• The Korean Journal of Ecology
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• v.25 no.1
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• pp.1-7
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• 2002

The ecological background of a restoration project is complex and difficult to betermine without experimentation. A useful context for experiments is the well-studied process of natural succession, because the factors that drive or inhibit succession are also at work during reclamation (a form of primary succession) and restoration (which often resembles secondary succession). Using experimental studies on urban wasteland reclamation, we have tested for factors that stimulate or inhibit succession during early phases of woodland development in the Northeastern United states. The emphasis has been on mutualisms (seed dispersal, pollination, and mycorrhizae) and microsite limitations in the recruitment, growth, and reproduction of woody plants. Using plantings of seeds, seedlings, and clusters of reproductively mature plants on abandoned landfills, we have observed that (1) soil microsite deficiencies lead to very poor germination (<0.1$\%$) and seedling survival (<0.01$\%$) of most native species; (2) seed dispersal by birds is a significant and reliable source of woody plant recruitment; however (3) proximity effects are strong, with most (up to 95$\%$) of seed rain falling in the vicinity of planted clusters that are closest to putative seed sources; and (4) remnant natural woodlands are critical components of the recruitment process. To emphasize the last point, in one case, we found that the destruction of approximately 50$\%$ of nearby natural woodland vegetation led to a commensurate decline in seed rain. In another case, we found that the species richness of recruits was strictly limited by the species composition of nearby source plant communities, with no evidence of community enrichment by long distance dispersal over 5 years. We conclude from these results that the size and proximity of remnant natural populations are critical considerations when planning reclamation and restoration programs that rely on natural successional processes.

• Journal of Ecology and Environment
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• v.41 no.8
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• pp.223-234
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• 2017

Background: Spatial structure of plants in a population reflects complex interactions of ecological and evolutionary processes. For dioecious plants, differences in reproduction cost between sexes and sizes might affect their spatial distribution. Abiotic heterogeneity may also affect adaptation activities, and result in a unique spatial structure of the population. Thus, we examined sex- and size-related spatial distributions of old-growth forest of dioecious tree Torreya nucifera in extremely heterogeneous Gotjawal terrain of Jeju Island, South Korea. Methods: We generated a database of location, sex, and size (DBH) of T. nucifera trees for each quadrat ($160{\times}300m$) in each of the three sites previously defined (quadrat A, B, C in Site I, II, and III, respectively). T. nucifera trees were categorized into eight groups based on sex (males vs. females), size (small vs. large trees), and sex by size (small vs. large males, and small vs. large females) for spatial point pattern analysis. Univariate and bivariate spatial analyses were conducted. Results: Univariate spatial analysis showed that spatial patterns of T. nucifera trees differed among the three quadrats. In quadrat A, individual trees showed random distribution at all scales regardless of sex and size groups. When assessing univariate patterns for sex by size groups in quadrat B, small males and small females were distributed randomly at all scales whereas large males and large females were clumped. All groups in quadrat C were clustered at short distances but the pattern changed as distance was increased. Bivariate spatial analyses testing the association between sex and size groups showed that spatial segregation occurred only in quadrat C. Males and females were spatially independent at all scales. However, after controlling for size, males and females were spatially separated. Conclusions: Diverse spatial patterns of T. nucifera trees across the three sites within the Torreya Forest imply that adaptive explanations are not sufficient for understanding spatial structure in this old-growth forest. If so, the role of Gotjawal terrain in terms of creating extremely diverse microhabitats and subsequently stochastic processes of survival and mortality of trees, both of which ultimately determine spatial patterns, needs to be further examined.

• Molecules and Cells
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• v.43 no.4
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• pp.331-339
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• 2020

Genetic modifications in noncoding regulatory regions are likely critical to human evolution. Human-accelerated noncoding elements are highly conserved noncoding regions among vertebrates but have large differences across humans, which implies human-specific regulatory potential. In this study, we found that human-accelerated noncoding elements were frequently coupled with DNase I hypersensitive sites (DHSs), together with monomethylated and trimethylated histone H3 lysine 4, which are active regulatory markers. This coupling was particularly pronounced in fetal brains relative to adult brains, non-brain fetal tissues, and embryonic stem cells. However, fetal brain DHSs were also specifically enriched in deeply conserved sequences, implying coexistence of universal maintenance and human-specific fitness in human brain development. We assessed whether this coexisting pattern was a general one by quantitatively measuring evolutionary rates of DHSs. As a result, fetal brain DHSs showed a mixed but distinct signature of regional conservation and outlier point acceleration as compared to other DHSs. This finding suggests that brain developmental sequences are selectively constrained in general, whereas specific nucleotides are under positive selection or constraint relaxation simultaneously. Hence, we hypothesize that human- or primate-specific changes to universally conserved regulatory codes of brain development may drive the accelerated, and most likely adaptive, evolution of the regulatory network of the human brain.

• BMB Reports
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• v.39 no.6
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• pp.749-758
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• 2006

The cytosolic members of the HSP70 family of proteins play key roles in the molecular chaperone machinery of the cell. In the study we cloned and sequenced the full-length cDNA of Delia antiqua HSP70 gene, which is 2461 bp long and encodes 643 a.a. with a calculated molecular mass of 70,787 Da. We investigated gene copies of cytosolic HSP70 members of 4 insect species with complete genome available, and found that they are quite variable with species. In order to characterize this protein we carried out an alignment and a phylogenetic analysis with 41 complete protein sequences from insects. The analysis divided the cytosolic members of the family into two classes, HSP70 and HSC70, distinguishable on the basis of 15 residues. HSP70 class members were slightly shorter in length and smaller in molecular mass relative to the HSC70 class members, and the conservative and functional regions in these sequences were documented. Mainly, we investigated the expression of Delia antiqua HSP70 gene, in response to diapauses and thermal stresses. Both summer and winter diapauses elevated HSP70 transcript levels. Cold-stress led to increased HSP70 expression levels in summer- and winter-diapausing pupae, but heat-stress elevated the levels only in the winter-diapausing pupae. In all cases, the expression levels, after being elevated, gradually decreased with time. HSP70 expression was low in non-diapausing pupae but was up-regulated following cold- and heat-stresses. Heat-stress gradually increased the mRNA level with time whereas cold-stress gradually decreased levels after an initial increase.

• Journal of Microbiology and Biotechnology
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• v.20 no.3
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• pp.447-459
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• 2010

Bacterial diversity of two distinct wastewater treatment systems, conventional activated sludge (CAS) and membrane bioreactor (MBR), of petroleum refineries were investigated through 16S rRNA gene libraries. Sequencing and phylogenetic analysis showed that the bacterial community composition of sludge samples was distinct between the two wastewater treatment systems. MBR clones belonged predominantly to Class Betaproteobacteria, represented mainly by genera Thiobacillus and Thauera, whereas CAS clones were mostly related to Class Alphaproteobacteria, represented by uncultured bacteria related to Order Parvularculales. Richness estimators ACE and Chao revealed that the diversity observed in both libraries at the species level is an underestimate of the total bacterial diversity present in the environment and further sampling would yield an increased observed diversity. Shannon and Simpson diversity indices were different between the libraries and revealed greater bacterial diversity for the MBR library, considering an evolutionary distance of 0.03. LIBSHUFF analyses revealed that MBR and CAS communities were significantly different at the 95% confidence level ($P{\leq}0.05$) for distances $0{\leq}D{\leq}0.20$. This work described, qualitatively and quantitatively, the structure of bacterial communities in industrial-scale MBR and CAS processes of the wastewater treatment system from petroleum refineries and demonstrated clearly differentiated communities responsible for the stable performance of wastewater treatment plants.

• Molecules and Cells
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• v.43 no.1
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• pp.86-95
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• 2020

The red-crowned crane (Grus japonensis) is an endangered, large-bodied crane native to East Asia. It is a traditional symbol of longevity and its long lifespan has been confirmed both in captivity and in the wild. Lifespan in birds is known to be positively correlated with body size and negatively correlated with metabolic rate, though the genetic mechanisms for the red-crowned crane's long lifespan have not previously been investigated. Using whole genome sequencing and comparative evolutionary analyses against the grey-crowned crane and other avian genomes, including the long-lived common ostrich, we identified redcrowned crane candidate genes with known associations with longevity. Among these are positively selected genes in metabolism and immunity pathways (NDUFA5, NDUFA8, NUDT12, SOD3, CTH, RPA1, PHAX, HNMT, HS2ST1, PPCDC, PSTK CD8B, GP9, IL-9R, and PTPRC). Our analyses provide genetic evidence for low metabolic rate and longevity, accompanied by possible convergent adaptation signatures among distantly related large and long-lived birds. Finally, we identified low genetic diversity in the red-crowned crane, consistent with its listing as an endangered species, and this genome should provide a useful genetic resource for future conservation studies of this rare and iconic species.

• Asian-Australasian Journal of Animal Sciences
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• v.12 no.1
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• pp.77-83
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• 1999

Molecular biological techniques that recently developed, have made it possible to realize some of new attempts in the research field of rumen microbiology. Those are 1) cloning of genes from rumen microorganisms mainly in E. coli, 2) transformation of rumen bacteria and 3) ecological analysis with nonculturing methods. Most of the cloned genes are for polysaccharidase enzymes such as endoglucanase, xylanase, amylase, chitinase and others, and the cloning rendered gene structural analyses by sequencing and also characterization of the translated products through easier purification. Electrotransformation of Butyrivibrio fibrisolvens and Prevotella ruminicola have been made toward the direction for obtaining more fibrolytic, acid-tolerant, depoisoning or essential amino acids-producing rumen bacterium. These primarily required stable and efficient gene transfer systems. Some vectors, constructed from native plasmids of rumen bacteria, are now available for successful gene introduction and expression in those rumen bacterial species. Probing and PCR-based methodologies have also been developed for detecting specific bacterial species and even strains. These are much due to accumulation of rRNA gene sequences of rumen microbes in databases. Although optimized analytical conditions are essential to reliable and reproducible estimation of the targeted microbes, the methods permit long term storage of frozen samples, providing us ease in analytical work as compared with a traditional method based on culturing. Moreover, the methods seem to be promissing for obtaining taxonomic and evolutionary information on all the rumen microbes, whether they are culturable or not.

• The Plant Pathology Journal
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• v.33 no.1
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• pp.34-42
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• 2017

Grapevine rupestris stem pitting-associated virus (GRSPaV) is a worldwide-distributed pathogen in grapevines with a high genetic variability. Our study revealed differences in the complexity of GRSPaV population in a single host. A single-variant GRSPaV infection was detected from the SK30 grapevine plant. On the contrary, SK704 grapevine was infected by three different GRSPaV variants. Variant-specific RT-PCR detection protocols have been developed in this work to study distribution of the three different variants in the same plant during the season. This study showed their randomized distribution in the infected SK704 grapevine plant. Comparative analysis of full-length genome sequences of four Slovak GRSPaV isolates determined in this work and 14 database sequences showed that population of the virus cluster into four major phylogenetic lineages. Moreover, our analyses suggest that genetic recombination along with point mutations could play a significant role in shaping evolutionary history of GRSPaV and contributed to its extant genetic diversification.

• BMB Reports
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• v.42 no.11
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• pp.725-730
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• 2009

Cyclin E1 (CCNE1), a positive regulator of the cell cycle, controls the transition of cells from G1 to S phase. In numerous human tumors, however, CCNE1 expression is frequently dysregulated, while the mechanism leading to its dysregulation remains incompletely defined. Herein, we showed that CCNE1 expression was subject to post-transcriptional regulation by a microRNA miR-16-1. This was evident at protein level of CCNE1 as well as its mRNA level. Further evident by dual luciferase reporter assay revealed that two evolutionary conserved binding sites on 3' UTR of CCNE1 were the direct functional target sites. Moreover, we showed that miR-16-1 induced G0/G1 cell cycle arrest by targeting CCNE1 and siRNA against CCNE1 partially phenocopied miR-16-1-induced cell cycle phenotype whereas substantially rescued anti-miR-16-1- induced phenotype. Together, all these results demonstrate that miR-16-1 plays a vital role in modulating cellular process in human cancers and indicate the therapeutic potential of miR-16-1 in cancer therapy.

• Journal of the Korean Society of Fisheries and Ocean Technology
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• v.54 no.3
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• pp.193-203
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• 2018

Capture efficiencies of commercial shrimp trawls may improve if their designs took into better account behavioral responses of wild shrimp to approaching cod-end of the trawls. Here we report results of water tunnel-based experimental studies of responses of wild California target prawns to several different near-realistic netting configurations over a range of water velocities (0.3-0.7 m/s). Netting panels were oriented at parallel to water flows (FP) on the bottom of test section, vertical (VT) or diagonal sloping backward (DG), bottom to top. Behavioral responses were recorded by video camera and analyzed frame by frame. Measured responses included rates of penetrating through netting by behavioral features and tail-flip frequencies. Frequencies of prawn passing through the nets increased with flow speed for both orientations and were higher at given speeds for sloped nets. Other behavioral features (e.g., passage head-or tail-first) also varied significantly with water velocities and netting orientation. Interactions of penetrating rates between netting orientations and flow speeds also were significantly dependent, except for prawn size. Additional studies are needed of other shrimp species and at higher water velocities more similar to actual field operations using trawls to improve size selectivity.