Integrity of hereditary material—the genome —is critical for species survival. Genomes need protection from agents that can cause mutations affecting DNA coding, regulatory functions, and duplication during cell division. DNA sequences called transposons, or jumping genes (discovered by Carnegie’s Barbara McClintock,) can multiply and randomly jump around the genome and cause mutations. About half of the sequence of the human and mouse genomes is derived from these mobile elements.  RNA interference (RNAi, codiscovered by Carnegie’s Andy Fire) and related processes are central to transposon control, particularly in egg and sperm precursor cells.  

The Bortvin lab, with colleagues, identified a key protein that suppresses jumping genes in mouse sperm and found that the protein is vital to sperm formation. It had been known previously that a similar element did this in the fruit fly. The protein, called Maelstrom, is old evolutionarily and found in many organisms. It is implicated in transposon silencing in flies and mice by means of specialized small RNAs known as Piwi-interacting RNAs (or piRNAs).  

Bortvin’s group showed the critical role of transposon silencing for normal fertility of male mice. But only recently did they discover the impact of transposons on the mammalian egg precursor.  The group found that mouse oocytes repress transposons inefficiently. Because of this poor transposon silencing, every oocyte stores this potent mutagen. Safia Malki in the lab correlated transposon abundance with oocyte viability and oocyte cell division reliability. She found that a burst of activity of a single transposon in transgenic mice increased oocyte death. Most strikingly, Malki improved oocyte viability and prevented errors in chromosome segregation by blocking the ability of the transposon to copy itself using a drug that blocks multiplication of HIV, the AIDS-causing virus.


This unique mode of transposon control in mouse oocytes sheds light on two puzzles—prenatal death of most oocytes and the age-related increase in chromosome errors, such as those that cause Down syndrome. Malki and Bortvin speculate that the lax control of transposons in mice, and perhaps human oocytes, causes the elimination of oocytes with either highly active transposons or those incapable of more stringent transposon control.

The surviving oocytes may prevent excessive transposon alterations to the genomes and be better suited to support the healthy development of the next generation. The Malki and Bortvin findings also suggest that an ovary of a newborn girl already contains “good” oocytes as well as those predisposed for chromosomal errors. It may be the case that “good” oocytes are ovulated during first two decades of a female’s reproductive life, while “bad” ones are ovulated later.

Bortvin received his Ph. D. in genetics from Harvard and was a postdoctoral fellow at the Whitehead Institute before joining the Carnegie staff in 2004. For more information see Bortvin lab


Explore Carnegie Science

This image shows an example of defects in the development of the embryonic central nervous system in stored eggs that lacked the Fmr1 gene.
August 15, 2018

Baltimore, MD—New work from Carnegie’s Ethan Greenblatt and Allan Spradling reveals that the genetic factors underlying fragile X syndrome, and potentially other autism-related disorders, stem from defects in the cell’s ability to create unusually large protein structures. Their findings are published in Science.

Their research focuses on a gene called Fmr1. Mutations in this gene create problems in the brain as well as the reproductive system. They can lead to the most-common form of inherited autism, fragile X syndrome, as well as to premature ovarian failure.

It was already thought that Fmr1 plays a pivotal part in the last stages of the process by which the recipe

July 26, 2018

Baltimore MD—Almost half of our DNA sequences are made up of jumping genes—also known as transposons. They jump around the genome in developing sperm and egg cells and are important to evolution. But their mobilization can also cause new mutations that lead to diseases, such as hemophilia and cancer. Remarkably little is known about when and where their movements occur in developing reproductive cells, the key process that ensures their propagation in future generations, but can lead to genetic disorders for the hosts.

To address this problem, a team* of Carnegie researchers developed new techniques to track the mobilization of jumping genes. They found that during a particular

June 28, 2018

Baltimore, MD—A tremendous amount of genetic material must be packed into the nucleus of every cell—a tiny compartment. One of the biggest challenges in biology is to understand how certain regions of this highly packaged DNA can be called upon, so that the genes encoded in them can be “turned on,” or expressed and used to manufacture RNA and proteins.

New work published in Molecular Cell by a team of biologists from Carnegie, Soonchunhyang University, and Johns Hopkins University has shed light on this process and their findings have implications for certain age-related diseases and organ decay.

The nucleus, where a cell’s DNA is housed, is surrounded by two membrane

May 7, 2018

Baltimore, MD—Allan C. Spradling, Director Emeritus of Carnegie’s Department of Embryology, has been awarded the 23rd March of Dimes and Richard B. Johnson, Jr., MD Prize in Developmental Biology as “an outstanding scientist who has profoundly advanced the science that underlies our understanding of prenatal development and pregnancy.”

Department director and Carnegie co-interim president Yixian Zheng remarked, “Allan is a legend in developmental biology. We are all delighted by this well- deserved recognition of Allan’s groundbreaking research.”

Spradling’s decades of scientific accomplishments cover a broad spectrum of advancements. Since the early 20th century, the fruit

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The Zheng lab studies cell division including the study of stem cells, genome organization, and lineage specification. They study the mechanism of genome organization in development, homeostasis—metabolic balance-- and aging; and the influence of cell morphogenesis, or cell shape and steructure,  on cell fate decisions. They use a wide range of tools and systems, including genetics in model organisms, cell culture, biochemistry, proteomics, and genomics.


The Spradling laboratory studies the biology of reproduction. By unknown means eggs reset the normally irreversible processes of differentiation and aging. The fruit fly Drosophila provides a favorable multicellular system for molecular genetic studies. The lab focuses on several aspects of egg development, called oogenesis, which promises to provide insight into the rejuvenation of the nucleus and surrounding cytoplasm. By studying ovarian stem cells, they are learning how cells maintain an undifferentiated state and how cell production is regulated by microenvironments known as niches. They are  also re-investigating the role of steroid and prostaglandin hormones in controlling the

Stem cells make headline news as potential treatments for a variety of diseases. But undertstanding the nuts and bolts of how they develop from an undifferentiated cell  that gives rise to cells that are specialized such as organs, or bones, and the nervous system, is not well understood. 

The Lepper lab studies the mechanics of these processes. overturned previous research that identified critical genes for making muscle stem cells. It turns out that the genes that make muscle stem cells in the embryo are surprisingly not needed in adult muscle stem cells to regenerate muscles after injury. The finding challenges the current course of research into muscular dystrophy, muscle

The Marnie Halpern laboratory studies how left-right differences arise in the developing brain and discovers the genes that control this asymmetry. Using the tiny zebrafish, Danio rerio, they explores how regional specializations occur within the neural tube, the embryonic tissue that develops into the brain and spinal cord.

The zebrafish is ideal for these studies because its basic body plan is set within 24 hours of fertilization. By day five, young larvae are able to feed and swim, and within three months they are ready to reproduce. They are also prolific breeders. Most importantly the embryos are transparent, allowing scientists to watch the nervous system develop and to

The Ludington lab investigates complex ecological dynamics from microbial community interactions using the fruit fly  Drosophila melanogaster. The fruit fly gut carries numerous microbial species, which can be cultured in the lab. The goal is to understand the gut ecology and how it relates to host health, among other questions, by taking advantage of the fast time-scale and ease of studying the fruit fly in controlled experiments. 

Nick Konidaris is a staff scientist at the Carnegie Observatories and Instrument Lead for the SDSS-V Local Volume Mapper (LVM). He works on a broad range of new optical instrumentation projects in astronomy and remote sensing. Nick's projects range from experimental to large workhorse facilities. On the experimental side, he recently began working on a new development platform for the 40-inch Swope telescope at Carnegie's Las Campanas Observatory that will be used to explore and understand the explosive universe.

 Nick and his colleagues at the Department of Global Ecology are leveraging the work on Swope to develop a new airborne spectrograph that will be used to provide a direct

Experimental petrologist Michael Walter became director of the Geophysical Laboratory beginning April 1, 2018. His recent research has focused on the period early in Earth’s history, shortly after the planet accreted from the cloud of gas and dust surrounding our young Sun, when the mantle and the core first separated into distinct layers. Current topics of investigation also include the structure and properties of various compounds under the extreme pressures and temperatures found deep inside the planet, and information about the pressure, temperature, and chemical conditions of the mantle that can be gleaned from mineral impurities preserved inside diamonds.

Walter had been at

Guoyin Shen's research interests lie in the quest to establish and to examine models for explaining and controlling the behavior of materials under extreme conditions. His research activities include investigation of phase transformations and melting lines in molecular solids, oxides and metals; polyamorphism in liquids and amorphous materials; new states of matter and their emergent properties under extreme conditions; and the development of enabling high-pressure synchrotron techniques for advancing compression science. 

He obtained a Ph.D. in mineral physics from Uppsala University, Sweden in 1994 and a B.S. in geochemistry from Zhejiang University, China in 1982. For more