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Bioscience, Biotechnology, and Biochemistry

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https://www.readbyqxmd.com/read/29792119/maple-2-3-0-an-improved-system-for-evaluating-the-functionomes-of-genomes-and-metagenomes
#1
Wataru Arai, Takeaki Taniguchi, Susumu Goto, Yuki Moriya, Hideya Uehara, Kazuhiro Takemoto, Hiroyuki Ogata, Hideto Takami
MAPLE is an automated system for inferring the potential comprehensive functions harbored by genomes and metagenomes. To reduce runtime in MAPLE analyzing the massive amino acid datasets of over 1 million sequences, we improved it by adapting the KEGG automatic annotation server to use GHOSTX and verified no substantial difference in the MAPLE results between the original and new implementations.
May 24, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29742980/bacterial-community-analysis-in-three-types-of-the-fermented-seafood-jeotgal-produced-in-south-korea
#2
Eun-Ji Song, Eun-Sook Lee, So-Lim Park, Hak-Jong Choi, Seong Woon Roh, Young-Do Nam
Jeotgal is a traditional Korean seafood fermented by indigenous microbes. The bacterial community in five myeolchi-jeot (Engraulis japonica), five meongge-jeot (Halocynthia roretzi), and six saeu-jeot (Acetes japonicas) produced in South Korea was analyzed by barcoded pyrosequencing targeting the V1/V2 hyper-variable regions of the 16S rRNA gene. All samples were dominated by the phyla Firmicutes, which represented 67.7% (SD = 27.2%) of the population. Tetragenococcus halophilus and Tetragenococcus muriaticus were the predominant species in myeolchi-jeot...
May 9, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29739279/murine-intestinal-organoids-resemble-intestinal-epithelium-in-their-microrna-profiles
#3
Fumina Ohsaka, Kei Sonoyama
Intestinal organoids were established as an ex vivo model of the intestinal epithelium. We investigated whether organoids resemble the intestinal epithelium in their microRNA (miRNA) profiles. Total RNA samples were obtained from crypt and villus fractions in murine intestine and from cultured organoids. Microarray analysis showed that organoids largely resembled intestinal epithelial cells in their miRNA profiles. In silico prediction followed by qRT-PCR suggested that six genes are regulated by corresponding miRNAs along the crypt-villus axis, suggesting miRNA regulation of epithelial cell renewal in the intestine...
May 8, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29739277/erratum
#4
(no author information available yet)
No abstract text is available yet for this article.
May 8, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29732953/suppressive-effects-of-the-peel-of-citrus-kawachiensis-kawachi-bankan-on-astroglial-activation-tau-phosphorylation-and-inhibition-of-neurogenesis-in-the-hippocampus-of-type-2-diabetic-db-db-mice
#5
Satoshi Okuyama, Wakana Shinoka, Kumi Nakamura, Maho Kotani, Atsushi Sawamoto, Kuniaki Sugawara, Masahiko Sudo, Mitsunari Nakajima, Yoshiko Furukawa
We previously reported that the dried peel powder of Citrus kawachiensis exerted anti-inflammatory effects in the brain in several animal models. Hyperglycemia induces inflammation and oxidative stress and causes massive damage in the brain; therefore, we herein examined the anti-inflammatory and other effects of the dried peel powder of C. kawachiensis in the streptozotocin-induced hyperglycemia mice model and in the type 2 diabetic db/db mice model. The C. kawachiensis administration inhibited microglial activation in the hippocampus in the streptozotocin-injected mice...
May 6, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29708475/direct-bioethanol-production-from-brown-macroalgae-by-co-culture-of-two-engineered-saccharomyces-cerevisiae-strains
#6
Yusuke Sasaki, Toshiyuki Takagi, Keisuke Motone, Toshiyuki Shibata, Kouichi Kuroda, Mitsuyoshi Ueda
A co-culture platform for bioethanol production from brown macroalgae was developed, consisting of two types of engineered Saccharomyces cerevisiae strains; alginate- and mannitol-assimilating yeast (AM1), and cellulase-displaying yeast (CDY). When the 5% (w/v) brown macroalgae Ecklonia kurome was used as the sole carbon source for this system, 2.1 g/L of ethanol was produced, along with simultaneous consumption of alginate, mannitol, and glucans.
April 30, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29699461/new-metabolites-sarcopodinols-a-and-b-isolated-from-deep-sea-derived-fungal-strain-sarcopodium-sp-fkj-0025
#7
Hirotaka Matsuo, Kenichi Nonaka, Yuriko Nagano, Akinori Yabuki, Katsunori Fujikura, Yōko Takahashi, Satoshi Ōmura, Takuji Nakashima
Fungal strain FKJ-0025 was isolated from deep-sea sediment collected at the Wakamiko Caldera in Kagoshima Bay (water depth: 200 m). The fungal strain FKJ-0025 was identified as the genus Sarcopodium based on its morphology and internal transcribed spacer (ITS) sequence. Two new compounds, designated sarcopodinols A (1) and B (2), were isolated together with the known compound SF-227 (3).
April 26, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29699448/comparative-study-of-polyethylene-polyamines-as-activator-molecules-for-a-structurally-unstable-group-i-ribozyme
#8
Mst Ara Gulshan, Shigeyoshi Matsumura, Tsunehiko Higuchi, Naoki Umezawa, Yoshiya Ikawa
Polyamines are a promising class of molecules that can modulate RNA enzyme activities. To analyze the effects of the number of amine moieties systematically, we employed four polyamines sharing dimethylene units to connect amine moieties. As a model RNA enzyme, we used a structurally unstable group I ribozyme, which was activated most and least efficiently by tetraethylenepentamine and diethylenetriamine respectively.
April 26, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29699439/synthesis-of-fisetin-and-2-4-6-trihydroxydihyrochalcone-4-o-%C3%AE-neohesperidoside-based-on-site-selective-deacetylation-and-deoxygenation
#9
Ryuji Tsunekawa, Kengo Hanaya, Shuhei Higashibayashi, Takeshi Sugai
Fisetin and 2',4',6'-trihydroxydihyrochalcone 4'-O-β-neohesperidoside were synthesized from commercially available quercetin and naringin in five steps. The key steps are site-selective deacetylation and subsequent deoxygenation. The target molecules were obtained in 37% and 23% yields from the starting materials, respectively.
April 26, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29699438/a-novel-thiamine-derived-pigment-pyrizepine-formed-by-the-maillard-reaction
#10
Asuka Igoshi, Kyoko Noda, Masatsune Murata
To find a Maillard pigment derived from thiamine, a solution containing glucose and thiamine was heated and analyzed with high-performance liquid chromatography equipped with diode-array detection. As a result, a unique peak showing an absorption maximum at 380 nm was detected. This peak was then isolated from a reaction solution containing glucose, lysine and thiamine, and was identified as 1-(2-methyl-6,9-dihydro-5H-pyrimido[4,5-e][1,4]diazepin-7-yl)ethan-1-one using instrumental analyses. This compound, named pyrizepine, was a novel yellow pigment having a fused ring consisting of pyrimidine and diazepine...
April 26, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29699437/a-fragmentation-study-of-isoflavones-by-it-tof-ms-using-biosynthesized-isotopes
#11
Ryu Nakata, Naoko Yoshinaga, Masayoshi Teraishi, Yutaka Okumoto, Alisa Huffaker, Eric A Schmelz, Naoki Mori
To aid in the identification and quantification of biologically and agriculturally significant natural products, tandem mass spectrometry can provide accurate structural information with high selectivity and sensitivity. In this study, diagnostic fragmentation patterns of isoflavonoids were examined by liquid chromatography-ion trap-time of flight-mass spectrometry (LC-IT-TOF-MS). The fragmentation scheme for [M+H-2CO]+ ions derived from isoflavones and [M+H-B-ring-CO]+ ions derived from 5-hydroxyisoflavones, were investigated using different isotopically labeled isoflavones, specifically [1',2',3',4',5',6',2,3,4-13 C9 ] and [2',3',5',6',2-D5 ] isoflavones...
April 26, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29690857/the-expression-of-transmembrane-protein-100-is-regulated-by-alterations-in-calcium-signaling-rather-than-endoplasmic-reticulum-stress
#12
Ayane Kuboyama, Takashi Sasaki, Makoto Shimizu, Jun Inoue, Ryuichiro Sato
Transmembrane protein 100 (TMEM100) comprises 134 amino acid residues and is highly conserved among vertebrates. Tmem100 has been recently reported as a key factor in angiogenesis, pain transmission, and tumor suppression. Although the importance of TMEM100 function is well supported, few studies have elucidated its expression mechanism. In the current study, we found that activating transcription factor 6α, a transcription factor activated by endoplasmic reticulum (ER) stress, enhanced Tmem100 promoter activity...
April 25, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29685096/effects-of-carbon-dioxide-on-metabolite-production-and-bacterial-communities-during-kimchi-fermentation
#13
Doo Hyun Park
Bacterial communities and metabolites in kimchi fermented under conventional conditions (CC) compared to CO2 -rich environments (CO2 ) were analyzed. After a 20-day fermentation, lactic and acetic acid productions were 54 and 69 mM under CC, and 19 and 12 mM under CO2 , respectively. The final pH of kimchi fermented under CC (CC-fermenting) and CO2 (CO2 -fermenting) were 4.1 and 4.7, respectively. For bacterial communities, OTU and Chao1 indices were both 35 in fresh kimchi, 10 and 15 in CC-fermenting kimchi, and 8 and 24 in CO2 -fermenting kimchi, respectively...
April 24, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29685095/zebularine-exerts-its-antiproliferative-activity-through-s-phase-delay-and-cell-death-in-human-malignant-mesothelioma-cells
#14
Yukitoshi Takemura, Motohiko Satoh, Kenichi Hatanaka, Shunichiro Kubota
Malignant mesothelioma is an asbestos-related aggressive tumor and current therapy remains ineffective. Zebularine as a DNA methyltransferase (DNMT) inhibitor has an anti-tumor effect in several human cancer cells. The aim of the present study was to investigate whether zebularine could induce antiproliferative effect in human malignant mesothelioma cells. Zebularine induced cell growth inhibition in a dose-dependent manner. In addition, zebularine dose-dependently decreased expression of DNMT1 in all malignant mesothelioma cells tested...
April 24, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29685094/effects-of-alcoholic-beverage-treatment-on-spatial-learning-and-fear-memory-in-mice
#15
Narumi Hashikawa-Hobara, Shuta Mishima, Shotaro Nagase, Keishi Morita, Ami Otsuka, Naoya Hashikawa
Although chronic ethanol treatment is known to impair learning and memory, humans commonly consume a range of alcoholic beverages. However, the specific effects of some alcoholic beverages on behavioral performance are largely unknown. The present study compared the effects of a range of alcoholic beverages (plain ethanol solution, red wine, sake and whiskey; with a matched alcohol concentration of 10%) on learning and memory. 6-week-old C57BL6J mice were orally administered alcohol for 7 weeks. The results revealed that red wine treatment exhibited a trend toward improvement of spatial memory and advanced extinction of fear memory...
April 24, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29685090/the-critical-role-of-his48-in-mouse-cytosolic-sulfotransferase-sult2a8-for-the-7%C3%AE-hydroxyl-sulfation-of-bile-acids
#16
Takehiko Shimohira, Katsuhisa Kurogi, Ming-Cheh Liu, Masahito Suiko, Yoichi Sakakibara
Members of the cytosolic sulfotransferase (SULT) SULT2A subfamily are known to be critically involved in the homeostasis of steroids and bile acids. SULT2A8, a 7α-hydroxyl bile acid-preferring mouse SULT, has been identified as the major enzyme responsible for the mouse-specific 7-O-sulfation of bile acids. Interestingly, SULT2A8 lacks a conservative catalytic His residue at position 99th. The catalytic mechanism underlying the SULT2A8-mediated 7-O-sulfation of bile acids thus remained unclear. In this study, we performed a mutational analysis in order to gain insight into this yet-unresolved issue...
April 24, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29678124/a-curcumin-diglutaric-acid-conjugated-prodrug-with-improved-water-solubility-and-antinociceptive-properties-compared-to-curcumin
#17
Chawanphat Muangnoi, Ponsiree Jithavech, Pahweenvaj Ratnatilaka Na Bhuket, Wiwat Supasena, Wisut Wichitnithad, Pasarapa Towiwat, Nuansri Niwattisaiwong, Ian S Haworth, Pornchai Rojsitthisak
In this work, a curcumin-diglutaric acid (CurDG) prodrug was synthesized by conjugation of curcumin with glutaric acid via an ester linkage. The water solubility, partition coefficient, release characteristics, and antinociceptive activity of CurDG were compared to those of curcumin. The aqueous solubility of CurDG (7.48 μg/mL) is significantly greater than that of curcumin (0.068 μg/mL). A study in human plasma showed that the CurDG completely releases curcumin within 2 h, suggesting the ability of CurDG to serve as a prodrug of curcumin...
April 20, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29678122/chemical-regulators-of-plant-hormones-and-their-applications-in-basic-research-and-agriculture
#18
Kai Jiang, Tadao Asami
Plant hormones are small molecules that play versatile roles in regulating plant growth, development, and responses to the environment. Classic methodologies, including genetics, analytic chemistry, biochemistry, and molecular biology, have contributed to the progress in plant hormone studies. In addition, chemical regulators of plant hormone functions have been important in such studies. Today, synthetic chemicals, including plant growth regulators, are used to study and manipulate biological systems, collectively referred to as chemical biology...
April 20, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29673297/characterization-of-copk02-a-ca-2-calmodulin-dependent-protein-kinase-in-mushroom-coprinopsis-cinerea
#19
Masashi Yamashita, Noriyuki Sueyoshi, Hiroki Yamada, Syouichi Katayama, Yukako Senga, Yasuhiro Takenaka, Atsuhiko Ishida, Isamu Kameshita, Yasushi Shigeri
We surveyed genome sequences from the basidiomycetous mushroom Coprinopsis cinerea and isolated a cDNA homologous to CMKA, a calmodulin-dependent protein kinase (CaMK) in Aspergillus nidulans. We designated this sequence, encoding 580 amino acids with a molecular weight of 63,987, as CoPK02. CoPK02 possessed twelve subdomains specific to protein kinases and exhibited 43, 35, 40% identity with rat CaMKI, CaMKII, CaMKIV, respectively, and 40% identity with CoPK12, one of the CaMK orthologs in C. cinerea. CoPK02 showed significant autophosphorylation activity and phosphorylated exogenous proteins in the presence of Ca2+ /CaM...
April 20, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29673281/construction-of-rhodococcus-expression-vectors-and-expression-of-the-aminoalcohol-dehydrogenase-gene-in-rhodococcus-erythropolis
#20
Ei-Tora Yamamura
NADP+ -dependent aminoalcohol dehydrogenase (AADH) of Rhodococcus erythropolis MAK154 produces double chiral aminoalcohols, which are used as pharmaceuticals. However, the genetic manipulation of Rhodococcus strains to increase their production of such industrially important enzymes is not well studied. Therefore, I aimed to construct Rhodococcus expression vectors, derived from the Rhodococcus-Escherichia coli shuttle vector pRET1102, to express aadh. The plasmid pRET1102 could be transformed into many actinomycete strains, including R...
April 20, 2018: Bioscience, Biotechnology, and Biochemistry
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