Adaptive laboratory evolution of a genome-reduced Escherichia coli.

Synthetic biology aims to design and construct bacterial genomes harboring the minimum number of genes required for self-replicable life. However, the genome-reduced bacteria often show impaired growth under laboratory conditions that cannot be understood based on the removed genes. The unexpected phenotypes highlight our limited understanding of bacterial genomes. Here, we deploy adaptive laboratory evolution (ALE) to re-optimize growth performance of a genome-reduced strain. The basis for suboptimal growth is the imbalanced metabolism that is rewired during ALE. The metabolic rewiring is globally orchestrated by mutations in rpoD altering promoter binding of RNA polymerase. Lastly, the evolved strain has no translational buffering capacity, enabling effective translation of abundant mRNAs. Multi-omic analysis of the evolved strain reveals transcriptome- and translatome-wide remodeling that orchestrate metabolism and growth. These results reveal that failure of prediction may not be associated with understanding individual genes, but rather from insufficient understanding of the strain's systems biology

An alternative approach of input-output tables to dynamic structure changes in Korean IT industries

The structure of the IT industry has always evolved in line with technological progresses and changes in consumer preferences, as well as with regulatory trends. This is why, when assessing the effect that a new technology or industry policy may have on the national economy, companies and policy-makers need to consider dynamic structural changes affecting the IT industry. One of the most popular existing methods for economic impact analysis is based on a traditional input-output table, and is conducted over a period between the current time and a given time in the future. In this study, we compare the accuracy of RAS and Cross Entropy (CE), the two most widely employed methods for updating input-output (IO) tables, by applying them to Korean IT industries. The main results of this study are the following. In terms of the accuracy of input coefficient estimates, we have found that both the RAS and CE methods have a tendency to overestimate or underestimate them. When the Korean industry was first divided into fourteen sectors, and the RAS and CE methods were applied to each of the fourteen industries, it was difficult to discern a consistent trend for the two methods concerning their accuracy in estimation of input coefficients. Secondly, when used to update an IO table in which the IT industry is subdivided into IT equipment and services, neither the CE nor RAS method proved distinctly superior to the other. Third, in light of the above two findings, we concluded that updating IO tables is best done through a hybrid method combining the CE and RAS methods. This paper proposes a procedure consisting of two steps: IO tables are first updated using the two methods, which are once again updated by employing the OLS average approach through the use of optimal weights

The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2)

Individual Streptomyces species have the genetic potential to produce a diverse array of natural products of commercial, medical and veterinary interest. However, these products are often not detectable under laboratory culture conditions. To harness their full biosynthetic potential, it is important to develop a detailed understanding of the regulatory networks that orchestrate their metabolism. Here we integrate nucleotide resolution genome-scale measurements of the transcriptome and translatome of Streptomyces coelicolor, the model antibiotic-producing actinomycete. Our systematic study determines 3,570 transcription start sites and identifies 230 small RNAs and a considerable proportion (∼21%) of leaderless mRNAs; this enables deduction of genome-wide promoter architecture. Ribosome profiling reveals that the translation efficiency of secondary metabolic genes is negatively correlated with transcription and that several key antibiotic regulatory genes are translationally induced at transition growth phase. These findings might facilitate the design of new approaches to antibiotic discovery and development

The architecture of ArgR-DNA complexes at the genome-scale in<i> Escherichia coli</i>

DNA-binding motifs that are recognized by transcription factors (TFs) have been well studied; however, challenges remain in determining the in vivo architecture of TF-DNA complexes on a genome-scale. Here, we determined the in vivo architecture of Escherichia coli arginine repressor (ArgR)-DNA complexes using high-throughput sequencing of exonuclease-treated chromatin-immunoprecipitated DNA (ChIP-exo). The ChIP-exo has a unique peak-pair pattern indicating 5′ and 3′ ends of ArgR-binding region. We identified 62 ArgR-binding loci, which were classified into three groups, comprising single, double and triple peak-pairs. Each peak-pair has a unique 93 base pair (bp)-long (±2 bp) ArgR-binding sequence containing two ARG boxes (39 bp) and residual sequences. Moreover, the three ArgR-binding modes defined by the position of the two ARG boxes indicate that DNA bends centered between the pair of ARG boxes facilitate the non-specific contacts between ArgR subunits and the residual sequences. Additionally, our approach may also reveal other fundamental structural features of TF-DNA interactions that have implications for studying genome-scale transcriptional regulatory networks

FREQUENCY AND LENGTH ADJUSTMENT OF A DUMBBELL FOR THE PEFP LOW-BETA SRF CAVITY*

Abstract This paper describes a method to adjust the frequency and the length of a dumbbell used to fabricate the PEFP low-beta superconducting RF cavity. A tuning program is used to calculate the π mode frequency of each half-cell according to the resonant frequency of a TM010 passband and the perturbation frequency shifts of a dumbbell. According to the frequency difference between the two half cells and the frequency sensitivity coefficients, we can determine the tuning length in the axial direction or the trimming length at the equator to make the two half cells have the same frequency and length. In order to measure the frequency and to compensate for the length of a PEFP dumbbell for a stiffening-ring welding shrinkage, a frequency measurement set and length tuning set have been fabricated

A Parametric Study on the Immunomodulatory Effects of Electroacupuncture in DNP-KLH Immunized Mice

This study was conducted to compare the effects of low frequency electroacupuncture (EA) and high frequency EA at acupoint ST36 on the production of IgE and Th1/Th2 cytokines in BALB/c mice that had been immunized with 2,4-dinitrophenylated keyhole limpet protein (DNP-KLH), as well as to investigate the difference in the immunomodulatory effects exerted by EA stimulations at acupoint ST36 and at a non-acupoint (tail). Female BALB/c mice were divided into seven groups: normal (no treatments), IM (immunization only), ST36-PA (IM + plain acupuncture at ST36), ST36-LEA (IM + low frequency (1 Hz) EA at ST36), ST36-HEA (IM + high frequency (120 Hz) EA at ST36), NA-LEA (IM + low frequency (1 Hz) EA at non-acupoint) and NA-HEA (IM + high frequency (120 Hz) EA at non-acupoint). EA stimulation was performed daily for two weeks, and total IgE, DNP-KLH specific IgE, IL-4 and IFN-γ levels were measured at the end of the experiment. The results of this study showed that the IgE and IL-4 levels were significantly suppressed in the ST36-LEA and ST36-HEA groups, but not in the NA-LEA and NA-HEA groups. However, there was little difference in the immunomodulatory effects observed in the ST36-LEA and ST36-HEA groups. Taken together, these results suggest that EA stimulation-induced immunomodulation is not frequency dependent, but that it is acupoint specific

Effect of 660 nm Light-Emitting Diode on the Wound Healing in Fibroblast-Like Cell Lines

Light in the red to near-infrared (NIR) range (630–1000 nm), which is generated using low energy laser or light-emitting diode (LED) arrays, was reported to have a range of beneficial biological effects in many injury models. NIR via a LED is a well-accepted therapeutic tool for the treatment of infected, ischemic, and hypoxic wounds as well as other soft tissue injuries in humans and animals. This study examined the effects of exposure to 660 nm red LED light at intensities of 2.5, 5.5, and 8.5 mW/cm2 for 5, 10, and 20 min on wound healing and proliferation in fibroblast-like cells, such as L929 mouse fibroblasts and human gingival fibroblasts (HGF-1). A photo illumination-cell culture system was designed to evaluate the cell proliferation and wound healing of fibroblast-like cells exposed to 600 nm LED light. The cell proliferation was evaluated by MTT assay, and a scratched wound assay was performed to assess the rate of migrating cells and the healing effect. Exposure to the 660 nm red LED resulted in an increase in cell proliferation and migration compared to the control, indicating its potential use as a phototherapeutic agent

Electro-Mechanical Safety Testing of Portable ECG Devices for Home Healthcare Usage

OBJECTIVES: This paper suggests the experimental guidelines to evaluate the electro-mechanical safety of belt type equipment. The electro-mechanical safety was determined by using the International Electrotechnical Commission guidelines, which are widely used as important factors for assessing the electro-mechanical safety of belt type equipment. However, the local guidelines on wearable healthcare sensors are currently not well-established. Therefore, safety guidelines suited for the actual circumstances in Korea are required, and this paper attempts to try a new experimental safety test procedure of the wearable healthcare sensor. METHODS: This belt type device measures the electrocardiogram (ECG) and heart rates by attaching to the chest. Examination lists were selected by analyzing the common standards ofelectro-mechanical safety (IEC 60601-1) and environment tests (IEC 60068-1, IEC 60068-2) of home-healthcare equipment. RESULTS: The essential electrical safety, which was required for the RS300G3 as a medical device, was evaluated, and most of the examination lists were selected by considering the circumstances of the users. The device passed all the selected examinable lists that are applicable to the Korean environment. CONCLUSIONS: This study has limitations to estimate and to conduct electro-mechanical safety experiments because our study focused on the belt type of heart-rates equipment. We are not taking into account the overall electro-mechanical home-healthcare measurements. According to industrial and technological development, there are infinite possibilities for the advancement of home-healthcare equipment, so more examination lists for safety are being added in addition to what we have doneope