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May 26

Congratulations Professor Byrne!

Very exciting news--postdoc Alex Byrne has accepted a faculty position in the Department of Neurobiology at UMass Medical School!! The Byrne lab will open this fall.

May 23

Huma Graduates!

Incredible undergrad Huma Baig graduated from Yale today. Huma graduated Cum Laude and with distinction in both of her majors, Latin American Studies and MCDB. She won the Edgar J. Boell Prize for the top senior in the MCDB major, based on her research in our lab. She also won a prize for the best senior thesis in the department of Latin American Studies. And she won an award for her civic contributions to her residential college community. Huma is currently working full time in the lab before heading to Brazil in September to study infectious disease.

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May 2

Welcome Alex Schulz and Chen Ding!!!

New postdoc Alex Schulz and new grad student Chen Ding start today.

April 29

Goodbye Ben!!!

Awesome undergrad Ben Meyer is off to medical school at Emory, with a prestigious Woodruff Fellowship. Go Ben!

April 18

Goodbye Sara!!!

Amazing grad student and postdoc Sara Kosmaczewski is starting a new phase in her scientific career with a postdoc at the Broad Institute in the Lindy Barrett lab. Look for great things to follow!

March 17

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February 26

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June 23

Our paper, "RNA ligation in neurons by RtcB inhibits axon regeneration", published in PNAS PDF

Activity of the RNA ligase RtcB has only two known functions: tRNA ligation after intron removal and XBP1 mRNA ligation during activation of the unfolded protein response. Here, we show that RtcB acts in neurons to inhibit axon regeneration after nerve injury. This function of RtcB is independent of its basal activities in tRNA ligation and the unfolded protein response. Furthermore, inhibition of axon regeneration is independent of the RtcB cofactor archease. Finally, RtcB is enriched at axon termini after nerve injury. Our data indicate that neurons have co-opted an ancient RNA modification mechanism to regulate specific and dynamic functions and identify neuronal RtcB activity as a critical regulator of neuronal growth potential.

March 18

Welcome new graduate students Alex Lin-Moore, Xiao Liu, and Alison Kochersberger!!


November 3

Our paper, "The RtcB RNA ligase is an essential component of the metazoan unfolded protein response", published in EMBO Reports PDF

RNA ligation can regulate RNA function by altering RNA sequence, structure and coding potential. For example, the function of XBP1 in mediating the unfolded protein response requires RNA ligation, as does the maturation of some tRNAs. Here, we describe a novel in vivo model in Caenorhabditis elegans for the conserved RNA ligase RtcB and show that RtcB ligates the xbp-1 mRNA during the IRE-1 branch of the unfolded protein response. Without RtcB, protein stress results in the accumulation of unligated xbp-1 mRNA fragments, defects in the unfolded protein response, and decreased lifespan. RtcB also ligates endogenous pre-tRNA halves, and RtcB mutants have defects in growth and lifespan that can be bypassed by expression of pre-spliced tRNAs. In addition, animals that lack RtcB have defects that are independent of tRNA maturation and the unfolded protein response. Thus, RNA ligation by RtcB is required for the function of multiple endogenous target RNAs including both xbp-1 and tRNAs. RtcB is uniquely capable of performing these ligation functions, and RNA ligation by RtcB mediates multiple essential processes in vivo.

August 2

Another great summer at the MBL Neurobiology course!

Thanks to Prahatha and Michael!

July 7

Our paper, "Syndecan Promotes Axon Regeneration by Stabilizing Growth Cone Migration", published in Cell Reports link

Growth cones facilitate the repair of nervous system damage by providing the driving force for axon regeneration. Using single-neuron laser axotomy and in vivo time-lapse imaging, we show that syndecan, a heparan sulfate (HS) proteoglycan, is required for growth cone function during axon regeneration in C. elegans. In the absence of syndecan, regenerating growth cones form but are unstable and collapse, decreasing the effective growth rate and impeding regrowth to target cells. We provide evidence that syndecan has two distinct functions during axon regeneration: (1) a canonical function in axon guidance that requires expression outside the nervous system and depends on HS chains and (2) an intrinsic function in growth cone stabilization that is mediated by the syndecan core protein, independently of HS. Thus, syndecan is a regulator of a critical choke point in nervous system repair.

April 29

Our review (with Yishi Jin), Axon Regeneration in C. elegans, published in Current Opinion in Neurobiology PDF

Single axon transection by laser surgery has made Caenorhabditis elegans a new model for axon regeneration. Multiple conserved molecular signaling modules have been discovered through powerful genetic screening. In vivo imaging with single cell and axon resolution has revealed unprecedented cellular dynamics in regenerating axons. Information from C. elegans has greatly expanded our knowledge of the molecular and cellular mechanisms of axon regeneration.

March 14

Really nice review of our paper on aging and regeneration, by Zhigang He and colleagues, published in Cell Metabolism PDF

Axon regeneration capacity often declines with age. One might assume that loss of regeneration is an obvious consequence of organismal aging. However, in the latest issue of Neuron, Byrne et al. (2014) demonstrate that regeneration ability and aging are regulated cell-autonomously within neurons, and can be decoupled.

January 17

Our paper, "Insulin/IGF1 Signaling Inhibits Age-Dependent Axon Regeneration", published in Neuron PDF

The ability of injured axons to regenerate declines with age, yet the mechanisms that regulate axon regeneration in response to age are not known. Here we show that axon regeneration in aging C. elegans motor neurons is inhibited by the conserved insulin/IGF1 receptor DAF-2. DAF-2’s function in regeneration is mediated by intrinsic neuronal activity of the forkhead transcription factor DAF-16/FOXO. DAF-16 regulates regeneration independently of lifespan, indicating that neuronal aging is an intrinsic, neuron-specific, and genetically regulated process. In addition, we found that DAF-18/ PTEN inhibits regeneration independently of age and FOXO signaling via the TOR pathway. Finally, DLK-1, a conserved regulator of regeneration, is downregulated by insulin/IGF1 signaling, bound by DAF-16 in neurons, and required for both DAF-16- and DAF-18-mediated regeneration. Together, our data establish that insulin signaling specifically inhibits regeneration in aging adult neurons and that this mechanism is independent of PTEN and TOR.

January 9

Our paper, "Axon Regeneration Genes Identified by RNAi Screening in C. elegans", published in Journal of Neuroscience PDF

Axons of the mammalian CNS lose the ability to regenerate soon after development due to both an inhibitory CNS environment and the loss of cell-intrinsic factors necessary for regeneration. The complex molecular events required for robust regeneration of mature neurons are not fully understood, particularly in vivo. To identify genes affecting axon regeneration in Caenorhabditis elegans, we performed both an RNAi-based screen for defective motor axon regeneration in unc-70/beta-spectrin mutants and a candidate gene screen. From these screens, we identified at least 50 conserved genes with growth-promoting or growth-inhibiting functions. Through our analysis of mutants, we shed new light on certain aspects of regeneration, including the role of beta-spectrin and membrane dynamics, the antagonistic activity of MAP kinase signaling pathways, and the role of stress in promoting axon regeneration. Many gene candidates had not previously been associated with axon regeneration and implicate new pathways of interest for therapeutic intervention.


December 16

Chris defends his thesis! Congratulations, Dr. Firnhaber!

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December 10

Tyson defends his thesis! Congratulations, Dr. Edwards!

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November 7

Our paper, "Neuron-Specific Feeding RNAi in C. elegans and Its Use in a Screen for Essential Genes Required for GABA Neuron Function", published in PLoS Genetics PDF

Forward genetic screens are important tools for exploring the genetic requirements for neuronal function. However, conventional forward screens often have difficulty identifying genes whose relevant functions are masked by pleiotropy. In particular, if loss of gene function results in sterility, lethality, or other severe pleiotropy, neuronal-specific functions cannot be readily analyzed. Here we describe a method in C. elegans for generating cell-specific knockdown in neurons using feeding RNAi and its application in a screen for the role of essential genes in GABAergic neurons. We combine manipulations that increase the sensitivity of select neurons to RNAi with manipulations that block RNAi in other cells. We produce animal strains in which feeding RNAi results in restricted gene knockdown in either GABA-, acetylcholine-, dopamine-, or glutamate-releasing neurons. In these strains, we observe neuron cell-type specific behavioral changes when we knock down genes required for these neurons to function, including genes encoding the basal neurotransmission machinery. These reagents enable high-throughput, cell-specific knockdown in the nervous system, facilitating rapid dissection of the site of gene action and screening for neuronal functions of essential genes. Using the GABA-specific RNAi strain, we screened 1,320 RNAi clones targeting essential genes on chromosomes I, II, and III for their effect on GABA neuron function. We identified 48 genes whose GABA cell-specific knockdown resulted in reduced GABA motor output. This screen extends our understanding of the genetic requirements for continued neuronal function in a mature organism.

October 30

Our paper, "Rapid and Permanent Neuronal Inactivation In Vivo via Subcellular Generation of Reactive Oxygen with the Use of KillerRed", published in Cell Reports PDF

Inactivation of selected neurons in vivo can define their contribution to specific developmental outcomes, circuit functions, and behaviors. Here, we show that the optogenetic tool KillerRed selectively, rapidly, and permanently inactivates different classes of neurons in C. elegans in response to a single light stimulus, through the generation of reactive oxygen species (ROS). Ablation scales from individual neurons in single animals to multiple neurons in populations and can be applied to freely behaving animals. Using spatially restricted illumination, we demonstrate that localized KillerRed activation in either the cell body or the axon triggers neuronal degeneration and death of the targeted cell. Finally, targeting KillerRed to mitochondria results in organelle fragmentation without killing the cell, in contrast to the cell death observed when KillerRed is targeted to the plasma membrane. We expect this genetic tool to have wide-ranging applications in studies of circuit function and subcellular responses to ROS.

September 20

Yet another classy happy hour...thanks everyone!


August 22

End-of-Summer Bash. Good weather, great food, and yes, a slack line!

Sara, Rachid and Chris just chill-axing
From Korean BBQ to cupcakes, we had it all!
Our fearless leader!
Sungmin is the ping-pong champion!
Victor, Lewie, and Sungmin after a challenging tournament
Alex has mad skills on the line!

May 17

Genetics Happy Hour a la Hammarlund. Always classy!

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September 15

Our paper, "Neural Regeneration in Caenorhabditis elegans", published in Annual Review of Genetics

Summary: Axon regeneration is a medically relevant process that can repair damaged neurons. This review describes current progress in understanding axon regeneration in the model organism Caenorhabditis elegans. Factors that regulate axon regeneration in C. elegans have broadly similar roles in vertebrate neurons. This means that using C. elegans as a tool to leverage discovery is a legitimate strategy for identifying conserved mechanisms of axon regeneration.

August 30

End of the 2012 Hammarlund Lab Summer Undergrad Program. Thanks to Will, Chukwuma, Kevin, and (amazing high school student) Austin!

April 13

Article about our Notch research published in Scientific American

March 9

Our meeting review, "Science in Suzhou: establishment and function of neural circuits", published in EMBO Reports! PDF

Summary: The CSH Asia conference ‘Assembly, Plasticity, Dysfunction and Repair of Neural Circuits’ brought together developmental, cell, molecular and systems neuroscientists to discuss the establishment, function and plasticity of neural circuits.

January 25

Our paper, "Notch Signaling Inhibits Axon Regeneration", published in Neuron! PDF

Summary: Many neurons have limited capacity to regenerate their axons after injury. Neurons in the mammalian central nervous system do not regenerate, and even neurons in the peripheral nervous system often fail to regenerate to their former targets. This failure is likely due in part to pathways that actively restrict regeneration; however, only a few factors that limit regeneration are known. Here, using single-neuron analysis of regeneration in vivo, we show that Notch/lin-12 signaling inhibits the regeneration of mature C. elegans neurons. Notch signaling suppresses regeneration by acting autonomously in the injured cell to prevent growth cone formation. The metalloprotease and gamma-secretase cleavage events that lead to Notch activation during development are also required for its activity in regeneration. Furthermore, blocking Notch activation immediately after injury improves regeneration. Our results define a postdevelopmental role for the Notch pathway as a repressor of axon regeneration in vivo.

Neuron Preview by Po, Calarco, and Zhen: PDF

Neuron 73 p. 208

January 10

Yale undergrad Trent Walradt joins the lab. Welcome Trent!

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December 19

Happy Holidays from the Hammarlund lab! (Cookies by Rebecca Brown from the CNNR Bakeoff)

Axon regeneration in C. chocolate

July 30

End of the 2011 Hammarlund Lab Summer Undergrad Program. Thanks to Jaimie, Quinn, Reba, and Yigit!

July 13

Sara passes her qualifying exams. Congratulations!

May 19

Our paper, In vivo Laser Axotomy in C. elegans, published in the Journal of Visualized Experiments! movie PDF

Summary: Neurons communicate with other cells via axons and dendrites, slender membrane extensions that contain pre- or post-synaptic specializations. If a neuron is damaged by injury or disease, it may regenerate. Cell-intrinsic and extrinsic factors influence the ability of a neuron to regenerate and restore function. Recently, the nematode C. elegans has emerged as an excellent model organism to identify genes and signaling pathways that influence the regeneration of neurons. The main way to initiate neuronal regeneration in C. elegans is laser-mediated cutting, or axotomy. During axotomy, a fluorescently-labeled neuronal process is severed using high-energy pulses. Initially, neuronal regeneration in C. elegans was examined using an amplified femtosecond laser. However, subsequent regeneration studies have shown that a conventional pulsed laser can be used to accurately sever neurons in vivo and elicit a similar regenerative response.
We present a protocol for performing in vivo laser axotomy in the worm using a MicroPoint® pulsed laser, a turnkey system that is readily available and that has been widely used for targeted cell ablation. We describe aligning the laser, mounting the worms, cutting specific neurons, and assessing subsequent regeneration. The system provides the ability to cut large numbers of neurons in multiple worms during one experiment. Thus, laser axotomy as described herein is an efficient system for initiating and analyzing the process of regeneration.

JoVE 51

May 6

Goodbye to new Yale Graduate and amazing lab member Ellie Hong!


December 9: Some of Marc's work from his first postdoc (Syntaxin N-terminal peptide motif is an initiation factor for the assembly of the SNARE–Sec1/Munc18 membrane fusion complex) published in PNAS

November 11: Chris passes his qualifying exam. Congratulations Chris!

November 5: Genetics Department Annual Retreat at Jiminy Peak. Faculty photo

October 19: Some of Chris' work from college (Modifiers of notch transcriptional activity identified by genome-wide RNAi) published in BMC Developmental Biology

August 12: Welcome postdoc Yasunori Saheki!

August 9: With a small tear in his eye, Dan heads west for a Visiting Assistant Professor position at Linfield College. Good Luck Dan!!

June 27-30: Neuronal Development, Synaptic Function, and Behavior C. elegans Topic Meeting.

June 15: Some of Alex's work from grad school (MADD-2, a Homolog of the Opitz Syndrome Protein MID1, Regulates Guidance to the Midline through UNC-40 in Caenorhabditis elegans) published in Developmental Cell

June 14: Welcome grad student Sara Kosmaczewski!

May 24: Welcome undergraduate Ellie Hong!

April 27: Tyson passes his qualifying exam. Congratulations Tyson!


October 6: Welcome postdoc Alexandra Byrne!

June 24-28: International C. elegans Meeting

June 10: "Imaging Axon Regeneration in vivo", Yale Microscopy Workshop

May 18: Welcome grad student Tyson Edwards!

May 7: Welcome grad student Christopher Firnhaber!

April 24: Arnold and Mabel Beckman Foundation Young Investigator Award.

Jan. 22: "Axon regeneration requires a conserved MAP kinase pathway" published in Science. PDF

Jan. 12: Welcome technician Laura Klein!


Dec. 12: Genetics Department Holiday Party

Dec. 11: CNNR Open House