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MOESM13 of Interaction of camel Lactoferrin derived peptides with DNA: a molecular dynamics study

Zana Pirkhezranian, Mojtaba Tahmoorespur, Xavier Daura, Hassan Monhemi & Mohammad Sekhavati
Additional file 13: Figure S12. Third replicate: Number of hydrogen bonds with DNA at different concentrations of CLFchimera, (A) CLFchimera, (B) 2-CLFchimera, (C) 3-CLFchimera, (D) 4-CLFchimera.

Pcdhβ deficiency affects hippocampal CA1 ensemble activity and contextual fear discrimination

Hirotaka Asai, Noriaki Ohkawa, Yoshito Saitoh, Khaled Ghandour, Emi Murayama, Hirofumi Nishizono, Mina Matsuo, Teruyoshi Hirayama, Ryosuke Kaneko, Shin-Ichi Muramatsu, Takeshi Yagi & Kaoru Inokuchi
Abstract Clustered protocadherins (Pcdhs), a large group of adhesion molecules, are important for axonal projections and dendritic spread, but little is known about how they influence neuronal activity. The Pcdhβ cluster is strongly expressed in the hippocampus, and in vivo Ca2+ imaging in Pcdhβ-deficient mice revealed altered activity of neuronal ensembles but not of individual cells in this region in freely moving animals. Specifically, Pcdhβ deficiency increased the number of large-size neuronal ensembles and the...

MOESM14 of Interaction of camel Lactoferrin derived peptides with DNA: a molecular dynamics study

Zana Pirkhezranian, Mojtaba Tahmoorespur, Xavier Daura, Hassan Monhemi & Mohammad Sekhavati
Additional file 14: Table S2. Interaction results from MD simulations of CLF-chimera concentration with DNA.

MOESM14 of Interaction of camel Lactoferrin derived peptides with DNA: a molecular dynamics study

Zana Pirkhezranian, Mojtaba Tahmoorespur, Xavier Daura, Hassan Monhemi & Mohammad Sekhavati
Additional file 14: Table S2. Interaction results from MD simulations of CLF-chimera concentration with DNA.

MOESM12 of Interaction of camel Lactoferrin derived peptides with DNA: a molecular dynamics study

Zana Pirkhezranian, Mojtaba Tahmoorespur, Xavier Daura, Hassan Monhemi & Mohammad Sekhavati
Additional file 12: Figure S11. Second replicate: Number of hydrogen bonds with DNA at different concentrations of CLFchimera, (A) CLFchimera, (B) 2-CLFchimera, (C) 3-CLFchimera, (D) 4-CLFchimera.

Pcdhβ deficiency affects hippocampal CA1 ensemble activity and contextual fear discrimination

Hirotaka Asai, Noriaki Ohkawa, Yoshito Saitoh, Khaled Ghandour, Emi Murayama, Hirofumi Nishizono, Mina Matsuo, Teruyoshi Hirayama, Ryosuke Kaneko, Shin-Ichi Muramatsu, Takeshi Yagi & Kaoru Inokuchi
Abstract Clustered protocadherins (Pcdhs), a large group of adhesion molecules, are important for axonal projections and dendritic spread, but little is known about how they influence neuronal activity. The Pcdhβ cluster is strongly expressed in the hippocampus, and in vivo Ca2+ imaging in Pcdhβ-deficient mice revealed altered activity of neuronal ensembles but not of individual cells in this region in freely moving animals. Specifically, Pcdhβ deficiency increased the number of large-size neuronal ensembles and the...

MOESM13 of Interaction of camel Lactoferrin derived peptides with DNA: a molecular dynamics study

Zana Pirkhezranian, Mojtaba Tahmoorespur, Xavier Daura, Hassan Monhemi & Mohammad Sekhavati
Additional file 13: Figure S12. Third replicate: Number of hydrogen bonds with DNA at different concentrations of CLFchimera, (A) CLFchimera, (B) 2-CLFchimera, (C) 3-CLFchimera, (D) 4-CLFchimera.

MOESM8 of Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Yan Qin, Shenglong Bai, Wenzheng Li, Ting Sun, David Galbraith, Zefeng Yang, Yun Zhou, Guiling Sun & Bingwu Wang
Additional file 8: Table S3. DEGs involved in nicotine biosynthesis and transport after topping.

MOESM5 of Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Yan Qin, Shenglong Bai, Wenzheng Li, Ting Sun, David Galbraith, Zefeng Yang, Yun Zhou, Guiling Sun & Bingwu Wang
Additional file 5: Figure S5. KEGG overview of DEGs after topping in tobacco. The numbers in the picture represent the DEGs that were annotated to the metabolic pathway, with the percentage representing the ratio of this count to the number of DEGs annotated to the total metabolic pathway.

MOESM11 of Interaction of camel Lactoferrin derived peptides with DNA: a molecular dynamics study

Zana Pirkhezranian, Mojtaba Tahmoorespur, Xavier Daura, Hassan Monhemi & Mohammad Sekhavati
Additional file 11: Figure S10. Minimum distances during 200 ns simulation.

MOESM10 of Interaction of camel Lactoferrin derived peptides with DNA: a molecular dynamics study

Zana Pirkhezranian, Mojtaba Tahmoorespur, Xavier Daura, Hassan Monhemi & Mohammad Sekhavati
Additional file 10: Figure S9. Second and Third Replicates: Contribution to DNA binding free energies of amino-acid residues in CLFchimera.

MOESM12 of Interaction of camel Lactoferrin derived peptides with DNA: a molecular dynamics study

Zana Pirkhezranian, Mojtaba Tahmoorespur, Xavier Daura, Hassan Monhemi & Mohammad Sekhavati
Additional file 12: Figure S11. Second replicate: Number of hydrogen bonds with DNA at different concentrations of CLFchimera, (A) CLFchimera, (B) 2-CLFchimera, (C) 3-CLFchimera, (D) 4-CLFchimera.

MOESM8 of Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Yan Qin, Shenglong Bai, Wenzheng Li, Ting Sun, David Galbraith, Zefeng Yang, Yun Zhou, Guiling Sun & Bingwu Wang
Additional file 8: Table S3. DEGs involved in nicotine biosynthesis and transport after topping.

MOESM9 of Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Yan Qin, Shenglong Bai, Wenzheng Li, Ting Sun, David Galbraith, Zefeng Yang, Yun Zhou, Guiling Sun & Bingwu Wang
Additional file 9: Table S4. Differentially transcribed transcription factors after topping.

MOESM9 of Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Yan Qin, Shenglong Bai, Wenzheng Li, Ting Sun, David Galbraith, Zefeng Yang, Yun Zhou, Guiling Sun & Bingwu Wang
Additional file 9: Table S4. Differentially transcribed transcription factors after topping.

MOESM7 of Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Yan Qin, Shenglong Bai, Wenzheng Li, Ting Sun, David Galbraith, Zefeng Yang, Yun Zhou, Guiling Sun & Bingwu Wang
Additional file 7: Table S2. List of DEGs in roots after topping.

MOESM11 of Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Yan Qin, Shenglong Bai, Wenzheng Li, Ting Sun, David Galbraith, Zefeng Yang, Yun Zhou, Guiling Sun & Bingwu Wang
Additional file 11: Table S6. DEGs involved in phytohormone signal transduction after topping.

MOESM10 of Interaction of camel Lactoferrin derived peptides with DNA: a molecular dynamics study

Zana Pirkhezranian, Mojtaba Tahmoorespur, Xavier Daura, Hassan Monhemi & Mohammad Sekhavati
Additional file 10: Figure S9. Second and Third Replicates: Contribution to DNA binding free energies of amino-acid residues in CLFchimera.

MOESM6 of Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Yan Qin, Shenglong Bai, Wenzheng Li, Ting Sun, David Galbraith, Zefeng Yang, Yun Zhou, Guiling Sun & Bingwu Wang
Additional file 6: Table S1. Quality and mapping rates of RNA-Seq data.

MOESM7 of Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Yan Qin, Shenglong Bai, Wenzheng Li, Ting Sun, David Galbraith, Zefeng Yang, Yun Zhou, Guiling Sun & Bingwu Wang
Additional file 7: Table S2. List of DEGs in roots after topping.

MOESM6 of Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Yan Qin, Shenglong Bai, Wenzheng Li, Ting Sun, David Galbraith, Zefeng Yang, Yun Zhou, Guiling Sun & Bingwu Wang
Additional file 6: Table S1. Quality and mapping rates of RNA-Seq data.

MOESM5 of Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Yan Qin, Shenglong Bai, Wenzheng Li, Ting Sun, David Galbraith, Zefeng Yang, Yun Zhou, Guiling Sun & Bingwu Wang
Additional file 5: Figure S5. KEGG overview of DEGs after topping in tobacco. The numbers in the picture represent the DEGs that were annotated to the metabolic pathway, with the percentage representing the ratio of this count to the number of DEGs annotated to the total metabolic pathway.

MOESM4 of Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Yan Qin, Shenglong Bai, Wenzheng Li, Ting Sun, David Galbraith, Zefeng Yang, Yun Zhou, Guiling Sun & Bingwu Wang
Additional file 4: Figure S4. Classification statistics of DEGs according to the GO annotations. The GO classification is indicated on the abscissa, with the ordinate providing the percentage of the number of genes (left) and the number of genes (right).

MOESM3 of Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Yan Qin, Shenglong Bai, Wenzheng Li, Ting Sun, David Galbraith, Zefeng Yang, Yun Zhou, Guiling Sun & Bingwu Wang
Additional file 3: Figure S3. Hierarchical cluster analysis of 4830 DEGs from different time points after topping in tobacco. The samples and treatments are indicated below each column. DEGs are defined by different colors, with the normalized expression levels employing a color gradient from low (blue) to high (red).

MOESM4 of Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Yan Qin, Shenglong Bai, Wenzheng Li, Ting Sun, David Galbraith, Zefeng Yang, Yun Zhou, Guiling Sun & Bingwu Wang
Additional file 4: Figure S4. Classification statistics of DEGs according to the GO annotations. The GO classification is indicated on the abscissa, with the ordinate providing the percentage of the number of genes (left) and the number of genes (right).

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