Papers Selected August- December  2013


 Insulin/IGF1 signaling inhibits axon regeneration and does so specifically in aged adult animals.  DAF-16/FOXO regulates regeneration independently of its role in lifespan determination.  DAF-18/PTEN inhibits regeneration independently of age and DAF-16/FOXO via TOR signaling.

 Free software from the Zhong lab to measure wom Lifespan, Locomotion,Length, and Eggs.

Also see these papers for tracking worms in 3 dimensions and Track-A-Worm, and WormBook


Coexpressed ephrins can inhibit the ability of EphA2 and EphA3 to bind ephrins in trans.The cis inhibition of EphA3 by ephrin-B2 implies that in some cases ephrins that cannot activate a particular Eph receptor in trans can inhibit its signaling ability through cis association. 

mTOR-independent signaling pathway by which PTEN can regulate in opposite directions the main mechanisms of intracellular protein degradation.


 Using C. elegans as a tool to screen for drugs that inhibit human EGFR signaling.  See also this paper.

  Molecular pathways needed for C. elegans desiccation tolerance.

Review on targeting EphR signaling for therapeutic intervention.

nlp-22 shows cyclical mRNA expression in synchrony with lethargus; it is regulated by LIN-42, an orthologue of the core circadian protein PERIOD.

The presence of males accelerated aging and shortened the life span of individuals of the opposite sex. A number of insulin like peptides genes (ins-4, ins-11, ins-23, and ins-31) are increased in the presence of males.

 The authors incorporated unnatrual amino acids in proteins and could use light to change the amino acids  (caged lysine to lysine in a NLS tagged  GFP).  


 This review summarizes the recent literature on neuronal aging in C. elegans

 USP13, stabilizes the PTEN protein through direct binding and deubiquitylation of PTEN.

CDC-42(G12V) gain of function caused  ectopic protrusions in neurons.  The Arp2/3 complex, UNC-115/abLIM and UNC-43/Ena as well as the Nck-interacting kinase MIG-15/NIK and p21-activated kinases (PAKs) and  PI3K signaling was required, specifically the Rictor/mTORC2 is required for these protrusions.


ELT-7 GATA factor, can convert the identity of fully differentiated, highly specialized non-endodermal cells of the pharynx into fully differentiated intestinal cells

Imaging system to record neuronal activity, detected by genetically encoded calcium indicators, simultaneously from 20 Caenorhabditis elegans animals in microfluidic arenas.

online database for the systematic investigation of C. elegans phenotype equivalents of human diseases by integrating known disease–gene associations, gene orthologue data, molecular phenotypes and QTL results. 

The authors used biolistic bombardment and  a different antibiotic, hygromycin B, and the hygromycin B phosphotranspherase gene – encoding a kinase that inactivates hygromycin by phosphorylation – to select transgenic C. elegans.  

 Ephs are frequently mutated in Non-small cell lung carcinoma (NSCLC) patients, and occur together with other known mutations relevant to the pathogenicity of NSCLC.

A Wormbook review on  more than 2,800 putative neuronal terminal differentiation genes.

mNeonGreen is the brightest monomeric green or yellow fluorescent protein. Link to sequence.

 A review on using C. elegans  to study neurodegenerative diseases.

 A preview on two new papers showing how PVD receives cues from the hypodermis (skin) to shape its dendrites.

See also:


 Sequencing now empowers clinical diagnostics and other aspects of medical care, including disease risk, therapeutic identification, and prenatal testing. This Review explores the current state of genomics in the massively parallel sequencing era.

It remains unclear what fraction of cancers follow the stem-cell model and what clinical behaviours the model explains. Studies using lineage tracing and deep sequencing could have implications for the cancer stem-cell model and may help to determine the extent to which it accounts for therapy resistance and disease progression.

InR is required for the formation of the peripheral nervous system during larval development and more particularly for the formation of sensory organ precursors (SOPs).

 HSPG core proteins Syndecan (SDN-1) and Glypican (LON-2) and the HS modifying enzymes in the dorsal guidance of D-type motor axons, a process controlled mainly by the conserved axon guidance molecule UNC-6/Netrin.

 Many first introns are large and thus may have a regulatory role. Transcription factors that bind first introns are largely different from those binding promoters, suggesting that the different interactions are complementary rather than redundant.

 The PTEN Long N-173 tail has a large intrinsically disordered region. and enriched in potential linear binding motifs, protein-binding sites and post-translational modifications (PTMs) indicating its probable role in PTEN function and transport across cells.

 Truncation of the C-terminal region of PTEN (Δ51) causes a neomorphic gain of function mutation that leads to an increase in NFκB activity, a transcription factor overactivated in astrocyte tumors.

 Proteoglycan biosynthesis is tightly regulated by a microRNA pathway to shape the cell surface glycosylation architecture required to direct neuronal migration.

 Impaired vMSP signaling to muscle triggers an energy deficiency, which induces a protective metabolic response involving FoxO. 

a href="http://www.biochemj.org/bj/imps/abs/BJ20131101.htm">  FGT-1 is the major glucose transporter in C. elegans. Knockdown of fgt-1 leads to an extension of lifespan equivalent, but not additive, to that observed in daf-2 and age-1 mutant worms. 

   New work in Mei Ding Lab shows PLM makes a gap junction connections to the BDU interneuron and regulated by Wnt, AHA-1 and the CAM-1 RTK.

  EBAX-1 specifically recognizes misfolded SAX-3 and promotes its degradation.


 Review on Eph Receptor signaling. [PDF]

  Our paper is out.  

 A complex humoral mix of monoamines is focused by more local, synaptic, neuropeptide release to modulate nociception

 A review on the mechanism of plasticity in the mechanosensory neurons. Depriving larval worms of mechanosensory stimulation early in development leads to fewer synaptic vesicles in the mechanosensory neurons and lower levels of an AMPA-type glutamate receptor subunit in the interneurons.

 Ephrin signaling is required for amphid axon ventral guidance.  VAB-1 acts in amphid neurons, interacting with EFN-1 expressed on surrounding cells. Interestingly left-hand neurons are more affected than right-hand neurons. An Eph kinase-independent pathway involves the ABL-1 nonreceptor tyrosine kinase and possibly the phosphatidylinositol 3-kinase pathway.

 A review on nuclear PTEN.

 A new study showing dentrite remodelling in C. elegans dauer formation.

   Individuals carrying melanocortin-1 receptor (MC1R) variants, especially those associated with red hair color, fair skin, and poor tanning ability (RHC trait), are more prone to melanoma. This paper shows that WT, but not MC1R RHC variants, protect PTEN from WWP2-mediated ubiquitination.

Chapter on how the C. elegans heterochronic gene pathway guides developmental transitions during continuous and interrupted larval development.


 Crystal structured of an ephrin-A5 and  EphA4  receptor complex.

 A biomarker for suicide prone people? A study with a small sample of men suggests that SAT1, PTEN, MARCKS and MAP3K3 might represent biomarkers for suicidality.

  This article surveys Lamarck’s ideas about the inheritance of acquired phenotypes.

 A wormbook chapter on statistical analysis.


 The naked mole rat is resistant to cancer and its fibroblasts secrete extremely high-molecular-mass hyaluronan (HA), which is over five times larger than human or mouse HA. This abundance is due to decreased activity of HA-degrading enzymes and a unique sequence of hyaluronan synthase 2 gene (HAS2).

 Oncogene review on HIF-1 in tumorigenesis.

RIN-1 acts as an effector for CED-10/Rac1 in the Slit/Robo pathway and regulates actin remodeling in axon guidance.