keyword
MENU ▼
Read by QxMD icon Read
search

folding

keyword
https://www.readbyqxmd.com/read/29224075/a-bloody-primer-analysis-of-rna-seq-from-tissue-admixtures
#1
Casey P Shannon, Chen Xi Yang, Scott J Tebbutt
RNA sequencing is a powerful technology that allows for unbiased profiling of the entire transcriptome. The analysis of transcriptome profiles from heterogeneous tissues, cell admixtures with relative proportions that can vary several fold across samples, poses a significant challenge. Blood is perhaps the most egregious example. Here, we describe in detail a computational pipeline for RNA-Seq data preparation and statistical analysis, with development of a means of estimating the cell type composition of blood samples from their bulk RNA-Seq profiles...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223921/metabolism-and-pharmacokinetics-of-alantolactone-and-isoalantolactone-in-rats-thiol-conjugation-as-a-potential-metabolic-pathway
#2
Bailun Zhou, Ji Ye, Niao Yang, Liping Chen, Zhiguo Zhuo, Ling Mao, Qun Liu, Gongcai Lan, Jing Ning, Guangbo Ge, Ling Yang, Yunheng Shen, Shumei Wang, Weidong Zhang
Alantolactone (AL) and isoalantolactone (IAL), two major active sesquiterpene lactones isolated from Radix Inulae extract, have a wide range of pharmacological activities. The predominant metabolic pathway of AL and IAL observed was glutathione (GSH) conjugation in vitro, which could occur in the absence of metabolic enzymes. Non-enzymatic conjugation with cysteine (Cys) couldalso be observed. Four metabolites (AL-GSH, AL-Cys, IAL-GSH, IAL-Cys) were subsequently isolated and confirmed by nuclear magnetic resonance (NMR)...
December 2, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/29223849/subcellular-distribution-of-molybdenum-ultrastructural-and-antioxidative-responses-in-soybean-seedlings-under-excess-molybdenum-stress
#3
Shoujun Xu, Chengxiao Hu, Qiling Tan, Shiyu Qin, Xuecheng Sun
Some studies have shown that excess molybdenum (Mo) could produce toxic effects on plants. However, little is known about the subcellular distribution of Mo and cell ultrastructure within plants under excess Mo stress. Here, we comprehensively analyzed the changes of Mo distribution in subcellular fractions, cell ultrastructure and antioxidant enzymes in leaves and roots of soybean seedlings in response to excess Mo stress. The results showed that roots exhibited higher Mo accumulation than leaves at the 100 mg L-1 Mo level, about 38...
December 5, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29223807/design-synthesis-and-biological-evaluation-of-deuterated-phenylpropionic-acid-derivatives-as-potent-and-long-acting-free-fatty-acid-receptor-1-agonists
#4
Zheng Li, Chunxia Liu, Xue Xu, Wei Shi, Huilan Li, Yuxuan Dai, Xingguang Cai, Wenlong Huang, Hai Qian
The free fatty acid receptor 1 (FFA1) is a potential target due to its function in enhancement of glucose-stimulated insulin secretion. Takeda's compound 1 has robustly in vitro activity for FFA1, but it has been suffered from poor pharmacokinetic (PK) profiles because the phenylpropanoic acid is vulnerable to β-oxidation. To identify orally available agonists, we tried to interdict the metabolically labile group by incorporating two deuterium atoms at the α-position of phenylpropionic acid. Interestingly, the differences of physicochemical properties between hydrogen and deuterium are quite small, but there are many differences in the structure-activity relationship between phenylpropionic acid series and present deuterated series...
December 5, 2017: Bioorganic Chemistry
https://www.readbyqxmd.com/read/29223776/impact-of-edaphic-factors-and-nutrient-management-on-the-hepatoprotective-efficiency-of-carlinoside-purified-from-pigeon-pea-leaves-an-evaluation-of-ugt1a1-activity-in-hepatitis-induced-organelles
#5
Subhasish Das, K Charan Teja, Sandip Mukherjee, Soma Seal, Rajesh Kumar Sah, Buddhadeb Duary, Ki-Hyun Kim, Satya Sundar Bhattacharya
Carlinoside is a unique compound well-known for its excellent curative potential in hepatitis. There is a substantial research gap regarding the medicinal use of carlinoside, as its concentrations are greatly variable (depending on locality). We cultivated Cajanus cajan using vermicompost as a major organic amendment at two locations (Sonitpur and Birbhum) with different soil types, but identical climate conditions. Sonitpur soils were richer in soil organic C (SOC), enzyme activation, and N/P content than Birbhum...
December 7, 2017: Environmental Research
https://www.readbyqxmd.com/read/29223533/atomic-structure-and-enzymatic-insights-into-the-vancomycin-resistant-enterococcus-faecalis-v583-alkylhydroperoxide-reductase-subunit-c
#6
Ankita Pan, Asha Manikkoth Balakrishna, Wilson Nartey, Andreas Kohlmeier, Phat Vinh Dip, Shashi Bhushan, Gerhard Grüber
The Enterococcus faecalis alkyl hydroperoxide reductase complex (AhpR) with its subunits AhpC (EfAhpC) and AhpF (EfAhpF) are of paramount importance to restore redox homeostasis. Recently, the novel phenomenon of swapping of the catalytic domains of EfAhpF was uncovered. Here, we visualized its counterpart EfAhpC (187 residues) from the vancomycin-resistant E. faecalis (V583) bacterium by electron microscopy and demonstrate, that in contrast to other bacterial AhpCs, EfAhpC forms a stable decamer-ring irrespective of the redox state...
December 6, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29223500/impact-of-chronic-kidney-disease-on-mortality-in-adults-undergoing-balloon-aortic-valvuloplasty
#7
Puja B Parikh, Samantha Novotny, Allen Jeremias, Javed Butler, Jie Yang, Donglei Yin, Luis Gruberg
BACKGROUND: Balloon aortic valvuloplasty (BAV) is often utilized as a bridge prior to surgical or transcatheter aortic valve replacement. Chronic kidney disease (CKD) is commonly present in patients with aortic stenosis, however, its association with outcomes following BAV has not been well studied. Accordingly, we sought to assess the impact of CKD on mortality in adults undergoing BAV. METHODS: The Nationwide Inpatient Sample was screened for hospitalizations involving adults undergoing BAV from 2006 to 2012...
October 26, 2017: Cardiovascular Revascularization Medicine: Including Molecular Interventions
https://www.readbyqxmd.com/read/29223416/cost-variation-across-centers-for-the-norwood-operation
#8
Kimberly E McHugh, Sara K Pasquali, Matthew A Hall, Mark A Scheurer
BACKGROUND: The Norwood operation is associated with high health care utilization, and prior studies reported substantial variability in Norwood costs across centers. However, specific factors driving this cost variation are unclear. We assessed center variability in Norwood costs and underlying mechanisms in a multicenter cohort. METHODS: Clinical data from the Pediatric Heart Network Single Ventricle Reconstruction trial were linked with cost data from the Children's Hospital Association Inpatient Essentials database...
December 6, 2017: Annals of Thoracic Surgery
https://www.readbyqxmd.com/read/29223402/genetic-regulation-mechanism-of-the-yjdf-riboswitch
#9
Sha Gong, Yanli Wang, Zhen Wang, Yujie Wang, Wenbing Zhang
The yjdF riboswitch resides in potential 5' UTRs of homologues of protein-coding gene yjdF in Firmicutes. Unlike other 30 riboswitch classes previously validated, this riboswitch class, can sense and bind to a broad collection of azaaromatic ligands. Among these compounds, some do activate production of yjdF protein driven by the riboswitch, while others are out of riboswitch-mediated modulation possibly because of the toxicity at high ligand concentrations. By incorporating the structures with pseudoknots and ligand binding kinetics into the co-transcriptional folding theory, we theoretically studied the co-transcriptional folding behaviors of the yjdF riboswitch from Bacillus subtilis at different transcription conditions...
December 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29223161/cell-free-expression-purification-and-characterization-of-the-functional-%C3%AE-2-adrenergic-receptor-for-multianalyte-detection-of-%C3%AE-agonists
#10
Jian Wang, Yuan Liu, Junhua Zhang, Zhengzheng Han, Wei Wang, Yang Liu, Dong Wei, Wei Huang
Large-scale expression of β2-adrenergic receptor (β2-AR) in functional form is necessary for establishment of receptor assays for detecting illegally abused β-adrenergic agonists (β-agonists). Cell-based heterologous expression systems have manycritical difficulties in synthesizing this membrane protein, such as low protein yields and aberrant folding. To overcome these challenges, the main objective of the present work was to synthesize large amounts of functional β2-AR in a cell-free system based on Escherichia coli extracts...
November 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29223157/self-organization-of-recombinant-membrane-porin-ompf-from-yersinia-pseudotuberculosis-in-aqueous-environments
#11
E V Sidorin, V A Khomenko, N Yu Kim, P S Dmitrenok, A M Stenkova, O D Novikova, T F Solov'eva
Recombinant porin OmpF (an integral protein of bacterial outer membrane) from Yersinia pseudotuberculosis was synthesized in Escherichia coli cells as inclusion bodies. By combining the methods of anion-exchange and gel filtration chromatographies, recombinant OmpF (rOmpF) was isolated as an individual protein in its denatured state, and its characteristic properties (molecular mass, N-terminal amino acid sequence, and hydrodynamic radius of the protein in 8 M urea solution) were determined. According to the data of gel filtration, dynamic light scattering, optical spectroscopy, and binding of the hydrophobic fluorescent probe 8-anilino-1-naphthalenesulfonic acid, the rOmpF is fully unfolded in 8 M urea and exists in random coil conformation...
November 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29223154/antiinflammatory-effect-of-rosiglitazone-via-modulation-of-mrna-stability-of-interleukin-10-and-cyclooxygenase-2-in-astrocytes
#12
E V Pankevich, A A Astakhova, D V Chistyakov, M G Sergeeva
Investigation of molecular mechanisms of proinflammatory stimuli signaling in astrocytes is important for understanding their role in pathogenesis of central nervous system diseases as well as in functioning of the innate immunity system in non-immune cells. Here we show that lipopolysaccharide (LPS) stimulation of primary rat astrocytes led to conventional inflammatory response: increase in both proinflammatory (tumor necrosis factor, TNFα; prostaglandin E2, PGE2) and antiinflammatory marker (interleukin 10, IL-10) levels...
November 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29223147/the-unmet-provision-of-allergy-services-in-hong-kong-impairs-capability-for-allergy-prevention-implications-for-the-asia-pacific-region
#13
Tak-Hong Lee, Ting-Fan Leung, Gary Wong, Marco Ho, Jaime Rosa Duque, Philip Hei Li, Chak-Sing Lau, Wai-Fan Lam, Adrian Wu, Eric Chan, Christopher Lai, Yu-Lung Lau
There is a high and rising prevalence of many allergic diseases in the Asia Pacific, including Hong Kong, which is unmatched by a commensurate provision of clinical allergy services. In the last 3 years, the allergy profile in Hong Kong has increased due to greater public engagement and more frequent educational activities, scientific outputs and publication of local guidelines on allergy prevention, diagnosis and treatment. Two new drug allergy clinics have been established in public hospitals, and for the first time in 20 years, Hong Kong has its first trainee in adult allergy...
December 10, 2017: Asian Pacific Journal of Allergy and Immunology
https://www.readbyqxmd.com/read/29223135/simultaneous-anti-diabetic-and-anti-vascular-calcification-activity-of-nocardia-sp-utmc-751
#14
Fatemeh Salimi, Saeedeh Jafari-Nodooshan, Nazanin Zohourian, Sedighe Kolivand, Javad Hamedi
Alpha-amylase can act as a significant player in causing hyperglycemia, leading to protein glycation, which is the main complication in this condition, besides causing vascular calcification (VC), an important vascular failure caused due to thisIn order to find a natural source of the biocompounds with inhibitory effects on alpha-amylase,, fifteen fermentation broth extracts of actinobacteria (FBEA) (200 μg mL-1 ) have been screened. Finally, the effects of the most efficient FBE have been investigated on osteopontin (OPN, a VC marker) mRNA level in the vascular smooth muscle cells under the calcification conditions, and the chemical constituents of the most efficient FBE were analyzed using GC-MS analysis...
December 9, 2017: Letters in Applied Microbiology
https://www.readbyqxmd.com/read/29223051/ultrasensitive-colorimetric-immunoassay-for-hcg-detection-based-on-dual-catalysis-of-au-pt-core-shell-nanoparticle-functionalized-by-horseradish-peroxidase
#15
Weiguo Wang, Yake Zou, Jinwu Yan, Jing Liu, Huixiong Chen, Shan Li, Lei Zhang
In this paper, an ultrasensitive colorimetric biosensor for human chorionic gonadotrophin (hCG) detection was designed from bottom-up method based on the dual catalysis of the horseradish peroxidase (HRP) and Au@Pt nanoparticles (NPs) relative to H2O2-TEM system. HRP and monoclonal mouse anti-hCG antibody (β-submit, mAb1) were co-immobilized onto the Au@Pt NP surface to improve catalytic efficiency and specificity, which formed a dual functionalized Au@Pt-HRP probe with the mean size of 42.8nm (D50). The colorimetric immunoassay was developed for the hCG detection, and the Au@Pt-HRP probe featured a higher sensitivity in the concentration range of 0...
December 5, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29223029/design-synthesis-and-evaluation-of-novel-n-hydroxybenzamides-n-hydroxypropenamides-incorporating-quinazolin-4-3h-ones-as-histone-deacetylase-inhibitors-and-antitumor-agents
#16
Doan Thanh Hieu, Duong Tien Anh, Nguyen Minh Tuan, Pham-The Hai, Le-Thi-Thu Huong, Jisung Kim, Jong Soon Kang, Tran Khac Vu, Phan Thi Phuong Dung, Sang-Bae Han, Nguyen-Hai Nam, Nguyen-Dang Hoa
In our search for novel small molecules targeting histone deacetylases, we have designed and synthesized several series of novel N-hydroxybenzamides/N-hydroxypropenamides incorporating quinazolin-4(3H)-ones (4a-h, 8a-d, 10a-d). Biological evaluation showed that these hydroxamic acids were generally cytotoxic against three human cancer cell lines (SW620, colon; PC-3, prostate; NCI-H23, lung cancer). It was found that the N-hydroxypropenamides (10a-d) were the most potent, both in term of HDAC inhibition and cytotoxicity...
December 5, 2017: Bioorganic Chemistry
https://www.readbyqxmd.com/read/29223024/genomic-integration-and-expression-of-the-aggregatibacter-actinomycetemcomitans-catalase-gene-in-aggregatibacter-aphrophilus
#17
Yuting Alice Yang, Ya-An Cheng, Casey Chen
OBJECTIVE: To test the hypothesis that virulence genes of Aggregatibacter actinomycetemcomitans can be expressed and confer fitness advantages in the closely related Aggregatibacter aphrophilus. DESIGN: Clinical isolates of A. aphrophilus were screened for natural competence with marked genomic DNA from A. actinomycetemcomitans and A. aphrophilus. The gene katA of A. actinomycetemcomitans D7S-1 and its flanking regions were constructed and inserted into a comparable locus in the genome of a naturally competent A...
December 5, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/29223015/thiamine-accumulation-and-thiamine-triphosphate-decline-occur-in-parallel-with-atp-exhaustion-during-postmortem-aging-of-pork-muscles
#18
S Muroya, M Oe, K Ojima
We aimed to clarify the mechanisms affecting postmortem thiamine and its phosphoester contents in major edible pork muscles, namely the longissimus lumborum (LL) in addition to vastus intermedius (VI). Metabolomic analysis by capillary electrophoresis-time of flight mass spectrometry revealed that the level of thiamine triphosphate (ThTP), approximately 1.8-fold higher in LL than in VI muscle at 0h postmortem, declined in the first 24h, resulting in an undetectable level at 168h postmortem in both muscles. In contrast, the thiamine content in both muscles increased after 24h postmortem during the aging process...
December 2, 2017: Meat Science
https://www.readbyqxmd.com/read/29223008/single-molecule-force-spectroscopy-a-new-tool-for-bioinorganic-chemistry
#19
REVIEW
Hongbin Li, Peng Zheng
Metalloproteins are essential in biology. The incorporation of metal ion into metalloproteins significantly expands protein functionality and enhances protein stability. Over the last few years, atomic force microscopy-based single molecule force spectroscopy (SMFS) has evolved into a unique tool allowing for probing metalloproteins and metalligand bonds one molecule/bond at a time. Mechanical strength of a wide variety of metalligand bonds has been measured in metal-ligand complexes as well as in metalloproteins, providing detailed information of their underlying free energy profiles and the influence of the protein environment on the bond strength...
December 6, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/29222954/evaluation-of-motion-artifact-metrics-for-coronary-ct-angiography
#20
Hongfeng Ma, Eric Gros, Aniko Szabo, Scott G Baginski, Zachary R Laste, Naveen M Kulkarni, Darin Okerlund, Taly G Schmidt
PURPOSE: This study quantified the performance of coronary artery motion artifact metrics relative to human observer ratings. Motion artifact metrics have been used as part of motion correction and best-phase selection algorithms for Coronary Computed Tomography Angiography (CCTA). However, the lack of ground truth makes it difficult to validate how well the metrics quantify the level of motion artifact. This study investigated five motion artifact metrics, including two novel metrics, using a dynamic phantom, clinical CCTA images, and an observer study that provided ground truth motion artifact scores from a series of pairwise comparisons...
December 9, 2017: Medical Physics
keyword
keyword
38814
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"