A budding yeast CAGE dataset comprising two cell types.

The budding yeast Saccharomyces cerevisiae is an excellent model organism for studying chromatin regulation with high-resolution genome-wide analyses. Since newly generated genome-wide data are often compared with publicly available datasets, expanding our dataset repertoire will be beneficial for the field. Information on transcription start sites (TSSs) determined at base pair resolution is essential for elucidating mechanisms of transcription and related chromatin regulation, yet no datasets that cover two different cell types are available.

Helical Three Dimensional Reconstruction Using Bayesian Optimization for Cryogenic Electron Microscopy.

Three-dimensional (3D) reconstruction for cryogenic electron microscopy (cryo-EM) often falls into an ill-posed problem owing to several uncertainties in observations, including noise. To reduce excessive degree of freedom and avoid overfitting, the structural symmetry is often used as a powerful constraint. In the case of the helix, the entire 3D structure is determined by the subunit 3D structure and two helical parameters.

Bayesian inference for three-dimensional helical reconstruction using a soft-body model.

Estimation of the three-dimensional (3D) structure of a protein using cryo transmission electron microscopy (cryo-TEM) is an inverse problem, which aims to estimate the parameters of a specific physical process from observations. In general, we need to model the observation process to estimate a structure. However, the inconsistency between the model and a real observation process decreases the estimation accuracy.

A Novel Bacterial Nitrate Transporter Composed of Small Transmembrane Proteins.

A putative silent gene of the freshwater cyanobacterium Synechococcus elongatus strain PCC 7942, encoding a small protein with two transmembrane helices, was named nrtS, since its overexpression from an inducible promoter conferred nitrate uptake activity on the nitrate transport-less NA4 mutant of S. elongatus. Homologs of nrtS, encoding proteins of 67-118 amino acid residues, are present in a limited number of eubacteria including mostly cyanobacteria and proteobacteria, but some others, e.

Virtual Adversarial Training: A Regularization Method for Supervised and Semi-Supervised Learning.

We propose a new regularization method based on virtual adversarial loss: a new measure of local smoothness of the conditional label distribution given input. Virtual adversarial loss is defined as the robustness of the conditional label distribution around each input data point against local perturbation. Unlike adversarial training, our method defines the adversarial direction without label information and is hence applicable to semi-supervised learning.

Removal of the product from the culture medium strongly enhances free fatty acid production by genetically engineered .

Background: Cyanobacterial mutants engineered for production of free fatty acids (FFAs) secrete the products to the medium and hence are thought to be useful for biofuel production. The dAS1T mutant constructed from PCC 7942 has indeed a large capacity of FFA production, which is comparable to that of triacylglycerol production in green algae, but the yield of secreted FFAs is low because the cells accumulate most of the FFAs intracellularly and eventually die of their toxicity. To increase the FFA productivity, enhancement of FFA secretion is required.

Constructing a meta-tracker using Dropout to imitate the behavior of an arbitrary black-box tracker.

Imitating the behaviors of an arbitrary visual tracking algorithm enables many higher level tasks such as tracker identification and efficient tracker-fusion. It is also useful for discovering the features essential in a black-box tracker or learning from several trackers to form a super-tracker. In this study, we propose a non-linear feature fusion framework, "MIMIC" that imitates many popular trackers by mixing a pool of heterogeneous features.

CyanoBase: a large-scale update on its 20th anniversary.

The first ever cyanobacterial genome sequence was determined two decades ago and CyanoBase (http://genome.microbedb.jp/cyanobase), the first database for cyanobacteria was simultaneously developed to allow this genomic information to be used more efficiently.

Modulation of the balance of fatty acid production and secretion is crucial for enhancement of growth and productivity of the engineered mutant of the cyanobacterium Synechococcus elongatus.

Background: Among the three model cyanobacterial species that have been used for engineering a system for photosynthetic production of free fatty acids (FFAs), Synechococcus elongatus PCC7942 has been the least successful; the FFA-excreting mutants constructed from this strain could attain lower rates of FFA excretion and lower final FFA concentrations than the mutants constructed from Synechocystis sp. PCC6803 and Synechococcus sp. PCC7002.

Identification of a Cyanobacterial RND-Type Efflux System Involved in Export of Free Fatty Acids.

An RND (resistance-nodulation-division)-type transporter having the capacity to export free fatty acids (FFAs) was identified in the cyanobacterium Synechococcus elongatus strain PCC 7942 during characterization of a mutant strain engineered to produce FFAs. The basic strategy for construction of the FFA-producing mutant was a commonly used one, involving inactivation of the endogenous acyl-acyl carrier protein synthetase gene (aas) and introduction of a foreign thioesterase gene ('tesA), but a nitrate transport mutant NA3 was used as the parental strain to achieve slow, nitrate-limited growth in batch cultures. Also, a nitrogen-regulated promoter PnirA was used to drive 'tesA to maximize thioesterase expression during the nitrate-limited growth.

Essential Role of Acyl-ACP Synthetase in Acclimation of the Cyanobacterium Synechococcus elongatus Strain PCC 7942 to High-Light Conditions.

Most organisms capable of oxygenic photosynthesis have an aas gene encoding an acyl-acyl carrier protein synthetase (Aas), which activates free fatty acids (FFAs) via esterification to acyl carrier protein. Cyanobacterial aas mutants are often used for studies aimed at photosynthetic production of biofuels because the mutation leads to intracellular accumulation of FFAs and their secretion into the external medium, but the physiological significance of the production of FFAs and their recycling involving Aas has remained unclear. Using an aas-deficient mutant of Synechococcus elongatus strain PCC 7942, we show here that remodeling of membrane lipids is activated by high-intensity light and that the recycling of FFAs is essential for acclimation to high-light conditions.

Efficient Monte Carlo image analysis for the location of vascular entity.

Tubular shaped networks appear not only in medical images like X-ray-, time-of-flight MRI- or CT-angiograms but also in microscopic images of neuronal networks. We present EMILOVE (Efficient Monte-carlo Image-analysis for the Location Of Vascular Entity), a novel modeling algorithm for tubular networks in biomedical images. The model is constructed using tablet shaped particles and edges connecting them.

Nitrite transport activity of a novel HPP family protein conserved in cyanobacteria and chloroplasts.

Some cyanobacterial genomes encode an integral membrane protein of the HPP family, which exhibited nitrite transport activity when expressed in the nitrite transport-less NA4 mutant of the cyanobacterium Synechococcus elongatus strain PCC 7942. AT5G62720 and AT3G47980 were found to encode Arabidopsis homologs of the cyanobacterial protein. The product of AT5G62720 was localized to the chloroplast envelope membrane and was shown to confer nitrite uptake activity on the NA4 mutant when expressed with an N-terminally truncated transit peptide or as a fusion with the N-terminal region of the cyanobacterial HPP family protein.

In vitro and in vivo analyses of the role of the carboxysomal β-type carbonic anhydrase of the cyanobacterium Synechococcus elongatus in carboxylation of ribulose-1,5-bisphosphate.

The carboxylase activities of crude carboxysome preparations obtained from the wild-type Synechococcus elongatus strain PCC 7942 strain and the mutant defective in the carboxysomal carbonic anhydrase (CA) were compared. The carboxylation reaction required high concentrations of bicarbonate and was not even saturated at 50 mM bicarbonate. With the initial concentrations of 50 mM and 25 mM for bicarbonate and ribulose-1,5-bisphosphate (RuBP), respectively, the initial rate of RuBP carboxylation by the mutant carboxysome (0.

Effects of high CO2 on growth and metabolism of Arabidopsis seedlings during growth with a constantly limited supply of nitrogen.

Elevated CO2 has been reported to stimulate plant growth under nitrogen-sufficient conditions, but the effects of CO2 on growth in a constantly nitrogen-limited state, which is relevant to most natural habitats of plants, remain unclear. Here, we maintained Arabidopsis seedlings under such conditions by growing a mutant with reduced nitrate uptake activity on a medium containing nitrate as the sole nitrogen source. Under nitrogen-sufficient conditions (i.

Evaluation of the effects of P(II) deficiency and the toxicity of PipX on growth characteristics of the P(II)-Less mutant of the cyanobacterium Synechococcus elongatus.

Among the known functions of the P(II) protein (the glnB gene product) in the cyanobacterium Synechococcus elongatus, negative regulation of the activity of PipX, a transcriptional co-activator of the NtcA regulon, has been thought to be essential for cell viability, because all the P(II)-less mutants thus far constructed carry spontaneous mutations in pipX. PipX is thus deduced to be a toxic protein, but its toxicity has not been clearly defined because of the lack of P(II)-deficient mutants carrying wild-type pipX. In this study, we developed a method to construct a targeted P(II)-less mutant of S.

Prevalence and morbidity of urethral Trichomonas vaginalis in Japanese men with or without urethritis.

Objectives: Trichomonas vaginalis is one of the pathogens causing sexually transmitted infections. This microorganism is a common pathogen among women, but its significance as a cause of morbidity among men remains uncertain. We sought to determine the prevalence and morbidity of T.

Antimicrobial chemotherapy of Mycoplasma genitalium-positive non-gonococcal urethritis.

Mycoplasma genitalium is an important pathogen of acute non-gonococcal urethritis (NGU) in men and plays a significant role in persistent or recurrent NGU. In the management of patients with M. genitalium-positive NGU, eradication of the mycoplasma from the urethra is necessary to prevent persistent or recurrent NGU.

In vitro activity of azithromycin against Mycoplasma genitalium and its efficacy in the treatment of male Mycoplasma genitalium-positive nongonococcal urethritis.

Many recent studies have shown that Mycoplasma genitalium is among the pathogens responsible for Chlamydia trachomatis-negative nongonococcal urethritis (NGU). A single 1-g dose of azithromycin (AZM) has been recommended for the treatment of NGU, including M. genitalium-positive NGU, irrespective of whether it is positive or negative for Chlamydia trachomatis.

Semaphorin 3A induces CaV2.3 channel-dependent conversion of axons to dendrites.

Polarized neurites (axons and dendrites) form the functional circuitry of the nervous system. Secreted guidance cues often control the polarity of neuron migration and neurite outgrowth by regulating ion channels. Here, we show that secreted semaphorin 3A (Sema3A) induces the neurite identity of Xenopus spinal commissural interneurons (xSCINs) by activating Ca(V)2.

Regulation of nitrate assimilation in cyanobacteria.

Nitrate assimilation by cyanobacteria is inhibited by the presence of ammonium in the growth medium. Both nitrate uptake and transcription of the nitrate assimilatory genes are regulated. The major intracellular signal for the regulation is, however, not ammonium or glutamine, but 2-oxoglutarate (2-OG), whose concentration changes according to the change in cellular C/N balance.

Emergence and spread of drug resistant Neisseria gonorrhoeae.

Purpose: The emergence and spread of Neisseria gonorrhoeae with resistance to oral antibiotics have led to difficulty in treating gonorrhea. We review drug resistance in N. gonorrhoeae with a particular emphasis on resistance to fluoroquinolones, cefixime and azithromycin.

Sparse bayesian learning of filters for efficient image expansion.

We propose a framework for expanding a given image using an interpolator that is trained in advance with training data, based on sparse bayesian estimation for determining the optimal and compact support for efficient image expansion. Experiments on test data show that learned interpolators are compact yet superior to classical ones.