The Chin-Sang Lab Reads

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The Chin-Sang Lab recommends…

Current papers/reviews (and refs within) you should read.


Papers selected in 2017

Papers selected 2017


PTEN interacts with DAXX and, in turn PTEN directly regulates oncogene expression by modulating DAXX-H3.3 association on the chromatin, independently of PTEN enzymatic activity. Furthermore, DAXX inhibition specifically suppresses tumour growth. 


The selfish gene element   is made up of sup-35, a maternal-effect toxin that kills developing embryos, and pha-1, its zygotically expressed antidote. pha-1 has long been considered essential for pharynx development on the basis of its mutant phenotype, but this phenotype arises from a loss of suppression of sup-35 toxicity.

EphA2 SAM domain inhibits kinase activity by reducing receptor oligomerization

The pre-Brenner history of using C. elegans and other nematodes as model organisms.

AMPK is required to block germ-line gene expression during starvation. In its absence the inappropriate activation of germ-line transcription results in sterility and transgenerational reproductive defects.


Using CRISPR they deleted genes that mice need to grow certain organs. When they introduced rat stem cells capable of producing those organs, those cells flourished and the chimeric mouse-rat lived to adulthood.  Interestingly rats do not make gallbladders (mice do) and the mouse cells could induce the rat stem cells to make gallbladders. Although very inefficient,  Human-pig chimeric embryos were also made but terminated after 28 days of development. 



Review on Sleep in C. elegans.

Heat and oxidative stress in combination with Hsp90 knockdown (daf-21 RNAi) caused transposon excision and transposition in C. elegans.


Papers selected January 2016-


SFA-1 the C. elegans homologue of SF1, also known as branchpoint binding protein, BBPis specifically required for lifespan extension by dietary restriction and by modulation of the TORC1 pathway components AMPK, RAGA-1 and RSKS-1/S6 kinase. Overexpression of SFA-1 is sufficient to extend lifespan. 


Use of daf-2  in modeling phenotypic consequences of candidate human pathogenic mutations.


Bidirectional signaling between EphrinB1 and EphB3b coordinates the movements of the hepatic endoderm and adjacent lateral plate mesoderm (LPM), resulting in asymmetric positioning of the zebrafish liver.  See also this Dev. Cell preview


These results support the existence of a conserved pathway for EphB trans-endocytosis that removes the physical tether between cells, thereby enabling cell repulsion.

Periodic A/T clusters (PATCs) can prevent transgenes from  stochastic silencing in germline.

ZIG-10 mediates an interaction between excitatory neurons and epidermis


A modular approach to synthesis of programmed polyproteams, through spontaneous isopeptide bond formation between peptide tags . The polyproteams are linked through irreversible amide bonds and so are stable over time (if protected from proteases) and allow easy analysis by SDS/PAGE.  Link to Addgene vectors

A improved version of proximity-dependent biotin identification (BioID)  method to detect protein-protein interactions in living cells. Link to Addgene vectors


Review on using C. elegans to study energy balance and feeding behaviour.

Linear DNAs with short homologies (∼35 bases) engage in a highly efficient gene conversion mechanism. There may be a size limitation as they got 0% edits a 2.4kb dsDNA.

β-amyloid may play a protective role in innate immunity and infectious or sterile inflammatory stimuli may drive amyloidosis

By duplicating the PVD neuron, Yip and Hieman show that dentrite tiling uses a mutual repulsion that rquires Netrin signaling.


Watch out Crispr/Cas9 there is a new kid on the block.  NgAgo a new gene editing too.  This protein uses a ssDNA guide (24nt with 5’Phosphate group) to make presice cuts in dsDNA.

Update:  There has been a lot of controversy about this method as many researcher are unable to reproduce the results. See Nature News


The Sherwood lab identified cdc-42 and gdi-1 are needed for invadopodia formation. CDC-42 is required for the invasive membrane localization of WSP-1 (N-WASP),  and GDI-1 mediates membrane trafficking.

sex-shared neurons adopt sex-specific synaptic wiring patterns. Reversal of the sexual identity of either the pre- or postsynaptic neuron alone transforms the patterns of synaptic connectivity to that of the opposite sex.  See Douglas Portman’s Nature News and Views article.

Review on Eph-ephrin signaling in the nervous system

A novel form of regeneration that is largely independent of defined regeneration pathways. This is similar to reduction of sensory activity which triggers axon regeneration in the mammalian CNS


3D graphic reconstruction of the developing intestine. LIN-12/Notch appears to modulate left-right adhesion in the primordium. Rotation appears to have a role in aligning the developing lumen of the intestine, and involves a conserved, UNC-6/netrin and other axon guidance genes.

Light-dependent activation of a guidance receptor, UNC-40/DCC using Arabidopsis thaliana Cryptochrome 2, which oligomerizes upon blue-light absorption. 

 

The GFP11 and sfCherry11 tags are only 18aa long and will reconstitute with FP1-10 to make a functional flourescent protein.  You can put these tags in tamdem to increase fluorescence. 

The Stome lab has shown that daf-2  long lived animals do not aquire a "germ cell program"  in the soma.  In contrast to this 2009 paper.

Optogenetics approach to control organelle transport.

 VAV-1, GEF activity acts in ALA to suppress locomotion and feeding during sleep-like behavioral quiescence in response to cellular stress. Additionally, VAV-1 activity is required for EGF-induced sleep-like quiescence and normal levels of EGFR and secretory dense core vesicles in ALA. 

vps-50 affects the behavioral state of C. elegans. VPS-50 and its murine homolog mVPS50 associate with synaptic and dense-core vesicles and function in acidification andmaturation of dense-core vesicles.


The authors extend the applicability of whole-genome sequencing to a broader spectrum of mutations, including classes that are difficult to map by traditional means.

EFN-4 has a new receptor.   L1 cell adhesion molecule LAD-2 acts as anephrin receptor to EFN-4 to promote axon guidance.  EFN-4 can function as a diffusible factor.


This paper supports our work we published in 2007 that EphR inhibits PTEN and in particular EphA7 overexpression role in promoting NSCLC.  Thus EphA7 may provide a targeted therapy for NSCLC.

Loss of the H3K4me3/2 histone emethylase, RBR-2 causes axon guidance defects due to the transcriptional up regulation of wsp-1.  The  NURF complex is required for the upreguation of wsp-1


PTEN deletion can rescue someof FGFR mutant phenotypes.

Drosphila insulin like peptide 8 works through the G protien coupled  Lgr3 relaxin receptor.


 

A new way to mutagenize worms using light and Histone-MiniSOG.


Trojanowski and Raizen Review on C. elegans sleep.

Papers selected January- 2015



C. elegans L1 straved animals  can metaboize EtOH to induced a aggregration behaviour.

Auxin induced protein degradation in C. elegans.

 rab-35, rab-10 and M04F3.2,  as well as vrp-1, ceh-60 and lrp-2  are need for abudant yolk protein.  Surprisingly, worms do fine with reduced yolk proteins.

Differential regulation of germline stem cell proliferation rates in C. elegans adults is accomplished through localized inhibition of insulin/IGF-1 signalling, requiring daf-18/PTEN, but not daf-16/FOXO. 

Review on PTEN Regualton

Starving C. elegans at L1 take longer to become reproductive, have lower fecundity and were smaller as adults. The progeny and grandprogeny of starved L1 animals were more resistant to starvation and heat stress. 

Paix et al. use synthesized tracrRNA and crRNAs and recobinant  Cas9 to inject into C. elegans. Supp. material.

We have tried this protocol and it works really well. E. coli will take linearized vector and insert with 20bp homology overlaps  (like Gibson assembly but without enzyme mix) and recombine the two pieces into a circular plasmid. We have tried with DH5 alpha, Top10 and XL1Blue.  We treat with  T4 DNA polymerase (3’ Exonuclease activity)  for 2.5 minutes  and this increases the efficiency.  See this SLIC paper and protocol.  Here is another paper that uses 40-50bp homolgy overlap and can recombine multiple fragments. And another one calle AQUA cloning. They also use this method for insertions, deletions, or substitutions. The method shows a broad compatibility with most widely used lab-strains of E. coli, including TOP10, NEB5α, NEB10β, BL21 (DE3) and JM109. 



Dickinson et al. revised their method for Crispr genome engineering in C. elegans. Improvements include drug selection and a Cre mediated self excision leaving only a small scar within an intron. In a single micro-injection they could isolate, 1) knock out for his-72 2) a his-72 transcriptional reporter and 3) a HIS-72 translational reporter. Detailed Protocol

Sense oligo for HR seems to work better than anti-sense and homology independent DNA repair  (like in zebrafish) works in C. elegans.

The sense oligo could be explained by this paper:


1) After duplex cleavage, Cas9 holds onto three ends of the target DNA (white crossed circles), but the PAM-distal non-target strand is released from the Cas9-DNA complex. 2) Complementary DNA anneals to released strand. 3) Branch migration results in extrusion from the Cas9-DNA complex.

Note that the pha-1 guide RNA targets the sense strand and thus the Oligo for repair does conform to this rule 

A new model, in addition to lagging strand hypothesis, to explain Gap repair in lambda Red recombineering.

The authors (Canadian) show the Crispr/Cas9 cleavage coupled to lambda Red recombineering can create large gene edits eg. deletions (94.3kb) or insertions  (3kb). Without any selection (just colony PCR).

Andrew Chisholm’s review on wound healing in C. elegans.

The authors report that they get higher efficiency of HDR  reporter knock-in mice by using  dual-crRNA:tracrRNA combined with Cas9 protein and repair template. A similar approach has been reported in zebrafish and C. elegans.

 A review on Eph–ephrin signaling in adhesion, repulsion and tension—that can in principle underlie the segregation of cells and formation of sharp borders. 


Recent experiments led to insights into how the widely used laboratory reference strain of the nematode Caenorhabditis elegans compares with natural strains. 

The natural history of C. elegans.


Methods Volumes 77–78, Pages 1-204 (1 May 2015) PTEN Function Methods

Designing your guide RNA to have GG just before the PAM site increases CRISPR/Cas9 edits.

Ploymerase theta is used in the C. elegans germline to to promote end joining after double strand break.  The authors show that  CRISPR/Cas9-induced genomic changes are exclusively generated through polymerase theta-mediated end joining, refuting a previously assumed requirement for NHEJ in their formation. 

Reduced insulin can increase longevity through a dauer independent pathway through SKN-1 (Nrf, NF-E2-related factor)which increases expression of collagens and other extracellular matrix genes.

 We tend to forget to understand how the pioneer researchers faced major questions. 

Lysomes have a signaling role in aging.

A review on transgenerational epigenetics.

Quality vs Quantity of life is addressed in C. elegans.

The E3 ubiquitin ligase substrate-recognition subunit ZIF-1, can be used to proteins and  can be quickly degraded in all somatic cell types examined with temporal and spatial control.

Review on monitoring autophagy in C. elgans.http://www.nature.com/ncomms/2015/151203/ncomms9868/full/ncomms9868.html



The Chin-Sang Lab reads


Papers selected January -December 2014





Jordan Ward has provided new improvements for better efficiency of CRISPR Cas9 HDR. 1) Use a better sgRNA (sgRNA F+E) 2) Use the conversion of pha-1(ts) as a selection and score these animals for conversion (co-conversion strategy) 3) Use ssODN as repair template 4) Inhibit NHEJ  (cku-80 RNAi). Update: At the last worm meeting they mentioned that inhibiting NHEJ doesn’t seem to help that much.

A nice history of the discovery of  Crispr Cas9 

Drosophila Eph RTK signaling required for compartment boundary formation.

 Optimization of CRISPR/Cas9 in fly shows that sgRNAs with high GC content before PAM and 18 nt seed vs. 20 nt is more efficient. 

Starvation in C. elegans induces transgenerational inheritance of small RNAs

Even without histone methyl transferase (PRC2), H3K27me is transmitted to daughter chromatids after ell division. In embryos with PRC2, H3K27me is only seen on chromosomes that had had  existing marks. See this preview.

Epidermal wounding triggers local production of the mitochondrial ROS (mtROS) superoxide and promotes actin mediated wound repair. Ca2+ uptake and inhibition of Rho activity is needed at wound site.

Review on the methods to study  PTEN subcellular localization

Chemosensation of  henazine-1-carboxamide and pyochelin produced by Pseudomonas aeruginosa activate a G-protein-signaling pathway that induces expression of the TGF-β and promotes avoidance behavior.

PHA-4, and SKN-1 regulate miR-71 and miR-228 are critical for dietary-restriction-induced longevity. PHA-4 and SKN-1 are negatively regulated by miR-228

Here Paix et al. report that CRISPR/Cas9  HDR can be done efficiently using just 30-60bp of homology arms.  Previously other groups would use about 1kb for homology arms. Detailed Protocol here.


A review on the molecular genetics of decision making.


ins-4, daf-28 and to a lesser extent ins-6 function redundantly  to  regulate L1 arrest.

 Sema1a reverse signaling promotes the phosphorylation and activation of Moesin (Moe), a member of the ezrin/radixin/moesin family of proteins, and downregulates the level of active Rho1 in photoreceptor axons. 


Grizzly bears prepare for hibernation by increased insulin sensitivity via down regulation of PTEN in fat tissue.

a three-dimensional scaffold of heparan sulfate mediates KAL-1/anosmin-1 

 insulin signaling strength can differentially affect specific neurons aging naturally or under proteotoxic stress

DAF-16/FOXO, and  DAF-18/PTEN and several components of the proteasome complex (rpn-6.1, rpn-7, rpn-9, rpn-10, rpt-6, pbs-3 and pbs-6) are essential for both lifespan and immunity of germline deficient animals. 

A review on the  mechanosensory systems of C. elegans, including the sensory neurons and circuitry involved in body touch, nose touch, and proprioception.

In the Q neuroblast lineage, loss of GRP- 1 (cytohesin)  led to the production of daughter cells that are more similar in size and the cells that should undergo apoptosis survives , resulting in the production of extra neurons.

The BK channel T352I missense mutation was insensitive to activation by ethanol.

Expression of vertebrate connexins in C. elegans  can be used to synthetically connect neurons.

A review on C. elegans approaches to target protein folding diseases.


ANI-2 promotes germ cell syncytial organization and allows for compensation of the mechanical stress associated with oogenesis by conferring stability and elasticity to germ cell intercellular bridges.


Review on the FMRF-amide neuropeptides.

Knocking out genes by feeding CRISPR guide RNAs.

During the oocyte to Embryo transition, many maternal mRNAs are cleared. A polyC motif in the 3′ UTR serves as a target for polyC binding proteins likely initiated by endogenous siRNAs.

The Wnt receptor Ryk, is increased in different animal models of HD. In C. elegans lin-18/Ryk represses daf-16/FOXO protective activity, possibly directly, through its intracellular domain, a product of γ-secretase–mediated cleavage previously implicated in the birth of new cortical neurons. 

Normally Q.aa and Q.pp are smaller cells that undergo apoptosis. The DEP domain-containing protein TOE-2 in promotes the apoptotic fate in the Q lineage. Interestingly in toe-2 mutants the Q.aa was a similar size to its sister but int he Q.pp daughter was smaller but did not undergo apoptosis.   Also see the PIG-1 paper1. and paper 2 

Metformin is able to extend lifespan by increasing the production of reactive oxygen species 

Some of the physiological phenotypes previously attributed to peripheral AAK-2 activity on metabolic targets may instead be due to the role of this kinase in neural serotonin signaling.


When C. elegans  L3 or L4 worms are removed form food development stops (eg. vulva formation).  DAF-16, a major target of insulin-like signaling, functions to arrest developmental upon nutrient removal. The effects of DAF-16 on progression through the L3 and L4 stages are mediated by DAF-9, a cytochrome P450 ortholog involved in the production of C. elegans steroid hormone.


The UNC-6/Netrin guidance cue has a conserved role in guiding cell and growth cone migrations along the dorso-ventral axis, whereas Wnts are critical for determining polarity and guidance along the antero-posterior axis. In this study we show that these two signaling pathways function redundantly in both antero-posterior and dorso-ventral guidance 

 The authors have made an enhanced PTEN (ePTEN) with approximately eightfold increased ability to suppress PIP3 signaling. This involved making 5 mutations in the PTEN protein: ePTEN Q17R, R41G, E73D, N262Y, N329H.

Deletion of TRPV1, an ion channel critical for nociception, extends mouse and C. elegans lifespan by regulating the activity of CRTC1 in peripheral sensory neurons.

 I motor neurons and mechanosensory neurons RPM-1 is localized to multiple, distinct subcellular compartments in a single cell to coordinate axon outgrowth and termination with synapse formation.

Actin polymerization and myosin II-mediated contractility may not be required for some cells in confined migration. Water permeation regulates cell volume and drives migration in narrow channels. 

Using a known to work sgRNA (unc-22) with your sgRNA you can let you know when the Cas9 activity has occurred. The authors also show you can directly select for GFP tagged genes by homologous recombination.

RPM-1 functions through a PP2C phosphatase, PPM-2, to regulate the activity of a MAP3 kinase, DLK-1. 

The authors use an In vivo sensor for mechanical tension to show differences in the front and back of migrating cells.

A web tool for identifying mutations from WGS.  Link to Mudi.  Also see CloudMap.

LIN-32 controls Q cell division and migrations.

 3 different imaging techniques that can be used to image live C. elegans without the use of microfluidic technologies

This paper presents a new type of nuclei segmentation method for automated analysis of cell lineage.

 Pheromones sensed by ciliated neurons in the Caenorhabditis elegans nose alter the lipid microenvironment within the oviduct, thereby affecting sperm motility. 

α-KG inhibits ATP synthase and,  and leads to reduced ATP content, decreased oxygen consumption, and increased autophagy in both C. elegans and mammalian cells.  This leads to extended lifespan.

WormNet v3 is freely accessible at http://www.inetbio.org/wormnet.


Deep sequencing strategies for simultaneously mapping and identifying causal mutations in Caenorhabditis elegans from mutagenesis screens. Have a look at CloudMap a cloud based pipeline for analysis of mutant genome sequences. 

Although CRISPR will likely replace Mos1 meditated genome editing there are two compelling uses for miniMos: 1) will be to probe the genome on a global scale for chromatin effects and to determine expression patterns using gene-trap constructs. 

Review of the CRISPR/Cas9 methods used in C. elegans.

daf-18 and shc-1;daf-18 mutants develop a disrupted gonad after L1 starvation. This is not dependent on the L1 arrest germline proliferation as daf-18(e1375) does not show proliferation at L1 arrest but nonetheless has a disrupted gonad.  hyper-proliferation and basement membrane disruption characterize this phenotype.  daf-2(lf) can suppress  proper gonad development in a DAF-16 independent manner.  Doxycyclin ( selectively inhibits mitochondrial protein synthesis) and reduced starvation temperature can suppress the phenotypic penetrance


Molecular mechanisms by which free radicals can have a pro-longevity effect. See below James Watson’s hypothesis on why causes type 2 diabetes.

Reduced insulin signaling restores germ cell immortality to prg-1.  This is accomplished by activating a parallel nuclear RNA-silencing pathway.


James Watson’s hypothesis of the cause of type 2 diabetes "“The fundamental cause, I suggest, is a lack of biological oxidants, not an excess,” he says. "Physical exercise prompts the body to make large numbers of oxidants — molecules called reactive oxygen species, or ROS," he continues, and that's why exercise is beneficial to our bodies.

Review on Axon regeneration in C. elegans.

EphA–Vav2–RhoA-mediated repulsion between contacting cancer cells at the tumour edge could enhance their local invasion away from the primary tumour.

PINK1-dependent phosphorylation of both parkin and ubiquitin is sufficient for full activation of parkin E3 activity.

Review on using C. elegans to model neurodegenerative diseases.


 PTEN alpha is longer isoform that uses a CUG start codon.PTENα induces cytochrome c oxidase activity and ATP production in mitochondria. 

Review on the mechanisms that control PTEN localization.


PTEN forms a dimer for active PIP3 phosphatase activity. Some PTEN missense mutations found cancers act as dominant negative.


RNA-binding protein Musashi regulates forgetting in C. elegans through translational repression of the actin-branching Arp2/3 complex. Memory length is regulated cooperatively through the activation of Adducin and by the glutamate-receptor/Musashi-1/Arp2/3 pathway

An automated system simultaneously images worm behavior and neuronal Ca2+ transients.

 Genome editing in adult animals.  CRISPR-Cas9–mediated correction of a Fah mutation in hepatocytes in a mouse model of the human disease hereditary tyrosinemia. They used hydrodynamic tail vein injection to get DNA into the liver cells.


The forty insulin-like peptides in the nematode C. elegans have specific and distinct effects on eight different physiological outputs that range from development, stress responses, lifespan and reproduction. Interestingly, we also find that these peptides regulate each other at the transcriptional


A method for single/low copy integration of transgenes.

 Cam Kinase II (UNC-43)  has a role in blocking the regulated exocytosis of Dense Core Vesicles  before they are transported into axons.


Review on microfluidic platforms for C. elegans research.


 A review on Ephrin signaling in the developing nervous system.


 A  review of the use of CRISP/Cas9 in Drosophila. 

PNKP is synthetic lethal with PTEN.  Cells have increased apoptosis and increased radiosensitivity in the double knock down. The worm homolog of PNKP is  F21D5.5   


 A method  to silence neurons by expressing an histamine-gated chloride channel (HisCl1) in specific neurons. The activity of HisCl1-expressing neurons is acutely and reversibly silenced by exogenous histamine, which C. elegans absorbs from the media. 

Reprogramming cells by stimulus-triggered acquisition of pluripotency (STAP), which requires neither nuclear transfer nor the introduction of transcription factors.


Genetics screens  identified at least 50 conserved genes with growth-promoting or growth-inhibiting functions for axon regeneration in C. elegans.





August 2013


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.

Papers Selected in 2013 (Jan.-July)




Long-term treatment with metformin starting at middle age extends healthspan and lifespan in male mice.

  SUMOylation (SUMO, small ubiquitin-like modifier) of PTEN controls its nuclear localization. See the Perspective by Leslie and Brunton.

Hours before it dies, a wave of blue fluorescence flows through the body of C. elegans.


A behavioral database for Caenorhabditis elegans strains. The database also has short videos that display behavior and morphology features.

 PTEN mediates chemorepulsion in growing axons.



Phosphorylated PTEN relative to its unphosphorylated counterpart shows reduced catalytic activity and membrane affinity and undergoes conformational compaction likely involving an intramolecular interaction between its C-tail and the C2 domain.

 Andrew Chisholm's review on cytoskeleton dynamics in axon regeneration.


a href="http://dev.biologists.org/content/140/10/2093.long">  EGL-18 and ELT-6  are  needed for seam cell fate during embryogenesis, are reused downstream of Wnt signaling in the maintenance of seam cell fates during the larval asymmetric stem cell-like divisions.


a negative feedback loop between the C. elegans detoxification/antioxidant response factor SKN-1/Nrf and its repressor wdr-23


Protein kinase A (PKA) stabilizes active wakefulness, at least in part through two of its downstream targets: neuropeptide release and CREB

  Biotechniques has a profile on Cori Bargmann.

CRISPR-Cas9 system for generating loss-of-function mutants in C. elegans. See  this paper too:


Dan Dickinson and Bob Goldstein run a website for information on Cas9 recombination in C. elegans.

See this commentary from Christian Frøkjær-Jensen . 

 New wormbook chapter on transcriptional regulation in C. elegans.


A library of 2,007 mutagenized C. elegans strains, with mutant alleles for each of the worm's more than 20,000 genes. The library contains over 800,000 unique single nucleotide changes.

Review on L1 arrest.

  PTEN-Long is a membrane permeable lipid phosphatase that is secreted from cells and can enter other cells. Also see this perspective and paper on intracellular PTEN.


 When fed the soil bacteria Comamonas, C. elegans develop faster, lay fewer eggs, and live shorter than when fed E. coli  OP50. Mixing of food experiments show that Comamonas DA1877 effect is “dominant” over that of E. coli OP50 . See this paper too:  

Forward and reverse genetic screens uncover diet-response network in C. elegans ► Mutations in human orthologs cause inborn metabolic disorders treated by diet ► Mitochondrial metabolic and nuclear regulatory networks communicate reciprocally ► Multiple transcription factors mediate the metabolic network perturbation response

AMPK contributes to survival during L1 diapause in a manner distinct from that by which it controls dauer diapause.  AMPK suppresses TORC1 activity to maintain stem cell quiescence but TORC1 activity appears to function independently for L1 diapause longevity.   

Novel lipid-TORC1 signaling pathway that coordinates nutrient and metabolic status with post embryonic growth.  See also this paper.


The tumor suppressor Rb and cell metabolism.  Dispatch for the paper below:

 Rb plays critical roles in promoting L1 starvation survival and function in both IIS-dependent and -independent pathways. 

 How can a cell control how big it is?

 

 New mechanisms that rely less on actomyosin contractility of purse-string bundles and more on dynamics in the global cortical actomyosin network of the cells. 

 Zou et al. report that the highly conserved let-7–LIN-41 heterochronic signaling pathway is responsible for part of the age-related decline in axon regeneration in the worm Caenorhabditis elegans.

 Understanding PTEN regulation may help us better interpret tumour development. Also see this review on non-genomic loss of PTEN function.

 Genetic similarities between sleep regulation during C. elegans lethargus and sleep regulation in other animals.

LAR modulates cell migration through EphA2 site-specific dephosphorylation

 Worms deprived of sleep die.  daf-16 mutants show an  are hypersensitive to the lethal effects of forced locomotion during lethargus.

 
 
This review describes several target sites that could help in the development of novel drug candidates to regulate or restore the normal physiological functions of PTEN and are essential in the treatment of human diseases where PTEN plays a pivotal role.

 

 Kinesin-2 motors mediate anterograde intraflagellar transport (IFT).  Bardet-Biedl syndrome (BBS) and IFT-A proteins are now implicated in regulation of IFT assembly at the ciliary base and tip.

EphA2 is expressed in human thyroid cancer. Phosphorylated Akt (pAkt), an important regulator of thyroid cancer metastasis, is attenuated by EphA2 knockdown, providing evidence that EphA2 may act through pAkt. Matrigel invasion of thyroid cancer cell lines correlates with EphA2 expression and loss of PTEN. This is consistent with what is seen in 

C. elegan  Eph and PTEN regulation.

 

 Axon tracts are critical for patterning the C. elegans body. The CAN neurons express the Ror family wnt receptor which "soaks" up wnt ligands in the posterior end. In vab-8 mutants the CAN cell body and posterior axons are anteriorly displaced leading to more wnts in the posterior end which induces ectopic  vulval cells in the posterior end. 

 Down regulation of the Insulin/IGF-1-like signaling (IIS) pathway protects neurons from degenerating in a DAF-16/FOXO-dependent manner and is related to superoxide dismutase and catalase-increased expression.

 Handedness in the worm is independent of body symmetry and may be is driven by epigenetic factors rather than by genetic variation.

 Protocol for C. elegans triple-fluorescence imaging approach for time-lapse imaging analysis such as Q neuroblast migration in the L1 larvae. 

 New mechanistic insights about the role of PTEN in metabolism.

 A method to express active ephrin in  bacteria. 

 Latest review on PTEN 


http://www.sciencemag.org/content/341/6144/395.long

Papers Selected in 2012


 MIG-10 isoforms, varying only in their N-terminal motifs, can localize to specific subcellular domains, organize the actin cytoskeleton at these domains, and instruct distinct neurodevelopmental outcomes downstream from Netrin.  AMPK contributes to survival during L1 diapause in a manner distinct from that by which it controls dauer diapause,  and AMPK suppresses TORC1 activity to maintain germline quiescence.

 

 

The B-type cholinergic motor neurons transduce the proprioceptive signal. A sensorimotor feedback loop operating within a specific type of motor neuron both drives and organizes body movement. See also this preview: 

                    

 Worm Developmental Dynamics Database (http://so.qbic.riken.jp/wddd/), which stores a collection of quantitative information about cell division dynamics in early Caenorhabditis elegans embryos with single genes silenced by RNA-mediated interference. 

Two recent studies describe mechanisms by which sexually dimorphic responses to pheromones in the nematode worm Caenorhabditis elegans are driven by differences in the balance of neural circuits that control attraction and repulsion behaviors.

 At present, of the 20,377 protein-coding genes in this organism, 6764 genes with associated molecular lesions are either deletions or null mutations 

 Perspective and link to paper that shows PTEN can be transferred between cells.

  

Scott Emmons' perspective on two new papers on oxytocin/vasopressin  signaling that regulates complex behaviors in C. elegans.

 

E. coli noncoding RNAs can regulate gene expression and physiological conditions of C. elegans and indicate that noncoding RNAs might have interspecies ecological roles.

How the stable MT cytoskeleton of a mature neuron is converted into the dynamically growing MT cytoskeleton of a regrowing axon.

Remote controlled worms: one interneuron pair (AIY) was sufficient to force the animal to locate, turn towards and track virtual light gradients.

 

performed RNA-seq of individually staged and dissected linker cells, comparing transcriptomes from linker cells of third-stage (L3) larvae, fourth-stage (L4) larvae, and nhr-67-RNAi-treated  (needed for linker cell migration) L4 larvae.

The endosome-associated protein, SID-5, promotes the transport of RNAi silencing signals between cells.

 

 insulin/IGF-1 signaling selectively engages AKT-2/DAF-16 to promote DNA damage-induced germ cell apoptosis downstream of CEP-1 through the Ras pathway.

Model figure.

 

DAF-18 PTEN inhibits, RAS/MAPK signaling in the vulval precursor cells and the inhibitory activity is partially independent of its PIP3 lipid phosphatase activity. Model figure.

 

The Caenorhabditis elegans TransgeneOme provides a platform for large-scale, tag-based protein function exploration under endogenous regulatory control.

 

Genome-wide RNA-interference-feeding screen for suppressors of lin-35/Rb. Of 26 suppressors identified, 17 fell into three functional classes: (1) ribosome biogenesis genes, (2) mitochondrial prohibitins, and (3) chromatin regulators. See this genetics primer on the screen.

 

 

UNC-40/DCC, SAX-3/Robo, and VAB-1/Eph differentially regulate the abundance and subcellular localization of the WAVE/SCAR actin nucleation complex and its activator, Rac1/CED-10 for epidermal morphogenesis.

 

Evidence for phosphorylation inhibiting PTEN.  IGFBP-2 bound RPTPβ which led to its dimerization and inactivation. This enhanced PTEN tyrosine phosphorylation and inhibited PTEN activity.

 

The authors describe a phenomenon, RNA-induced epigenetic silencing (RNAe) , in which the C. elegans Piwi pathway can initiate a state of gene silencing that is extremely stable across generations.

 

The wiring diagram of the male tail form a neural network for mating.  See also this perspective:

.  Can this be done in humans? Watch this TED talk.

 

 

The Drosophila AF-6/afadin homolog Canoe (Cno) functionally interacts with the slit-Robo pathway.

 

See also:

Driver Mutations in Melanoma: Lessons Learned From Bench-to-Bedside Studies. Domain landscapes of somatic mutations in cancer.

 

Use the C. elegans OrthoList to find cancer genes in C. elegans:

 

 

 

Acoustic tweezers can manipulate C. elegans. See movie

Engineering to go beyond the constraints of the C. elegans genome to extend its lifespan.

 

Is ventral enclsoure the nematode phylotypic stage. Also see this preiview.

 

Rac GTPase activity is controlled by different GEFs in distinct axon guidance contexts, explaining how Rac GTPases can specifically control multiple cellular functions.

 

An photo-inducible cell ablation method.

 

 

The ATPase ASNA-1 is required for both growth and the L1 diapause. ykt-6, mrps-2, mrps-10 and mrpl-43 were identified genes that cause asna-1 like larval arrest.

 

 

In Zebrafish  hypoxia induces ephrinB2a activation and disrupts axon pathfinding. Interestingly magnesium sulfate (used to improve neurodevelopmental outcomes in preterm births) protects against pathfinding errors by preventing the upregulation of ephrinB2a.

 

A role of EphA:ephrinA attractive reverse signaling in motor axon guidance and in vivo evidence of in-parallel forward Eph and reverse ephrin signaling function in the same neuronal population

 

Review on the mechanisms regulating PTEN expression and function, including transcriptional regulation, post-transcriptional regulation by non-coding RNAs, post-translational modifications and protein–protein interactions.

 

PTEN is involved in the control of cell proliferation, migration, and survival of both cancer and tumor-associated endothelial cells. Ideally, combining PTEN-targeted therapy to classical chemotherapy should be a promising strategy.

 

This review is on cellular mechanisms underlying directional motility of the growth cone. The cellular ensemble of cytoskeleton, adhesion, and membrane orchestrates the directed movement of growth cones. 

UNC-6 (Netrin), is required for self-avoidance of sister dendrites from the PVD nociceptive neuron in Caenorhabditis elegans. UNC-40 receptor captures UNC-6 at the tips of growing dendrites for interaction with UNC-5 on the apposing branch to induce mutual repulsion.

 

New reagents that improve the efficiency, facilitate the selection for transgenic strains and expand the set of MosSCI insertion sites. See also:

 and this chapter.

 

 

The ability of PTEN to decrease neuronal spine density depended upon its protein phosphatase activity (not lipid) and its own phosphorylation status.

Short review on PTEN.

Super-PTEN mice have resistance to cancer and are less prone to obese due to increased energy expenditure and reduced body fat.

 

A summary of common genes that are regulators of neurodegenerative diseases obtained from model organism research.

 

While most genes when mutated don't lead to a gross observable phenotype, the Fraser lab demonstrate that, most agenes affect fitness, and this suggests that genetic networks are not robust to mutation.

 

RAE-1 binds RPM-1 and functions downstream of rpm-1 in neurons.

This is the first time that a key player of the PCP pathway is shown to be involved in the insulin/IGF-1-like signaling dependent modulation of life span in C. elegans.

 

VAPB/ALS8 major sperm protein domain (vMSP) are secreted by neurons act on Lar-like protein-tyrosine phosphatase (CLR-1) and Roundabout (SAX-3) growth cone guidance receptors expressed in striated muscle. This promotes striated muscle energy production and metabolism, in part through the regulation of mitochondrial localization and function.

 

 

A novel molecular "clutch" which anchors the preexisting contracting network of actomyosin in cells to contact points on neighbouring cells.

 

Selected by: Lois Mulligan. Ephrin A reverse signaling is mediated by Ret RTK.

Papers Selected in 2011


VAB-1 can function in P9/10 epidermal cells as well as in neurons in the  pocket cell ventral enclosure and functions redundantly with PLX-2/plexin to prevent gaps in the bridge used for P9/10 cell migration in body wall closure.

 

Ephrins (B1 and B2) bind to IL-7 receptor alpha to modulate its internalization and signaling.

 

EphA and B receptors cocluster, such that specific ligation of one receptor promotes recruitment and cross-activation of the other.

 

An explanation for incomplete penetrance.  See this News and Views.

 

Viral silencing agents, viRNAs, are transgenerationally transmitted in a template-independent manner and work in trans to silence viral genomes present in animals that are deficient in producing their own viRNAs.

 

This review focuses on recent progress in elucidating molecular interaction networks using different kinds of functional assays in the classical genetic model for animal development.

 

An automated system simultaneously images worm behavior and neuronal Ca2+ transients .

 

A Caenorhabditis elegans heterologous expression system able to produce milligram amounts of functional native and engineered GPCRs. Both bovine opsin [(b)opsin] and human adenosine A(2A) subtype receptor [(h)A(2A)R] expressed in neurons or muscles of C. elegans were localized to cell membranes. Worms expressing these GPCRs manifested changes in motor behavior in response to light and ligands, respectively. Also see this paper.

 

MiniSOG may do for EM what Green Fluorescent Protein did for fluorescence microscopy. See also this paper on using Mito-MiniSOG for targeted cell ablations.

 

 

hif-1 is required for most, if not all, early transcriptional changes in H2S. Moreover, SKN-1, the C. elegans homologue of NRF2, also contributes to H2S-dependent changes in transcription asskn-1 is essential to survive exposure to H2S.

 

Skin wounding in C. elegans triggers a Ca2+-dependent signaling cascade that promotes wound closure, in parallel to the innate immune response to damage. Wound closure requires actin polymerization and is negatively regulated by nonmuscle myosin.

 

 

 

 

A novel role for DAF-18 in promoting neurite outgrowth during development in Caenorhabditis elegans.  DAF-18/PTEN acts cell-autonomously to control neurite length in the AIY interneurons. DAF-16B isoform is required downstream of DAF-18 for outgrowth

 

MADD-4 is secreted by the dorsal and ventral nerve cords of the nematode C. elegans to attract sensory axons and muscle membrane extensions called muscle arms. MADD-4's activity is dependent on UNC-40/DCC, a netrin receptor, which functions cell-autonomously to direct membrane extension.

 

 

Another successful chemical genomics project from the Peter Roy's lab. Dafadine an inhibitor of DAF-9.

 

These results indicate that the maternal environment affects both progeny reproduction and development in C. elegans and therefore that all progeny are not equal.

Both the initial double-stranded RNA (dsRNA), which triggers RNAi, and at least one dsRNA intermediate produced during RNAi can act as or generate mobile silencing RNA in C. elegans.

 

 

The transgenerational inheritance of lifespan extension by members of the ASH-2 complex is dependent on the H3K4me3 demethylase RBR-2, and requires the presence of a functioning germline in the descendants.

 

New technologies for C. elegans.

 

New method to follow RNA in vivo.

 

Selected >650 C. elegans genes based on their orthology to human genes and potential neuronal function or known biochemical role were crossed to the mec-4::gfp or mec-7::gfp markers and looked at PLM regeneration. Arf Guanine nucleotide Exchange Factor (GEF), EFA-6, acts as an intrinsic inhibitor of regrowth. They also report PLM overshoot and undershoot for many mutants tested.

 

motoneuron commissural axon morphology defects in mig-15 mutants result from impaired growth cone motility and subsequent failure to migrate across longitudinal obstacles or retract extra processes. ezrin/radixin/moesin ortholog ERM-1, the kinesin-1 motor UNC-116 and the actin regulator WVE-1 complex. Genetic analysis indicates that mig-15 and erm-1 act in the same genetic pathway to regulate growth cone migration and that this pathway functions in parallel to the UNC-116/WVE-1 pathway.

 

 

 

 

 

 

The hemidesmosome is not only structural but a mechanosensor that responds to tension that can stimulate signalling pathways. See Dispatch by Jeff Hardin

http://dx.doi.org/10.1016/j.cub.2011.03.052

 

 

A 554 essential genes network based on gonad phenotypes.  Watch Cell Paperclip

movies\Green et al 2011 High resolution C. elegans essential gene network.mp4

 

Selected by Ahmed: Robo1 interacts with Nrp1 to modulate semaphorin signaling in the developing forebrain. another example of Robo receptors forming putative hetero-receptor complexes. 

 

 

 

The decision for worms to leave their food is multigenic trait that is regulated by non-coding plymorphisms in tyra-3 (tyramine receptor 3). 

 

An update of Cell's most cited article.

The complete genomes of seven prostate tumours. Many rearrangements found. Rearrangement breakpoints were enriched near open chromatin, androgen receptor and ERG DNA binding sites in the setting of the ETS gene fusion TMPRSS2–ERG, but inversely correlated with these regions in tumours lacking ETS fusions.  Prostate cancer genes include PTEN, MAGI2, CADM2, 

 

Latest review of Eph in stem cells and cancer.

 

Yang et al. show that ephrin-A1 ligand-dependent activation of EphA2 decreases the growth of PC3 prostate cancer cells and profoundly inhibits the Akt-mTORC1 pathway, which is hyperactivated due to loss of the PTEN tumor suppressor. Their data suggest a novel signaling mechanism whereby EphA2 inactivates the Akt-mTORC1 oncogenic pathway through Aktdephosphorylation mediated by a serine/threonine phosphatase (PP1-like?).

Papers Selected in 2010


 Review on Cancer models in C. elegans.


 Mechanisms of trastuzumab (Herceptin) resistance.

  

Peroxidasins play crucial roles in development and reveal a new role for peroxidasins as extracellular inhibitors of axonal regeneration.

 

Review on morphogenesis: novel imaging methods, modeling, mechanical tension, and the role of junctions as signal integrators.

 

FMI-1 is a cell-type dependent axon guidance factor with different domain requirements for its different functions in pioneers and followers.

 

 

trans-generational inheritance of olfactory imprinting in C. elegans

 

P granules are not required to specify the germline in C. elegans.

 

Roles for PVD and FLP neurons:Noxious signals perceived by PVD and FLP promote an escape behavior consisting of increased speed, reduced pauses and reversals, and inhibition of egg-laying.

 

Review of trans generational epigenetic regulation in the germline.

 

Hemmingsson et al. show that C. elegans can be used to characterize cisplatin resistance mechanisms and propose that rationally designed drugs against ASNA-1 can sensitize cancer cells to cisplatin.

 

A way to visualize alternative splicing in vivo.

Using a C. elegans mutant as a drug screening toll of r spinal muscular atrophy.

 

An example of the TAT peptide crossing membranes in C. elegans.

 

kat-1 is required for the extension of lifespan and enhanced thermotolerance mediated by overexpression of the deacetylase gene sir-2.1

 

Reproductive aging in C. elegans and humans share many aspects including oocyte quality

 

Review on autophagy and longevity in C. elegans.

 

Diverse cell fate and cell polarity regulators control common mechanisms of morphogenesis in C. elegans.

 

The worm is even more like bacteria! Now you can use plasmids that carry antibiotic resistance genes to select for transgenic worms.

 

Inappropriate protein aggregation are hallmarks of neurodegenerative disorders including Parkinson's Huntington's and Alzheimer's disease.  van Ham et al. conducted a suppressor C. elegans screen for protein aggregation and identified MOAG-4 (modifier of aggregation 4) which is homologus to  SERF1A and SERF2 in humans.  See also:

 

Who would have thought your online gaming could lead to a nature paper! Link to Foldit

 

http://www.genemania.org

The evolution of trans-splicing. 

 

Theveneau et al. used xenopus neural crest cells as a models to show groups of cells (attached by  N-cadherin) are better at interpreting and responding to a chemotactic gradient (Sdf1) when compared to single cells.

 

ERK MAPK pathway increases longevity.  This longevity is consistent to what we see in vab-1 mutant worms, which have increased MAPK in oocyte maturation as well as increased DAF-18/PTEN.

 

 A review on RTK signaling [PDF]

 

Mice housed in an enriched environment (EE) showed decreased tumor growth. This is mediated through the expression of BDNF in the hypothalamus, which in turn shuts down the the fat hormone leptin.

Note EE is complex as the stress hormone levels are actually higher in EE mice. 

 

Here the authors show that the "pseudo gene" PTENP1 competes with micro RNAs that inhibit the PTEN gene. Therefore they provide a functional role for PTENP1 where it can protect the PTEN gene by sequestering away mircro RNAS that would normally target the 3'UTR of the PTEN gene. Thus PTENP1 "pseudo gene" acts as a bona fide tumour suppressor. This provocative regulation opens up the possibility of other so called "pseudo genes" have similar function.

 

Overlap extension PCR: A neat way to clone PCR products into any plasmid without using restriction enzymes or ligase. Note constructs used in this paper conform to the iGEM BioBrick standard. See Supplementary Material. Here is another method called Inverse Fusion PCR cloning. And another one called Exponential Megapriming PCR.  Also see Gibson Assembly method and follow up.

 

Is the concept of free will an illusion that has been selected for in human evolution? 

 

There is increased EGFR activity in PTEN deficient cells, and .PTEN knockdown confers resistance to EGFR kinase inhibitors. Vivanco et al. show that  PTEN  stabilizes a complex between the  Cbl E3 igase with EGFR, which targets EGFR for ubiquitinylation and degradation.

 

Phototransduction in the photoreceptor cell ASJ required a G protein–dependent cGMP pathway and the taste receptor homolog LITE-1. Phototransduction in ASJ does not required typical PDEs.

 

Modified FACS to sort worms!

 

Fleming et al. report on the phenotypic characterization of unc-34 the C. elegans  Ena/VASP ortholog. UNC-34 has roles in cell migration and genetically interacts with Wnt signaling in ALM polarity. 

 

 

More microfluidic devices for C. elegans.

 

The first report of a ser/thr phosphatase  (LET-92) regulating axon guidance.

 

Gene targeting in C. elegans!

 

A novel approach to use a temperature sensitive MEC-8 dependent RNA splicing to turn genes on or off. The mec-2

intron is specifically spliced out by MEC-8. Therefore you can insert this intron into any gene to regulate its splicing in a temperature dependent manner. The authors used this method for therde-1 gene to show you can get temperature sensitive RNAi. 

 

ten-1 encodes a transmembrane protein called Teneurin.  It is synthetic lethal with sax-3, unc-34 and unc-73.

 

Burns et al. provide structural features of drug-like small molecules that increase the likelihood of it working on C.elegans.

 

Morgan et al. used a small molecules that inhibit Ras-ERK signalling and showed that they could reprogram germ cells to switch from sperm production to oocytes.

 

 

HIF-1 prevents DNA-damaged induced germline apoptosis by inhbiting CEP-1/p53. Surprisingly, it does this in a differen tissue by transcriptionally up regulating  the tyrosinase TYR-2 in the ASJ sensory neurons. TYR-2 in turn is secreted by ASJ to antagonize CEP-1 in the germline.

 

 

Two papers from the Hobert and Moerman labs showing the feasibility of whole genome sequencing to identify EMS induced mutations.

 

Selected by Jun: Recent review that cites our work and possible connection of Eph and mTOR pathways.

 

Monoclonal antibodies for C. elegans available here.

 

Selected by Jun:  Expressing the SID-1 receptor in neurons (normally they don't) causes worms to be more sensitive to neuronal RNAi by feeding. Interestingly the SID-1 receptor acts as a sink for the dsRNA an non-neuronal tissues are reduced in their RNAi ability making this strain a useful tool to study the role of lethal genes in the nervous system.

 

Review on C. elegans sperm and oocyte signaling. With insight into understanding human diseases like ALS and cancer.

 

DCC associates with the translation initiation machinery and when the netrin ligand binds DCC it causes the the release of ribosomes and translation initiation factors to promote localized protein translation. Also see this preview.

 

Selected by Jun: A brief report that ROBO1 is cleaved and the intracellular part is found in the nucleus. What is the role of this receptor in the nucleus? That is the key question.

 

 

Matus et al. used previous genome-wide RNAi data to identify genes that gave a Protruding Vulva (Pvul) phenotype. Using these genes, they further tested which ones caused specific defects in Anchor Cell (AC) basement invasions. They identified 99 genes that promote cell invasion. They identified know genes involved in cell invasions verifying the validity of their screen. But, but most of the genes identified have not been previously been implicated in invasion or metastasis, in particular genes that encode for the cct complex (eg. cct-5) and lit-1 (a NEMO-like kinase). They went on to show the human orthologs of CCT-5 and LIT-1/NLK indeed have pro-invasion roles using a human carcinoma metastasis assay. This work is a beautiful example of how studying an in vivo process like AC invasion in C. elegans can identify human genes that regulate cell invasion and metastasis. 

 

A role for Ephrin-B2 independent of receptor binding. The PDZ binding domain is necessary for cell contraction and membrane blebbing.

 

Ghosh and Emmons use a swimming assay to quiescence in C. elegans. PKG (EGL-4) promotes quiescence as expected from previous results and here they report that the protein phosphatase calcineurin (TAX-6) promotes swimming. TAX-6 appears to function in the sensory neurons while EGL-4 appears to act downstream of acetylcholine release from motor neurons.

 

 

Some advice on lab management

 

Genetic and biochemical analysis reveal that ARR-1 functions to regulate DAF-2 signaling via direct interaction with MPZ 1 PDZ domain. ARR 1 and MPZ 1 are found in a complex with the PTEN ortholog DAF 18, and regulates DAF-2 signaling in vivo.

 

Elena Pasquale reviews Eph Receptor signalling in cancer and highlights some of the new research that makes Eph receptors promising targets for cancer therapy. Note there is mention of our Eph/PTEN interaction in C. elegans.

 

Selected by Jun: This paper gives a possible reason that accounts for "incomplete penetrance". They found "that expression in the wild-type network was highly regular, but that mutations to components of this network that are incompletely penetrant for loss of intestinal cells led to large variations in the expression of a downstream gene. These variations were subsequently thresholded to yield alternative cell fates, showing that incomplete penetrance can result from stochastic fluctuations in gene expression when mutations compromise mechanisms that normally buffer such variability.

    A novel method to image individual mRNA molecules was used:

see also Tuning In to Noise: Epigenetics and Intangible Variation

A preview on a paper describing how two small molecule inhibitors are rendered ineffective when their target kinases are involved in protein-protein interaction.  This highlights the need for in vivo kinetics of inhibition. Original paper Hoshi et al. (2010).

 

The authors express each of the 2 Robo receptors in each of the three distinct spatial and temporal patterns of the three robo genes (termed "robo swap"). It's not a Robo combinatorial protein code per se that is required for lateral positioning of axons but  but the difference in gene expression.  In contrast, structural differences are critical in midline crossing decisions, Robo 1 to prevent crossing and Robo2 to promote crossing.

 

Science news report on a recent article in BMC Evolutionary Biology suggesting that the "Asian Flush" mutation may have shaped human evolution as it might have protected farmers from the hazards of drinking alcohol. Many East Asian populations have mutations in alcohol dehydrogenase (ADH)  or aldehyde dehdrogenase (ALDH). Which can lead to high levels of acetlyaldehyde  (metabolic product of ADH on ethanol) leading to the red face, nausea headaches etc.

Zhuang et al. show that the over expression of EphA2 is an contributor to trastuzumab (aka Herceptin)) resistance. Activated EphA2 amplifies signaling through the phosphoinositide 3-kinase(PI3K)/Akt and MAPK pathways in resistant cells.

A Review on signal transduction synthetic biology some recent progress and limitations are discussed. Also, see this essay.

 

 

Sex determining genes regulate Robo signaling to influence midline crossing in Drosophila.

 

PTEN loss reduces eIF2alpha phosphoylation. The PKR kinase  is required to phosphorylate eIF2alpha and is dependent on the PTEN PDZ-binding motif. Thus PTEN can regulate protein synthesis (loss of PTEN has reduction of eIF2alpha phosphoylation) and they provide another example of PTEN function of the PI3K signaling pathway.  Note in worms the homolog of PKR ispek-1.  Also in worms loss of semaphorin/plexin signaling leads to increased eIF2alpha  phosphorylation and causes translation repression.

 

 

The Wellcome Trust Sanger Institute sequence the genomes from a malignant melanoma and a lung cancer patient. The melanoma genome contained more than 30,000 mutations (187 with non-synonymous a.a. changes)  and the lung cancer contained more than 23,000 mutations.  This implies that a typical smoker would acquire one mutation for every 15 cigarettes smoked.   There is not one gene that stands out as a "lung cancer gene" But the CHD7 was found to be mutated in several SCLC.  From the melanoma BRAF V600E and a deletion of PTEN confirm these as "driver" mutations.

Papers Selected in 2009


  The Worm Breeder's Gazette has returned after a 6 year hiatus.

Turning of FOXL2 in female mice caused ovary cells to change to testicular cells. This study challenges the assumption that the female fate is default pathway in sex determination.  In males SOX9 seems to be the key gene that keeps FOXL2 off.

 

A systems approach to look at ephrin-B1 and EphB2 cell-specific  signaling

during cell sorting.

 

Most oncogenic mutation of PI3K are in the p110 catalytic subunit but Jaiswal et al. report mutations in the p85alpha subunit that promotes tumor formation.  These mutation affect the inhibitory role of p85 on p110.

 

Defective autophagy can lead to tumors through the inability to eliminate p62 through autophagy. p62 is a multifunctional protein that binds polyubiquitinated proteins  and forms aggregates to target proteins to the autophagosomes for degradation. p62 also up regulates NF-kB to promote tumorgenesis.

 

 

Two reviews on next-generation sequencing

 

$5000 Prize for finding a new Caenorhabditis species has still yet to be won. How to isolate wild  C. elegans and other related nematodes. 

 

Another example that introns are not junk DNA: Myosin genes have a intronic miRNAs that control muscle gene expression and performance.

 

Alterations in DNA (mutation) can lead to uncontrolled and invasive growth (cancer).  Here the authors describe a mechanism for an epigentic switch (no alteration in DNA sequence) that promotes transformation of breast cancer cells through multiple generations. This switch mechanism they describe could allow transient events like inflammation or exposure to environmental factors (not necessarily altering DNA sequence) to produce a cancerous state just like a mutations that inactivate a tumor suppressor or activate and oncogene.

From 1959: Can a single injury cause cancer? This author says no. But these new epigenetic mechanisms suggest maybe.

A new role for slit and robo in keeping cell boundaries and compartments.  This role is similar to what the Eph Receptors do.

 

A perspective on the following two papers:

Two  G-protein coupled receptors mediate the dauer pheromone signal.


 

Another form of C. elegans diapuse (in addition to L1 arrest and dauer).  Adult reproductive diapuase (ARD) in C. elegans allows the worm to delay reproduction by 15 fold and extend life span at least threefold. ARD requires apoptotic death of the germline, except for the germline stem cells.  The NHR-49 nuclear receptor is required for entry and recovery of ARD.

 

EphB receptors have a paradoxical function: int intestinal epithelium they can promote cell proliferation (i.e. oncogenic) but can also act as a tumor suppressor in colon cancer development.

Here Genander et al. report that the EphB2 receptors regulates two separate pathways. EphB2  suppresses cell migration through the PI3K pathway in a kinase independent manner and regulates cell proliferation through Abl-cyclin D1 in a kinase dependent manner.  See preview by Roberta Noberini and Elena Pasquale.

 

PI(4,5)P2 and NCK cooperate in N-WASP-stimulated actin polymerization.

Review on the field of developmental neuroscience.

Herbert et al. show that coordinated signaling mechanisms including Ephrin B2 and EphB4 drives angioblast migration and arterial-venous segregation during vessel development.

P-REX2a (phosphatidylinositol 3,4,5-trisphosphate RAC exchanger 2a (P-REX2a) binds to PTEN to inhibit PTEN lipid phohsphatase to increase PI3K/AKT signaling. See also this perspecitve.

Tips on how to give a good talk. See also my tips.

The budding yeast Saccharomyces cerevisiae lacks RNAi. But now Dinnernberg et al. show that RNAi can be restored in S. cerevisiae, by introducing Dicer and Argonaute genes of S. castellii.

Nile Red on live worms does not correlate with fat biochemical quantification. Nutritional cues perceive in the intestine regulate fat independent of neuroendocrine cues. Specific peptides may provide regulating fat metabolism and fat storage.

Janes et al. show that tyrosine phosphorylation of EphA3 changes the tyrosine kinase domain conformation away from the plama membrane to allow ADAM10 to come in contact with its substrate, ephrinA5.

Injection of  miR-124 into fertilized mouse eggs resulted in a 30% increase in body size. But the surprising part is that it lasted into adulthood and the males could epigenetically pass this phenotype to their offspring.  The researchers suggest that modification of the Sox-9 gene is involved.

LTR is a leucine-rich repeat transmembrane protein expressed in tendons. LTR  acts as a lignad for Robo during muscle cell migration towards the tendon cells.

Goldstein lab review on apical constriction mechanisms.

A gene targeting approach for C. elegans.

Mechanism of transcription termination in C. elegans and the importance of the first intron downstream of polycistronic pre-mRNAs in expression a role in preventing premature pol II transcription termination.

 

A mathematical model shows PTEN protein expression to be the key determinant of resistance to anti-HER2 therapy (eg. trastuzumab aka Herceptin). Note that Nagata  et al (2004) also showed that PTEN deficiency is a powerful predictor for trastuzumab.

 

Bruce Alberts' editorial encouraging research funding agencies to fund research in more accessible organisms not just human cells. The most profound impact on cancer treatments  comes form basic research on model organisms, rather than form studies of highly complex human tumors. 

 

Qian et al. have provided a novel mode of regulation for an SH2 domain.  The SH2 domain of tensin-3 is phosphoylated by Src tyrosine kinase and this phosphorylation promotes the oncogenic function of tensin-3. Whether other SH2 domins are regulated by tyrosine kinases remains to be shown.

 

 

Andrew Chisholm and Yishi Jin Labs' show thai in C. elegans neurons the DLK-1 pathway acts via the MAPKAP kinase, MAK-2, to promote stabilization of the mRNA of the bZip protein CEBP-1, resulting in enhanced CEBP-1 translation. This mechanism is also required for the regenerative responses of adult neurons.

 

Fine et al. identified P-REX2a, a guanine nucleotide exchange factor (GEF) for the RAC small guanosine triphosphatase as a binding partner for PTEN. P-REX2a inhibited catalytic activity of PTEN.  P-REX2a thus provides a mechanism through which tumor cells may inactivate PTEN. Ian's notes: The closest match to P-REX2a in C. elegans is VAV-1 which is a Rho/Rac GEF and orthologous to the Vav prto-oncogene.  VAB-1 has been shown to function with VAB-1/EphR in oocytes Govindan et al. 2006 and Cheng et al. 2008.

Here, Bear and Gertler try to resolve the controversy of the anti-capping role for Ena/VASP.  In addition, they describe several alternate mechanisms that Ena/VASP proteins may utilize to regulate actin dynamics in vivo, including inhibition of branching, bundling and profilin-actin recruitment. 

 

 

Review on PI3K signaling in cancer. 

Review on mutations that affect sleep. [PDF]

Selected by Jun: This new Cell paper shows that SH2 domain also binds to a non-canonical site on the RTK (non pY) in a kinase independent manner. They discover that "N-SH2 domain of PLCγ utilizes an additional region separate from its canonical pY binding site for binding to a region in the C-lobe of the tyrosine kinase domain of FGFR1 in a phosphorylation-independent manner"

A description of Pdk-1 dependent and independent  effects  in different cells with pten deleted.

Integrin clustering can be initiated by Eph/Ephrin reverse signaling to form the ECM.

 

 

Some evidence to support the apparent paradox of EphA2  roles in cell migration and invasion. The oncogenic role of EphA2 is ligand independent and required the S897 phosphorylation by AKT. Interestingly ephrin-A1 stimulation could reverse the S897 caused by AKT. 

An interesting paper describing how a subunit of the WAVE complex (Cyfip1) may act as a invasion suppression gene. This is a surprising result given that proteins that promote actin-based protrusions (i.e. WAVE/SCAR) are thought to be needed for invasion during metastasis. 

Review on the roles of Eph signaling at the synapse.

A-class Eph receptor/ephrin interactions involve smaller rearrangements in the interacting partners, better described by a 'lock-and-key'-type binding mechanism, in contrast to the 'induced fit' mechanism defining the B-class molecules.

selected by Jun: Long lived C. elegans (due to decreased insulin-like signalling) have misexpression of germline genes (eg. pie-1  and pgl-1 ) in somatic tissues. DAF-16, the major transcriptional effector of insulin-like signalling, regulates pie-1 expression by directly binding to the pie-1 promoter. Thus the somatic tissues of insulin-like mutants are more germline-like and protected from genotoxic stress.

Selected by Jun. Another Eph Receptor (EphA3) binds to the NCK1 adaptor. PY602 of EphA3 binds tot he SH2 domain of NCK1. The interaction is much greater on "activated" EphA3 when stimulated with Ephrin-A5.

Talking mice? The Foxp2 gene is thought to be involved in the evolution of human speech and language.  This group put the human version of Fox2p in mice and found that these mice have different vocalizations (lower pitched) and have increased synaptic plasticity in the brain regions thought to be important for speech.

XIAP closest match in C. elegans is encoded by the  bir-2

MicroRNA miR-26a negatively regulates PTEN

 

Selected by Jun: Dendrite shape is not only cause by an "out growth" but instead the dendritic tip can anchor itself and  and the cell body migrates away from it. DEX-1 and DYF-7 are Transmembrane proteins (Tectorin-like) that are required for proper anchoring of the dendrites.

 

Using a novel genetic screen Hammarlund et al.  identified DLK-1 MAP kinase kinase kinase (MAPKKK) as a protein requierd of axon regenration.  Also see O'Brien and Sagasti Science signalling [perpespetive]

An interesting study that shows the Src family tyrosine kinase, Rak,  binds to and can phosphorylate PTEN and stabilizes it by protecting it from ubiquitin-mediated degradation. As such, Rak acts as a strong tumor suppressor.  However, it should be noted that this paper has results that are opposite to what Lu et al 2003 found  which shows Src kinase family inhibits PTEN activity and stability. See: http://www.jbc.org/cgi/content/full/278/41/40057

 

Review on vertebrate cilia and physiological consequences of abnormal cilliogenesis.

Definition: “An epigenetic trait is a stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence.”

During L1 arrest RNA Polymerase II binds to promoters of growth and development genes in anticipation of favorable condition.

Review on protein phophatases

 

crml-1 was identified as a suppressor of unc-34/ena.  CRML-1 inhibitory binding to UNC-73 causes lower SAX-3/Robo levels

P granule components are degraded by autophagy.

 

the role of phosphoinositides in developmental signaling

 

A new model for apical constriction: In contrast to a "purse-string " model constriction pulses (asynchronous) are powered by actin-myosin network of contractions that occur at the medial apical cortex and pull discrete adherens junction sites inwards. The transcription factors snail and   twist  regulate the pulse constrictions.  See preview in DevCell

15 examples published by Nature that provide evidence for evolution by natural selection.