https://wiki.sine.space/api.php?action=feedcontributions&user=Answerform0&feedformat=atom wiki.sine.space - User contributions [en] 2019-06-15T20:56:32Z User contributions MediaWiki 1.26.3 https://wiki.sine.space/index.php?title=Ulated_based_on_normalized,_log2-transformed_gene_expression_values_from_the&diff=83333 Ulated based on normalized, log2-transformed gene expression values from the 2019-05-05T13:23:12Z <p>Answerform0: </p> <hr /> <div>However, for some non-model organisms and minor species, it is not feasible to perform whole genome sequencing [http://www.aqqagency.com/comment/html/?239605.html Urakami T, Kanemoto S, Kondo S, Saitoh M, PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28388412 Analyzer system platform, HiSeq2000, with a 100 bp paired-end read. A paired-end sequencing protocol was selected for this study because it is critical for the assembly of short (]</div> Answerform0 https://wiki.sine.space/index.php?title=Ulated_based_on_normalized,_log2-transformed_gene_expression_values_from_the&diff=83321 Ulated based on normalized, log2-transformed gene expression values from the 2019-05-05T11:12:26Z <p>Answerform0: </p> <hr /> <div>The transcriptomic sequencing was completed using the Illumina Genome [https://www.ncbi.nlm.nih.gov/pubmed/28388412 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28388412] Analyzer system [http://mythailand.ru/album/473940 Rface in mediating the symbiotic and pathogenic interactions of Photorhabdus.Background] platform, HiSeq2000, with a 100 bp paired-end read. It is generally recognized that EBN is one of the most expensive animal-based products; it is often known as the &quot;caviar of the East&quot; [4]. Nevertheless, the transcriptomic profiles of swiftlets have not been established. The current study focused on de novo RNA sequencing of the salivary glands of both EBN-producing swiftlets and non-EBN-producing swiftlets. The transcriptomic sequencing was completed using the Illumina Genome [https://www.ncbi.nlm.nih.gov/pubmed/28388412 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28388412] Analyzer system platform, HiSeq2000, with a 100 bp paired-end read. A paired-end sequencing protocol was selected for this study because it is critical for the assembly of short (</div> Answerform0 https://wiki.sine.space/index.php?title=Ulated_based_on_normalized,_log2-transformed_gene_expression_values_from_the&diff=82646 Ulated based on normalized, log2-transformed gene expression values from the 2019-04-29T12:01:44Z <p>Answerform0: </p> <hr /> <div>The current study focused on de novo RNA sequencing of the salivary [http://mythailand.ru/album/464520 Mmon carp. PLoS A single. 2012;7(1):e30925. Xu PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28388412 Analyzer Ulated based on normalized, log2-transformed gene expression values from the system platform, HiSeq2000, with a 100 bp paired-end read. A paired-end sequencing protocol was selected for this study because it is critical for the assembly of short (]</div> Answerform0 https://wiki.sine.space/index.php?title=Ulated_based_on_normalized,_log2-transformed_gene_expression_values_from_the&diff=82522 Ulated based on normalized, log2-transformed gene expression values from the 2019-04-28T23:00:35Z <p>Answerform0: </p> <hr /> <div>The current study focused on de novo RNA sequencing of the salivary glands of both [http://www.fcxjsm.com/comment/html/?237107.html Ddle line). In the presence in the nocodazole, the distribution of] EBN-producing swiftlets and non-EBN-producing swiftlets. BMC Genomics (2017) 18:Page 9 ofTable 4 Expression profiles of genes of potential importance in salivary gland development and EBN compositionsGene function Salivary development Gene CREB3L2 SEC63 SEC24A SAR1 AA versus Aerodramus species Gene function EGFR signalling pathway Gene ARF4 BCAR1 CAV1 CEBPA ELF3 EPS15 EPS8 JUN PLEC RAB5A REPS1 ZPR1 VAV2 STAT3 N-glycan biosynthesis ALG2 MGAT1 RPN1 FUT8 RPN2 AMC versus AFC Gene function EGFR signalling pathway Gene JUND HDAC BCAR N-glycan biosynthesis Alanine and Aspartate metabolism MGAT GOT1 PDHB AFM versus AFC Gene function MAPK signalling pathway BMP signalling pathway Fatty acid synthesis Gender comparison of AFC Gene function N-glycan trimming Gene EDEM2 Male 3.951 Female 0.359 log2 3.459 q-value 0.008 Gene HMGN1 TOB2 ACADVL AFM 23,486.800 20.463 10.909 AFC 2685.98 0.959 50.803 log2 -3.128 -4.414 2.219 q-value 0.001 0.001 0.001 AMC 4.911 1.357 7.776 20.278 226.741 894.023 AFC 39.541 580.771 200.736 256.555 7.0263 135.641 log2 3.009 8.740 4.690 3.661 -5.012 -2.721 q-value 0.001 0.001 0.001 0.046 0.000 0.000 AA 0.683 6.407 0.695 8.626 6.816 0.198 0.754 0.411 6.047 17.934 6.795 1.079 49.553 2.453 6.546 4.617 66.407 13.173 1.069 Aerodramus spp 48.954 51.836 50.207 49.820 603.607 10.035 13.668 11.504 31.197 47.435 21.529 13.242 239.912 53.308 90.860 91.067 552.366 84.076 71.026 log2 6.162 3.016 6.174 2.529 6.468 5.657 4.178 4.803 2.367 1.403 1.663 3.617 2.275 4.441 3.794 4.301 3.056 2.674 6.053 q-value 0.026 0.003 0.026 0.018 0.001 0.026 0.026 0.021 0.005 0.046 0.040 0.001 0.011 0.001 0.001 0.004 0.003 0.003 0.001 AFM 65.608 36.723 15.763 38.916 AFC 76.666 34.793 15.414 23.855 AMC 51.669 50.081 19.240 16.996 AA 0.000 5.926 19.20 6.AFC Aerodramu.Ulated based on normalized, log2-transformed gene expression values from the nCounter data and the RNA-Seq FPKM data of the 36 genes. The mean correlation was 0.54 with a 95 bootstrap confidence interval.DiscussionCharacterization of the swiftlet transcriptomeWith the advancements in sequencing technologies, the genomes of several avian species, including Peking ducks [30], passenger pigeons [15], and vultures [31], have been sequenced and characterized, whereby this inclusion has accelerated the research [https://www.ncbi.nlm.nih.gov/pubmed/28724915 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28724915] on functional genomics and improved our understanding of the genetic regulation of important traits. However, for some non-model organisms and minor species, it is not feasible to perform whole genome sequencing because of the expensive cost. Sequencing based on NGS technology has provided an opportunity to use a transcriptomic approach to study mechanisms that control certain traits in non-model organisms [32]. It is generally recognized that EBN is one of the most expensive animal-based products; it is often known as the &quot;caviar of the East&quot; [4]. Nevertheless, the transcriptomic profiles of swiftlets have not been established. The current study focused on de novo RNA sequencing of the salivary glands of both EBN-producing swiftlets and non-EBN-producing swiftlets. The transcriptomic sequencing was completed using the Illumina Genome [https://www.ncbi.nlm.nih.gov/pubmed/28388412 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28388412] Analyzer system platform, HiSeq2000, with a 100 bp paired-end read. A paired-end sequencing protocol was selected for this study because it is critical for the assembly of short (</div> Answerform0 https://wiki.sine.space/index.php?title=Es_among_A._fuciphagus_and_a._maximus_from_organic_habitat_(cave&diff=82507 Es among A. fuciphagus and a. maximus from organic habitat (cave 2019-04-28T20:57:30Z <p>Answerform0: Created page with &quot;Es between A. fuciphagus and a. maximus from natural habitat (cave). Genes were identified working with a mixture of ANOVA with [http://www.chemscene.com/1187595-84-1.html 118...&quot;</p> <hr /> <div>Es between A. fuciphagus and a. maximus from natural habitat (cave). Genes were identified working with a mixture of ANOVA with [http://www.chemscene.com/1187595-84-1.html 1187595-84-1 biological activity] Bonferroni-corrected 0.05. d Top-10 differential expressed genes involving A. fuciphagus from organic habitat (cave) and man-made habitat (property). Genes had been identified making use of a mixture of ANOVA with Bonferroni-corrected 0.05. Expression data had been Z-score standardized per geneup-regulated in AFC and AMC samples, respectively (Table 2). All round [http://www.chemscene.com/66575-29-9.html Forskolin web] evaluation of log2-fold transform information suggested that 98 on the considerably regulated genes have less than four folds unique.Pathway prediction and enrichment analysisA total of 14,835 annotated genes were exported for the Enricher tool for pathway enrichment evaluation against several publicly out there databases. The outcomes indicated a total of 41, 75, 11, 69, and 34 pathways from KEGG, WIKI pathway, Reactome, Biocarta, and PANTHER databases, respectively. All genes that have been considerably regulated having a q-value significantly less than or equal to 0.05 and a log2-fold alter of extra than two were identified and subjected [http://www.ncbi.nlm.nih.gov/pubmed/27324125 PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27324125] to pathways enrichment evaluation. Pathway enrichment analysis amongst EBN and nonEBN-producing swiftlets indicated that a total of 341 pathways were up-regulated in EBN-producing swiftlet salivary glands, having a majority of your pathways involved in mRNA processing (15.five ), protein export (14.4 ), and squamous cell TarBase (9.1 ), when 328 pathways were up-regulated in AA samples. The major 3 upregulated pathways identified in AA were associated with translation aspects (27.four ), mRNA processing (ten.9 ) and spliceosomes (8.8 ). Further evaluation showed a total of 152 and 120 up-regulated pathways detected amongst AFC and AMC samples, respectively. The majority from the up-regulation in AFC samples involved the PI3K-Akt signaling pathway (46 ), ribosome biogenesis (12.5 ), and cardiac muscle contraction (six.5 ). Meanwhile, analysis of AMC samples showed that the prime three up-regulated pathways have been the Ras signaling pathway (38 ), the MAPK signaling pathway (29 ), plus the proteasome pathway (20 ). As anticipated, comparisons involving AFM and AFC showed only 34 and 7 pathways that have been substantially up-regulated inAFM and AFC samples, respectively. The majority with the detected pathways in AFM samples have been related with galactose metabolism (38 ), endocytosis (15 ), and oxidative phosphorylation (15 ), when the top rated three upregulated pathways in AFC samples have been mitochondrial fatty acid oxidation (43 ), RNA transport (29 ), and proteoglycan (29 ) (Table three). Gender primarily based analysis showed that a total of 34 pathways have been considerably up-regulated in female AFC samples, and also the majority of these pathways have been associated with DNA repair (61 ), circadian clock (20 ), and cell cycle (12 ). Furthermore, 25 pathways have been upregulated in male samples, and 40 of the identified pathways were involved in mitochondrial protein synthesis. Evaluation of AFM information didn't indicate [https://www.ncbi.nlm.nih.gov/pubmed/27385778 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27385778] considerable regulated pathways in female samples, whereas 15 pathways were considerably up-regulated in male samples. The majority on the detected pathways were connected with molecule transport (17.5 ), protein metabolism (five.eight ), and signal transduction (5.1 ). Lastly, a total of 13 and five pathways have been up-regulated in female and male samples from AMC, respectively.Es between A.</div> Answerform0 https://wiki.sine.space/index.php?title=Three_regulated_pathways_in_male_samples_were_vesicle-mediated_transport_(38_),_extracellular_matrix&diff=82043 Three regulated pathways in male samples were vesicle-mediated transport (38 ), extracellular matrix 2019-04-24T09:02:21Z <p>Answerform0: </p> <hr /> <div>These genes are involved in salivary gland development, the epidermal growth factor receptor (EGFR) signaling pathway, the bone morphogenetic protein (BMP) signaling pathway, the mitogen-activated protein kinases (MAPK) signaling pathway, the fatty acid synthesis pathway, the N-glycan trimming in endoplasmic reticulum, and the N-glycan biosynthesis pathway (Table 4).NanoString nCounter?Gene expression assayTable 2 Number of up-[http://eversunny.org/comment/html/?302041.html Robiology 2010, 10:45 http://www.biomedcentral.com/1471-2180/10/Page 3 ofFigure 1 Visualization of P.] regulated genes of male and [http://listensounds.com/comment/html/?276021.html S for anti-C-26 antibody cross-reactivity. 2010;84(14):6909?two. Hai R, Schmolke M, Varga ZT] Mitochondrial fatty acid oxidation (43 ) - RNA transport (29 ) - Proteoglycan (29 ) Gender comparison AFC Female Number of pathways up-regulated 34 Top 3 regulated pathway -DNA repair (61 ) -Circadian clock (20 ) -Cell cycle (12 ) Male 25 -Mitochondrial protein (40 ) -Peptide hormone metabolism (23 ) -Muscle contraction (15 ) AFM Female Male Number of pathways up-regulated 0 15 Top 3 regulated pathway -NA -Transmembrane transport of small molecule (17.5 ) -Protein metabolism (5.8 ) -Signal transduction (5.1 ) AMC Female Number of pathways up-regulated 13 Top 3 regulated pathway -Organelle biogenesis and maintenance (23 ) -Muscle contraction (17 ) -Axon guidance (9 )Table 3 Pathway enrichment analysis of up-regulated pathways in swiftlet salivary glands (Continued)Male 5 -Vesicle-mediated transport (38 ) -Extracellular [https://www.ncbi.nlm.nih.gov/pubmed/27385778 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27385778] matrix transport (29 ) -Signal transduction (23 ) AFC Aerodramus fuciphagus from cave AFM Aerodramus fuciphagus from man-made house AMC Aerodramus maximus from cave AA Apus affinis NA No regulated pathways with p-value [https://www.ncbi.nlm.nih.gov/pubmed/28506461 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28506461] up-regulated pathways in swiftlet salivary glandsAA versus Aerodramus species AA Number of pathways up-regulated 328 Top 3 regulated pathway - Translation factors (27.4 ) - mRNA processing (10.9 ) - Spliceosome (8.8 ) Aerodramus species 341 - mRNA processing (15.5 ) - Protein export (14.4 ) - Squamous cell TarBase (9.1 ) AFC versus AMC AFC Number of pathways up-regulated 152 Top 3 regulated pathway - PI3K-Akt signaling pathway (46 ) - Ribosome biogenesis in eukaryotes (12.5 ) - Cardiac muscle contraction (6.5 ) AMC 120 - Ras signalling pathway (38 ) - MAPK signalling pathway (29 ) - Proteasome (20 ) AFM versus AFC AFM Number of pathways up-regulated 34 Top 3 regulated pathway - Galactose metabolism (38 ) - Endocytosis (15 ) - Oxidative phosphorylation (15 ) AFC 7 - Mitochondrial fatty acid oxidation (43 ) - RNA transport (29 ) - Proteoglycan (29 ) Gender comparison AFC Female Number of pathways up-regulated 34 Top 3 regulated pathway -DNA repair (61 ) -Circadian clock (20 ) -Cell cycle (12 ) Male 25 -Mitochondrial protein (40 ) -Peptide hormone metabolism (23 ) -Muscle contraction (15 ) AFM Female Male Number of pathways up-regulated 0 15 Top 3 regulated pathway -NA -Transmembrane transport of small molecule (17.5 ) -Protein metabolism (5.8 ) -Signal transduction (5.1 ) AMC Female Number of pathways up-regulated 13 Top 3 regulated pathway -Organelle biogenesis and maintenance (23 ) -Muscle contraction (17 ) -Axon guidance (9 )Table 3 Pathway enrichment analysis of up-regulated pathways in swiftlet salivary glands (Continued)Male 5 -Vesicle-mediated transport (38 ) -Extracellular [https://www.ncbi.nlm.nih.gov/pubmed/27385778 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27385778] matrix transport (29 ) -Signal transduction (23 ) AFC Aerodramus fuciphagus from cave AFM Aerodramus fuciphagus from man-made house AMC Aerodramus maximus from cave AA Apus affinis NA No regulated pathways with p-value</div> Answerform0 https://wiki.sine.space/index.php?title=Importance_in_salivary_gland_development_and_EBN_composition_were_selected_for&diff=81857 Importance in salivary gland development and EBN composition were selected for 2019-04-22T23:00:02Z <p>Answerform0: Created page with &quot;The array contained four internal positive control probes and five negative controls for data normalization. Seven housekeeping genes were selected based on expression profile...&quot;</p> <hr /> <div>The array contained four internal positive control probes and five negative controls for data normalization. Seven housekeeping genes were selected based on expression profile analysis to [http://hmaoyl.com/comment/html/?231325.html Ing for the prescene of your polymyxin B. The hdfR and] determine [https://www.ncbi.nlm.nih.gov/pubmed/28724915 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28724915] the appropriate thresholds for measuring significant hybridization signals over the background. After pre-processing and normalization, log2-transformed RNA-Seq and nCounter data from 36 genes were compared, and the [http://wazock.com/comment/html/?180511.html E.) Figure 6 Organ comparison. (A): Left panel: Spleen size comparison of] concordance of the data from both technologies were evaluated.the completeness of the assembled transcript sequences. A total of 142 (57.66 ) Core Eukaryotic Genes (CEGs) were identified as full-length, whereas a total of 185 (74.6 ) core genes were retrieved as partial CEGs (Additional file 4: Table S3).Functional annotation and classification of the assembled UnigenesResultsOverview of the swiftlets' transcriptome landscapeAfter removing the amplification adapters and the ambiguous reads, we generated a total of 17.4 million, 17.7 million, 19.6 million, and 15.1 million clean reads for AFC, AFM, AMC, and AA, respectively [https://www.ncbi.nlm.nih.gov/pubmed/28388412 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28388412] (Table 1). The results showed that 99 of the sequenced reads passed quality control with Phred scores of more than 20, indicating that the error rate of the sequencing process was less than 0.01 . SOAPdenovo-Trans software was used to perform de novo assembly and generated 47,596 (AFC), 55,331 (AFM), 40,330 (AMC), and 44,145 (AA) contigs; the average contig size exceeded 200 bp for all four libraries (Table 3). More than 65 of the reads could be mapped back to the reference transcripts in all four experimental groups. Furthermore, for all four groups, more than 96 of the genes were longer than 100 bp, more than 20 of the genes were 500 to 1000 bp, 11 of the genes were longer than 1000 bp, and 0.01 of the genes for AFC, AFM, and AA exceeded 10 kbp (Table 1). CEGMA analysis was used to analyzeTable 1 Overview of the sequencing and assemblySequencing parameters Contig (n) Contig N50 size Total length of contig Scaffolds (n) Scaffold N50 size Maximum length of scaffold Species and location AFC 47,596 252 AFM 55,331 269 AMC 40,330 256 AA 44,145 244 9,807,398 28,051 1143 15,348The generated, non-redundant, reference transcript was used for gene predictions by AUGUSTUS and a total of 14,835 genes were predicted. The functional annotation of genes was first performed using the BLASTx function in the Blast2GO tool against the non-redundant (NR) protein database from NCBI and the UniProt database with an E-value of</div> Answerform0 https://wiki.sine.space/index.php?title=Ree_main_categories,_namely_cellular_components,_molecular_function,_and_biological_processes.&diff=81534 Ree main categories, namely cellular components, molecular function, and biological processes. 2019-04-20T01:06:42Z <p>Answerform0: Created page with &quot;1 Gene annotation and gene ontology of [http://www.aqqagency.com/comment/html/?239596.html Ftlet Aerodramus Fuciphagus (thunberg)(aves: apodidae) in farmed colonies. Raffles B...&quot;</p> <hr /> <div>1 Gene annotation and gene ontology of [http://www.aqqagency.com/comment/html/?239596.html Ftlet Aerodramus Fuciphagus (thunberg)(aves: apodidae) in farmed colonies. Raffles Bull] swiftlet transcriptome. maximus) and non-EBN generating swiftlets (AA).Ree primary categories, namely cellular elements, molecular function, and biological processes. The molecular function category consisted of 11 GO groups, the largest group was that of binding (60.1 ), plus the cellular element category consisted of 15 GO groups; the largest group was that of cell/cell parts (90.six ). Lastly, the biological [https://www.ncbi.nlm.nih.gov/pubmed/27527552 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27527552] processes category consisted of 23 GO groups; the largest group was that of cellular course of action (77.4 ) (Figure 1b). Additional gene ontology enrichment analysis showed that extra genes were involved in salivary gland morphogenesis and regulation in Aerodramus than in Apus affinis (Figure 1c).Gene expression analysis10,865,350 12,946,212 9,192,670 28,471 1521 15,860 32,337 1560 15,605 one hundred 25,185 1362 10,769Minimum length of scaffold 100 Total length of scaffolds GC percentage13,284,125 15,888,505 11,131,881 11,571,111 46.72 44.30 47.94 50.73Data from EBN-producing swiftlets (AFC, AFM, and AMC) was in comparison to data from non-EBN-producing swiftlets (AA); interspecies comparisons of information from EBN-producing swiftlets in the cave (AFC and AMC), and comparisons of white-nest making swiftlets from two distinctive habitats (AFC and AFM) (Figure two). Furthermore, the effects of gender on gene expression patterns had been also studied for EBN-producing swiftlets. As anticipated, the greatest differential gene expression profile was observed in between EBN-producing swiftlets (AFC, AFM, and AMC) and non-EBN-producing swiftlets (AA). Comparisons among the data from EBNproducing swiftlets and non-EBN-producing swiftletsLooi et al. BMC Genomics (2017) 18:Web page five ofFig. 1 Gene annotation and gene ontology of swiftlet transcriptome. [https://www.ncbi.nlm.nih.gov/pubmed/26795252 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26795252] a Venn diagram displaying exceptional and shared proteins following annotation according to Non-redundant, InterProsca and Pfam databases. b You can find 14,107 proteins assigned towards the cellular component, biological approach and molecular function by Gene Ontology classification technique. The y-axis indicates the percentage of genes for each category, along with the y-axis around the right side shows the number of genes. c The amount of genes involved in salivary gland improvement among Apus affinis and Aerodramus species. The y-axis indicates the percentage of genes for every category, plus the y-axis on the proper side shows the amount of genesshowed that a total of 2037 genes were drastically upregulated and 1450 genes had been substantially downregulated. An interspecies comparison between AFC and AMC from equivalent habitats showed a fewer variety of differentially regulated genes; only expressions of 124 genes have been up-regulated and 118 genes were downregulated. Lastly, expression profiles involving AFC andAFM only identified 16 up-regulated genes and 32 down-regulated genes out of 14,835 annotated genes. Analysis of male and female samples indicated that AFM possess the highest number of regulated genes, whereby a total of 180 genes were significantly up-regulated in male samples and 37 genes in female samples (Table 2). On the other hand, only 102 genes and 45 genes were significantlyLooi et al.</div> Answerform0 https://wiki.sine.space/index.php?title=Three_regulated_pathways_in_male_samples_were_vesicle-mediated_transport_(38_),_extracellular_matrix&diff=80667 Three regulated pathways in male samples were vesicle-mediated transport (38 ), extracellular matrix 2019-04-16T02:36:59Z <p>Answerform0: </p> <hr /> <div>BMC Genomics (2017) 18:Page 8 ofTable 3 Pathway enrichment analysis of [https://www.ncbi.nlm.nih.gov/pubmed/28506461 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28506461] up-regulated pathways in swiftlet salivary glandsAA versus Aerodramus species AA Number of pathways up-regulated 328 Top 3 regulated pathway - Translation factors (27.4 ) - mRNA processing (10.9 ) - Spliceosome (8.8 ) Aerodramus species 341 - mRNA processing (15.5 ) - Protein export (14.4 ) - Squamous cell TarBase (9.1 ) AFC versus AMC AFC Number of pathways up-regulated 152 Top 3 regulated pathway - PI3K-Akt signaling pathway (46 ) - Ribosome biogenesis in eukaryotes (12.5 ) - Cardiac muscle contraction (6.5 ) AMC 120 - Ras signalling pathway (38 ) - MAPK signalling pathway (29 ) - Proteasome (20 ) AFM versus AFC AFM Number of pathways up-regulated 34 Top 3 regulated pathway - Galactose metabolism (38 ) - Endocytosis (15 ) - Oxidative phosphorylation (15 ) AFC 7 - Mitochondrial fatty acid oxidation (43 ) - RNA transport (29 ) - Proteoglycan (29 ) Gender comparison AFC Female Number of pathways up-regulated 34 Top 3 regulated pathway -DNA repair (61 ) -[http://lauraldaniels.com/comment/html/?211270.html Nt information. W.L., and Y.D. generated stable cell line] Circadian clock (20 ) -Cell cycle (12 ) Male 25 -Mitochondrial protein (40 ) -Peptide hormone metabolism (23 ) -Muscle contraction (15 ) AFM Female Male Number of pathways up-regulated 0 15 Top 3 regulated pathway -NA -Transmembrane transport of small molecule (17.5 ) -Protein metabolism (5.8 ) -Signal transduction (5.1 ) AMC Female Number of pathways up-regulated 13 Top 3 regulated pathway -Organelle biogenesis and maintenance (23 ) -Muscle contraction (17 ) -Axon guidance (9 )Table 3 Pathway enrichment analysis of up-regulated pathways in swiftlet salivary glands (Continued)Male 5 -Vesicle-mediated transport (38 ) -Extracellular [https://www.ncbi.nlm.nih.gov/pubmed/27385778 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27385778] matrix transport (29 ) -Signal transduction (23 ) AFC Aerodramus fuciphagus from cave AFM Aerodramus fuciphagus from man-made house AMC Aerodramus maximus from cave AA Apus affinis NA No regulated pathways with p-value [https://www.ncbi.nlm.nih.gov/pubmed/28506461 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28506461] up-regulated pathways in swiftlet salivary glandsAA versus Aerodramus species AA Number of pathways up-regulated 328 Top 3 regulated pathway - Translation factors (27.4 ) - mRNA processing (10.9 ) - Spliceosome (8.8 ) Aerodramus species 341 - mRNA processing (15.5 ) - Protein export (14.4 ) - Squamous cell TarBase (9.1 ) AFC versus AMC AFC Number of pathways up-regulated 152 Top 3 regulated pathway - PI3K-Akt signaling pathway (46 ) - Ribosome biogenesis in eukaryotes (12.5 ) - Cardiac muscle contraction (6.5 ) AMC 120 - Ras signalling pathway (38 ) - MAPK signalling pathway (29 ) - Proteasome (20 ) AFM versus AFC AFM Number of pathways up-regulated 34 Top 3 regulated pathway - Galactose metabolism (38 ) - Endocytosis (15 ) - Oxidative phosphorylation (15 ) AFC 7 - Mitochondrial fatty acid oxidation (43 ) - RNA transport (29 ) - Proteoglycan (29 ) Gender comparison AFC Female Number of pathways up-regulated 34 Top 3 regulated pathway -DNA repair (61 ) -Circadian clock (20 ) -Cell cycle (12 ) Male 25 -Mitochondrial protein (40 ) -Peptide hormone metabolism (23 ) -Muscle contraction (15 ) AFM Female Male Number of pathways up-regulated 0 15 Top 3 regulated pathway -NA -Transmembrane transport of small molecule (17.5 ) -Protein metabolism (5.8 ) -Signal transduction (5.1 ) AMC Female Number of pathways up-regulated 13 Top 3 regulated pathway -Organelle biogenesis and maintenance (23 ) -Muscle contraction (17 ) -Axon guidance (9 )Table 3 Pathway enrichment analysis of up-regulated pathways in swiftlet salivary glands (Continued)Male 5 -Vesicle-mediated transport (38 ) -Extracellular [https://www.ncbi.nlm.nih.gov/pubmed/27385778 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27385778] matrix transport (29 ) -Signal transduction (23 ) AFC Aerodramus fuciphagus from cave AFM Aerodramus fuciphagus from man-made house AMC Aerodramus maximus from cave AA Apus affinis NA No regulated pathways with p-value</div> Answerform0 https://wiki.sine.space/index.php?title=Ffecting_swimming_motility_and_the_pbgE1_mutant_was_also_shown_to&diff=80570 Ffecting swimming motility and the pbgE1 mutant was also shown to 2019-04-15T13:40:41Z <p>Answerform0: </p> <hr /> <div>The arn operon has been shown to be involved in the modification of the lipid A moiety of LPS with L-aminoarabinose in response to the presence of cationic antimicrobial peptides (CAMPs) [6-8]. The pbgE1 mutant did produce altered LPS [http://worldhcy.com/comment/html/?75612.html By Ariel Quintana [20]. Moreover, TG treatment can result in maximal] compared to the wildtype implicating LPS structure as [https://www.ncbi.nlm.nih.gov/pubmed/28724915 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28724915] a nematode colonization factor in Photorhabdus [5]. In this study we screened a library of Photorhabdus mutants with the aim of extending our understanding of the transmission process by identifying genes important in the colonization of the H. bacteriophora IJ nematode by P. luminescens TT01.ResultsConstruction of a GFP-tagged strain of P. luminescens TTIn order to facilitate a relatively rapid screening method for the identification of transmission mutants we decided to tag TT01 with a constitutively expressed gfp using a mini-Tn7 transposon (see Methods). This would enable the translucent IJs to be viewed beneath a fluorescent microscope and be scored qualitatively for the presence/absence of bacteria. Colonies of the gfp-tagged strain (called TT01gfp) were initially checked for fluorescence using a UV light box before overnight cultures were checked for gfp expression using a fluorescent microscope. This confirmed that the vast majority of cells in an overnight population of TT01gfp were expressing gfp (see Figure 1A). Phenotypic comparisons of TT01 and TT01gfp confirmed that there was no difference in growth rate, bioluminescence, pigmentation or virulence to insect larvae. Furthermore we also verified that TT01gfp was able to colonize IJ nematodes (see Figure 1B) with a transmission [http://4189.kqmj.net/comment/html/?206733.html Chondria play an essential part in Ca2+ homeostasis in T cells] frequency identical to TT01 (between 80-85 ). As has been previously shown, the TT01gfp bacteria were confirmed to occupy the proximal region of the nematode gut extending from just below the pharynx of the IJ (see Figure 1C).Identification of TT01gfp mutants affected in colonization of the IJIn this study we were using a qualitative screen that was designed to identify mutants that were affected in transmission frequency i.e. we were looking for mutants that colonized significantly fewer IJs than the 80 level observed with TT01gfp. Therefore [https://www.ncbi.nlm.nih.gov/pubmed/27663262 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27663262] TT01gfp was subjected to transposon mutagenesis using the Tn5 interposon delivered by plasmid pUT-Km2 and individual mutants were arrayed into 96 well plates and frozen. From this arrayed library 3271 mutants were screened for a defect in transmission frequency by growing the mutant on a lipid agar plate and inoculating the biomass with 30 surface-sterilized H. bacteriophora IJs. After 21 days incubation the new generation of IJs were collected and checked for colonization using a fluorescent microscope. In this way 40 mutants were identified as having a qualitative defect in transmission frequency i.e.</div> Answerform0 https://wiki.sine.space/index.php?title=Three_regulated_pathways_in_male_samples_were_vesicle-mediated_transport_(38_),_extracellular_matrix&diff=80513 Three regulated pathways in male samples were vesicle-mediated transport (38 ), extracellular matrix 2019-04-15T08:28:28Z <p>Answerform0: </p> <hr /> <div>Three [http://www.chemscene.com/1005342-46-0.html buy CS-1630] regulated pathways in male samples were vesicle-mediated transport (38 ), extracellular matrix transport (29 ), and signal transduction (23 ) (Table 3). A Pearson correlation was calc.Three regulated pathways in male samples were vesicle-mediated transport (38 ), extracellular matrix transport (29 ), and signal transduction (23 ) (Table 3). A total of 24 genes of interest, that are associated with salivary gland development and EBN composition, were identified for further discussion. These genes are involved in salivary gland development, the epidermal growth factor receptor (EGFR) signaling pathway, the bone morphogenetic protein (BMP) signaling pathway, the mitogen-activated protein kinases (MAPK) signaling pathway, the fatty acid synthesis pathway, the N-glycan trimming in endoplasmic reticulum, and the N-glycan biosynthesis pathway (Table 4).NanoString nCounter?Gene expression assayTable 2 Number of up-regulated genes of male and female swiftlet salivary glandsGender of the swiftlets Malea FemaleaSampling groups AFC 46 56 AFM 180 37 AMC 20Samples from male swiftlets were used as baseline for differential expression analysisA total of 36 genes associated with salivary gland development and EBN compositions were analyzed using the NanoString nCounter?gene expression assay. All the analyzed genes showed a normal distribution of log2 expression values with a median value of 10.5-folds compared with the negative control. Out of these genes,Looi et al. BMC Genomics (2017) 18:Page 8 ofTable 3 Pathway enrichment analysis of [https://www.ncbi.nlm.nih.gov/pubmed/28506461 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28506461] up-regulated pathways in swiftlet salivary glandsAA versus Aerodramus species AA Number of pathways up-regulated 328 Top 3 regulated pathway - Translation factors (27.4 ) - mRNA processing (10.9 ) - Spliceosome (8.8 ) Aerodramus species 341 - mRNA processing (15.5 ) - Protein export (14.4 ) - Squamous cell TarBase (9.1 ) AFC versus AMC AFC Number of pathways up-regulated 152 Top 3 regulated pathway - PI3K-Akt signaling pathway (46 ) - Ribosome biogenesis in eukaryotes (12.5 ) - Cardiac muscle contraction (6.5 ) AMC 120 - Ras signalling pathway (38 ) - MAPK signalling pathway (29 ) - Proteasome (20 ) AFM versus AFC AFM Number of pathways up-regulated 34 Top 3 regulated pathway - Galactose metabolism (38 ) - Endocytosis (15 ) - Oxidative phosphorylation (15 ) AFC 7 - Mitochondrial fatty acid oxidation (43 ) - RNA transport (29 ) - Proteoglycan (29 ) Gender comparison AFC Female Number of pathways up-regulated 34 Top 3 regulated pathway -DNA repair (61 ) -Circadian clock (20 ) -Cell cycle (12 ) Male 25 -Mitochondrial protein (40 ) -Peptide hormone metabolism (23 ) -Muscle contraction (15 ) AFM Female Male Number of pathways up-regulated 0 15 Top 3 regulated pathway -NA -Transmembrane transport of small molecule (17.5 ) -Protein metabolism (5.8 ) -Signal transduction (5.1 ) AMC Female Number of pathways up-regulated 13 Top 3 regulated pathway -Organelle biogenesis and maintenance (23 ) -Muscle contraction (17 ) -Axon guidance (9 )Table 3 Pathway enrichment analysis of up-regulated pathways in swiftlet salivary glands (Continued)Male 5 -Vesicle-mediated transport (38 ) -Extracellular [https://www.ncbi.nlm.nih.gov/pubmed/27385778 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27385778] matrix transport (29 ) -Signal transduction (23 ) AFC Aerodramus fuciphagus from cave AFM Aerodramus fuciphagus from man-made house AMC Aerodramus maximus from cave AA Apus affinis NA No regulated pathways with p-value</div> Answerform0 https://wiki.sine.space/index.php?title=Three_regulated_pathways_in_male_samples_were_vesicle-mediated_transport_(38_),_extracellular_matrix&diff=80090 Three regulated pathways in male samples were vesicle-mediated transport (38 ), extracellular matrix 2019-04-11T08:02:19Z <p>Answerform0: </p> <hr /> <div>Three regulated pathways in male samples were vesicle-mediated transport (38 ), extracellular matrix transport (29 ), and signal transduction (23 ) (Table 3). A total of 24 genes of interest, that are associated with salivary gland development and EBN composition, were identified for further discussion. These genes are involved in salivary gland development, the epidermal growth factor receptor (EGFR) signaling pathway, the bone morphogenetic protein (BMP) signaling pathway, the mitogen-activated protein kinases (MAPK) signaling pathway, the fatty acid synthesis pathway, the N-glycan trimming in endoplasmic reticulum, and the N-glycan biosynthesis [http://www.chemscene.com/1202757-89-8.html 1202757-89-8] pathway (Table 4).NanoString nCounter?Gene expression assayTable 2 Number of up-regulated genes of male and female swiftlet salivary glandsGender of the swiftlets Malea FemaleaSampling groups AFC 46 56 AFM 180 37 AMC 20Samples from male swiftlets were used as baseline for differential expression analysisA total of 36 genes associated with salivary gland development and EBN compositions were analyzed using the NanoString nCounter?gene expression assay. All the analyzed genes showed a normal distribution of log2 expression values with a median value of 10.5-folds compared with the negative control. Out of these genes,Looi et al. BMC Genomics (2017) 18:Page 8 ofTable 3 Pathway enrichment analysis of [https://www.ncbi.nlm.nih.gov/pubmed/28506461 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28506461] up-regulated pathways in swiftlet salivary glandsAA [http://www.chemscene.com/290315-45-6.html CS-1339 chemical information] versus Aerodramus species AA Number of pathways up-regulated 328 Top 3 regulated pathway - Translation factors (27.4 ) - mRNA processing (10.9 ) - Spliceosome (8.8 ) Aerodramus species 341 - mRNA processing (15.5 ) - Protein export (14.4 ) - Squamous cell TarBase (9.1 ) AFC versus AMC AFC Number of pathways up-regulated 152 Top 3 regulated pathway - PI3K-Akt signaling pathway (46 ) - Ribosome biogenesis in eukaryotes (12.5 ) - Cardiac muscle contraction (6.5 ) AMC 120 - Ras signalling pathway (38 ) - MAPK signalling pathway (29 ) - Proteasome (20 ) AFM versus AFC AFM Number of pathways up-regulated 34 Top 3 regulated pathway - Galactose metabolism (38 ) - Endocytosis (15 ) - Oxidative phosphorylation (15 ) AFC 7 - Mitochondrial fatty acid oxidation (43 ) - RNA transport (29 ) - Proteoglycan (29 ) Gender comparison AFC Female Number of pathways up-regulated 34 Top 3 regulated pathway -DNA repair (61 ) -Circadian clock (20 ) -Cell cycle (12 ) Male 25 -Mitochondrial protein (40 ) -Peptide hormone metabolism (23 ) -Muscle contraction (15 ) AFM Female Male Number of pathways up-regulated 0 15 Top 3 regulated pathway -NA -Transmembrane transport of small molecule (17.5 ) -Protein metabolism (5.8 ) -Signal transduction (5.1 ) AMC Female Number of pathways up-regulated 13 Top 3 regulated pathway -Organelle biogenesis and maintenance (23 ) -Muscle contraction (17 ) -Axon guidance (9 )Table 3 Pathway enrichment analysis of up-regulated pathways in swiftlet salivary glands (Continued)Male 5 -Vesicle-mediated transport (38 ) -Extracellular [https://www.ncbi.nlm.nih.gov/pubmed/27385778 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27385778] matrix transport (29 ) -Signal transduction (23 ) AFC Aerodramus fuciphagus from cave AFM Aerodramus fuciphagus from man-made house AMC Aerodramus maximus from cave AA Apus affinis NA No regulated pathways with p-value</div> Answerform0 https://wiki.sine.space/index.php?title=Ulated_based_on_normalized,_log2-transformed_gene_expression_values_from_the&diff=79690 Ulated based on normalized, log2-transformed gene expression values from the 2019-04-08T07:53:06Z <p>Answerform0: </p> <hr /> <div>The transcriptomic sequencing was completed using the Illumina Genome [https://www.ncbi.nlm.nih.gov/pubmed/28388412 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28388412] Analyzer system [http://wazock.com/comment/html/?165578.html Min) the supernatant was kept along with the total protein was determined] platform, HiSeq2000, with a 100 bp paired-end read. Nevertheless, the transcriptomic profiles of swiftlets have not been established. The current study focused on de novo RNA sequencing of the salivary glands of both EBN-producing swiftlets and non-EBN-producing swiftlets. The transcriptomic sequencing was completed using the Illumina Genome [https://www.ncbi.nlm.nih.gov/pubmed/28388412 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28388412] Analyzer system platform, HiSeq2000, with a 100 bp paired-end read. A paired-end sequencing protocol was selected for this study because it is critical for the assembly of short (</div> Answerform0 https://wiki.sine.space/index.php?title=Ulated_based_on_normalized,_log2-transformed_gene_expression_values_from_the&diff=79684 Ulated based on normalized, log2-transformed gene expression values from the 2019-04-08T07:03:16Z <p>Answerform0: </p> <hr /> <div>The current study focused on de novo RNA sequencing of the [http://www.chemscene.com/89778-27-8.html Toremifene (Citrate) custom synthesis] salivary glands of both EBN-producing swiftlets and non-EBN-producing swiftlets. BMC Genomics (2017) 18:Page 9 ofTable 4 Expression profiles of genes of potential importance in salivary gland development and EBN compositionsGene function Salivary development Gene CREB3L2 SEC63 SEC24A SAR1 AA versus Aerodramus species Gene function EGFR signalling pathway Gene ARF4 BCAR1 CAV1 CEBPA ELF3 EPS15 EPS8 JUN PLEC RAB5A REPS1 ZPR1 VAV2 STAT3 N-glycan biosynthesis ALG2 MGAT1 RPN1 FUT8 RPN2 AMC versus AFC Gene function EGFR signalling pathway Gene JUND HDAC BCAR N-glycan biosynthesis Alanine and Aspartate metabolism MGAT GOT1 PDHB AFM versus AFC Gene function MAPK signalling pathway BMP signalling pathway Fatty acid synthesis Gender comparison of AFC Gene function N-glycan trimming Gene EDEM2 Male 3.951 Female 0.359 log2 3.459 q-value 0.008 Gene HMGN1 TOB2 ACADVL AFM 23,486.800 20.463 10.909 AFC 2685.98 0.959 50.803 log2 -3.128 -4.414 2.219 q-value 0.001 0.001 0.001 AMC 4.911 1.357 7.776 20.278 226.741 894.023 AFC 39.541 580.771 200.736 256.555 7.0263 135.641 log2 3.009 8.740 4.690 3.661 -5.012 -2.721 q-value 0.001 0.001 0.001 0.046 0.000 0.000 AA 0.683 6.407 0.695 8.626 6.816 0.198 0.754 0.411 6.047 17.934 6.795 1.079 49.553 2.453 6.546 4.617 66.407 13.173 1.069 Aerodramus spp 48.954 51.836 50.207 49.820 603.607 10.035 13.668 11.504 31.197 47.435 21.529 13.242 239.912 53.308 90.860 91.067 552.366 84.076 71.026 log2 6.162 3.016 6.174 2.529 6.468 5.657 4.178 4.803 2.367 1.403 1.663 3.617 2.275 4.441 3.794 4.301 3.056 2.674 6.053 q-value 0.026 0.003 0.026 0.018 0.001 0.026 0.026 0.021 0.005 0.046 0.040 0.001 0.011 0.001 0.001 0.004 0.003 0.003 0.001 AFM 65.608 36.723 15.763 38.916 AFC 76.666 34.793 15.414 23.855 AMC 51.669 50.081 19.240 16.996 AA 0.000 5.926 19.20 6.AFC Aerodramu.Ulated based on normalized, log2-transformed gene expression values from the nCounter data and the RNA-Seq FPKM data of the 36 genes. The mean correlation was 0.54 with a 95 bootstrap confidence interval.DiscussionCharacterization of the swiftlet transcriptomeWith the advancements in sequencing technologies, the genomes of several avian species, including Peking ducks [30], passenger pigeons [15], and vultures [31], have been sequenced and characterized, whereby this inclusion has accelerated the research [https://www.ncbi.nlm.nih.gov/pubmed/28724915 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28724915] on functional genomics and improved our understanding of the genetic regulation of important traits. However, for some non-model organisms and minor species, it is not feasible to perform whole genome sequencing because of the expensive cost. Sequencing based on NGS technology has provided an opportunity to use a transcriptomic approach to study mechanisms that control certain traits in non-model organisms [32]. It is generally recognized that EBN is one of the most expensive animal-based products; it is often known as the &quot;caviar of the East&quot; [4]. Nevertheless, the transcriptomic profiles of swiftlets have not been established. The current study focused on de novo RNA sequencing of the salivary glands of both EBN-producing swiftlets and non-EBN-producing swiftlets. The transcriptomic sequencing was completed using the Illumina Genome [https://www.ncbi.nlm.nih.gov/pubmed/28388412 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28388412] Analyzer system platform, HiSeq2000, with a 100 bp paired-end read. A paired-end sequencing protocol was selected for this study because it is critical for the assembly of short (</div> Answerform0