how_to_run_simulation

Procedures to run the simulation of the resistance evolution and draw plots (Figure 2, 3 and 4 on the article) on your R environment. Installation of "ResistanceDLDP" package is required

ResistanceDLDP_1.1.tar

R package source to define functions for the simulation of resistance evolution

Novel diphenylmethyl-Derived Amide Protecting Group for Efficient Liquid-Phase Peptide Synthesis: AJIPHASE

An efficient method for the synthesis of peptides bearing an amide at the C-terminal is described. This method involves the attachment of a C-terminal protecting group bearing long aliphatic chains, followed by the repetition of simple reaction and precipitation steps with the combined advantages of liquid-phase peptide synthesis (LPPS) and solid-phase peptide synthesis (SPPS). Using this method, a hydrophobic peptide was successfully synthesized in good yield and high purity, which cannot be obtained satisfactorily by SPPS

Changes of Detergent-Resistant Plasma Membrane Proteins in Oat and Rye during Cold Acclimation: Association with Differential Freezing Tolerance

Cold acclimation (CA) results in an increase in freezing tolerance of plants, which is closely associated to functional changes of the plasma membrane (PM). Although proteomic studies have revealed compositional changes of the PM during CA, there has been no large-scale study of how the microdomains in the PM, which contains specific lipids and proteins, change during CA. Therefore, we conducted semiquantitative shotgun proteomics using microdomain-enriched detergent-resistant membrane (DRM) fractions extracted from low freezing-tolerant oat and highly freezing-tolerant rye. We identified 740 and 809 DRM proteins in oat and rye, respectively. Among the proteins identified, the abundances of a variety of proteins, such as P-type ATPase and aquaporins, were affected by CA in both oat and rye. Some CA-responsive proteins in the DRM fractions, such as heat shock protein 70, changed differently in oat and rye. In addition, changes in lipocalins and sugar transporters in the DRM fractions were different from those found in total PM fraction during CA. This is the first report to describe compositional changes in the DRM during CA. The proteomic profiles obtained in the present study hint at many possible microdomain functions associated with CA and freezing tolerance

1,2-<i>cis</i>-α-Stereoselective Glycosylation Utilizing a Glycosyl-Acceptor-Derived Borinic Ester and Its Application to the Total Synthesis of Natural Glycosphingolipids

1,2-<i>cis</i>-α-Stereoselective glycosylations were conducted using a 1,2-anhydroglucose donor and mono-ol acceptors in the presence of a glycosyl-acceptor-derived borinic ester. Reactions proceeded smoothly under mild conditions to provide the corresponding α-glycosides with high stereoselectivity in moderate to high yields. In addition, the present method was applied successfully to the direct glycosylation of a protected ceramide acceptor and the total synthesis of natural glycosphingolipids (GSLs)

Changes of Detergent-Resistant Plasma Membrane Proteins in Oat and Rye during Cold Acclimation: Association with Differential Freezing Tolerance

Cold acclimation (CA) results in an increase in freezing tolerance of plants, which is closely associated to functional changes of the plasma membrane (PM). Although proteomic studies have revealed compositional changes of the PM during CA, there has been no large-scale study of how the microdomains in the PM, which contains specific lipids and proteins, change during CA. Therefore, we conducted semiquantitative shotgun proteomics using microdomain-enriched detergent-resistant membrane (DRM) fractions extracted from low freezing-tolerant oat and highly freezing-tolerant rye. We identified 740 and 809 DRM proteins in oat and rye, respectively. Among the proteins identified, the abundances of a variety of proteins, such as P-type ATPase and aquaporins, were affected by CA in both oat and rye. Some CA-responsive proteins in the DRM fractions, such as heat shock protein 70, changed differently in oat and rye. In addition, changes in lipocalins and sugar transporters in the DRM fractions were different from those found in total PM fraction during CA. This is the first report to describe compositional changes in the DRM during CA. The proteomic profiles obtained in the present study hint at many possible microdomain functions associated with CA and freezing tolerance

Glycosylations of Glycals using <i>N</i>‑Iodosuccinimide (NIS) and Phosphorus Compounds for Syntheses of 2‑Iodo- and 2‑Deoxyglycosides

The glycosylations of glycals and alcohols using <i>N</i>-iodosuccinimide (NIS) and a catalytic amount of PPh₃ effectively proceeded under mild conditions to provide the corresponding 2-deoxy-2-iodoglycosides in high yields. The reactivity of the iodoglycosylations with PPh₃ significantly increased in comparison to that using NIS alone as an activator. In addition, the glycosylations of glycals and alcohols using catalytic amounts of NIS and P­(OPh)₃ were effectively realized to give the corresponding 2-deoxyglycosides in high yields

Changes of Detergent-Resistant Plasma Membrane Proteins in Oat and Rye during Cold Acclimation: Association with Differential Freezing Tolerance

Cold acclimation (CA) results in an increase in freezing tolerance of plants, which is closely associated to functional changes of the plasma membrane (PM). Although proteomic studies have revealed compositional changes of the PM during CA, there has been no large-scale study of how the microdomains in the PM, which contains specific lipids and proteins, change during CA. Therefore, we conducted semiquantitative shotgun proteomics using microdomain-enriched detergent-resistant membrane (DRM) fractions extracted from low freezing-tolerant oat and highly freezing-tolerant rye. We identified 740 and 809 DRM proteins in oat and rye, respectively. Among the proteins identified, the abundances of a variety of proteins, such as P-type ATPase and aquaporins, were affected by CA in both oat and rye. Some CA-responsive proteins in the DRM fractions, such as heat shock protein 70, changed differently in oat and rye. In addition, changes in lipocalins and sugar transporters in the DRM fractions were different from those found in total PM fraction during CA. This is the first report to describe compositional changes in the DRM during CA. The proteomic profiles obtained in the present study hint at many possible microdomain functions associated with CA and freezing tolerance

R script to compute models

model.R implements the simple Comins model (eq.1) and our approximation (eq.5). The code generates all plots in the main text and the supplemental information

Detergent-resistant Plasma Membrane Proteome in Oat and Rye: Similarities and Dissimilarities between Two Monocotyledonous Plants

The plasma membrane (PM) is involved in important cellular processes that determine the growth, development, differentiation, and environmental signal responses of plant cells. Some of these dynamic reactions occur in specific domains in the PM. In this study, we performed comparable nano-LC–MS/MS-based large-scale proteomic analysis of detergent-resistant membrane (DRM) fractions prepared from the PM of oat and rye. A number of proteins showed differential accumulation between the PM and DRM, and some proteins were only found in the DRM. Numerous proteins were identified as DRM proteins in oat (219 proteins) and rye (213 proteins), of which about half were identified only in the DRM. The DRM proteins were largely common to those found in dicotyledonous plants (<i>Arabidopsis</i> and tobacco), which suggests common functions associated with the DRM in plants. Combination of semiquantitative proteomic analysis and prediction of post-translational protein modification sites revealed differences in several proteins associated with the DRM in oat and rye. It is concluded that protein distribution in the DRM is unique from that in the PM, partly because of the physicochemical properties of the proteins, and the unique distribution of these proteins may define the functions of the specific domains in the PM in various physiological processes in plant cells