The Xing lab published a research article in FEBS Letters

The Xing lab published a research article in FEBS Letters.


miRNAs serve as crucial post-transcriptional regulators in a variety of essential cell fate decisions. However, the contribution of the mRNA-miRNA mutual regulation to bistability is not fully understood. Here, we built a set of mathematical models of mRNA-miRNA interactions and systematically analyzed the sensitivity of the response curves under various conditions. Our findings indicate that mRNA-miRNA reciprocal regulation could manifest ultrasensitivity to subserve the generation of bistability when equipped with a positive feedback loop. We also find that the region of bistability is expanded by a stronger competing endogenous mRNA (ceRNA). Interestingly, bistability can be generated without a feedback loop if multiple miRNA binding sites exist on a target mRNA. Thus, we demonstrate the importance of simple mRNA-miRNA reciprocal regulation in cell fate decisions.

This article is protected by copyright. All rights reserved.

Tian X-J, Zhang H, Zhang J, Xing J (2016) Reciprocal Regulation Between mRNA and miRNA Enables a Bistable Switch That Directs Cell Fate Decisions FEBS Letters doi: 10.1002/1873-3468.12379.

Bing Liu’s Work Published in Science Signaling

“Crosstalk Between Toll-like Receptor Pathways”Bing figure
A collaboration between the Bahar lab, the Ding lab (National Singapore University), and the Thiagarajan lab (Harvard), led by Dr. Liu in the Bahar lab.

Toll-like receptors (TLRs) recognize pathogens and stimulate the innate immune response. Liu et al uncovers how the crosstalk between TLR pathways enables macrophages to fine-tune their responses to multiple infection events. In particular, macropahges can “memorize” the first pathogen attack and boost the immune response to subsequent attacks. The crosstalk also helps to avoid the harmful excessive inflammatory responses.

Clark and Chikina publish their study of Marine Mammal Evolution

Clark and Chikina publish their study of Marine Mammal Evolution in Molecular Biology and Evolution. One of the authors was their former TECBio REU student, Joe Robinson. Congrats to everyone!


Mammal species have made the transition to the marine environment several times, and their lineages represent one of the classical examples of convergent evolution in morphological and physiological traits. Nevertheless, the genetic mechanisms of their phenotypic transition are poorly understood, and investigations into convergence at the molecular level have been inconclusive. While past studies have searched for convergent changes at specific amino acid sites, we propose an alternative strategy to identify those genes that experienced convergent changes in their selective pressures, visible as changes in evolutionary rate specifically in the marine lineages. We present evidence of widespread convergence at the gene level by identifying parallel shifts in evolutionary rate during three independent episodes of mammalian adaptation to the marine environment. Hundreds of genes accelerated their evolutionary rates in all three marine mammal lineages during their transition to aquatic life. These marine-accelerated genes are highly enriched for pathways that control recognized functional adaptations in marine mammals, including muscle physiology, lipid-metabolism, sensory systems, and skin and connective tissue. The accelerations resulted from both adaptive evolution as seen in skin and lung genes, and loss of function as in gustatory and olfactory genes. In regard to sensory systems, this finding provides further evidence that reduced senses of taste and smell are ubiquitous in marine mammals. Our analysis demonstrates the feasibility of identifying genes underlying convergent organism-level characteristics on a genome-wide scale and without prior knowledge of adaptations, and provides a powerful approach for investigating the physiological functions of mammalian genes.

Maria Chikina, Joe Robinson, Nathan Clark. “Hundreds of genes experienced convergent shifts in selective pressure in marine mammals.” Molecular Biology and Evolution. 2016.

Dr. Robin Lee Receives R35

RobinDr. Lee’s grant proposal entitled “Deciphering dynamic signals in control of cell fate decisions”  has been selected to receive an R35 Outstanding Investigator ‘MIRA’ award from the NIGMS.


It is an emerging principle that dynamic properties of molecules within a signaling network, such as sub-cellular changes in protein localization or abundance, provide a temporal codes that mediate cellular responses to stimuli. How dynamic molecular signals relay, and process, information is a critical gap in our understanding of how healthy and diseased cells make decisions. Here we propose a hybrid experimental and computational framework to decipher dynamic signals induced by inflammatory factors in single cells, and understand how cells interpret these signals to decide between inflammation, proliferation, or cell death.

Congratulations, Robin!

Berg Named Editor-in-Chief of Science

BergCongratulations to Dr. Jeremy M. Berg for his appointment as Editor-in-Chief of Science!

Berg, Associate Senior Vice Chancellor for Science Strategy and Planning in the Health Sciences, who also holds positions as Pittsburgh Foundation Professor and Director of the Institute for Personalized Medicine, Professor of Computational and Systems Biology, and Professor of Chemistry at the University of Pittsburgh, will start his appointment on July 1, 2016. He will be the 20th Editor-in-Chief since the journal’s start in 1880 and will serve a 5-year term.

“I am thrilled and humbled by the opportunity to work with the team at Science and AAAS,” said Berg.

Berg will continue to hold his roles at the University. Dr. Arthur S. Levine said, “Dr. Berg is one of the nation’s leading scientists, with many landmark achievements in biomedical research, a broad and deep sense of all of the sciences, and a profound interest in science policy and the dynamics of the scientific community. I am proud indeed that Dr. Berg has been given this rare recognition, and especially proud that he is, and will remain, a member of our faculty.”

AAAS announcement
Pitt annoucement