Biology subjects

Kang, J.

Publications and source records attributed to Kang, J..

9 recordsLinked to original sources

bioRxiv2018

SmbHLH37 functions antagonistically with SmMYC2 in regulating jasmonate-mediated biosynthesis of phenolic acids in Salvia miltiorrhiza

Jasmonates (JAs) are integral to various defense responses and induce biosynthesis of many secondary metabolites. MYC2, a basic helix-loop-helix (bHLH) transcription factor (TF), acts as a transcriptional activator of JA signaling. MYC2 is repressed by the JASMONATE ZIM-domain (JAZ) proteins in the absence of JA, but de-repressed by the protein complex SCFCOI1 on perception of JA. We previously reported that overexpression of SmMYC2 promotes the production of salvianolic acid B (Sal B) in Salvia miltiorrhiza. However, the responsible molecular mechanism is unclear. Here, we showed that SmMYC2 binds to and activates the promoters of its target genes SmTAT1, SmPAL1, and SmCYP98A14 to activate Sal B accumulations. SmbHLH37, a novel bHLH gene significantly up-regulated by constitutive expression of SmMYC2, was isolated from S. miltiorrhiza for detailed functional characterization. SmbHLH37 forms a homodimer and interacts with SmJAZ3/8. Overexpression of SmbHLH37 substantially decreased yields of Sal B. SmbHLH37 binds to the promoters of its target genes SmTAT1 and SmPAL1 and blocks their expression to suppress the pathway for Sal B biosynthesis. These results indicate that SmbHLH37 negatively regulates JA signaling and functions antagonistically with SmMYC2 in regulating Sal B biosynthesis in S. miltiorrhiza.

plant biology↗

bioRxiv2018

Organization of state transitions in the resting-state human cerebral cortex

The resting-state brain is often considered a nonlinear dynamic system transitioning among multiple coexisting stable states. Despite the increasing number of studies on the multistability of the brain system, the processes of state transitions have rarely been systematically explored. Thus, we investigated the state transition processes of the human cerebral cortex system at rest by introducing a graph-theoretic analysis of the state transition network. The energy landscape analysis of brain state occurrences, estimated using the pairwise maximum entropy model for resting-state fMRI data, identified multiple local minima, some of which mediate multi-step transitions toward the global minimum. The state transition among local minima is clustered into two groups according to state transition rates and most inter-group state transitions were mediated by a hub transition state. The distance to the hub transition state determined the path length of the inter-group transition. The cortical system appeared to have redundancy in inter-group transitions when the hub transition state was removed. Such a hub-like organization of transition processes disappeared when the connectivity of the cortical system was altered from the resting-state configuration. In summary, the resting-state cerebral cortex has a well-organized architecture of state transitions among stable states, when evaluated by nonlinear systematic approach.

neuroscience↗

bioRxiv2018

Metabolic engineering of Escherichia coli for de novo biosynthesis of vitamin B12

The only known source of vitamin B12 (adenosylcobalamin) is from bacteria and archaea, and the only unknown step in its biosynthesis is the production of the intermediate adenosylcobinamide phosphate. Here, using genetic and metabolic engineering, we generated an Escherichia coli strain that produces vitamin B12 via an engineered de novo aerobic biosynthetic pathway. Excitingly, the BluE and CobC enzymes from Rhodobacter capsulatus transform L-threonine into (R)-1-Amino-2-propanol O-2-Phosphate, which is then condensed with adenosylcobyric acid to yield adenosylcobinamide phosphate by either CobD from the aeroic R. capsulatus or CbiB from the anerobic Salmonella typhimurium. These findings suggest that the biosynthetic steps from co(II)byrinic acid a,c-diamide to adocobalamin are the same in both the aerobic and anaerobic pathways. Finally, we increased the vitamin B12 yield of a recombinant E. coli strain by more than [~]250-fold to 307.00 {micro}g/g DCW via metabolic engineering and optimization of fermentation conditions. Beyond our scientific insights about the aerobic and anaerobic pathways and our demonstration of E. coli as a microbial biosynthetic platform for vitamin B12 production, our study offers an encouraging example of how the several dozen proteins of a complex biosynthetic pathway can be transferred between organisms to facilitate industrial production.

synthetic biology↗

bioRxiv2018

TMEM106B, a risk factor for FTLD and aging, has an intrinsically disordered cytoplasmic domain

TMEM106B was initially identified as a risk factor for FTLD, but recent studies highlighted its general role in neurodegenerative diseases. Very recently TMEM106B has also been characterized to regulate aging phenotypes. TMEM106B is a 274-residue lysosomal protein whose cytoplasmic domain functions in the endosomal/autophagy pathway by dynamically and transiently interacting with diverse categories of proteins but the underlying structural basis remains completely unknown. Here we conducted bioinformatics analysis and biophysical characterization by CD and NMR spectroscopy, and obtained results reveal that the TMEM106B cytoplasmic domain is intrinsically disordered with no well-defined three-dimensional structure. Nevertheless, detailed analysis of various multi-dimensional NMR spectra allowed defining residue-specific conformations and dynamics. Overall, the TMEM106B cytoplasmic domain is lacking of any tight tertiary packing and relatively flexible. However, several segments are populated with dynamic/nascent secondary structures and have relatively restricted backbone motions. In particular, the fragment Ser12-Met36 is highly populated with - helix conformation. Our study thus decodes that being intrinsically disordered allows the TMEM106B cytoplasmic domain to dynamically and transiently interact with a variety of distinct partners.

biophysics↗

bioRxiv2018

Misfolded proteins share a common capacity in disrupting LLPS organizing membrane-less organelles

Profilin-1 mutants cause ALS by gain of toxicity but the underlying mechanism remains unknown. Here we showed that three PFN1 mutants have differential capacity in disrupting dynamics of FUS liquid droplets underlying the formation of stress granules (SGs). Subsequently we extensively characterized conformations, dynamics and hydrodynamic properties of C71G-PFN1, FUS droplets and their interaction by NMR spectroscopy. C71G-PFN1 co-exists between the folded (55.2%) and unfolded (44.8%) states undergoing exchanges at 11.7 Hz, while its unfolded state non-specifically interacts with FUS droplets. Results together lead to a model for dynamic droplets to recruit misfolded proteins, which functions seemingly at great cost: simple accumulation of misfolded proteins within liquid droplets is sufficient to reduce their dynamics. Further aggregation of misfolded proteins within droplets might irreversibly disrupt/destroy structures and dynamics of droplets, as increasingly observed on SGs, an emerging target for various neurodegenerative diseases. Therefore, our study implies that other misfolded proteins might also share the capacity in disrupting LLPS.

biophysics↗

bioRxiv2018

Voltage-sensitive dye delivery through the blood brain barrier using adenosine receptor agonist Regadenoson

Optical imaging of brain activity has mostly employed genetically manipulated mice, which cannot be translated to clinical human usage. Observation of brain activity directly is challenging due to difficulty in delivering dyes and other agents through the blood brain barrier (BBB). Using fluorescence imaging, we have demonstrated the feasibility of delivering the near-infrared voltage-sensitive dye (VSD) IR-780 perchlorate to the brain tissue through pharmacological techniques, via an adenosine agonist (Regadenoson). Comparison of VSD fluorescence of mouse brains without and with Regadenoson showed significantly increased residence time of the fluorescence signal in the latter case, indicative of VSD diffusion into the brain tissue. Dose and timing of Regadenoson were varied to optimize BBB permeability for VSD delivery.

bioengineering↗

bioRxiv2018

Transcranial photoacoustic imaging of NMDA-evoked focal circuit dynamics in rat forebrain

Transcranial functional photoacoustic (fPA) voltage-sensitive dye (VSD) imaging promises to overcome current temporal and spatial limitations of current neuroimaging modalities. The technique previously distinguished global seizure activity from control neural activity in groups of rats. To validate the focal specificity of transcranial fPA neuroimaging in vivo, we now present proofs-of-concept that the results differentiate between low- and high-dose N-methyl-D-aspartate (NMDA) evoked neural activity in rat hippocampus. Concurrent quantitative EEG (qEEG) and microdialysis recorded real-time circuit dynamics and glutamate concentration change, respectively. We hypothesized that location-specific fPA VSD contrast would identify the neural dynamics in hippocampus with the correlation to NMDA evoked focal glutamate release and time-specific EEG signals. To test the hypothesis, we infused 0.3 to 3.0 mM NMDA at 2 l/min over 60 min via an implanted microdialysis probe. The dialysate samples collected every 20 min during the infusion were analyzed for focal changes in extracellular glutamate release. Transcranial fPA VSD imaging provided NMDA-evoked VSD responses with positive correlation to extracellular glutamate concentration change at the contralateral side of the microdialysis probe. The graded response represents the all-or-none gating system of the dentate gyrus (DG) in hippocampus. Quantitative EEG (qEEG) successfully confirmed induction of focal seizure activity during NMDA infusion. We conclude that transcranial fPA VSD imaging distinguished graded DG gatekeeping functions, based on the VSD redistribution mechanism sensitive to electrophysiologic membrane potential. The results suggest the potential future use of this emerging technology in clinics and science as an innovative and significant functional neuroimaging modality.

neuroscience↗

bioRxiv2017

Transcranial real-time in vivo recording of electrophysiological neural activity in the rodent brain with near-infrared photoacoustic voltage-sensitive dye imaging

Minimally-invasive monitoring of electrophysiological neural activities in real-time--that enables quantification of neural functions without a need for invasive craniotomy and the longer time constants of fMRI and PET--presents a very challenging yet significant task for neuroimaging. In this paper, we present in vivo functional PA (fPA) imaging of chemoconvulsant rat seizure model with intact scalp using a fluorescence quenching-based cyanine voltage-sensitive dye (VSD) characterized by a lipid vesicle model mimicking different levels of membrane potential variation. The framework also involves use of a near-infrared VSD delivered through the blood-brain barrier (BBB), opened by pharmacological modulation of adenosine receptor signaling. Our normalized time-frequency analysis presented in vivo VSD response in the seizure group significantly distinguishable from those of the control groups at sub-mm spatial resolution. Electroencephalogram (EEG) recording confirmed the changes of severity and frequency of brain activities, induced by chemoconvulsant seizures of the rat brain. The findings demonstrate that the near-infrared fPA VSD imaging is a promising tool for in vivo recording of brain activities through intact scalp, which would pave a way to its future translation.

neuroscience↗

bioRxiv2017

Community assessment of cancer drug combination screens identifies strategies for synergy prediction

The effectiveness of most cancer targeted therapies is short lived since tumors evolve and develop resistance. Combinations of drugs offer the potential to overcome resistance, however the number of possible combinations is vast necessitating data-driven approaches to find optimal treatments tailored to a patients tumor. AstraZeneca carried out 11,576 experiments on 910 drug combinations across 85 cancer cell lines, recapitulating in vivo response profiles. These data, the largest openly available screen, were hosted by DREAM alongside deep molecular characterization from the Sanger Institute for a Challenge to computationally predict synergistic drug pairs and associated biomarkers. 160 teams participated to provide the most comprehensive methodological development and subsequent benchmarking to date. Winning methods incorporated prior knowledge of putative drug target interactions. For >60% of drug combinations synergy was reproducibly predicted with an accuracy matching biological replicate experiments, however 20% of drug combinations were poorly predicted by all methods. Genomic rationale for synergy predictions were identified, including antagonism unique to combined PIK3CB/D inhibition with the ADAM17 inhibitor where synergy is seen with other PI3K pathway inhibitors. All data, methods and code are freely available as a resource to the community.

bioinformatics↗