Jonghoon Kang

Spinal AMPA receptor inhibition attenuates mechanical allodynia and neuronal hyperexcitability following spinal cord injury in rats.

In this study, we examined whether a competitive AMPA receptor antagonist, NBQX, attenuates mechanical allodynia and hyperexcitability of spinal neurons in remote, caudal regions in persistent central neuropathic pain following spinal cord injury in rats. Spinal cord injury was produced by unilateral T13 transverse spinal hemisection, from dorsal to ventral, in male Sprague Dawley rats (200–250 g). Mechanical thresholds were measured behaviorally, and the excitability of wide‐dynamic‐range (WDR) dorsal horn neurons in the lumbar cord (L4–L5) was measured to assess central neuropathicpain. On postoperation day (POD) 28 after spinalhemisection, mechanical thresholds were significantly decreased in both injured (ipsilateral) and noninjured (contralateral) hindpaws compared with preinjury and sham control, respectively (P < 0.05). Intrathecal administration of NBQX (0.25, 0.5, 1 mM) significantly reversed the decreased mechanical thresholds in both hindpaws, dose dependently (P < 0.05). The excitability of WDR neurons was significantly enhanced on both sides of the lumbar dorsal horn 28 days following spinal hemisection (P < 0.05). The hyperexcitability of WDR neurons was attenuated by topical administration of NBQX (0.125, 0.25, 0.5, 1 mM), dose dependently (P < 0.05). Regression analysis indicated that at least three molecules of NBQX bond per receptor complex, and are needed to achieve inhibition of WDR hyperexcitability. In conclusion, our study demonstrates that the AMPA receptor plays an important role in behaviors related to the maintenance of central neuropathic pain below the level of spinal cord injury.

Combinatorial selection of a RNA thioaptamer that binds to Venezuelan equine encephalitis virus capsid protein

A phosphorothioate RNA aptamer (thioaptamer) targeting the capsid protein of Venezuelan equine encephalitis virus (VEEV) was isolated by in vitro combinatorial selection. The selected thioaptamer had a strong binding affinity (∼7 nM) and high specificity for the target protein. For the binding to the protein, the overall tertiary structure of the thioaptamer is required. We introduce two theoretical methods to examine the effect of phosphorothioate modification on the enhancement of binding affinity and one experimental method to examine the nature of the multiple bands of thioaptamer in a native gel.

The evidence that the DNC (SLC25A19) is not the mitochondrial deoxyribonucleotide carrier

We review the evidence that the function of the SLC25A19 gene product, previously identified as the mitochondrial deoxyribonucleotide carrier (DNC), is actually the transport of thiamine pyrophosphate. This evidence comes from enzyme kinetics, homologous yeast protein alignments, gene knockout studies, and clinical samples from Amish Microcephaly patients. This diverse body of evidence consistently points to the conclusion that SLC25A19 is not the true mitochondrial DNC gene. The identification of the correct mitochondrial DNC is important for research on the genetic diseases of mitochondrial DNA maintenance and the toxicity experienced by many HIV patients undergoing antiretroviral therapy involving nucleoside analogs.

Study to find the best extraction solvent for use with guava leaves (Psidium guajava L.) for high antioxidant efficacy.

The effects of guava leaves extracted using solvents of water, ethanol, methanol, and different concentrations of hydroethanolic solvents on phenolic compounds and flavonoids, and antioxidant properties have been investigated. The antioxidant capability was assessed based on 2,2-diphenyl-1-picrylhydrazyl radical and 2,2′-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) radical-scavenging abilities, reducing power, and nitric oxide-and nitrate-scavenging activities. The results demonstrated that the antioxidant ability of guava leaf extracts has a strong relationship with phenolic compound content rather than flavonoid content. Phenolic compound content of water extracted guava leaves was higher compared to pure ethanol and methanol extracts. However, phenolic compound content extracted using hydroethanolic solvent was higher than water, whereas 50% hydroethanolic was observed to be the most effective solvent showing high antioxidant ability.

Thermostability of seven hepatitis C virus genotypes in vitro and in vivo.

Hepatitis C virus (HCV) is transmitted primarily through percutaneous exposure to contaminated blood especially in healthcare settings and among people who inject drugs. The environmental stability of HCV has been extrapolated from studies with the bovine viral diarrhoea virus or was so far only addressed with HCV genotype 2a viruses. The aim of this study was to compare the environmental and thermostability of all so far known seven HCV genotypes in vitro and in vivo. Incubation experiments at room temperature revealed that all HCV genotypes showed similar environmental stabilities in suspension with viral infectivity detectable for up to 28 days. The risk of HCV infection may not accurately be reflected by determination of HCV RNA levels. However, viral stability and transmission risks assessed from in vitro experiments correlated with viral infectivity in transgenic mice containing human liver xenografts. A reduced viral stability for up to 2 days was observed at 37 °C with comparable decays for all HCV genotypes confirmed by thermodynamic analysis. These results demonstrate that different HCV genotypes possess comparable stability in the environment and that noninfectious particles after incubation in vitro do not cause infection in an HCV in vivo model. These findings are important for estimation of HCV cross‐transmission in the environment and indicate that different HCV genotypes do not display an altered stability or resistance at certain temperatures.

Thermodynamic characterization of dissociation rate variations of human leukocyte antigen and peptide complexes

Stability of minor histocompatibility antigen-MHC molecule complexes is a major requirement for the successful presentation of the antigen to T cell receptors. In this letter we show thermodynamic features of the complexes made of a peptide antigen and its three variants to explain molecular basis of variable stability of the complexes. Our analysis suggests that enthalpy is a major factor in determining the stability of the complexes. We also found that the dissociation of the peptides from the complexes exhibits enthalpy-entropy compensation. Two structural features of the complexes, noncovalent chemical bondings and flexibility of the peptides in the complexes, are in a good agreement with our thermodynamic analysis. We expect thermodynamic investigation of peptide antigen-MHC protein complexes will provide valuable information on the stability.

Implications for undergraduate education of two interdisciplinary biological sciences: biochemistry and biophysics.

Dear Editor: As CBE—Life Sciences Education readers know, modern biology has become more quantitative and mechanistic rather than qualitative and phenomenological. Indeed, the American Society for Cell Biology (2010) notes that “biology learning encompasses diverse fields, including math, chemistry, physics, engineering, and computer science, as well as the interdisciplinary intersections of biology with these fields.” Because of this, interdisciplinary biology courses are increasingly critical for preparing undergraduates for further education and careers in the life sciences. The problem is that many institutions do not reflect this in their undergraduate course offerings. In this letter, we show that the growth of two biological disciplines, namely biochemistry and biophysics, can be described in terms of their representation in the research literature. On this basis, we make predictions about the future trends of research in these disciplines and the implications of these trends for undergraduate education. The most widely taught interdisciplinary biological science is probably biochemistry. Many undergraduate biology and chemistry departments recognize its importance and offer it as a core course in their curricula. Biophysics is another interdisciplinary biological science. Although it is not as popular as biochemistry, the growing importance of the subject should be recognized by teaching institutions and reflected in their course offerings. Unfortunately, it seems that the number of institutions that have noticed the demand for it is limited. For example, out of 34 undergraduate institutions in the University of Georgia System (2010) , only 5 offer an undergraduate biophysics course or related courses, such as physical biochemistry. In contrast, 8 of the top 10 universities listed in U.S. News and World Report (2010) teach biophysics or physical biochemistry. Here, we offer a brief analysis of the primary life sciences literature to support our argument for widespread teaching of biophysics at the undergraduate level. Specifically, we used the number of papers indexed by PubMed (National Center for Biotechnology Information, 2010 ) as a measure of subject importance. We searched PubMed with search terms “biochemistry OR biochemical” for biochemistry and “biophysics OR biophysical” for biophysics with a limit of the search to title/abstract for each year from 1950 to 2009. We then normalized the number of papers for each subject to the total number of papers in each year. We recognize that there are limitations to this approach. For example, the DNA structure paper by Watson and Crick (1953 ) is not counted as either a biophysics or a biochemistry paper because it does not contain the search terms in its title or abstract. Yet we believe that this metric reasonably represents the activity of the subjects relative to one another. Figure ​Figure11 shows the normalized number of papers of biochemistry and biophysics, from which we draw three conclusions. First, biochemistry has been continuously growing, with a large increase between 1974 and 1975. This growth may explain why biochemistry is now widely taught. Second, the normalized number of biochemistry publications approaches an asymptotic value suggesting saturation (Figure ​(Figure1A),1A), although we cannot rule out the potential for major transitions in biochemistry research to prompt new growth in the field in the future. Third, although the discipline of biophysics is younger than that of biochemistry, it has been growing exponentially (Figure ​(Figure1B).1B). This feature can be more clearly seen in Figure ​Figure1C,1C, where the number of biophysics papers was normalized to that of the biochemistry papers. Figure ​Figure1C1C indicates that the relative importance of biophysics was ∼12% in year 2009, but if the trend of the last 25 years is maintained for the next 10 years, it will be ∼20% in year 2020. Current biology seems to be facing the same “cultural transition” that chemistry faced ∼100 years ago when it started including physics-based approaches in education and research. This incorporation of physics in chemistry resulted in physical chemistry, one of the core areas in chemistry today (Servos, 1996 ). Figure 1. Proportion of biochemistry (A) and biophysics (B) papers in PubMed and their ratio ( = biophysics/biochemistry) (C). Extrapolation of the fitting equation is shown as a dashed line (C). Nonlinear curve fitting was performed using SigmaPlot (version 11; ... This analysis reveals the major upswing in biochemistry publications that occurred between 1974 and 1975. We offer a hypothesis to explain this phenomenon: the introduction of a great textbook. We propose that Biochemistry by Lehninger (1970) , which has been widely recognized since its initial publication (Sable, 1971 ), is the original modern biochemistry textbook. Perhaps groundbreaking instructional resources such as this can trigger a quantum leap in research in the discipline. Unlike biochemistry, biophysics suffers from the lack of consensus on the standard topics and skills that should comprise an undergraduate course. This is an issue that biologists and biophysicists need to solve together. In conclusion, if training future biologists is one of the goals of undergraduate biology education, then our analysis indicates that we need to make biophysics a standard component of the curriculum, similar to biochemistry.

Quantitative Analysis of the Trends Exhibited by the Three Interdisciplinary Biological Sciences: Biophysics, Bioinformatics, and Systems Biology.

New interdisciplinary biological sciences like bioinformatics, biophysics, and systems biology have become increasingly relevant in modern science. Many papers have suggested the importance of adding these subjects, particularly bioinformatics, to an undergraduate curriculum; however, most of their assertions have relied on qualitative arguments. In this paper, we will show our metadata analysis of a scientific literature database (PubMed) that quantitatively describes the importance of the subjects of bioinformatics, systems biology, and biophysics as compared with a well-established interdisciplinary subject, biochemistry. Specifically, we found that the development of each subject assessed by its publication volume was well described by a set of simple nonlinear equations, allowing us to characterize them quantitatively. Bioinformatics, which had the highest ratio of publications produced, was predicted to grow between 77% and 93% by 2025 according to the model. Due to the large number of publications produced in bioinformatics, which nearly matches the number published in biochemistry, it can be inferred that bioinformatics is almost equal in significance to biochemistry. Based on our analysis, we suggest that bioinformatics be added to the standard biology undergraduate curriculum. Adding this course to an undergraduate curriculum will better prepare students for future research in biology.

Thermodynamic analysis of intracellular ice recrystallization in mouse oocytes

In a recent article published in Cryobiology, Seki and Mazur performed kinetic analysis to investigate the physicochemical mechanism of the intracellular ice formation in mouse oocytes subjected to rapid cooling. Based on their results, the authors calculated the activation energy for the ice recrystallization process to be 27.5 kcal/mol. In this letter, we report our analysis of the result in terms of the transition-state theory to show that the process is unfavorable in terms of enthalpy but favorable in terms of entropy accompanying molecular expansions. This report is expected to evoke interests in applying thermodynamics to the investigation of the intracellular ice formation.

Thermodynamic Analysis of Hepatitis C Virus Vitality in Syringes

TO THE EDITOR—We read with interest the article by Paintsil et al [1], and we found that the experimental technique reported could be directly applied to the study of an important topic, hepatitis C virus (HCV) vitality. In this letter, we show our own analysis of the results in the article, and suggest a means of applying the technique to examine HCV infectivity (ie, vitality). One of the main results reported by Paintsil et al [1] is temperature-dependent HCV vitality. Assuming the HCV decay (losing infectivity) as a chemical reaction, we can analyze it in terms of chemical kinetics, which will allow us to characterize it quantitatively. This approach has been found to be useful in understanding molecular phenomena [2, 3]. Among the 2 different examinations that the authors performed, we found that the one conducted with the low-void volume syringes to be suitable for quantitative analysis because it showed a monotonic decrease in HCV infectivity [1]. First, the half-life (t1/2) of HCV vitality was obtained from the article’s Figure 3A. The half-life we used corresponds to the time point for 50% HCV-positive syringes. From the halflife values, we can obtain the rateconstant (k) of HCV decay using Equation(1), assuming it follows firstorder kinetics: