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Investigation of the parallel tempering method for protein folding
Schug, Alexander,Herges, Thomas,Verma, Abhinav,Wenzel, Wolfgang IOP Pub 2005 Journal of physics, an Institute of Physics journa Vol.17 No.18
<P>We investigate the suitability and efficiency of an adapted version of the parallel tempering method for all-atom protein folding. We have recently developed an all-atom free energy force field (PFF01) for protein structure prediction with stochastic optimization methods. Here we report reproducible folding of the 20-amino-acid trp-cage protein and the conserved 40-amino-acid three-helix HIV accessory protein with an adapted parallel tempering method. We find that the native state, for both proteins, is correctly predicted to 2?Šbackbone root mean square deviation and analyse the efficiency of the simulation approach. </P>
Thomson, Robert,Yuki, Masaki,Talhelm, Thomas,Schug, Joanna,Kito, Mie,Ayanian, Arin H.,Becker, Julia C.,Becker, Maja,Chiu, Chi-yue,Choi, Hoon-Seok,Ferreira, Carolina M.,Fü,lö,p, Marta,Gul, Peli National Academy of Sciences 2018 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.115 No.29
<▼1><P><B>Significance</B></P><P>Biologists and social scientists have long tried to understand why some societies have more fluid and open interpersonal relationships—differences in relational mobility—and how those differences influence individual behaviors. We measure relational mobility in 39 societies and find that relationships are more stable and hard to form in east Asia, North Africa, and the Middle East, while they are more fluid in the West and Latin America. Results show that relationally mobile cultures tend to have higher interpersonal trust and intimacy. Exploring potential causes, we find greater environmental threats (like disease and warfare) and sedentary farming are associated with lower relational mobility. Our society-level index of relational mobility for 39 societies is a resource for future studies.</P></▼1><▼2><P>Biologists and social scientists have long tried to understand why some societies have more fluid and open interpersonal relationships and how those differences influence culture. This study measures relational mobility, a socioecological variable quantifying voluntary (high relational mobility) vs. fixed (low relational mobility) interpersonal relationships. We measure relational mobility in 39 societies and test whether it predicts social behavior. People in societies with higher relational mobility report more proactive interpersonal behaviors (e.g., self-disclosure and social support) and psychological tendencies that help them build and retain relationships (e.g., general trust, intimacy, self-esteem). Finally, we explore ecological factors that could explain relational mobility differences across societies. Relational mobility was lower in societies that practiced settled, interdependent subsistence styles, such as rice farming, and in societies that had stronger ecological and historical threats.</P></▼2>
A miRNA181a/NFAT5 axis links impaired T cell tolerance induction with autoimmune type 1 diabetes
Serr, Isabelle,Scherm, Martin G.,Zahm, Adam M.,Schug, Jonathan,Flynn, Victoria K.,Hippich, Markus,Kalin, Stefanie,Becker, Maike,Achenbach, Peter,Nikolaev, Alexei,Gerlach, Katharina,Liebsch, Nicole,Lor American Association for the Advancement of Scienc 2018 Science Translational Medicine Vol.10 No.422
<P>Molecular checkpoints that trigger the onset of islet autoimmunity or progression to human type 1 diabetes (T1D) are incompletely understood. Using T cells from children at an early stage of islet autoimmunity without clinical T1D, we find that a microRNA181a (miRNA181a)-mediated increase in signal strength of stimulation and costimulation links nuclear factor of activated T cells 5 (NFAT5) with impaired tolerance induction and autoimmune activation. We show that enhancing miRNA181a activity increases NFAT5 expression while inhibiting FOXP3+ regulatory T cell (T-reg) induction in vitro. Accordingly, Treg induction is improved using T cells from NFAT5 knockout (NFAT5ko) animals, whereas altering miRNA181a activity does not affect T-reg induction in NFAT5ko T cells. Moreover, high costimulatory signals result in phosphoinositide 3-kinase (PI3K)-mediated NFAT5, which interferes with FoxP(3+) Treg induction. Blocking miRNA181a or NFAT5 increases Treg induction in murine and humanized models and reduces murine islet autoimmunity in vivo. These findings suggest targeting miRNA181a and/or NFAT5 signaling for the development of innovative personalized medicines to limit islet autoimmunity.</P>
Santos, Inê,s C.,Smuts, Jonathan,Choi, Woo-Sik,Kim, Younghoon,Kim, Seoung Bum,Schug, Kevin A. Elsevier 2018 Talanta Vol.182 No.-
<P><B>Abstract</B></P> <P>The identification of microorganisms is very important in different fields and alternative methods are necessary for a rapid and simple identification. The use of fatty acids for bacterial identification is gaining attention as phenotypic characteristics are reflective of the genotype and are more easily analyzed. In this work, gas chromatography-vacuum ultraviolet spectroscopy (GC-VUV) was used to determine bacteria fatty acid methyl esters (FAMEs), to identify and discriminate different environmental bacteria based on their fatty acid profile. Microorganisms were grown in agar and their fatty acids extracted, saponified, and esterified before analysis. Unique FAME profiles were obtained for each microorganism mainly composed of branched, cyclopropane, hydroxy, saturated, and unsaturated fatty acid methyl esters. <I>S. maltophilia</I> showed a higher diversity of fatty acids while <I>Bacillus</I> species showed higher complexity in terms of branched-chain FAMEs, with several <I>iso</I> and <I>anteiso</I> forms. 12 different bacteria genera and 15 species were successfully differentiated based on their fatty acid profiles after performing PCA and cluster analysis. Some difficult to differentiate species, such as <I>Bacillus</I> sp., which are genetically very similar, were differentiated with the developed method.</P> <P><B>Highlights</B></P> <P> <UL> <LI> GC-VUV of FAMEs can effectively differentiate a wide range of environmental bacteria. </LI> <LI> A fast method for FAMEs is featured; chromatographic resolution can be sacrificed for spectral resolution. </LI> <LI> Multivariate statistical methods indicate high classification accuracy. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>