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Additional file 1: Figure S1. of Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance

Maureen Carey, Jason Papin & Jennifer Guler
Distribution of genome-wide expression data demonstrates moderate differential expression between sensitive and resistant parasites. Fold change values from differential expression between sensitive and resistant parasites from Cambodia (A) and Vietnam (B) with significantly differentially expressed genes in red. Fold change is the ratio of mean expression in resistant parasites to mean expression in sensitive parasites, for each respective country. (PDF 820 kb)

Additional file 14: of Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China

Jian-Qiang Su, Xin-Li An, Bing Li, Qing-Lin Chen, Michael Gillings, Hong Chen, Tong Zhang & Yong-Guan Zhu
Dataset 4. Characteristics of network analysis of bacterial taxa and ARGs in summer and winter. (XLSX 35 kb)

Additional file 8: of Genome analysis of E. coli isolated from Crohn’s disease patients

Daria Rakitina, Alexander Manolov, Alexandra Kanygina, Sofya Garushyants, Julia Baikova, Dmitry Alexeev, Valentina Ladygina, Elena Kostryukova, Andrei Larin, Tatiana Semashko, Irina Karpova, Vladislav Babenko, Ruzilya Ismagilova, Sergei Malanin, Mikhail Gelfand, Elena Ilina, Roman Gorodnichev, Eugenia Lisitsyna, Gennady Aleshkin, Petr Scherbakov, Igor Khalif, Marina Shapina, Igor Maev, Dmitry Andreev & Vadim Govorun
Comparison of the OG content of CD-isolates and commensal strains. Columns: OG – orthologous group number; Function – orthologous group function; gene group / global function – function of the operon or a major pathway in which OG participates; crohnall.yes − number of genomes from CrohnAll group containing the OG; crohnall.no − number of genomes from CrohnAll group not containing the OG; commensal.yes − number of genomes from commensal group containing the OG; commensal.no −...

Additional file 1: Figure S1. of O-GlcNAc regulation of autophagy and α-synuclein homeostasis; implications for Parkinson’s disease

Willayat Wani, Xiaosen Ouyang, Gloria Benavides, Matthew Redmann, Stacey Cofield, John Shacka, John Chatham, Victor Darley-Usmar & Jianhua Zhang
Inhibition of OGA by thiamet G (TG) did not significantly change mitochondrial mass or function. (JPEG 500 kb)

Additional file 13: of Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China

Jian-Qiang Su, Xin-Li An, Bing Li, Qing-Lin Chen, Michael Gillings, Hong Chen, Tong Zhang & Yong-Guan Zhu
Figure S8. Co-occurrence patterns of summer (a) and winter (b) antibiotic resistome and summer (c) and winter (d) microbiome in urban sewages. A connection stands for a strong (Spearman’s ρ > 0.7) and significant (P value 

Additional file 7: of Genome analysis of E. coli isolated from Crohnâ s disease patients

Daria Rakitina, Alexander Manolov, Alexandra Kanygina, Sofya Garushyants, Julia Baikova, Dmitry Alexeev, Valentina Ladygina, Elena Kostryukova, Andrei Larin, Tatiana Semashko, Irina Karpova, Vladislav Babenko, Ruzilya Ismagilova, Sergei Malanin, Mikhail Gelfand, Elena Ilina, Roman Gorodnichev, Eugenia Lisitsyna, Gennady Aleshkin, Petr Scherbakov, Igor Khalif, Marina Shapina, Igor Maev, Dmitry Andreev & Vadim Govorun
plLF82 homologs in CD-associated E. coli. (A) Sequence similarity of CD isolates with the plasmid pLF82 (100 kb), (B) and (C) functions of proteins common between pLF82 or pJJ1886_4 and CD isolates The functions were obtained from original annotation, complemented by Prokka annotation and BLAST protein similarity search. (D) Sequence similarity of commensal E. coli isolates with plasmids plLF82 and pJJ1886_4 (script for the data is described in supplementary data https://github.com/paraslonic/Rakitina_etal_Crohn_paper/tree/master/plasmidCoverage [41]. (DOC 228 kb)

Additional file 2: Table S2. of 16S rRNA gene-based association study identified microbial taxa associated with pork intramuscular fat content in feces and cecum lumen

Shaoming Fang, Xingwei Xiong, Ying Su, Lusheng Huang & Congying Chen
OTUs significantly associated with IMF content (FDR 

Use of a special Brazilian red-light emitting railroad worm Luciferase in bioassays of NEK7 protein Kinase and Creatine Kinase

Arina Perez, Bruno Aquino, Vadim Viviani & JĂśrg Kobarg
Abstract Background Luciferases, enzymes that catalyze bioluminescent reactions in different organisms, have been extensively used for bioanalytical purposes. The most well studied bioluminescent system is that of firefly and other beetles, which depends on a luciferase, a benzothiazolic luciferin and ATP, and it is being widely used as a bioanalytical reagent to quantify ATP. Protein kinases are proteins that modify other proteins by transferring phosphate groups from a nucleoside triphosphate, usually ATP. Methods Here, we...

Additional file 1: of Risk factors for acute surgical site infections after lumbar surgery: a retrospective study

Qi Lai, Quanwei Song, Runsheng Guo, Haidi Bi, Xuqiang Liu, Xiaolong Yu, Jianghao Zhu, Min Dai & Bin Zhang
Original data of 26 patients with ASSI. (XLS 13 kb)

Real-life clinical practice results with vinflunine in patients with relapsed platinum-treated metastatic urothelial carcinoma: an Italian multicenter study (MOVIE-GOIRC 01–2014)

Rodolfo Passalacqua, Silvia Lazzarelli, Maddalena Donini, Rodolfo Montironi, Rosa Tambaro, Ugo De Giorgi, Sandro Pignata, Raffaella Palumbo, Giovanni Ceresoli, Gianluca Del Conte, Giuseppe Tonini, Franco Morelli, Franco Nolè, Stefano Panni, Ermanno Rondini, Annalisa Guida, Paolo Zucali, Laura Doni, Elisa Iezzi & Caterina Caminiti
Abstract Background Vinflunine is the only chemotherapeutic agent shown to improve survival in platinum-refractory patients with metastatic transitional cell carcinoma of the urothelium (TCCU) in a phase III clinical trial, which led to product registration for this indication in Europe. The aim of this study was to assess the efficacy of vinflunine and to evaluate the prognostic significance of risk factors in a large, unselected cohort of patients with metastatic TCCU treated according to routine...

16S rRNA gene-based association study identified microbial taxa associated with pork intramuscular fat content in feces and cecum lumen

Shaoming Fang, Xingwei Xiong, Ying Su, Lusheng Huang & Congying Chen
Abstract Background Intramuscular fat (IMF) that deposits among muscle fibers or within muscle cells is an important meat quality trait in pigs. Previous studies observed the effects of dietary nutrients and additives on improving the pork IMF. Gut microbiome plays an important role in host metabolism and energy harvest. Whether gut microbiota exerts effect on IMF remains unknown. Results In this study, we investigated the microbial community structure of 500 samples from porcine cecum and...

Additional file 12: of Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China

Jian-Qiang Su, Xin-Li An, Bing Li, Qing-Lin Chen, Michael Gillings, Hong Chen, Tong Zhang & Yong-Guan Zhu
Figure S7. Seasonal variation of antibiotic resistomes and microbial communities in sewage. a Percentage of the core resistomes in urban sewage samples. MLS Macrolide-Lincosamide-Streptogramin resistance. b NMDS analysis revealing the distribution pattern of the core resistomes at subtype level (Adonis tests, P 

Additional file 6: of Genome analysis of E. coli isolated from Crohnâ s disease patients

Daria Rakitina, Alexander Manolov, Alexandra Kanygina, Sofya Garushyants, Julia Baikova, Dmitry Alexeev, Valentina Ladygina, Elena Kostryukova, Andrei Larin, Tatiana Semashko, Irina Karpova, Vladislav Babenko, Ruzilya Ismagilova, Sergei Malanin, Mikhail Gelfand, Elena Ilina, Roman Gorodnichev, Eugenia Lisitsyna, Gennady Aleshkin, Petr Scherbakov, Igor Khalif, Marina Shapina, Igor Maev, Dmitry Andreev & Vadim Govorun
Multi locus sequence types (MLST) were determined by the sequence of seven housekeeping genes with web server mlst.warwick.ac.uk [48]. (XLS 17 kb)

Additional file 1: of Real-life clinical practice results with vinflunine in patients with relapsed platinum-treated metastatic urothelial carcinoma: an Italian multicenter study (MOVIE-GOIRC 01â 2014)

Rodolfo Passalacqua, Silvia Lazzarelli, Maddalena Donini, Rodolfo Montironi, Rosa Tambaro, Ugo De Giorgi, Sandro Pignata, Raffaella Palumbo, Giovanni Ceresoli, Gianluca Del Conte, Giuseppe Tonini, Franco Morelli, Franco Nolè, Stefano Panni, Ermanno Rondini, Annalisa Guida, Paolo Zucali, Laura Doni, Elisa Iezzi & Caterina Caminiti
List of participating centers. Table S1. Stratified analysis of overall survival (OS) and progression-free survival (PFS) according to previous Cisplatin or Carboplatin treatment and to the number of cycles received. (DOCX 46 kb)

Risk factors for acute surgical site infections after lumbar surgery: a retrospective study

Qi Lai, Quanwei Song, Runsheng Guo, Haidi Bi, Xuqiang Liu, Xiaolong Yu, Jianghao Zhu, Min Dai & Bin Zhang
Abstract Background Currently, many scholars are concerned about the treatment of postoperative infection; however, few have completed multivariate analyses to determine factors that contribute to the risk of infection. Therefore, we conducted a multivariate analysis of a retrospectively collected database to analyze the risk factors for acute surgical site infection following lumbar surgery, including fracture fixation, lumbar fusion, and minimally invasive lumbar surgery. Methods We retrospectively reviewed data from patients who underwent lumbar surgery between...

Additional file 1: Figure S1. of Use of a special Brazilian red-light emitting railroad worm Luciferase in bioassays of NEK7 protein Kinase and Creatine Kinase

Arina Perez, Bruno Aquino, Vadim Viviani & JĂśrg Kobarg
Lack of ATPase contamination in luciferase purification analysis. Demonstrates that the used luciferase preparation is not contaminated with ATP consuming enzymes derived from E.coli. Figure S2. Purification of proteins used in the assays. Shows purity of the protein samples (luciferase, creatin kinase, NEK7 and 9, Mat1 and CC2D1A) used in the experiments of the paper. (DOCX 252 kb)

Additional file 1: Table S1. of 16S rRNA gene-based association study identified microbial taxa associated with pork intramuscular fat content in feces and cecum lumen

Shaoming Fang, Xingwei Xiong, Ying Su, Lusheng Huang & Congying Chen
OTUs significantly associated with IMF content (FDR 

Additional file 11: of Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China

Jian-Qiang Su, Xin-Li An, Bing Li, Qing-Lin Chen, Michael Gillings, Hong Chen, Tong Zhang & Yong-Guan Zhu
Figure S6. Relative abundances of the bacterial genera in all the WWTP sewage samples. Genera are colored by their respective phylum. a The relative abundance of the top 30 abundant genera, representing as the relative abundance of each genus. b The relative abundance of the 33 shared, classified bacterial genera. c The relative abundance of top 30 human gut microbial genera. (PDF 559 kb)

Additional file 5: of Genome analysis of E. coli isolated from Crohnâ s disease patients

Daria Rakitina, Alexander Manolov, Alexandra Kanygina, Sofya Garushyants, Julia Baikova, Dmitry Alexeev, Valentina Ladygina, Elena Kostryukova, Andrei Larin, Tatiana Semashko, Irina Karpova, Vladislav Babenko, Ruzilya Ismagilova, Sergei Malanin, Mikhail Gelfand, Elena Ilina, Roman Gorodnichev, Eugenia Lisitsyna, Gennady Aleshkin, Petr Scherbakov, Igor Khalif, Marina Shapina, Igor Maev, Dmitry Andreev & Vadim Govorun
Phage sensitivity test of E. coli CD-isolates (see Methods). (DOC 45 kb)

Deciphering functional diversification within the lichen microbiota by meta-omics

Tomislav Cernava, Armin Erlacher, Ines Aschenbrenner, Lisa Krug, Christian Lassek, Katharina Riedel, Martin Grube & Gabriele Berg
Abstract Background Recent evidence of specific bacterial communities extended the traditional concept of fungal-algal lichen symbioses by a further organismal kingdom. Although functional roles were already assigned to dominant members of the highly diversified microbiota, a substantial fraction of the ubiquitous colonizers remained unexplored. We employed a multi-omics approach to further characterize functional guilds in an unconventional model system. Results The general community structure of the lichen-associated microbiota was shown to be highly similar irrespective...

Additional file 10: of Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China

Jian-Qiang Su, Xin-Li An, Bing Li, Qing-Lin Chen, Michael Gillings, Hong Chen, Tong Zhang & Yong-Guan Zhu
Figure S5. Bacterial community compositions in sewage samples. a The relative abundance of major phyla in each city. b Comparison of the relative abundance of major phyla between summer and winter samples at the phylum level. ANOVA, * represents P 

Additional file 4: of Genome analysis of E. coli isolated from Crohnâ s disease patients

Daria Rakitina, Alexander Manolov, Alexandra Kanygina, Sofya Garushyants, Julia Baikova, Dmitry Alexeev, Valentina Ladygina, Elena Kostryukova, Andrei Larin, Tatiana Semashko, Irina Karpova, Vladislav Babenko, Ruzilya Ismagilova, Sergei Malanin, Mikhail Gelfand, Elena Ilina, Roman Gorodnichev, Eugenia Lisitsyna, Gennady Aleshkin, Petr Scherbakov, Igor Khalif, Marina Shapina, Igor Maev, Dmitry Andreev & Vadim Govorun
(A) Mauve alignment of CD-E. coli isolates from one patient (alignment made for RCE01, RCE02, RCE03, RCE03 and RCE06). (B) Heatmap of the phylogenetic distance between E. coli strains. Distances between strains are calculated as the median distance of core genes (see Methods). Phylogroups of E. coli are designated (A, B1, E, B2, D, F). RCE03 is not shown because of its low similarity to other E. coli strains. (DOC 4350 kb)

Deficiency of PI3-Kinase catalytic isoforms p110γ and p110δ in mice enhances the IL-17/G-CSF axis and induces neutrophilia

Kirsten Bucher, Fee Schmitt, Benedikt Mothes, Carolin Blumendeller, Daniel Schäll, Roland Piekorz, Emilio Hirsch, Bernd Nürnberg & Sandra Beer-Hammer
Abstract Background Phosphoinositide 3-kinase γ (PI3Kγ) and PI3Kδ are second messenger-generating enzymes with key roles in proliferation, differentiation, survival, and function of leukocytes. Deficiency of the catalytic subunits p110γ and p110δ of PI3Kγ and PI3Kδ in p110γ/δ−/− mice leads to defective B- and T-cell homeostasis. Here we examined the role of p110γ and p110δ in the homeostasis of neutrophils by analyzing p110γ−/−, p110δ−/− and p110γ/δ−/− mice. Methods Neutrophils and T cells in leukocyte suspensions from...

Additional file 4: Figure S4. of Deficiency of PI3-Kinase catalytic isoforms p110γ and p110δ in mice enhances the IL-17/G-CSF axis and induces neutrophilia

Kirsten Bucher, Fee Schmitt, Benedikt Mothes, Carolin Blumendeller, Daniel Schäll, Roland Piekorz, Emilio Hirsch, Bernd Nürnberg & Sandra Beer-Hammer
Migration of neutrophils from WT and p110−/− mice upon CXCL12/SDF-1. Transwells inserts (3.0 μm pore size, Costar) were placed in 24-well plates containing CXCL12/SDF-1(10 nM or 50 nM). BM cells labeled with 40 Ly6G-APC were seeded on the upper chamber of each well at 3 × 106 cells per well. In parallel, cells were directly seeded into wells without transwell inserts and served as positive controls (100% migration). Cells were incubated for 60 or 110 min. Then Ly6G+ neutrophils in the...

Additional file 1: Table S1. of Deciphering functional diversification within the lichen microbiota by meta-omics

Tomislav Cernava, Armin Erlacher, Ines Aschenbrenner, Lisa Krug, Christian Lassek, Katharina Riedel, Martin Grube & Gabriele Berg
Metadata and basic information related to the DNA/RNA-based omic approaches. Table S2: Primer sets for eukaryotic and prokaryotic rRNA gene fragment amplification. Bold: T7 promoter sequence; blue: enhancer sequence. Table S3: Taxonomical assignments. Fig. S1: Molecular fingerprints of 16S rRNA gene fragments from total DNA (Tot DNA) from the lichen, isolates from the lichen thalli (L. pulmonaria) and control strains (E. coli, S. aureus, P. aeruginosa). Fig. S2: Phylogenetic tree of bacteria-strains within the phylum...

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