Joshua J Yim

All Publications

• Linking Genomic and Metabolomic Natural Variation Uncovers Nematode Pheromone Biosynthesis CELL CHEMICAL BIOLOGY Falcke, J. M., Bose, N., Artyukhin, A. B., Roedelsperger, C., Markov, G. V., Yim, J. J., Grimm, D., Claassen, M. H., Panda, O., Baccile, J. A., Zhang, Y. K., Le, H. H., Jolic, D., Schroeder, F. C., Sommer, R. J. 2018; 25 (6): 787-+

  Abstract

  In the nematodes Caenorhabditis elegans and Pristionchus pacificus, a modular library of small molecules control behavior, lifespan, and development. However, little is known about the final steps of their biosynthesis, in which diverse building blocks from primary metabolism are attached to glycosides of the dideoxysugar ascarylose, the ascarosides. We combine metabolomic analysis of natural isolates of P. pacificus with genome-wide association mapping to identify a putative carboxylesterase, Ppa-uar-1, that is required for attachment of a pyrimidine-derived moiety in the biosynthesis of ubas#1, a major dauer pheromone component. Comparative metabolomic analysis of wild-type and Ppa-uar-1 mutants showed that Ppa-uar-1 is required specifically for the biosynthesis of ubas#1 and related metabolites. Heterologous expression of Ppa-UAR-1 in C. elegans yielded a non-endogenous ascaroside, whose structure confirmed that Ppa-uar-1 is involved in modification of a specific position in ascarosides. Our study demonstrates the utility of natural variation-based approaches for uncovering biosynthetic pathways.

  View details for DOI 10.1016/j.chembiol.2018.04.004

  View details for Web of Science ID 000436822100014

  View details for PubMedID 29779955

  View details for PubMedCentralID PMC6014897

• Optimization of a Protease Activated Probe for Optical Surgical Navigation. Molecular pharmaceutics Yim, J. J., Tholen, M., Klaassen, A., Sorger, J., Bogyo, M. 2018; 15 (3): 750–58

  Abstract

  Molecularly targeted optical contrast agents have the potential to enable surgeons to visualize specific molecular markers that can help improve surgical precision and thus outcomes. Fluorescently quenched substrates can be used to highlight tumor lesions by targeting proteases that are highly abundant in the tumor microenvironment. However, the majority of these and other molecularly targeted optical contrast agents are labeled with reporter dyes that are not ideally matched to the properties of clinical camera systems, which are typically optimized for detection of indocyanine-green (ICG). While a wide range of near-infrared (NIR) dyes are suitable for use with highly sensitive and highly tunable research-focused small animal imaging systems, most have not been evaluated for use with commonly used clinical imaging systems. Here we report the optimization of a small molecule fluorescently quenched protease substrate probe 6QC-ICG, which uses the indocyanine green (ICG) dye as its optical reporter. We evaluated dosing and kinetic parameters of this molecule in tumor-bearing mice and observed optimal tumor over background signals in as little as 90 min with a dose of 2.3 mg/kg. Importantly, the fluorescence intensity of the probe signal in tumors did not linearly scale with dose, suggesting the importance of detailed dosing studies. Furthermore, when imaged using the FDA approved da Vinci Si surgical system with Firefly detection, signals were significantly higher for the ICG probe compared to a corresponding probe containing a dye with similar quantum yield but with a slightly shifted excitation and emission profile. The increased signal intensity generated by the optimal dye and dose of the ICG labeled probe enabled detection of small, flat lesions that were less than 5 mm in diameter. Therefore, 6QC-ICG is a highly sensitive probe that performs optimally with clinical imaging systems and has great potential for applications in optical surgical navigation.

  View details for DOI 10.1021/acs.molpharmaceut.7b00822

  View details for PubMedID 29172524

• New Blood Test SEEKs To Detect and Localize Cancer before It's Too Late. Biochemistry Bogyo, M., Yim, J. J., Rosenthal, E. L. 2018; 57 (10): 1561–62

  View details for DOI 10.1021/acs.biochem.8b00179

  View details for PubMedID 29489339

• A Bright Future for Precision Medicine: Advances in Fluorescent Chemical Probe Design and Their Clinical Application. Cell chemical biology Garland, M., Yim, J. J., Bogyo, M. 2016; 23 (1): 122-136

  Abstract

  The Precision Medicine Initiative aims to use advances in basic and clinical research to develop therapeutics that selectively target and kill cancer cells. Under the same doctrine of precision medicine, there is an equally important need to visualize these diseased cells to enable diagnosis, facilitate surgical resection, and monitor therapeutic response. Therefore, there is a great opportunity for chemists to develop chemically tractable probes that can image cancer in vivo. This review focuses on recent advances in the development of optical probes, as well as their current and future applications in the clinical management of cancer. The progress in probe development described here suggests that optical imaging is an important and rapidly developing field of study that encourages continued collaboration among chemists, biologists, and clinicians to further refine these tools for interventional surgical imaging, as well as for diagnostic and therapeutic applications.

  View details for DOI 10.1016/j.chembiol.2015.12.003

  View details for PubMedID 26933740

  View details for PubMedCentralID PMC4779185

• Starvation-induced collective behavior in C-elegans SCIENTIFIC REPORTS Artyukhin, A. B., Yim, J. J., Cheong, M. C., Avery, L. 2015; 5

  Abstract

  We describe a new type of collective behavior in C. elegans nematodes, aggregation of starved L1 larvae. Shortly after hatching in the absence of food, L1 larvae arrest their development and disperse in search for food. In contrast, after two or more days without food, the worms change their behavior--they start to aggregate. The aggregation requires a small amount of ethanol or acetate in the environment. In the case of ethanol, it has to be metabolized, which requires functional alcohol dehydrogenase sodh-1. The resulting acetate is used in de novo fatty acid synthesis, and some of the newly made fatty acids are then derivatized to glycerophosphoethanolamides and released into the surrounding medium. We examined several other Caenorhabditis species and found an apparent correlation between propensity of starved L1s to aggregate and density dependence of their survival in starvation. Aggregation locally concentrates worms and may help the larvae to survive long starvation. This work demonstrates how presence of ethanol or acetate, relatively abundant small molecules in the environment, induces collective behavior in C. elegans associated with different survival strategies.

  View details for DOI 10.1038/srep10647

  View details for Web of Science ID 000355542100001

  View details for PubMedID 26013573

  View details for PubMedCentralID PMC4445038

• Nematode signaling molecules derived from multimodular assembly of primary metabolic building blocks. Organic letters Yim, J. J., Bose, N., Meyer, J. M., Sommer, R. J., Schroeder, F. C. 2015; 17 (7): 1648–51

  Abstract

  In the nematode model organisms Caenorhabditis elegans and Pristionchus pacificus, a new class of natural products based on modular assembly of primary-metabolism-derived building blocks control organismal development and behavior. We report identification and biological activities of the first pentamodular metabolite, pasa#9, and the 8-oxoadenine-containing npar#3 from P. pacificus. These structures suggest co-option of nucleoside and tryptophan metabolic pathways for the biosynthesis of endogenous metabolite libraries that transcend the dichotomy between "primary" and "secondary" metabolism.

  View details for DOI 10.1021/acs.orglett.5b00329

  View details for PubMedID 25782998

  View details for PubMedCentralID PMC4878434

• B. subtilis GS67 Protects C. elegans from Gram-Positive Pathogens via Fengycin-Mediated Microbial Antagonism CURRENT BIOLOGY Iatsenko, I., Yim, J. J., Schroeder, F. C., Sommer, R. J. 2014; 24 (22): 2720-2727

  Abstract

  Studies on Caenorhabditis elegans have provided detailed insight into host-pathogen interactions. Usually, the E. coli strain OP50 is used as food source for laboratory studies, but recent work has shown that a variety of bacteria have dramatic effects on C. elegans physiology, including immune responses. However, the mechanisms by which different bacteria impact worm resistance to pathogens are poorly understood. Although pathogen-specific immune priming is often discussed as a mechanism underlying such observations, interspecies microbial antagonism might represent an alternative mode of action. Here, we use several natural Bacillus strains to study their effects on nematode survival upon pathogen challenge. We show that B. subtilis GS67 persists in the C. elegans intestine and increases worm resistance to Gram-positive pathogens, suggesting that direct inhibition of pathogens might be the primary protective mechanism. Indeed, chemical and genetic analyses identified the lipopeptide fengycin as the major inhibitory molecule produced by B. subtilis GS67. Specifically, a fengycin-defective mutant of B. subtilis GS67 lost inhibitory activity against pathogens and was unable to protect C. elegans from infections. Furthermore, we found that purified fengycin cures infected worms in a dose-dependent manner, indicating that it acts as an antibiotic. Our results reveal a molecular mechanism for commensal-mediated C. elegans protection and highlight the importance of interspecies microbial antagonism for the outcome of animal-pathogen interactions. Furthermore, our work strengthens C. elegans as an in vivo model to reveal protective mechanisms of commensal bacteria, including those relevant to mammalian hosts.

  View details for DOI 10.1016/j.cub.2014.09.055

  View details for Web of Science ID 000345189700027

  View details for PubMedID 25448001

• Natural Variation in Dauer Pheromone Production and Sensing Supports Intraspecific Competition in Nematodes CURRENT BIOLOGY Bose, N., Meyer, J. M., Yim, J. J., Mayer, M. G., Markov, G. V., Ogawa, A., Schroeder, F. C., Sommer, R. J. 2014; 24 (13): 1536-1541

  Abstract

  Dauer formation, a major nematode survival strategy, represents a model for small-molecule regulation of metazoan development [1-10]. Free-living nematodes excrete dauer-inducing pheromones that have been assumed to target conspecifics of the same genotype [9, 11]. However, recent studies in Pristionchus pacificus revealed that the dauer pheromone of some strains affects conspecifics of other genotypes more strongly than individuals of the same genotype [12]. To elucidate the mechanistic basis for this intriguing cross-preference, we compared six P. pacificus wild isolates to determine the chemical composition of their dauer-inducing metabolomes and responses to individual pheromone components. We found that these isolates produce dauer pheromone blends of different composition and respond differently to individual pheromone components. Strikingly, there is no correlation between production of and dauer response to a specific compound in individual strains. Specifically, pheromone components that are abundantly produced by one genotype induce dauer formation in other genotypes, but not necessarily in the abundant producer. Furthermore, some genotypes respond to pheromone components they do not produce themselves. These results support a model of intraspecific competition in nematode dauer formation. Indeed, we observed intraspecific competition among sympatric strains in a novel experimental assay, suggesting a new role of small molecules in nematode ecology.

  View details for DOI 10.1016/j.cub.2014.05.045

  View details for Web of Science ID 000338799800030

  View details for PubMedID 24980503

  View details for PubMedCentralID PMC4437242

• Succinylated Octopamine Ascarosides and a New Pathway of Biogenic Amine Metabolism in Caenorhabditis elegans JOURNAL OF BIOLOGICAL CHEMISTRY Artyukhin, A. B., Yim, J. J., Srinivasan, J., Izrayelit, Y., Bose, N., von Reuss, S. H., Jo, Y., Jordan, J. M., Baugh, L. R., Cheong, M., Sternberg, P. W., Avery, L., Schroeder, F. C. 2013; 288 (26): 18778-18783

  Abstract

  The ascarosides, small-molecule signals derived from combinatorial assembly of primary metabolism-derived building blocks, play a central role in Caenorhabditis elegans biology and regulate many aspects of development and behavior in this model organism as well as in other nematodes. Using HPLC-MS/MS-based targeted metabolomics, we identified novel ascarosides incorporating a side chain derived from succinylation of the neurotransmitter octopamine. These compounds, named osas#2, osas#9, and osas#10, are produced predominantly by L1 larvae, where they serve as part of a dispersal signal, whereas these ascarosides are largely absent from the metabolomes of other life stages. Investigating the biogenesis of these octopamine-derived ascarosides, we found that succinylation represents a previously unrecognized pathway of biogenic amine metabolism. At physiological concentrations, the neurotransmitters serotonin, dopamine, and octopamine are converted to a large extent into the corresponding succinates, in addition to the previously described acetates. Chemically, bimodal deactivation of biogenic amines via acetylation and succinylation parallels posttranslational modification of proteins via acetylation and succinylation of L-lysine. Our results reveal a small-molecule connection between neurotransmitter signaling and interorganismal regulation of behavior and suggest that ascaroside biosynthesis is based in part on co-option of degradative biochemical pathways.

  View details for DOI 10.1074/jbc.C113.477000

  View details for Web of Science ID 000321335800015

  View details for PubMedID 23689506

  View details for PubMedCentralID PMC3696653

• Sex-specific mating pheromones in the nematode Panagrellus redivivus PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Choe, A., Chuman, T., von Reuss, S. H., Dossey, A. T., Yim, J. J., Ajredini, R., Kolawa, A. A., Kaplan, F., Alborn, H. T., Teal, P. E., Schroeder, F. C., Sternberg, P. W., Edison, A. S. 2012; 109 (51): 20949-20954

  Abstract

  Nematodes use an extensive chemical language based on glycosides of the dideoxysugar ascarylose for developmental regulation (dauer formation), male sex attraction, aggregation, and dispersal. However, no examples of a female- or hermaphrodite-specific sex attractant have been identified to date. In this study, we investigated the pheromone system of the gonochoristic sour paste nematode Panagrellus redivivus, which produces sex-specific attractants of the opposite sex. Activity-guided fractionation of the P. redivivus exometabolome revealed that males are strongly attracted to ascr#1 (also known as daumone), an ascaroside previously identified from Caenorhabditis elegans hermaphrodites. Female P. redivivus are repelled by high concentrations of ascr#1 but are specifically attracted to a previously unknown ascaroside that we named dhas#18, a dihydroxy derivative of the known ascr#18 and an ascaroside that features extensive functionalization of the lipid-derived side chain. Targeted profiling of the P. redivivus exometabolome revealed several additional ascarosides that did not induce strong chemotaxis. We show that P. redivivus females, but not males, produce the male-attracting ascr#1, whereas males, but not females, produce the female-attracting dhas#18. These results show that ascaroside biosynthesis in P. redivivus is highly sex-specific. Furthermore, the extensive side chain functionalization in dhas#18, which is reminiscent of polyketide-derived natural products, indicates unanticipated biosynthetic capabilities in nematodes.

  View details for DOI 10.1073/pnas.1218302109

  View details for Web of Science ID 000313123700045

  View details for PubMedID 23213209

  View details for PubMedCentralID PMC3529029

• Comparative Metabolomics Reveals Biogenesis of Ascarosides, a Modular Library of Small-Molecule Signals in C. elegans JOURNAL OF THE AMERICAN CHEMICAL SOCIETY von Reuss, S. H., Bose, N., Srinivasan, J., Yim, J. J., Judkins, J. C., Sternberg, P. W., Schroeder, F. C. 2012; 134 (3): 1817-1824

  Abstract

  In the model organism Caenorhabditis elegans, a family of endogenous small molecules, the ascarosides function as key regulators of developmental timing and behavior that act upstream of conserved signaling pathways. The ascarosides are based on the dideoxysugar ascarylose, which is linked to fatty-acid-like side chains of varying lengths derived from peroxisomal β-oxidation. Despite the importance of ascarosides for many aspects of C. elegans biology, knowledge of their structures, biosynthesis, and homeostasis remains incomplete. We used an MS/MS-based screen to profile ascarosides in C. elegans wild-type and mutant metabolomes, which revealed a much greater structural diversity of ascaroside derivatives than previously reported. Comparison of the metabolomes from wild-type and a series of peroxisomal β-oxidation mutants showed that the enoyl CoA-hydratase MAOC-1 serves an important role in ascaroside biosynthesis and clarified the functions of two other enzymes, ACOX-1 and DHS-28. We show that, following peroxisomal β-oxidation, the ascarosides are selectively derivatized with moieties of varied biogenetic origin and that such modifications can dramatically affect biological activity, producing signaling molecules active at low femtomolar concentrations. Based on these results, the ascarosides appear as a modular library of small-molecule signals, integrating building blocks from three major metabolic pathways: carbohydrate metabolism, peroxisomal β-oxidation of fatty acids, and amino acid catabolism. Our screen further demonstrates that ascaroside biosynthesis is directly affected by nutritional status and that excretion of the final products is highly selective.

  View details for DOI 10.1021/ja210202y

  View details for Web of Science ID 000301084400069

  View details for PubMedID 22239548

  View details for PubMedCentralID PMC3269134

• Complex Small-Molecule Architectures Regulate Phenotypic Plasticity in a Nematode ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Bose, N., Ogawa, A., von Reuss, S. H., Yim, J. J., Ragsdale, E. J., Sommer, R. J., Schroeder, F. C. 2012; 51 (50): 12438-12443

  Abstract

  Chemistry the worm's way: The nematode Pristionchus pacificus constructs elaborate small molecules from modified building blocks of primary metabolism, including an unusual xylopyranose-based nucleoside (see scheme). These compounds act as signaling molecules to control adult phenotypic plasticity and dauer development and provide examples of modular generation of structural diversity in metazoans.

  View details for DOI 10.1002/anie.201206797

  View details for Web of Science ID 000312213800006

  View details for PubMedID 23161728

  View details for PubMedCentralID PMC3733369

• Synthesis of Caeliferins, Elicitors of Plant Immune Responses: Accessing Lipophilic Natural Products via Cross Metathesis ORGANIC LETTERS O'Doherty, I., Yim, J. J., Schmelz, E. A., Schroeder, F. C. 2011; 13 (21): 5900-5903

  Abstract

  A cross metathesis (CM)-based synthesis of the caeliferins, a family of sulfooxy fatty acids that elicit plant immune responses, is reported. Unexpectedly, detailed NMR spectroscopic and mass spectrometric analyses of CM reaction mixtures revealed extensive isomerization and homologation of starting materials and products. It is shown that the degree of isomerization and homologation in CM strongly correlates with substrate chain length and lipophilicity. Side-product suppression requires appropriate catalyst selection and use of 1,4-benzoquinone as a hydride scavenger.

  View details for DOI 10.1021/ol202541b

  View details for Web of Science ID 000296212200050

  View details for PubMedID 21992613

  View details for PubMedCentralID PMC3216471

• Transcranial magnetic stimulation in ALS Utility of central motor conduction tests NEUROLOGY Floyd, A. G., Yu, Q. P., Piboolnurak, P., Tang, M. X., Fang, Y., Smith, W. A., Yim, J., Rowland, L. P., Mitsumoto, H., Pullman, S. L. 2009; 72 (6): 498-504

  Abstract

  To investigate transcranial magnetic stimulation (TMS) measures as clinical correlates and longitudinal markers of amyotrophic lateral sclerosis (ALS).We prospectively studied 60 patients with ALS subtypes (sporadic ALS, familial ALS, progressive muscular atrophy, and primary lateral sclerosis) using single pulse TMS, recording from abductor digiti minimi (ADM) and tibialis anterior (TA) muscles. We evaluated three measures: 1) TMS motor response threshold to the ADM, 2) central motor conduction time (CMCT), and 3) motor evoked potential amplitude (correcting for peripheral changes). Patients were evaluated at baseline, compared with controls, and followed every 3 months for up to six visits. Changes were analyzed using generalized estimation equations to test linear trends with time.TMS threshold, CMCT, and TMS amplitude correlated (p < 0.05) with clinical upper motor neuron (UMN) signs at baseline and were different (p < 0.05) from normal controls in at least one response. Seventy-eight percent of patients with UMN (41/52) and 50% (4/8) of patients without clinical UMN signs had prolonged CMCT. All three measures revealed significant deterioration over time: TMS amplitude showed the greatest change, decreasing 8% per month; threshold increased 1.8% per month; and CMCT increased by 0.9% per month.Transcranial magnetic stimulation (TMS) findings, particularly TMS amplitude, can objectively discriminate corticospinal tract involvement in amyotrophic lateral sclerosis (ALS) from controls and assess the progression of ALS. While central motor conduction time and response threshold worsen by less than 2% per month, TMS amplitude decrease averages 8% per month, and may be a useful objective marker of disease progression.

  View details for DOI 10.1212/01.wnl.0000341933.97883.a4

  View details for Web of Science ID 000263187000005

  View details for PubMedID 19204259

  View details for PubMedCentralID PMC2677511