Isozymes of Alginate Lyase in the Mid-gut Gland of Turbo cornutus

Alginate lyase, SP2, from Turbo cornutus was separated on an SP-Sephadex C-50 column from SP1, whose properties have already been reported, and purified according to the method employed for SP1, to obtain information on SP2. The profiles of the optimal pH, pH-stability, thermal inactivation and molecular size of SP2 were entirely the same as those of SP1. The isoelectric point of SP1 and SP2 was 7.5 and 7.7, respectively. The action of SP2 on Alginate caused a rapid decrease in solution viscosity. Analysis of digestion products of alginate with SP2 showed that the enzyme had an affinity toward the mannuronate-rich domains of the alginate molecule and released unsaturated oligomers mostly composed of mannuronic acid as final product. Alginate lyases, SP1 and SP2, were shown to be isozymes in the mid-gut gland of Turbo cornutus.     

Characterization of Starch Granules from Waxy,Nonwaxy, and Hybrid Seeds of Amaranthus hypochondriacus L.

Perisperm starch granules of the dicotyledonous plant Amaranthus hypochondriacus L. were prepared from two homozygous lines (WxWx and wxwx) and their hybrid (Wxwx). The hybrid line was obtained by natural hybridization. By Sephadex G-75 column chromatography of isoamylase-debranched starches, the amylose content of WxWx starch was 16.9%, that of Wxwx was 10.7, and wxwx was zero. SDS-polyacrylamide gel electrophoresis showed that starch granules from two genotypes (WxWx and Wxwx) contained a Wx protein (MW = 68,000) which was supposed to be a starch granule-bound starch synthase and was associated with amylose synthesis, as observed in nonwaxy maize. The intensities of the stained protein bands were apparently correlated with the number of the Wx alleles. The Wx protein was not detected in the wxwx starch. These findings suggest that the Wx allele produces the Wx protein and amylose in the perisperm of A. hypochondriacus, with incomplete dominance over the wx allele. The Wx allele did not affect the fine structure of amylopectin and had little if any effect on susceptibility to glucoamylase and pasting properties of starch granules from these genotypes.     

Primary Drug-Resistant Tuberculosis in Hanoi,Viet Nam: Present Status and Risk Factors

Introduction

Resistance of Mycobacterium tuberculosis (MTB) to anti-tuberculosis (TB) drugs presents a serious challenge to TB control worldwide. We investigated the status of drug resistance, including multidrug-resistant (MDR) TB, and possible risk factors among newly diagnosed TB patients in Hanoi, the capital of Viet Nam.

Methods

Clinical and epidemiological information was collected from 506 newly diagnosed patients with sputum smear- and culture-positive TB, and 489 (96.6%) MTB isolates were subjected to conventional drug susceptibility testing, spoligotyping, and 15-locus variable numbers of tandem repeats typing. Adjusted odds ratios (aORs) were calculated to analyze the risk factors for primary drug resistance.

Results

Of 489 isolates, 298 (60.9%) were sensitive to all drugs tested. Resistance to isoniazid, rifampicin, streptomycin, ethambutol, and MDR accounted for 28.2%, 4.9%, 28.2%, 2.9%, and 4.5%, respectively. Of 24 isolates with rifampicin resistance, 22 (91.7%) were MDR and also resistant to streptomycin, except one case. Factors associated with isoniazid resistance included living in old urban areas, presence of the Beijing genotype, and clustered strains [aOR = 2.23, 95% confidence interval (CI) 1.15–4.35; 1.91, 1.18–3.10; and 1.69, 1.06–2.69, respectively). The Beijing genotype was also associated with streptomycin resistance (aOR = 2.10, 95% CI 1.29–3.40). Human immunodeficiency virus (HIV) coinfection was associated with rifampicin resistance and MDR (aOR = 5.42, 95% CI 2.07–14.14; 6.23, 2.34–16.58, respectively).

Conclusion

Isoniazid and streptomycin resistance was observed in more than a quarter of TB patients without treatment history in Hanoi. Transmission of isoniazid-resistant TB among younger people should be carefully monitored in urban areas, where Beijing strains and HIV coinfection are prevalent. Choosing an optimal treatment regimen on the basis of the results of drug susceptibility tests and monitoring of treatment adherence would minimize further development of drug resistance strains.     

Quantifying Collective Attention from Tweet Stream

Online social media are increasingly facilitating our social interactions, thereby making available a massive “digital fossil” of human behavior. Discovering and quantifying distinct patterns using these data is important for studying social behavior, although the rapid time-variant nature and large volumes of these data make this task difficult and challenging. In this study, we focused on the emergence of “collective attention” on Twitter, a popular social networking service. We propose a simple method for detecting and measuring the collective attention evoked by various types of events. This method exploits the fact that tweeting activity exhibits a burst-like increase and an irregular oscillation when a particular real-world event occurs; otherwise, it follows regular circadian rhythms. The difference between regular and irregular states in the tweet stream was measured using the Jensen-Shannon divergence, which corresponds to the intensity of collective attention. We then associated irregular incidents with their corresponding events that attracted the attention and elicited responses from large numbers of people, based on the popularity and the enhancement of key terms in posted messages or “tweets.” Next, we demonstrate the effectiveness of this method using a large dataset that contained approximately 490 million Japanese tweets by over 400,000 users, in which we identified 60 cases of collective attentions, including one related to the Tohoku-oki earthquake. “Retweet” networks were also investigated to understand collective attention in terms of social interactions. This simple method provides a retrospective summary of collective attention, thereby contributing to the fundamental understanding of social behavior in the digital era.     

Phosphorylase coupling as a tool to convert cellobiose into amylose

This work aims to establish the enzymatic process to produce amylose from cellobiose. Incubation of cellobiose with cellobiose phosphorylase and alpha-glucan phosphorylase in the presence of maltotetraose and a catalytic amount of inorganic phosphate at 45 degrees C for 16 h resulted in the production of linear alpha-1,4-glucan with a 19.3% (w/v, against cellobiose weight) yield. The yield was successfully improved (32.4%) when mutarotase and glucose oxidase were added to remove glucose in the reaction mixture. The weight-average molecular weight of the product was precisely controlled from 42 to 720 kDa by changing the initial molar ratio of cellobiose to maltotetraose. The combined use of two different phosphorylases should be a useful tool in converting beta-1,4-linked-polysaccharide into alpha-1,4-linked-polysaccharide.     

Rare carotenoids, (3R)-saproxanthin and (3R,2'S)-myxol, isolated from novel marine bacteria (Flavobacteriaceae) and their antioxidative activities

We isolated three orange or yellow pigment-producing marine bacteria, strains 04OKA-13-27 (MBIC08261), 04OKA-17-12 (MBIC08260), and YM6-073 (MBIC06409), off the coast of Okinawa Prefecture in Japan. These strains were classified as novel species of the family Flavobacteriaceae based on their 16S rRNA gene sequence. They were cultured, and the major carotenoids produced were purified by chromatographic methods. Their structures were determined by spectral data to be (3R)-saproxanthin (strain 04OKA-13-27), (3R,2'S)-myxol (strain YM6-073), and (3R,3'R)-zeaxanthin (strains YM6-073 and 04OKA-17-12). Saproxanthin and myxol, which are monocyclic carotenoids rarely found in nature, demonstrated significant antioxidative activities against lipid peroxidation in the rat brain homogenate model and a neuro-protective effect from L-glutamate toxicity.     

Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes

Background

The availability of diverse second- and third-generation sequencing technologies enables the rapid determination of the sequences of bacterial genomes. However, identifying the sequencing technology most suitable for producing a finished genome with multiple chromosomes remains a challenge. We evaluated the abilities of the following three second-generation sequencers: Roche 454 GS Junior (GS Jr), Life Technologies Ion PGM (Ion PGM), and Illumina MiSeq (MiSeq) and a third-generation sequencer, the Pacific Biosciences RS sequencer (PacBio), by sequencing and assembling the genome of Vibrio parahaemolyticus, which consists of a 5-Mb genome comprising two circular chromosomes.

Results

We sequenced the genome of V. parahaemolyticus with GS Jr, Ion PGM, MiSeq, and PacBio and performed de novo assembly with several genome assemblers. Although GS Jr generated the longest mean read length of 418 bp among the second-generation sequencers, the maximum contig length of the best assembly from GS Jr was 165 kbp, and the number of contigs was 309. Single runs of Ion PGM and MiSeq produced data of considerably greater sequencing coverage, 279× and 1,927×, respectively. The optimized result for Ion PGM contained 61 contigs assembled from reads of 77× coverage, and the longest contig was 895 kbp in size. Those for MiSeq were 34 contigs, 58× coverage, and 733 kbp, respectively. These results suggest that higher coverage depth is unnecessary for a better assembly result. We observed that multiple rRNA coding regions were fragmented in the assemblies from the second-generation sequencers, whereas PacBio generated two exceptionally long contigs of 3,288,561 and 1,875,537 bps, each of which was from a single chromosome, with 73× coverage and mean read length 3,119 bp, allowing us to determine the absolute positions of all rRNA operons.

Conclusions

PacBio outperformed the other sequencers in terms of the length of contigs and reconstructed the greatest portion of the genome, achieving a genome assembly of “finished grade” because of its long reads. It showed the potential to assemble more complex genomes with multiple chromosomes containing more repetitive sequences.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-699) contains supplementary material, which is available to authorized users.     

Effects of Cholesterol-Loaded Cyclodextrins on the Rate and the Quality of Motility in Frozen and Thawed Rabbit Sperm

The motility of sperm after freezing and thawing is critical for effective cryopreservation. It is known that supplementation with cholesterol-loaded cyclodextrin (CLC) improves cryosurvival of sperm in various animals. To clarify the effects of supplementation with CLC on rabbit sperm motility after freezing and thawing, rabbit sperm motility was analyzed using a computer-assisted sperm analysis system. Sperm motility with CLC supplementation was 29.4 ± 9.6% (mean ± SD), which was significantly higher than that of controls (20.8 ± 7.1%, P<0.05). The curvilinear velocity of sperm with CLC exceeded that of controls, whereas the values for linearity and wobble were significantly lower in sperm with CLC compared with controls. After artificial insemination, 44.3% of recovered ova were fertilized in the CLC-supplemented group, which was higher than the percentage in the control group (36.4%). The results indicate that supplementation with CLC improves the rate and quality of motility in rabbit sperm after freezing and thawing, and would be advantageous for successful cryopreservation.     

Isolation of Dermatophytes and Related Species from Domestic Fowl (Gallus gallus domesticus)

We investigated 793 bird combs [645 chickens and 148 fighting cocks (Shamo)] to determine the prevalence of dermatophytes and their related fungal species. The targeted fungal species were recovered from 195 of the 793 examined birds (24.6 %). Prevalence ratios were compared in temperate (the mainland) and subtropical (Nansei Islands) areas, genders, strains, breeding scale (individual and farm), and housing system (in cage and free ranging). The frequency of the fungal species in the mainland, males, fighting cocks, breeding scale by individual nursing, and free-range housing system exhibited significantly higher positive ratios than that in the other groups. A total of 224 dermatophytes and related species were isolated, including 101 Arthroderma (Ar.) multifidum, 83 Aphanoascus (Ap.) terreus, five Uncinocarpus queenslandicus, two U. reesii, two Ap. pinarensis, one Amauroascus kuehnii, one Ar. simii, one Gymnoascus petalosporus, one Microsporum gallinae, and 28 Chrysosporium-like (Chrysosporium spp.) isolates, which were identified using internal transcribed spacer regions of ribosomal RNA gene sequences. The predominant fungal species in the mainland was Ap. terreus and that in the Nansei Islands was Ar. multifidum. Pathogenic fungal species to humans and animals were limited to M. gallinae and Ar. simii, which corresponded to 0.025 % of the isolates in this study.     

Functional analysis of three novel cell lines derived from human papillary thyroid carcinomas with three different clinical courses

Papillary thyroid carcinoma (PTC) is the most frequent thyroid carcinoma. PTC cell lines have been of considerable value in studying aspects of thyroid cancer, such as gene expression, cell proliferation, and differentiation. Here we report three novel PTC lines established from three patients with different backgrounds. Case 1 was a 38-year-old woman with PTC in the right thyroid lobe, with no metastasis. The cell line was established from the resection sample and named D-PTC. The cell line consisted of epithelial cells with few lysosomes and showed a pavement structure and follicular formation at confluency. There was a little pilling up. The secretion of free thyroxin (fT4) and thyroglobulin (Tg) was increased by TSH, or GH and IGF-I treatment. Case 2 was a 22-year-old woman with PTC initially in the right thyroid lobe, but 4 years after the right lobe resection, PTC metastasis was observed in left lobe. The cell line was established from a sample of the second resection and named UD-PTC. This cell line consisted of small epithelial cells with evident lysosomes and exhibited floating cell clusters. The secretion of fT4 and Tg was slightly increased by TSH, or GH and IGF-I treatment. Case 3 was an 85-year-old man with PTC and with acromegaly. Metastasis was observed at cervical lymph nodes. The cell line was derived from the metastasis region and named A-PTC. This cell line consisted of small epithelial cells and many lysosomes. The cells frequently showed pilling up. The secretion of fT4 and Tg was significantly increased by GH and IGF-I treatment. We have established three PTC cell lines with substantial variation in their phenotype. The cell lines may be useful for thyroid cancer research.