Review
Biotechnology & Applied Microbiology
Dmytro Kukhtar, Martin Fussenegger
Summary: Synthetic biology has traditionally focused on single cell systems, such as bacteria, yeast, or mammalian cells, for introducing new or altered functionality. This article extends the field of synthetic biology to nematodes, particularly the well-studied organism Caenorhabditis elegans, as a practical platform for developing applications in a multicellular context. The authors review transgenesis techniques for nematodes and discuss the application of synthetic biology principles in constructing nematode gene switches and genetic devices for controlling motility. Potential applications of engineered nematodes are also discussed.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Cell Biology
Catia Igreja, Tobias Loschko, Alejandra Schaefer, Radhika Sharma, Shiela Pearl Quiobe, Elbin Aloshy, Hanh Witte, Ralf J. Sommer
Summary: The detection, manipulation and purification of proteins are crucial in modern life sciences studies. The introduction of the ALFA-tag provides a novel epitope tag for nematode research with a wide range of applications, such as super-resolution microscopy and immunoprecipitation. This study successfully demonstrates the utilization of ALFA-tagging in nematode model organisms, leading to high-resolution protein expression and successful pulldown experiments.
Article
Biology
Xinwei Yu, Matthew S. Creamer, Francesco Randi, Anuj K. Sharma, Scott W. Linderman, Andrew M. Leifer
Summary: A method called fDNC, based on the transformer network architecture, is proposed for automated tracking and identifying neurons in C. elegans. This method predicts neural correspondence quickly without requiring straightening or transforming the animal into a canonical coordinate system, making it suitable for future real-time applications.
Article
Pharmacology & Pharmacy
Nicholas Osborne, Charles Leahy, Yoon-Kwang Lee, Paula Rote, Byoung-Joon Song, James P. Hardwick
Summary: Fatty acids play a vital role in maintaining cellular homeostasis and influencing various cellular processes. The CYP4 Omega hydroxylase gene family metabolizes different types of fatty acids. The CYP4V2 gene is important in the progression of metabolic syndrome and nonalcoholic fatty liver disease.
BIOCHEMICAL PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Fabian Schmitt, Lukas Babylon, Fabian Dieter, Gunter P. Eckert
Summary: This study investigated the impact of environmentally hazardous substances on the healthspan and mitochondrial functions of invertebrates, finding that pesticides can decrease heat stress resistance but can be improved by polyphenolic metabolites.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Pharmacology & Pharmacy
Jiayue Wang, Xiuhua Zhu, Shenrui Wang, Yingjie Zhang, Wenjie Hua, Zhenyu Liu, Yu Zheng, Xiao Lu
Summary: Global quantitative phosphoproteomic and proteomic analysis revealed differentially expressed phosphorylated proteins (DPPs) and proteins in post-infarction chronic heart failure. These DPPs were mainly enriched in nucleocytoplasmic transport and mRNA surveillance pathway. A critical protein related to apoptosis in heart failure and potential therapeutic targets were identified.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Biochemical Research Methods
James A. Sanford, Yang Wang, Joshua R. Hansen, Marina A. Gritsenko, Karl K. Weitz, Tyler J. Sagendorf, Cristina E. Tognon, Vladislav A. Petyuk, Wei-Jun Qian, Tao Liu, Brian J. Druker, Karin D. Rodland, Paul D. Piehowski
Summary: Global and phosphoproteome profiling is useful in clinical specimen analysis, but requires a large amount of biological material. This study investigates the impact of differential peptide loading on proteomic data quality and finds that decreased loading amounts result in increased missing values, higher quantitative variability, and fewer statistical differences.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Zoology
Dorothy Maushe, Vera Ogi, Keerthi Divakaran, Arletys Maria Verdecia Mogena, Paul Anton Himmighofen, Ricardo A. R. Machado, Benjamin Daniel Towbin, Ralf-Udo Ehlers, Carlos Molina, Christian Parisod, Christelle Aurelie Maud Robert
Summary: This review provides a comprehensive overview of the response of entomopathogenic nematodes (EPNs) to various stresses, including starvation, temperature, desiccation, osmotic stress, hypoxia, and ultra-violet light. It also discusses EPN defense strategies against biotic stressors such as viruses, bacteria, fungi, and predatory insects. By comparing these strategies to the nematode model Caenorhabditis elegans, new avenues and targets for selecting and engineering precision nematodes adapted to specific field conditions are proposed.
JOURNAL OF INVERTEBRATE PATHOLOGY
(2023)
Article
Biology
Vasin Dumrongprechachan, Ryan B. Salisbury, Lindsey Butler, Matthew L. MacDonald, Yevgenia Kozorovitskiy
Summary: In this study, the researchers used APEX2 transgenic technology to analyze cell-type-specific axonal proteomes during mammalian postnatal neurodevelopment. They identified co-regulated proteins and phosphorylations associated with genetic risk for human brain disorders and discovered proline-directed kinases as major developmental regulators.
Article
Biochemistry & Molecular Biology
Van Thi Nguyen, Ae Ran Park, Kalaiselvi Duraisamy, Duc Duy Vo, Jin-Cheol Kim
Summary: In this study, it was found that Grammicin (Gra) can kill the devastating root-knot nematode by inducing oxidative stress response. Gra interacts with multiple genes in C. elegans, resulting in oxidative stress response and nematode death. The mode of action of Gra is different from traditional nematicides, suggesting its potential application in controlling plant-parasitic nematodes.
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
(2022)
Article
Biochemical Research Methods
Mallory I. Frederick, Owen F. J. Hovey, Jenica H. Kakadia, Trevor G. Shepherd, Shawn S. C. Li, Ilka U. Heinemann
Summary: This study investigated the cellular signaling dynamics during epithelial ovarian cancer (EOC) metastasis using cellular models. The results showed that spheroid cells in the metastatic process exhibited hypoxia and cell cycle arrest, and stimulated Rho-associated kinase 1 (ROCK1)-mediated signaling related to cytoskeletal organization. Aurora kinase B and ROCK1 were identified as major drivers of metastatic behavior in EOC cells.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Biochemical Research Methods
Bram Cockx, Sven Van Bael, Rose Boelen, Elke Vandewyer, Heeseung Yang, Tuan Anh Le, Johnathan J. Dalzell, Isabel Beets, Christina Ludwig, Junho Lee, Liesbet Temmerman
Summary: Neuropeptides play a crucial role in regulating animal physiology and behavior. This study developed a targeted peptidomics method for C.elegans and identified numerous neuropeptides that are more abundant in its dauer stage compared to L3 juveniles. Through further experiments, flp-7 and flp-11 were identified as novel regulators of nictation behavior.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Multidisciplinary Sciences
Hailey Sounart, Denis Voronin, Yuvarani Masarapu, Matthew Chung, Sami Saarenpaa, Elodie Ghedin, Stefania Giacomello
Summary: The study investigates the interaction between the parasitic nematode Brugia malayi and its symbiotic bacteria Wolbachia. Using spatial transcriptomics, the researchers were able to uncover the spatial gene expression patterns and localization of key genes in the reproductive system of the worms. This approach has the potential to advance our understanding of infectious diseases caused by micro-scale parasitic worms.
NATURE COMMUNICATIONS
(2023)
Article
Parasitology
Milena Lubisch, Sven Moyzio, Charlotte Sophia Kaiser, Isabel Krafeld, Dustin Leusder, Martin Scholz, Lara Hoepfner, Michael Hippler, Eva Liebau, Janina Kahl
Summary: This study examines the feasibility of using the free-living nematode Caenorhabditis elegans as an expression system for proteins from parasitic nematodes, successfully expressing functional proteins for subsequent immunological and biochemical studies.
Article
Biochemical Research Methods
Khaled Youssef, Daphne Archonta, Terrance J. Kubiseski, Anurag Tandon, Pouya Rezai
Summary: This paper reveals the novel effect of electric field on adult C. elegans egg-laying behavior, showing that the electric egg-laying rate is significantly influenced by EF strength, direction, and exposure duration, as well as worm aging. The involvement and sensitivity of specific neurons and muscles to the EF are demonstrated, and the assay can be used for cellular screening and mapping of the neural basis of electrosensation.
Article
Pharmacology & Pharmacy
Anne E. Zepeski, Brett A. Faine, Anna E. Merrill, Grerk Sutamtewagul, Sharathkumar Bhagavathi
Summary: This study evaluated the role of chromogenic anti-factor Xa assays in the emergency department for patients requiring anticoagulation reversal. Results showed that anti-Xa levels can aid in determining the need for reversal agents in patients with emergent anticoagulation needs.
AMERICAN JOURNAL OF HEALTH-SYSTEM PHARMACY
(2022)
Article
Medical Laboratory Technology
William S. Phipps, Dina N. Greene, Hannah Pflaum, Thomas J. Laha, Jane A. Dickerson, Jill Irvine, Anna E. Merrill, Pratistha Ranjitkar, Clark M. Henderson, Andrew N. Hoofnagle
Summary: A new method for quantifying retinol binding protein in neonatal plasma was developed, allowing for increased monitoring of key nutritional markers in premature infants. Results obtained with the new method differed from those obtained with traditional nephelometry, casting doubt on lower concentration results obtained with immunoassay.
CLINICAL BIOCHEMISTRY
(2022)
Editorial Material
Multidisciplinary Sciences
Timothy W. Rhoads, Rozalyn M. Anderson
Article
Multidisciplinary Sciences
Maximilian J. Helf, Bennett W. Fox, Alexander B. Artyukhin, Ying K. Zhang, Frank C. Schroeder
Summary: In this study, untargeted metabolomics using high-resolution mass spectrometry and Metaboseek software was applied to uncover the biosynthetic functions of a fat metabolism pathway in C. elegans. Over 200 previously uncharacterized metabolites related to the alpha-oxidation pathway were identified, highlighting the importance of alpha-oxidation in fatty acid and lipid metabolism.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Jingfang Yu, Merly C. Vogt, Bennett W. Fox, Chester J. J. Wrobel, Diana Fajardo Palomino, Brian J. Curtis, Bingsen Zhang, Henry H. Le, Arnaud Tauffenberger, Oliver Hobert, Frank C. Schroeder
Summary: Untargeted comparative metabolomics revealed the biosynthesis and metabolism pathways of serotonin in nonneuronal tissues, suggesting its important roles in serotonin-dependent phenotypes in C. elegans. Serotonin is abundantly produced in nonneuronal tissues via phenylalanine hydroxylase, in addition to its canonical biosynthesis in neurons via tryptophan hydroxylase. Most serotonin in C. elegans is incorporated into N-acetylserotonin-derived glucosides and further modified via the carboxylesterase CEST-4. Bacterial indole production interacts with serotonin metabolism via CEST-4. These findings indicate the significance of nonneuronal serotonin biosynthesis and metabolism in contributing to serotonin-dependent phenotypes.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Pharmacology & Pharmacy
Briana J. Negaard, Ryan Hobbs, Jared R. Frye, Anna E. Merrill
Summary: This study found that approximately half of ICU patients receiving both propofol and heparin infusions experienced interference with aPTT measurements. Ultracentrifugation of samples can remove the optical interference, but it significantly delays aPTT reporting and adjustments to heparin dosing.
AMERICAN JOURNAL OF HEALTH-SYSTEM PHARMACY
(2023)
Article
Multidisciplinary Sciences
Russell N. Burkhardt, Alexander B. Artyukhin, Erin Z. Aprison, Brian J. Curtis, Bennett W. Fox, Andreas H. Ludewig, Diana Fajardo Palomino, Jintao Luo, Amaresh Chaturbedi, Oishika Panda, Chester J. J. Wrobel, Victor Baumann, Douglas S. Portman, Siu Sylvia Lee, Ilya Ruvinsky, Frank C. Schroeder
Summary: Recent studies have shown that there are pervasive metabolomic differences between hermaphrodites and males of the C. elegans nematode. Numerous new metabolites that incorporate building blocks from various metabolic pathways have been identified, some of which are specifically associated with the male germline or soma. One male germline-dependent metabolite, a dipeptide incorporating N,N-dimethyltryptophan, has been found to affect food consumption, lifespan, and larval development in hermaphrodites. These findings provide a foundation for understanding how the genetic sex influences the metabolome and offer insights into sex-dependent metabolites in other animals.
NATURE COMMUNICATIONS
(2023)
Letter
Obstetrics & Gynecology
Renee G. Cafun, Anna Merrill, Sharathkumar M. Bhagavathi, Karen M. Summers, Brittany A. Bettendorf, Bradley J. Van Voorhis
FERTILITY AND STERILITY
(2023)
Article
Medical Laboratory Technology
Kai J. Rogers, Tracy S. Halvorson, Matthew D. Krasowski, Anna E. Merrill
Summary: This study used a two-assay algorithm to improve the positive predictive value of HCV screening in specimens with borderline or weakly positive anti-HCV results. The algorithm involved a second anti-HCV assay for samples with borderline or weakly positive results in the screening assay.
JOURNAL OF CLINICAL LABORATORY ANALYSIS
(2023)
Article
Chemistry, Multidisciplinary
Brian J. Curtis, Tyler J. Schwertfeger, Russell N. Burkhardt, Bennett W. Fox, Jude Andrzejewski, Chester J. J. Wrobel, Jingfang Yu, Pedro R. Rodrigues, Arnaud Tauffenberger, Frank C. Schroeder
Summary: Glucose-based nucleosides with diverse modifications were discovered in C. elegans and related nematodes. These gluconucleosides exist in phosphorylated and non-phosphorylated forms, and can be further modified with acyl moieties from amino acid catabolism. Stable-isotope labeling experiments indicated that these gluconucleosides incorporate modified nucleobases derived from RNA and possibly DNA breakdown.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Chester J. J. Wrobel, Frank C. Schroeder
Summary: Recent studies have found that nematodes, including Caenorhabditis elegans, use products from biochemical degradation pathways to assemble complex modular structures for various signaling functions. These structures, called ascarosides and glucosides, are made up of building blocks from neurotransmitter, amino acid, nucleoside, and fatty acid metabolism. Carboxylesterases are key enzymes that mediate the assembly of these modular structures, which are derived from conserved detoxification mechanisms. These modular metabolites represent a distinct biosynthetic strategy for generating diversity in nematodes and complement the microbial natural products derived from polyketide synthase and nonribosomal peptide synthetase. They also serve as a target for compound discovery using metabolomics and genomic approaches.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Daehan Lee, Bennett W. Fox, Diana Fajardo Palomino, Oishika Panda, Francisco J. Tenjo, Emily J. Koury, Kathryn S. Evans, Lewis Stevens, Pedro R. Rodrigues, Aiden R. Kolodziej, Frank C. Schroeder, Erik C. Andersen
Summary: From bacterial quorum sensing to human language, communication is essential for social interactions. Nematodes produce and sense pheromones to communicate among individuals and respond to environmental changes. The genetic basis and molecular mechanisms underlying the variation in the nematode pheromone language remain largely unknown, but our study provides valuable insights into the genetic mechanisms underlying the evolution of chemical communication.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Olga B. Ponomarova, Hefei W. Zhang, Xuhang N. Li, Shivani E. Nanda, Thomas C. Leland, Bennett Fox, Alyxandra Starbard, Gabrielle Giese, Frank Schroeder, L. Safak Yilmaz, Albertha J. M. Walhout
Summary: In humans, mutations in D-2-hydroxyglutarate (D-2HG) dehydrogenase (D2HGDH) lead to the accumulation of D-2HG, causing delayed development, seizures, and ataxia. Using Caenorhabditis elegans as a model organism, researchers found that D-2HG is produced in the propionate shunt pathway when the vitamin B12-dependent propionate breakdown pathway is disrupted. Loss of the D2HGDH ortholog, dhgd-1, leads to embryonic lethality and mitochondrial defects, but can be rescued by RNAi of hphd-1 or supplementation of vitamin B12 or ketone bodies. This study reveals the role of ketone bodies in energy production when vitamin B12 levels are low and highlights the importance of dhgd-1 in ketone body production.
Meeting Abstract
Geriatrics & Gerontology
Timothy Rhoads
INNOVATION IN AGING
(2022)
Meeting Abstract
Geriatrics & Gerontology
Timothy Rhoads, Josef Clark, Rozalyn Anderson
INNOVATION IN AGING
(2022)