Browsing by Author "Chen, Ying"

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    The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation
    Kosch, Tiffany A.; Torres-Sánchez, María; Liedtke, H. C.; Summers, Kyle; Yun, Maximina H.; Crawford, Andrew J.; Maddock, Simon T.; Ahammed, Md. S.; Araújo, Victor L. N.; Bertola, Lorenzo V.; Bucciarelli, Gary M.; Carné, Albert; Carneiro, Céline M.; Chan, Kin O.; Chen, Ying; Crottini, Angelica; da Silva, Jessica M.; Denton, Robert D.; Dittrich, Carolin; Espregueira Themudo, Gonçalo; Farquharson, Katherine A.; Forsdick, Natalie J.; Gilbert, Edward; Che, Jing; Katzenback, Barbara A.; Kotharambath, Ramachandran; Levis, Nicholas A.; Márquez, Roberto; Mazepa, Glib; Mulder, Kevin P.; Müller, Hendrik; O’Connell, Mary J.; Orozco-terWengel, Pablo; Palomar, Gemma; Petzold, Alice; Pfennig, David W.; Pfennig, Karin S.; Reichert, Michael S.; Robert, Jacques; Scherz, Mark D.; Siu-Ting, Karen; Snead, Anthony A.; Stöck, Matthias; Stuckert, Adam M. M.; Stynoski, Jennifer L.; Tarvin, Rebecca D.; Wollenberg Valero, Katharina C. (2024-11-01)
    Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to “leap” to the next level.
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    Diminished satellite cell fusion and S6K1 expression in myotubes derived from skeletal muscle of low birth weight neonatal pigs
    Chen, Ying; Zhu, Haibo; McCauley, Sydney R.; Zhao, Lidan; Johnson, Sally E.; Rhoads, Robert P.; El-Kadi, Samer Wassim (The American Physiological Society, 2017-02-09)
    Low birth weight (LBWT) is consistently associated with impaired postnatal muscle growth in mammals. Satellite cell (SC)‐mediated myonuclear incorporation precedes protein accumulation in the early stages of postnatal muscle development and growth. The objective of this study was to investigate proliferation and differentiation of SCs and the regulation of protein synthesis signaling in response to insulin‐like growth factor (IGF)‐I stimulation in SC‐derived myotubes of LBWT neonatal pigs. SCs isolated from Longissimus dorsi muscle of LBWT and NBWT pigs (3‐d‐old, n = 8) were cultured and induced to proliferate and differentiate to myotubes in vitro. On day 3 of differentiation, myotubes were fasted in serum‐free media for 3 h and treated with human recombinant R³‐insulin‐like growth factor‐I (rh IGF‐I) at 0, 25, and 50 ng × mL⁻¹ for 30 min. There was no difference in proliferation rates of SCs from LBWT and NBWT pigs. However, LBWT SC fusion was 15% lower (P ≤ 0.05) without a difference in MyoD or myogenin mRNA expression in comparison with NBWT pigs, suggesting SCs are not intrinsically different between the two groups. IGF‐Ι stimulation at physiological concentrations activated downstream effectors of mTOR similarly in myotubes from LBWT and NBWT pigs. However, abundance of ribosomal protein S6 kinase 1(S6K1) was lower in myotubes of LBWT compared to their NBWT siblings (P ≤ 0.05). These results indicate that the modest reduction in SC fusion and S6K1 expression are not the major contributors to the impaired postnatal muscle growth of LBWT pigs.
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    Formulation of a Multi-Disciplinary Design Optimization of Containerships
    Chen, Ying (Virginia Tech, 1999-05-17)
    To develop a computer tool that will give the best ship design using an optimization technique is one of the objects of the FIRST project. Choosing a containership design as a test case, the Design Optimization Tools (DOT) package is used as the optimization tool. The problem is tackled from the ship owner's point of view. The required freight rate is chosen as the objective function because the most important thing that concerns the ship owner is whether the ship will make a profit or not, and if so, how much profit it can make. DOT, as well as any other numerical optimization tool, only gives an approximation of the optimum design and uses numerical approximation during the optimization. It is very important for the users to formulate carefully the optimization problem so that it will give a stable and reasonable solution. Development of a geometric module and choosing suitable empirical formulas for performance evaluation are also major issues of the project.
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    In vivo metal substitution in bacteroides superoxide dismutase
    Chen, Ying (Virginia Tech, 1989-12-08)
    The effect of various growth conditions on the type of superoxide dismutase (SGD) formed anaerobically in three Bacteriodes species was studied. B. fragilis, B. distasonis, and B. thetaiotaomicron were grown in ironâ restricted media with or without manganese supplementation. Iron availability was decreased by treatment of the media with chelex-100, a metal-chelating resin, and addition of desferrioxamine mesylate (desferal, Ciba-Geigy), an iron chelator. Mn-containing (MnSOD) and Fe-containing superoxide dismutase (EeSOD) activities in cell extracts were differentiated by inhibition with azide and inactivation by H₂0₂. The amount of Mn-containing superoxide dismutase was estimated by the fraction of azide- and H₂0₂, -resistant activity. Cells grown in untreated media contained approximately 90% FeSOD and 10% MnSOD. Cells grown in Fe-restricted media supplemented with graded amounts of manganese synthesized a progressively larger fraction of MnSOD. Hemin, added to the Fe-restricted media, did not serve as an iron source for FeSOD formation. Superoxide dismutase specific activities varied (3-6 U/mg) in each extract but not as a function of manganese concentration.
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    NMR Applications in Soft Materials Science:  Correlation of Structure, Dynamics, and Transport
    Chen, Ying (Virginia Tech, 2015-09-05)
    This dissertation aims to investigate and correlate structure, dynamics and transport properties of several novel soft materials systems using multiple Nuclear Magnetic Resonance (NMR) methodologies, including solid-state NMR (SSNMR), diffusometry, and imaging, and with the help of X-ray scattering. First, we report the investigation of structure and dynamics of three polymeric membranes: hydroxyalkyl-containing imidazolium homopolymers, poly(arylene ether sulfone) segmented copolymers, and disulfonated poly(arylene ether sulfone) random copolymers using a wide array of SSNMR techniques, including: 1) ¹³C cross-polarization magic angle spinning (CPMAS) with varying cross-polarization (CP) contact time, 2) ¹³C single-pulse magic angle spinning (MAS) with varying delay time, 3) ²³Na single-pulse MAS, 4) two dimensional phaseadjusted spinning sideband (2D PASS), 5) proton spin−lattice relaxation (T₁), 6) rotating frame spin−lattice relaxation (T₁ρ), and 7) center-band-only detection of exchange (CODEX). These various types of SSNMR spectroscopic methods provide a wealth of structural and dynamic information over a wide range of time scales from a few nanoseconds to seconds. We further present a picture of rich structural and transport behaviors in supramolecular assemblies formed by amphiphilic wedge molecules using a combination of ²³Na solid-state NMR, ¹H/²H PFG NMR diffusion, relaxation and grazing-incidence small-angle X-ray scattering. Our results show that the liquid crystalline domains in these materials undergo a transition from columnar to bicontinuous cubic phases with a simple increase in humidity, while the amorphous domain boundaries consist of individual wedge molecules with a significant fraction (~ 10%) of total wedge molecules. Multiple-component diffusion of both wedges and water further confirms the structural and dynamic heterogeneity, with the bicontinous cubic phase being able to facilitate much faster water and ion transport than the columnar phase. We then develop a quantitative approach to probe the migration of two novel “theranostic” polymeric agents (combining “therapeutic” and “diagnostic” functions) into bulk hydrogels using two distinct time-resolved magnetic resonance imaging (MRI) methods. To the best of our knowledge, this is the first work that combines time-resolved MRI experiments to reliably quantify diffusivity of paramagnetic and superparamagnetic nanoparticles in bulk biological media. Our results agree closely with those obtained from fluorescence techniques, yet the capability of our approach allows the analysis of actual nanoparticles diffusion through biogels on mm to cm scales during a range of time periods. Finally, we employ a combination of NMR techniques to obtain a comprehensive understanding of ion clustering and transport behaviors of ionic liquids inside the benchmark ionic polymer Nafion. Spin relaxation shows that anion relaxation is more influenced by the fixed sulfonate groups than cation relaxation. 2D ¹H-¹⁹F heteronuclear Overhauser effect spectroscopy (HOESY) and 1D ¹⁹F¹⁹F selective nuclear Overhauser effect (NOE) spectroscopy confirm our assumption of the formation of ion clusters at low water content in the ionomer. While we observe non-restricted diffusion behavior for cations, anion diffusion is strongly restricted both between domain boundaries and within domains in the absence of water. The restricted anion diffusion can serve as a reliable probe for detailed multiscale structures of the ionomer.
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    Regulation of protein metabolism in skeletal muscle of low-birth-weight neonatal pigs
    Chen, Ying (Virginia Tech, 2017-09-27)
    The neonatal period in mammals is characterized by high rates of growth, attributed to rapid myonuclear accretion and protein deposition in muscle. Low-birth-weight (LBWT) neonates experience restricted muscle development, which leads to impaired postnatal growth and metabolic disorders later in life. The overall hypothesis of this dissertation was that dysfunction of myogenic satellite cells and aberrant regulation of protein synthesis and degradation signaling predispose LBWT neonatal pigs to slower postnatal growth. We sought to determine the proliferation and differentiation of satellite cells (SCs) derived from skeletal muscle of LBWT neonatal pigs and to elucidate the cellular mechanisms that regulate protein synthesis and degradation in LBWT pig muscles. Newborn pigs were considered as normal-birth-weight (NBWT) or LBWT when weight at birth was within 0.5 SD and below 2 SD of litter average respectively. SCs isolated from longissimus dorsi (LD) muscle of NBWT and LBWT neonatal pigs displayed similar proliferation rates. Fusion was modestly diminished in SCs from muscle of LBWT pigs compared with their NBWT siblings, suggesting SCs were not intrinsically different between the two groups and were unlikely a major contributor to the impaired muscle growth of LBWT pigs. Plasma and muscle insulin-like growth factor (IGF)-I was diminished in LBWT compared with NBWT pigs. In addition, reduced activation of key components of IGF-I downstream signaling pathway in LBWT pigs muscle may lead to diminished translation initiation signaling and thus decreased protein synthesis in these animals. However, IGF-I receptor expression and myostatin signaling inversely correlated to LBWT, indicating they may participate in compensatory responses for the reduction in protein synthesis signaling. Expression of eukaryotic initiation factor (eIF) 4F complex subunits, eIF4E, eIF4G, and eIF4A was reduced in LBWT compared with NBWT pigs. This would suggest that diminished translation initiation signaling in skeletal muscle of LBWT pigs is the main factor that predisposes LBWT pigs to slower growth rates in the neonatal period. In contrast, changes in protein degradation signaling do not appear to affect protein turnover in LBWT neonatal pigs.