Post-transcriptional gene regulation in vertebrates

We are passionate about understanding how genes are regulated and how that regulation can impact development or affect human diseases. We seek to understand what dictates the stability and the level of translation of messenger RNA (mRNA) in vertebrates.

Lab Mates

Ariel Bazzini

Assistant Investigator
Hometown
Buenos Aires, Argentina

Research interests
I am fascinated about gene regulation and how mis-regulation can affect normal development or cause human diseases.

Hobbies
Playing futbol, soccer or football, depending where are you coming from!

Qiushuang Wu (Q)

Predoctoral Researcher

Hometown
Xiangyang, China

Research interests

Q has strong interest in molecular biology, especially for post-transcriptional gene expression regulation in vertebrates. For her PhD, she studies codon optimality to regulate mRNA stability and also downstream open reading frames (dORF) to regulate translation efficiency.

Hobby
cooking

Santiago Medina

Bioinformatics Technician
Hometown
Guanajuato, Mexico

Research interests
I am interested in understanding how the regulatory information is encoded in codons to affect gene expression. I am passionate about computational biology and statistics.

Hobbies
I enjoy reading, biking, and horseback riding.

Webpage
https://santiagogmedina.com/about/

Luciana Castellano

Predoctoral Researcher 
Hometown
Buenos Aires, Argentina

Research interests
I am passionate about cell biology. I love studying the mechanisms that regulate gene expression and cell fate specification. In particular, I am truly intrigued by how viruses can impact host gene regulation and which factors orchestrate this phenomenon.

Hobbies
I enjoy playing different sports, such as volleyball, field hockey and tennis. I love dancing too! In my free time, I also enjoy chatting with friends while sharing some mate (traditional Argentinian drink).

Michelle DeVore

Predoctoral Researcher
Hometown
Ellicott, Colorado

Research interests
A single cell contains an extraordinary amount of ever-changing  information. I am interested in trying to understand more about how cells maintain their individual identities and functions within an organism, and how mismanagement of even the smallest piece of that information can result in disease. 

Hobbies
I love spending time with and learning about animals, gardening, creating art, reading, and being in nature. 

Michay Diez

(soon to be) Predoctoral Researcher
Hometown
Ituzaingó, Buenos Aires, Argentina

Research interests
I am focused on employing biochemistry, proteomics, and molecular biology to understand the role of novel post-transcriptional regulators in human disease, with the hope of finding new therapeutic targets.

Hobbies
Reading suspense novels, baking Argentinian pastries, and dancing tango.

Gopal Kushawah

Postdoctoral Research Associate
Hometown
Uttar Pradesh, India

Research interest
I am interested in the noncoding genome, how with increase in the complexity of the organism the content of noncoding genome increases. Even during the early embryonic development, how the noncoding regions of the genes regulate the fate of the early embryo development. Now with the advent of CRISPR-Cas system it has become more fascinating to understand the role of such sequences both at DNA and RNA levels. Recently we have developed CRISPR-Cas13d tool for higher vertebrate models.  Using CRISPR-Cas13d, one can target different kinds of RNA in the genome and decipher the complex regulatory lexicon of early embryonic development in higher vertebrate systems.  

Hobbies
Playing cricket, volleyball, cooking, watching sci-fi movies.

Gabriel da Silva Pescador

Predoctoral Researcher
Hometown
Florianópolis, SC, Brazil

Research interests
I am fascinated by developmental biology and understanding how a single cell becomes a full developed embryo. During my undergraduate and master studies I focused on how neural crest cells differentiate into skin pigmented cells. Nowadays, I am interested in understanding how embryos regulate cell differentiation and promote tissue specificity

Hobbies
I enjoy reading and playing soccer.

Danielson B. Amaral (Dany)

Predoctoral Researcher
Hometown
Cametá, PA, Brazil

Research interests
I have an ever growing passion for Biology since elementary school, exploring ideas and testing hypothesis is exciting! For my PhD I’m very interested in investigating the mechanisms that regulate mRNA degradation rate, both normally and in aberrant molecules, how they affect gene expression, embryo development and their role in evolution.

Hobbies
I enjoy outdoors activities, camping and swimming in rivers/lakes. While at home I like having friends over, watching anime, reading manga and playing online survivor games.

Open Positions

We are always looking for talented scientists (Post-docs, students and technicians) who want to work collaboratively to find the next discovery in RNA. If you are interested in gene regulation, development, computational biology, or molecular biology, send us a very short (half a page) summary of your interest, why you want to work with us, and your resume.

Ariel Bazzini
arb@stowers.org

Publications

Translation of small downstream ORFs enhances translation of canonical main open reading frames
Wu Q, Wright M, Gogol MM, Bradford WD, Zhang N, Bazzini AA. The EMBO Journal (Accepted).

CRISPR-Cas13d induces efficient mRNA knock-down in animal embryos
Kushawah G, Hernandez-Huertas L, Abugattas-Nuñez del Prado J, Martinez-Morales JR, DeVore ML, Hassan H, Moreno-SanchezI, Tomas-Gallardo L, Diaz-Moscoso A, Monges DE, Guelfo JR, Theune WC, Brannan E, Wang W, Corbin TJ, Moran AM, Sánchez Alvarado A, Málaga-Trillo E, Takacs CM, Bazzini AA, Moreno-Mateos MA.Dev Cell (Accepted).

Translation affects mRNA stability in a codon-dependent manner in human cells.
Wu Q, Medina SG, Kushawah G, DeVore ML, Castellano LA, Hand JM, Wright M, Bazzini AA. Elife. 2019 Apr 23;8. pii: e45396. doi: 10.7554/eLife.45396.

Brd4 and P300 Confer Transcriptional Competency during Zygotic Genome Activation.
Chan SH, Tang Y, Miao L, Darwich-Codore H, Vejnar CE, Beaudoin JD, Musaev D, Fernandez JP, Benitez MDJ, Bazzini AA, Moreno-Mateos MA, Giraldez AJ. Dev Cell. 2019 Jun 17;49(6):867-881.e8. doi: 10.1016/j.devcel.2019.05.037.

Poly(A) tails: longer is not always better.
Castellano LA, Bazzini AA. Nat Struct Mol Biol. 2017 Dec 7;24(12):1010-1011.

Systems to study codon effect on post-transcriptional regulation of gene expression
Wu Q, Bazzini AA. Methods. 2017 Nov 21; pii: S1046-2023(17)30272-4.

When LIN41 Comes to a Fork in the Road, It Takes BOTH Paths: Translational Repression OR mRNA Decay, Depending on the Target Site Position
Hand JM1, Bazzini AA. Mol Cell. 2017 Feb 2;65(3):375-377.

Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
Bazzini AA, Del Viso F, Moreno-Mateos MA, Johnstone TG, Vejnar CE, Qin Y, Yao J, Khokha MK, Giraldez AJ. The EMBO Journal 2016;35:2087-2103.

Optimized CRISPR-Cas9 System for Genome Editing in Zebrafish
Vejnar CE, Moreno-Mateos MA, Cifuentes D, Bazzini AA, Giraldez AJ. Cold Spring Harb Protoc. 2016;2016:pdb prot086850.

Upstream ORFs are prevalent translational repressors in vertebrates
Johnstone TG, Bazzini AA, Giraldez AJ. The EMBO Journal. 2016;35:706-723.

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation
Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ. The EMBO Journal. 2014;33:981-993.

Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition
Lee MT, Bonneau AR, Takacs CM, Bazzini AA, DiVito KR, Fleming ES, Giraldez AJ. Nature. 2013;503:360-364.

Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish
Bazzini AA, Lee MT, Giraldez AJ. Science. 2012;336:233-237.

MicroRNAs sculpt gene expression in embryonic development: new insights from plants
Bazzini AA, Giraldez AJ.  Developmental Cell. 2011;20:3-4.

Infection and coaccumulation of tobacco mosaic virus proteins alter microRNA levels, correlating with symptom and plant development
Bazzini AA, Hopp HE, Beachy RN, Asurmendi S.  Proceedings of the National Academy of Sciences of the United States of America. 2007;104:12157-12162.

News

March 2020
Q Friday Science Club
Q presented a wonderful presentation on her research on dORFs at the Friday Science Club at Stowers Institute. We all celebrated her achievement at the reception following.
February 2020
Dany Rotation Lunch
The end to a fantastic rotation with Dany called for a group lunch in the Stowers café.
August 2019
Q's Birthday
We celebrated Q’s birthday with fun desserts and cake.
July 2019
Luli's Birthday
Luli celebrated her first birthday as a PhD student.

The Institute

The Stowers Institute for Medical Research is a non-profit, basic biomedical research organization dedicated to improving human health by studying the fundamental processes of life. Researchers at Stowers aim to understand genetic programs and molecular mechanisms that underlie biological development, health, and disease. Discoveries resulting from this type of foundational research frequently prove to be major milestones along the path toward advances in medicine and human health, including novel therapies and cures. Jim Stowers Jr., founder of American Century Investments, and his wife, Virginia, opened the Institute in 2000. Currently, the Institute is home to about 500 researchers and support personnel, more than 20 independent research programs, and more than a dozen scientific support teams and facilities.

Living in Kansas City

From plains settlers and Civil War battles to jazz clubs and the Negro League, Kansas City has grown into a diverse and vibrant city. It is rich with live music, theater, museums and professional sports, with free public transportation downtown. The restaurants range from fine dining to farm-to-table, with an emphasis on Kansas City barbecue. For weekend fun, choose from amusement parks, pickleball courts, and the nation’s first outdoor shopping district. With all of these benefits, it might not come as big surprise that Kansas City made it onto National Geographic’s list of Best Trips 2019 worldwide. Add in excellent area schools, an affordable cost of living, and easy travel to either coast, it’s clear there is something for everyone in Kansas City, Missouri.

Arts

The Kauffman Center for the Performing Arts was designed by Moshe Safdie whose works are known for their dramatic curves and arrays of simple geometric patterns. The Kansas City Ballet, the Lyric Opera of Kansas City, and the Kansas City Symphony each share space in the architecturally distinctive building that graces the downtown skyline.

Minutes from the performing arts center is the Crossroads Arts District. It is home to an eclectic mix of shops, studios, galleries, and boutiques. Local artists and designers converged to create a diverse arts community offering everything from furniture, flowers, chocolates, and baked goods to watercolors, oils, photographs and glass and metal sculptures. The Crossroads Arts District hosts monthly events dubbed First Fridays and Second Saturdays that open the area to visitors in a street fair-like atmosphere.

Located in the heart of Kansas City, the Nelson Atkins Museum of Art stands as a monolith of limestone in a beautifully manicured landscape of gardens. A recent modern addition to the building strikingly reflects the contrast of new architecture to old. The Nelson houses a world-class permanent collection of art and regularly features special exhibitions. The Kemper Museum of Contemporary Art and the Kansas City Art Institute are both situated within blocks of the Nelson. All three offer workshops and art classes for children and adults.

Included in the diverse arts abounding in Kansas City is the Jazz District. This district is anchored by the American Jazz Museum and the Negro Leagues Baseball Museum. Live jazz entertainment, reminiscent of the days when Charlie Parker, John Coltrane, or Count Basie played here, is available almost nightly in either the Blue Room or the Gem Theater.

Sports

The Kansas City area is the proud home to multiple professional athletic clubs including the Kansas City Chiefs football team, the Kansas City Royals baseball team, the Sporting Kansas City soccer team and the Missouri Mavericks hockey team. Both the Chiefs and the Royals are housed in recently renovated, state-of-the-art stadiums with arguably the best fan base in the country. Sporting Kansas City inaugurated its new soccer stadium, Children's Mercy Park, in June of 2011.

Next door to Children's Mercy Park are the Kansas Speedway and the Community America Ballpark, where the American Association baseball team, the Kansas City T-Bones plays. The Speedway hosts both NASCAR and Indy Car Races. A single NASCAR event at the Speedway can draw a stunning crowd of over 120,000 people.

In addition to multiple professional sports, Kansas City is a hot bed for college sports. With several Big 12 Conference colleges located within a few hours either side of the city, rivalries abound. The basketball competition culminates at the NCAA Big 12 Tournament at the Kansas City based Sprint Center. Connected to the Sprint Center is the College Basketball Experience, a total immersion entertainment adventure into the sport of men’s college basketball, and the National Collegiate Basketball Hall of Fame.

Professional golfer and Kansas Citian, Tom Watson, hosts a charity golf tournament that brings the largest names in golf to Kansas City every year: Arnold Palmer, Jack Nicklaus, Phil Mickelson are just a few of the many. Golfers can choose from over 45 public courses and numerous private courses including The National Golf Club designed by legendary golfer Tom Watson.

Recreation

Whether your interests are geared to the outdoors or indoors, you will find something in Kansas City to suit you. For thrill seekers, there is the World’s of Fun Amusement Park with a roller coaster touting a daring 205-foot drop. There are two outdoor and two indoor water-amusement parks.

The Kansas City Zoo encompasses over 200 acres of land with more than 1000 animals on exhibit. But, that doesn’t compare with the Powell Gardens’ 915 acres of garden displays. This botanical garden was designed to “embrace the Midwest spirit” with its gardens and gently flowing meadows.

Multiple area lakes offer summer opportunities for boating, sailing and skiing. The Missouri River serves as a base for multiple river boat casinos moored within city limits. In addition to being a gambler’s paradise, they house a variety of restaurants and concert venues.

Other concerts, plays and Broadway style shows are available through multiple theaters and stages. The Midland and The Folly Theaters both feature early 1900’s architecture.  The Midland caters to the concert scene, while The Folly is geared more toward the fine arts. The Coterie Theater is specifically oriented to families and young audiences and is nationally rated as one of the top 5 theaters in this category. Outdoor summertime productions are offered at the Starlight Theater and Providence Medical Center/Sandstone Amphitheater.

Kansas City’s past meets with its present each October during the American Royal horse show and rodeo. Originally a small livestock show, the event has grown to include a horse and livestock show, professional and youth rodeo, entertainment events with some of country music’s top performers and a top-ranked barbecue contest.

Foods

Barbecue may be synonymous with Kansas City but there is much more to the local food scene than just ribs and burnt ends. Kansas City’s Boulevard Brewery is the largest specialty brewer in the Midwest producing about 600,000 barrels of beer a year. One of the best selling seasonal beers is the Chocolate Ale, designed in conjunction with local chocolatier, Christopher Elbow.

Christopher Elbow Artisanal Chocolates mixes chocolate with a variety of other flavors such as lavender, grapefruit, chili, and elderflower to create a small work of edible art.  The chocolatier gained national acclaim when Oprah Winfrey named his chocolates one of her “Favorite Things”.

And again, it wouldn’t be Kansas City without barbeque. Gates and Sons, Arthur Bryant’s, Fiorella’s Jack Stack, Joe’s Kansas City, BB’s Lawnside, Danny Edward’s, Winslow’s, Hayward’s, and Smokestack—just to name a few of the local joints. The typical long and slow smoking process and the prolific use of sauce rather than dry rub has attracted a loyal following: The Kansas City Barbecue Society boasts over 20,000 members worldwide.

But if barbecue is not your style you will still find a big variety of restaurants and specialty shops offering everything from burgers to sushi to foie gras to tapas.

Schools

The Kansas City metropolitan area spans two states and covers 7952 square miles.  41 school districts provide services in that area. There are multiple urban, suburban, private, parochial, and charter schools from which to choose. Since 1992, 70 local schools have been awarded the Department of Education’s prestigious Blue Ribbon School Award.  This award recognizes both high performing schools and schools that have significantly improved student achievement.

Based on 2010 SAT scores both Kansas and Missouri scored an average of 595 on the math section of the exam.  The national average for that section is 516—both states beating that average by 79 points.

There are 34 colleges, universities and technical schools in the area.  They include both University of Missouri-Kansas City and University of Kansas Medical School. Smaller distinguished schools include Rockhurst University and William Jewell College, both ranked well by the US News and World Report College rankings.

Economy

Kansas City has an important and influential economy that impacts the entire region. The centrally located city is well suited to accommodate a large manufacturing base and is home to one of the country’s biggest foreign trade zones. Both benefit from an expansive rail network. It is home to several Fortune 500 and 1000 companies and is the headquarters to more than 47 companies and organizations. Major employers include Garmin, Hallmark Cards, General Motors, Ford, Honeywell, Citigroup and American Century Investments.

A low cost of living allows Kansas City to be consistently ranked as one of the most affordable major markets to live and work aided by a strong transportation network and low energy costs. While the national housing market is unsteady, Kansas City’s market has remained relatively unmarred.

Contact

BAZZINI LAB

816-926-4113

Dr. Ariel Bazzini
arb@stowers.org

Stowers Institute for Medical Research
1000 E 50th Street
Kansas City, Missouri 64110