• ALGAE
• /
• v.21 no.1
• /
• pp.1-10
• /
• 2006

Genomic data is accumulating in public database at an unprecedented rate. Although presently dominated by the sequences of metazoan, plant, parasitic, and picoeukaryotic taxa, both expressed sequence tag (EST) and complete genomes of free-living algae are also slowly appearing. This wealth of information offers the opportunity to clarify many long-standing issues in algal and plant evolution such as the contribution of the plastid endosymbiont to nuclear genome evolution using the tools of comparative genomics and multi-gene phylogenetics. A particularly powerful approach for the automated analysis of genome data from multiple taxa is termed phylogenomics. Phylogenomics is the convergence of genomics science (the study of the function and structure of genes and genomes) and molecular phylogenetics (the study of the hierarchical evolutionary relationships among organisms, their genes and genomes). The use of phylogenetics to drive comparative genome analyses has facilitated the reconstruction of the evolutionary history of genes, gene families, and organisms. Here we survey the available genome data, introduce phylogenomic pipelines, and review some initial results of phylogenomic analyses of algal genome data.

• ALGAE
• /
• v.30 no.2
• /
• pp.103-119
• /
• 2015

Photosynthetic rates of the large centric diatom Coscinodiscus granii were measured by means of multicolor variable chlorophyll fluorescence imaging, single cell $^{14}C$ assimilation, and optical $O_2$ sensor measurements during light acclimatization of cultures grown at five different irradiances: 50, 150, 235, 332, and $450{\mu}mol$ photons $m^{-2}\;s^{-1}$. Photo-acclimatization was evident from changes of cellular chlorophyll a content, growth rates, and light response curves. Each of the applied methods evaluates different parts and reactions in the photosynthetic apparatus, which makes a direct quantitative comparison of rates difficult, although a different degree of correlation were found between all three methods. However, when used in combination, they provide information about the internal relationship of photosynthetic pathways as well as the variation in photosynthetic capacity between individual cells within a single algal culture.

• Rapid Communication in Photoscience
• /
• v.2 no.2
• /
• pp.60-63
• /
• 2013

Rhodopsins belong to a family of membrane-embedded photoactive retinylidene proteins. One opsin gene was isolated from ${\beta}$-proteobacterium (IMCC9480) which had been collected at the North Pole. It is very similar to Xanthorhodopin (XR) of HTCC2181. In this study, we carried out basic characterization of the rhodopsin. It has ${\lambda}max$ of 536, 554, and 546 nm at pH 4.0, 7.0, and 10.0, respectively. Since the pKa of its proton acceptor is around 6.27, we measured its proton pumping activity and photocycling rate at pH 8.0. It has a typical proton acceptor (D99) and donor (E110) which mediate proton translocation from intracellular to extracellular region when deduced from the sequence alignments. On the basis of in vitro proton pumping activity, it was proposed to have fast photocycling rate with M and O intermediates, indicating that it is a typical ion-pumping rhodopsin. Since the XR has not yet been expressed in any other heterologous expression system, we tried to get much more information about the XR through the XR-homologue rhodopsin.

• Transactions of the Korean Society of Mechanical Engineers A
• /
• v.27 no.12
• /
• pp.2079-2084
• /
• 2003

In biological cell manipulation, manual thrust or penetration of an injection pipette into an embryo cell is currently performed by a skilled operator, relying on visual feedback information only. Accurately measuring cellular forces is a requirement for minimally invasive cell injections. Moreover, the cellular force sensing is essential in investigating the biophysical properties for cell injury and membrane modeling studies. This paper presents cellular force measurements for the force feedback-based biomanipulation. Cellular force measurement system using piezoelectric polymer sensor is implemented to measure the penetration force of a zebrafish egg cell. First, measurement system setup and calibration are described. Second, the force feedback-based biomanipulation is experimentally carried out. Experimental results show that it successfully supplies real-time cellular force feedback to the operator at tens of uN and thus plays a main role in improving the reliability of biological cell injection tasks.

• Proceedings of the Korean Society for Noise and Vibration Engineering Conference
• /
• 2008.04a
• /
• pp.476-479
• /
• 2008

Understanding the dynamics of proteins is essential to gain insight into biological functions of proteins. The protein dynamics is delineated by conformational fluctuation (i.e. thermal vibration), and thus, thermal vibration of proteins has to be understood. In this paper, a simple mechanical model was considered for understanding protein's dynamics. Specifically, a mechanical vibration model was developed for understanding the large protein dynamics related to biological functions. The mechanical model for large proteins was constructed based on simple elastic model (i.e. Tirion's elastic model) and model reduction methods (dynamic model condensation). The large protein structure was described by minimal degrees of freedom on the basis of model reduction method that allows one to transform the refined structure into the coarse-grained structure. In this model, it is shown that a simple reduced model is able to reproduce the thermal fluctuation behavior of proteins qualitatively comparable to original molecular model. Moreover, the protein's dynamic behavior such as collective dynamics is well depicted by a simple reduced mechanical model. This sheds light on that the model reduction may provide the information about large protein dynamics, and consequently, the biological functions of large proteins.

• Korean Journal Plant Pathology
• /
• v.14 no.3
• /
• pp.268-277
• /
• 1998

The production of Korean ginseng, one of the most important medicinal root crops, is limited by many factors including soil sickness, root rots in fields as well as during storage prior to consumption. Although much research has been conducted on the diseases in field condition, little information is available on the control of postharvest roots rots. To obtain better management strategy of postharvest root rots in ginseng, biological control using antagonistic bacteria was attempted. Of 208 bacteria obtained form suppressive soil samples, 4 were selected based on the inhibitory effect on mycelial growth of two major causal fungi for postharvest root rots in ginseng, Botrytis cinerea and Fusarium solani. The culture filtrates of these bacterial antagonists greatly inhibited the conidial germination of both pathogenic fungi and produced abnormal morphology such as swollen germ tubes in F. solani and vacuolation of nongerminated conidia in B. cinerea. The population levels of bacterial antagonists on the ginseng roots were gradually increased up to 8 days of incubation. Postharvest root rots of ginseng caused by f. solani and B. cinerea were controlled in dipping tests in the ranges of 60∼80% by antagonistic Bacillus spp. obtained from suppressive soil. These results suggest that biological control using these antagonistic bacteria would be an alternative strategy to control postharvest root rots in ginseng.

• Korea-Australia Rheology Journal
• /
• v.19 no.1
• /
• pp.27-33
• /
• 2007

The co-extrusion of multi-layer films has been studied with the focus on its process stability. As in the single-layer film casting process, the productivity of the industrially important multi-layer film casting and the quality of thus produced films have often been hampered by various instabilities occurring in the process including draw resonance, a supercritical Hopfbifurcation instability, frequently encountered when the draw ratio is raised beyond a certain critical value. In this study, this draw resonance instability along with the neck-in of the film width has been investigated for a three-layer film casting using a varying width non-isothermal 1-D model of the system with Phan-Thien and Tanner (PTT) constitutive equation known for its robustness in portraying extensional deformation processes. The effects of various process conditions, e.g., the aspect ratio, the thickness ratio of the individual film layers, and cooling of the process, on the stability have been examined through the nonlinear stability analysis.

• The Korean Journal of Soil Zoology
• /
• v.10 no.1_2
• /
• pp.55-64
• /
• 2005

Predatory nematodes are ubiquitous and feed on soil microorganisms including plant parasitic nematodes. They reduce populations of plant parasitic nematodes in virtually all soils because of their constant association with plant parasitic nematodes in the rhizosphere. Predatory potential of several species of predacious nematodes, belonging to the orders Mononchida, Diplogasterida, Dorylaimida and Aphelenchida, have been studied in detail on plant parasitic nematodes but most of the studies were based on in vitro experiments. A review of progress on the use of predatory nematodes as biological control agents of plant parasitic nematodes reveals that advocacy for predatory nematodes dates back to the early $20^{th}$ century; nevertheless, their potential has begun to be studied in recent years. Information on the efficacy of predatory nematodes under field conditions is lacking; however, some predatory nematodes have given very promising results against plant parasitic nematodes. This article summarizes research progress to date on predatory nematodes and discusses about their possible use in the management of plant parasitic nematodes.

• Clinical and Experimental Reproductive Medicine
• /
• v.43 no.2
• /
• pp.59-81
• /
• 2016

It is well established that there is a heritable element of susceptibility to chronic human ailments, yet there is compelling evidence that some components of such heritability are transmitted through non-genetic factors. Due to the complexity of reproductive processes, identifying the inheritance patterns of these factors is not easy. But little doubt exists that besides the genomic backbone, a range of epigenetic cues affect our genetic programme. The inter-generational transmission of epigenetic marks is believed to operate via four principal means that dramatically differ in their information content: DNA methylation, histone modifications, microRNAs and nucleosome positioning. These epigenetic signatures influence the cellular machinery through positive and negative feedback mechanisms either alone or interactively. Understanding how these mechanisms work to activate or deactivate parts of our genetic programme not only on a day-to-day basis but also over generations is an important area of reproductive health research.

• Plant Resources
• /
• v.6 no.2
• /
• pp.108-113
• /
• 2003

This study was carried out to obtain basic information for possibility of oral vaccine in carrot using Agrobacteruim -mediated transformation system. The epitope region of porcine epidemic diarrhea virus (PEDV) spike gene which is classified as a member of the Coronaviridae and causes an acute enteritis in pigs was successfully expressed in carrot (Daucus carota) using the Agrobacterium-mediated transformation system. Hypocotyl segments of in vitro germinated plantlets were infected with Agrobacteriun tumefaciens LBA 4404 harboring PEDV spike gene. Embryogenic callus (EC) was induced on MS selection medium with 1 mg/L 2,4-D, 50 mg/L kanamycin and 300 mg/L cefotaxime after 45 days of culture. Subcultured ECs on MS selection medium without 2,4-D were converted to somatic embryos (SE) of various stage; globular, heart and torpedo stage. Putative transgenic embryos were selected on MS medium with 50 mg/L kanamycin and 300 mg/L cefotaxime. Regenerated plantlets from transformed SE were induced on MS medium containing 50 mg/L kanamycin after 30 days of culture. Genomic PCR confirmed the integration of PEDV spike gene into nuclear genome of carrot and northern blot analysis demonstrated the expression of PEDV spike gene in transgenic carrot.