Biology subjects

Song, J.

Publications and source records attributed to Song, J..

312 records · Page 18Linked to original sources

bioRxiv2017

NMR studies reveal that protein dynamics critically mediate aggregation of the well-folded and very soluble E. coli S1 ribosomal protein

Unlike mammalian aging associated with many hallmarks, E. coli aging is only significantly characterized by protein aggregation, thus offering an excellent model for addressing the relationship between protein aggregation and aging. Here we characterized conformations, unfolding and dynamics of ribosomal protein S1 and its D3/D5 domains using NMR, CD and fluorescence spectroscopy. S1 is a 557-residue modular protein containing six S1 motifs. Paradoxically, while S1 is well-folded and very soluble in vitro, it was found in various lists of aggregated E. coli proteins. Our results decipher: 1) S1 has dynamic inter-domain interactions. Strikingly, S1 and its D3/D5 domains have significantly exposed hydrophobic patches characterized by irreversible unfolding. 2) Although D5 has significantly restricted backbone motion on ps-ns time scale, it has global s-ms conformational dynamics and particularly high \"global breathing\" motions. 3) D5 assumes the conserved {beta}-barrel fold but contains large hydrophobic patches at least dynamically accessible. Taken together, our study reveals that S1 could be prone to aggregation due to significant dynamics at two levels: inter-domain interactions and individual domains, which may even render buried hydrophobic patches/cores accessible for driving aggregation. This mechanism is most likely to operate in many proteins of E. coli and other organisms including human.

biophysics↗

bioRxiv2017

TDCPP exposure affects the concentrations of thyroid hormones in zebrafish

Previous studies show that TDCPP may interrupt the thyroid endocrine system, however, the potential mechanisms involved in these processes were largely unknown. In this study, zebrafish embryos/larvae were exposed to TDCPP until 120 hpf, by which time most of the organs of the larvae have completed development. In this study, the effects of TDCPP on HPT axis were examined and the thyroid hormone levels were measured after TDCPP treatment. Zebrafish (Danio rerio) embryos were treated with a series concentration of TDCPP (10, 20, 40, 80, 160 and 320 g/L) from 1 day post-fertilization (dpf) to 5 dpf. Exposure concentrations of TDCPP were determined based on the survival rates in each group. Total mRNA were isolated, first-strand cDNA were synthesis and qPCR were performed to detect the mRNA expression levels in hypothalamic-pituitary-thyroid (HPT) axis. The mRNA expression levels of genes involved in thyroid hormone homeostasis were increased in the TDCPP-treated larvae. The mRNA levels of genes involved in thyroid hormone synthesis were also increased in the embryos treated with TDCPP. Furthermore, exposure to TDCPP led to a dose-dependent effect on zebrafish development, including diminished hatching and survival rates, increased malformation. TDCPP treatment significantly reduced the T4 concentration in the 5 dpf zebrafish larvae, but increased the concentration of T3, suggesting the function of thyroid endocrine were interrupted in the TDCPP-exposed zebrafish. Taken together, these data indicated that TDCPP affected the thyroid hormone levels in the zebrafish larvae and could increased the mRNA expression levels of genes related to HPT axis, which further impaired the endocrine homeostasis and thyroid system.

pharmacology and toxicology↗

bioRxiv2017

RRM domain of ALS/FTD-causing FUS interacts with membrane: an anchor of membraneless organelles to membranes?

526-residue FUS functions to self-assemble into reversible droplets/hydrogels, which could be further solidified into pathological fibrils. FUS is composed of N-terminal low-sequence complexity (LC); RNA-recognition motif (RRM) and C-terminal LC domains. FUS belongs to an emerging category of proteins which are capable of forming membraneless organelles in cells via phase separation. On the other hand, eukaryotic cells contain a large network of internal membrane systems. Therefore, it is of fundamental importance to address whether membraneless organelles can interact with membranes. Here we attempted to explore this by NMR HSQC titrations of three FUS domains with gradual addition of DMPC/DHPC bicelle, which mimics the bilayer membrane. We found that both N- and C-terminal LC domains showed no significant interaction with bicelle, but its well-folded RRM domain does dynamically interact with bicelle with an interface opposite to that for binding nucleic acids including RNA and ssDNA. If this in vitro observation also occurs in cells, to interact with membrane might represent a mechanism for dynamically organizing membraneless organelles to membranes to facilitate their physiological functions.

biophysics↗

bioRxiv2017

TeachEnG: a Teaching Engine for Genomics

MotivationBioinformatics is a rapidly growing field that has emerged from the synergy of computer science, statistics, and biology. Given the interdisciplinary nature of bioinformatics, many students from diverse fields struggle with grasping bioinformatic concepts only from classroom lectures. Interactive tools for helping students reinforce their learning would be thus desirable. Here, we present an interactive online educational tool called TeachEnG (acronym for Teaching Engine for Genomics) for reinforcing key concepts in sequence alignment and phylogenetic tree reconstruction. Our instructional games allow students to align sequences by hand, fill out the dynamic programming matrix in the Needleman-Wunsch global sequence alignment algorithm, and reconstruct phylogenetic trees via the maximum parsimony and Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithms. With an easily accessible interface and instant visual feedback, TeachEnG will help promote active learning in bioinformatics.\n\nAvailability and Implementation: TeachEnG is freely available at http://song.igb.illinois.edu/TeachEnG/. It is written in JavaScript and compatible with Firefox, Safari, Chrome, and Microsoft Edge.\n\nContact: songi@illinois.edu

bioinformatics↗

bioRxiv2017

Multiple roles of PIWIL1 in mouse neocorticogenesis

PIWI-interacting RNAs (piRNAs) and their associated PIWI proteins play an important role in repressing transposable elements in animal germlines. However, little is known about the function of PIWI proteins and piRNAs in the developing brain. Here, we investigated the role of an important PIWI family member, Piwi-like protein 1 (Piwil1; also known as Miwi in mouse) in the developing mouse neocortex. Using a Piwil1 knock-out (Piwil1 KO) mouse strain, we found that Piwil1 is essential for several steps of neocorticogenesis, including neocortical cell cycle, neuron migration and dendritogenesis. Piwil1 deletion resulted in increased cell cycle re-entry at embryonic day 17 (E17) when predominantly intracortically projecting neurons are being produced. Prenatal Piwil1 deletion increased the number of Pax6+ radial glia at postnatal day 0 (P0). Furthermore, Piwil1 deletion disrupted migration of Satb2+ neurons within deep layers at E17, P0 and P7. Satb2+ neurons showed increased co-localization with Bcl11b (also known as Ctip2), marker of subcortically projecting neurons. Piwil1 knockouts had disrupted neocortical circuitry represented by thinning of the corpus callosum and altered dendritogenesis. We further investigated if Piwil1 deletion disrupted expression levels of neocortical piRNAs by small RNA-sequencing in neocortex. We did not find differential expression of piRNAs in the neocortices of Piwil1 KO, while differences were observed in other Piwil1 KO tissues. This result suggests that Piwil1 may act independently of piRNAs and have novel roles in higher cognitive centers, such as neocortex. In addition, we report a screen of piRNAs derived from tRNA fragments in developing neocortices. Our result is the first report of selective subsets of piRNAs and tRNA fragments in developing prenatal neocortices and helps clarify some outstanding questions about the role of the piRNA pathway in the brain.

neuroscience↗

bioRxiv2016

Repliscan: a tool for classifying replication timing regions

BackgroundReplication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replicating timing.\n\nResultsTo accurately detect and classify regions of replication across the genome, we present Repliscan. Repliscan robustly normalizes, automatically removes outlying and uninformative data points, and classifies Repli-seq signals into discrete combinations of replication signatures. The quality control steps and self-fitting methods makes Repliscan generally applicable and superior to previous methods with thresholds inapplicable to different genomes.\n\nConclusionsRepliscan is simple and effective to use on organisms with different magnitude genome sizes and sequencing coverage as low as 2.4x.

bioinformatics↗