Calendar
Upcoming events
Minflux Cluster Meeting: "Building Research Minfluxes"
All interested are invited to join the Minflux Cluster Meeting to hear Drs. Jonas Ries & Martin Gruebele: "Building Research Minfluxes." The meeting will be held via Zoom.
QCB Seminar featuring Anthony Bae: Integration of nonlinear optical microscopy with computational models for analysis of the morphological and metabolic dynamics of live mitochondria
Beckman Institute 3269 (third floor tower room)
Join us from 2-3 p.m. in Beckman 3269 or on Zoom for QCB Seminar featuring Anthony Bae, QCB/University of Illinois. Refreshments prior outside Beckman 3151.
Title:
Integration of nonlinear optical microscopy with computational models for analysis of the morphological and metabolic dynamics of live mitochondriaAbstract:
Mitochondrial dynamics are crucial for metabolic homeostasis, quality control, and apoptosis regulation. Disruptions in these dynamics can cause neurodegenerative disorders, cardiovascular diseases, and cancer. Fluorescence microscopy enables real-time observation of mitochondrial events but faces challenges in simultaneously capturing dynamics and metabolism due to photobleaching, chemical toxicity, and limited temporal resolution. Nonlinear optical (NLO) microscopy, generating signals without dyes, has been demonstrated to allow label-free monitoring of key metabolic coenzymes and lipid accumulation within mitochondria. This project has developed a novel multiplexed NLO imaging platform integrated with computational modeling to simultaneously capture both morphological and metabolic changes in mitochondria. The integration of NLO microscopy and computational modeling is anticipated to reveal new correlations between mitochondrial dynamics and cellular metabolism, potentially uncovering unknown disease mechanisms related to mitochondrial dysfunction.
Beckman Friends and Family Night
Beckman Institute
Bring your friends and family for this sneak peak to explore the research happening at the Beckman Institute, including the QCB CraftCells (Minecraft worlds).
Beckman Open House
Beckman Institute
Beckman’s annual open house will take place 9 a.m. to 4 p.m. Friday, April 4, and 9 a.m. to 3 p.m. Saturday, April 5. In addition to QCB's Minecraft worlds demonstrations, the event features hands-on science experiments, opportunities to participate in research and the debut read-aloud of a Beckman-themed children’s book in English and Spanish.
QCB Seminar featuring Carolyn Larabell: Quantitative 3D Imaging of Whole Cells Using Soft X-ray Tomography
Beckman Institute 3269 (third floor tower room)
Join us from 2-3 p.m. in Beckman 3269 or on Zoom for QCB Seminar featuring Carolyn Larabell, University of California San Francisco and Lawrence Berkeley National Lab. Refreshments prior outside Beckman 3151.
Title:
Quantitative 3D Imaging of Whole Cells Using Soft X-ray TomographyAbstract:
Soft x-ray tomography (SXT) visualizes and quantifies the structural organization ofbiological organisms up to 20 um diameter. Specimens are imaged in the near-nativestate - rapidly frozen in their normal growth conditions - at a resolution up to 35 nm.Large numbers of cells can be imaged since it takes only 5-10 min to go from the frozenspecimen to a reconstructed tomogram. Imaging is based primarily on the absorption ofCarbon, a common element of all known life. At the same time, water (ice) is virtuallyinvisible so that high-contrast images are obtained based solely on the inherentproperties of the structures examined. This is accomplished by imaging with x-rayphotons in the 'water window' (between 284 – 543eV), where x-ray photons areabsorbed an order of magnitude more strongly by carbon- and nitrogen-containingorganic material than by water. The absorption of soft x-rays adheres to the Beer-Lambert Law and is, therefore, a function of the chemical composition andconcentration of organic material, yielding unique quantitative Linear AbsorptionCoefficient (LAC) measurements for specimen components. We have used this label-free imaging technology to image and quantify a wide variety of structures, includingisolated organic particles, bacteria, yeast, spores, algae, larger mammalian cells andtissue. I will present examples of SXT data that enabled biological findings that couldn’t be obtained with other technologies.
GPU Programming Using OpenACC
NCSA Room 3000
Contact name: Sandie Kappes
Contact email: kappes@illinois.edu
The Pittsburgh Supercomputing Center (PSC) is presenting an OpenACC GPU programming workshop on April 9, 2025.
OpenACC is the accepted standard using compiler directives to allow quick development of GPU-capable codes using standard languages and compilers. It has successfully accelerated real applications within very short development periods. This workshop assumes knowledge of either C or Fortran programming. Hands-on exercises using the Bridges-2 computing platform at the Pittsburgh Supercomputing Center are included to give attendees practice with the concepts presented.
This event will be presented virtually from PSC with onsite attendance at NCSA. NCSA staff will be available to assist attendees with hands-on exercises and provide technical support. There WILL NOT be a direct-to-desktop option.
You must have an ACCESS ID to register for this event.
If you do not have an ACCESS ID, please visit this page to create one:
QCB Seminar featuring Bernhard Palsson: What are iModulons?
Beckman Institute 3269 (third floor tower room)
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oin us from 2-3 p.m. in Beckman 3269 or on Zoom for QCB Seminar featuring Bernhard Palsson, University of California, San Diego. Refreshments prior outside Beckman 3151.Title:
What are iModulons?Abstract:
The first microbial genome sequences appeared in the mid to late 1990s. In the 2000s, computational biology at the genome-scale arose through the reconstruction of metabolic networks based on functional gene annotation. In the late 2000s, the cost of DNA sequencing dropped massively, leading to rapidly expanding data bases of microbial genome sequences and microbial transcriptomes. These data sets could be knowledge-enriched and decomposed into coherently functioning sets of genes using machine learning methods. A growing number of data types can be processed in a similar fashion. Multiple data types can now be made interoperable based on known mechanisms and molecular functions. The 2020s are likely to see an accelerating fine-grained understanding of microbial physiology.
Analysis of large biological data sets can take place at four levels. At level 1 we perform multi-variate statistics, at level 2 knowledge-enrichment of large data sets, at level 3 systems biology and computational modeling, and at level 4 detailed biophysical modeling. Levels 1 and 4 are well developed in the literature. The history of genome-scale models, level 3, is about 20 years old with much progress made. Level 2 is the least developed and is focused on knowledge mapping and the use of machine learning and explanatory AI.
This talk will focus on progress at levels 2 with transcriptomes. Large compendia of high-quality RNAseq profiles can now be decomposed using Independent Component Analysis (ICA). ICA identifies independently modulated sets of genes, called iModulons. This talk will show the uses of iModulons for metabolic engineering and bioprocess development: including cross-species transfer of iModulons, Media composition, expression of heterologous genes, and y-gene discovery.
QCB Seminar featuring Andrew Pountain: Inferring bacterial cell biology and gene regulation from transcriptional "noise"
Beckman Institute 3269 (third floor tower room)
Join us from 2-3 p.m. in Beckman 3269 or on Zoom for QCB Seminar featuring Andrew Pountain, UTHealth Houston. Refreshments prior outside Beckman 3151.
Titlez:
Inferring bacterial cell biology and gene regulation from transcriptional "noise"Abstract:
Gene expression varies between individual cells, even those with identical genomes in a homogeneous environment. In bacteria, our understanding of what drives this variation has been obscured by a lack of methods to measure single-cell gene expression at the genome-wide scale. By applying a recently developed single cell RNA sequencing protocol, we showed that interactions between transcription and chromosomal replication drive global heterogeneity in gene expression. Analyzing genome-wide patterns of covariance, we could reconstruct DNA replication patterns and use these to infer cell cycle transcriptional dynamics in these organisms for the first time. We found that replication itself impacts transcription of each gene, but that the response of individual genes to this perturbation is shaped by a gene’s local regulatory context, from its turnover rate to its repression state. We are continuing to develop our understanding of transcription-replication interactions, as well as expanding our analysis across different states of growth. Overall, bacterial transcriptional variation, far from being simply “noise”, contains quantitatively reproducible information about the state of the underlying biological system, far beyond what can be inferred from bulk measurement.
Minflux Cluster Meeting
All interested are invited to join the Minflux Cluster Meeting to hear our speaker (TBD). The meeting will be held via Zoom.
QCB Seminar featuring Yingjie Zhang
Beckman Institute 3269 (third floor tower room)
Join us from 2-3 p.m. in Beckman 3269 or on Zoom for QCB Seminar featuring Yingjie Zhang, QCB/University of Illinois. Refreshments prior outside Beckman 3151.
QCB Site Visit Preparation Mini-Retreat (Internal Event)
Beckman Institute
All QCB members are asked to attend this session to prepare our posters for the upcoming QCB site visit. Students will share their posters, faculty members will be the mock review panel. Continental breakfast and lunch provided.
QCB Seminar featuring Marie-Cristen Spindler
Beckman Institute 3269 (third floor tower room)
Join us from 2-3 p.m. in Beckman 3269 or on Zoom for QCB Seminar featuring Marie-Cristen Spindler, QCB/European Molecular Biology Laboratory. Refreshments prior outside Beckman 3151.
NSF Site Visit (Internal Event)
Beckman Institute
The NSF Site Visit is an internal event for QCB members and invited guests.
QCB Seminar featuring Taekjip Ha: Biophysical Principles of Genome Organization Across Multiple Scales
Beckman Institute 3269 (third floor tower room)
Join us in Beckman 3269 and on Zoom for Taekjip Ha, Please note the change of day and time: this is a Thursday at 11 a.m.!
Title: Biophysical Principles of Genome Organization Across Multiple Scales
Abstract:
Recent advances in genetics, biochemistry, cell biology, and biophysics have contributed to our understanding that the genome is organized hierarchically, with higher-order macromolecular assemblies spanning spatial and temporal orders of magnitude. Beyond being wrapped around histones as irregular groups of “beads on a string”, chromatin is organized into topologically associated domains, which are composed of small and large loops, and form euchromatic and heterochromatic compartments. In this talk, I will present biophysical principles we are uncovering about genome organization across three different scales, including sequence-dependent DNA mechanics [1], chromatin loops for homology search [2], and polyamines' role in translating nucleosome condensability into 3D genome organization [3].
[1] doi:10.1101/2024.12.22.629997
Minflux Cluster Meeting featuring Minxue Liu and Oraya Zinder
All interested are invited to join the Minflux Cluster Meeting hear Minxue Liu, "Spatial organization of nuclear speckle during stress response" and Oraya Zinder, "Quantifying DNA replication components using super resolution microscopy." The meeting will be held via Zoom.
MINFLUX Workshop
Carl R. Woese Institute for Genomic Biology
Details to come.
QCB 2nd Annual Summer School in Quantitative Cell Biology
Beckman Institute
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Summer School in Quantitative Cell Biology
is designed for graduate students, postdoctoral fellows, and researchers in physics, biophysics, chemical and life sciences, and engineering who seek to expand their research skills in quantitative methods for studying and modelling cells. The workshop will include lectures, mini-courses, and hands-on training in experimental and computational techniques. No charge to attend but must apply.
NSF iPOLS Meeting
Beckman Institute
The Physics of Living Systems (PoLS) Student Research Network (SRN) is funded by the National Science Foundation award PHY-2014141, from the Division of Physics, Directorate of Mathematical and Physical Sciences, and hosted by the Center for Theoretical Biological Physics at Rice University. It is a trans-institutional community-based network of graduate students and graduate student educators all working on the physics of living systems. This is the annual meeting, hosted this year by the Center for Quantitative Cell Biology.