Contributors: Griffin Walker
... Griffin Walker's demo, released in 2004. It's not mastered, please be kind.
Data for: The first mitochondrial genome for Phaudidae (Lepidoptera) with phylogenetic analyses of Zygaenoidea
Contributors: Yuyu Wang, Jing Li, Xiaoying Li, Shuo Geng, Ruyue Zhang, Yuxin An, Xiao Zhang, Haoran Cui, Juan Yang, Cong Li
... complete genome.fas The sequence of complete genome of the Phauda flammans. We checked by manual proofreading according to its relative species. tree.fas The dateset is what we used in the tree reconstruction.
A new live-attenuated polio vaccine constructed by rational design improves safety by preventing reversion to virulence
Contributors: Ming-Te Yeh, Patrick Dolan, Raul Andino
... Variant calls for the in vivo and in vitro studies of virus diversity and genetic stability reported in the manuscript, "A new live-attenuated polio vaccine constructed by rational design improves safety by preventing reversion to virulence", by Yeh, et al.
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First record of the rare freshwater alga Tetrasporopsis fuscescens (Chrysomerophyceae, Ochrophyta) in North America
Contributors: Pavel Skaloud
... Multiple alignments of the nuclear SSU rDNA and plastid rbcL, psaA, psbA and psbC loci sequences built either manually in MEGA6 or using MAFFT v6, applying the Q-INS-i strategy.
Contributors: Alberto Ciccia
... Sanger sequencing files for ICE and EditR analyses Raw gel images and qPCR data for DTECT
Symbiosis between river and dry lands: phycobiont dynamics on river gravel bars (Supplementary datasets))
Contributors: Lucie Vancurova, Veronika Kalníková, Ondrej Peksa, Zuzana Škvorová, Jiří Malíček, Patricia Moya, Kryštof Chytrý, Ivana Cernajova, Pavel Skaloud
... Multiple alignments of the ITS rDNA (of Asterochloris and Stereocaulon) and actin type I loci sequences built using MAFFT v7, applying the Q-INS-i strategy.
Data for: Insights into Features of Novel Type 1½ Inhibitors of p38αMitogen-Activated Protein Kinase Using QSAR, E-Pharmacophore Modeling, Quantum Mechanics, Bioisostere Replacement and ADMET Studies.
Contributors: Ireoluwa Joel
... In this dataset, we provide mechanistic insights into novel type 1 1/2 inhibitors developed by Walter et al., (2017) using: Combi-QSAR, E-pharmacophore modeling, Molecular docking, and Quantum mechanics (HOMO, LUMO, and MESP) methods. Finally, we generated 592 unique lead compounds using Bioisostere replacement methods. 474 were within the applicability domain (AD) of our QSAR model. The biological activities (pIC50) of the compounds (474) were predicted using our QSAR model and the binding free energy of the top compounds (pIC50 > 3.0) was calculated by docking.
The Binding Prediction Model of The Iron-responsive Element Binding Protein and Iron-responsive Elements
Contributors: Kevin Nathanael Ramanto, Arli Aditya Parikesit
... Iron is essential to fulfilling an indispensable role in the biological process in human physiology. Various proteins were known involved in iron metabolism. One of the proteins called iron-responsive element binding protein (IRP) which acts as master iron of cellular iron homeostasis. There are two IRP known to date, which is: IRP1 and IRP2. Previous studies showed IRP bind to iron-responsive elements (IRE) located in 5’-UTR of the transferrin receptor 1. The interaction of IRP/IRE is well studied through many years to find a better treatment for the cellular disorder in iron metabolism. However, the structural differences of both IRP and the binding prediction model of IRP/IRE remain unclear. This dataset provides structure predictions of IRP/IRE by using reliable bioinformatics tools .
Data for: Cystoisospora felis infection in a captive jaguar cub (Panthera onca) in Michoacán, México
Contributors: John Barta, Edgardo Soriano Vargas, Perryn Kruth, Josué Rangel-Díaz, Marco Antonio Juárez-Estrada, claudia guzmán
... Sequence-based genotyping of a Cystoisospora species infecting a captive jaguar cub based on the mitochondrial cytochrome c oxidase subunit I. Primer Info - Primers were originally described here: https://doi.org/10.1017/pao.2015.7. JPEG - Amplicon sequencing of PCR product aligned to reference Cystoisospora felis sequence (GenBank KT184386) - 100% identity. FASTA - Conseq from ABI reads (not submitted to GenBank) - 100% pairwise identity to Cystoisospora felis sequence (GenBank KT184386) from domestic cat.
Contributors: Bram Lories
... A differential fluorescence induction screening was performed in order to identify genes of Salmonella Typhimurium SL1344 that respond to conditions of high bacterial competition. This dataset contains the sequences of all positives hits after two rounds of positive and one round of negative selection. Description of the methods and experimental details of the DFI screening can be found at: Lories et al. (2020). Biofilm bacteria use stress responses to detect and respond to competitors. Current Biology.