Matthew K. Daddysman

Matthew K. Daddysman

Data Analysis & Visualization | R, Python, Matlab, C, C++, Labview | Biophysicist | Microscopist

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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.

Pages

Posts

Simulating Anomalous Diffusion using Matlab

4 minute read

Published:

Matlab provides a function for simulating anomalous diffusion from fractional Brownian motion theory. I show how I used this function to generate a simulated anomalous diffusion data set with random lengths, diffusion constants, and anomalous diffusion exponents. Read more

portfolio

publications

Kaempferol inhibits angiogenesis and VEGF expression through both HIF dependent and independent pathways in human ovarian cancer cells

Published in Nutrition and Cancer, 2009

The antiangiogenesis potential of kaempferol and its underlying mechanisms were investigated in two ovarian cancer cell lines, OVCAR-3 and A2780/CP70. Read more

Recommended citation: Luo H, Rankin GO, Liu L, Daddysman MK, Jiang BH and Chen YC (2009) "Kaempferol inhibits angiogenesis and VEGF expression through both HIF dependent and independent pathways in human ovarian cancer cells", Nutr Cancer, 61:4, 554 – 563. https://dx.doi.org/10.1080/01635580802666281

Kaempferol enhances cisplatin's effect on ovarian cancer cells through promoting apoptosis caused by down regulation of cMyc

Published in Cancer Cell International, 2010

Kaempferol enhances the effect of cisplatin through down regulation of cMyc in promoting apoptosis of ovarian cancer cells. As a dietary component, kaempferol sensitizes ovarian cancer cells to cisplatin treatment and deserves further studies for possible applications in chemotherapy of ovarian cancers. Read more

Recommended citation: Luo H, Daddysman MK, Rankin GO, Jiang BH and Chen YC (2010) "Kaempferol enhances cisplatin's effect on ovarian cancer cells through promoting apoptosis caused by down regulation of cMyc", Cancer Cell Int, 10:16. https://dx.doi.org/10.1186/1475-2867-10-16

DNA multiphoton absorption generates localized damage for studying repair dynamics in live cells

Published in Biophysical Journal, 2011

Multiphoton excitation of DNA in live cells with visible femtosecond pulses produces thymine cyclopyrimidine dimers (CPDs), the primary ultraviolet DNA photoproduct. We demonstrate the utility of this method by applying it to investigate the spatiotemporal recruitment of GFP-tagged topoisomerase I (TopI) to sites of localized DNA damage in polytene chromosomes within live cells of optically thick Drosophila salivary glands. Read more

Recommended citation: Daddysman MK and Fecko CJ (2011) "DNA multiphoton absorption generates localized damage for studying repair dynamics in live cells", Biophys J, 101:9, 2294-2303. https://dx.doi.org/10.1016/j.bpj.2011.09.031

Revisiting point FRAP to quantitatively characterize anomalous diffusion in live cells

Published in Journal of Physical Chemistry B, 2013

We apply two-photon excited FRAP with a diffraction limited bleaching and observation volume to study anomalous diffusion of unconjugated green fluorescence protein (GFP) in vitro and in cells. We find that GFP exhibits anomalous diffusion in chromosomal regions but diffuses normally in regions devoid of chromatin. Read more

Recommended citation: Daddysman MK and Fecko CJ (2013) "Revisiting point FRAP to quantitatively characterize anomalous diffusion in live cells", J Phys Chem B, 117:5, 1241-1251. https://dx.doi.org/10.1021/jp310348s

RNA Polymerase II Subunits Exhibit a Broad Distribution of Macromolecular Assembly States in the Interchromatin Space of Cell Nuclei

Published in Journal of Physical Chemistry B, 2014

We investigate the diffusion dynamics of two RNA polymerase II subunits, Rpb3 and Rpb9, in regions of live Drosophila cell nuclei that are devoid of chromatin binding sites. Using FRAP microscopy, we demonstrate that both unengaged subunits are incorporated into a broad distribution of complexes, with sizes ranging from free (unincorporated) proteins to those that have been predicted for fully assembled gene transcription units. Read more

Recommended citation: Tycon MA, Daddysman MK and Fecko CJ (2014) "RNA polymerase II subunits exhibit a broad distribution of macromolecular assembly states in the interchromatin space of cell nuclei", J Phys Chem B, 118:2, 423-433. https://dx.doi.org/10.1021/jp4082933

Photoinduced damage resulting from fluorescence imaging of live cells

Published in Methods in Molecular Biology: Photoswitching Proteins, 2014

The photochemistry of nonnative compounds and the deposition of energy into the cell during imaging can result in unexpected and unwanted side effects. We examine potential live cell damage by first discussing common imaging considerations and modalities in fluorescence microscopy. Read more

Recommended citation: Daddysman MK, Tycon MA and Fecko CJ (2014) "Photoinduced damage resulting from fluorescence imaging of live cells", Methods Mol Bio, 1148, 1-17. https://dx.doi.org/10.1007/978-1-4939-0470-9_1

Correlative imaging across microscopy platforms using the fast and accurate relocation of microscopic experimental regions (FARMER) method

Published in Review of Scientific Instruments, 2017

Imaging specific regions of interest (ROIs) of nanomaterials or biological samples with different imaging modalities (e.g., light and electron microscopy) or at subsequent time points (e.g., before and after off-microscope procedures) requires relocating the ROIs. Unfortunately, relocation is typically difficult and very time consuming to achieve. We report the Fast and Accurate Relocation of Microscopic Experimental Regions (FARMER) method, which only requires determining the coordinates of 3 (or more) conspicuous reference points (REFs) and employs an algorithm based on geometric operators to relocate ROIs in subsequent imaging sessions. Read more

Recommended citation: Huynh T, Daddysman MK, Bao Y, Selewa A, Kuznetsov A, Philipson LH and Scherer NF (2017) "Correlative imaging across microscopy platforms using the fast and accurate relocation of microscopic experimental regions (FARMER) method", Rev Sci Instrum, 88(5):053702. https://dx.doi.org/10.1063/1.4982818

Biphasic growth dynamics control cell division in Caulobacter crescentus

Published in Nature Microbiology, 2017

Cell size is specific to each species and impacts cell function. Here, we investigate size control and the cell cycle dependence of bacterial growth using multigenerational cell growth and shape data for single Caulobacter crescentus cells. Our analysis reveals a biphasic mode of growth: a relative timer phase before constriction where cell growth is correlated to its initial size, followed by a pure adder phase during constriction. Cell wall labelling measurements reinforce this biphasic model, in which a crossover from uniform lateral growth to localized septal growth is observed. We present a mathematical model that quantitatively explains this biphasic 'mixer' model for cell size control. Read more

Recommended citation: Banerjee S, Lo K, Daddysman MK, Selewa A, Kuntz T, Dinner AR and Scherer NF (2017) "Biphasic growth dynamics control cell division in Caulobacter crescentus", Nat Microbiol, 2:17116. https://dx.doi.org/10.1038/nmicrobiol.2017.116

Particle tracking by repetitive phase-shift interferometric super resolution microscopy

Published in Optics Letters, 2018

Accurate and rapid particle tracking is essential for addressing many research problems in single molecule and cellular biophysics and colloidal soft condensed matter physics. We developed a novel three-dimensional interferometric fluorescent particle tracking approach that does not require any sample scanning. By periodically shifting the interferometer phase, the information stored in the interference pattern of the emitted light allows localizing particles positions with nanometer resolution. This tracking protocol was demonstrated by measuring a known trajectory of a fluorescent bead with sub-5 nm axial localization error at 5 Hz. The interferometric microscopy was used to track the RecA protein in Bacillus subtilis bacteria to demonstrate its compatibility with biological systems. Read more

Recommended citation: Gdor I, Wang X, Daddysman MK, Yifat Y, Wilton R, Hereld M, Noirot-Gros MF and Scherer NF (2018) "Particle tracking by repetitive phase-shift interferometric super resolution microscopy", Opt Lett, 43:2819-2822. https://doi.org/10.1364/OL.43.002819

Distinct Sub- to Superdiffuse Insulin Granule Transport Behaviors in β-Cells Are Strongly Affected by Granule Age

Published in Journal of Physical Chemistry B, 2024

Intracellular transport is a complex process that is difficult to describe by a single general model for motion. Here, we study the transport of insulin containing vesicles, termed granules, in live MIN6 cells. We characterize how the observed heterogeneity is affected by different intracellular factors. Read more

Recommended citation: Yi H, Gong D, Daddysman MK, Renn M and Scherer NF (2024) "Distinct Sub- to Superdiffuse Insulin Granule Transport Behaviors in β-Cells Are Strongly Affected by Granule Age", J Phys Chem B, 128:26, 6246-6256. https://doi.org/10.1021/acs.jpcb.4c01403

talks

teaching

Organic Chemistry Lab Instructor

Undergraduate course, Alderson Broaddus University, 2009

I was the organic chemistry lab instructor for 2 health science majors in summer 2009. The course was an experimental and instrumentation survey lab course. I prepared and designed experiments, graded lab reports, and wrote lab exams. Read more

Physical Chemistry Computational Lab (Chem 481L) Instructor

Undergraduate course, University of North Carolina, Department of Chemistry, 2013

I was the instructor of record for fall 2013 physical chemistry computational lab (Chem 481L) course at UNC. The course involved preforming numerical calculations of quantum mechanical and thermodynamic problems. I prepare the course materials, conducted lectures, and wrote and graded exams and lab reports. Additionally, I supervised two teaching assistants who assisted in grading and managing office help hours. The course enrolled 40 senior chemistry majors. I was previously a teaching assistant in the same course in the fall 2011 & spring 2012. I received the 2012 Albert R. Ledoux Teaching Award for this TA assignment. Read more

Research Mentorship

Mentorship, University of Chicago; University of North Carolina, 2017

I’ve mentored four undergraduates in research. As a graduate student I tutored eighteen undergraduates in various chemistry classes. Read more