scholarly journals ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms’ proteomes

2018 ◽  
Vol 34 (20) ◽  
pp. 3557-3565 ◽  
Author(s):  
Rostam M Razban ◽  
Amy I Gilson ◽  
Niamh Durfee ◽  
Hendrik Strobelt ◽  
Kasper Dinkla ◽  
...  
Keyword(s):  
Sequence Evolution ◽  
Protein Properties ◽  
Web App

scholarly journals ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms’ proteomes

2018 ◽  
Vol 34 (23) ◽  
pp. 4140-4140
Author(s):  
Rostam M Razban ◽  
Amy I Gilson ◽  
Niamh Durfee ◽  
Hendrik Strobelt ◽  
Kasper Dinkla ◽  
...  
Keyword(s):  
Sequence Evolution ◽  
Protein Properties ◽  
Web App

scholarly journals ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms’ proteomes

2017 ◽  
Author(s):  
Amy I. Gilson ◽  
Niamh Durfee ◽  
Rostam M. Razban ◽  
Hendrick Strobelt ◽  
Kasper Dinkla ◽  
...  
Keyword(s):  
Protein Structure ◽  
Protein Evolution ◽  
Scale Effects ◽  
Structure Evolution ◽  
P Value ◽  
Sequence Evolution ◽  
Protein Chain ◽  
E Coli ◽  
Protein Properties ◽  
Web App

AbstractMotivationProtein evolution spans time scales and its effects span the length of an organism. A web app named ProteomeVis is developed to provide a comprehensive view of protein evolution in the S. cerevisiae and E. coli proteomes. ProteomeVis interactively creates protein chain graphs, where edges between nodes represent structure and sequence similarities within user-defined ranges, to study the long time scale effects of protein structure evolution. The short time scale effects of protein sequence evolution is studied by sequence evolutionary rate (ER) correlation analyses with protein properties that span from the molecular to the organismal level.ResultsWe demonstrate the utility and versatility of ProteomeVis by investigating the distribution of edges per node in organismal protein chain universe graphs (oPCUGs) and putative ER determinants. S. cerevisiae and E. coli oPCUGs are scale-free with scaling constants of 1.78 and 1.50, respectively. Both scaling constants can be explained by a previously reported theoretical model describing protein structure evolution (Dokholyan et al., 2002). Protein abundance most strongly correlates with ER among properties in ProteomeVis, with Spearman correlations of −0.51 (p-value<10−10) and −0.46 (p-value<10−10) for S. cerevisiae and E. coli, respectively. This result is consistent with previous reports that found protein expression to be the most important ER determinant (Zhang and Yang, 2015).AvailabilityProteomeVis is freely accessible at http://proteomevis.chem.harvard.edu/proteomevis/[email protected] informationAvailable to download on bioRxiv.

The Infancy of Solar-Type Stars and its Relevance for the Origin of Life

1997 ◽  
Vol 161 ◽  
pp. 267-282 ◽  
Author(s):  
Thierry Montmerle
Keyword(s):  
Main Sequence ◽  
Solar Nebula ◽  
Circumstellar Disks ◽  
T Tauri Stars ◽  
Necessary Condition ◽  
Sequence Evolution ◽  
T Tauri ◽  
Solar Type ◽  
Optical Domain ◽  
The Origin Of Life

AbstractFor life to develop, planets are a necessary condition. Likewise, for planets to form, stars must be surrounded by circumstellar disks, at least some time during their pre-main sequence evolution. Much progress has been made recently in the study of young solar-like stars. In the optical domain, these stars are known as «T Tauri stars». A significant number show IR excess, and other phenomena indirectly suggesting the presence of circumstellar disks. The current wisdom is that there is an evolutionary sequence from protostars to T Tauri stars. This sequence is characterized by the initial presence of disks, with lifetimes ~ 1-10 Myr after the intial collapse of a dense envelope having given birth to a star. While they are present, about 30% of the disks have masses larger than the minimum solar nebula. Their disappearance may correspond to the growth of dust grains, followed by planetesimal and planet formation, but this is not yet demonstrated.

SISTEM MONITORING EVALUASI DAN PELAPORAN KEGIATAN TARUNA ATKP MEDAN

2020 ◽  
Vol 4 (2) ◽  
pp. 82
Author(s):  
Albert Panjaitan ◽  
Hairul Amren ◽  
Darmeli Nasution ◽  
Rizaldy Khair ◽  
Iswandi Idris
Keyword(s):  
Short Message Service ◽  
Short Message ◽  
Message Service ◽  
Web App

Perkembangan yang sangat pesat terjadi pada bidang teknologi informasi dan telekomunikasi saat ini mendorong masyarakta dunia memasuki era revolusi industri 4.0 yang serba cepat, sekaligus menjadikan informasi sentral dalam dunia industri maupun dunia usaha hingga dunia pendidikan. Akademi Teknik dan Keselamatan Penerbangan (ATKP) Medan merupakan institusi pendidikan di bawah naungan pemerintah yang sudah mulai menggunakan berbagai hal teknologi informasi dan telekomunikasi. Dengan adanya perkembangan tersebut berdampak memeberikan fasilitas yang dapat digunakan oleh pengguna layanan komunikasi, dan informasi, seperti Short Message Service (SMS) hingga sistem berbasis aplikasi menggunakan smartphone android maupun iOS. Layanan aplikasi sms hingga sistem aplikasi tersebut adalah teknologi yang memungkinkan manusia untuk mendapatkan atau mengirimkankan informasi kapanpun dan dimanapun dibutuhkan. Penelitian ini bertujuan untuk membuat sistem aplikasi monitoring evaluasi pelaporan kegiatan taruna di ATKP medan berbasis web app. Dalam pembuatannya, aplikasi ini disesuaikan dengan kenutuhan user/orang tua taruna dan institusi ATKP secara umum. Sistem aplikasi ini akan memberikan kemudahan kepada orang tua taruna dalam memonitoring, kegiatan hingga prilaku taruna selama pendidikan di ATKP Medan serta  kemudahan mengakses nilai dengan cepat. Sistem aplikasi ini dibuat dengan menggunakan bahasa pemrograman php (web).

From Levinthal’s Paradox to the Effects of Cell Environmental Perturbation on Protein Folding

2020 ◽  
Vol 26 (42) ◽  
pp. 7537-7554 ◽  
Author(s):  
Juan Zeng ◽  
Zunnan Huang
Keyword(s):  
Protein Folding ◽  
Posttranslational Modifications ◽  
Three Dimensional ◽  
Rational Drug Design ◽  
Basic Knowledge ◽  
Sequence Evolution ◽  
3D Structures ◽  
Folding Mechanism ◽  
Cellular Environment ◽  
Environment Temperature

Background: The rapidly increasing number of known protein sequences calls for more efficient methods to predict the Three-Dimensional (3D) structures of proteins, thus providing basic knowledge for rational drug design. Understanding the folding mechanism of proteins is valuable for predicting their 3D structures and for designing proteins with new functions and medicinal applications. Levinthal’s paradox is that although the astronomical number of conformations possible even for proteins as small as 100 residues cannot be fully sampled, proteins in nature normally fold into the native state within timescales ranging from microseconds to hours. These conflicting results reveal that there are factors in organisms that can assist in protein folding. Methods: In this paper, we selected a crowded cell-like environment and temperature, and the top three Posttranslational Modifications (PTMs) as examples to show that Levinthal’s paradox does not reflect the folding mechanism of proteins. We then revealed the effects of these factors on protein folding. Results: The results summarized in this review indicate that a crowded cell-like environment, temperature, and the top three PTMs reshape the Free Energy Landscapes (FELs) of proteins, thereby regulating the folding process. The balance between entropy and enthalpy is the key to understanding the effect of the crowded cell-like environment and PTMs on protein folding. In addition, the stability/flexibility of proteins is regulated by temperature. Conclusion: This paper concludes that the cellular environment could directly intervene in protein folding. The long-term interactions of the cellular environment and sequence evolution may enable proteins to fold efficiently. Therefore, to correctly understand the folding mechanism of proteins, the effect of the cellular environment on protein folding should be considered.

scholarly journals Adventure Code Camp: Library Mobile Design in the Backcountry

2014 ◽  
Vol 33 (3) ◽  
pp. 45 ◽  
Author(s):  
David Ward ◽  
James Hahn ◽  
Lori Mestre
Keyword(s):  
Mobile Devices ◽  
Design Process ◽  
Mobile Apps ◽  
Library Services ◽  
Mobile Web ◽  
Process Outcomes ◽  
Mobile Design ◽  
Web App ◽  
Software Services

<p>This article presents a case study exploring the use of a student Coding Camp as a bottom-up mobile design process to generate library mobile apps. A code camp sources student programmer talent and ideas for designing software services and features.  This case study reviews process, outcomes, and next steps in mobile web app coding camps. It concludes by offering implications for services design beyond the local camp presented in this study. By understanding how patrons expect to integrate library services and resources into their use of mobile devices, librarians can better design the user experience for this environment.</p>

Usability Testing of VLASTWA: A Vocabulary and Strategy Teaching Web App

2020 ◽  
Author(s):  
Siamak Mirzaei ◽  
Trent Lewis ◽  
Mirella Wyra ◽  
Brett Wilkinson
Keyword(s):  
Usability Testing ◽  
Web App
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