Helicoverpa armigera (Hübner) is one of the most destructive lepidopteran pests, which causes enormous economic losses in agricultural production worldwide. The components of the immune system are largely unknown in this insect. The application of entomopathogens is considered as an alternative to the chemical insecticides for its control. However, few studies have focused on the molecular mechanisms of host-pathogen interactions between pest insects and their pathogens. Here, we investigated the immunotranscriptome of H. armigera larvae and examined gene expression changes after pathogen infections. This study provided insights into the potential immunity-related genes and pathways in H. armigera larvae.Innate immunity is essential in defending against invading pathogens in invertebrates. The cotton bollworm, H. armigera larvae injected with buffer, fungal pathogen Beauveria bassiana, or Gram-negative bacterium Enterobacter cloacae. Based on sequence similarity to those homologs known to participate in immune responses in other insects, we identified immunity-related genes encoding pattern recognition receptors, signal modulators, immune effectors, and nearly all members of the Toll, IMD and JAK/STAT pathways. The RNA-seq data indicated that some immunity-related genes were activated in fungus- and bacterium-challenged fat body while others were suppressed in B. bassiana challenged hemocytes, including the putative IMD and JAK-STAT pathway members. Bacterial infection elevated the expression of recognition and modulator genes in the fat body and signal pathway genes in hemocytes. Although fat body and hemocytes both are important organs involved in the immune response, our transcriptome analysis revealed that more immunity-related genes were induced in the fat body than that hemocytes. Furthermore, quantitative real-time PCR analysis confirmed that, consistent with the RNA-seq data, the transcript abundances of putative PGRP-SA1, Serpin1, Toll-14, and Spz2 genes were elevated in fat body upon B. bassiana infection, while the mRNA levels of defensin, moricin1, and gloverin1 were up-regulated in hemocytes.Here, we adopted a high throughput RNA-seq approach to determine the immunotranscriptome of H. armigera are acquired. This study provided valuable information for future functional investigations as well as development of specific and effective agents to control this pest.In this study, a global survey of the host defense against fungal and bacterial infection was performed on the non-model lepidopteran pest species. The comprehensive sequence resource and expression profiles of the immunity-related genes in The online version of this article (doi:10.1186/s12864-015-1509-1) contains supplementary material, which is available to authorized users. Helicoverpa armigera, is a destructive and highly polyphagous insect pest in Asia, Europe, Africa, and Australia. It causes serious damage to cotton, sorghum, corn and several other crops. Further aggravating the situation, this pest is spreading geographically by invading newer territory. Recently, their presence outside the Asian continent has been confirmed with reports of establishment of this species in Brazil [Beauveria bassiana has been widely considered as a potent eco-friendly bio-control agent [B. bassiana as an effective suppressant of H. armigera and other lepidopteran pests is under consideration [B. bassiana kills the pest, it needs to invade and overcome the host immune responses that have not been well understood in H. armigera.The cotton bollworm n Brazil . Primaryol agent . The potderation . Before The invasion of pathogens and parasites into an insect is defended by innate immune system, a strong universal defense mechanism shared by both vertebrates and invertebrates . This syB. bassiana triggers the cellular and humoral immune mechanism of the host resulting in melanized nodules and activation of Toll pathway [B. bassiana infection of mosquito Aedes aegypti enhances the cleavage of hemolymph PPO and its conversion to phenoloxidase (PO), the rate limiting enzyme in melanogenesis [Anopheles gambiae retarded the growth and dissemination of B. bassiana [After invading the host,  pathway ,10. The  pathway . Several pathway . Besidesogenesis . SimilarB. bassiana parasitizes a wide range of hosts including H. armigera and other lepidopteran pests. Most studies on insect immunity were performed in model organisms, such as Drosophila melanogaster [Manduca sexta [Tenebrio molitor [A. gambiae, A. aegypti, Bombyx mori, Apis mellifera and Tribolium castaneum, whose genome sequences are available. It is only recently that H. armigera immunity started to attract some researchers’ attentions [H. armigera interaction with Bacillus thuringiensis and Autographa californica multiple nucleocapsid nucleopolyhedrovirus were obtained [H. armigera genome is still unavailable and its immune response to B. bassiana remains largely unexplored, restricting its further development and adoption as a biological agent in the control of lepidopteran pests.nogaster , Manducaca sexta , and Ten molitor . Systematentions . Fourteeobtained . The expobtained -17. HoweH. armigera is of great importance for understanding the origin and evolution of immune systems, which is a challenging task since genetic backgrounds of non-model insects are unclear, let alone expression profiling. In this work, RNA-seq was employed to perform immunotranscriptome analysis of H. armigera larval hemocytes and fat body in response to the challenges of entomopathogenic fungi B. bassiana and Gram-negative bacteria Enterobactor cloacae. In an attempt to gain insights into the H. armigera immune response against pathogens, we characterized 233 such genes and divided them into pattern recognition, signal transduction, execution, and cellular responses. Hierarchical clustering analyses of differentially expressed gene (DEG) cohorts indicated that the fungi and bacteria elicited distinct expression profiles of genes in hemocytes and fat body. These results provide an overview of the tissue-specific expression profiles in response to infections and a platform for further exploring the molecular basis of host antimicrobial response.More interestingly, systematic survey on Drosophila and mosquitoes are often injected with live pathogens, which eventually kill the hosts. In order to decipher host-pathogen interactions and develop better pest control methods, we performed septic injury on day 2 fifth instar larvae using two entomopathogens, B. bassiana, and E. cloacae, which elicit an inefficient immune response compared with the challenge by dead pathogens. The immunity-related genes based on their expression profiles in fat body or hemocytes were obtained through comparison of the immune challenged transcriptomes. These two entomopathogenic agents had distinct morphological characteristics on plates and under light microscope , fungus-induced fat body (FB_Bb), bacterium-induced fat body (FB_Ec), control hemocytes (HC_Mock), fungus-induced hemocytes (HC_Bb), and bacterium-induced hemocytes (HC_Ec) , totally yielded 150,606 contigs  . Only fewer transcripts were matched to the ones from H. armigera (0.6%), probably due to the unavailability of its genome sequences  and increases the chances of full length gene predictions. Based on the unigene information   of them displaying homology to the known proteins    transcripts that were significantly changed in the fat body elicited by B. bassiana, while more transcripts (496 up- and 2081 down-regulated) suppressed in hemocytes were observed.To gain insights into the tissue-specific transcriptional changes in B. bassiana infected larvae, respectively, among all the experimental conditions  to compare changes in the transcriptomes and found clear variation between fat body and hemocyte samples  enrichment and KEGG analysis were further performed for DETs ,25. Funcunctions . There wB. bassiana and E. cloacae infection.Taken together, our results clearly indicated that global gene expression profiles varied among different tissues and treatments Figures  and 2. WH. armigera and pathogens, we annotated the insect defense genes and examined their phylogenetic relationships. By sequencing the tissues that were enriched in the immune-related transcripts at sufficient depth, followed by the BLAST search [A. mellifera, but similar to that in B. mori. This result indicated that H. armigera, well adapted to various plant hosts and environment, has a sizable repertoire of genes related to the cellular and humoral immune responses against the wounding and infection.For in-depth analysis of the interactions between T search , we weree.g. lipopolysaccharide, peptidoglycan, lipoteichoic acid, β-1,3-glucan) on the pathogen surface to trigger host defense reactions [e.g. AMPs) via immune signaling pathways [H. armigera immunotranscriptome has at least 41 PRR transcripts, including 9 PGRPs, 5 βGRPs, 24 CTLs, and 3 galectins  essential for amidase activity, indicating that they can not only bind but also degrade peptidoglycan  with QPD signature sequence. However, we could not find H. armigera homologue of A. gambiae CTL4 and CTLMA2, which prevented Plasmodium from melanization [H. armigera CTLs are much more diversified than other insect groups and may arise from gene duplications catering to specific pathogen interactions. Apart from CTLs, another class of lectins-Galectins that were found in diverse groups of insects and known to bind to β-galactoside were also essential for pathogen recognition [H. armigera immunotranscriptome revealed three galectins, displaying 1 to 1 orthologous relationship with B. mori galectins  are a sub-group of carbohydrate binding lectin proteins that require the presence of calcium for its association with various types of sugar moieties like mannose and galactose. The protein family shows a considerable amount of diversity in terms of structure and function and can occur in membrane bound or soluble forms. Several insect CTLs have been implicated to play a role in host defense functioning as PRRs and eliciting multiple immune responses including PPO activation, hemocyte-mediated nodule formation, encapsulation and opsonization finally resulting in microbial clearance ,36. Prevtination ,38. Anottination ,16. Our a Figure . The phyal cells ,40. Alonnization . Our finognition . H. armiA. gambiae, 8 in A. aegypti, and 10 in C. pipiens [A. gambiae, TEP1 played the key role in blocking Plasmodium oocyst proliferation in the midgut [Helicoverpa, however, has a relatively small TEP family with only four members which are homologous to B. mori TEPs , belonging to C3/α-2 macroglobulin superfamily, harbor an intrachain β-cysteinyl-γ-glutamyl thioester bond, which is used for self- or non-self-identification . α2-macr pipiens . In A. ge midgut . HelicovH. armigera PRRs encoded by 10 scavenger receptors class B (ScR-Bs), 1 hemocytin, 1 hemolin, 1 DSCAM, 1 Draper, 1 RhoL, 1 Rap1, 1 enabled, 1 Fascin, 1 Scar, 1 Dizzy, 1 TM9SF4, 1 Integrin, 1 Noduler, and 4 Eater, which are involved in phagocytosis, encapsulation, and various other cellular immune responses . The presence of a large number of PRR genes in the immunotranscriptome of H. armigera, indicated their involvement in the immune response to the infection of B. bassiana and E. cloacae.Based on sequence homology search, we have also identified other o-diphenols and further oxidation of o-diphenols to quinones, which then polymerize to form melanin that entraps and kills microbial pathogens and parasites [H. armigera transcriptome. The H. armigera PPO1 and PPO2 share 80.3% and 79% of identity in amino acid sequence to the B. mori PPO1 and PPO2  and their non-catalytic homologs (SPHs) constitute one of the largest protein family in insects that are functionally involved in various physiological processes such as digestion, development, hemolymph clotting, and immune responses . Hemolymocessing ,52. ThusHelicoverpa transcriptome, 10 cSPs (cSP1-10) and 2 cSPHs (cSPH11-12) were identified  but much lower than that of D. melanogaster (57) [H. armigera cSPs and cSPHs are divided into four subfamilies based on their evolutionary relatedness , although lacking catalytic serine residue, act as cofactors for cSP mediated reactions. In ter 57) ,50, partB. mori 1 but muchredicted ,56. Simi ,50, parprotease . Structus cSPH11- were idetivation . CLIPC iH. armigera unigenes yields 22 serpin transcripts, most of which have putative orthologs in B. mori , a detailed study of Serpin1 and 2 gene sequences will reveal the scope of this phenomenon. 1:1 orthologous relationship between H. armigera, B. mori, and M. sexta Serpins3, 4 and 5 allowed us to make predictions about the putative functions of these HaSerpins as summarized below [D. melanogaster Spn27A, M. sexta serpin-3 and B. mori Serpin3 are negative regulators of the melanization cascade. In the phylogenetic tree, H. armigera Serpin3 was located in the same clade with them and also contained the conserved P2-P2′ sequence (NK-FG)  acts as the ligand for this pathway, binding to Toll receptors and triggering its dimerization between leucine-rich repeats [H. armigera transcriptome  played an important role in killing microbes and parasites [GSTs, 3 SODs, and 6 peroxiredoxin transcripts  proteins forming amphiphilic α-helix, hairpin-like β-sheet, or structures stabilized by disulfide bonds . Inducti B. mori ,31. AnalM. sexta , probablarasites . HoweverB. bassiana-, E cloacae- and buffer-injected H. armigera larvae. The results, consistent with the deep RNA-seq data, provide an overview of tissue-specific gene expression patterns of H. armigera larvae in response to B. bassiana infection  occurred in fat body elicited by B. bassiana, suggesting their involvement in antifungal immunity. The gloverin1, lysozyme2, and lysozyme4 mRNA levels increased most dramatically to defend the fungal infection. Notably, most of these genes did not change sharply at transcript level in the other experiment conditions, indicating that fat body plays a major role in the antifungal response.Humoral defense proteins are mainly produced and secreted by fat body, an insect tissue analogous to liver and adipose tissue of mammals in terms of immunity and metabolism. For PRR genes, RNA-seq based transcriptome analysis indicated that short PGRPs  were induced in fat body after the fungal challenge. Similarly, transcription of ScR-B1, B4, B8, TEP2, TEP3, CTL9 ~ 11, 18, 20 ~ 24 and galectins is up-regulated. This change is not limited to PRRs, some signal transducers and regulators are also induced. Cluster analysis of expression patterns revealed that cSP5, 8 ~ 10, cSPH11, 12, Serpin6, 14, 20, 21 mRNAs became much more abundant in fat body after the fungal challenge whereas higher levels of cSP2 ~ 4 and cSP6 transcripts were detected in hemocytes. The pronounced up-regulation of Toll pathway genes  in response to such bacterial infection. This number was apparently lower than that elicited by fungi, which is 24 , signaling modulators , and effector molecules . The mRNA abundances of FADD, Fos, JNK significantly increased in fat body elicited by B. bassiana induced hemocytes, including βGRP1, βGRP2, hemolin, cSP2, cSP6, Serpin2, Serpin5, lysozyme1, lysozyme3 and so on. Immune activation by E. cloacae is also noticeable as demonstrated by induction of PRRs  and immune modulators .Hemocyte mediated defense reactions such as phagocytosis and encapsulation also depend on the recognition of foreign pathogens to trigger downstream immune signaling pathways. The expression profiles of immunity-related genes in hemocytes elicited by the pathogens were highly different from those in fat body. To better understand the complexity of responses of hemocytes against pathogens, the expression profile of immunity-related genes elicited by fungi and bacteria was compared. Gene cohorts of cluster 1 include 21 such genes induced in B. bassiana elicited hemocytes. RNA-seq based transcriptome analysis indicated that long PGRPs  were strongly suppressed by B. bassiana but induced by E. cloacae. Quantitative real-time PCR also revealed that the βGRP1 mRNA level dramatically increased in hemocytes elicited by B. bassiana. In contrast, CTL mRNA levels did not change significantly in hemocytes. The transcript levels of PPOs were high in hemocytes, but significantly decreased in response to fungal challenge. Likewise, components of the IMD pathway , JNK and JAK-STAT pathways  were all dramatically suppressed in hemocytes in response to the fungal infection but moderately induced by bacterial infection, as validated by the quantitative real-time PCR assay of Domeless, JAK, and STAT transcripts. This indicated that signal transduction in hemocytes responds differently to bacterial and fungal infection. More immunity-related genes were regulated by fungi (60) than bacteria (18) in hemocytes, and most of them tended to be suppressed  than hemocytes (cluster 1). The expression of immune recognition and modulation molecules was mainly controlled in fat body, while genes involved in signal transduction, such as JAK-STAT and IMD, were regulated more drastically in hemocytes Figure . In Tolls Figure , which iB. mori and M. sexta, H. armigera, as a notorious lepidopteran pest affecting world agriculture, has not yet been systematically investigated on aspects of immunity until now. In order to develop and apply better pest control methods, we used high throughput sequencing to analyze the transcriptome of hemocytes and fat body in response to bacterial and fungal infection. The 233 immunity-related transcripts discovered are involved in recognition, signal transduction and modulation, and execution mechanisms. This number is certainly going to increase when its genomic information is available, based on the information acquired from this study, we can conclude that the repertoire of immunity-related genes is well conserved in H. armigera. Moreover, we find that these genes displayed distinct mRNA profiles in response to B. bassiana and E. cloacae infection. Their products may constitute an integrated pathway of antifungal immunity, which provide valuable clues for further functional studies in H. armigera responding to B. bassiana, and pave the way for using H. armigera as a model system to study fungal-host interaction [While many immunological studies are focused on eraction . We haveTaken together, this study provided a global view of host defense gene expression profiles in response to bacterial and fungal challenges in a non-model insect. The results could benefit future in-depth study on the role of candidate genes involved in anti-fungal and -bacterial immunity, thereby helping improve the understanding of host-pathogen interactions and evolutionary history of immunogenetics from insects to mammals.H. armigera was obtained from Dr. Qi-Lian Qin at Institute of Zoology, Chinese Academy of Sciences, and maintained in the laboratory. Larvae were reared on an artificial diet at 28 ± 1°C under a photoperiod of 14:10 (l: d) and 70% relative humidity. Male and female pupae were placed in separate glass dishes under the same conditions for eclosion. Adults were fed with 10% honey solution. The colony of H. armigera in the laboratory was maintained for over five generations before experiments. E. cloacae strain (strain no. 1.2022) was obtained from China General Microbiological Culture Collection Center. The bacteria at stationary phase in LB broth (A600 ≈ 2.0) were diluted four times (A600 ≈ 0.5) and used for septic injury. B. bassiana strain ARSEF 2860, was cultured on potato dextrose agar (PDA) plates at 25°C and 80% humidity [A colony of humidity .B. bassiana suspension (1 × 107 conidia/ml), E. cloacae suspension (A600 ≈ 0.5), or sterile PBS using a microinjector. Then all the larvae were kept under the same rearing conditions. The samples were collected from E. cloacae infected larvae at 6 h and B. bassiana infected larvae at 48 h, respectively, at which time larvae started to die. Hemolymph samples were individually collected into ice-cold PBS containing 0.1% 1-phenyl-2-thiourea. Suspensions were pooled in a 1.5 ml Eppendorf tubes and centrifuged at 500 g for 5 min at 4°C to collect hemocytes. Fat body tissues were removed from larvae under a dissection microscope. Control samples from the PBS-injected larvae were prepared at 6 h and 48 h in the same way, and RNA was combined in equal amount.At day 2 after molting, approximately 120 fifth instar larvae from the same batch were divided into three groups. Each larva in the treated groups was inoculated in hemocoel with 2 μl of the Samples of hemocytes and fat body were homogenized using a motor-driven pellet pestle mixer  and lysed in 1.0 ml of TRI Reagent . Total RNA was extracted using RNeasy Mini Kit  according to the manufacturer’s instructions. RNA concentrations were determined on a Nanodrop ND-2000 spectrophotometer . RNA integrity was verified on Agilent 2100 BioAnalyzer .H. armigera larvae (24 in each group) were individually challenged with B. bassiana or E. cloacae. Insects in the treatment groups and control group of buffer injection were maintained in individual containers and fed on the standard diet. Dead larvae were counted at different time intervals for calculation of mortality rate. The survival curves were compared using the Kaplan-Meier and Cox’s proportional hazards model to assess variables that affected survival [Day 2 fifth instar survival . The thrTen μg of total RNA from each treatment or control group was used to enrich poly(A) mRNA using oligo(dT) magnetic beads . In the next step, paired-end RNA-seq libraries were prepared by following the Illumina’s library construction protocol. The challenged and control libraries were sequenced on Illumina HiSeq 2000 platform  in the Beijing Institutes of Biological Sciences (Chinese Academy of Sciences). FASTQ files of raw-reads were produced and sorted out by barcodes for further analysis.de novo assembled to produce contigs using Trinity, the short reads assembling program [Prior to assembly, 2 × 100 bp paired-end raw reads from each cDNA library were processed to remove adaptors, low quality sequences Q < 20), and reads contaminated with microbes using Trimmomatic package . The Fas program ,20 using, and rea program  was used−5. An in-house Perl script was used to identify putative coding regions from the sequences, and translate them into amino acid sequences for further analysis. To determine enriched GO terms, significantly up- and down-regulated genes were subjected to gene ontology enrichment analysis through BLAST2GO against GO database [Non-coding RNAs were obtained using homologous search NONCODE . For fundatabase ,25. Finadatabase . In addiH. armigera unigenes using Bowtie [average method was used to compute the hierarchical clustering and Pearson correlation method was adopted to calculate the distance between both rows and columns. For principal component analysis (PCA), PCs, PC variances, and PC scores were calculated using eigen function in R language [Transcripts abundance were quantified as follows: First, aligning the filtered raw paired-end reads from each of the six tissue-specific library to the corresponding non-redundant g Bowtie . Next, Rg Bowtie  package g Bowtie . These tlanguage .H. armigera unigene sequence collection. The reference insect species include D. melanogaster [A. gambiae [A. mellifera [B. mori [T. castaneum [H. armigera immunity-related genes were confirmed by searching the BLASTX algorithm against the Nr database using a cut-off E-value of 0.1. The deduced amino acid sequences were analyzed by Pfam (http://pfam.xfam.org/) and SMART (http://smart.embl-heidelberg.de/) to detect conserved domain structures required for specific functions. Signal peptide predictions were determined by SignalP4.0.The available immunity-related gene sequences from other model insect species were used as templates to search the nogaster , A. gamb gambiae , A. mellellifera , B. mori[B. mori , and T. astaneum . The potH. armigera sequences were aligned with their homologues from other representative insect species from holometabolous insect orders, including D. melanogaster, A. gambiae, A. mellifera, T. castaneum, and B. mori. The sequences were retrieved from NCBI, Immunodb, or Ensembl. Multiple sequence alignments were performed by CLUSTALX software with BLOSUM series of weight matrices [matrices . Phylogematrices .To validate the expression profile from RNA-seq results, specific primers were designed to perform a quantitative real-time PCR analysis of selected immunity-related genes . H. armigera unigenes are available under NCBI TSA accession number affiliated with the same BioProject.All the raw sequence data and the final


Rhodococcus sp. B7740 was isolated from Arctic seawater and selected for its capacity to synthesize carotenoids. Here, we report the complete genome sequence of Rhodococcus sp. B7740 to provide the genetic basis for a better understanding of its carotenoid-accumulating capabilities, and we describe the major features of the genome. Rhodococcus . Genomic DNA was prepared using a DNA extraction kit (BioTech) following the manufacturer’s instructions. Complete genome sequencing was performed by Nextomics Biosciences Co., Ltd.  using single-molecule real-time sequencing (SMRT) technology. Genomic DNA was interrupted randomly and repaired to construct a DNA library, which was then qualified using an Agilent 2100 Bioanalyzer high-sensitivity kit. The DNA fragments were then sequenced using a PacBio RS II SMRT DNA sequencing system (g system . Finallyg system . Two SMRg system . Annotatg system  and GLIMg system , RNAmmerg system , and Rfag system  databaseRhodococcus sp. B7740 genome resulted in the identification of some key carotenoid-biosynthesis genes, including geranylgeranyl pyrophosphate synthetase, phytoene synthase, and phytoene dehydrogenase. A more detailed analysis of this genome and its comparison with the genomes of other carotenoid-producing bacteria may provide further insight into the mechanisms of carotenoid synthesis.The complete genome comprised 5,341,557 bases, including 5,149 predicted coding sequences, with a G+C content of 64.93%. Forty-seven tRNAs, four 5S rRNAs, four large subunit rRNAs, and four small subunit rRNAs were detected in the genome. The genome encoded a total of 468 subsystems, some of which showed carbohydrate subsystem features. Analysis of the Rhodococcus sp. B7740 has been deposited in GenBank under the accession no. CP010797.The complete genome sequence of


Cordyceps sinensis, also called DongChongXiaCao  in Chinese, is becoming increasingly popular and important in the public and scientific communities. This study summarizes the chemical constituents and their corresponding pharmacological actions of Cordyceps sinensis. Many bioactive components of Cordyceps sinensis have been extracted including nucleoside, polysaccharide, sterol, protein, amino acid, and polypeptide. In addition, these constituents' corresponding pharmacological actions were also shown in the study such as anti-inflammatory, antioxidant, antitumour, antiapoptosis, and immunomodulatory actions. Therefore can use different effects of C. sinensis against different diseases and provide reference for the study of Cordyceps sinensis in the future. Cordyceps is an important kind of medicinal fungi belonging to the Ascomycota, Pyrenomycetes, Hypocreales, and Clavicipitaceae [ Cordyceps are specific macrofungi because of their characteristic parasitic habit on larvae and pupae of insects. As a pleomorphic fungus distributed worldwide, Cordyceps is particularly abundant in tropical forests and humid temperate [ Cordyceps, over 400 species have been described so far [ Cordyceps sinensis, also called as “winter worm, summer grass,” is recognized as the most famous tonic herb in traditional Chinese medicine (TCM) for centuries.The genuspitaceae –5. Cordyemperate –5. WithiCordyceps sinensis is an abundant resource in nature with various biological activity and has been used extensively as a tonic and health supplement for subhealth patients especially seniors in China and other Asian countries. Till now, numerous bioactive constituents have been extracted such as cordycepin, polysaccharides, ergosterol, mannitol, and adenosine [ C. sinensis may be caused by a single active ingredient or by the combined action of many active agents that existed in the extract.denosine , 7. Meandenosine –14. To s Cordyceps sinensis because of the increasing interest both for medicine and mycology [ Cordyceps sinensis for its significant role in the development of new drugs and therapeutics for various diseases. Moreover, realizing the pharmacological action of the monomer composition could strengthen the drug efficacy through extracting a single ingredient in Cordyceps sinensis. Therefore, it is necessary to review the development on the research of C. sinensis.Research is necessary to get an overview about the genusmycology , 16. The C. sinensis, are used as a valuable chemical marker for quality control of Cordyceps [ Cordyceps militaris, nucleosides in Cordyceps have become a focus [ Cordyceps sinensis. Almost all of the nucleotides and nucleosides in C. sinensis can be transformed reciprocally [ Cordyceps sinensis [ C. sinensis and its products.Nucleosides, a major active component ofordyceps . Besides a focus . In succprocally . Furtherprocally , 19. An sinensis . Then, asinensis . Therefo C. militaris and its structural formula was confirmed as 3′-deoxyadenosine but it is only found in natural C. sinensis with very low content and cannot be detected in the cultured ones [ Cordyceps [Early in 1950, cordycepin was first isolated fromred ones . Cordyceordyceps , which iordyceps . C. sinensis stimulates steroidogenesis in primary mouse Leydig cell and activates apoptosis in MA-10 mouse Leydig tumor cells in dose- and time-dependent manners [ C. militaris within the content profiles of nucleosides in Cordyceps product [Cordycepin is a category of compounds that exhibits significant therapeutic potential and has many intracellular targets, including nucleic acid, apoptosis, and cell cycle. Tuli et al. researched the variety of molecular mechanisms that mediate the pharmacological effects of cordycepin. Besides, they deem that cordycepin can participate in various molecular processes in cells because of its similarity with adenosine . Wang et manners , 28. The manners . In addi manners . Besides Cordyceps spp. [ Cordyceps sinensis than in the natural one. Among them, cultured C. sinensis has a large number of adenosines, which are much higher than those in cultured C. militaris [ C. sinensis may be the oxidative deamination of adenosine [ Cordyceps sinensis [ Cordyceps sinensis may contain some enzymes which can decompose adenosine [Adenosine , which peps spp. . The conilitaris , 31. Nucdenosine . Many otdenosine –34.1, A2A, A2B, and A3 [2A plays an important role in depression, locomotion, and anxiety [Also, adenosine is an energy transfer and signal transductant in cells and can still exert a wide spectrum of cytoprotection or prevent tissue damage such as treating chronic heart failure, anti-inflammatory properties, and anticonvulsant activity –38. In a, and A3 . This nu anxiety . In part Cordyceps sinensis. The overall content of nucleosides is much higher in cultured Cordyceps sinensis than in natural ones by comparison [To date, six nucleobases , includimparison . A methomparison . As a remparison . However Cordyceps sinensis showed by many investigations [Three nucleotides, namely, uridine-5′-monophosphate (UMP), adenosine-5′-monophosphate (AMP), and guanosine-5′-monophosphate (GMP), were separated by ion-pairing reversed-phase liquid chromatography-mass spectrometry (IP-RP-LC-MS) developed by Yang et al. . In the igations . Nucleotigations .Cordyceps sinensis contains a great deal of polysaccharides, which can be in the range of 3–8% of the total weight [ Cordyceps polysaccharides mainly include extracellular polysaccharide and intracellular polysaccharide. A large amount of experimental evidence has shown that fungal polysaccharides have a wide range of bioactivities including antitumor [ C. sinensis, were qualitatively and quantitatively analyzed [ Cordyceps polysaccharides were usually composed of these monosaccharides and they play a prominent role in the organism. Polysaccharides are the main contributor towards the pharmacological properties of C. sinensis. Nevertheless, its application has been limited so far because of its limited supply. It is an endangered species due to the excessive harvest of the natural fungus [ C. sinensis has shown as many pharmacological properties as natural C. sinensis [l weight , 51. Corntitumor , anti-inntitumor , immunopntitumor , hypoglyntitumor , hypochontitumor , and antntitumor . In otheanalyzed . Howeverl fungus , 60. Measinensis . C. sinensis. The cultured supernatant was collected and then treated with three times volume of 95% ethanol for precipitation. As a result, the sediment contains a large number of EPSF [22 tumor cells' injection. The data of these studies show that EPSF could elevate the immunocytes' activities in H22 tumor-bearing mice, which might be closely related to elevating peritoneal macrophages' and splenic lymphocytes' activity [ Cordyceps sinensis, has been specifically named and widely concerned. A recent study has shown that the sulfated EPS-1 derivatives have remarkable antioxidant activities. So, sulfation was an effective and favorable strategy for improving the physicochemical properties and bioactivities of fungal polysaccharides [Exopolysaccharide fraction (EPSF), a heteropolysaccharide, was extracted from the cultured supernatant of of EPSF . EPSF ha of EPSF . Previou of EPSF . Thus itactivity . Studiesactivity . Song etactivity . This isactivity . As mentcharides , which i C. sinensis mycelia by ion-exchange and sizing chromatography. APS is composed of mannose, glucose, and galactose in an approximate molar ratio of 3.3 : 2.3 : 1 [12 cells with APS could reduce H2O2-induced cell death, which was investigated by measuring cell viability, lactate dehydrogenase (LDH) release, antioxidant enzyme activity, malondialdehyde (MDA) levels, and intracellular accumulation of reactive oxygen species (ROS) and Ca2+ [12 cells against H2O2-induced injury [ C. sinensis fungus, has stimulating effects on macrophages [2 macrophages to M1 phenotype by activating NF-κB pathway. So APSF also has immunomodulatory effects as many other polysaccharides [An acid polysaccharide (APS) was isolated from cultivated 2.3 : 1 . In the and Ca2+ . In concd injury . Howeverrophages , Chen etcharides . C. sinensis mycelium by hot water extraction, ethanol precipitation, anion-exchange, and gel permeation chromatography [2+-chelating. That indicated a connection between antioxidant activity and reparation of renal failure. On the other hand, CPS-1 stimulates pancreatic release of insulin and/or reduces insulin metabolism, so the polysaccharide can treat diabetes. Especially, the reducing power of CPS-1 was very potent and nearly as effective as ascorbic acid [A water-soluble polysaccharide named CPS-1 had been isolated fromtography . CPS-1 wtography  and treatography . On one bic acid . Cordyceps sinensis polysaccharide, was found to be mostly of α-(1 → 4)-D-glucose and α-(1 → 3)-D-mannose, branched with α--D-glucose every twelve residues on average - and (1→3)-linked D-glucosyl residues. Moreover, mannoglucan showed weak cytotoxicity activity against SPC-I cancer line and no obvious cytotoxicity activities against BCAP37 and SW480 cancer line [ Cordyceps sinensis mycelia and identified by NMR and GC-MS [16- and C18-ceramide levels [β-D-glucan linkages [ Cordyceps sinensis, respectively. The former has the hypoglycemic activity, which can lower the plasma glucose level and decrease protein content of facilitative glucose transporter isoform 2 from rat liver following i.p. administration [A neutral mannoglucan with a molecular weight of 7.7 × 10cer line . Similarnd GC-MS . Wang ete levels . In addilinkages . Besidesstration  and the stration .Sterols components of fungus have important physiological function; they also have a variety of biological activities at the same time. So studying sterols has important theoretical significance and application prospects.2 [ C. sinensis although it is a characteristic of fungi sterol [ Cordyceps sinensis with HPLC method and obtained a high yield. They also presented that ergosterol existed in free and combined states [ E. aerogenes and P. aeruginosa and the fungus C. albicans [Ergosterol  is a cha2 . Ergostei sterol . Y. H. Ld states . It is id states . Zheng ealbicans . At presalbicans . C. sinensis. To clarify the pharmacologic properties of H1-A, a series of researches studied its effect on mesangial cell proliferation, cytotoxicity, cell cycles, and apoptosis. These findings suggest that H1-A modulates some subcellular signal transduction pathways and changes the balance between proliferation and apoptosis of mesangial cells in vitro or in vivo. H1-A may be effective in the management of autoimmune disorders, and the modulation of the signal transduction proteins Bcl-2 and Bcl-XL may represent a target for future pharmacologic interventions [H1-A , a pure ventions . As earlventions . Meanwhiventions .β-D-glucopyranoside (a) and 22,23-dihydroergosteryl-3-O-β-D-glucopyranoside (b), were isolated during the fractionation of the methanol extract of C. sinensis [α,8α-epidioxy-24(R)-methylcholesta-6,22-dien-3β-D-glucopyranoside (c) and 5α,6α-epoxy-24(R)-methylcholesta-7,22-dien-3β-ol (d) are two glycoside derivatives of a sterol and they also exist in the methanol extract of C. sinensis [Two identified compounds, ergosteryl-3-O-sinensis . Besidessinensis , 88. The C. sinensis are enzymes, including the intracellular proteases and extracellular proteases.Most of the proteins in C. sinensis and designated CSDNase. Although acid DNase was first studied biochemically in the 1960s [4)2SO4 precipitation and a series of chromatographic separations. It was found to be single-chained with an apparent molecular mass of 34 kDa and act on both dsDNA and ssDNA as a deoxyribonuclease but act preferentially on dsDNA. The activity of CSDNase was primarily expressed during fungal mycelium growth and it was an endocellular enzyme [A new acid deoxyribonuclease (DNase) that acted at an acidic pH without divalent ions was extracted fromhe 1960s , its strr enzyme . Further Cordyceps sinensis. CSP is a single polypeptide chain with an apparent molecular weight of 31 kD. It is a novel extracellular protease with a free cysteine residue near the active site. It also can hydrolyse bovine serum albumin (BSA) and human serum albumin (HSA) to a lesser extent. Li et al. have found that CSP was a plasmin-link protease but not a plasminogen activator, and it preferentially cleaved the Aα chain of fibrinogen and the α-chain of fibrin. In conclusion, the presence of CSP possibly linked C. sinensis to its pharmacological use for cardiovascular disease, which will provide a new insight into the protein engineering of new thrombolytic agents [A novel serine protease with fibrinolytic activity named CSP was purified from the culture supernatant of the fungusc agents .C. sinensis contains many amino acids and polypeptides, which played an important role in clinical trials. For example, some polypeptide macromolecule in C. sinensis could significantly reduce the mean arterial pressure of rats and induce a direct endothelium-dependent vasorelaxant effect by stimulating the production of nitric oxide and endothelium-derived hyperpolarizing factor [ C. sinensis.g factor . Thus, i Cordyceps sinensis with the putative beneficial effect on diabetic osteopenia in diabetic rats. The relationship between diabetes and osteoporosis is widely studied [β cells and lowering the concentration of serum glucose, which subsequently triggered a lower extent of oxidative stress in diabetic rats [Cordymin is a peptide from the medicinal mushroom studied , 94. Howtic rats . All tho Cordyceps sinensis (A new cyclodipeptide named cordycedipeptide A was isolated from the culture liquid ofsinensis . Its str Cordyceps sinensis (Two new aurantiamides named as cordyceamides A and B were isolated from the culture liquid ofsinensis . Their s C. sinensis and they mainly played a sedative hypnotic effect. Tryptophan is the most effective ingredient among them. Tryptophan is the precursor of serotonin material, which has close relationship with animals' insomnia [There are 18 kinds of amino acids ininsomnia . OtherwiC. sinensis contains a lot of D-mannitol, also known as cordycepic acid, and the content in insect body is higher than that in stroma. Its structure has been determined as 1,3,4,5-tetrahydroxy-cyclohexanoic acid, isomeric with quinic acid. It differs mainly from the natural quinic acid in being dextrorotatory and not forming the lactone [β1-induced fibrogenic response of cultured HSCs, which are the drug's therapeutic mechanisms to inhibit and resolve liver fibrosis [ C. sinensis has effects on diuretic, improving the plasma osmotic pressure and anti-free radical according to pharmacological research and clinical reports [ C. sinensis. lactone . Cordyce lactone . Cordycefibrosis . Additio reports , 103. So C. sinensis. It displayed very good antitumor activity, but the content of the mycelia was very low [A new monosaccharide saponin, whose structure is 3-O-glucopyranoside, was isolated and identified from the mycelia ofvery low . C. sinensis, for example, alkane, polyamine, vitamin, and microelement. Each of these has its own pharmacological effects. More constituents need to be separated and studied in the future research work, however.Moreover, there are many other ingredients in the fungiC. sinensis, a macro fungus of biomedical importance, contains a number of bioactive components ( C. sinensis. Many ingredients in C. sinensis have the antitumour activity as shown above, such as cordycepin, adenosine, EPSF, cordyglucans, and monosaccharide saponins. As investigation into this fungus continues, more bioactive constituents with potential therapeutic value will be isolated. However, new methods and technologies need to be adopted to extract and analyse the components, requiring evaluation along the modern scientific line. Overall, so far, we know only a little of the wonders of this creature and it still has many secrets for us to discover. More research is needed on the herbal medicine and its related species.mponents . Many of


Caulobacter crescentus, a Gram-negative bacterium that divides asymmetrically and is a commonly used model organism to study the cell cycle, asymmetric cell division, and cell differentiation. Here, we announce the sequence and annotated complete genome of the phiKMV-like podophage Percy and note its prominent features.Podophage Percy infects  Caulobacter crescentus is a nonpathogenic bacterium that is found in diverse environments, especially fresh water lakes and soil . Morphology was determined using transmission electron microscopy performed at the Texas A&M University Microscopy and Imaging Center.Bacteriophage Percy was isolated from a water sample collected in College Station, Texas, USA. Phage DNA was sequenced using 454 pyrosequencing at the Emory GRA Genome Center . Trimmed FLX Titanium reads were assembled to a single contig at 41.7-fold coverage using the Newbler assembler version 2.5.3 (454 Life Sciences) at default settings. The contig was confirmed to be complete by PCR using primers that face the upstream and downstream ends of the contig. Products from the PCR amplification of the junctions of concatemeric molecules were sequenced by Sanger sequencing . Genes were predicted using GeneMarkS  and corrhttps://cpt.tamu.edu/pause), resulting in a packaged genome of 44,974 bp. Percy shares 49.7% and 53.8% nucleotide sequence identity across the genome with Pseudomonas phage phiKMV (NC_005045) and Caulobacter phage Cd1 (GU393987), respectively, as determined by Emboss Stretcher , a coding density of 94%, 55 predicted coding sequences, and a G+C content of 60.9%. Of the 55 predicted coding sequences, 21 are novel, 9 are conserved, and 25 have an annotated gene function predicted by BLASTp, InterPro Scan, and CDD analyses 79. The G+tretcher . Core getretcher . Most ofEnterobacteria phage T7 (NC_001604)  . The DNA_001604) . Percy a_001604) , 16. To _001604) –19.KT381879.The genome sequence of phage Percy was deposited in GenBank under the accession number


Helicobacter pylori infection in Indonesia is still controversial and mainly investigated in the largest ethnic group, Javanese. We examined the prevalence of H. pylori infection using four different tests including culture, histology confirmed by immunohistochemistry and rapid urease test. We also analyzed risk factors associated with H. pylori infection in five largest islands in Indonesia. From January 2014–February 2015 we consecutively recruited a total of 267 patients with dyspeptic symptoms in Java, Papua, Sulawesi, Borneo and Sumatera Island. Overall, the prevalence of H. pylori infection was 22.1% (59/267). Papuan, Batak and Buginese ethnics had higher risk for H. pylori infection than Javanese, Dayak and Chinese ethnics . The sensitivity and specificity for RUT and culture were 90.2%, 92.9% and 80.5%, 98.2%, respectively. The patients aged 50–59 years group had significantly higher H. pylori infection than 30–39 years group . Protestant had significantly higher H. pylori infection rate than that among Catholic . It was also significantly lower among peoples who used tap water as source of drinking water than from Wells/river . However only ethnics as become independent risk factors for H. pylori infection. Although we confirmed low prevalence of H. pylori in Javanese; predominant ethnic in Indonesia, several ethnic groups had higher risk of H. pylori infection. The age, religion and water source may implicate as a risk factor for H. pylori infection in Indonesia.The prevalence of  Helicobacter pylori infection has been recognized as one of the most common chronic bacterial infections in humans and associated with peptic ulcer disease, gastric adenocarcinoma, and primary gastric B-cell lymphoma [http://www.bps.go.id/).lymphoma . The ovelymphoma . JavanesH. pylori in Indonesia (H. pylori diagnosis [H. pylori infection in Surabaya (Java island) was low, only 11.5% using five different methods to diagnose H. pylori infection [http://globocan.iarc.fr/). We also found that the highest prevalence of H. pylori was observed in patients from the Chinese Indonesian population instead of patients from the Javanese population. Another our study also found unexpected result about the prevalence of H. pylori infection in minor group in North Sulawesi. The overall H. pylori prevalence was only 14.3% for adults and 3.8% for children [ndonesia . Althougiagnosis . Moreoveiagnosis ,4,6–10. H. pylori in saliva, dental plaque [H. pylori. A number of studies have found poor hygiene standards, crowded households and deficient sanitation are important to both acquisition of infection in childhood and spreading of this disease. Lower social economic status, non-filtered water, and smoking to be a risk factor for H. pylori [H. pylori infection was higher among individuals born before 1950 and lower in those born thereafter; the data indicated a rapid change in the sanitary conditions and standard of living in Japan after the World War II, and clean public water systems were introduced in Japan in the 1950s. Therefore, sanitary conditions, such as a full equipment rate of water and sewage, are considered to be important factors for H. pylori infection [The presence of l plaque , and fecl plaque  indicate. pylori . On the . pylori . In Japanfection .H. pylori in non-Javanese ethnics [H. pylori infection from several islands in Indonesia using same methods. In this study, we examined the prevalence of H. pylori infection in five largest islands using four different tests. We also identified and analyzed environmental factors on different ethnics in Indonesia.To our knowledge, very few reports had investigated  ethnics ,14,15 anH. pylori culture, rapid urease test (RUT), and histological examination. One corporal specimen was used for histological examination. Peptic ulcers and erosive gastritis were identified by endoscopy. Written informed consent was obtained from all participants, and the study protocol was approved by the Ethics Committee of Dr. Cipto Mangunkusumo Teaching Hospital , Dr. Soetomo Teaching Hospital , Dr. Wahidin Sudirohusodo Teaching Hospital  and Oita University Faculty of Medicine .We performed prospective study from January 2014 until February 2015. The survey took place on Jakarta (n = 31) and Surabaya (n = 50) in Java island, Jayapura (n = 21) in Papua island, Makassar (n = 30) in Sulawesi island, Pontianak (n = 64) in Borneo island and Medan (n = 71) in Sumatera island . ExperieH. pylori infections were diagnosed based on the combined results of three methods from four different tests; culture, histology confirmed by immunohistochemistry (IHC) and rapid urease test . For H. pylori culture, one antral biopsy specimen was homogenized and directly inoculated onto Mueller Hinton II Agar medium  supplemented with 7% horse blood without antibiotics. The plates were incubated for up to 10 days at 37°C under microaerophilic conditions . H. pylori were identified on the basis of colony morphology, Gram staining results, and positive reactions for oxidase, catalase, and urease. Isolated strains were stored at -80°C in Brucella Broth  containing 10% dimethylsulfoxide and 10% horse serum.To maximize diagnostic accuracy, H. pylori. IHC was also performed as previously described [H. pylori antibody  overnight at 4°C. After washing, the sections were incubated with biotinylated goat antirabbit IgG , followed by incubation with an avidin-conjugated horseradish peroxidase solution . Peroxidase activity was detected using an H2O2/diaminobenzidine substrate solution.All biopsy materials for histological testing were fixed in 10% buffered formalin and embedded in paraffin. Serial sections were stained with hematoxylin and eosin as well as May–Giemsa stain. Samples with bacterial loads greater than or equal to grade 1 by updated Sydney system were considered positive for escribed . BrieflyU and t-tests. A multivariate logistic regression model was used to calculate the odds ratios (OR) of the clinical outcomes that included age, sex, H. pylori infection status, demographic and environment information. All determinants with P values of < 0.10 were entered together into the full logistic regression model, and the model was reduced by excluding variables with P values of > 0.10. The OR and 95% confidence interval (CI) were used to estimate the risk. A P value of < 0.05 was accepted as statistically significant. The SPSS statistical software package version 18.0  was used for all statistical analyses.Discrete variables were tested using the chi-square test; continuous variables were tested using the Mann-Whitney A total of 267 patients with dyspeptic symptoms  were recruited including 39 patients aged ≤29 years, 40 patients aged 30–39 years, 67 patients aged 40–49 years, 57 patients aged 50–59 years, and 64 patients aged ≥60 years. Based on ethnic group they were consisted of 70 Batak subjects, 54 Chinese Indonesian, 42 Javanese, 30 Buginese, 40 Dayak, 21 Papuan, three Madurese, two Acehnese, two Sundanese, one Banjarese, one Balinese, and one Ambonese subject. Among three tests, RUT showed higher positive rate compared with other tests (both P <0.001).H. pylori-positive rates for each test. Thirty-two patients were positive by all three tests. Fourteen patients were positive only by the RUT. Three and two patients were positive only by histology and culture, respectively. Using histology confirmed IHC as a gold standard, the sensitivity and specificity of RUT and culture were 90.2%, 92.9% and 80.5%, 98.2%, respectively. Negative predictive value (NPV) and positive predictive value (PPV) were 98.1%, 69.8% and 96.5%, 89.2%, respectively. Overall accuracy rates were 92.5% and, 95.5%, respectively. Using histology confirmed IHC, the prevalence of H. pylori infection was 15.4% (41/267), whereas using culture it was 13.9% (37/267) . In the subsequent analyses, patients were considered to be negative for H. pylori infection when all test results were negative, whereas patients with at least one positive test result were considered positive for H. pylori infection ((37/267) . Howevernfection .H. pylori infection with variables relating to gastrointestinal symptoms and past illness history   were infected with H. pylori. There was no difference the proportion of patients were infected with H. pylori in gastritis  and peptic ulcer group  (P = 0.66).Epigastric pain and bloating were the highest symptoms. There were no significant difference between positivity of ctively) . In endoH. pylori infection related with ethnics group (P <0.001). The highest prevalence of H. pylori infection was Papuan patients; nine of 21 (42.9%) were positive for H. pylori. Among 70 Batak patients, 28 (40.0%) was positive for H. pylori. H. pylori infection was found in 11 of 30 Buginese (36.7%) patients. On the other hand, seven of 54 (13.0%) Chinese were positive for H. pylori infection; Chinese-Surabaya  was no significance difference of H. pylori infection compared to Chinese Pontianak (12.5% (3/24), P = 0.93). Three Dayak (7.5%) were positive for H. pylori infection. Among 42 Javanese patients, only one (2.4%) was positive for H. pylori infection. Madurese, Acehnese, Sundanese, Banjarese, Balinese and Ambonese patients were negative for H. pylori infection.There were significant difference on the prevalence of H. pylori infection in the sixth largest ethnics number group according to various range age groups. Interestingly when we just analyzed Papuans, Batak and Buginese, the youngest group aged ≤29 had high prevalence of H. pylori infection contrary with the low H. pylori prevalence group . The ethnic groups also had significant difference with religion, monthly income, source of water, type of latrine, history of drugs, smoking habit and alcohol consumption . Moreover the next analysis on the sixth largest ethnics in this study; Papuan, Batak and Buginese ethnics had higher risk for H. pylori infection than Javanese, Dayak and Chinese ethnics  after adjusted for age and sex. The patients aged 50–59 years group had significantly higher H. pylori infection rate than 30–39 years group . It was also significantly lower among peoples who used tap water as source of drinking water than from Wells/river although after adjusted age and sex. However final model analysis found only ethnics was significantly as independent risk factor for H. pylori infection . There were no statistically significant relationship between H. pylori infection rate and gender, social economic status, type of occupation, marital status, body mass index, type of symptoms, type of latrine, history of drugs, smoking habit and alcohol consumption.Adjusted OR were calculated for analysis . We enters group . The preH. pylori organisms, it have limited sensitivity. Moreover guideline mentioned there was no single test can be considered as the gold standard for the diagnosis of H. pylori infection [H. pylori tests to increase diagnostic accuracy as well as to compare results among tests. We confirmed that the H. pylori infection prevalence in five largest islands in Indonesia using combination of the diagnostic tests to be 22.1%, contrast with several Southeast Asian countries with high H. pylori infection prevalence such as Thailand and the Philippines  [H. pylori infection in Orang Asli, the aboriginal community, residing in the state of Kelantan, Malaysia has been reported to be 19% [Although culture remains a reference method due to ability to directly detect nfection . In the ctively) ,27, but o be 19% .H. pylori in Indonesia should be observed by considering ethno-geographic group. Moreover, several ethnics had higher prevalence of H. pylori infection than Chinese Indonesian, the highest prevalence ethnic was reported in previous study [H, pylori ethnic, Papuans, is various indigenous peoples of Papua island and neighboring islands. They are speakers of the Papuan languages and often distinguished ethnically and linguistically from Austronesians. Most of them quite maintain their traditions, especially who living in central mountainous region/highland zones [H. pylori infection in Papuans concordance with previous study which reported the prevalence was 58% in Papua New Guinea, eastern part of Papua island [H. pylori strains of Papuans peoples which may have similarity with New Guinea and Aborigines Australia strains. The eastern sections of Indonesia, especially Papua, were geographically connected to Australia as a single continent (Sahul) about 60,000 years ago.However as a wide country with spans almost 2 million square kilometers between Asia and Australia and consist of 300 distinct native ethnic groups, the prevalence of us study . The hignd zones . The higet al. reported that seroprevalence of Chinese which born in Malaysia/Singapore (43.1%) were lower than those born in China/Hong Kong (68.2%) [H. pylori infection in chopsticks users which suggests person-to-person transmission of H. pylori via the oral-oral route with ethno-specific food practices an important risk factor. Environmental factors might contribute to the lower H. pylori infection rate in Chinese Indonesians. Beside use Chinese cuisine legacy, Chinese Indonesian also modified some of the dishes with addition of Indonesian local ingredients [H. pylori as same as ‘budu’ or local anchovy sauce, and ‘pegaga’ or centenella asiatica have also been reported to be associated with the low prevalence of H. pylori in Malaysia [The lower prevalence of Chinese descent than that of Chinese non-immigrants was reported in previous studies ,31. Chowredients  which miMalaysia .H. pylori (36.7%), however still lower than that in Philippines [H. pylori infection in North Sulawesi was very low (14.3%) by urine test confirmed with serology [H. pylori prevalence within Sulawesi island. We should remark that Sulawesi island consist of various indigenous ethnic groups which have different phenotype. Although we observed hspMaori type in North Sulawesi, a subpopulation of East Asian type, often isolated from native Taiwanese and Maori tribe as well as some subjects in Philippines [Another interesting result we found was that Buginese, a majority numerous ethnic in the southern part of Sulawesi had also high prevalence of lippines . Sulaweslippines . Alfred lippines . Contrarserology . Recentl. pylori .7%, howeH. pylori infection in Javanese group also confirmed our previous study in Surabaya, Java island [H. pylori prevalence as well as Malay ethnic group in Malaysia which have the similar host genetic factors that reduced susceptibility to H. pylori infection [H. pylori infection. Dayak is the indigenous peoples of Borneo which was categorized on Malayo-Polynesian linguistic subgroup speakers. Europeans created the term `Dayak`to refer to the non-Malay inhabitants of Borneo [The extremely low prevalence of a island . Javanesnfection ,38. In tf Borneo .H. pylori infection. Genotyping of H. pylori strains and host factors analysis from Batak ethnic may partly explain the reason of these differences. The transmission routes of H. pylori are still not entirely understood, but human-to-human spread through oral-oral or faecal-oral routes are considered the most plausible routes for infection [H. pylori infection rates.However it is still questionable why Batak ethnic in North Sumatera had high prevalence of nfection . TherefoH. pylori infection in developing countries that H. pylori infections occur earlier in life and with high frequency [H. pylori infection in Protestant was higher than that in Catholic. The religious beliefs and practices might be as important factors for spreading H. pylori in Indonesia. However it may also due to that in this study, the majority of Protestant were Papuan and Batak ethnics which have the highest prevalence of H. pylori. The use of well or river water was associated with increased risk of infection. Therefore, consistent with several previous studies [H. pylori could survive and contaminate the local water supplies to be the most plausible. However in fact, only ethnics as independent risk factor for H. pylori infection. Further studies in each group is needed to clarify the most influenced variables of demographic and sanitation which related prevalence patterns of H. pylori infection in Indonesia, especially in high prevalence area.Our data showed there were difference of several demographic and environmental factors between ethnic groups; age, religion and the source of drinking water were associated with increased risk of infection. Several ethnics showed the age-related prevalence pattern of requency . We also studies ,40, H. pH. pylori infection is higher in dyspeptic patients than in the general population. Currently we are still continuing surveys to add the sample numbers and expand to other islands, including collecting serum. A larger sample size is necessary to elucidate the prevalence of H. pylori in Indonesia. We just performed survey in 1–2 cities every island. Most of the cities is a capitol of province which may have better sanitary and socio-economic condition than the rural part. Therefore, our results cannot be generalized across Indonesia. A study to investigate genotypes of H. pylori strains in Indonesia is now in progress. Genotyping information may partly explain the differences of H. pylori infection among ethnic group in Indonesia.Similar with our previous study , rapid uH. pylori infection than Javanese group, predominantly ethnic which reported have low prevalence of H. pylori infection in previous study. The age, religion and water source may implicated as a risk factor for H. pylori infection in Indonesia. Improving the sanitary conditions to decrease the prevalence of H. pylori in Indonesia is important.Several ethnics group have higher risk for S1 TableH. pylori positive in case at least one test showed positive, the prevalence of H. pylori infection was 22.1% (59/267).When patients were considered to be (PDF)Click here for additional data file.


We report that a subset of avian genes is characterized by very high GC content and long G/C stretches. These sequence characteristics correlate with the frequent absence of these genes from genomic databases. We provide several examples where genes in this subset are mistakenly reported as missing in birds.www.dx.doi.org/10.1186/s13059-015-0725-yThe online version of this article (doi:10.1186/s13059-015-0724-z) contains supplementary material, which is available to authorized users. A recent paper reported 274 genes as missing in birds but present in the genomes of most other vertebrate lineages . Here, wet al.  in P. humilis as EPOR and SWSAP1. This is in keeping with gene arrangement in mammals.Pursuing our long-term interest in chicken hematopoiesis, we noticed that the gene cluster reported in Figure 2 of Lovell et al.  next to in birds . Using mMMP14 and MRPL2 genes also showed the GC-rich sequence characteristics. To show that this sequence pattern causes persistent problems for correct gene assembly, we analyzed the 89 genes   and EPOR genes , EPOR, its genomic neighbor SWSAP1, and other GC-rich genes reported here (e.g. MMP14 and LPPR2, as shown in Fig. All these newly assembled avian genes previously considered missing in all birds or in the chicken share similar GC-rich sequence characteristics. GC-rich genes are extremely hard to amplify by PCR, a key step in NGS library preparation , 8. Thesent Fig. . TherefoEPO and EPOR loci, we analyzed the gene set reported as missing in birds [et al. [et al. [We report the existence of avian genes with strongly biased GC patterns. These genes have been underrepresented in genomic databases, probably due to technical obstacles to genomic library preparation. In addition to identifying chicken in birds  and foun [et al.  was not  [et al.  are prob [et al. . Here, w


Pulmonary exacerbations (PEx) are critical events in cystic fibrosis (CF), responsible for reduced quality of life and permanent loss of lung function. Approximately 1/4 of PEx are associated with failure to recover lung function and/or resolve symptoms. Developing tools to optimize PEx treatment is of paramount importance.We retrospectively audited all adults infected with Pseudomonas aeruginosa, experiencing PEx necessitating parenteral antibiotic therapy from 2006–2012 from our center. Quantitative analysis of sputum at admission, twice-weekly during hospitalization, and end of therapy were compared to baseline  and follow-up (after PEx) samples. Change in P. aeruginosa burden from baseline was assessed for any and all morphotypes (ALL), as well as mucoid (MUC) and non-mucoid (NON) isolates specifically. PEx were identified as failures if >90% of baseline pulmonary function was not recovered.Forty-six patients meeting the above inclusion and exclusion criteria experienced 144 PEx during this time . Patients were treated for a median 14 days (IQR 13–16). No increase in ALL, MUC or NON were detected at PEx, nor was there an association between change in sputum density and magnitude of lung function decline. PEx failures were observed in 30% of events. Reductions of at least 1-log and 2 log P. aeruginosa sputum density was observed in 57% and 46% (ALL), 73% and 55% (MUC) and 58% and 46% (NON) of PEx, respectively. Factors associated with greater reduction of P. aeruginosa sputum density included choice of β-lactam antibiotic, antibiotics with in vitro predicted activity and treatment duration. PEx associated with reductions in P. aeruginosa sputum density were not associated with a reduced risk of PEx failure.Enhanced killing of P. aeruginosa during PEx does not predict improved clinical outcomes. Studies accounting for the polymicrobial nature of CF respiratory disease and the heterogeneity of P. aeruginosa causing chronic infection may enable the identification of a more appropriate pathogen(s) based biomarker of PEx outcomes. Pseudomonas aeruginosa infects 50-70% of patients  whereas concomitant ICS were associated with a trend to increased risk  of failure. Antibiotic choice did not impact PEx outcome, nor did the number of antibiotics with in vitro predicted activity against ALL, MUC or NON (not shown). Failure risk did not differ based on delivery of PEx treatment; 33/68 (49%) in hospital, 18/42 (43%) HPTP, 9/32 (28%) transitioned from hospital to HPTP, 1/2 (50%) admitted to hospital from HPTP, p = 0.24. Concurrent use of additional anti-staphylococcal agents did not reduce failure risk .PEx treatment failures, as defined by failing to recover 90% of baseline FEV6 CFU/ml (IQR 105-106), S. aureus 106 (IQR 105-106), P. aeruginosa ALL 106 (IQR 106-107), MUC 106 (IQR 105-106) and NON 106 (IQR 105-107). Relative to baseline, admission PEx samples did not demonstrate an increase in P. aeruginosa burden . An association between number of antibiotics with in vitro predicted activity and reduction of P. aeruginosa density was observed although this reached statistical significance only for regimens with activity against the NON-isolates  of PEx had ≥1 isolate that was resistant. At least one isolate was resistant to tobramycin, in 54.3% (77/142) of PEx. Highly resistant isolates were rare in admission PEx samples and over a one-year period prior to PEx , 22% (25/116); NON 41% (45/110), 50% (57/113) and PDR; MUC 1% (1/103), 3% (3/115) and NON 12% (13/109), 22% (25/113), respectively. Antibiotic choice impacted 2/142 of P. aeruginosa sputum density. In particular, concurrent chronic azithromycin, DNase, nor hypertonic saline impacted P. aeruginosa density. A trend was observed in individuals receiving concurrent ICS at having a lower likelihood of reducing P. aeruginosa sputum burden (not shown). Venue for antibiotic delivery did not impact bacteriologic response (not shown). Treatments <14 days produced an inferior bacteriologic response, although this met statistical significance for only the NON-isolates , Group C Streptococcus (3), and one each of MSSA, MRSA and H. influenzae. None of these resulted in changed antimicrobial management (with the exception of TMP/SMX for MRSA) and none manifested in chronic infection. Exacerbations associated with the emergence of new pathogens did not impact risk of PEx failure .MSSA was a chronic colonizer of patients in 31/146 (21.2%) of PEx, and two had a history of recent-prior MRSA transient colonization, though none on admission. MSSA was more likely to demonstrate a significant bacteriologic response with 26/30 (81%), 20/30 (67%), 14/30 (46%) experiencing at least a 2-log, 4-log or 6-log drop in MSSA, respectively at the end of therapy. Bacteriologic responses of MSSA and OF during PEx did not predict clinical success , MUC  and NON-MUC  .Change in CFU of ) Figure . EARLY cPEx are increasingly recognized as a significant contributor to the progressive nature of CF lung disease . AvoidinP. aeruginosa burden [P. aeruginosa killing. Smith et al., followed 75 patients chronically infected with P. aeruginosa through PEx managed with single or dual agent anti-pseudomonals [P. aeruginosa, reduced sputum DNA and protein levels, none of these factors correlated with absolute change in pulmonary function. Similarly, Mclaughlin et al., did not observe a correlation between burden of P. aeruginosa and absolute lung function recovery [P. aeruginosa density using quantitative PCR [Anti-pseudomonal antibiotics are an integral component of PEx management. Independent of enhanced airway clearance, anti-pseudomonal antibacterials have been shown to improve pulmonary function in a linear capacity relative to reducing a burden . Few studomonals . While trecovery . More retive PCR . These sP. aeruginosa burden was noted in approximately 60% of patients. This decline was predictable based on early changes in P. aeruginosa burden after only four days of treatment. Reduction in total P. aeruginosa burden, nor mucoid or non-mucoid isolates specifically did not, however, correlate with risk of failing to recover lung function. Enhanced killing of P. aeruginosa was observed in patients receiving antibacterials estimated to have more potent in vitro activity. This was particularly true when antibiotics had greater activity against non-mucoid isolates that were more readily reduced with antibiotics. Furthermore, we have observed like others, that in those few patients who transiently achieve clearance of P. aeruginosa during PEx treatments, no enhancement in clinical outcomes was afforded [We sought to determine if bacteriologic killing as a measure of effectiveness of antibacterial therapies correlated with clinical outcomes in PEx. During antibacterial treatment of PEx, a progressive decline in afforded .P. aeruginosa treated with regimens devoid of anti-pseudomonal activity suggesting response is more complicated than a one-host and one-pathogen model [Streptococcus milleri group , 40% of PEx were identified to have this organism emerge as numerically dominant at the onset of PEx, and resolution of symptoms correlated with reduction in sputum burden [Prevotella and Chrysiogenales, levels of other microbiome constituents do not correlate with improvements in lung function [To complicate matters, studies have shown resolution of PEx in patients chronically infected with en model ,32. Accom burden ,33,34. Ufunction ,36.P. aeruginosa load, or specifically MUC or NON morphotypes associated with an exacerbation. Nor was there an association between change in P. aeruginosa sputum density and extent of decline in pulmonary function. This data mirrors that of other recent studies that have challenged the long held belief that an increase in P. aeruginosa triggers PEx [P. aeruginosa morphotypes are involved. These factors may include: environmental exposures such as pollution [P. aeruginosa sub-populations [We did not detect an increase in either total gers PEx -39. Cleaollution  and alleollution ; host faollution  and co-mollution ,43,44 paollution , changesollution ,46 and sulations ,48. FurtP. aeruginosa burden [P. aeruginosa sputum density.Many contentious issues exist in PEx management strategies. Data in these areas are difficult to interpret as outcomes have traditionally focused on absolute improvement in pulmonary function, as opposed to a more appropriate model of proportional recovery ,47 Wherea burden ,47. Likea burden . Herein P. aeruginosa burden. In particular, cefepime was inferior at reducing P. aeruginosa sputum burden, although no impact on PEx outcome was noted. Interestingly, meta-analyses have demonstrated patients treated with cefepime relative to an alternate β-lactam with a similar spectrum of activity may be associated with an increased risk of mortality [The effectiveness of different antibiotics in achieving good PEx outcomes has been previously assessed. Herein we did observe differential abilities of antibiotics to reduce ortality ,51. Whilortality ,53. BaseP. aeruginosa during antibacterial treatment and may warrant further caution with these agents in CF.ICS are common agents in CF, with approximately one third of patients receiving them. However, their utility has not clearly been established and the general consensus is that they are over used and may even be harmful . Indeed,P. aeruginosa sputum density. To do so we have utilized a proportional lung function recovery model to overcome the deficiency whereby other studies using absolute improvement fail to account for the extent of initial decline and therefore are poor predictors of success or failure [P. aeruginosa reported routinely by clinical laboratories [P. aeruginosa using qPCR would not distinguish between mucoid and non-mucoid isolates. As infection with mucoid isolates of P. aeruginosa is associated with reduced success of eradication treatment in patients with new infection [Herein we have attempted to expand upon other studies assessing PEx outcomes and changes in  failure . While t failure . Furtherratories . Indeed,nfection ,58 and anfection ,59, it mP. aeruginosa drug resistance observed herein relative to other works [Several limitations of this work deserve consideration. Because diagnosis of PEx were collected and analyzed retrospectively, the data is not as robust as prospectively collected data. Symptoms or signs not documented in clinical records may inadvertently be documented as absent. This may be somewhat mitigated, as these findings were collected at a single CF clinic over a short time period, where practice patterns were relatively uniform. Our study excluded PEx not requiring parenteral antibiotics. We observed a significantly higher rate of PEx failures than in other works ,11,15. Wer works . Whetherin vitro predicted activity against all morphotypes, and in particular non-mucoid isolates was more likely to result in enhanced P. aeruginosa killing during PEx. However, patients who experienced enhanced killing of P. aeruginosa after completion of therapy were not afforded a reduced risk of PEx failure. Accordingly, bacteriologic response during PEx treatment cannot be used to predict success.In this work we identified that while the majority of patients treated with parenteral anti-pseudomonals experienced a temporary reduction in sputum burden, approximately 40% did not. This bacteriologic response could be predicted on the basis of sputum samples collected early into antibiotic treatment. Antibacterial treatments with a greater number of agents with


Infections caused by multidrug resistant organisms (MDRO) are associated with higher morbidity, mortality and healthcare costs. WHO recommends hospitals to monitor antimicrobial use to reduce MDRO prevalence.This 4-year study described the annual MDRO prevalence and annual antimicrobial consumption. It also investigated their relationship.S.aureus(MRSA), ESBL E.coli, ESBL K.pneumoniae, and MDR P.aeruginosa were evaluated. Data on annual consumption (Defined Daily Dose) of selected antimicrobials were analyzed. Linear regression was used to analyze trend in antimicrobial consumption and MDRO prevalence. Pearson’s correlation coefficient was used to determine their relationship. A p-value<0.05 and r2>0.5 were considered statistically significant.Annual antibiogram of Methicillin Resistant E.coli significantly increased, ESBL K.pneumoniae and MRSA remained stable and MDR P.aeruginosa significantly decreased. The increased consumption of cefazolin, cefepime, meropenem and cotrimoxazole were positively correlated with increased ESBL E.coli prevalence. The higher use of antimicrobials without anti-Pseudomonal activity ceftriaxone and ertapenem versus piperacillin-tazobactam were positively correlated with decreased MDR P.aeruginosa prevalence. MRSA prevalence positively correlated and mirrored linezolid usage as it is a 2nd line agent for it. The absence of increase in ESBL K.pneumoniae prevalence may be due to decreased fluoroquinolone use.There was a significant increase in annual patient days while annual antibiotic usage decreased. The most common antibiotic class used was cephalosporin, followed by beta-lactam/beta-lactamase inhibitors then fluoroquinolones. Individually, piperacillin-tazobactam, ceftriaxone and ertapenem use significantly increased. The prevalence of ESBL E.coli increased, ESBL K.pneumoniae and MRSA remained stable; MDR P.aeruginosa decreased. A positive correlation between antimicrobial use and MDRO prevalence was established. Establishing an antibiotic restriction program is recommended to address the significant prevalence of MDRO.This study at our institution found that antimicrobial use did not increase despite increase in annual patient days. The prevalence of ESBL None declared.


Paenibacillus darwinianus owe their resilience to substantial genomic changes. For this, genome-based comparative analyses were performed on three P. darwinianus strains, isolated from gamma-irradiated RSR soils, together with nine temperate, soil-dwelling Paenibacillus spp. The genome of each strain was sequenced to over 1,000-fold coverage, then assembled into contigs totalling approximately 3 Mbp per genome. Based on the occurrence of essential, single-copy genes, genome completeness was estimated at approximately 88%. Genome analysis revealed between 3,043–3,091 protein-coding sequences (CDSs), primarily associated with two-component systems, sigma factors, transporters, sporulation and genes induced by cold-shock, oxidative and osmotic stresses. These comparative analyses provide an insight into the metabolic potential of P. darwinianus, revealing potential adaptive mechanisms for survival in Antarctic soils. However, a large proportion of these mechanisms were also identified in temperate Paenibacillus spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. These analyses have also revealed that the P. darwinianus genomes contain significantly fewer CDSs and have a lower paralogous content. Notwithstanding the incompleteness of the assemblies, the large differences in genome sizes, determined by the number of genes in paralogous clusters and the CDS content, are indicative of genome content scaling. Finally, these sequences are a resource for further investigations into the expression of physiological attributes that enable survival under extreme conditions and selection processes that affect prokaryotic genome evolution.Antarctic soils represent a unique environment characterised by extremes of temperature, salinity, elevated UV radiation, low nutrient and low water content. Despite the harshness of this environment, members of 15 bacterial phyla have been identified in soils of the Ross Sea Region (RSR). However, the survival mechanisms and ecological roles of these phyla are largely unknown. The aim of this study was to investigate whether strains of  Firmicutes represents one of the most abundant and ubiquitous bacterial groups in the environment. Members of this phylum have been identified in a wide variety of habitats that vary in physical and biochemical characteristics, including the vertebrate gut Firmicutes typically form a minor, yet consistent, component of microbial communities Firmicutes can be locally abundant, as observed in grassland soils of The Netherlands Firmicutes, members of the genera Bacillus, Clostridium, and Paenibacillus are commonly identified in soil microbial communities The phylum Paenibacillus contains a monophyletic lineage of endospore-forming bacteria represented by over 100 described species Paenibacillus genomes have been sequenced, of which two, those of P. larvaeP. vortexP. larvae was investigated for its ability to cause American foulbrood, a disease of honey bees, and P. vortex for its social organisation and complex pattern-forming behaviours.The genus P. darwinianus strains, isolated from gamma-irradiated soils of the Ross Sea Region (RSR), Antarctica Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Gemmatimonadetes, Nitrospira, Planctomycetes, Proteobacteria, Spirochaetes, Verrucomicrobia and Candidate ‘TM7’ Firmicutes were identified in most soil microbial communities, but their relative abundance was variable, and they typically formed a minor component of the community. However, they can be abundant, as observed in ornithogenic soils of Cape Hallett Paenibacillaceae (of phylum Firmicutes) amongst the most abundant OTUs  Here, we report genome analyses of three Paenibacillus are commonly cultured and identified in polar and permafrost soil communities. Despite this, only six novel Paenibacillus spp., namely P. antarcticusP. cineris, P. cookiiP. darwinianusP. macquariensisP. wynniiP. darwinianus owe their resilience to substantial genomic changes compared to Paenibacillus spp. isolated from temperate soil environments. Therefore, the objective of this study was to compare genomes of three strains of P. darwinianus with nine temperate, soil-dwelling Paenibacillus spp., focusing on traits that may contribute to survival and growth in soil, including signal transduction pathways, sigma factors, sporulation, motility and their ability to cope with oxidative and osmotic stress. This study has demonstrated that, while the genomic content investigated is largely similar across all 12 Paenibacillus isolates, there is some evidence for genome content scaling.Members of the genus P. darwinianus genomes are composed of the chromosome (approx. 3 Mbp), each containing a varying number of DNA scaffolds ranging from 107 to 111. The genome completeness was approx. 88%, assessed by the occurrence of essential, single-copy genes. Due to this incompleteness, we have regarded the apparent absence or low copy number of a given gene with caution. General genome features of the P. darwinianus strains compared with nine temperate Paenibacillus spp. are listed in P. darwinianus genomes were generated on the IMG website. These plots revealed high levels of synteny between the three strains . The genomes contained 3,101–3,123 open reading frames with an average coding density of 87.4%. These genomes comprised approx. 3,000 protein coding sequences (CDSs). For each genome, approx. 77% of the total CDSs were assigned to clusters of orthologous groups (COG) categories. Notably, the highest proportion of genes was assigned to COG categories including amino acid transport and metabolism [E], carbohydrate transport and metabolism [G], transcription [K], and translation, ribosomal structure and biogenesis [J] (P. darwinianus genomes as compared to the temperate Paenibacillus spp. (P<0.01). Temperature range data indicated that P. darwinianus strains are psychrotolerant with optimal, minimal and maximal growth occurring at 18, 10 and 37°C, respectively Paenibacillus spp. exhibit growth over a wide range of temperatures (10–45°C) with optimal growth occurring between 25 and 30°C The three  strains . The genesis [J] . TransmeP. darwinianus strains and nine temperate Paenibacillus spp. were carried out using CMG-Biotools Paenibacillus spp. was determined. This analysis revealed broad similarities in genome-wide amino acid usage profiles for all 12 Paenibacillus spp. with Ala, Leu, Gly, and Val the most frequently used amino acids across all genomes (Paenibacillus genomes using CMG-Biotools P. darwinianus strains exhibited a high level of conservation of gene families (89.2–90.3%). This observation was also supported by the pan- and core-genome analysis, as the P. darwinianus core- and pan-genome comprised 2,735 and 3,194 gene families, respectively. A large proportion of genes in the P. darwinianus core-genome were assigned to COG categories including carbohydrate transport and metabolism [G], amino acid transport and metabolism [E], and transcription [K]. In contrast, the temperate Paenibacillus core- and pan-genome comprised 1,139 and 25,493 gene families, respectively. Genes in the temperate Paenibacillus core-genome were assigned to COG categories including translation, ribosomal structure and biogenesis [J], amino acid transport and metabolism [E], and transcription [K]. Overall, the temperate and Antarctic core- and pan-genome comprised 998 and 26,612 gene families, respectively. Finally, up to 6% of the CDSs were in paralogous clusters for temperate Paenibacillus spp., whereas approx. 2.4% of the CDSs were in paralogous clusters for all P. darwinianus strains  were attributed to TCS in genomes of the temperate Paenibacillus species. Genes for TCS, DesK-DesR for low temperature Paenibacillus genomes , was not identified in P. darwinianus genomes Flavobacterium psychrophilum, expression of the sensor kinase LytS was cold-induced, with expression significantly upregulated at 8°C compared to its expression at 20°C Two-component signal transduction systems (TCS) represent a primary means by which a bacterial cell senses and responds to a variety of stresses and to the changing environment. gulators . A large genomes . Notably−1 soil 4-dicarboxylates, oxalate and succinate have been identified in aerosol particles over coastal East Antarctica 4-dicarboxylates, namely succinate, fumarate, malate, and oxaloacetate) were identified in the P. darwinianus genomes and in the genomes of just two temperate Paenibacillus spp., P. mucilaginosus and P. terrae. Genes encoding additional proteins required for the function of sensor kinase, DctS including DctA and DctB, were also identified in all P. darwinianus genomes With the exception of ornithogenic soils formed under penguin rookeries, RSR soils typically contain low concentrations of organic carbon, ranging from 0.01 to 0.96 mg C gP. darwinianus genomes contained genes associated with a diverse set of sigma factors similar to the multiple copies observed in psychrophilic bacteria Planococcus halocryophilusPsychromonas ingrahamiiA and alternative sigma factors including general stress response factor, σB, chemotaxis and flagellar motility associated factor, σD, cell envelope stress associated factor, σECF, cold shock response factor, σL, and sporulation-specific factors, σE σF, σG, and σHB is crucial as it controls the expression of an estimated 150 or more genes in response to a wide range of stress and starvation conditions B, including RsbW and RsbV, were also identified in all P. darwinianus strains.Sigma factors are dissociable units of RNA polymerase that activate the conditional expression of a specific set of genes in response to a particular stress or stimulus, thus implementing compensatory physiological changes. 2−), hydrogen peroxide (H2O2), hydroxyl radical molecules (⋅OH) and lipid peroxides, are both produced and accumulated as a result of aerobic metabolism P. darwinianus strains contained two copies of the catalase gene, two of the superoxide dismutase gene sodA and one of the DNA oxidative damage protectant gene dps. Additionally, up to six copies of the peroxiredoxin genes, ahpCF, bcp and tpx and nine copies of the thioredoxin genes, trxA and trxB were identified in all P. darwinianus strains  including superoxides (O strains . Other b−2 soil opuA) comprising three components: OpuAA, the ATPase component, OpuAB, the permease component and OpuAC, the periplasmic component, were identified in all P. darwinianus strains and in most temperate Paenibacillus spp. P. darwinianus genomes and in the genome of just one temperate species, P. terrae. Proline biosynthesis enzymes, γ-glutamyl kinase (proB), γ-glutamyl phosphate reductase (proA) and Pyrroline-5-carboxylate reductase (proC) were also identified in all Paenibacillus genomes psychrerythraeaP. halocryophilusPseudoalteromonas haloplanktisP. ingrahamiiP. darwinianus strains contained genes for mechanosensitive ion channels (MScL), responsible for the release of cytoplasmic solutes Paenibacillus spp. -type transporters associated with amino acid, antimicrobial peptide, sugar, nitrate and proline/glycine betaine transport, comprised approx. 60% of the membrane transporter genes (P. darwinianus strains as compared to the temperate species (P<0.01). While temperate Paenibacillus spp. contained several copies of genes encoding ABC-type oligopeptide, ABC-type dipeptide/oligopeptide/nickel, and ABC-type polysaccharide/polyol phosphate transport systems, no copies of genes associated with these transport systems were identified in the P. darwinianus genomes. However, a similar proportion of CDSs were associated with carbohydrate metabolism across all Paenibacillus genomes  responsible for various facets of sporulation including DNA replication and translocation, formation of the sporulation septum, engulfment, spore morphogenesis and germination  associated with sporulation  associated with flagella biosynthesis and chemosensory pathways . In addition, of the total CDSs identified in the P. darwinianus genomes, significantly fewer CDSs were assigned to COG category, transcription [K] (P<0.01). Finally, P. darwinianus strain BrT showed limited catabolic activity Previous studies have shown that, in bacteria, an increase in genome size is often linked with an increase in metabolic complexity, allowing bacteria to produce new enzymes that exploit environmental conditions P. darwinianus genomes contained several features that were also identified in genomes of cold-adapted bacteria and archaea. These included genes for signal transduction pathways, sigma factors, membrane transporters, motility and sporulation associated genes and mechanisms to deal with cold shock, oxidative and osmotic stresses, thus suggesting their importance in cold adaptation and survival. However, comparative analyses revealed that a large proportion of these features were also present in genomes of temperate species. This suggests that these physiological traits, while not unique to Antarctic soils, are beneficial for growth and survival in a range of soil environments. Transcriptomic- and proteomic-based studies comparing the expression profiles of P. darwinianus strains and temperate Paenibacillus spp., at relatively low versus high temperatures may elucidate the exact mechanisms for cold-adaptation in these strains.The P. darwinianus a growth advantage in the Antarctic soil environment. Although this study has provided an insight into the metabolic potential of this species in RSR soils, it draws attention to our limited knowledge about the expression of physiological traits that enable survival under extreme conditions and, more importantly, to the lack of complete prokaryotic genomes from Antarctic soil environments. Complete genomes will not only reveal genes essential for survival in the harsh Antarctic soil environment but also assist with the characterisation of selection processes that affect prokaryotic genomes in this environment.In conclusion, fewer CDSs, lower paralogous content and the limited catabolic activity suggest the occurrence of genome content scaling, offering 6°Co γ-rays for 80 h at a dose of 288 Gy/h and plated onto PYGV (Peptone Yeast extract Glucose Vitamin) gellan gum-based solid medium at 15°C for up to two months T, CE1 and MB1 were identified as strains of P. darwinianus by 16S rRNA gene sequencing. P. darwinianus BrT was deposited at the International Collection of Microorganisms from Plants (ICMP), Landcare Research, New Zealand (ICMP no. 19912) and at DSMZ, Germany (DSM 27245). P. darwinianus strains CE1 (ICMP no. 20538) and MB1 (ICMP no. 20539) were also deposited at ICMP.Soil samples were collected from three sites: Cape Evans  on Ross Island, Minna Bluff  on the mainland coast and the Britannia Drift, Lake Wellman Region  in south-eastern Darwin Mountains T, CE1 and MB1 by growth on PYGV (Peptone Yeast Glucose Vitamin) medium solidified by gellan gum Temperature range data were obtained for strains BrPaenibacillus strains were routinely cultured on PYGV gellan gum plates at 15–18°C. High molecular weight DNA was extracted by a modified CTAB (hexadecyltrimethylammonium) and protein lysis method 260/A280) was assessed on a NanoDrop ND-1000 Spectrophotometer (Biolab). The quality of each DNA extract was tested by electrophoresis on a 1% agarose gel. Following extraction, high molecular weight DNA was sent to Macrogen  for sequencing on the Illumina HiSeq 2000 platform using 100 bp paired end libraries. With a sequencing output of 35 Gb, estimated coverage was over 1,000× per genome.The three Antarctic https://github.com/ucdavis-bioinformatics/sickle). High-quality reads (Q>30) were assembled into contigs by Velvet v1.2.10 FASTQ files obtained for each genome were trimmed by the FASTQ Trimmer tool of the FASTX-toolkit v0.0.13 Paenibacillus species, namely P. curdlanolyticus YK9, P. daejeonensis DSM 15491, P. mucilaginosus K02, P. panacisoli DSM 21345, P. pinihumi DSM 23905, P. polymyxa SC2, P. taiwanensis DSM 18679, P. terrae HPL-003, and P. terrigena DSM 21567 were selected For comparative analyses, nine temperate, soil-dwelling This whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the following accession numbers: JFHT00000000 for strain Br, JFHU00000000 for strain CE1, and JFHV00000000 for MB1.Figure S1P. darwinianus strains.Dot plot comparisons of the three (PPTX)Click here for additional data file.Table S1Paenibacillus spp. and P. darwinianus strains.List of Pfam domains associated with Two-Component Systems in genomes of temperate (XLSX)Click here for additional data file.Table S2Paenibacillus spp. and P. darwinianus strains.List of genes associated with Two-Component Systems in genomes of temperate (XLSX)Click here for additional data file.Table S3P. darwinianus strains.List of sigma factors identified in genomes of the (XLSX)Click here for additional data file.Table S4Paenibacillus spp. and P. darwinianus strains.List of genes associated with transporter proteins in genomes of temperate (XLSX)Click here for additional data file.Table S5Paenibacillus spp. and P. darwinianus strains.List of genes associated with ABC-type transport systems in genomes of temperate (XLSX)Click here for additional data file.Table S6Paenibacillus spp. and P. darwinianus strains.List of COGs associated with carbohydrate metabolism in genomes of temperate (XLSX)Click here for additional data file.Table S7P. darwinianus strains.Sporulation associated genes identified in genomes of the (XLSX)Click here for additional data file.Table S8Paenibacillus spp.Sporulation associated genes identified in genomes of temperate (XLSX)Click here for additional data file.Table S9Paenibacillus spp. and P. darwinianus strains.List of flagellar assembly and chemotaxis associated genes in genomes of temperate (XLSX)Click here for additional data file.Table S10Paenibacillus spp. and P. darwinianus strains.List of genes associated with oxidative and osmotic stress response in genomes of temperate (XLSX)Click here for additional data file.Table S11Paenibacillus spp. and P. darwinianus strains.List of cold-shock induced genes identified in genomes of temperate (XLSX)Click here for additional data file.