Linear Pathway Research Articles

Studying Cancer Evolution in Barrett's Esophagus and Esophageal Adenocarcinoma.

Technological advances in genome sequencing and copy number analysis have allowed researchers to catalog the wide variety of genomic alterations that occur across diverse cancer types. For most cancer types, the lack of high-frequency alterations and the heterogeneity observed both within and between tumors suggest neoplastic progression proceeds through a branched evolutionary pathway as proposed by Nowell in 1976, as opposed to the linear pathway that has dominated medical science for the last century. To understand how cancer evolves over time and space in the body, new study designs are needed that can distinguish between alterations that develop in patients who progress to cancer from to those who don't. Here we present approaches developed in the study of Barrett's esophagus, a premalignant precursor of esophageal adenocarcinoma, and discuss strategies for applying the results from these analyses to address the critical clinical problems of overdiagnosis of benign disease, early detection of life-threatening cancer, and effective risk stratification.

Noncanonical Activin A Signaling in PC12 Cells: A Self-Limiting Feedback Loop.

Activin A (Act A), a member of transforming growth factor-β superfamily, plays a neuroprotective role in multiple neurological diseases through Act A/Smads signal activation. Traditionally, the up-regulation of Act A gene and extracellular Act A accumulation show the signal activation as a linear pathway. However, one of our discoveries indicated that Act A could lead a loop signaling in ischemic injury. To clarify the characteristic of this loop signaling in a non-pathological state, we up-regulated the expression of Act A, monitored extracellular Act A accumulation and examined the activity of Act A signaling, which was quantified by the expression of phosphorylated Smad3 and the fluorescence intensity of Smad4 in nuclei. The results demonstrated a noncanonical Act A signal loop with self-amplifying property in PC12 cells. Further, it showed self-limiting behavior due to temporary activation and spontaneous attenuation. This periodic behavior of Act A signal loop was found to be regulated by the level of Smad anchor for receptor activation (SARA). Moreover, increased activity of Act A signal loop could promote PC12 cell proliferation and enhance the survival rate of cells to Oxygen-Glucose Deprivation. These practical discoveries will bring new insight on the functional outcome of Act A signaling in neurological diseases by the further understanding: loop signaling.

Solving linear unbranched pathways with Michaelis–Menten kinetics using the Lambert W-function

In this paper, an n-step, linear and unbranched pathway with Michaelis–Menten kinetics is solved in a quasi-analytical way. The method, based on the optimal control theory, calculates the optimal enzyme concentrations while minimizing the operation time. In the computation of the solution, the Lambert W-function plays a fundamental role, due to the presence of a non-linear kinetic model. Our method allows us to obtain the generalized solution and to perform the sensitivity analysis of the catalytic parameters.

Process evaluation in drugs trials within adult learning disability populations: a systematic review

The majority of RCTs focus on outcomes rather than on the processes involved in implementing an intervention. Process evaluations within trials examine not only the implementation but also the receipt and setting of an intervention which aids the interpretation of outcome results. Currently, process evaluations tend to be the domain of ‘complex interventions’ in health and public health research rather than drugs trials (CTIMPs). CTIMPs tend to be thought of as more ‘simple’ interventions having linear pathways from the intervention to the outcome. However, as pharmacological interventions move past early stage research and are rolled out into practice, their implementation shifts to becoming complex in nature. This is particularly true when implementing interventions in populations where neurodevelopmental impairments mean an individual may lack capacity. Parents/carers looking after the best interests of such individuals effectively become extra ‘layers’ through which the intervention needs to be administered. This added degree of complexity is something which is perhaps not routinely addressed. This systematic review is of drug trials that have been carried out in adult populations with neurodevelopmental impairments which incorporat a process evaluation element. A systematic search of PsycINFO, EMBASE, MEDline, CINAHL and the Cochrane Central Register of Controlled Trials will be undertaken. The aim being to identify existing methods of evaluating interventions and provide a qualitative narrative of these. Results will be used to develop the approach taken to later stage CTIMPs particularly in this population and to explore the potential for a new framework for evaluating interventions of this nature.

Designing overall stoichiometric conversions and intervening metabolic reactions.

Existing computational tools for de novo metabolic pathway assembly, either based on mixed integer linear programming techniques or graph-search applications, generally only find linear pathways connecting the source to the target metabolite. The overall stoichiometry of conversion along with alternate co-reactant (or co-product) combinations is not part of the pathway design. Therefore, global carbon and energy efficiency is in essence fixed with no opportunities to identify more efficient routes for recycling carbon flux closer to the thermodynamic limit. Here, we introduce a two-stage computational procedure that both identifies the optimum overall stoichiometry (i.e., optStoic) and selects for (non-)native reactions (i.e., minRxn/minFlux) that maximize carbon, energy or price efficiency while satisfying thermodynamic feasibility requirements. Implementation for recent pathway design studies identified non-intuitive designs with improved efficiencies. Specifically, multiple alternatives for non-oxidative glycolysis are generated and non-intuitive ways of co-utilizing carbon dioxide with methanol are revealed for the production of C2+ metabolites with higher carbon efficiency.

“Should I stay or should I go?” Exploring high school apprentices’ pathways

Completion rates are one measure of the success of apprenticeship training. But little is known about outcomes for youth who begin an apprenticeship in high school. This paper draws primarily on interviews with youth who did not continue training or work in their high school apprenticeship trade in two Canadian provinces. Our analysis focuses on why these youth decided to enrol in high school apprenticeship, why they did not continue and what they did afterwards. Findings suggest that a narrow focus on apprenticeship training completion diverts attention from the complex learning and work transitions experienced by most youth. Instead of assuming a linear pathway from school-to-trades work, we argue that partners involved in high school apprenticeship and policy-makers could do more to raise student awareness of multiple trajectories and skills transfer, make apprenticeship training more expansive, and increase the flexibility of pathways by providing greater articulation between different post-secondary education pathways and opportunities to change direction.

Ethylene Control of Fruit Ripening: Revisiting the Complex Network of Transcriptional Regulation.

The plant hormone ethylene plays a key role in climacteric fruit ripening. Studies on components of ethylene signaling have revealed a linear transduction pathway leading to the activation of ethylene response factors. However, the means by which ethylene selects the ripening-related genes and interacts with other signaling pathways to regulate the ripening process are still to be elucidated. Using tomato (Solanum lycopersicum) as a reference species, the present review aims to revisit the mechanisms by which ethylene regulates fruit ripening by taking advantage of new tools available to perform in silico studies at the genome-wide scale, leading to a global view on the expression pattern of ethylene biosynthesis and response genes throughout ripening. Overall, it provides new insights on the transcriptional network by which this hormone coordinates the ripening process and emphasizes the interplay between ethylene and ripening-associated developmental factors and the link between epigenetic regulation and ethylene during fruit ripening.

Metalloregulator CueR biases RNA polymerase’s kinetic sampling of dead-end or open complex to repress or activate transcription

Metalloregulators respond to metal ions to regulate transcription of metal homeostasis genes. MerR-family metalloregulators act on σ(70)-dependent suboptimal promoters and operate via a unique DNA distortion mechanism in which both the apo and holo forms of the regulators bind tightly to their operator sequence, distorting DNA structure and leading to transcription repression or activation, respectively. It remains unclear how these metalloregulator-DNA interactions are coupled dynamically to RNA polymerase (RNAP) interactions with DNA for transcription regulation. Using single-molecule FRET, we study how the copper efflux regulator (CueR)--a Cu(+)-responsive MerR-family metalloregulator--modulates RNAP interactions with CueR's cognate suboptimal promoter PcopA, and how RNAP affects CueR-PcopA interactions. We find that RNAP can form two noninterconverting complexes at PcopA in the absence of nucleotides: a dead-end complex and an open complex, constituting a branched interaction pathway that is distinct from the linear pathway prevalent for transcription initiation at optimal promoters. Capitalizing on this branched pathway, CueR operates via a "biased sampling" instead of "dynamic equilibrium shifting" mechanism in regulating transcription initiation; it modulates RNAP's binding-unbinding kinetics, without allowing interconversions between the dead-end and open complexes. Instead, the apo-repressor form reinforces the dominance of the dead-end complex to repress transcription, and the holo-activator form shifts the interactions toward the open complex to activate transcription. RNAP, in turn, locks CueR binding at PcopA into its specific binding mode, likely helping amplify the differences between apo- and holo-CueR in imposing DNA structural changes. Therefore, RNAP and CueR work synergistically in regulating transcription.

Identification of two mutations increasing the methanol tolerance of Corynebacterium glutamicum.

BackgroundMethanol is present in most ecosystems and may also occur in industrial applications, e.g. as an impurity of carbon sources such as technical glycerol. Methanol often inhibits growth of bacteria, thus, methanol tolerance may limit fermentative production processes.ResultsThe methanol tolerance of the amino acid producing soil bacterium Corynebacterium glutamicum was improved by experimental evolution in the presence of methanol. The resulting strain Tol1 exhibited significantly increased growth rates in the presence of up to 1 M methanol. However, neither transcriptional changes nor increased enzyme activities of the linear methanol oxidation pathway were observed, which was in accordance with the finding that tolerance to the downstream metabolites formaldehyde and formate was not improved. Genome sequence analysis of strain Tol1 revealed two point mutations potentially relevant to enhanced methanol tolerance: one leading to the amino acid exchange A165T of O-acetylhomoserine sulfhydrolase MetY and the other leading to shortened CoA transferase Cat (Q342*). Introduction of either mutation into the genome of C. glutamicum wild type increased methanol tolerance and introduction of both mutations into C. glutamicum was sufficient to achieve methanol tolerance almost indistinguishable from that of strain Tol1.ConclusionThe methanol tolerance of C. glutamicum can be increased by two point mutations leading to amino acid exchange of O-acetylhomoserine sulfhydrolase MetY and shortened CoA transferase Cat. Introduction of these mutations into producer strains may be helpful when using carbon sources containing methanol as component or impurity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0558-6) contains supplementary material, which is available to authorized users.

Design Principles as a Guide for Constraint Based and Dynamic Modeling: Towards an Integrative Workflow.

During the last 10 years, systems biology has matured from a fuzzy concept combining omics, mathematical modeling and computers into a scientific field on its own right. In spite of its incredible potential, the multilevel complexity of its objects of study makes it very difficult to establish a reliable connection between data and models. The great number of degrees of freedom often results in situations, where many different models can explain/fit all available datasets. This has resulted in a shift of paradigm from the initially dominant, maybe naive, idea of inferring the system out of a number of datasets to the application of different techniques that reduce the degrees of freedom before any data set is analyzed. There is a wide variety of techniques available, each of them can contribute a piece of the puzzle and include different kinds of experimental information. But the challenge that remains is their meaningful integration. Here we show some theoretical results that enable some of the main modeling approaches to be applied sequentially in a complementary manner, and how this workflow can benefit from evolutionary reasoning to keep the complexity of the problem in check. As a proof of concept, we show how the synergies between these modeling techniques can provide insight into some well studied problems: Ammonia assimilation in bacteria and an unbranched linear pathway with end-product inhibition.

A kinetic model for analysis of physical tunnels in sequentially acting enzymes with direct proximity channeling

Direct channeling is a well-known process in which intermediates are funneled between enzyme active sites through a physical tunnel and can be a potential way to enhance the biocatalytic efficiency for cascading bioreactions. However, the exact mechanism of the substrate channeling remains unclear. In this work, we used mathematical models to describe the mass transfer in the physical tunnels and to gain further understanding of direct proximity channeling. Simulation with a diffusion-reaction model showed that the reduction of the diffusion distance of intermediates could not cause proximity channeling. A second kinetic model, which considered the physical tunnel as a small sphere capable of preventing diffusion of the intermediate into the bulk, was then constructed. It was used to show that the maximum channeling degree in branched pathways depends on the strength of the side reactions, suggesting that proximity channeling in a physical tunnel is more suitable for a pathway with strong side reactions. On the other hand, for a linear pathway, proximity channeling is more beneficial when the constituting enzymes have relatively low activities and expression levels. Our kinetic model provides a theoretical basis for engineering proximity channeling between sequentially acting enzymes in microbial cell factories and enzyme engineering.

Production of carbon-13-labeled cadaverine by engineered Corynebacterium glutamicum using carbon-13-labeled methanol as co-substrate.

Methanol, a one-carbon compound, can be utilized by a variety of bacteria and other organisms as carbon and energy source and is regarded as a promising substrate for biotechnological production. In this study, a strain of non-methylotrophic Corynebacterium glutamicum, which was able to produce the polyamide building block cadaverine as non-native product, was engineered for co-utilization of methanol. Expression of the gene encoding NAD+-dependent methanol dehydrogenase (Mdh) from the natural methylotroph Bacillus methanolicus increased methanol oxidation. Deletion of the endogenous aldehyde dehydrogenase genes ald and fadH prevented methanol oxidation to carbon dioxide and formaldehyde detoxification via the linear formaldehyde dissimilation pathway. Heterologous expression of genes for the key enzymes hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase of the ribulose monophosphate (RuMP) pathway in this strain restored growth in the presence of methanol or formaldehyde, which suggested efficient formaldehyde detoxification involving RuMP key enzymes. While growth with methanol as sole carbon source was not observed, the fate of 13C-methanol added as co-substrate to sugars was followed and the isotopologue distribution indicated incorporation into central metabolites and in vivo activity of the RuMP pathway. In addition, 13C-label from methanol was traced to the secreted product cadaverine. Thus, this synthetic biology approach led to a C. glutamicum strain that converted the non-natural carbon substrate methanol at least partially to the non-native product cadaverine.

Abstract 2158: PDK1-dependent activation of RSK is an absolute requirement for PI3K oncogenic activity in the thyroid gland

Abstract Aberrant activation of the phosphatidylinositol-3 kinase (PI3K)/Akt pathway plays a key role in thyroid tumorigenesis, particularly in follicular thyroid cancer (FTC) and anaplastic thyroid cancer (ATC). Accordingly, conditional deletion of Pten in the mouse thyroid epithelium induces constitutive activation of the PI3K/AKT pathway, and causes thyroid hyperplasia at birth that progresses to invasive and metastatic follicular carcinoma. This phenotype is dramatically accelerated by simultaneous deletion of Trp53, leading to the development of ATC, or activation of Kras, leading to poorly differentiated carcinomas. The PDK1 kinase plays a central role in the PI3K signaling cascade, acting as a master regulator of PI3K downstream effectors belonging to the AGC kinases family, such as AKT and S6K1. Additional AGC kinases are controlled by PDK1 independent of PI3K activity. PDK1 possesses a substrate docking site, the “PIF pocket”, required for the phosphorylation of most AGC kinases (including S6K, PKC, SGK, and RSK) but not of AKT. The L155E PDK1 mutant disrupts the PIF pocket and impairs AGC kinase activation, without any effect on AKT activation. Thanks to this differential mechanism of substrate activation, we are defining the relative contribution of AKT and other PDK1 targets to the neoplastic transformation process in Pten-/- thyrocytes. Surprisingly, in vivo disruption of the PIF-pocket completely abrogates neoplastic transformation of Pten-/- thyroids, even in the face of AKT constitutive activation. This finding supports the hypothesis that the linear PI3K-AKT pathway is not sufficient to drive thyroid transformation and that concomitant activation of additional PDK1-dependent pathways is absolutely required. We now show that RSK family members (RSK1-3) are essential components of this PDK1-dependent accessory pathway. Remarkably, RSK3 levels in the thyroid are increased in the absence of Pten, and RSK activity in thyroid cells is abrogated when PDK1 PIF-pocket is mutated. Genetic and pharmacological inhibition of RSK drastically impairs [Pten,Trp53]-/- ATC cell proliferation both in vitro and in vivo, in syngeneic allograft models. Taken together, our data identify a new signaling cascade that is essential for neoplastic transformation of thyroid epithelial cells, and thus a new critical candidate for drug development. Citation Format: Arturo Orlacchio, Antonio Di Cristofano. PDK1-dependent activation of RSK is an absolute requirement for PI3K oncogenic activity in the thyroid gland. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2158. doi:10.1158/1538-7445.AM2015-2158

Short-term regulation and alternative pathways of photosynthetic electron transport in Hibiscus rosa-sinensis leaves

In this work, using the EPR and PAM-fluorometry methods, we have studied induction events of photosynthetic electron transport in Hibiscus rosa-sinensis leaves. The methods used are complementary, providing efficient tools for in situ monitoring of P700 redox transients and photochemical activity of photosystem II (PSII). The induction of P700+ in dark-adapted leaves is characterized by the multiphase kinetics with a lag-phase, which duration elongates with the dark-adaptation time. Analyzing effects of the uncoupler monensin and artificial electron carrier methylviologen (MV) on photooxidation of P700 and slow induction of chlorophyll a fluorescence (SIF), we could ascribe different phases of transient kinetics of electron transport processes in dark-adapted leaves to the following regulatory mechanisms: (i) acceleration of electron transfer on the acceptor side of PSI, (ii) pH-dependent modulation of the intersystem electron flow, and (iii) re-distribution of electron fluxes between alternative (linear, cyclic, and pseudocyclic) pathways. Monensin significantly decreases a level of P700+ and inhibits SIF. MV, which mediates electron flow from PSI to O2 with consequent formation of H2O2, promotes a rapid photooxidation of P700 without any lag-phase peculiar to untreated leaves. MV-mediated water–water cycle (H2O→PSII→PSI→MV→O2→H2O2→H2O) is accompanied by generation of ascorbate free radicals. This suggests that the ascorbate peroxidase system of defense against reactive oxygen species is active in chloroplasts of H. rosa-sinensis leaves. In DCMU-treated chloroplasts with inhibited PSII, the contribution of cyclic electron flow is insignificant as compared to linear electron flow. For analysis of induction events, we have simulated electron transport processes within the framework of our generalized mathematical model of oxygenic photosynthesis, which takes into account pH-dependent mechanisms of electron transport control and re-distribution of electron fluxes between alternative pathways. The model adequately describes the main peculiarities of P700+ induction and dynamics of the intersystem electron transport.

Non-monotonic dynamics and crosstalk in signaling pathways and their implications for pharmacology.

Currently, drug discovery approaches commonly assume a monotonic dose-response relationship. However, the assumption of monotonicity is increasingly being challenged. Here we show that for two simple interacting linear signaling pathways that carry two different signals with different physiological responses, a non-monotonic input-output relation can arise with simple network topologies including coherent and incoherent feed-forward loops. We show that non-monotonicity of the response functions has severe implications for pharmacological treatment. Fundamental constraints are imposed on the effectiveness and toxicity of any drug independent of its chemical nature and selectivity due to the specific network structure.

New features of triacylglycerol biosynthetic pathways of peanut seeds in early developmental stages.

The peanut (Arachis hypogaea L.) is one of the three most important oil crops in the world due to its high average oil content (50 %). To reveal the biosynthetic pathways of seed oil in the early developmental stages of peanut pods with the goal of improving the oil quality, we presented a method combining deep sequencing analysis of the peanut pod transcriptome and quantitative real-time PCR (RT-PCR) verification of seed oil-related genes. From the sequencing data, approximately 1500 lipid metabolism-associated Unigenes were identified. The RT-PCR results quantified the different expression patterns of these triacylglycerol (TAG) synthesis-related genes in the early developmental stages of peanut pods. Based on these results and analysis, we proposed a novel construct of the metabolic pathways involved in the biosynthesis of TAG, including the Kennedy pathway, acyl-CoA-independent pathway and proposed monoacylglycerol pathway. It showed that the biosynthetic pathways of TAG in the early developmental stages of peanut pods were much more complicated than a simple, unidirectional, linear pathway.

Atrioventricular nodal block with atrioventricular nodal reentrant tachycardia ablation.

The initial model of atrioventricular nodal tachycardia (AVNRT) as a small circuit of reentry within the AV node precluded a catheter-based cure for this arrhythmia without the occurrence of AV conduction block. Landmark observations that the atria were part of the circuit of AVNRT1 and that the arrhythmia could be reset with paced beats placed at sites anatomically distant from the compact AV node2 set the stage for the present expectation of curative ablation without AV block. Despite this understanding of the AVNRT mechanism and the large accrued operator experience during the past 3 decades when ablating this arrhythmia, AV block still occurs in ≈1% to 2.3% as a complication of ablation.3 See Article p 739 In this installment of teaching rounds, Chen et al4 share with us what we can learn from a series of patients with permanent or transient AV block noted during and soon after radiofrequency energy delivery. The authors provide an honest, transparent, and instructive view of their 5 cases. The fact that we are successful ≈99% of the time without complication suggests that the present methods for maintaining safety, including monitoring junctional rhythm during ablation and relating catheter position to the fluoroscopic anatomic approximation of the AV node location are mostly successful. The student of electrophysiology must, however, be aware of how these precautions can fail us. Even closely spaced bipolar electrodes placed over the compact AV node are not able to record electrograms from the node itself. Because we cannot map the structure we need to avoid, we must estimate anatomically its location and correlate this information with our standard fluoroscopic views. ### Utility The compact AV node is located within Koch’s triangle, approximately in its mid and central position. Using the His bundle as a surrogate for the superior vertex and …

Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation.

BackgroundAdjusting the capacity of metabolic pathways in response to rapidly changing environmental conditions is an important component of microbial adaptation strategies to stochastic environments. In this work, we use advanced dynamic optimization techniques combined with theoretical models to study which reactions in pathways are optimally targeted by regulatory interactions in order to minimize the regulatory effort that is required to adjust the flux through a complex metabolic network. Moreover, we analyze how constraints in the speed at which an organism can respond on a proteomic level influences these optimal targets of pathway control.ResultsWe find that limitations in protein biosynthetic rates have a strong influence. With increasing protein biosynthetic rates the regulatory effort targeting the initial enzyme in a pathway is reduced while the regulatory effort in the terminal enzyme is increased. Studying the impact of allosteric regulation for different pathway topologies, we find that the presence of feedback inhibition by products of metabolic pathways allows organisms to reduce the regulatory effort that is required to control a metabolic pathway in all cases. In a linear pathway this even leads to the case where the sole transcriptional regulatory control of the terminal enzyme is sufficient to control flux through the entire pathway. We confirm the utilization of these pathway regulation strategies through the large-scale analysis of transcriptional regulation in several hundred prokaryotes.ConclusionsThis work expands our knowledge about optimal programs of pathway control. Optimal targets of pathway control strongly depend on the speed at which proteins can be synthesized. Moreover, post-translational regulation such as allosteric regulation allows to strongly reduce the number of transcriptional regulatory interactions required to control a metabolic pathway across different pathway topologies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0587-z) contains supplementary material, which is available to authorized users.

On the Mathematical Modelling of Linear Metabolic Networks

We consider metabolic networks of simple enzymatic reactions of V.Henri type. Applying the mass action law the reactions lead to a system of ordinary diferential equations. For a linear chain of reactions we propose certain simplications of the ODE system as well as a solution of the initial problem for the system. Some numerical examples are presented.

A Synthetic Lethal Screen Identifies a Role for Lin-44/Wnt in C. elegans Embryogenesis.

BackgroundThe C. elegans proteins PTP-3/LAR-RPTP and SDN-1/Syndecan are conserved cell adhesion molecules. Loss-of-function (LOF) mutations in either ptp-3 or sdn-1 result in low penetrance embryonic developmental defects. Work from other systems has shown that syndecans can function as ligands for LAR receptors in vivo. We used double mutant analysis to test whether ptp-3 and sdn-1 function in a linear genetic pathway during C. elegans embryogenesis.ResultsWe found animals with LOF in both sdn-1 and ptp-3 exhibited a highly penetrant synthetic lethality (SynLet), with only a small percentage of animals surviving to adulthood. Analysis of the survivors demonstrated that these animals had a synergistic increase in the penetrance of embryonic developmental defects. Together, these data strongly suggested PTP-3 and SDN-1 function in parallel during embryogenesis. We subsequently used RNAi to knockdown ~3,600 genes predicted to encode secreted and/or transmembrane molecules to identify genes that interacted with ptp-3 or sdn-1. We found that the Wnt ligand, lin-44, was SynLet with sdn-1, but not ptp-3. We used 4-dimensional time-lapse analysis to characterize the interaction between lin-44 and sdn-1. We found evidence that loss of lin-44 caused defects in the polarization and migration of endodermal precursors during gastrulation, a previously undescribed role for lin-44 that is strongly enhanced by the loss of sdn-1.ConclusionsPTP-3 and SDN-1 function in compensatory pathways during C. elegans embryonic and larval development, as simultaneous loss of both genes has dire consequences for organismal survival. The Wnt ligand lin-44 contributes to the early stages of gastrulation in parallel to sdn-1, but in a genetic pathway with ptp-3. Overall, the SynLet phenotype provides a robust platform to identify ptp-3 and sdn-1 interacting genes, as well as other genes that function in development, yet might be missed in traditional forward genetic screens.