33 research outputs found
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 PPh<sub>3</sub> effectively
proceeded under mild conditions to provide the corresponding 2-deoxy-2-iodoglycosides
in high yields. The reactivity of the iodoglycosylations with PPh<sub>3</sub> 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 PÂ(OPh)<sub>3</sub> 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