis) Michener, 2007: 518. http://species-id.net/wiki/Rhynostelis_multiplicataAnthidium multiplicatum Smith 1879: 87.Rhynostelis multiplicata ; Hoplostelis (Rhynostelis) multiplicata ; Integument black, with wide yellow areas in both sexes. Scutum with a large, reverse U-shaped macula; scutellum almost totally yellow; axillae yellow and all terga with yellow bands . Male anApproximate body length 13.29; forewing length 10.45; head width 4.02; head length 3.67; eye length 2.55. Head integument yellow except: distal margin of mandible and apical tooth black; labrum blackened; frons black, bands above superior margin of antennal sockets extending to vertex, including ocelli and finely attached with black spot above compound eyes. Antennae with ventral face of pedicel darkish yellow, remaining segments light brown; dorsal face with scape and pedicel light brown and flagellum amber . PronotaPubescence. Light yellow with predominantly short hairs (less than ocellus diameter). Pilosity longer and denser among ocelli, above antennal sockets and clypeus apex. Hairs of mesepisternum little longer than mesoscutum, curved on scutellum and propodeum. Fore leg with coxa and trochanter covered by dense pilosity. Third to fifth sterna with apical dense and long slight curved hairs.Sculpturing. Head finely punctate with sparser punctures on clypeal protuberance and at supraclypeal area. Mandibles with punctures smaller than that of head. Mesoscutum with integument microreticulated, punctures deeper than head. Gibbous area of mesepisternum with larger and sparser punctures; distance between punctures at least half width a puncture diameter. Punctures of terga fine and shallow; punctures on yellow bands larger and sparser than those on black areas.Pará, Belém: one male, “IPEAN  / 105-2 / EU” (DZUP); andPageBreak one female “IPEAN / 105-1/ EU” (DZUP). Amazonas, Manaus: one female “Proj. DBFF.WWF/ Manaus-AM/ Brasil 04/11/89 / M. B. V. Garcia (DZUP).Material examined. BRAZIL, PageBreakPageBreakonly posteriorly at middle; sixth tergum with subapical band and blackish margin. All sterna yellow; distal sternum with medioapical spot and black margin. The female collected in Manaus is a little smaller than the female from Belém and the integument of the head is darker and with irregular macula. Such differences in color might be caused by some chemical product used during collection or preservation.Remarks on the female from Pará. Approximate body length 16.13; forewing length 12.38; head width 4.90; length head 4.16, eye length 3.18. Integument predominantly yellow. The female differs from the male as follows: black maculae on vertex and frons larger than in male. All terga with yellow bands; basal tergum with complete band; second and third terga with bands slightly interrupted at middle; fourth tergum with band interrupted anteriorly only at middle, fifth tergum with band interrupted Rhynostelis multiplicata emerged from a test-tube placed on a termite nest where an orchid bee was previously seen ). However, the record of the host was never confirmed. The specimens from Belém studied herein emerged from one nest of Eufriesea laniventris , (DZUP), according the identification of Dr. Gabriel A. R. Melo. Thus, the cleptoparasitism of Rhynostelis multiplicata on orchid bees of the genus Eufriesea is confirmed.Host records. Urban and Moure (1995) commented that one female of


H. pylori was a cause of GOO. Both patients presented with a history of weight loss, vomiting, and abdominal pain. Their diagnosis of PUD and GOO was made by EGD and UGI. H. pylori testing was negative for both on multiple occasions but still received H. pylori eradication therapy. Patient 1 after failing pharmaceutical management underwent surgery for definitive treatment. Patient 2 underwent six therapeutic pyloric dilations before undergoing surgery as definitive treatment. These cases suggest that GOO secondary to PUD occurs in the absence of H. pylori infection and surgical management can provide definitive therapy.Gastric outlet obstruction (GOO) in children is most commonly caused by idiopathic hypertrophic pyloric stenosis. Prior to proton pump inhibitors and H2 blockers, peptic ulcer disease (PUD) secondary to  H. pylori infection was recognized as a common cause of GOO. In infants, GOO is usually caused by idiopathic hypertrophic pyloric stenosis (IHPS) [Gastric outlet obstruction (GOO) is a well-identified entity leading to the clinical symptoms of abdominal pain and vomiting. Prior to the introduction of proton pump inhibitors (PPIs) and H2 blockers (H2Bs) peptic ulcer disease (PUD) secondary to s (IHPS) , althougH. pylori antigen, hemoccult, bacteria, and viruses were negative. Patient 1 is an 11-year-old male who presented with a 3-year history of postprandial vomiting and abdominal pain, 1.5 kg weight loss, and plateau in height. Weight at presentation was 28.3 kg (7th percentile), height 144.5 cm (54th percentile), and BMI 13.5 (<5 percentile). On examination only asthenia was noted. The complete blood count, electrolytes, erythrocyte sedimentation rate, stool elastase, and 72-hour fecal fat were normal. Stool examinations for An esophagogastroduodenoscopy (EGD) with a standard endoscope showed retained food and liquid in the stomach despite 18 hours of fasting. Visual examination showed thickened mucosal folds along the lesser curvature and stenosis of the pylorus with no visible ulcers. The patient was started on lansoprazole 30 mg daily. Campylobacter-like organism, CLO test, Kimberly-Clark, Roswell, GA) of the gastric antrum and fundus was negative, upper gastrointestinal series (UGI) showed a narrowed pyloric channel, and computed tomography (CT) of the abdomen/pelvis and pyloric ultrasound were normal. The patient became asymptomatic, and the lansoprazole was stopped after 6 months of therapy.Rapid urease test . Histology of the duodenum showed benign mucosa containing a lymphoid follicle and no active inflammation. The antrum showed mild active gastritis. Serum studies and colonoscopy were not suggestive of Crohn's disease. The patient was referred for surgical intervention. In the operating room a dilated stomach and a 1–1.5 cm thickened area of the pyloric channel were observed. A Jaboulay pyloroplasty was performed. The resected section showed an ulcer, with normal smooth muscle and hypertrophic nerves. The surface epithelium was replaced by granulation tissue. The lamina propria showed mild active chronic inflammation. No etiologic source for the hypertrophy was identified.Three months following surgery, 10 months after initial presentation, the patient was asymptomatic; his weight was 41.2 kg (48th percentile) and height 148 cm (38th percentile).H. pylori IgG and abdominal ultrasound. A large pyloric channel ulcer was seen on UGI. Weight was 53.8 kg (50% tile), height 160 cm (35% tile), and physical exam unremarkable. Patient 2 is a 15-year-old female who presented with a 2-month history of vomiting and weight loss. Laboratory evaluation prior to referral included normal H. pylori. The EGD demonstrated a narrowed pyloric channel  is usually managed with dilatation and PPI. Lau et al. [ therapy –8. H. pyu et al.  in a casu et al.  identifiH. pylori therapy in PUD-related GOO is less clear although eradication is warranted as a primary intervention [H. pylori-negative patients undergoing dilatation, the rate of recurrent obstruction was 4/11 and was not significantly different from the rate of recurrent obstruction in the H. pylori-positive group. Gibson et al. [H. pylori-negative PUD leading to GOO should have early surgery because of high recurrence of obstruction. In addition to PPI therapy benign GOO can be treated with serial dilations , 12 howervention . Lam et rvention  reportedn et al.  concludeH. pylori was not routinely assessed, and these patients were not treated with PPI and/or dilitations. Yen and Kong [H. pylori negative. In the H. pylori negative cohort only one patient required surgical intervention; the other two patients had resolution with PPI therapy only. In children, cases of GOO outside of infancy have been reported that are non-PUD-related . Edwardsand Kong  identifiH. pylori infection. Our patients demonstrate that medical management was palliative but definitive management was surgical.We conclude that GOO secondary to ulceration can occur in the absence of


Terriglobus saanensis SP1PR4T is a novel species of the genus Terriglobus. T. saanensis is of ecological interest because it is a representative of the phylum Acidobacteria, which are dominant members of bacterial soil microbiota in Arctic ecosystems. T. saanensis is a cold-adapted acidophile and a versatile heterotroph utilizing a suite of simple sugars and complex polysaccharides. The genome contained an abundance of genes assigned to metabolism and transport of carbohydrates including gene modules encoding for carbohydrate-active enzyme (CAZyme) family involved in breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides. T. saanensis SP1PR4T represents the first member of genus Terriglobus with a completed genome sequence, consisting of a single replicon of 5,095,226 base pairs (bp), 54 RNA genes and 4,279 protein-coding genes. We infer that the physiology and metabolic potential of T. saanensis is adapted to allow for resilience to the nutrient-deficient conditions and fluctuating temperatures of Arctic tundra soils. T (= DSM 23119 = ATCC BAA-1853) is the type strain of Terriglobus saanensis. It is second of two validly ascribed species of the genus Terriglobus, with T. roseus first isolated from agricultural soils in 2007 , starch glucosyl transferase, ceramide β-glucosyltransferase involved in biosynthesis of cellulose, trehalose, starch, hopanoid, and capsular/free exopolysaccharide (EPS) [T. saanensis is involved in hydrolysis of lignocellulosic soil organic matter, utilization of stored carbohydrates and biosynthesis of exopolysaccharides. Therefore, we surmise that T. saanensis may be central to carbon cycling processes in Arctic and boreal soil ecosystems.Genome analysis of n (9.2%) . This ines (CAZy ) family es (CAZy . T. saanin (yhj) . In addide (EPS) . This su


Chloroplast is an essential organelle in plants which contains independent genome. Chloroplast genomes have been widely used for plant phylogenetic inference recently. The number of complete chloroplast genomes increases rapidly with the development of various genome sequencing projects. However, no comprehensive platform or tool has been developed for the comparative and phylogenetic analysis of chloroplast genomes. Thus, we constructed a comprehensive platform for the comparative and phylogenetic analysis of complete chloroplast genomes which was named as chloroplast genome analysis platform (CGAP).CGAP is an interactive web-based platform which was designed for the comparative analysis of complete chloroplast genomes. CGAP integrated genome collection, visualization, content comparison, phylogeny analysis and annotation functions together. CGAP implemented four web servers including creating complete and regional genome maps of high quality, comparing genome features, constructing phylogenetic trees using complete genome sequences, and annotating draft chloroplast genomes submitted by users.http://www.herbbol.org:8000/chloroplast. CGAP will facilitate the collection, visualization, comparison and annotation of complete chloroplast genomes. Users can customize the comparative and phylogenetic analysis using their own unpublished chloroplast genomes.Both CGAP and source code are available at  Chloroplast contains independent genome derived from a cyanobacterial ancestor . ChloroppsbA-trnH,4. BecaupsbA-trnH-7.http://nar.oxfordjournals.org/content/34/suppl_1/D692.full) and GOBASE  are specialized chloroplast repositories [http://dogma.ccbb.utexas.edu/) is a web-based annotation tool for chloroplast and mitochondrial genomes [http://binf.gmu.edu:8080/GeneOrder3.0/) and BADGER  can be used for comparative analysis of gene arrangements in small genomes [http://www.cs.unm.edu/~moret/GRAPPA/) and MGR (http://grimm.ucsd.edu/MGR/) perform phylogenetic analysis based on gene order changes [As the number of sequenced chloroplast genomes increases rapidly, bioinformatics tools become more critical for the analysis of complete chloroplast genomes. GenBank, EMBL and DDBJ are the primary nucleotide sequences databases. The chloroplast genome database . Entire platform was constructed on a machine with 16 GB RAM. The performances of the database and web servers were tested via a variety of web browsers . As of writing this article, CGAP has been running for half a year.CGAP contains a built-in database and four web servers including visualization of genomes, comparison of genome features, phylogeny analysis and genome annotation. The architecture of the platform was showed in Figure http://www.ncbi.nlm.nih.gov/genomes). According to the annotation information stored in the GenBank format file, CGAP extracted all types of genome features including Gene, CDS, tRNA, rRNA, Exon, Intron, Promoter, RepeatRegion, StemLoop, -10 Signal and -35 Signal. Complete chloroplast genomes and all genome features were stored in CGAP chloroplast database. You can view and download all genomes and features in Fasta format online.CGAP collected 284 complete chloroplast genomes from NCBI Organelle Genome Resources  [CGAP annotated new chloroplast genomes based on feature sequences of the chloroplast genomes collected in CGAP database and basic local alignment method (BLAST 2.2.25+: ih.gov/) . CGAP idih.gov/) -32. FinaCGAP was developed for the comparative analysis of complete chloroplast genomes. It integrated genome collection, visualization, content comparison, phylogeny analysis and annotation functions together. CGAP implemented feature content comparison of chloroplast genomes and a novel alignment-free method for the phylogenetic analysis. Users can customize the comparative and phylogenetic analysis using their own unpublished genomes. To our knowledge, CGAP represents the first comprehensive platform for the comparative analysis of chloroplast genomes. It would facilitate the researches and applications of complete chloroplast genomes.Project name: CGAPProject home page: http://www.herbbol.org:8000/chloroplastOperating system(s): Linux for the distributed source code and operating system independent for the web serversProgramming language: Python 2.6License: Free for academic useCGAP: Chloroplast genome analysis platform; IRs: Inverted repeats; LSC: Large single-copy; SSC: Small single-copy; BBC: Base-base correlation; NJ: Neighbor-joiningThe authors declare that they have no competing interests.JC implemented the programs, and wrote the initial manuscript draft. XZ supplied constructive suggestions for the functions of the platform. GR set up the frame work for the web server. ZL designed the whole study, proposed the alignment-free method and revised the manuscript extensively. All authors read and approved the final manuscript.One by one regional comparison results of genomes.Click here for fileOne by more regional comparison results of genomes.Click here for fileOverview of the phylogenetic tree constructed in phylogeny analysis.Click here for file