Dr. Xiangjia “Jack” Min, Associate Professor in Biological Science, published a research article in Computational Molecular Biology in September 2017.
Title: Comprehensive Cataloging and Analysis of Alternative Splicing in Maize
Author: Dr. Xiangjia “Jack” Min
Gene expression is a key step in developmental regulation and responses in changing environments in plants. Alternative splicing (AS) is a process generating multiple RNA isoforms from a single gene pre-mRNA transcript that increases the diversity of functional proteins and RNAs. Identification and analysis of alternatively splicing events are critical for crop improvement and understanding regulatory mechanisms. In maize large numbers of transcripts generated by RNA-seq technology are available, we incorporated these data with data assembled with ESTs and mRNAs to comprehensively catalog all genes undergoing AS. A total of 192,624 AS events were detected and classified, including 103,566 (53.8%) basic events and 89,058 (46.2%) complex events which were formed by combination of various types of basic events. Intron retention was the dominant type of basic AS event, accounting for 24.1%. These AS events were identified from 91,128 transcripts which were generated from 26,669 genomic loci, of which consisted of 20,860 gene models. It was estimated that 55.3% maize genes may be subjected to AS. The transcripts mapping information can be used to improve the predicted gene models in maize. The data can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/).
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Dr. Michael Butcher, Associate Professor in Biological Science, in collaboration with Dr. Gary Walker, Chairperson and Professor of Biological Sciences, Mr. Julio “Ed” Budde, and student Dylan Thomas published a research article in Journal of Applied Physiology in September 2017.
Title: Ontogeny of myosin isoform expression and prehensile function in the tail of the gray short-tailed opossum (Monodelphis domestica)
Authors: Dylan R. Thomas, Brad A. Chadwell, Gary R. Walker, Julio E. Budde, John L. VandeBerg, Michael T. Butcher
Terrestrial opossums use their semiprehensile tail for grasping nesting materials as opposed to arboreal maneuvering. We relate the development of this adaptive behavior with ontogenetic changes in myosin heavy chain (MHC) isoform expression from 21 days to adulthood. Monodelphis domestica is expected to demonstrate a progressive ability to flex the distal tail up to age 7 mo, when it should exhibit routine nest construction. We hypothesize that juvenile stages (3–7 mo) will be characterized by retention of the neonatal isoform (MHC-Neo), along with predominant expression of fast MHC-2X and -2B, which will transition into greater MHC-1β and -2A isoform content as development progresses. This hypothesis was tested using Q-PCR to quantify and compare gene expression of each isoform with its protein content determined by gel electrophoresis and densitometry. These data were correlated with nesting activity in an age-matched sample of each age group studied. Shifts in regulation of MHC gene transcripts matched well with isoform expression. Notably, mRNA for MHC-Neo and -2B decrease, resulting in little-to-no isoform translation after age 7 mo, whereas mRNA for MHC-1β and -2A increase, and this corresponds with subtle increases in content for these isoforms into late adulthood. Despite the tail remaining intrinsically fast-contracting, a critical growth period for isoform transition is observed between 7 and 13 mo, correlating primarily with use of the tail during nesting activities. Functional transitions in MHC isoforms and fiber type properties may be associated with muscle “tuning” repetitive nest remodeling tasks requiring sustained contractions of the caudal flexors.
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Dr. Michael Butcher, Associate Professor in Biological Science, in collaboration with biology student Zachary Glenn, published a research article in Journal of Mammalian Evolution in September 2017.
Title: Architectural Properties of Sloth Forelimb Muscles (Pilosa: Bradypodidae)
Authors: Rachel A. Olson, Zachary D. Glenn, Rebecca N. Cliffe, Michael T. Butcher
Tree sloths have reduced skeletal muscle mass, and yet they are able to perform suspensory behaviors that require both strength and fatigue resistance to suspend their body mass for extended periods of time. The muscle architecture of sloths is hypothesized to be modified in ways that will enhance force production to compensate for this reduction in limb muscle mass. Our objective is to test this hypothesis by quantifying architecture properties in the forelimb musculature of the brown-throated three-toed sloth (Bradypus variegatus: N = 4). We evaluated architecture from 52 forelimb muscles by measuring muscle moment arm (rm), muscle mass (MM), belly length (ML), fascicle length (LF), pennation angle (θ), and physiological cross-sectional area (PCSA), and these metrics were used to estimate isometric force, joint torque, and power. Overall, the musculature becomes progressively more pennate from the extrinsic to intrinsic regions of the forelimb, and the flexors are more well developed than the extensors as predicted. However, most muscles are indicative of a mechanical design for fast joint rotational velocity instead of large joint torque (i.e., strength), although certain large, parallel-fibered shoulder (e.g., m. latissimus dorsi) and elbow (e.g., m. brachioradialis) flexors are capable of producing appreciable torques by having elongated moment arms. This type of functional tradeoff between joint rotational velocity and mechanical advantage is further exemplified by muscle gearing in Bradypus that pairs synergistic muscles with opposing LF/rm ratios in each functional group. These properties are suggested to facilitate the slow, controlled movements in sloths. In addition, the carpal/digital flexors have variable architectural properties, but their collective PCSA and joint torque indicates the capability for maintaining grip force and carpal stability while distributing load from the manus to the shoulder. The observed specializations provide a basis for understanding sustained suspension in sloths.
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Dr. Xiangjia “Jack” Min, Associate Professor in Biological Science, in collaboration with Dr. Feng Yu, Assistant Professor in Computer Science and Information Systems published a research article in Current Plant Biology in July 2017.
Title: “Comparative landscape of alternative splicing in fruit plants”
Authors: G Sablok, B Powell, J Braessler, F Yu F, XJ Min
Alternative splicing (AS) has played a major role in defining the protein diversity, which could be linked to phenotypic alternations. It is imperative to have a comparative resolution of AS to understand the pre-mRNAs splicing diversity. In the present research, we present a comparative assessment of the AS events in four different fruit plants including apple (Malus domestica), grape (Vitis vinifera), sweet orange (Citrus sinensis), and woodland strawberry (Fragaria vesca), using spliced mapping of the expressed sequence tags and mRNA sequences. We identified a total of 2039 AS events in apple, 2454 in grape, 1425 in orange, and 631 in strawberry, respectively. In this study grape displayed the maximum number of genes (1588) associated with the splicing, followed by apple (1580), orange (1133) and strawberry (444). Transcripts mapping analysis shows that grape plant has relatively larger intron sizes than introns in other fruit species. The data provide a basis for further functional characterization of the genes undergoing AS and can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/plant/).
Full article link: http://www.sciencedirect.com/science/article/pii/S2214662817300439
“Sex and regional differences in rabbit right ventricular L-type calcium current levels and mathematical modeling of arrhythmia vulnerability.” Experimental Physiology 102 (7): 804-817, 2017.
*A figure from this paper was used as the cover illustration for the July 1 edition of this journal.
What is the central question of this study?
Regional variations of ventricular L-type calcium current (ICa-L) amplitude may underlie the increased arrhythmia risk in adult females. Current amplitude variations have been described for the left ventricle but not for the right ventricle.
What is the main finding and its importance?
Adult female rabbit right ventricular base myocytes exhibit elevated ICa-L compared with female apex or male myocytes. Oestrogen upregulated ICa-L in cultured female myocytes. Mathematical simulations modelling long QT syndrome type 2 demonstrated that elevated ICa-L prolonged action potentials and induced early after-depolarizations. Thus, ventricular arrhythmias in adult females may be associated with an oestrogen-induced upregulation of ICa-L.
Previous studies have shown that adult rabbit left ventricular myocytes exhibit sex and regional differences in L-type calcium current (ICa-L) levels that contribute to increased female susceptibility to arrhythmogenic early after-depolarizations (EADs). We used patch-clamp recordings from isolated adult male and female rabbit right ventricular myocytes to determine apex–base differences in ICa-L density and used mathematical modelling to examine the contribution of ICa-L to EAD formation. Current density measured at 0 mV in female base myocytes was 67% higher than in male base myocytes and 55% higher than in female apex myocytes. No differences were observed between male and female apex myocytes, between male apex and base myocytes, or in the voltage dependences of ICa-L activation or inactivation. The role of oestrogen was investigated using cultured adult female right ventricular base myocytes. After 2 days, 17β-estradiol (1 nm) produced a 65% increase in ICa-L density compared with untreated control myocytes, suggesting an oestrogen-induced upregulation of ICa-L. Action potential simulations using a modified Luo–Rudy cardiomyocyte model showed that increased ICa-L density, at the level observed in female base myocytes, resulted in longer duration action potentials, and when combined with a 50% reduction of the rapidly inactivating delayed rectifier potassium current conductance to model long QT syndrome type 2, the action potential was accompanied by one or more EADs. Thus, we found higher levels of ICa-L in adult female right ventricle base myocytes and the upregulation of this current by oestrogen. Simulations of long QT syndrome type 2 showed that elevated ICa-L contributed to genesis of EADs.
Information regarding the authors:
YSU Faculty: Dr. Mark D. Womble (Department of Biological Sciences; senior author) and Dr. Jozsi Z. Jalics (Department of Mathematics and Statistics; contributing author).
YSU Students: At the time that this research was performed, Zane M. Kalik (lead author) was an undergraduate Biology student, Joshua L. Mike (contributing author) was an undergraduate Mathematics and Chemistry student, Moriah Wright (contributing author) was an undergraduate Mathematics student, and Cassandra Slipski (contributing author) was a Biology graduate student.
Thomas DR, Chadwell BA, Walker GR, Budde JE, Vandeberg JL, Butcher MT. “Ontogeny of myosin isoform expression and prehensile function in the tail of the gray short-tailed opossum (Monodelphis domestica),” Journal of Applied Physiology, May 2017. DOI: 10.1152/japplphysiol.00651.2016
Former YSU biology student Dylan Thomas authored this paper in collaboration with faculty and staff from YSU, Ohio University, and the University of Texas Rio Grande Valley. The paper was submitted in July 2016 and was accepted and published in May 2017 by the American Physiological Society.
Terrestrial opossums use their semi-prehensile tail for grasping nesting materials as opposed to arboreal maneuvering. We relate the development of this adaptive behavior with ontogenetic changes in myosin heavy chain (MHC) isoform expression from 21 days to adulthood. Monodelphis domestica is expected to demonstrate a progressive ability to flex the distal tail up to age 7 months, when it should exhibit routine nest construction. We hypothesize that juvenile stages (3-7 months) will be characterized by retention of the neonatal isoform (MHC-Neo), along with predominant expression of fast MHC-2X and 2B, which will transition into greater MHC-1β and 2A isoform content as development progresses. This hypothesis was tested using Q-PCR to quantify and compare gene expression of each isoform to its protein content determined by gel electrophoresis and densitometry. These data were correlated with nesting activity in an age-matched sample of each age group studied. Shifts in regulation of MHC gene transcripts matched well with isoform expression. Notably, mRNA for MHC-Neo and 2B decrease, resulting in little-to-no isoform translation after age 7 months, whereas mRNA for MHC-1β and 2A increase, and this corresponds with subtle increases in content for these isoforms into late adulthood. Despite the tail remaining intrinsically fast-contracting, a critical growth period for isoform transition is observed between 7 and 13 months, correlating primarily with use of the tail during nesting activities. Functional transitions in MHC isoforms and fiber type properties may be associated with muscle ‘tuning’ repetitive nest remodeling tasks requiring sustained contractions of the caudal flexors.
Daniel Wehrung, Elaheh. A. Chamsaz, James H. Andrews, Abraham Joy, and Moses O. Oyewumi, “Engineering Alkoxyphenacyl-Polycarbonate Nanoparticles for Potential Application in Near-Infrared Light-Modulated Drug Delivery via Photon Up-Conversion Process,” Journal of Nanoscience and Nanotechnology 17, 4867-4881 (2017).
This publication describes the results of experiments primarily done at NEOMED, but also at YSU’s Dept. of Physics & Astronomy, using nano-crystals to convert near infrared light to ultraviolet light. Typically, ultraviolet light is difficult to apply as a form of medical phototherapy due to its harmful effects to other tissues. Using the materials studied in this paper, the primary exposure would instead be to infrared light that is then converted to ultraviolet at the site of the phototherapy for localized treatment. This work was led by Daniel Wehrung as part of his successful PhD dissertation work at NEOMED under the supervision of Dr. Moses Oyewumi in the Department of Pharmaceutical Sciences. Dr. Andrews assisted with experiments at YSU as part of this study.
Photoresponsive delivery systems that are activated by high energy photo-triggers have been accorded much attention because of the capability of achieving reliable photoreactions at short irradiation times. However, the application of a high energy photo-trigger (UV light) is not clinically viable. Meanwhile, the process of photon-upconversion is an effective strategy to generate a high energy photo-trigger in-situ through exposure to clinically relevant near-infrared (NIR) light. In this regard, we synthesized photon upconverting nanocrystals (UCNCs) that were subsequently loaded into photoresponsive nanoparticles (NPs) prepared using alkoxyphenacyl-based polycar- bonate homopolymer (UCNC-APP-NPs). UCNC loading affected resultant NP size, size distribu- tion, colloidal stability but not the zeta potential. The efficiency of NIR-modulated drug delivery was impacted by the heterogenetic nature of the resultant UCNC-APP-NPs which was plausibly formed through a combination of UCNC entrapment within the polymeric NP matrix and nucleation of polymer coating on the surface of the UCNCs. The biocompatibility of UCNC-APP-NPs was demonstrated through cytotoxicity, macrophage activation, and red blood cell lysis assays. Studies in tumor-bearing (nu/nu) athymic mice showed a negligible distribution of UCNC-APP-NPs to retic- uloendothelial tissues. Further, distribution of UCNC-APP-NPs to various tissues was in the order (highest to lowest): Lungs > Tumor > Kidneys > Liver > Spleen > Brain > Blood > Heart. In all, the work highlighted some important factors that may influence the effectiveness, reproducibility biocompatibility of drug delivery systems that operate on the process of photon-upconversion.
Robert J. Korenic, Associate Professor, Civil and Construction Engineering Technology, presented a paper entitled “Youngstown State University ‘Gateway Project’ Rain Garden Design Upgrades.” The paper was presented at the Engineering Sustainability Innovation and the Triple Bottom Line Conference on April 10, 2017 in Pittsburgh, PA. This is a national conference affiliated with the University of Pittsburgh Swanson School of Engineering and the Mascaro Center for Sustainable Innovation.
The Youngstown State University (YSU) “Gateway Project,” completed several years ago, was a large scale grounds and facilities project intended to upgrade several campus buildings and the grounds surrounding these facilities. Many of the upgrades utilized Leadership in Energy and Environmental Design (LEED) sustainable design criteria. Included in these upgrades was the installation of bioswale and rain garden areas intended to help manage storm water runoff from new parking facilities. While the bioswales are functioning as intended, the rain garden has never maintained plant life and is not functioning to manage storm water runoff. Phase one of this research involved testing the hydraulic conductivity of the soil in the garden, sampling the soil for its pH and identifying the soil stratification in the garden by digging test pits. This document will recap the results of that research and build on those results by specifying how the rain garden can be rebuilt in order to properly manage the storm water runoff.
Paper Title: “Hidden Markov Model for Portfolio Management with Mortgage-Backed Securities Exchange-Traded Fund” was published on the Society of Actuaries website in April. This project was funded by the finance research grants from SOA, from June 2016-June 2017.
The hidden Markov model (HMM) is a regime-shift model that assumes observation data were driven by hidden regimes (or states). The model has been used in many fields, such as speech recognition, handwriting recognition, biomathematics and financial economics. In this paper, we describe HMM and its application in finance and actuarial areas. We then develop a new application of HMM in mortgage-backed securities exchange-traded funds (MBS ETFs). We begin with a primer on the hidden Markov model, covering main concepts, the model’s algorithms and examples to demonstrate the concepts. Next, we introduce some applications of the model in actuarial and financial areas. We then present applications of HMM on MBS ETFs. Finally, we establish a new use of HMM for a portfolio management with MBS ETFs: predicting prices and trading some MBS ETFs. Data, algorithms and codes generated in this paper can be used for future research in actuarial science and finance.
Paper Title: “Using the Hidden Markov Model to Improve the Hull-White Model for Short Rate”, a collaboration work with Thomas Wakefield, YSU, and Dung Nguyen, Ned Davis Research Group, was accepted to publish in the International Journal of Trade, Economics and Finance.
Abdullah M. Kuraan, Stefan I. Moldovan, Kyosung Choo, “Heat transfer and hydrodynamics of free water jet impingement at low nozzle-to-plate spacings,” International Journal of Heat and Mass Transfer 108 (2017) 2211-2216.
In this study, heat transfer and hydrodynamics of a free water jet impinging a flat plate surface are experimentally investigated. The effects of the nozzle-to-plate spacing, which is equal to or less than one nozzle diameter (H/d = 0.08–1), on the Nusselt number, hydraulic jump diameter, and pressure at the stagnation point are considered. The results show that the normalized stagnation Nusselt number, pressure, and hydraulic jump diameter are divided into two regions: Region (I) jet deflection region (H/d ⩽ 0.4) and Region (II) inertia dominant region (0.4 < H/d ⩽ 1). In region I, the normalized stagnation Nusselt number and hydraulic jump diameter drastically increase with decreasing the nozzle-to-plate spacing, since the stagnation pressure increases due to the jet deflection effect. In region II, the effect of the nozzle-to-plate spacing is negligible on the normalized stagnation Nusselt number and hydraulic jump diameter since the average velocity of the jet is constant, which means the jet deflection effect disappears. Based on the experimental results, new correlations for the normalized hydraulic jump diameter, stagnation Nusselt number, and pressure are developed as a function of the nozzle-to-plate spacing alone.
STEM faculty members on the paper: Xiangjia “Jack” Min, Feng Yu, Chester Cooper
STEM graduate students: Brian Powell, Vamshi Amerishetty, John Meinken
STEM undergraduate student: Geneva Knott
Powell B., Amerishetty V., Meinken J., Knott G., Feng Y., Cooper C., and Min X.J., 2016, “ProtSecKB: the protist secretome and subcellular proteome knowledgebase,” Computational Molecular Biolog 6(4): 1-12.
Kingdom Protista contains a large group of eukaryotic organisms with diverse lifestyles. We developed the Protist Secretome and Subcellular Proteome Knowledgebase (ProtSecKB) to host information of curated and predicted subcellular locations of all protist proteins. The protist protein sequences were retrieved from UniProtKB, consisting of 1.97 million entries generated from 7,024 species with 101 species including 127 organisms having complete proteomes. The protein subcellular locations were based on curated information and predictions using a set of well evaluated computational tools. The database can be searched using several different types of identifiers, gene names or keyword(s). Secretomes and other subcellular proteomes can be searched or downloaded. BLAST searching against the complete set of protist proteins or secretomes is available. Protein family analysis of secretomes from representing protist species, including Dictyostelium discoideum, Phytophthora infestans, and Trypanosoma cruzi, showed that species with different lifestyles had drastic differences of protein families in their secretomes, which may determine their lifestyles. The database provides an important resource for the protist and biomedical research community. The database is available at http://bioinformatics.ysu.edu/secretomes/protist/index.php.
Editors’ Choice – Canadian Geotechnical Journal – December 201
Jai K. Jung, Thomas D. O’Rourke, Christina Argyrou. “Multi-directional force–displacement response of underground pipe in sand,” Canadian Geotechnical Journal, 2016, 53(11): 1763-1781.
This paper is part of a Special Issue entitled “Pipeline geotechnics”.
A methodology is presented to evaluate multi-directional force–displacement relationships for soil–pipeline interaction analysis and design. Large-scale tests of soil reaction to pipe lateral and uplift movement in dry and partially saturated sand are used to validate plane strain, finite element (FE) soil, and pipe continuum models. The FE models are then used to characterize force versus displacement performance for lateral, vertical upward, vertical downward, and oblique orientations of pipeline movement in soil. Using the force versus displacement relationships, the analytical results for pipeline response to strike-slip fault rupture are shown to compare favorably with the results of large-scale tests in which strike-slip fault movement was imposed on 250 and 400 mm diameter high-density polyethylene pipelines in partially saturated sand. Analytical results normalized with respect to maximum lateral force are provided on 360° plots to predict maximum pipe loads for any movement direction. The resulting methodology and dimensionless plots are applicable for underground pipelines and conduits at any depth, subjected to relative soil movement in any direction in dry or saturated and partially saturated medium to very dense sands.
Brian K. Friedrich, Tamira D. Ford, Aspen W. Glaspell, Kyosung Choo, “Experimental study of the hydrodynamic and heat transfer of air-assistant circular water jet impinging a flat circular disk,” International Journal of Heat and Mass Transfer Volume 106 (March 2017) 804-809.
Hydrodynamic and heat transfer characteristics of the circular hydraulic jump by air-assistant water jet impingement was experimentally investigated using water and air as the test fluid. The effects of volumetric quality (β = 0–0.9) on the hydraulic jump radius, local Nusselt number and, pressure at the stagnation point were considered under fixed water-flow-rate condition. The results showed that the dimensionless hydraulic jump radius increased with volumetric quality, attained a maximum value at around 0.8 of the volumetric quality, and then decreased. The hydraulic jump of two phase impinging jet is governed by the stagnation pressure and the lateral variation of Nusselt number is governed by hydraulic jump radius. Based on the experimental results, a new correlation for the normalized hydraulic jump radius of the impinging jet are developed as a function of the normalized stagnation pressure alone.
John Martin, an assistant professor of engineering technology at Youngstown State University, has recently presented for the American Society for Engineering Education and the American Society of Mechanical Engineers. Martin holds a bachelor’s and master’s degree in mechanical engineering and his research area is in engineering education.
“Work in Progress: The Effects of Concurrent Presentation of Engineering Concepts and FEA Applications”, Martin, J., Martin, A., Proceedings of the 2016 ASEE Annual Conference and Expo, New Orleans, LA, June, 2016.
“CFD Analysis Comparing Steady Flow and Pulsatile Flow through the Aorta and its Main Branches”, Martin, J., Proceedings for the 2016 ASME International Mechanical Engineering Congress & Exposition, Phoenix, AZ, November, 2016.
Michael Crescimanno and Jim Andrews, Professors in Physics & Astronomy, together with students Brandon Latronica and Maddie Smotzer, co-authored the paper “Linear distributed Bragg cavity effects on optical limiting in two- and three-level media,” to appear in a special December issue of the Journal of the Optical Society of America on the topic “Nonlinear Optics near the Fundamental Limit.” This work was funded through grants from the National Science Foundation.
A lumped distributed Bragg reflector (DBR)-nonlinear layer-DBR system is used to explore how nonlinear optical effects (in particular, optical limiting) are modulated by the dispersive character of the (optically linear) DBR. A three-level quantum optics model of the nonlinear layer is used to find self-consistent numerical solutions to the (nonlinear) optical transport in the composite system. We find that the intensity dependence of the real part of the index can be combined with the dispersion in the (linear) DBR to cause optical limiting even for materials that have only a saturated absorber (two-level) response.