Seungmin Lee

FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors

SUMMARY Genomes of more than 60 fungal species have been sequenced to date, yet there has been no systematic approach to analyze fungal transcription factors (TFs) kingdom widely. We developed a standardized pipeline for annotating TFs in fungal genomes. Resulting data have been archived in a new database termed the Fungal Transcription Factor Database (FTFD). In FTFD, 31,832 putative fungal TFs, identified from 62 fungal and 3 Oomycete species, were classified into 61 families and phylogenetically analyzed. The FTFD will serve as a community resource supporting comparative analyses of the distribution and domain structure of TFs within and across species. AVAILABILITY All data described in this study can be browsed through the FTFD web site at http://ftfd.snu.ac.kr/.

Fungal cytochrome P450 database.

BackgroundCytochrome P450 enzymes play critical roles in fungal biology and ecology. To support studies on the roles and evolution of cytochrome P450 enzymes in fungi based on rapidly accumulating genome sequences from diverse fungal species, an efficient bioinformatics platform specialized for this super family of proteins is highly desirable.ResultsThe Fungal Cytochrome P450 Database (FCPD) archives genes encoding P450s in the genomes of 66 fungal and 4 oomycete species (4,538 in total) and supports analyses of their sequences, chromosomal distribution pattern, and evolutionary histories and relationships. The archived P450s were classified into 16 classes based on InterPro terms and clustered into 141 groups using tribe-MCL. The proportion of P450s in the total proteome and class distribution in individual species exhibited certain taxon-specific characteristics.ConclusionThe FCPD will facilitate systematic identification and multifaceted analyses of P450s at multiple taxon levels via the web. All data and functions are available at the web site http://p450.riceblast.snu.ac.kr/.

Tris-(8-hydroxyquinoline)aluminum-based organic light-emitting devices with Al/CaF2 cathode: Performance enhancement and interface electronic structures

The device characteristics and the interface electronic structures of organic light-emitting devices based on tris-(8-hydroxyquinoline)aluminum were investigated with Al/CaF2, Al/LiF, and Al-only cathodes. Similar to the Al/LiF cathode, the Al/CaF2 cathode greatly improved the performance of the device over the Al-only cathode. However, a photoelectron spectroscopy study revealed that despite the performance improvement, the evolution of the new peaks during the Al/CaF2 cathode formation closely resembled those of the Al-only cathode rather than the Al/LiF cathode.

Low-level laser therapy promotes the osteogenic potential of adipose-derived mesenchymal stem cells seeded on an acellular dermal matrix.

This study investigates the feasibility of using an adipose-derived mesenchymal stem cell (ASC)-seeded acellular dermal matrix (ADM) along with low-level laser therapy (LLLT) to repair bone defect in athymic nude mice. Critical-sized calvarial defects were treated either with ADM, ADM/LLLT, ADM/ASCs, or ADM/ASCs/LLLT. In micro-computed tomography scans, the ADM/ASCs and the ADM/ASCs/LLLT groups showed remarkable bone formation after 14 days. Additionally, bone regeneration in the ADM/ASCs/LLLT group was obvious at 28 days, but in the ADM/ASCs group at 56 days. Bone mineral density and bone tissue volume in the ADM/ASCs/LLLT group significantly increased after 7 days, but in the ADM/ASCs group after 14 days. Histological analysis revealed that the defects were repaired in the ADM/ASCs and the ADM/ASCs/LLLT group, while the defects in the ADM and the ADM/LLLT groups exhibited few bone islands at 28 and 56 days. The successful seeding of ASCs onto ADM was confirmed, and LLLT enhanced the proliferation and the survival of ASCs at 14 days. Our results indicate that ASC-seeded grafts promote bone regeneration, and the application of LLLT on ASC-seeded ADM results in rapid bone formation. The implantation of an ASC-seeded ADM combined with LLLT may be used effectively for bone regeneration.

Heat capacity measurement of dielectric solids using a linear surface heater: Application to ferroelectrics

A new ac calorimetry for dielectric solids was developed. A long and thin metal strip directly evaporated onto the surface of the sample is used as a heater and thermometer. Temperature oscillation of the heater is measured from the third harmonic voltage at the heater. Both the heat capacity and thermal conductivity of the sample are obtained by the frequency dependent phase and amplitude of the third harmonic voltage. Since heat capacity addenda and heat leaks in the measurement are extremely small, prior calibration is not required. The calorimeter is fully automated and has been tested on two ferroelectrics, KH2PO4 and triglycine sulfate, at temperatures above 77 K. The optimal frequency region for the calorimetry is also discussed.

Field emission characteristics of CuO nanowires grown on brown-oxide-coated Cu films on Si substrates by conductive heating in air

CuO nanowires were grown on brown-oxide-coated Cu films on Si substrates by conductive heating in air and their field emission characteristics were investigated. High resolution scanning electron microscopy showed that the CuO nanowires grew perpendicularly to the substrate, and their length and radius could be controlled by varying heating temperature and time. It was found that the lengths of the CuO nanowires were saturated to a certain point with respect to the heating temperature, and the increasing heating time increased the uniformity of the CuO nanowires in length. The field emission characteristics were strongly affected by the formation of the brown-oxide layer and the morphologies of the CuO nanowires governed by heating temperature and time.

Numerical modeling of wind turbine aerodynamic noise in the time domain.

Aerodynamic noise from a wind turbine is numerically modeled in the time domain. An analytic trailing edge noise model is used to determine the unsteady pressure on the blade surface. The far-field noise due to the unsteady pressure is calculated using the acoustic analogy theory. By using a strip theory approach, the two-dimensional noise model is applied to rotating wind turbine blades. The numerical results indicate that, although the operating and atmospheric conditions are identical, the acoustical characteristics of wind turbine noise can be quite different with respect to the distance and direction from the wind turbine.

Optically pumped GaN vertical cavity surface emitting laser with high index-contrast nanoporous distributed Bragg reflector

Laser operation of a GaN vertical cavity surface emitting laser (VCSEL) is demonstrated under optical pumping with a nanoporous distributed Bragg reflector (DBR). High reflectivity, approaching 100%, is obtained due to the high index-contrast of the nanoporous DBR. The VCSEL system exhibits low threshold power density due to the formation of high Q-factor cavity, which shows the potential of nanoporous medium for optical devices.

Mode Selection-Based Channel Feedback Reduction Schemes for Opportunistic Scheduling in OFDMA Systems

In this paper, we present two new feedback schemes, namely the network mode selection-based feedback (NMF) and the user mode selection-based feedback (UMF), that reduce the feedback load needed for opportunistic scheduling in the OFDMA downlink system. The two schemes are designed to select either the selective feedback (SF) mode which feeds back the fine-grained condition of a part of the channels or the bit-map based feedback (BF) mode which feeds back the coarse-grained condition of all the channels using 1 bit for each channel, depending on the channel conditions of the users. Specifically, the NMF scheme makes the BS determine the more desirable feedback mode by predicting and comparing the average total throughputs of the two modes for the given statistical channel characteristics of the users. The UMF scheme makes each user determine its own feedback mode based on both its channel realization and the recommendation of the network. Numerical results reveal that the proposed NMF and UMF schemes achieve significant performance gain over the existing feedback reduction schemes with similar feedback load.

Fabrication of Field Emitters with Carbon Nanotubes Using Triboelectricity

The triboelectricity method uses no adhesives but it induced by the difference of triboelectric series between materials can vertically align the carbon nanotube (CNT) emitters. CNTs are attached on a silicon wafer by dip-coating method, and then vertically aligned by the triboelectricity. The field emission property is enhanced up to 270 µA/cm2 at 4 V/µm after the activation of the emitters but no emission is observed at the same electric field before activation. The triboelectricity method avoids inevitable contamination due to the adhesives of taping method and is suitable for the conventional fabrication process which uses indirect-attachment method of CNTs.