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https://www.readbyqxmd.com/read/28432324/optimization-of-amino-acid-replacement-costs-by-mutational-pressure-in-bacterial-genomes
#1
Paweł Błażej, Dorota Mackiewicz, Małgorzata Grabińska, Małgorzata Wnętrzak, Paweł Mackiewicz
Mutations are considered a spontaneous and random process, which is important component of evolution because it generates genetic variation. On the other hand, mutations are deleterious leading to non-functional genes and energetically costly repairs. Therefore, one can expect that the mutational pressure is optimized to simultaneously generate genetic diversity and preserve genetic information. To check if empirical mutational pressures are optimized in these ways, we compared matrices of nucleotide mutation rates derived from bacterial genomes with their best possible alternatives that minimized or maximized costs of amino acid replacements associated with differences in their physicochemical properties (e...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28431152/insights-into-the-existence-of-isomeric-plastomes-in-cupressoideae-cupressaceae
#2
Xiao-Jian Qu, Chung-Shien Wu, Shu-Miaw Chaw, Ting-Shuang Yi
The cypress family (Cupressaceae) possesses highly rearranged plastomes that lack a pair of large inverted repeats typically found in land plants. A few cypress species have been reported to contain isomeric plastomes, but whether the existence of isomeric plastomes is ubiquitous in the family remains to be investigated with a broader taxon sampling. In this study, we sequenced the complete plastomes of ten species in Cupressoideae, the largest cypress subfamily. Cupressoideae showed relatively accelerated rates of substitutions at both nonsynonymous and synonymous sites as compared with other subfamilies of Cupressaceae...
April 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28431121/starbeast2-brings-faster-species-tree-inference-and-accurate-estimates-of-substitution-rates
#3
Huw A Ogilvie, Remco R Bouckaert, Alexei J Drummond
Fully Bayesian multispecies coalescent (MSC) methods like *BEAST estimate species trees from multiple sequence alignments. Today thousands of genes can be sequenced for a given study, but using that many genes with *BEAST is intractably slow. An alternative is to use heuristic methods which compromise accuracy or completeness in return for speed. A common heuristic is concatenation, which assumes that the evolutionary history of each gene tree is identical to the species tree. This is an inconsistent estimator of species tree topology, a worse estimator of divergence times, and induces spurious substitution rate variation when incomplete lineage sorting is present...
April 14, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28430414/dynamic-and-energetic-signatures-of-adenine-tracts-in-a-ra-dt-rna-dna-hybrid-and-in-homologous-rna-dna-rna-rna-and-dna-dna-double-helices
#4
Yuegao Huang, Irina M Russu
Nuclear magnetic resonance spectroscopy and proton exchange are being used to characterize the opening reactions of individual base pairs in the RNA-DNA hybrid 5'-rGCGAUAAAAAGGCC-3'/5'-dGGCCTTTTTATCGC-3'. The hybrid contains a central tract of five rA-dT base pairs. The rates and the equilibrium constant of the opening reaction for each base pair are determined from the dependence of the exchange rates of imino protons on ammonia concentration, at 10°C. The results are compared to those previously obtained by our laboratory for three homologous duplexes of the same base sequence (except for the appropriate T/U substitution), containing tracts of dA-rU, rA-rU or dA-dT base pairs...
April 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28429503/cleavage-of-a-p-p-double-bond-mediated-by-n-heterocyclic-carbenes
#5
Naoki Hayakawa, Kazuya Sadamori, Shota Tsujimoto, Miho Hatanaka, Tomonari Wakabayashi, Tsukasa Matsuo
The reaction of the bulky diphosphenes (Rind)P=P(Rind) (1; Rind=1,1,3,3,5,5,7,7-octa-R-substituted s-hydrindacen-4-yl) with two molecules of N-heterocyclic carbene (NHC; 1,3,4,5-tetramethylimidazol-2-ylidene) resulted in the quantitative formation of the NHC-bound phosphinidenes NHC→P(Rind) (2), along with the cleavage of the P=P double bond. The reaction times are dependent on the steric size of the Rind groups (11 days for 2 a (R=Et) and 2 h for 2 b (R=Et, Me) at room temperature). The mechanism for the double bond-breaking is proposed to proceed via the formation of the NHC-coordinated, highly polarized diphospehenes 3 as an intermediate...
April 21, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28429390/microporous-polyamide-membranes-for-molecular-sieving-of-nitrogen-from-volatile-organic-compounds
#6
Haoli Zhou, Fei Tao, Quan Liu, Chunxin Zong, Wenchao Yang, Xingzhong Cao, Wanqin Jin, Nanping Xu
Microporous polymer membranes continue to receive tremendous attention for energy-efficient gas separation processes owing to their high separation performances. A new network microporous polyamide membrane with good molecular-sieving performance for the separation of N2 from a volatile organic compound (VOC) mixture is described. Triple-substituted triptycene was used as the main monomer to form a fisherman's net-shaped polymer, which readily forms a composite membrane by solution casting. This membrane exhibited outstanding separation performance and good stability for the molecular-sieving separation of N2 over VOCs such as cyclohexane...
April 21, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28429059/a-novel-method-to-recover-inclusion-body-protein-from-recombinant-e-coli-fed-batch-processes-based-on-phage-%C3%AE-x174-derived-lysis-protein-e
#7
Daniela Ehgartner, Patrick Sagmeister, Timo Langemann, Andrea Meitz, Werner Lubitz, Christoph Herwig
Production of recombinant proteins as inclusion bodies is an important strategy in the production of technical enzymes and biopharmaceutical products. So far, protein from inclusion bodies has been recovered from the cell factory through mechanical or chemical disruption methods, requiring additional cost-intensive unit operations. We describe a novel method that is using a bacteriophage-derived lysis protein to directly recover inclusion body protein from Escherichia coli from high cell density fermentation process: The recombinant inclusion body product is expressed by using a mixed feed fed-batch process which allows expression tuning via adjusting the specific uptake rate of the inducing substrate...
April 20, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28428609/socket-preservation
#8
L Fee
Socket preservation maintains bone volume post-extraction in anticipation of an implant placement or fixed partial denture pontic site. This procedure helps compensate for the resorption of the facial bone wall. Socket preservation should be considered when implant placement needs to be delayed for patient or site-related reasons. The ideal healing time before implant placement is six months. Socket preservation can reduce the need for later bone augmentation. By reducing bone resorption and accelerating bone formation it increases implant success and survival...
April 21, 2017: British Dental Journal
https://www.readbyqxmd.com/read/28427865/dynamics-and-energetics-of-cyanobacterial-photosystem-i-ferredoxin-complexes-in-different-redox-states
#9
Pierre Sétif, Risa Mutoh, Genji Kurisu
Fast turnover of ferredoxin/Fd reduction by photosystem-I/PSI requires that it dissociates rapidly after it has been reduced by PSI:Fd intracomplex electron transfer. The rate constants of Fd dissociation from PSI have been determined by flash-absorption spectroscopy with different combinations of cyanobacterial PSIs and Fds, and different redox states of Fd and of the terminal PSI acceptor (FAFB). Newly obtained values were derived firstly from the fact that the dissociation constant between PSI and redox-inactive gallium-substituted Fd increases upon (FAFB) reduction and secondly from the characterization and elucidation of a kinetic phase following intracomplex Fd reduction to binding of oxidized Fd to PSI, a process which is rate-limited by the foregoing dissociation of reduced Fd from PSI...
April 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28427322/dental-pulp-pluripotent-like-stem-cells-dppsc-a-new-stem-cell-population-with-chromosomal-stability-and-osteogenic-capacity-for-biomaterials-evaluation
#10
Raquel Núñez-Toldrà, Ester Martínez-Sarrà, Carlos Gil-Recio, Miguel Ángel Carrasco, Ashraf Al Madhoun, Sheyla Montori, Maher Atari
BACKGROUND: Biomaterials are widely used to regenerate or substitute bone tissue. In order to evaluate their potential use for clinical applications, these need to be tested and evaluated in vitro with cell culture models. Frequently, immortalized osteoblastic cell lines are used in these studies. However, their uncontrolled proliferation rate, phenotypic changes or aberrations in mitotic processes limits their use in long-term investigations. Recently, we described a new pluripotent-like subpopulation of dental pulp stem cells derived from the third molars (DPPSC) that shows genetic stability and shares some pluripotent characteristics with embryonic stem cells...
April 21, 2017: BMC Cell Biology
https://www.readbyqxmd.com/read/28425716/reactions-of-n2o5-with-salty-and-surfactant-coated-glycerol-interfacial-conversion-of-br-to-br2-mediated-by-alkylammonium-cations
#11
Michael A Shaloski, Joseph R Gord, Sean Staudt, Sarah L Quinn, Timothy H Bertram, Gilbert Maker Nathanson
Gas-liquid scattering and product-yield experiments are used to investigate reactions of N2O5 with glycerol containing Br(-) and surfactant ions. N2O5 oxidizes Br(-) to Br2 for every solution tested: 2.7 M NaBr, 0.03 M tetrahexylammonium bromide (THABr), 0.03 M THABr + 0.5 M NaBr, 0.03 M THABr + 0.5 M NaCl, 0.03 M THABr + 0.01 M sodium dodecyl sulfate (SDS), and 0.01 M cetyltrimethylammonium bromide (CTABr). N2O5 also reacts with glycerol itself to produce mono- and dinitroglycerin. Surface tension measurements indicate that 0...
April 20, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28423875/adaptive-selection-at-agouti-gene-inferred-breed-specific-selection-signature-within-the-indigenous-goat-populations
#12
Hafiz Ishfaq Ahmad, Guiqiong Liu, Xunping Jiang, Chenhui Liu, Xu Fangzheng, Yuqing Chong, Nabeel Ijaz, Huang Huarong
Objective: The aim of this study was to calculate selection signatures at possible loci leading to population differentiation, as well as pattern of selection of agouti gene within the local goat breeds and its correlation among other animal species to reveal molecular evolution. Methods: The high Fst outlier method corresponding to Fst distribution was used to identify the loci subject to positive selection. According to the empirical distribution of Fst estimates, we selected the SNPs having high Fst outlier corresponded to the upper 1% of the distribution as the loci under selection...
April 19, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28423873/replacing-groundnut-cake-with-gluten-meals-of-rice-and-maize-in-diets-for-growing-sahiwal-cattle
#13
Tariq A Malik, S S Thakur, M S Mahesh, R K Yogi
Objective: This experiment aimed to investigate the effect of isonitrogenous replacement of Groundnut cake (GNC) by Rice gluten meal (RGM) and Maize gluten meal (MGM) at 75% level on nutrient intake, apparent digestibility, growth performance and related blood constituents in growing Sahiwal cattle. Methods: Eighteen Sahiwal calves were divided into three groups, based on average body weight (BW: 87.24 kg) and age (6-12 m), and treatments were assigned to the different groups randomly...
April 19, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28423022/bioactivity-and-structure-activity-relationship-of-cinnamic-acid-esters-and-their-derivatives-as-potential-antifungal-agents-for-plant-protection
#14
Kun Zhou, Dongdong Chen, Bin Li, Bingyu Zhang, Fang Miao, Le Zhou
A series of cinnamic acid esters and their derivatives were synthesized and evaluated for antifungal activities in vitro against four plant pathogenic fungi by using the mycelium growth rate method. Structure-activity relationship was derived also. Almost all of the compounds showed some inhibition activity on each of the fungi at 0.5 mM. Eight compounds showed the higher average activity with average EC50 values of 17.4-28.6 μg/mL for the fungi than kresoxim-methyl, a commercial fungicide standard, and ten compounds were much more active than commercial fungicide standards carbendazim against P...
2017: PloS One
https://www.readbyqxmd.com/read/28422442/effect-of-hepatitis-b-virus-subgenotype-on-antiviral-response-in-nucleoside-treated-hepatitis-b-e-antigen-positive-patients
#15
Sheng Shen, Xieer Liang, Kamal Hamed, Yasuhito Tanaka, Katsumi Omagari, Rong Fan, Qing Xie, Deming Tan, Bin Zhou, Ji-Dong Jia, Jinlin Hou, Jian Sun
BACKGROUND: Previous studies have reported that hepatitis B virus (HBV) genotype is not a predictor of treatment response with nucleos(t)ide analogue (NUC) therapy. However, the impact of subgenotype on treatment response is unknown. AIM: To identify the effect of HBV subgenotype on treatment response. METHODS: In this retrospective study, the derivation dataset comprised patients from the EFFORT study (NCT00962533) telbivudine monotherapy group; patients infected with genotypes B or C from the GLOBE (NCT00057265) and 015 (NCT00131742) studies formed the validation dataset...
April 19, 2017: Hepatology Research: the Official Journal of the Japan Society of Hepatology
https://www.readbyqxmd.com/read/28421616/the-validity-of-the-montgomery-asberg-depression-rating-scale-in-an-inpatient-sample-with-alcohol-dependence
#16
Breanne Hobden, Melanie L Schwandt, Mariko Carey, Mary R Lee, Mehdi Farokhnia, Sofia Bouhlal, Christopher Oldmeadow, Lorenzo Leggio
BACKGROUND: The Montgomery-Asberg Depression Rating Scale (MADRS) is commonly used to examine depressive symptoms in clinical settings, including facilities treating patients for alcohol addiction. No studies have examined the validity of the MADRS compared to an established clinical diagnostic tool of depression in this population. This study aimed to examine: 1) the validity of the MADRS compared to a clinical diagnosis of a depressive disorder (using the Structured Clinical Interview for DSM-IV (SCID)) in patients seeking treatment for alcohol dependence (AD); 2) whether the validity of the MADRS differs by type of SCID-based diagnosis of depression; and 3) which items contribute to the optimal predictive model of the MADRS compared to a SCID diagnosis of a depressive disorder...
April 19, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/28421567/early-biomarker-response-and-patient-preferences-to-oral-and-intramuscular-vitamin-b12-substitution-in-primary-care-a-randomised-parallel-group-trial
#17
Corina Metaxas, Deborah Mathis, Cyrill Jeger, Kurt Eduard Hersberger, Isabelle Arnet, Philipp Walter
BACKGROUND: Vitamin B12 (VB12) deficiency can be treated with oral high-dose substitution or intramuscular (i.m.) injection of VB12. Whenever alternative routes of administration exist, patient preferences should be considered when choosing the treatment. We aimed to assess outpatient preferences towards oral or IM VB12 substitution and confirm noninferiority of early biomarker response with oral treatment, in a typical primary care population. METHODS: Prospective randomised nonblinded parallel-group trial...
April 19, 2017: Swiss Medical Weekly
https://www.readbyqxmd.com/read/28419941/pamam-generation-4-incorporated-gelatin-3d-matrix-as-an-improved-dermal-substitute-for-skin-tissue-engineering
#18
Somnath Maji, Tarun Agarwal, Tapas Kumar Maiti
The study explored the prospects of PAMAM (generation 4) applicability in gelatin based scaffolds for skin tissue engineering. The effect of PAMAM on physico-chemical and biological characteristics of gelatin scaffolds was evaluated. Gelatin scaffolds (with/without PAMAM) were prepared by lyophilization, chemically crosslinked by glutaraldehyde and characterized for their morphology (pore size), chemical features (bond nature), water adsorption, biodegradation and biological compatibility. The study demonstrated that addition of PAMAM did not significantly alter the pore size distribution or porosity of the scaffolds...
April 5, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28419579/erdj3-has-an-essential-role-for-z-variant-alpha-1-antitrypsin-degradation
#19
Nazli Khodayari, George Marek, Yuanqing Lu, Karina Krotova, Rejean Liqun Wang, Mark Brantly
Alpha-1-antitrypsin deficiency (AATD) is an inherited disease characterized by emphysema and liver disease. AATD is most often caused by a single amino acid substitution at amino acid 342 in the mature protein, resulting in the Z mutation of the alpha-1-antitrypsin gene (ZAAT). This substitution is associated with misfolding and accumulation of ZAAT in the endoplasmic reticulum (ER) of hepatocytes and monocytes, causing a toxic gain of function. Retained ZAAT is eliminated by ER-associated degradation and autophagy...
April 17, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28418755/recommendations-for-adopting-the-international-code-of-marketing-of-breast-milk-substitutes-into-u-s-policy
#20
Jessica Soldavini, Lindsey Smith Taillie
In 1981, the World Health Organization adopted the International Code of Marketing of Breast-milk Substitutes ( International Code), with subsequent resolutions adopted since then. The International Code contributes to the safe and adequate provision of nutrition for infants by protecting and promoting breastfeeding and ensuring that human milk substitutes, when necessary, are used properly through adequate information and appropriate marketing and distribution. Despite the World Health Organization recommendations for all member nations to implement the International Code in its entirety, the United States has yet to take action to translate it into any national measures...
April 1, 2017: Journal of Human Lactation: Official Journal of International Lactation Consultant Association
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