UNC Biology's Joe Kieber, an important plant cell biologist

Reading this interview with Professor Kieber is pretty much like chatting one-on-one with Prof Kieber, who is simultaneously no-nonsense, gentle and curious.

Joe Kieber gravitated towards a life in science by spending a lot of his childhood playing outdoors. He also had key professors and mentors that inspired him and guided his path towards mechanistic plant biology.

When he was a trainee, the concept that plant cells could communicate via tiny simple molecules was just beginning to be appreciated.

Prof Kieber took an unbiased approach to discover genes involved in plant signaling by randomly mutagenizing a large population of seeds and looking for the ones with characteristic malformations. While mutation in a wide range of "housekeeping genes" like those encoding ribosomal proteins, lipid synthesis enzymes, and the cytoskeleton might have led to certain developmental defects, Prof Kieber looked for a special combination of triple-malformation. This phenotype was characteristic of problems with the signaling molecule (ethylene), so he reasoned it would be characteristic of proteins involved in the signal transduction between the signal-receptor ligation and the changes in cell and tissue behavior.

Professor Kieber did discover several proteins involved in ethylene signaling and has defined much of the signaling downstream of another plant hormone, cytokinin. His collective contributions have been recognized with several awards including the election to the National Academies of Sciences, an honor earned by very few UNC scientists (the short list includes Professors Ted Salmon and Kerry Bloom whose work you already know about!).

Stem cell biology Nobel Prize (2012)

We now take for granted that every cell in our body contains the identical genetic material, and that this material has the capacity to encode all the molecules needed to create and operate any cell in the body. But this notion was once revolutionary, and one research team, led by John Gurdon, had to push through this resistance and persevere despite doubt and distrust.

Gurdon was awarded the Nobel Prize 50 years after discovering that the DNA in a differentiated cell could replace the nucleus of an egg, and support the development of an entire organism. Gurdon's lab did this work with frog eggs, which are popular for experimental biology because they are so huge (1mm+ across).

Gurdon shared the Nobel with Shinya Yamanaka, who worked out what very few genes are sufficient to keep cells acting like stem cells, keeping them from differentiating. Stem cells don't express -every- gene, but any gene could be turned on. This is as opposed to the epigenetic process of shutting down the genome so that only a subset of genes, such as those required to carry out the functions of a differentiated cell, can be expressed.

Yamanaka's "factors" keep epigenetic genome closure from happening.

And Gurdon's experiments worked because oocytes have the ability to strip off whatever epigenetic marks had closed down the DNA from the differentiated cell.

Their discoveries have led to an entire field of stem cell biology, including fundamental mechanistic research and a vast array of "applied" research like implant and repair technologies. These discoveries have had a massive economic impact, including the creation of a journal (and jobs there): Cell Stem Cell, as mentioned in the previous post!

Frugal Scientists in the Prakash Lab Create "Paperfuge"

 Much of the global population most susceptible to devastating disease is also susceptible to inadequate medical care. Some of the limitations to medicine involve the dependence of modern medicine on technologies including electricity. How can key diagnostics like centrifugal sample separation and light microscopy be done without electricity?

The brilliant team in Manu Prakash's lab at Stanford has invented several inexpensive, lightweight, and electricity-independent tools to make modern diagnostics accessible to populations with little or no industrialized infrastructure.

For example, the paperfuge enables rural medicine by leveraging a millennia-old toy technology by which a disc is spun. When thin tubes of blood samples are mounted on a disc of paper and spun (fast!), the different materials of blood separate according to their density and the portion containing malaria parasites can be observed (with a foldscope!) even when present at very low levels, accelerating diagnosis and treatment.

In developing the paperfuge, the Prakash lab not only created the tool, but they also uncovered and documented its underlying physics: the strings that spin the central paper disc supercoil.

Wired Magazine picked up this story! Even more fun than reading the general-audience press is seeing the instrument in action via a movie on YouTube.

Stem Cells in Oral Biology - UNC Dentistry & collaborators

UNC researcher Scott Williams and his team discovered that there are several distinct kinds of stem cells in the mouth. They used mice to test how cells of the palate (~skin internal to the mouth) are renewed. They are all renewed by proliferation of stem cells in a basal layer and population of the suprabasal layers via the asymmetry of stem cell division. 

But this renewal happens differently along the ridges on the roof of the mouth. Where there is more wear and tear on the mouth from chewing hard food, stem cells proliferate more. This suggests that stem cells respond to physical stress by boosting their proliferation rate. The Williams lab discovered which protein is important for oral "skin" stem cells to remain quiescent (not dividing) and a different protein that becomes highly expressed in clones of cells that result from rapid divisions of stem cells. 

They noted that these regional differences correspond to parts of the mouth more and less likely to develop cancer - their work will help us understand how tissues are susceptible or refractory to cancerous transformation. 

They published this very comprehensively-documented discovery in the prestigious journal Cell Stem Cell (one of the "Cell" journals).

Undergraduate Jeet Patel, who did an Honors Thesis in Biology on his research, was a contributing author!

EVERYTHING ABOVE HERE WAS POSTED AFTER EXAM 3

Weaponizing matrix metalloproteinases

Matrix metalloproteinases (MMPs) are proteins that when bound to a metal (such as zinc) can break down other proteins. They are typically secreted into the extracellular space. When cancer cells express MMPs, they can invade from one tissue to another, by breaking down basal lamina.

MMPs weren't "invented" for cancer, though; they're important for development, when cells need to break from one compartment of the body to another in order to set up the body plan and build organs.

MMPs are seen in the genomes of organisms besides humans (and related mammals) - they're expressed by venomous snakes! It turns out snake venom is so destructive because it contains MMPs. Venoms can induce much of their harm by causing hemorrhage (breaking down blood vessels and inhibiting clotting).

There is a whole field of Venomics (get it? Like genomics, transcriptomics, proteomics, etc) in which folks are working to better understand the molecular and cellular biology and the biochemistry of venom proteins including MMPs in order to engineer them for therapies, develop anti-venom treatments, and widen our understanding of the diversity of protein function.

Feedback loops aren't just for signaling

 

My lab has
a pre-print* about the interplay between biochemical and mechanical feedback loops.You already know how time-delayed negative feedback loops can cause oscillations. Positive feedback ramps M-Cdk activity up, which in turn leads to satisfaction of the spindle assembly / kinetochore attachment checkpoint, which degrades M-cyclins and destroys M-Cdk activity. These processes collectively = the oscillation of the cell into and out of mitosis. 

On a shorter timescale, Rho proteins' activity oscillates because downstream of their activation, effector proteins boost GAP activity, turning Rho proteins off. This biochemical feedback had been well-described in several papers with experimental (wet-lab) work and models (dry-lab work).

It was also appreciated that Rho proteins cause contractility, which I taught you builds tension along a linear bundle - in 2D this causes the compaction of material towards a point. This increase in local concentration of everything in the Rho pathway constitutes mechanical positive feedback.

These biochemical and mechanical feedbacks had never been considered together, until a 2022 paper from our now-collaborators Mike Staddon and Shiladitya Banerjee. Their modeling of this combination of feedback predicted that contractility should not just oscillate, but should be very complex, with a wide range of amplitudes and periods, much longer than the period of the biochemical oscillator.

We performed high resolution imaging and discovered that this is exactly the case in cytokinesis. We collaborated with Mike and Shila to extend their model and the analysis of model outputs, and created an interdisciplinary paper about non-muscle contractility. We will send it back in, having revised it according to anonymous peer reviewer comments, and we're optimistic that it'll soon be accepted.

* pre-prints are manuscripts shared globally via the open repository BioRxiv. "Open" means anyone can access the contents - they don't have to pay $35 per paper they want to read, like for lots of for-profit journals; their university library doesn't have to pay hundreds or thousands of dollars for access to the repository like they have to for journals.

Pre-prints are not peer-reviewed. Peer review is the process by which 2, 3, or 4 (or sometimes more) usually-anonymous "peers" (research faculty at universities around the world) evaluate a manuscript according to the standards of a the journal where they paper is being considered, and their own experience and standards. They give a yes, no, or revisions required answer, and usually many comments ranging from typos to perceived conceptual errors to recommended extensions of the work. The journal editor summarizes all the comments and tells the authors what they need to do to get accepted and published. Sometimes they just reject the paper and the authors need to try somewhere else.

Pre-prints can receive comments and suggestions, but people don't do that very much yet. This could help prepare the manuscript for anonymous peer review.

Peer-reviewed publication is still the gold standard for showing you've advanced a field, but pre-prints allow the community to see what you've done even before that long process is complete.

Truly interdisciplinary research

 Retired UNC professor Keith Burridge worked for decades on the cell biology of the cytoskeleton, adhesion, cell shape, and movement. He discovered and named several cytoskeletal proteins including the Tar Heel protein, talin.

Even before he retired, he was a secret playwright! Now he spends even more of his time creating art in this way. He loves history, controversy, and telling the stories of those whose voices haven't been heard. He wrote a one-person play about Edith Wilson, who truly ran this country after Woodrow Wilson became incapacitated, keeping the degree of his inability a secret. 

The most science-y play I've seen from him was about the discovery of mRNA: "The Message." It was read by local actors for the celebration of Keith's retirement. Keith was present for some of the moments of discovery in Cambridge England, and also carefully researched the events and people depicted in the play. Can you imagine a time before we knew about mRNA?! I love that art like theatre can afford us time-travel, to explore other perspectives and vicariously enjoy the thrill of discovery.

Keith lives near campus and can be spotted on long walks. Since he's my PhD advisor, I'm grateful to be near him still!

The probability of improbable events

 The other day at the Biology Department's Undergraduate Honors Thesis Symposium, two separate student groups decided to take advantage of the fact that it was April 1st and play an April Fools' joke on the audience. One teased the audience that they'd be tested on their knowledge of epigenetics. The other led us, momentarily, to believe their general audience introduction was going to be about the Loch Ness Monster. 

What are the chances that all those stories, accounts, and grainy photos are true? Those are not good odds.

One scientist is actually working on the probability of goofy things like seeing the Loch Ness Monster and BigFoot. I love how this work interrogates humorous topics with solid statistical approaches.

It reminds me of how biophysical modeler Rob Phillips says you can't claim to be surprised by your own data unless you've done the (well-informed) math and find contradictory predictions.

Are mitochondria (not just the powerhouse of the cell but also) light sensors?!

Vision is so important to people - to most animals, really! We have specific and special eyes that collect light and code images, and a big part of our brain is dedicated to decoding that information. But the eye and optic nerve and brain are all made up of cells - so can any individual cells actually see or is vision an emergent behavior of cells, tissues and organs? When I saw this paper about vision in single cells, I as amused to learn about the hypothesis that mitochondria form part of see-ing parts of simple tiny organisms. I wondered what else was known about the evolution of sight and stumbled across this TedX talk. You might find it fun, too!

^ EVERYTHING ABOVE HERE IS POSTED BY DR. MADDOX ^

Celebrate all that you've learned

Celebrate all that you've learned so far by setting this video to 'full screen', turning up the sound, and marveling at how many things you recognize — and understand how they work.

 

John Liebler - The Inner Life of the Cell from John Liebler on Vimeo.

You can find a narrated version here. And you can read a little more about how the video was made here, and more about molecular animation here. If you want to see more about how molecular animators work, here's a lab at University of Utah that does terrific work.

Curiosity creates cures

Want some help explaining to others how studying bacteria, or yeast, or flies can tell us something important about human health? How curiosity is an engine to important discoveries? Here's a video and a great summary from the NIH.

How unfolded proteins are recognized in the ER

How are unfolded proteins recognized in the ER, and what happens next? The Lasker Award web site describes the discovery of the unfolded protein response and its molecular mechanisms (click "see more" to get a fuller story including the figure below).

One of the scientists whose lab made some of the key discoveries, Peter Walter, describes his science and art projects in a video here:

Kizzmekia Corbett, a Tar Heel and a science hero

"Kizzmekia Corbett had gone home to North Carolina for the holidays in 2019 when the headlines began to trickle in: A strange, pneumonialike illness was making dozens of people sick...."

Among the scientists we have to thank for the COVID vaccines that transformed the pandemic is one person who played a central role in the development of RNA-based vaccines, Dr. Kizzmekia Corbett.

Dr. Corbett grew up near Chapel Hill in Hillsborough, worked in a UNC lab for a summer in high school, and then moved back and forth between North Carolina and the DC/Baltimore area as a researcher: she was a student in the famous Meyerhoff Scholars Program at UMBC, then did her PhD at Carolina, and then moved to the National Institutes of Health.

At the NIH, Corbett was scientific lead of the Vaccine Research Center's COVID-19 team that developed mRNA-based vaccines by making use of the Cryo-EM structure and her and colleague's previous work on MERS virus to design an mRNA vaccine rapidly. Corbett and colleagues discovered that the mRNA vaccines worked in mice and in primates, leading to the now-famous Moderna and Pfizer vaccines that have transformed the pandemic.

December 2020: The efficacy of the Moderna (see p. 30) and Pfizer (see p. 58) mRNA vaccines was shockingly good! Whew!

Now she's a professor at Harvard, running a lab that studies vaccines and the immune system, to inform the development of new vaccines including (fingers crossed) a vaccine that might work against all SARS-COV-2 variants. She's active on Twitter, which has given people an almost-live, inside view of what must be a fascinating path.

Here's a general-interest interview with then-NIH chief Francis Collins...

... and I recommend especially another interview that spans from her initial interest in science to some more in-depth virology:

 

Try your hand at some simple bioinformatics

You can try some simple bioinformatics yourself if you like. Here are two things to try:

 

(1) Get a gene sequence and see what predictions can be made from it. I recommend starting by thinking of a protein or gene of interest — find a disease gene in a news article for example. Then get the protein sequence. You can find sequences here -- type in the name of any protein or gene (here for example is a resident ER protein, i.e. a protein that stays in the ER). Click on a specific protein's name and the sequence will be at the bottom of the next page. Click "FASTA" near the top of this page to get the sequence in a simpler format, and copy and paste that sequence into any of the programs below to try them out.

To start with, you might try a program that can predict the arrangement of transmembrane proteins based on sequence. The program, described in more detail than most people will want to see here, uses rules deduced by biologists, and was then fine-tuned with an artificial intelligence algorithm, training the program using transmembrane proteins with known orientations.  There is a similar program that can predict where in a cell a protein will end up.  

Then you can try other predictions that can be made based solely on sequence by searching online for other predictor tools.

(2) See how little a well-conserved protein has changed through evolution. Let's look at the current versions of beta-tubulin from yeast and human, and see how similar they are. Try this: copy the text of the yeast beta-tubulin sequence from here (from MREI... to the end of the protein's sequence), then paste it into the Enter Query Sequence box here, and next to Organism, type "human" and then select human from the dropdown menu that appears (2nd or 3rd one down - 'human' or 'humans'). Then click BLAST at the bottom. The page will automatically update for seconds or minutes, depending on how busy servers are. When it's done, you'll see the results in a section headed "Sequences producing significant alignments". Click on the top link ("... tubulin.... [Homo sapiens]") in that long list of links. Now you'll see the sequence you queried (the yeast beta-tubulin) and the subject sequence - the closest protein sequence that it found among all known human proteins. In between is a list of identical amino acids, and + signs for similar amino acids. Tubulin, actin, and histones are remarkably well conserved proteins. If you try the exercise with other kinds of proteins, you'll see that only parts of them are well conserved across diverse organisms, or that some don't exist in certain organisms.

More about Bioinformatics at Wikipedia.

(image: a 7-transmembrane protein from Wikimedia Commons)

Cystic fibrosis and drug development

Trikafta is a 3-part drug that helps deltaF508 cystic fibrosis patients. Trikafta was approved by the FDA in 2019 based on studies testing efficacy and safety [1],[2]. The figure below illustrates mechanisms of action for a previous 2-part drug and the new 3-part drug. 

 Bad news though: the new drug costs more than $300,000 per year (so research on more cost-effective solutions is critically important). Developing drugs like these costs a lot, and drug companies need to recoup costs and make a profit to justify investing in possible new drugs, so the FDA gives companies a 5-7 year monopoly when a drug is developed, before generic versions of drugs can be sold. The complex issues involved are covered well, I think, here.

You can find info about cystic fibrosis from the NIH, and current clinical trials here.

Here's an old but really interesting article about Cystic Fibrosis, and a source for up-to-date information on the disease and its effects on patients.

Nobel Prizes

UNC's Aziz Sancar on a Turkish postage stamp

The Nobel Prize web site has great, clear explanations of the important discoveries that have been recognized with the award, along with the key experiments that led to these discoveries. The newest ones have both introductory and advanced explanations as pdf files. 

The Nobel Prizes are announced each October. Most of the ones below were awarded for discoveries that we're discussing in class.

• 1974: George Palade and the secretory process
• 1986: Cell-cell signaling by growth factors 

• 

  location to get your selfie!
  

  
  

  1992: Reversible protein phosphorylation as a biological switch 
• 1997: Certain proteins (prions) can act as infectious agents 
• 1999: Discovery of signal sequences for protein sorting 
• 2001: The cell cycle
  
• 2007: Oliver Smithies at UNC! (Oliver passed away in 2017, but his spouse – also a scientist – uses his old Nobel parking space on campus).
• 2008: GFP
• 2012: G protein-coupled receptors in cell communication
• 2014: Super-resolution microscopy
• 2015: UNC's Aziz Sancar for DNA repair mechanisms! Go Heels!
• 2017: CryoEM
• 2020: CRISPR 

Charpentier and Doudna, from a great video about their work on CRISPR and their 2020 Nobel Prize.

Turning a molecular wheel with a flow of protons

(image source)

A scientist's story of first hearing Peter Mitchell's proposal that a concentration gradient of protons was the energy source for ATP synthase. I recommend reading this starting in the middle, with "In 1955..." (highlighted, second sentence of the 3rd paragraph) and then looping back to the beginning of the article afterwards.

"I remember thinking... that I would bet anything that ATP synthesis didn’t work that way."

Mitchell was an unusual scientist:

"For much of his career he worked in his own lab in a... house... his research funded in part by a herd of dairy cows." (source)

In this video, see how ATP synthase works with key molecular details gained in part from solving protein structures in different states (ATP-bound, ADP-bound states etc) mostly from John Walker's lab in Cambridge, England. Walker shared the Nobel Prize for deciphering the structure of ATP synthase.

 

* EVERYTHING ABOVE WAS POSTED AFTER THE 1ST EXAM *

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How many diseases are linked to specific genes?

(image credit)

How many diseases have genes associated with their malfunctions? Check back on the links below and watch the numbers go up throughout the course!

• HERE is a periodically-updated list. As of 13 years ago (Jan 27, 2011), 2949 diseases were known with "Phenotype description, molecular basis known: Total". Today (Feb 1, 2024), it's 6784 diseases—an average increase of about a new one discovered per day!
• How many disease genes are there? See "Total number of genes with phenotype-causing mutation" here. As of Feb 1, 2024, it's 4876 genes.  

Identifying a gene associated with a disease can be a big step toward developing both diagnostics and treatments. What kinds of genes are being discovered now? HERE is a link to news stories on discoveries made in the past month. HERE's how they're discovered.

Sickle cell anemia

Learn more about sickle cell anemia, the most common inherited blood disorder in the US, at an NIH web site or the Sickle Cell Disease Association of America web site.

Here's a NY Times story about very-recently approved gene therapy that we discussed in class (for those interested in science writing, the author Gina Kolata is a great writer who tells engaging stories while reliably getting the science right, and she has several books out). Gene therapy is an important step forward, but sadly, as this story covers, the current cost of gene therapy makes it unavailable to many patients.

Here's an earlier 22-minute radio story about the first US patient whose bone marrow cells' genes were edited using CRISPR. 

Get an idea of what else is being tried right now toward cures or treatments for symptoms by seeing current clinical trials.

Brownian motion simulation

Try out this simulator to get an intuitive sense for how Brownian motion works. Slide the "energy" slider to the right to see what happens at higher temperatures. And be sure to "drag to see what's actually going on". Much of the theory here was worked out by Einstein. Here's a translated version of Einstein's original 1905 publication that began to explain what causes Brownian motion.

Dorothy Crowfoot Hodgkin

Read about Dorothy Crowfoot Hodgkin here, on Wikipedia, and in her biography. Here you can read a little detail about the exclusion of women in research discussions at the time.

(Image: British postage stamp honoring Hodgkin)

For those interested in gender bias in science journalism, here's a headline from when she won the Nobel Prize, and another, plus a newer checklist to help science journalists think clearly about whether their writing rehashes cliches about women in science at the expense of explaining the science and the scientist's achievements.

Breaking the resolution limit of light microscopy

A photo of the original PALM microscope in the living room where it was developed, and a story about this and related technologies. The Wikipedia page on Super-resolution Microscopy discusses PALM and several other tricks for breaking the diffraction limit.

"...that’s where we learned about photoactivatable fluorescent proteins.... it became obvious to Harald and me that this was the missing link for the idea that I had pitched after I left Bell: we could isolate a few molecules at a time by activating limited subsets of photoactivatable proteins. It seemed so easy."

"...We were both unemployed, but Harald had some of his equipment from Bell [Labs]..."

-from Betzig's Nobel speech

image credit: HHMI

 

Henrietta Lacks

Henrietta Lacks
(image credit)

Learn more about Henrietta Lacks starting at her Wikipedia page. Below, author Rebecca Skloot talks about her book about Henrietta Lacks and science writing more generally, and historian and filmmaker Henry Louis Gates talks about Henrietta Lacks and the history of medical consent and race.

About the book: "...the science end of this story is enough to blow one's mind... But what's truly remarkable... is that we also get the rest of the story, the part that could have easily remained hidden had she not spent ten years unearthing it: Who was Henrietta Lacks? How did she live? How she did die? Did her family know that she'd become, in some sense, immortal, and how did that affect them?" -Jad Abumrad (founder of the podcast Radiolab)

There's a movie too.

Our images from microscope-building day

Images uploaded so far are here.

Amazing images from microscopes

The Nikon Small World web site has some stunning images and videos.

Image: Growing tip of a red algae by UNC's own Dr. Nat Prunet. Go Heels!

Struggling with your grades? Fear not!

Watch the 45 seconds between 1:45 and 2:30 to see how Chemistry Nobel Laureate Marty Chalfie (of Green Fluorescent Protein fame) did in Chemistry classes in college.

 

Beautiful animation of a cell

This animation shown in class can be seen here:
https://www.youtube.com/watch?v=wJyUtbn0O5Y

Microns, nanometers, etc.

Powers of Ten, a classic Charles & Ray-Bernice Eames film on grasping the sizes of things from human scale out to the then-known universe, and back in to subatomic particles.

More images from Robert Hooke's Micrographia

Here's the whole book.

 Hooke's book begins with an apology to the King of England, for, well, discovering things.

 Hooke's methods for immobilizing some of the insects he observed were creative:

...I gave it a Gill of Brandy, or Spirit of Wine, which after a while e'en knock'd him down dead drunk, so that he became moveless...

Hooke's engraving of a head of a hoverfly, from Micrographia

My favorite of van Leeuwenhoek's letters, with a surprise ending

"Concerning the Worms in Sheeps Livers, Gnats, and Animalcula in the Excrements of Frogs" (van Leeuwenhoek, 1700)

In this letter, he describes finding microscopic life in frog poop. I especially like the surprise ending in the last 3 paragraphs – starting, "On the fifth day the Frog had dung'd again...." Scientific papers never end the way this one did.

Google Doodle from van Leeuwenhoek's 384th birthday

A popular book about cell biology

A great, vivid exploration of some fascinating topics in cell biology. See the "Read sample" button on the left side of this page to read parts of the book now. Also available as an audiobook.