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Additional file 16: Figure S4. of Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection

Yachun Su, Yuye Zhang, Ning Huang, Feng Liu, Weihua Su, Liping Xu, Waqar Ahmad, Qibin Wu, Jinlong Guo & Youxiong Que
GO categories and distribution of novel miRNAs targets in RT/RCK (A) and YAT/YACK (B), respectively. RCK and YACK: ROC22 and YA05-179 under sterile water stress after 48 h, respectively; RT and YAT: ROC22 and YA05-179 under Sporisorium scitamineum stress after 48 h, respectively. (TIF 1606 kb)

Insertion and deletion polymorphisms of the ancient AluS family in the human genome

Maria Kryatova, Jared Steranka, Kathleen Burns & Lindsay Payer
Abstract Background Polymorphic Alu elements account for 17% of structural variants in the human genome. The majority of these belong to the youngest AluY subfamilies, and most structural variant discovery efforts have focused on identifying Alu polymorphisms from these currently retrotranspositionally active subfamilies. In this report we analyze polymorphisms from the evolutionarily older AluS subfamily, whose peak activity was tens of millions of years ago. We annotate the AluS polymorphisms, assess their likely mechanism of...

Additional file 15: Figure S3. of Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection

Yachun Su, Yuye Zhang, Ning Huang, Feng Liu, Weihua Su, Liping Xu, Waqar Ahmad, Qibin Wu, Jinlong Guo & Youxiong Que
GO categories and distribution of known miRNAs targets in RT/RCK (A) and YAT/YACK (B), respectively. RCK and YACK: ROC22 and YA05-179 under sterile water stress after 48 h, respectively; RT and YAT: ROC22 and YA05-179 under Sporisorium scitamineum stress after 48 h, respectively. (TIF 3774 kb)

Additional file 14: Table S12. of Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection

Yachun Su, Yuye Zhang, Ning Huang, Feng Liu, Weihua Su, Liping Xu, Waqar Ahmad, Qibin Wu, Jinlong Guo & Youxiong Que
The prediction results for partial target genes of differentially expressed miRNAs. (DOC 41 kb)

Additional file 5: Figure S2. of Insertion and deletion polymorphisms of the ancient AluS family in the human genome

Maria Kryatova, Jared Steranka, Kathleen Burns & Lindsay Payer
Functionally significant Alu sequence features annotated in TPRT insertion candidates (nâ =â 7). (PDF 203 kb)

Additional file 13: Table S11. of Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection

Yachun Su, Yuye Zhang, Ning Huang, Feng Liu, Weihua Su, Liping Xu, Waqar Ahmad, Qibin Wu, Jinlong Guo & Youxiong Que
Prediction of target genes of known and novel miRNAs. (DOC 30 kb)

Additional file 4: Table S3. of Insertion and deletion polymorphisms of the ancient AluS family in the human genome

Maria Kryatova, Jared Steranka, Kathleen Burns & Lindsay Payer
Sequences of deletion and Alu-containing alleles of AluS deletion polymorphisms (nâ =â 37) [2]. (XLSX 16 kb)

Amelioration of amyloid-β-induced deficits by DcR3 in an Alzheimer’s disease model

Yi-Ling Liu, Wei-Ting Chen, Yu-Yi Lin, Po-Hung Lu, Shie-Liang Hsieh & Irene Cheng
Abstract Background Microglia mediate amyloid-beta peptide (Aβ)-induced neuroinflammation, which is one of the key events in the pathogenesis of Alzheimer’s disease (AD). Decoy receptor 3 (DcR3)/TNFRSF6B is a pleiotropic immunomodulator that promotes macrophage differentiation toward the M2 anti-inflammatory phenotype. Based on its role as an immunosupressor, we examined whether DcR3 could alleviate neuroinflammation and AD-like deficits in the central nervous system. Method We crossed human APP transgenic mice (line J20) with human DcR3 transgenic mice...

Additional file 9: Figure S7. of Amelioration of amyloid-β-induced deficits by DcR3 in an Alzheimer’s disease model

Yi-Ling Liu, Wei-Ting Chen, Yu-Yi Lin, Po-Hung Lu, Shie-Liang Hsieh & Irene Cheng
Expression inflammatory-related genes in mice of four genotypes. The mRNA levels of (a) M2a, (b, c) M2b, (c-f) M2c, and (g-i) inflammasome related proteins were examined by using qPCR. *P ≤ 0.05. (PDF 52 kb)

Additional file 8: Figure S6. of Amelioration of amyloid-β-induced deficits by DcR3 in an Alzheimer’s disease model

Yi-Ling Liu, Wei-Ting Chen, Yu-Yi Lin, Po-Hung Lu, Shie-Liang Hsieh & Irene Cheng
Morphological changes of primary microglia in vitro under Aβ or Aβ/DcR3 treatment. The representative fluorescent images were labeled with microglia marker (Iba1, red) and nucleus (DAPI, blue) in microglia culture. Scale bar: 20 μm. (PDF 8273 kb)

Additional file 12: Table S10. of Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection

Yachun Su, Yuye Zhang, Ning Huang, Feng Liu, Weihua Su, Liping Xu, Waqar Ahmad, Qibin Wu, Jinlong Guo & Youxiong Que
The significantly differentially expressed novel miRNAs in the YAT/YACK. (DOC 32 kb)

Additional file 7: Figure S5. of Amelioration of amyloid-β-induced deficits by DcR3 in an Alzheimer’s disease model

Yi-Ling Liu, Wei-Ting Chen, Yu-Yi Lin, Po-Hung Lu, Shie-Liang Hsieh & Irene Cheng
Effect of DcR3 on Aβ deposition in the hippocampus. (a) Immunostaining of total Aβ (6E10, Red) and nucleus (DAPI, Blue) of the hippocampus. Scale bar: 200 μm. (b, c) Quantification data of (b) total numbers of Aβ plaques and (c) plaque coverage (N = 4 mice per genotype, N = 8 brain slices per mouse). (PDF 119 kb)

Additional file 3: Table S2. of Insertion and deletion polymorphisms of the ancient AluS family in the human genome

Maria Kryatova, Jared Steranka, Kathleen Burns & Lindsay Payer
Polymorphic AluS insertion candidates (nâ =â 11). (XLSX 17 kb)

Additional file 6: Figure S4. of Amelioration of amyloid-β-induced deficits by DcR3 in an Alzheimer’s disease model

Yi-Ling Liu, Wei-Ting Chen, Yu-Yi Lin, Po-Hung Lu, Shie-Liang Hsieh & Irene Cheng
Aβ aggregation status and DcR3 immuno-depletion control for the conditioned media experiment. (a-c) Western blotting were applied to determine the aggregation state of Aβ peptide in (a) fresh prepared oAβ or fAβ, (b) after 72 h incubating with microglia, (c) after 72 h incubating with neuron. (d) Representative Western blotting image of DcR3 protein levels after immuno-depletion. (e) DcR3 depletion conditioned treatment had no protective function on neuronal survival under Aβ stress (n = 4). *P ≤ 0.05,***P ≤ 0.001. The neuronal survival...

Additional file 11:Table S9. of Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection

Yachun Su, Yuye Zhang, Ning Huang, Feng Liu, Weihua Su, Liping Xu, Waqar Ahmad, Qibin Wu, Jinlong Guo & Youxiong Que
The significantly differentially expressed novel miRNAs in the RT/RCK. (DOC 42 kb)

Additional file 5: Figure S3. of Amelioration of amyloid-β-induced deficits by DcR3 in an Alzheimer’s disease model

Yi-Ling Liu, Wei-Ting Chen, Yu-Yi Lin, Po-Hung Lu, Shie-Liang Hsieh & Irene Cheng
DcR3 protected neurons against Aβ stress in vitro. (a) Representative illustrations of PI staining used to measure the number of dead neurons after CM treatment. Red: dead cells (PI); Blue: nucleus (DAPI). Scale bar: 20 μm. (b) The ratio of PI/DAPI indicates the change in the number of dead neurons after treatment with the conditioned medium. (c) Primary neurons were labeled with neuronal markers (MAP2, Green), and nucleus (DAPI, Blue). Arrow indicated broken and swelling neurites....

Additional file 4: Figure S2. of Amelioration of amyloid-β-induced deficits by DcR3 in an Alzheimer’s disease model

Yi-Ling Liu, Wei-Ting Chen, Yu-Yi Lin, Po-Hung Lu, Shie-Liang Hsieh & Irene Cheng
Synaptophysin and MAP2 immunostaining in the hippocampus. (a)Enlarged view of synaptophysin staining in Fig. 2a. Scale bar: 100 μm. (b)Representative immunofluorescence images labeled with neuronal marker MAP2 in the mouse brain slice. Scale bar: 100 μm. (c) Quantification graph comparing the average intensity in CA3-mossy fibers, CA1, and DG region (N = 7-13 mice per genotype). (PDF 4774 kb)

Additional file 2: Figure S1. of Insertion and deletion polymorphisms of the ancient AluS family in the human genome

Maria Kryatova, Jared Steranka, Kathleen Burns & Lindsay Payer
Diagnostic nucleotides differentiate AluS and AluY subfamily consensus sequences. a. To identify diagnostic nucleotides differentiating AluS and AluY subfamily consensus sequences, RepBase consensus sequences of all six AluS subfamilies (AluSc, AluSg, AluSp, AluSq, AluSx, AluSz,) and the most common AluY subfamilies (AluY, AluYa5, AluYa8, AluYb8, AluYb9, AluYc1) were aligned. Five diagnostic nucleotides that distinguish all six AluS subfamilies from six AluY subfamilies included in the alignment were identified (highlighted in magenta). Seven additional positions that...

Additional file 3: Figure S1. of Amelioration of amyloid-β-induced deficits by DcR3 in an Alzheimer’s disease model

Yi-Ling Liu, Wei-Ting Chen, Yu-Yi Lin, Po-Hung Lu, Shie-Liang Hsieh & Irene Cheng
Full-length APP and DcR3 expression in four genotypes of mice at 6 months of age. (a, b) Levels of full-length APP did not change between the APP and APP/DcR3 mice (c) Levels of DcR3 did not change between the DcR3 and APP/DcR3 mice (N = 18-22 mice per genotype). *P ≤ 0.05. NS, not significant. (PDF 8354 kb)

Process relevant screening of cellulolytic organisms for consolidated bioprocessing

Elena Antonov, Ivan Schlembach, Lars Regestein, Miriam Rosenbaum & Jochen Büchs
Abstract Background Although the biocatalytic conversion of cellulosic biomass could replace fossil oil for the production of various compounds, it is often not economically viable due to the high costs of cellulolytic enzymes. One possibility to reduce costs is consolidated bioprocessing (CBP), integrating cellulase production, hydrolysis of cellulose, and the fermentation of the released sugars to the desired product into one process step. To establish such a process, the most suitable cellulase-producing organism has to...

Additional file 2: Table S2. of Amelioration of amyloid-β-induced deficits by DcR3 in an Alzheimerâ s disease model

Yi-Ling Liu, Wei-Ting Chen, Yu-Yi Lin, Po-Hung Lu, Shie-Liang Hsieh & Irene Cheng
Statement on sample size and statistical measures. (PDF 1351 kb)

MOESM2 of Process relevant screening of cellulolytic organisms for consolidated bioprocessing

Elena Antonov, Ivan Schlembach, Lars Regestein, Miriam Rosenbaum & Jochen Büchs
Additional file 2: Figure S2. Characteristic growth and enzyme production properties of T. terrestris. (A) Biological duplicates of oxygen transfer rate (OTR) and cumulative oxygen transfer. For clarity of the depicted values, only every third measuring point of OTR and every eighth measuring point of cumulative oxygen transfer over time is represented by a symbol. (B) pH value and protein content in the culture supernatant; (C) Residual cellulose concentration and standard filter paper activity; RAMOS...

MOESM1 of Process relevant screening of cellulolytic organisms for consolidated bioprocessing

Elena Antonov, Ivan Schlembach, Lars Regestein, Miriam Rosenbaum & Jochen Büchs
Additional file 1: Figure S1. Screening for cellulase synergism with A. terreus culture broth using the freeze assay. Freeze assay was performed at the indicated cultivation temperatures with 0.5 mL suspended full culture broth of A. terreus mixed with 0.5 mL full culture broth of different candidate organisms. Full culture broth was harvested after 5 days of cultivation in modified Pakula medium with 5 g L−1 glucose and 30 g L−1 α-cellulose. Bars show overall carbon release rate calculated as...

Additional file 1: Table S1. of Amelioration of amyloid-β-induced deficits by DcR3 in an Alzheimer’s disease model

Yi-Ling Liu, Wei-Ting Chen, Yu-Yi Lin, Po-Hung Lu, Shie-Liang Hsieh & Irene Cheng
List of the real-time PCR primers sets (5′-3′) for the target genes. (PDF 4549 kb)

Additional file 10: Table S8. of Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection

Yachun Su, Yuye Zhang, Ning Huang, Feng Liu, Weihua Su, Liping Xu, Waqar Ahmad, Qibin Wu, Jinlong Guo & Youxiong Que
The significantly differentially expressed known miRNAs in the YAT/YACK. (DOC 37 kb)

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