Ma C et al. (2015) Molecules "Potent Activities of Roemerine against Candida albicans and the Underlying Mechanisms."

Yan L, Xu G, Wang C, He G, Du F, Jiang Y, Ma C, Rao G, He J

[Molecules, 2015]

Roemerine (RM) is an aporphine alkaloid isolated from the fresh rattan stem of Fibraurea recisa, and it has been demonstrated to have certain antifungal activity. This study aimed to investigate the antifungal activity of RM and the underlying mechanisms in Candida albicans (C. albicans). The in vitro antifungal activity of RM was evaluated by a series of experiments, including the XTT reduction assay, confocal laser scanning microscopy assay, scanning electron microscope assay. Results showed that 1 g/mL RM inhibited biofilm formation significantly (p < 0.01) both in Spider medium and Lee's medium. In addition, RM could inhibit yeast-to-hyphae transition of C. albicans in a dose-dependent manner. The biofilm-specific and hypha-specific genes such as YWP1, SAP5, SAP6, HWP1, ECE1 were up-regulated and EFG1 was down-regulated after 8 g/mL RM treatment. Furthermore, the toxicity of RM was investigated using C. elegans worms, three cancer cells and one normal cell. The date showed that RM had no significant toxicity. In conclusion, RM could inhibited the formation of C. albicans biofilm in vitro, but it had no fungicidal effect on planktonic C. albicans cells, and the anti-biofilm mechanism may be related to the cAMP pathway.

Gouveia GJ et al. (2021) Anal Chem "Long-Term Metabolomics Reference Material."

Andersen EC, Morse AM, Garcia BM, Edison AS, Shaver AO, Gouveia GJ, McIntyre LM

[Anal Chem, 2021]

The use of quality control samples in metabolomics ensures data quality, reproducibility, and comparability between studies, analytical platforms, and laboratories. Long-term, stable, and sustainable reference materials (RMs) are a critical component of the quality assurance/quality control (QA/QC) system; however, the limited selection of currently available matrix-matched RMs reduces their applicability for widespread use. To produce an RM in any context, for any matrix that is robust to changes over the course of time, we developed iterative batch averaging method (IBAT). To illustrate this method, we generated 11 independently grown <i>Escherichia coli</i> batches and made an RM over the course of 10 IBAT iterations. We measured the variance of these materials by nuclear magnetic resonance (NMR) and showed that IBAT produces a stable and sustainable RM over time. This <i>E. coli</i> RM was then used as a food source to produce a <i>Caenorhabditis elegans</i> RM for a metabolomics experiment. The metabolite extraction of this material, alongside 41 independently grown individual <i>C. elegans</i> samples of the same genotype, allowed us to estimate the proportion of sample variation in preanalytical steps. From the NMR data, we found that 40% of the metabolite variance is due to the metabolite extraction process and analysis and 60% is due to sample-to-sample variance. The availability of RMs in untargeted metabolomics is one of the predominant needs of the metabolomics community that reach beyond quality control practices. IBAT addresses this need by facilitating the production of biologically relevant RMs and increasing their widespread use.

Monoson HL et al. (1973) Mycopathologia et Mycologia Applicata "Endoparasitic nematode-trapping fungi of Mason State Forest."

Monoson HL, Williams SA

[Mycopathologia et Mycologia Applicata, 1973]

An initial survey involving the endoparasitic nematode-trapping fungi of Mason State Forest in Illinois was conducted from 15 May to 26 July 1971. Three endoparasitic forms were isolated from the soil samples collected; one non-endoparasitic form was also isolated. Soil pH's and soil nutrient levels were determined for the investigation period.

Lawal TA et al. (2020) Orphanet J Rare Dis "Preclinical model systems of ryanodine receptor 1-related myopathies and malignant hyperthermia: a comprehensive scoping review of works published 1990-2019."

Dowling JJ, Terry NL, Todd JJ, Wires ES, Lawal TA

[Orphanet J Rare Dis, 2020]

BACKGROUND: Pathogenic variations in the gene encoding the skeletal muscle ryanodine receptor (RyR1) are associated with malignant hyperthermia (MH) susceptibility, a life-threatening hypermetabolic condition and RYR1-related myopathies (RYR1-RM), a spectrum of rare neuromuscular disorders. In RYR1-RM, intracellular calcium dysregulation, post-translational modifications, and decreased protein expression lead to a heterogenous clinical presentation including proximal muscle weakness, contractures, scoliosis, respiratory insufficiency, and ophthalmoplegia. Preclinical model systems of RYR1-RM and MH have been developed to better understand underlying pathomechanisms and test potential therapeutics. METHODS: We conducted a comprehensive scoping review of scientific literature pertaining to RYR1-RM and MH preclinical model systems in accordance with the PRISMA Scoping Reviews Checklist and the framework proposed by Arksey and O'Malley. Two major electronic databases (PubMed and EMBASE) were searched without language restriction for articles and abstracts published between January 1, 1990 and July 3, 2019. RESULTS: Our search yielded 5049 publications from which 262 were included in this review. A majority of variants tested in RYR1 preclinical models were localized to established MH/central core disease (MH/CCD) hot spots. A total of 250 unique RYR1 variations were reported in human/rodent/porcine models with 95% being missense substitutions. The most frequently reported RYR1 variant was R614C/R615C (human/porcine total n=39), followed by Y523S/Y524S (rabbit/mouse total n=30), I4898T/I4897T/I4895T (human/rabbit/mouse total n=20), and R163C/R165C (human/mouse total n=18). The dyspedic mouse was utilized by 47% of publications in the rodent category and its RyR1-null (1B5) myotubes were transfected in 23% of publications in the cellular model category. In studies of transfected HEK-293 cells, 57% of RYR1 variations affected the RyR1 channel and activation core domain. A total of 15 RYR1 mutant mouse strains were identified of which ten were heterozygous, three were compound heterozygous, and a further two were knockout. Porcine, avian, zebrafish, C. elegans, canine, equine, and drosophila model systems were also reported. CONCLUSIONS: Over the past 30years, there were 262 publications on MH and RYR1-RM preclinical model systems featuring more than 200 unique RYR1 variations tested in a broad range of species. Findings from these studies have set the foundation for therapeutic development for MH and RYR1-RM.

Volpatti JR et al. (2020) Elife "Identification of drug modifiers for RYR1 related myopathy using a multi-species discovery pipeline."

Groom L, Endo Y, Volpatti JR, Zuercher WJ, Brennan S, Roy P, Dirksen RT, Dowling JJ, Knox J, Noche R

[Elife, 2020]

Ryanodine receptor type I-related myopathies (RYR1-RMs) are a common group of childhood muscle diseases associated with severe disabilities and early mortality for which there are no available treatments. The goal of this study is to identify new therapeutic targets for RYR1-RMs. To accomplish this, we developed a discovery pipeline using nematode, zebrafish, and mammalian cell models. We first performed large-scale drug screens in <i>C. elegans</i> which uncovered 74 hits. Targeted testing in zebrafish yielded positive results for two p38 inhibitors. Using mouse myotubes, we found that either pharmacological inhibition or siRNA silencing of p38 impaired caffeine-induced Ca²⁺ release from wild type cells while promoting intracellular Ca²⁺ release in <i>Ryr1</i> knockout cells. Lastly, we demonstrated that p38 inhibition blunts the aberrant temperature-dependent increase in resting Ca²⁺ in myotubes from an RYR1-RM mouse model. This unique platform for RYR1-RM therapy development is potentially applicable to a broad range of neuromuscular disorders.

Yu Z et al. (2011) J Environ Sci (China) "Behavior toxicity to Caenorhabditis elegans transferred to the progeny after exposure to sulfamethoxazole at environmentally relevant concentrations."

Yu Z, Jiang L, Yin D

[J Environ Sci (China), 2011]

Sulfamethoxazole (SMX) is one of the most common detected antibiotics in the environment. In order to study whether SMX can affect behavior and growth and whether these effects could be transferred to the progeny, Caenorhabditis elegans was exposed at environmentally relevant concentrations for 24, 48, 72 and 96 hr, respectively. After exposure, the exposed parent generation (P0) was measured for behavior and growth indicators, which were presented as percentage of controls (POC). Then their corresponding unexposed progeny (F1) was separated and measured for the same indicators. The lowest POC for P0 after 96 hr-exposure at 100 mg/L were 37.8%, 12.7%, 45.8% and 70.1% for body bending frequency (BBF), reversal movement (RM), Omega turns (OT) and body length (BL), respectively. And F1 suffered defects with the lowest POC as 55.8%, 24.1%, 48.5% and 60.7% for BBF, RM, OT and BL, respectively. Defects in both P0 and F1 showed a time- and concentration-dependent fashion and behavior indicators showed better sensitivity than growth indicator. The observed effects on F1 demonstrated the transferable properties of SMX. Defects of SMX at environmental concentrations suggested that it is necessary to perform further systematical studies on its ecological risk in actual conditions.

Zaridah MZ et al. (2001) J Ethnopharmacol "In vitro antifilarial effects of three plant species against adult worms of subperiodic Brugia malayi."

Omar AW, Idid SZ, Zaridah MZ, Khozirah S

[J Ethnopharmacol, 2001]

Five aqueous extracts from three plant species, i.e., dried husks (HX), dried seeds (SX) and dried leaves (LX) of Xylocarpus granatum (Meliaceae), dried stems (ST) of Tinospora crispa (Menispermaceae) and dried leaves (LA) of Andrographis paniculata (Acanthaceae) were tested in vitro against adult worms of subperiodic Brugia malayi. The relative movability (RM) value of the adult worms over the 24-h observation period was used as a measure of the antifilarial activity of the aqueous extracts. SX extract of X. granatum demonstrated the strongest activity, followed by the LA extract of A. paniculata, ST extract of T. crispa, HX extract and LX extract of X. granatum.

Zhou, Y et al. (2017) International Worm Meeting "Genetic and chemical modulation of C. elegans intestinal antiviral innate immunity."

Zhou, Y, Tao, Y, Bedian, L, Zhong, W

[International Worm Meeting, 2017]

The RNA virus Orsay is the only known natural viral pathogen infecting the intestine cells of the nematode C. elegans. The C. elegans intestine cells resemble human intestinal epithelial cells not only in morphological features such as microvilli, but also in molecular mechanisms such as antibacterial innate immune response. As Orsay was discovered only six years ago, the C. elegans antiviral innate immune system remains largely unknown. Only two pathways, RNAi and ubiquitin-mediated protein degradation, have been discovered to be involved in the C. elegans antiviral innate immunity. To explore the genetic landscape of the C. elegans antiviral innate immunity, we conducted a genome-wide RNAi screen for genes whose inactivation sensitizes worms to Orsay infection. 110 genes were identified to be required for C. elegans antiviral innate immunity. 72 of these genes have human orthologs. Tissue-specific RNAi experiments showed that the majority of these genes function in the intestine cells to modulate antiviral innate immunity. In addition to RNAi and ubiquitin-mediated protein degradation, these genes encompass pathways in autophagy, mitochondrial unfolded protein responses, collagens, cytoskeletal organization, RNA processing, and transcription. To identify the gene products that are druggable, we screened 2000 chemicals for drugs that can alleviate Orsay infection symptoms, and discovered four innate immunity enhancing drugs, resorcinol monoacetate (RM), berberine (BBR), bismuth subsalicylate, 3,3'- diindolymethane (DIM). BBR and bismuth subsalicylate are known antidiarrhea drugs, with possible antiviral functions against human gastrointestinal viruses. Chemical-genetic experiments revealed that these drugs have different mechanism of actions: RM strengthens the collagen barrier for viral entry; BBR and DIM enhances the ubiquitin-mediated protein degradation pathway. Together, these data revealed a multifaceted antiviral innate immune system in the C. elegans intestine. Aspects of genetic and chemical modulation of this system may be conserved in human innate immunity against gastrointestinal viruses.

Littleford, H. et al. (2013) International Worm Meeting "Identification of DMD-3 targets in the C. elegans male tail tip."

Ercan, S., Fitch, D., Yang, J-S., Kiontke, K., Mason, A., Herrera, R. A., Littleford, H.

[International Worm Meeting, 2013]

Morphogenesis is a fundamental developmental process in which cells can change shape and identity, migrate, and fuse to form a variety of structures. Despite its importance in development, little is known about how transcriptional regulation is linked to cytoskeletal processes that facilitate morphogenesis. Morphogenesis occurs in 4 cells of the C. elegans male tail tip as it retracts and changes shape during L4. Previous work demonstrated that DMD-3, a conserved, DM-domain transcription factor related to the human male fate-determining gene DMRT1, is necessary and sufficient for male tail tip retraction (Mason et al. 2008). DMD-3 is at the center of a genetic network with a bow-tie structure, regulated by pathways including Wnt signaling and heterochronic regulation, and in turn regulating genes involved in cellular processes such as vesicle trafficking and cytoskeletal rearrangement (Nelson et al 2011). However, while some of the regulatory pathways involved in specifying DMD-3 expression are known, the structure of the network downstream of DMD-3 is uncharacterized. We are using two methods to investigate downstream targets of DMD-3. To identify tail tip-specific targets, we are performing transcriptome profiling of tail tip tissue from worms that undergo tail tip morphogenesis (wild-type males and hermaphrodites ectopically expressing dmd-3), and worms that do not (wild-type hermaphrodites and dmd-3 mutant males). To identify direct DMD-3 transcriptional targets, we are employing chromatin immunoprecipitation and next-generation sequencing (ChIP-Seq), using an epitope-tagged DMD-3::GFP::FLAG transgene. Preliminary microarray transcriptome analysis on tail tip-specific RNA identified 134 significantly differentially-expressed genes (alpha = 0.05) in the dmd-3 mutant relative to wild-type. Combining the results of both approaches will yield direct targets of DMD-3 that act in the male tail tip. References: Mason et al. 2008. Development 135:2373-2382. Nelson et al. 2011. PLoS Genetics 7(3):e1002010.

Wilson DL (1993) Mech Ageing Dev "A comparison of methods for estimating mortality parameters from survival data."

Wilson DL

[Mech Ageing Dev, 1993]

The Gompertz mortality function, Rm = R0e alpha t, is frequently used to describe changes in mortality rate (Rm) with time (t). In this paper, four methods for determining the best fit values of the two parameters, R0 and alpha, are compared. Three of the four methods use the Gompertz mortality function with mortality rate estimates derived from survival data to determine the best fit values for the two parameters. All three confront problems. The fourth method uses the Gompertz survival function, which can be derived from the Gompertz mortality function and which allows one to use survival data directly. It thereby avoids the problems and generally gives the best estimates for the two parameters. The use of the mortality function, with mortality rate estimates, confronts four distinct problems. One of these is caused by time intervals when zero organisms die. A second is caused by errors produced in estimating mortality rates from survival data. If too high a proportion of a population die in a given time interval, the mortality rate estimates are too low. A third problem is the sensitivity of the mortality-equation-based analyses to values at the end of the survival curve, where scatter in mortality values tends to be greater. A final problem occurs when time intervals greater than one time unit (day, week, year, etc.) are used in the analysis. Such problems with the use of mortality rates to estimate parameter values are revealed when the calculated parameters are used to produce a survival curve, or when known values of R0 and alpha are used to generate survival data. This paper introduces a non-linear regression analysis, using a Simplex algorithm to fit parameters R0 and alpha in the Gompertz Survival function and concludes that it gives more reliable and consistent results with a variety of data than do three methods that use the mortality function.