As of this week, the omicron variant makes up the majority of new coronavirus cases in the U.S. Omicron is more contagious than previous variants and has caused a spike in cases across the nation, including locally.

The same prevention measures that have been put in place previously can still help slow the spread of this variant — vaccination, wearing a face covering, physical distancing, and regular surveillance testing. A well-fitting mask with good filtration is a strong defense for when you are out in public, even if you are fully vaccinated.

As the campus community looks toward winter break, Georgia Tech encourages all students, faculty, and staff to get fully vaccinated, including a booster shot. Campus vaccination clinics will resume in January; to find a vaccination site before that, visit vaccines.gov. Vaccines help reduce the risk of severe illness and hospitalization.

Anyone with Covid-19 symptoms — even mild ones — should get tested and wait for a negative result before interacting with others. Testing on campus is closed through winter break and will resume Tuesday, Jan. 4, 2022. Until then, you can find an alternate testing site.

We recommend all students, faculty, and staff plan to get tested off-campus before returning for the spring semester, and we recommend each person test again on campus upon their return. Campus testing sites will reopen at full capacity on Jan. 4th to accommodate those returning to campus.

Joanne Cole, Ph.D.
Harvard Medical School
The Broad Institute of MIT and Harvard

BlueJeans Livestream

SPEAKER BIO
Dr. Joanne Cole is an Instructor at Harvard Medical School conducting research with Drs. Joel Hirschhorn and Jose Florez at The Broad Institute of MIT and Harvard, Massachusetts General Hospital, and Boston Children’s Hospital. Currently supported by an NIDDK K99/R00 Pathway to Independence Award, her research focuses on using statistical genetics as a tool to determine diet’s relationship with human health, with an emphasis on cardiometabolic diseases. Dr. Cole received her PhD in Human Genetics and Genomics at the University of Colorado Anschutz Medical Campus under the mentorship of Dr. Richard Spritz studying the genetic determinants of normal human facial shape and body size in children and adolescents from Tanzania. In 2016, she went to Boston to pursue her postdoctoral training with Drs. Florez and Hirschhorn to apply her skillset in quantitative genetics to disease biology as a lead analyst in the ‘Genetics of Nephropathy – an International Effort’ (GENIE) consortium whose goal is to identify and characterize the genetics of diabetic kidney disease. Combining her interests from her graduate and postdoctoral training in complex human phenotypes and metabolic disease, she ventured into studying the biological basis of dietary intake as an American Diabetes Association postdoctoral fellow. Dr. Cole continues to pursue the genetics of dietary intake with three interconnected goals, 1) improve dietary phenotypes using genetics, 2) decipher the mechanisms mediating genetic influences on dietary intake, and 3) use genetics to elucidate the underlying causal relationships between nutrition and human health.

Event Details

Brandon (Brady) Weissbourd, Ph.D.
Division of Biology
California Institute of Technology

BlueJeans Livestream

ABSTRACT
Jellyfish are radially symmetric organisms without a brain that arose more than 500 million years ago. They achieve complex organismal behaviors through coordinated interactions between autonomously functional body parts. While jellyfish neurons have been studied electrophysiologically, it has not been possible to investigate their neural function at the systems level. Here I introduce Clytia hemisphaerica as a transparent and genetically tractable jellyfish model for neuroscience. I report efficient generation of stable transgenic and knock-out lines for whole-organism GCaMP imaging and conditional cell ablation. Using these tools and computational analyses we find that an apparently unstructured subnetwork of RFamide-expressing neurons gives rise to spatiotemporally structured ensemble activity that controls localized umbrella infolding during feeding. Looking forward, Clytia affords a tractable platform for high resolution studies at the interface of nervous system development, regeneration, evolution, and function.

Event Details

PingHsun (Benson) Hsieh, Ph.D.
Department of Genome Sciences
University of Washington

BlueJeans Livestream

ABSTRACT
Evolutionary theory provides a critical framework for studying human biology and health, from identifying variants that could lead to genetic novelties through evolutionary processes, such as hybridization and selection, to understanding the genetic basis of adaptive traits and disease risk in populations. With the recent long-read sequencing technologies, we are now able to study previously inaccessible DNA and RNA variants in some of the most challenging regions in the human genome and discover disease mechanisms. In this talk, I will focus on the evolution and fitness implications of structural variants (SVs, e.g., deletions, duplications, inversions)—an important but understudied genomic variation that affects many more bases than single-nucleotide variants in the genome. Using evolutionary theory and long-read sequencing, I will first provide evidence for hybridization and adaptation events in the evolution of humans, including a large (>380,000 bp), complex duplication in an Oceanic population that has an origin from a now-extinct human species. I will then delineate the structure of this duplication, including its novel protein-coding gene content, and hypothesize its biomedical implication in the population. In addition, I will discuss unique insights of SVs for biologically important traits, such as dietary and cold adaptations in humans. Finally, I will show evidence for recurrent SVs in the human genome and their implications in predispositions to recurrent disease-causing rearrangements in humans. Together, these works demonstrate the untapped diversity and fitness effect of uncharacterized SVs in humans and how evolutionary inferences help improve our understanding of human biology and health.

Event Details

Black soldier fly larvae devour food waste and other organic matter and are made of 60% protein, making them an attractive sustainable food source in agriculture. But increasingly, black soldier larvae are dying before they reach livestock facilities as animal feed. 

Georgia Tech researchers, recognizing the culprit is the collective heat generated when the maggots eat in crowded conditions, have found that delivering the right amount of airflow could help solve the overheating issue. Their findings were published this month in Frontiers in Physics as part of a special issue on the “Physics of Social Interactions.”

“Black soldier fly larvae are widely used in an emerging food-recycling industry. The idea is to feed the larvae with food waste and then turn them into chicken feed,” explained first author Hungtang Ko, a Ph.D. student in the George W. Woodruff School of Mechanical Engineering.  “These larvae make a great candidate for this process because they eat just about everything.”

Each year humans waste more than one billion tons of food, or a third of all food production, and many countries are running out of options for disposing of this waste.

The larvae thrive in and around compost piles, where their larvae help break down organic material, from rotten produce to animal remains and manure. Black soldier fly larvae commonly grow to about 1,000 times their size, noted David Hu, professor in the School of Mechanical Engineering.

“It’s like going from the size of a person to the size of a big truck,” he said of the larvae’s growth from eggs to adults.

Hu has appeared on Science Friday graphically showing the voracious appetite of black soldier fly larvae, which can eat twice their body mass in food per day. But when these maggots feed while tightly packed in container bins, they generate metabolic heat that collectively can turn lethal for them.

Air Flow Matters

Ko and Hu collaborated with Daniel Goldman, Dunn Family Professor in the School of Physics, to set up the experiments. Goldman uses fluidized beds —widely used in industrial applications like oil refining ― to control properties of granular media in animal and robot locomotion studies. Fluidized beds operate by forcing a vertical flow of fluid through a collection of particulate matter; above a certain flow rate, the grains transition from a solid pile to a fluid-like arrangement, where they collide and jostle.  

The researchers placed the larvae in a container subjected to regular air flow at a consistent temperature. They then attached a leaf blower to supply air flow into the chamber, manually ramping up and down the air speed in five-minute trials.

Because of the larvae’s constant activity, the collectives’ behavior under air fluidization differs from what is observed in traditional fluidized beds: larvae were un-jammable when air flow became low. Instead, they behave like a fluid that adapted and adjusted to external forces.

“An interesting aspect of this work is that it probes a regime of ‘active matter,’ which has received less attention from physicists: Instead of 3D swarms composed of widely separated, non-colliding flying birds and insects, our `swarm’ exists in another regime, where animals are packed tightly together,” Goldman said.

In a second experiment, the team used x-ray imaging and constant air speed to see how fast larvae eat. Specifically, Ko measured the average velocity and pressure of the larvae, as well as how much food they ate under various airflow speeds.

“As you continue to increase the flow, you’ll reach a point where all the larvae are flying [through the air]. The airflow is too fast, and they won’t eat well,” he said.   

Optimal air velocity will ensure the larvae are cooled off properly and can still feed effectively. “Probing optimal flow velocity will be a good next step. Also, from an engineering perspective, we need to consider other ways that we can cool the larvae down, including using heat transfer,” he added. 

The results indicated that as larvae are agitated by rapid flows, the insects are more likely to be suspended in mid-air without contacting the food, suggesting that a moderate flow rate would be optimal for feeding dense groups of larvae.

The researchers also hope this work will enable black soldier fly larvae to be more readily available as recyclers of food waste, which totals 1.3 billion tons per year, according to the Food and Agriculture Organization of the United Nations. But just as important is the potential of these protein-rich insects to reduce the carbon effects of feeding animals. Global food production contributes more than 17 billion metric tons of human-made greenhouse gas emissions every year, according to a study published in September in Nature Food. Animal-based foods produce more than twice the emissions of plant-based food, the study found. 

“There's no sustainable protein source for the animals that we eat,” noted Ko. “The black soldier fly larvae could play a role in reducing the environmental impact of feeding these animals.”

CITATION: H. Ko, et. all, “Air-Fluidized Aggregates of Black Soldier Fly Larvae,” (Frontiers in Physics, 2021) https://doi.org/10.3389/fphy.2021.734447

Cancer chemotherapy has undergone a paradigm shift in recent years with traditional treatments like broad-spectrum cytotoxic agents being complemented or replaced by drugs that target specific genes believed to drive the onset and progression of the disease.

This more personalized approach to chemotherapy became possible when genomic profiling of individual patient tumors led researchers to identify specific "cancer driver genes" that, when mutated or abnormally expressed, led to the onset and development of cancer.

Different types of cancer — like lung cancer versus breast cancer — and, to some extent, different patients diagnosed with the same cancer type — show variations in the cancer driver genes believed to be responsible for disease onset and progression. “For example, the therapeutic drug Herceptin is commonly used to treat breast cancer patients when its target gene, HER-2, is found to be over-expressed,” says John F. McDonald, professor in the School of Biological Sciences.

McDonald explains that, currently, the identification of potential targets for gene therapy relies almost exclusively on genomic analyses of tumors that identify cancer driver genes that are significantly over-expressed.

But in their latest study, McDonald and Bioinformatics Ph.D. student Zainab Arshad have found that another important class of genetic changes may be happening in places where scientists don’t normally look: the network of gene-gene interactions associated with cancer onset and progression.

“Genes and the proteins they encode do not operate in isolation from one another,” McDonald says. “Rather, they communicate with one another in a highly integrated network of interactions.”

“What I think is most remarkable about our findings is that the vast majority of changes — more than 90% — in the network of interactions accompanying cancer are not associated with genes displaying changes in their expression,” adds Arshad, co-author of the paper. “What this means is that genes playing a central role in bringing about changes in network structure associated with cancer — the ‘hub genes’ — may be important new targets for gene therapy that can go undetected by gene expression analyses.”

Their research paper “Changes in gene-gene interactions associated with cancer onset and progression are largely independent of changes in gene expression” is published in the journal iScience.

Mutations, expression — and changes in network structure

In the study, Arshad and McDonald worked with samples of brain, thyroid, breast, lung adenocarcinoma, lung squamous cell carcinoma, skin, kidney, ovarian, and acute myeloid leukemia cancers — and they noticed differences in cell network structure for each of these cancers as they progressed from early to later stages.

When early-stage cancers develop, and stayed confined to their body tissue of origin, they noted a reduction in network complexity relative to normal pre-cursor cells. Normal, healthy cells are highly differentiated, but as they transition to cancer, “[T]hey go through a process of de-differentiation to a more primitive or stem cell-like state. It’s known from developmental biology that as cells transition from early embryonic stem cells to highly specialized fully differentiated cells, network complexity increases. What we see in the transition from normal to early-stage cancers is a reversal of this process,” McDonald explains.

McDonald says as the cancers progress to advanced stages, when they can spread or metastasize to other parts of the body, “[W]e observe re-establishment of high levels of network complexity, but the genes comprising the complex networks associated with advanced cancers are quite different from those comprising the complex networks associated with the precursor normal tissues.”

“As cancers evolve in function, they are typically associated with changes in DNA structure, and/or with changes in the RNA expression of cancer driver genes. Our results indicate that there’s an important third class of changes going on — changes in gene interactions — and many of these changes are not detectable if all you’re looking for are changes in gene expression.”

 

DOI: https://doi.org/10.1016/j.isci.2021.103522

Acknowledgments: This research was supported by the Mark Light Integrated Cancer Research Center Student Fellowship , the Deborah Nash Endowment Fund , and the Ovarian Cancer Institute (Atlanta), where John F. McDonald serves as chief research officer. The results shown here are based upon data generated by the TCGA Research Network: http://cancergenome.nih.gov/.

 

About Georgia Institute of Technology

The Georgia Institute of Technology, or Georgia Tech, is a top 10 public research university developing leaders who advance technology and improve the human condition. The Institute offers business, computing, design, engineering, liberal arts, and sciences degrees. Its nearly 40,000 students representing 50 states and 149 countries, study at the main campus in Atlanta, at campuses in France and China, and through distance and online learning. As a leading technological university, Georgia Tech is an engine of economic development for Georgia, the Southeast, and the nation, conducting more than $1 billion in research annually for government, industry, and society.

 

A free, four-day online event!

REGISTER HERE

Join us for a lively exploration of the math-bio interface. 

The Symposium will host daily panel discussion about important issues in math-bio research and traineeship. How can we productively embed ourselves in a second discipline? What paths have led to successful math-bio careers in academia? In industry? 

Support the next generation of math-bio researchers.

Following each panel, the Symposium will spotlight work being done by junior researchers from all 4 NSF-Simons MathBioSys research centers. Come support these young scientists who are forging new connections at the interface between mathematics and the bio-sciences!

Featuring plenary lecture by Belinda Akpa, Ph.D.

SCMB is happy to feature Belinda Akpa, senior scientist at Oak Ridge National Laboratory, as the Symposium's plenary speaker. Akpa, who holds a joint appointment as Associate Professor of Chemical and Biomedical Engineering at UTK, will speak on "Making the most of 'tiny data' in systems biomedicine" in the 12 noon plenary session on Thursday 12/16. 
 
Contribute your own work to our poster session.

Following the plenary session, the Symposium will host a poster session via spatial conferencing platform spatial.chat. Enhace the scientific reach of our event by contributing your own work!

Poster presenters are also invited to contribute a 90 second pre-recorded "microtalk". The microtalks will run on loop in our spatial.chat coffee break space, serving as an advertisement for your work in the lead up to the poster session.
 
SCMB, a National Science Foundation-Simons MathBioSys Research Center, is a collaborative partnership of seven institutions united in advancing the mathematics of complex biological systems and expanding communities at the math-bio interface.
 

Event Details

An interdisciplinary team of researchers from the Georgia Institute of Technology has received a $2 million federal grant to create tools that will provide the clearest three-dimensional images yet of the chemical and biomolecular interactions between plants and the soil in which they grow.

At just a few inches underground, the rhizosphere — the thin strip of earth that includes the soil-root interface — has so far been difficult to visualize on site. If scientists can build instruments that capture in real-time clearer images of the physical associations of microbes attached to roots, along with the oxygen-carbon-nitrogen chemical exchanges they mediate, it could help mitigate the effects of climate change and lead to the development of more sustainable fuels and fertilizers.

“From a microbiological perspective, we have catalogued what microbes are in the root zone and how abundant they are,” said Joel Kostka, professor in the School of Biological Sciences and School of Earth and Atmospheric Sciences at Georgia Tech. “But there's been very little work to understand their dynamics under real soil conditions.”

Kostka, who also serves as associate chair for Research in Biological Sciences, joins Marcus Cicerone, professor in the School of Chemistry and Biochemistry and principal investigator for the new grant from the U.S. Department of Energy’s Office of Biological and Environmental Research. The research team also includes Francisco Robles, assistant professor in the Wallace H. Coulter Department of Biomedical Engineering, and Lily Cheung, assistant professor in the School of Chemical and Biomolecular Engineering in the College of Engineering.

Together, the researchers plan to produce a new optical instrument that will provide 3D images of dynamic metabolic processes with chemical specificity — meaning it will be able to identify carbon sources (sugars, organic acids) exuded by plant roots and nitrogen-rich compounds provided to the root by nitrogen-fixing (diazotrophic) microbes. The instrument will be built with commercially available components, and with an eye towards simplicity so that it can be easily leveraged by Department of Energy (DOE) Bioenergy Research Centers and field sites.

A ‘hotspot for microbes in 3D

Understanding more about the metabolic processes happening in the rhizosphere will help the DOE develop a wider range of sustainable products like new types of biofertilizers and biofuels. The research will also help create practices for better crop management — and will help researchers use plants and soil as more effective carbon traps that sequester greenhouse gases from the atmosphere into the soil.

“The problem is that we don’t know much about the free-living bacteria in the soil, because we can’t get in there and look,” Cicerone said. “The DOE wanted somebody to build an instrument that would allow them to image or gather information about the metabolic processes, the interaction — the metabolic interactions between the microbes and the plants, in real time.”

Kostka adds that the rhizosphere is “a hotspot for microbes.”

“It’s often where the plant is communicating with the outside world,” he explained. “Our goal is to develop an instrument that they (the DOE) can use to better understand those interactions between plants and microbes and how those can be tweaked, say, to optimize plant production, crop production, biofuels and biomass production. And that's the long-term goal for us.”

How light gets scattered, smothered, and covered in soil

Cicerone says the visibility issue with soil involves how photons — or particles of light — scatter once they hit the soil. He likens it to someone putting a red light up to the back of their thumb.

“You turn your thumb around, your thumb glows red, right? So, the light comes through, but most of it scatters. The unscattered light contains the spatial information, but it is so weak that you can’t detect it by eye, and you lose the spatial information. The same thing happens with the soils. You get a lot of light scattering, and you lose spatial information,” Cicerone said.

Cicerone and Robles will build instrumentation that will focus light into the soil and that is “exquisitely sensitive to the minuscule amount of light that only scatters when it reaches its target.” Evaluating that light will help scientists learn even more about the chemical processes in the rhizosphere.

The visibility enhancements will be implemented in optical techniques with names like coherent Raman scattering and optical coherence tomography, which are commonly used for non-invasive imaging of thin biological material, like the retina of the eye — or the tiniest of plant roots.

“We learn two things from the light coming out of the sample. The amount of light coming out tells you about the refractive index of the material, and the light’s frequency change tells you about the chemical composition of the material,” Cicerone explained.

It’s through imaging and then optimizing those microbe-plant interactions that the DOE aims to design more sustainable products and practices, based on the chemistry to be learned from the team’s new optical instruments.

“This is a three-year funded project, and we hope at the end of the three years to have an experimental system, where we can do something that nobody else can do,” Cicerone added. “And that is that we can follow the biochemistry under the soil, in situ, in real time, to clearly see what's going on there and find out what the microbes really are doing in natural conditions. At that point, we can start manipulating the biology, start doing the experiments that the DOE is primarily interested in.”

 

Award Number: DE-SC0022121
Title: Deep Chemical Imaging of the Rhizosphere
Institution: Georgia Tech Research Corporation, Atlanta, GA
Principal Investigator: Cicerone, Marcus

About Georgia Institute of Technology

The Georgia Institute of Technology, or Georgia Tech, is a top 10 public research university developing leaders who advance technology and improve the human condition. The Institute offers business, computing, design, engineering, liberal arts, and sciences degrees. Its nearly 40,000 students representing 50 states and 149 countries, study at the main campus in Atlanta, at campuses in France and China, and through distance and online learning. As a leading technological university, Georgia Tech is an engine of economic development for Georgia, the Southeast, and the nation, conducting more than $1 billion in research annually for government, industry, and society.

No RSVP and totally free! Join us for the first live stress reduction comedy show since the beginning of the COVID-19 pandemic, featuring student and faculty comedians from the Georgia Tech Stand-up Comedy Club and the Geekapalooza Comedy Tour.

The show is Wed. Dec. 8th (Reading Day) at 7:00pm in room 205Q in the Clough Undergraduate Learning Commons.

It is your chance to enjoy some humor and mediate your stress levels in advance of final exams. We strongly encourage all attendees to wear masks during the performance.

Event Details

Members of the Georgia Tech community are opening their doors for the Atlanta Science Festival. Whether you’re interested in robotics, brains, biology, space, art, nanotechnology, paper, computer science, wearables, bioengineering, chemical engineering, or systems engineering, there will be activities for you. Visit campus for lab tours, hands-on STEAM activities, exhibits, demonstrations, opportunities to meet student researchers, and learn about the research and so much more happening at Tech.

 
Biomechanics Basics
Learn how scientists research human motion for innovations in robotics, prosthetics and exoskeletons + ultrasound demonstrations to show muscles in action.

Through the Lenses of your Senses
A tour of the senses from a Neuroscience perspective.

Fundamentals of Electrical Energy
Build a simple electric motor (yours to keep!) and see demonstrations of a electrostatic Van de Graaff generator and a plasma globe.

Garcia Lab for Regenerative Medicine
Learn About the Intersection of Engineering, Materials Science, & Cell Biology.

Introduction to Chemical Engineering
See how various labs at GT use Chemical Engineering research to innovate across technology applications.

Intro to Industrial & Systems Engineering
Participants will Build Lego structures using Industrial & Systems Engineering principles.

Introduction to Mechanical Engineering
Learn about the broad areas of Mechanical Engineering research at Georgia Tech!

LaserFest
The Georgia Tech Research Institute presents its traveling, laser-themed museum. Interactive exhibits teach the history of lasers, how they work, and how they are used in our modern, technological society.

Learn to Code With BBUGS
Learn to code with games

Physics of Flight
Aviation Demonstrations

What is Blood Composed Of?
Learn the different components of blood and their different functions.

Need an Arm with That?
Learn how humans and robots collaborate by building simple structures with a
robot arm as your partner.

Papermaking: History & Hands-On
Participants will learn to make a handcrafted sheet of paper and tour the Robert C. Williams Museum of Papermaking Spring Exhibit “Pulp + Fiber”.

retroTECH Exhibit & VR for Science Education
View an amazing collection of retro video games on vintage consoles + the Data Visualization Lab is offering demonstrations of virtual reality games that explore science.

Stem Cell Plinko
Learn how stem cells differentiate using a Plinko game example

Virtual Reality & 3D Printing: Bioapplications
Demonstrations of VR and 3D printing technologies and lab tours.

Distracted Calling
A competitive racing-game that shows how much impact cell phone operation has on driving performance + demonstrations on improving everyday tasks with ergonomic design.

BRAINS!!!!!
Tour a cutting edge brain imaging facility, make a paper brain hat, and see electroencephalogram and transcranial magnetic stimulation demos.

Introduction to Microfluidics
Microfluidic devices have myriad applications in biomedical engineering; they can be used for the analysis of biological fluids, separation and sorting of different cell types, and can even be used to grow 3-dimensional tissues and live organisms! The Bioengineering Graduate Association will demonstrate the capabilities of microfluidics and provide hands-on examples so visitors can see for themselves!

What’s the “A” in STEAM?
A gallery exhibit of research-inspired artwork + interactive science-themed arts & crafts.

What’s the Big Deal About Nanotechnology?
How do scientists and engineers make and see nanoscale objects? What does your hair or an insect’s eye look like under a scanning electron microscope (SEM)? Through hands-on demos, learn what makes the nanoscale different. Take a cleanroom tour and bring a sample (not wet and not greater than an inch in diameter) to scan with our tabletop SEM.

Event Details

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