Liu D et al. (2018) BMC Bioinformatics "Inferring synteny between genome assemblies: a systematic evaluation."

Hunt M, Liu D, Tsai IJ

[BMC Bioinformatics, 2018]

BACKGROUND: Genome assemblies across all domains of life are being produced routinely. Initial analysis of a new genome usually includes annotation and comparative genomics. Synteny provides a framework in which conservation of homologous genes and gene order is identified between genomes of different species. The availability of human and mouse genomes paved the way for algorithm development in large-scale synteny mapping, which eventually became an integral part of comparative genomics. Synteny analysis is regularly performed on assembled sequences that are fragmented, neglecting the fact that most methods were developed using complete genomes. It is unknown to what extent draft assemblies lead to errors in such analysis. RESULTS: We fragmented genome assemblies of model nematodes to various extents and conducted synteny identification and downstream analysis. We first show that synteny between species can be underestimated up to 40% and find disagreements between popular tools that infer synteny blocks. This inconsistency and further demonstration of erroneous gene ontology enrichment tests raise questions about the robustness of previous synteny analysis when gold standard genome sequences remain limited. In addition, assembly scaffolding using a reference guided approach with a closely related species may result in chimeric scaffolds with inflated assembly metrics if a true evolutionary relationship was overlooked. Annotation quality, however, has minimal effect on synteny if the assembled genome is highly contiguous. CONCLUSIONS: Our results show that a minimum N50 of 1Mb is required for robust downstream synteny analysis, which emphasizes the importance of gold standard genomes to the science community, and should be achieved given the current progress in sequencing technology.

Liu D et al. (2016) Biomicrofluidics "An automated microfluidic system for screening Caenorhabditis elegans behaviors using electrotaxis."

Gupta B, Liu D, Selvaganapathy PR

[Biomicrofluidics, 2016]

Caenorhabditis elegans (C. elegans) is a widely used animal model to study mechanisms of biological processes and human diseases. To facilitate manipulations of C. elegans in the laboratory, researchers have developed various tools that permit careful monitoring of behavior and changes in cellular processes. Earlier, we had reported a novel microfluidic assay device to study the neuronal basis of movement and to investigate the effects of cellular and environmental factors that can induce degeneration in certain neurons leading to movement disorder. The system involved the use of an electric field to perform electrotaxis assays, which allows detailed examination of movement responses of animals. One of the potential uses of this system is to perform genetic and chemical screenings for neuroprotective factors; however, it could not be done due to manual operations and low throughput. In this paper, we present an integrated microfluidic system that automates screening of C. elegans behavioral response using electrotaxis. The core component of system is a multilayer poly dimethyl siloxane (PDMS) device, which enables C. elegans loading, capture, flush, release, electrotaxis, and clean sequentially with the help of other components. The system is capable of screening C. elegans, at a throughput of more than 20 worms per hour, automatically and continually without human intervention. To demonstrate the effectiveness of the system, C. elegans neuronal mutants were screened, and the phenotype data were extracted and analyzed. We envision that the automatic screening potential of the system will accelerate the study of neuroscience, drug discovery, and genetic screens in C. elegans.

Liu D et al. (2007) Mol Cell Biol "The human SETMAR protein preserves most of the activities of the ancestral Hsmar1 transposase."

Chalmers R, Siddique A, Buisine N, Liu D, Bischerour J, Bigot Y

[Mol Cell Biol, 2007]

Transposons have contributed protein coding sequences to a unexpectedly large number of human genes. Except for the V(D)J recombinase and telomerase, all remain of unknown function. Here we investigate the activity of the human SETMAR protein, a highly expressed fusion between a histone H3 methylase and a mariner family transposase. Although SETMAR has demonstrated methylase activity and a DNA repair phenotype, its mode of action and the role of the transposase domain remain obscure. As a starting point to address this problem, we have dissected the activity of the transposase domain in the context of the full-length protein and the isolated transposase domain. Complete transposition of an engineered Hsmar1 transposon by the transposase domain was detected, although the extent of the reaction was limited by a severe defect for cleavage at the 3'' ends of the element. Despite this problem, SETMAR retains robust activity for the other stages of the Hsmar1 transposition reaction, namely, site-specific DNA binding to the transposon ends, assembly of a paired-ends complex, cleavage of the 5'' end of the element in Mn(2+), and integration at a TA dinucleotide target site. SETMAR is unlikely to catalyze transposition in the human genome, although the nicking activity may have a role in the DNA repair phenotype. The key activity for the mariner domain is therefore the robust DNA-binding and looping activity which has a high potential for targeting the histone methylase domain to the many thousands of specific binding sites in the human genome provided by copies of the Hsmar1 transposon.

Liu D et al. (2020) Aging (Albany NY) "Carnitine promotes recovery from oxidative stress and extends lifespan in C. elegans."

Liu D, Li L, Ou ZL, Zeng X

[Aging (Albany NY), 2020]

Carnitine is required for transporting fatty acids into the mitochondria for -oxidation. Carnitine has been used as an energy supplement but the roles in improving health and delaying aging remain unclear. Here we show in <i>C. elegans</i> that L-carnitine improves recovery from oxidative stress and extends lifespan. L-carnitine promotes recovery from oxidative stress induced by paraquat or juglone and improves mobility and survival in response to H₂O₂ and human amyloid (A) toxicity. L-carnitine also alleviates the oxidative stress during aging, resulting in moderate but significant lifespan extension, which was dependent on SKN-1 and DAF-16. Long-lived worms with germline loss (<i>glp-1</i>) or reduced insulin receptor activity (<i>daf-2)</i> recover from aging-associated oxidative stress faster than wild-type controls and their long lifespans were not further increased by L-carnitine. A new gene, T08B1.1, aligned to a known carnitine transporter OCTN1 in humans, is required for L-carnitine uptake in <i>C. elegans</i>. T08B1.1 expression is elevated in <i>daf-2</i> and <i>glp-1</i> mutants and its knockdown prevents L-carnitine from improving oxidative stress recovery and prolonging lifespan. Together, our study suggests an important role of L-carnitine in oxidative stress recovery that might be important for healthy aging in humans.

Liu D et al. (2013) Environ Toxicol Pharmacol "Realgar bioleaching solution is a less toxic arsenic agent in suppressing the Ras/MAPK pathway in Caenorhabditis elegans."

Li H, Bai Y, Zhou T, Zhi D, Liu D, Yu Q, Wan F

[Environ Toxicol Pharmacol, 2013]

To explore other arsenic derivatives with anticancer effects and fewer adverse effects, realgar bioleaching solution (RBS) has been found to be a viable approach. Here we used C. elegans as a model organism to its possible efficacy for anti-cancer effect of RBS. Our results indicated that RBS significantly suppressed the multivulva (Muv) phenotype of let-60 ras(gf) mutant that was positive correlated to arsenic concentrations in worms and also inhibited Muv phenotype of lin-15(lf) upstream of Ras/MAPK pathway, but did not affect the Muv phenotype resulting from loss-of-function mutations of lin-l(lf) downstream of Ras/MAPK pathway, which may be mechanism-based. In toxicity tests, RBS did not lead to reduction resulting from arsenic trioxide (ATO) in the number of pharyngeal pumping which was orthologous to vertebrate heart beating in wild type C. elegans. Overall, RBS was likely to be a potential anti-cancer drug candidate with high efficiency and low toxicity.

Liu D et al. (2019) Theranostics "Using near-infrared enhanced thermozyme and scFv dual-conjugated Au nanorods for detection and targeted photothermal treatment of Alzheimer's disease."

Liu J, Kuai Z, Liu D, Jiang X, Kong W, Gao R, Liu X, Shi Y, Bai S, Shan Y, Li W

[Theranostics, 2019]

Investigation of targeting inhibitors of A aggregation, heme-A peroxidase-like activity and efficient detectors of A aggregation, are of therapeutic value and diagnostics significance for the treatment of Alzheimer's disease (AD). Due to the complex pathogenesis of AD, theranostics treatment with multiple functions are necessary. Herein we constructed the NIR absorption property of gold nanorods (GNRs) loaded with single chain variable fragment (<i>scFv</i>) 12B4 and thermophilic acylpeptide hydrolase (APH) ST0779 as a smart theranostic complex (GNRs-APH-<i>scFv</i>, GAS), which possesses both rapid detection of A aggregates and NIR photothermal treatment that effectively disassembles A aggregates and inhibits A-mediated toxicity. <b>Methods</b>: We screened targeting anti-A <i>scFv</i> 12B4 and thermophilic acylpeptide hydrolase as amyloid-degrading enzyme, synthesized GAS gold nanorods complex. The GAS was evalued by A inhibition and disaggregation assays, A detection assays, A mediated toxicity assays <i>in vitro</i>. <i>In vivo,</i> delaying A-induced paralysis in AD model of <i>Caenorhabditis elegans</i> was also tested by GAS. <b>Results</b>: <i>In vitro</i>, GAS has a synergistic effect to inhibit and disassociate A aggregates, in addition to decrease heme-A peroxidase-like activity. In cultured cells, treatment with GAS reduces A-induced cytotoxicity, while also delaying A-mediated paralysis in CL4176 <i>C.elegans</i> model of AD. Furthermore, the photothermal effect of the GAS upon NIR laser irradiation not only helps disassociate the A aggregates but also boosts APH activity to clear A. The GAS, as a targeting detector and inhibitor, allows real-time detection of A aggregates. <b>Conclusion</b>: These results firstly highlight the combination of <i>scFv</i>, APH and nanoparticles to be theranostic AD drugs. Taken together, our strategy provides a new thought into the design of smart compounds for use as efficiently therapeutic and preventive agents against AD. Moreover, our design provides broad prospects of biomedical strategy for further theranostics application in those diseases caused by abnormal protein.

Sakoguchi H et al. (2016) Biosci Biotechnol Biochem "Screening of biologically active monosaccharides: growth inhibitory effects of d-allose, d-talose, and l-idose against the nematode Caenorhabditis elegans."

Izumori K, Yoshihara A, Sakoguchi H, Sato M

[Biosci Biotechnol Biochem, 2016]

We compared the growth inhibitory effects of all aldohexose stereoisomers against the model animal Caenorhabditis elegans. Among the tested compounds, the rare sugars d-allose (d-All), d-talose (d-Tal), and l-idose (l-Ido) showed considerable growth inhibition under both monoxenic and axenic culture conditions. 6-Deoxy-d-All had no effect on growth, which suggests that C6-phosphorylation by hexokinase is essential for inhibition by d-All.

Sakoguchi H et al. (2016) Bioorg Med Chem Lett "Growth inhibitory effect of d-arabinose against the nematode Caenorhabditis elegans: Discovery of a novel bioactive monosaccharide."

Shintani T, Izumori K, Sato M, Sakoguchi H, Okuma K, Yoshihara A

[Bioorg Med Chem Lett, 2016]

Biological activities of unusual monosaccharides (rare sugars) have largely remained unstudied until recently. We compared the growth inhibitory effects of aldohexose stereoisomers against the animal model Caenorhabditis elegans cultured in monoxenic conditions with Escherichia coli as food. Among these stereoisomers, the rare sugar d-arabinose (d-Ara) showed particularly strong growth inhibition. The IC50 value for d-Ara was estimated to be 7.5mM, which surpassed that of the potent glycolytic inhibitor 2-deoxy-d-glucose (19.5mM) used as a positive control. The inhibitory effect of d-Ara was also observed in animals cultured in axenic conditions using a chemically defined medium; this excluded the possible influence of E. coli. To our knowledge, this is the first report of biological activity of d-Ara. The d-Ara-induced inhibition was recovered by adding either d-ribose or d-fructose, but not d-glucose. These findings suggest that the inhibition could be induced by multiple mechanisms, for example, disturbance of d-ribose and d-fructose metabolism.

Yoshihara A et al. (2019) Bioorg Med Chem Lett "Growth inhibition by 1-deoxy-d-allulose, a novel bioactive deoxy sugar, screened using Caenorhabditis elegans assay."

Sakoguchi H, Fleet GWJ, Izumori K, Shintani T, Sato M, Yoshihara A

[Bioorg Med Chem Lett, 2019]

The biological activities of deoxy sugars (deoxy monosaccharides) have remained largely unstudied until recently. We compared the growth inhibition by all 1-deoxyketohexoses using the animal model Caenorhabditis elegans. Among the eight stereoisomers, 1-deoxy-d-allulose (1d-d-Alu) showed particularly strong growth inhibition. The 50% inhibition of growth (GI₅₀) concentration by 1d-d-Alu was estimated to be 5.4mM, which is approximately 10 times lower than that of d-allulose (52.7mM), and even lower than that of the potent glycolytic inhibitor, 2-deoxy-d-glucose (19.5mM), implying that 1d-d-Alu has a strong growth inhibition. In contrast, 5-deoxy- and 6-deoxy-d-allulose showed no growth inhibition of C. elegans. The inhibition by 1d-d-Alu was alleviated by the addition of d-ribose or d-fructose. Our findings suggest that 1d-d-Alu-mediated growth inhibition could be induced by the imbalance in d-ribose metabolism. To our knowledge, this is the first report of biological activity of 1d-d-Alu which may be considered as an antimetabolite drug candidate.

Katane M et al. (2020) Biochim Biophys Acta Proteins Proteom "Biochemical characterization of d-aspartate oxidase from Caenorhabditis elegans: Its potential use in the determination of free D-glutamate in biological samples."

Katane M, Sekine M, Nakayama K, Homma H, Kuwabara H, Saitoh Y, Miyamoto T

[Biochim Biophys Acta Proteins Proteom, 2020]

d-Aspartate oxidase (DDO) is a flavin adenine dinucleotide (FAD)-containing flavoprotein that stereospecifically acts on acidic D-amino acids (i.e., free d-aspartate and D-glutamate). Mammalian DDO, which exhibits higher activity toward d-aspartate than D-glutamate, is presumed to regulate levels of d-aspartate in the body and is not thought to degrade D-glutamate in vivo. By contrast, three DDO isoforms are present in the nematode Caenorhabditis elegans, DDO-1, DDO-2, and DDO-3, all of which exhibit substantial activity toward D-glutamate as well as d-aspartate. In this study, we optimized the Escherichia coli culture conditions for production of recombinant C. elegans DDO-1, purified the protein, and showed that it is a flavoprotein with a noncovalently but tightly attached FAD. Furthermore, C. elegans DDO-1, but not mammalian (rat) DDO, efficiently and selectively degraded D-glutamate in addition to d-aspartate, even in the presence of various other amino acids. Thus, C. elegans DDO-1 might be a useful tool for determining these acidic D-amino acids in biological samples.