Project description:The Ion Torrent Personal Genome Machine (PGM) is a new sequencing platform that substantially differs from other sequencing technologies by measuring pH rather than light to detect polymerisation events. Using re-sequencing datasets, we comprehensively characterise the biases and errors introduced by the PGM at both the base and flow level, across a combination of factors, including chip density, sequencing kit, template species and machine. We found two distinct insertion/deletion (indel) error types that accounted for the majority of errors introduced by the PGM. The main error source was inaccurate flow-calls, which introduced indels at a raw rate of 2.84% (1.38% after quality clipping) using the OneTouch 200 bp kit. Inaccurate flow-calls typically resulted in over-called short-homopolymers and under-called long-homopolymers. Flow-call accuracy decreased with consecutive flow cycles, but we also found significant periodic fluctuations in the flow error-rate, corresponding to specific positions within the flow-cycle pattern. Another less common PGM error, high frequency indel (HFI) errors, are indels that occur at very high frequency in the reads relative to a given base position in the reference genome, but in the majority of instances were not replicated consistently across separate runs. HFI errors occur approximately once every thousand bases in the reference, and correspond to 0.06% of bases in reads. Currently, the PGM does not achieve the accuracy of competing light-based technologies. However, flow-call inaccuracy is systematic and the statistical models of flow-values developed here will enable PGM-specific bioinformatics approaches to be developed, which will account for these errors. HFI errors may prove more challenging to address, especially for polymorphism and amplicon applications, but may be overcome by sequencing the same DNA template across multiple chips.
Project description:Inflammatory bowel disease (IBD), encompassing Crohn's disease and ulcerative colitis, is associated with enhanced leukocyte infiltration to the gut, which is directly linked to the clinical aspects of these disorders. Thus, leukocyte trafficking is a major target for IBD therapy. Past and emerging techniques to study leukocyte trafficking both in vitro and in vivo have expanded our knowledge of the leukocyte migration process and the role of inhibitors. Various strategies have been employed to target chemokine- and integrin-ligand interactions within the multistep adhesion cascade and the S1P/S1PR1 axis in leukocyte migration. Though there is an abundance of preclinical data demonstrating efficacy of leukocyte trafficking inhibitors, many have yet to be confirmed in clinical studies. Vigilance for toxicity and further research is required into this complex and emerging area of IBD therapy.
Project description:A first approach toward understanding the targeted design of molecular photoacoustic contrast agents (MPACs) is presented. Optical and photoacoustic Z-scan spectroscopy was used to identify how nonlinear (excited-state) absorption contributes to enhancing the photoacoustic emission of the curcuminBF2 and bis-styryl (MeOPh)2BODIPY dyes relative to Cy3.
Project description:In this issue of Cell Chemical Biology, Seneviratne et al. (2020) combine photoaffinity labeling and quantitative chemical proteomics to identify the molecular target of a lead compound discovered from a phenotypic drug screen. Their work showcase the power of coupling a photoreactive group to screening hits for rapid target deconvolution.
Project description:The inversion of the lowest singlet and triplet excited states, observed in several triangle-shaped organic molecules containing conjugated carbon and nitrogen atoms, is an astonishing result that implies the breakdown of Hund's rule. The phenomenon attracted interest for its potential toward triplet harvesting in organic LEDs. On a more fundamental vein, the singlet-triplet (ST) inversion sheds new light on the role of electron correlations in the excited-state landscape of π-conjugated molecules. Relying on the celebrated Pariser-Parr-Pople model, the simplest model for correlated electrons in π-conjugated systems, we demonstrate that the ST inversion does not require triangle-shaped molecules nor any specific molecular symmetry. Indeed, the ST inversion does not require strictly non-overlapping HOMO and LUMO orbitals but rather a small gap and a small exchange integral between the frontier orbitals.
Project description:Surgical excision of brain tumors provides a means of cytoreduction and diagnosis while minimizing neurologic deficit and improving overall survival. Despite advances in functional and three-dimensional stereotactic navigation and intraoperative magnetic resonance imaging, delineating tissue in real time with physiological confirmation is challenging. Raman spectroscopy is a promising investigative and diagnostic tool for neurosurgery, which provides rapid, non-destructive molecular characterization in vivo or in vitro for biopsy, margin assessment, or laboratory uses. The Raman Effect occurs when light temporarily changes a bond's polarizability, causing change in the vibrational frequency, with a corresponding change in energy/wavelength of the scattered photon. The recorded inelastic scattering results in a "fingerprint" or Raman spectrum of the constituent under investigation. The amount, location, and intensity of peaks in the fingerprint vary based on the amount of vibrational bonds in a molecule and their ensemble interactions with each other. Distinct differences between various pathologic conditions are shown as different intensities of the same peak, or shifting of a peak based on the binding conformation. Raman spectroscopy has potential for integration into clinical practice, particularly in distinguishing normal and diseased tissue as an adjunct to standard pathologic diagnosis. Further, development of fiber-optic Raman probes that fit through the instrument port of a standard endoscope now allows researchers and clinicians to utilize spectroscopic information for evaluation of in vivo tissue. This review highlights the need for such an instrument, summarizes neurosurgical Raman work performed to date, and discusses the future applications of neurosurgical Raman spectroscopy.
Project description:In this article we revisit the much-studied behavior of self-assembled aggregates of gold colloidal particles. In the literature, the electrostatic interactions, van der Waals interactions, and the change in free energy due to ligand-ligand or ligand-solvent interactions are mainly considered to be the dominating factors in determining the characteristics of the gold aggregates. However, our light scattering and imaging experiments clearly indicate a distinct effect of light in the growth structure of the gold colloidal particles. We attribute this to the effect of a non-uniform distribution of the electric field in aggregated gold colloids under the influence of light.
Project description:Nitrogen and light availability are well-known to influence photosynthesis, having both individual and synergistic effects. However, the regulatory interactions between these signaling pathways, especially the transcription factors that perceive and integrate these cues remain to be elucidated. Arabidopsis grown in a matrix of nitrogen and light treatments exhibited distinct physiological and transcriptomic responses. Notably, the effect of nitrogen dose on biomass, nitrogen use efficiency, carbon:nitrogen ratio, and gene expression was highly dependent on light intensity. Genes differentially expressed across the treatments were enriched for photosynthetic processes, including pentose-phosphate cycle, light-harvesting and chlorophyll biosynthesis. We identified bZIP and MYB-related family transcription factors as key regulators of photosynthesis, nitrogen assimilation, and light response using gene regulatory network analysis. The transcription factors unveiled in this study have the potential to unlock new strategies for enhancing photosynthetic activity and nutrient-use efficiency in plants.