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https://www.readbyqxmd.com/read/28438015/genome-characteristics-of-lactobacillus-fermentum-strain-jdfm216-for-application-as-probiotic-bacteria
#1
Sung Yong Jang, Jaeyoung Heo, Mi Ri Park, Min-Ho Song, Jong Nam Kim, Sung Ho Jo, Do-Youn Jeong, Hak Kyo Lee, Younghoon Kim, Sangnam Oh
Lactobacillus fermentum strain JDFM216, isolated from a Korean infant feces, possesses an enhancement of longevity and immune response on Caenorhabditis elegans host. To explore the molecular characteristics of strain JDFM216, we performed a whole-genome sequencing using PacBio system. The single circular DNA chromosome of 2,076,427 bp was completely assembled and 2,623 encoding sequences were predicted. Phylogenetically featured five genes possibly related to longevity and immune response of host were identified in L...
April 25, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28437774/bacterial-community-dynamics-and-functional-variation-during-the-long-term-decomposition-of-cyanobacterial-blooms-in-vitro
#2
Limei Shi, Yaxin Huang, Min Zhang, Yang Yu, Yaping Lu, Fanxiang Kong
Cyanobacterial blooms drastically influence carbon and nutrient cycling in eutrophic freshwater lakes. To understand the mineralization process of cyanobacteria-derived particulate organic matter (CyanPOM), the aerobic degradation of cyanobacterial blooms dominated by Microcystis sp. was investigated over a 95-day microcosm experiment. Approximately 91%, 95% and 83% of the initial particulate organic carbon (POC), particulate organic nitrogen (PON), and particulate organic phosphorus (POP) were decomposed, respectively...
April 21, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28437629/design-and-development-of-benzoxazole-derivatives-with-toll-like-receptor-9-antagonism
#3
Swarnali Roy, Ayan Mukherjee, Barnali Paul, Oindrila Rahaman, Shounak Roy, Gundaram Maithri, Bandaru Ramya, Sourav Pal, Dipyaman Ganguly, Arindam Talukdar
Toll-like receptor 9 (TLR9) is a major therapeutic target for numerous inflammatory disorders. Development of small molecule inhibitors for TLR9 remains largely empirical due to lack of structural understanding of potential TLR9 antagonism by small molecules and due to the unusual topology of the ligand binding surface of the receptor. To develop a structural model for rational design of small molecule TLR9 antagonists, an enhanced homology model of human TLR9 (hTLR9) was constructed. Binding mode analysis of a series of molecules having characteristic molecular geometry, flexibility and basicity was conducted based on crystal structure of the inhibitory DNA (iDNA) bound to horse and bovine TLR9...
April 5, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28437610/long-acting-release-formulation-of-exendin-4-based-on-biomimetic-mineralization-for-type-2-diabetes-therapy
#4
Wei Chen, Guohao Wang, Bryant C Yung, Gang Liu, Zhiyong Qian, Xiaoyuan Chen
Exendin-4 has been clinically exploited for treating type 2 diabetes, but the short circulation half-life and multiple daily injections limit its widespread application with respect to poor patient compliance, low efficacy, and high treatment cost. In this study, a potent long-acting release system based on biomimetic mineralization was constructed for biocompatible and sustained exendin-4 delivery. Similar to natural biomineralization, exendin-4 can be mineralized to form nano-sized mineral solids by means of the reaction between acidic amino acid residues and calcium ions in a supersaturated environment with negligible influence on peptide bioactivity...
April 24, 2017: ACS Nano
https://www.readbyqxmd.com/read/28437605/aqueously-released-graphene-oxide-embedded-in-epoxy-resin-exhibits-different-characteristics-and-phytotoxicity-of-chlorella-vulgaris-from-the-pristine-form
#5
Xiangang Hu, Weilu Kang, Li Mu
The environmental release of nanoparticles is attracting increasing attention. Graphene oxide (GO) embedded in epoxy resin (ER) is a popular composite that has been used in various fields, but the environmental release of GO-ER composites and the effects on organisms in the environment remain unknown. The present work found that GO-ER composites in water for 2-7 days resulted in the release of 0.3-2.1% GO-ER at nanoscale (2-3 nm thickness and approximately 70-130 nm lateral length). Interestingly, pristine GO quenched 30-45% hydroxyl and 12% nitroxide free radicals, whereas this capacity was not observed for the released particles from GO-ER...
April 24, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28437555/polymorphisms-of-alui-and-hin1i-loci-of-the-igf-1r-gene-and-their-genetic-effects-on-growth-traits-in-bian-chickens
#6
P F Wu, D Wang, C F Jin, X Q Zhang, H Q Wu, L Zhang, F X Ding, K Z Xie, G X Zhang
Growth traits are important economic traits in broiler chicken production. AluI and Hin1I loci are two restriction sites, which are respectively located in exons 2 and 3 of the IGF-1R gene. These two loci are significantly related to the growth traits in Jinghai Yellow chickens. In this study, a correlation analysis was performed between these two loci and the growth traits of Bian chickens. The results showed a G376A mutation at the AluI site and a C919A mutation at the Hin1I site, which respectively resulted in three genotypes AA, AB, and BB in exon 2 and three genotypes CC, CD, and DD in exon 3...
April 20, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28437394/selective-degradation-of-splicing-factor-caper%C3%AE-by-anticancer-sulfonamides
#7
Taisuke Uehara, Yukinori Minoshima, Koji Sagane, Naoko Hata Sugi, Kaoru Ogawa Mitsuhashi, Noboru Yamamoto, Hiroshi Kamiyama, Kentaro Takahashi, Yoshihiko Kotake, Mai Uesugi, Akira Yokoi, Atsushi Inoue, Taku Yoshida, Miyuki Mabuchi, Akito Tanaka, Takashi Owa
Target-protein degradation is an emerging field in drug discovery and development. In particular, the substrate-receptor proteins of the cullin-ubiquitin ligase system play a key role in selective protein degradation, which is an essential component of the anti-myeloma activity of immunomodulatory drugs (IMiDs), such as lenalidomide. Here, we demonstrate that a series of anticancer sulfonamides NSC 719239 (E7820), indisulam, and NSC 339004 (chloroquinoxaline sulfonamide, CQS) induce proteasomal degradation of the U2AF-related splicing factor coactivator of activating protein-1 and estrogen receptors (CAPERα) via CRL4(DCAF15) mediated ubiquitination in human cancer cell lines...
April 24, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28437282/inhibition-of-mid-chain-hetes-protects-against-angiotensin-ii-induced-cardiac-hypertrophy
#8
Samya Elkhatali, Zaid H Maayah, Ahmed A El-Sherbeni, Osama H Elshenawy, Ghada Abdelhamid, Sherif M Shoieb, Ayman O S El-Kadi
Recent data demonstrated the role of CYP1B1 in cardiovascular disease. It was, therefore, necessary to examine whether the inhibition of CYP1B1 and hence inhibiting the formation of its metabolites, using 2,4,3',5'-tetramethoxystilbene (TMS), would have a cardioprotective effect against angiotensin II (Ang II)-induced cardiac hypertrophy. For this purpose, male Sprague-Dawley rats were treated with Ang II with or without TMS (300 μg/kg every 3day3 i.p). Thereafter, cardiac hypertrophy and the formation of mid-chain HETEs and AA were assessed...
April 18, 2017: Journal of Cardiovascular Pharmacology
https://www.readbyqxmd.com/read/28437198/branched-chain-amino-acids-are-associated-with-insulin-resistance-independent-of-leptin-and-adiponectin-in-subjects-with-varying-degrees-of-glucose-tolerance
#9
Margery A Connelly, Justyna Wolak-Dinsmore, Robin P F Dullaart
BACKGROUND: Branched chain amino acids (BCAA) may be involved in the pathogenesis of insulin resistance and are associated with type 2 diabetes mellitus (T2DM) development. Adipokines such as leptin and adiponectin influence insulin resistance and reflect adipocyte dysfunction. We examined the extent to which the association of BCAA with insulin resistance is attributable to altered leptin and adiponectin levels in individuals with varying degrees of glucose tolerance. METHODS: BCAA were measured by nuclear magnetic resonance, whereas leptin and adiponectin were measured by immunoassay, in subjects with normal fasting glucose (n = 30), impaired fasting glucose (n = 25), and T2DM (n = 15)...
February 21, 2017: Metabolic Syndrome and related Disorders
https://www.readbyqxmd.com/read/28437100/reparameterization-of-solute-solute-interactions-for-amino-acid-sugar-systems-using-isopiestic-osmotic-pressure-molecular-dynamics-simulations
#10
Wesley Kayser Lay, Mark S Miller, Adrian Hamilton Elcock
AMBER/GLYCAM and CHARMM are popular force fields for simulations of amino acids and sugars. Here we report excessively attractive amino acid-sugar interactions in both force fields, and corrections to nonbonded interactions that match experimental osmotic pressures of mixed aqueous solutions of diglycine and sucrose. The modified parameters also improve the ∆Gtrans of diglycine from water to aqueous sucrose and, with AMBERff99SB/GLYCAM06, eliminate a caging effect seen in previous simulations of the protein ubiquitin with glucose...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28437098/interaction-of-fibrin-with-the-very-low-density-lipoprotein-receptor-further-characterization-and-localization-of-the-vldl-receptor-binding-site-in-fibrin-%C3%AE-n-domains
#11
Sergiy Yakovlev, Leonid Medved
Our recent study revealed that fibrin and the VLDL receptor (VLDLR) interact with each other through a pair of fibrin βN-domains and CR domains of the receptor and this interaction promotes transendothelial migration of leukocytes and thereby inflammation. The major objectives of the present study were to further clarify the molecular mechanism of fibrin-VLDLR interaction and to identify amino acid residues in the βN-domains involved in this interaction. Our binding experiments with the (β15-66)2 fragment, which corresponds to a pair of fibrin βN-domains, and the VLDLR(1-8) fragment consisting of eight CR domains of VLDLR, revealed that interaction between them strongly depends on ionic strength and chemical modification of all Lys or Arg residues in (β15-66)2 results in abrogation of this interaction...
April 24, 2017: Biochemistry
https://www.readbyqxmd.com/read/28437060/high-throughput-and-quantitative-measurement-of-microbial-metabolome-by-gas-chromatography-mass-spectrometry-using-automated-alkyl-chloroformate-derivatization
#12
Linjing Zhao, Yan Ni, Mingming Su, Hongsen Li, Fangcong Dong, Wenlian Chen, Runmin Wei, Lulu Zhang, Seu-Ping Guiraud, François-Pierre J Martin, Cynthia Rajani, Guoxiang Xie, Wei Jia
The ability to identify and quantify small molecule metabolites derived from gut microbial-mammalian co-metabolism is essential for the understanding of the distinct metabolic functions of the microbiome. To date, analytical protocols that quantitatively measure a complete panel of microbial metabolites in biological samples have not been established, but urgently needed by the microbiome research community. Here, we report an automated high-throughput quantitative method using a gas chromatography/time-of-flight mass spectrometry (GC/TOFMS) platform to simultaneously measure over one hundred microbial metabolites in human serum, urine, feces and Escherichia coli cell samples within 15 minutes per sample...
April 24, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28437009/conformational-changes-of-ubiquitin-under-high-pressure-conditions-a-pressure-simulated-tempering-molecular-dynamics-study
#13
Yoshiharu Mori, Yuko Okamoto
Molecular dynamics simulations for the system of ubiquitin were performed with pressure simulated tempering to study pressure-induced conformational changes of ubiquitin. The pressure dependence of ubiquitin was analyzed in a wide range of pressure from atmospheric pressure (0.1 MPa) to 1.0 GPa. The fluctuation of the distance between amino-acid residues and the distribution of a largely fluctuating distance were calculated. The large fluctuation of the L8-E34 distance induced by pressure means that the conformation of ubiquitin changes under high pressure conditions...
June 5, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28436990/tcrp1-promotes-nih-3t3-cell-transformation-by-over-activating-pdk1-and-akt1
#14
C Wang, H Liu, Q Qiu, Z Zhang, Y Gu, Z He
Tongue cancer resistance-related protein 1 (TCRP1) gene was first cloned from the multidrug resistance tongue cancer cell (Tca8113/pingyangmycin) in our lab. Our precious studies demonstrated that TCRP1 was involving in chemotherapy and radiotherapy resistance of tongue cancer cells, lung cancer cells and ovarian cancer cells. In this study, we showed that TCRP1 overexpression promotes cell transformation and tumorigenesis through hyperphosphorylation of the oncogenic kinase 3-phosphoinositide-dependent protein kinase-1 (PDK1) and AKT1, whereas inhibition of PDK1 by OSU-03012 or PDK1 small interfering RNA reversed TCRP1-mediated cell transformation...
April 24, 2017: Oncogenesis
https://www.readbyqxmd.com/read/28436674/general-dialdehyde-click-chemistry-for-amine-bioconjugation
#15
Sina Elahipanah, Paul J O'Brien, Dmitry Rogozhnikov, Muhammad N Yousaf
The development of methods for conjugating a range of molecules to primary amine functional groups has revolutionized the fields of chemistry, biology, and material science. The primary amine is a key functional group and one of the most important nucleophiles and bases used in all of synthetic chemistry. Therefore, tremendous interest in the synthesis of molecules containing primary amines and strategies to devise chemical reactions to react with primary amines has been at the core of chemical research. In particular, primary amines are a ubiquitous functional group found in biological systems as free amino acids, as key side chain lysines in proteins, and in signaling molecules and metabolites and are also present in many natural product classes...
April 24, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28436673/unique-rhizosphere-micro-characteristics-facilitate-phytoextraction-of-multiple-metals-in-soil-by-the-hyperaccumulating-plant-sedum-alfredii
#16
Dandi Hou, Kai Wang, Ting Liu, Haixin Wang, Zhi Lin, Jie Qian, Lingli Lu, Shengke Tian
Understanding the strategies that the roots of hyperaccumulating plants use to extract heavy metals from soils is important for optimizing phytoremediation. The rhizosphere characteristics of Sedum alfredii, a hyperaccumulator, were investigated 6 months after planting in weathered field soils contaminated with 5.8 μg·g-1 Cd, 1985.1 μg·g-1 Zn, 667.5 μg·g-1 Pb, and 698.8 μg·g-1 Cu. In contrast with the non-hyperaccumulating ecotype (NHE), the hyperaccumulating ecotype (HE) of S. alfredii was more tolerant to the metals and accumulated higher levels of Cd and Zn...
April 24, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28436534/a-novel-trpa1-variant-is-associated-with-carbamazepine-responsive-cramp-fasciculation-syndrome
#17
M J Nirenberg, R Chaouni, T M Biller, R M Gilbert, C Paisán-Ruiz
Cramp-fasciculation syndrome (CFS) is a rare muscle hyperexcitability syndrome that presents with muscle cramps, fasciculations, and stiffness, as well as pain, fatigue, anxiety, hyperreflexia, and paresthesias. Although familial cases have been reported, a genetic etiology has not yet been identified. We performed whole-exome sequencing followed by validation and cosegregation analyses on a father-son pair with CFS. Both subjects manifested other hypersensitivity-hyperexcitability symptoms, including asthma, gastroesophageal reflux, migraine, restless legs syndrome, tremor, cold hyperalgesia, and cardiac conduction defects...
April 24, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28436486/muscle-wasting-and-cachexia-in-heart-failure-mechanisms-and-therapies
#18
REVIEW
Stephan von Haehling, Nicole Ebner, Marcelo R Dos Santos, Jochen Springer, Stefan D Anker
Body wasting is a serious complication that affects a large proportion of patients with heart failure. Muscle wasting, also known as sarcopenia, is the loss of muscle mass and strength, whereas cachexia describes loss of weight. After reaching guideline-recommended doses of heart failure therapies, the most promising approach to treating body wasting seems to be combined therapy that includes exercise, nutritional counselling, and drug treatment. Nutritional considerations include avoiding excessive salt and fluid intake, and replenishment of deficiencies in trace elements...
April 24, 2017: Nature Reviews. Cardiology
https://www.readbyqxmd.com/read/28436444/transcriptome-profiling-of-sulfate-deprivation-responses-in-two-agarophytes-gracilaria-changii-and-gracilaria-salicornia-rhodophyta
#19
Wei-Kang Lee, Parameswari Namasivayam, Janna Ong Abdullah, Chai-Ling Ho
Seaweeds survive in marine waters with high sulfate concentration compared to those living at freshwater habitats. The cell wall polymer of Gracilaria spp. which supplies more than 50% of the world agar is heavily sulfated. Since sulfation reduces the agar quality, it is interesting to investigate the effects of sulfate deprivation on the sulfate contents of seaweed and agar, as well as the metabolic pathways of these seaweeds. In this study, two agarophytes G. changii and G. salicornia were treated under sulfate deprivation for 5 days...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28436422/rational-design-of-non-resistant-targeted-cancer-therapies
#20
Francisco Martínez-Jiménez, John P Overington, Bissan Al-Lazikani, Marc A Marti-Renom
Drug resistance is one of the major problems in targeted cancer therapy. A major cause of resistance is changes in the amino acids that form the drug-target binding site. Despite of the numerous efforts made to individually understand and overcome these mutations, there is a lack of comprehensive analysis of the mutational landscape that can prospectively estimate drug-resistance mutations. Here we describe and computationally validate a framework that combines the cancer-specific likelihood with the resistance impact to enable the detection of single point mutations with the highest chance to be responsible of resistance to a particular targeted cancer therapy...
April 24, 2017: Scientific Reports
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