SOLiDzipper: A High Speed Encoding Method for the Next-Generation Sequencing Data

Background Next-generation sequencing (NGS) methods pose computational challenges of handling large volumes of data. Although cloud computing offers a potential solution to these challenges, transferring a large data set across the internet is the biggest obstacle, which may be overcome by efficient encoding methods. When encoding is used to facilitate data transfer to the cloud, the time factor is equally as important as the encoding efficiency. Moreover, to take advantage of parallel processing in cloud computing, a parallel technique to decode and split compressed data in the cloud is essential. Hence in this review, we present SOLiDzipper, a new encoding method for NGS data. Methods The basic strategy of SOLiDzipper is to divide and encode. NGS data files contain both the sequence and non-sequence information whose encoding efficiencies are different. In SOLiDzipper, encoded data are stored in binary data block that does not contain the characteristic information of a specific sequence platform, which means that data can be decoded according to a desired platform even in cases of Illumina, Solexa or Roche 454 data. Results The main calculation time using Crossbow was 173 minutes when 40 EC2 nodes were involved. In that case, an analysis preparation time of 464 minutes is required to encode data in the latest DNA compression method like G-SQZ and transmit it on a 183 Mbit/s bandwidth. However, it takes 194 minutes to encode and transmit data with SOLiDzipper under the same bandwidth conditions. These results indicate that the entire processing time can be reduced according to the encoding methods used, under the same network bandwidth conditions. Considering the limited network bandwidth, high-speed, high-efficiency encoding methods such as SOLiDzipper can make a significant contribution to higher productivity in labs seeking to take advantage of the cloud as an alternative to local computing. Availability http://szipper.dinfree.com . Academic/non-profit: Binary available for direct download at no cost. For-profit: Submit request for for-profit license from the web-site

Measuring the maturity of open access: a preliminary study

Open access is an important part of scholarly communication, and it has been a global phenomenon. The growth of open access brings several signif-icant benefits to the general public as well as researchers, ultimately leads to the advancement of science. For the continuous growth and development of open access, it is necessary to measure the degree of maturity of open ac-cess. However, there is not much discussion about the assessment frame-work for open access. This study aims to propose an assessment framework of open access maturity. For the purpose of this study, we conducted an analysis with a total of 24 literatures relevant to the digital maturity, the ma-turity of open data/open science, and major open access initiatives. For digi-tal maturity, 18 articles were analyzed: 10 articles for generic purpose model, and 8 articles for industry-specific model. In addition, three articles on the maturity of open data/open science were analyzed and three major open ac-cess initiatives. In preliminary analysis results, three dimensions with 13 be-longing items were proposed for measuring the maturity of open access. Three dimensions are OA Policy, OA capability, and Openness quality. For OA policy, there are three items such as OA policy document, OA govern-ance, and OA strategy. For OA Capability, finance for OA, people for OA, culture for OA, and collaboration for OA are proposed. For Openness Quali-ty dimension, six items are suggested: submission and review, author rights, user rights, findability, accessibility, and monitoring

An isoform of the plastid RNA polymerase-associated protein FSD3 negatively regulates chloroplast development

Background Plastid-encoded RNA polymerase (PEP) plays an essential role in chloroplast development by governing the expression of genes involved in photosynthesis. At least 12 PEP-associated proteins (PAPs), including FSD3/PAP4, regulate PEP activity and chloroplast development by modulating formation of the PEP complex. Results In this study, we identified FSD3S, a splicing variant of FSD3; the FSD3 and FSD3S transcripts encode proteins with identical N-termini, but different C-termini. Characterization of FSD3 and FSD3S proteins showed that the C-terminal region of FSD3S contains a transmembrane domain, which promotes FSD3S localization to the chloroplast membrane but not to nucleoids, in contrast to FSD3, which localizes to the chloroplast nucleoid. We also found that overexpression of FSD3S negatively affects photosynthetic activity and chloroplast development by reducing expression of genes involved in photosynthesis. In addition, FSD3S failed to complement the chloroplast developmental defects in the fsd3 mutant. Conclusion These results suggest FSD3 and FSD3S, with their distinct localization patterns, have different functions in chloroplast development, and FSD3S negatively regulates expression of PEP-dependent chloroplast genes, and development of chloroplasts.This work was carried out with the support of the Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ01323901 and PJ01364301) Rural Development Administration, Republic of Korea, and the National Research Foundation of Korea Grant funded by the Korean Government (MOE) [NRF-2019R1A2C1007103]

Antibacterial and synergistic effects of Nardostachytis rhizoma extracts on methicillin-resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is a serious clinical problem worldwide. Few new drugs are available against MRSA, because it has the ability to acquire resistance to most antibiotics which consequently increases the cost of medication. In the present study, the antibacterial activity of Nardostachytis rhizoma was investigated. The most effective method is to develop antibiotics from the natural products without having any toxic or side effects. Therefore, there is a need to develop alternative antimicrobial drugs for the treatment of infectious diseases. The use of two drugs in combination is a good alternative to slow the process of developing drug resistance and to restore the effectiveness of drugs that are no longer prescribed. Combination therapy is the most commonly recommended empirical treatment for bacterial infections in intensive care units, where monotherapy may not be effective against all potential pathogens, and for preventing the emergence of resistant. Five clinical isolates (MRSA) were obtained from five different patients at Wonkwang University Hospital (Iksan, South Korea). The other two strains were S. aureus ATCC 33591 (methicillin-resistant strain) and S. aureus ATCC 25923 (methicillin-susceptible strain). Antibacterial activity (minimal inhibitory concentrations, MICs) was determined by broth dilution method, disc diffusion method, MTT test and checkerboard dilution test. Antimicrobial activity of n-hexane fraction of N. rhizoma was significant. Against the seven strains, the disc diffusion test was in the range of 14 to 18 mm and had a MICs ranging from 31.25 to 125 ìg/ml. FICI values for n-hexane fraction (HFL) of N. rhizome + ampicillin (AM) and HFL + oxacillin (OX) were 0.1875 and 0.078125-0.09375, showing the increase of synergistic effect. When combined together, these antibiotic effects were dramatically increased. These effective combinations could be new promising agents in the management of MRSA and MSSA.Key words: Nardostachytis rhizoma, synergism, antibacterial, methicillin-resistant Staphylococcus aureus (MRSA)

Characterization of diverse natural variants of CYP102A1 found within a species of Bacillus megaterium

An extreme diversity of substrates and catalytic reactions of cytochrome P450 (P450) enzymes is considered to be the consequence of evolutionary adaptation driven by different metabolic or environmental demands. Here we report the presence of numerous natural variants of P450 BM3 (CYP102A1) within a species of Bacillus megaterium. Extensive amino acid substitutions (up to 5% of the total 1049 amino acid residues) were identified from the variants. Phylogenetic analyses suggest that this P450 gene evolve more rapidly than the rRNA gene locus. It was found that key catalytic residues in the substrate channel and active site are retained. Although there were no apparent variations in hydroxylation activity towards myristic acid (C14) and palmitic acid (C16), the hydroxylation rates of lauric acid (C12) by the variants varied in the range of >25-fold. Interestingly, catalytic activities of the variants are promiscuous towards non-natural substrates including human P450 substrates. It can be suggested that CYP102A1 variants can acquire new catalytic activities through site-specific mutations distal to the active site

Precise Temperature Mapping of GaN-Based LEDs by Quantitative Infrared Micro-Thermography

A method of measuring the precise temperature distribution of GaN-based light-emitting diodes (LEDs) by quantitative infrared micro-thermography is reported. To reduce the calibration error, the same measuring conditions were used for both calibration and thermal imaging; calibration was conducted on a highly emissive black-painted area on a dummy sapphire wafer loaded near the LED wafer on a thermoelectric cooler mount. We used infrared thermal radiation images of the black-painted area on the dummy wafer and an unbiased LED wafer at two different temperatures to determine the factors that degrade the accuracy of temperature measurement, i.e., the non-uniform response of the instrument, superimposed offset radiation, reflected radiation, and emissivity map of the LED surface. By correcting these factors from the measured infrared thermal radiation images of biased LEDs, we determined a precise absolute temperature image. Consequently, we could observe from where the local self-heat emerges and how it distributes on the emitting area of the LEDs. The experimental results demonstrated that highly localized self-heating and a remarkable temperature gradient, which are detrimental to LED performance and reliability, arise near the p-contact edge of the LED surface at high injection levels owing to the current crowding effect

P-glycoprotein confers acquired resistance to 17-DMAG in lung cancers with an ALK rearrangement

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.Background Because anaplastic lymphoma kinase (ALK) is dependent on Hsp90 for protein stability, Hsp90 inhibitors are effective in controlling growth of lung cancer cells with ALK rearrangement. We investigated the mechanism of acquired resistance to 17-(Dimethylaminoethylamino)-17-demethoxygeldanamycin (17-DMAG), a geldanamycin analogue Hsp90 inhibitor, in H3122 and H2228 non-small cell lung cancer cell lines with ALK rearrangement. Methods Resistant cell lines (H3122/DR-1, H3122/DR-2 and H2228/DR) were established by repeated exposure to increasing concentrations of 17-DMAG. Mechanisms for resistance by either NAD(P)H/quinone oxidoreductase 1 (NQO1), previously known as a factor related to 17-DMAG resistance, or P-glycoprotein (P-gp; ABCB1/MDR1) were queried using RT-PCR, western blot analysis, chemical inhibitors, the MTT cell proliferation/survival assay, and cellular efflux of rhodamine 123. Results The resistant cells showed no cross-resistance to AUY922 or ALK inhibitors, suggesting that ALK dependency persists in cells with acquired resistance to 17-DMAG. Although expression of NQO1 was decreased in H3122/DR-1 and H3122/DR-2, NQO1 inhibition by dicumarol did not affect the response of parental cells (H2228 and H3122) to 17-DMAG. Interestingly, all resistant cells showed the induction of P-gp at the protein and RNA levels, which was associated with an increased efflux of the P-gp substrate rhodamine 123 (Rho123). Transfection with siRNA directed against P-gp or treatment with verapamil, an inhibitor of P-gp, restored the sensitivity to the drug in all cells with acquired resistance to 17-DMAG. Furthermore, we also observed that the growth-inhibitory effect of 17-DMAG was decreased in A549/PR and H460/PR cells generated to over-express P-gp by long-term exposure to paclitaxel, and these cells recovered their sensitivity to 17-DMAG through the inhibition of P-gp. Conclusion P-gp over-expression is a possible mechanism of acquired resistance to 17-DMAG in cells with ALK rearrangement