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https://www.readbyqxmd.com/read/28454482/effects-of-environmental-factors-and-metallic-electrodes-on-ac-electrical-conduction-through-dna-molecule
#1
S Abdalla, A Obaid, F M Al-Marzouki
BACKGROUND: Deoxyribonucleic acid (DNA) is one of the best candidate materials for various device applications such as in electrodes for rechargeable batteries, biosensors, molecular electronics, medical- and biomedical-applications etc. Hence, it is worthwhile to examine the mechanism of charge transport in the DNA molecule, however, still a question without a clear answer is DNA a molecular conducting material (wire), semiconductor, or insulator? The answer, after the published data, is still ambiguous without any confirmed and clear scientific answer...
December 2017: Nanoscale Research Letters
https://www.readbyqxmd.com/read/28454466/identification-of-molecular-characteristics-induced-by-radiotherapy-in-rectal-cancer-based-on-microarray-data
#2
Chang Ge, Mengxia Wu, Guifang Chen, Guanying Yu, Dehui Ji, Shaozhao Wang
The present study aimed to reveal the molecular characteristics induced by radiotherapy in rectal cancer at the transcriptome level. Microarray data (ID, GSE26027) downloaded from the Gene Expression Omnibus database were re-analyzed to identify differentially expressed genes (DEGs) between rectal cancer tissues during and prior to radiotherapy. The DEGs were then inputted into the database for annotation, visualization and integrated discovery, an online tool to perform enrichment analyses, and into the search tool for the retrieval of interacting genes/proteins database to identify protein-protein interactions (PPIs)...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28453939/all-atom-molecular-dynamics-simulations-of-peptide-amphiphile-assemblies-that-spontaneously-form-twisted-and-helical-ribbon-structures
#3
Cheng-Tsung Lai, Nathaniel L Rosi, George C Schatz
Self-assembly of peptide amphiphiles (PAs) has been an active research area as the assemblies can be programmed into various shaped nanostructures. Although cylindrical micelles are common structures, gold-binding peptide conjugates PEPAu can self-assemble into chiral nanofibers with single or double helices. When gold nanoparticles bind to the helices, the resulting chiral nanoparticle assemblies have a collective plasmonic circular dichroism signal that can serve as nanoscale circular polarizers or chiroptical sensors...
April 28, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28453914/the-shape-of-things-to-come-the-formation-of-modulated-nematic-mesophases-at-various-length-scales
#4
Richard J Mandle
The twist-bend nematic phase is a recently discovered liquid-crystalline phase that exhibits macroscopic chirality even when formed from achiral materials, and as such presents a unique testbed for studies concerning the spontaneous breaking of mirror symmetry in soft matter. It is primarily exhibited by materials whose molecular structure is composed of two rigid aromatic units (such as biphenyl connected by a flexible spacer). The local structure of the NTB phase is nematic-like - with molecules having an average orientational order but no positional order - with a nanoscale helix where the pitch is of the order of several nanometres...
April 28, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28448050/single-molecule-analysis-of-laser-localized-psoralen-adducts
#5
Jing Huang, Himabindu Gali, Julia Gichimu, Marina A Bellani, Durga Pokharel, Manikandan Paramasivam, Michael M Seidman
The DNA Damage Response (DDR) has been extensively characterized in studies of double strand breaks (DSBs) induced by laser micro beam irradiation in live cells. The DDR to helix distorting covalent DNA modifications, including interstrand DNA crosslinks (ICLs), is not as well defined. We have studied the DDR stimulated by ICLs, localized by laser photoactivation of immunotagged psoralens, in the nuclei of live cells. In order to address fundamental questions about adduct distribution and replication fork encounters, we combined laser localization with two other technologies...
April 20, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28445763/myosin-rod-hypophosphorylation-and-cb-kinetics-in-papillary-muscles-from-a-tnc-a8v-ki-mouse-model
#6
Masataka Kawai, Jamie R Johnston, Tarek Karam, Li Wang, Rakesh K Singh, Jose R Pinto
The cardiac troponin C (TnC)-A8V mutation is associated with hypertrophic and restrictive cardiomyopathy (HCM and RCM) in human and mice. The residue affected lies in the N-helix, a region known to affect Ca(2+)-binding affinity to the N-terminal domain. Here we report on the functional effects of this mutation in skinned papillary muscle fibers from homozygous knock-in TnC-A8V mice. Muscle fibers from left ventricle were activated at 25°C under the ionic conditions of working cardiomyocytes. The pCa-tension relationship showed a 3× increase in Ca(2+)-sensitivity and a decrease (0...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28444797/the-transcription-factor-myb115-contributes-to-the-regulation-of-proanthocyanidin-biosynthesis-and-enhances-fungal-resistance-in-poplar
#7
Lijun Wang, Lingyu Ran, Yisu Hou, Qiaoyan Tian, Chaofeng Li, Rui Liu, Di Fan, Keming Luo
Proanthocyanidins (PAs) are major defense phenolic compounds in the leaves of poplar (Populus spp.) in response to abiotic and biotic stresses. Transcriptional regulation of PA biosynthetic genes by the MYB-basic helix-loop-helix (bHLH)-WD40 complexes in poplar is not still fully understood. Here, an Arabidopsis TT2-like gene MYB115 was isolated from Populus tomentosa and characterized by various molecular, genetic and biochemical approaches. MYB115 restored PA productions in the seed coat of the Arabidopsis tt2 mutant...
April 26, 2017: New Phytologist
https://www.readbyqxmd.com/read/28444795/systematics-and-molecular-phylogeny-of-the-ciliate-genus-pseudokeronopsis-ciliophora-hypotrichia
#8
Ju Li, Zifeng Zhan, Kuidong Xu
A still challenging study on ciliate systematics is to clarify the taxonomic and phylogenetic confusions of the fascinating pigmented Pseudokeronopsis species because of their high inter-specific similarities. We evaluated the identities and internal relationships within Pseudokeronopsis based on morphological descriptions in combination with the 18S and ITS-5.8S rDNA genetic distances, ITS2 secondary structures and phylogenetic analyses. Results showed that (1) Pseudokeronopsis pararubra, a species ever synonymized as Pseudokeronopsis carnea, is a valid species; (2) most Chinese populations identified as Pseudokeronopsis rubra represent a new species namely Pseudokeronopsis songi sp...
April 26, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28444690/strobilurins-as-growth-promoting-compounds-how-stroby-regulates-arabidopsis-leaf-growth
#9
Judith Van Dingenen, Chrystalla Antoniou, Panagiota Filippou, Jacob Pollier, Nathalie Gonzalez, Stijn Dhondt, Alain Goossens, Vasileios Fotopoulos, Dirk Inzé
Strobilurins are an important class of agrochemical fungicides used throughout the world on a wide variety of crops as protection against fungal pathogens. In addition to this protective role, they are reported to also positively influence plant physiology. In this study, we analyzed the effect of Stroby® WG, a commercially available fungicide consisting of 50% (w/w) kresoxim-methyl (KM) as active strobilurin compound, on Arabidopsis leaf growth. Treatment of seedlings with Stroby resulted in larger leaves due to an increase in cell number...
April 25, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28444308/investigating-dna-supercoiling-in-eukaryotic-genomes
#10
Samuel Corless, Nick Gilbert
Supercoiling is a fundamental property of DNA, generated by polymerases and other DNA-binding proteins as a consequence of separating/bending the DNA double helix. DNA supercoiling plays a key role in gene expression and genome organization, but has proved difficult to study in eukaryotes because of the large, complex and chromatinized genomes. Key approaches to study DNA supercoiling in eukaryotes are (1) centrifugation-based or electrophoresis-based techniques in which supercoiled plasmids extracted from eukaryotic cells form a compacted writhed structure that migrates at a rate proportional to the level of DNA supercoiling; (2) in vivo approaches based on the preferential intercalation of psoralen molecules into under-wound DNA...
April 24, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28443104/genome-wide-identification-and-characterization-of-apple-bhlh-transcription-factors-and-expression-analysis-in-response-to-drought-and-salt-stress
#11
Ke Mao, Qinglong Dong, Chao Li, Changhai Liu, Fengwang Ma
The bHLH (basic helix-loop-helix) transcription factor family is the second largest in plants. It occurs in all three eukaryotic kingdoms, and plays important roles in regulating growth and development. However, family members have not previously been studied in apple. Here, we identified 188 MdbHLH proteins in apple "Golden Delicious" (Malus × domestica Borkh.), which could be classified into 18 groups. We also investigated the gene structures and 12 conserved motifs in these MdbHLHs. Coupled with expression analysis and protein interaction network prediction, we identified several genes that might be responsible for abiotic stress responses...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28442432/fibre-diffraction-studies-of-biological-macromolecules
#12
REVIEW
D A Marvin
Two fundamental structures in molecular biology, DNA and the α-helix, were determined using X-ray fibre diffraction data, and yet fibre diffraction occupies an obscure niche in structural biology. Relatively few structures are appropriate for the technique, and it seldom supplies data of the quality common in protein crystallography; however, it has proven indispensable in some cases. Here we outline some aspects of helix diffraction mathematics, and then illustrate the application of fibre diffraction by three case studies: DNA, filamentous bacterial viruses, and bacterial pili...
April 22, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28442331/non-covalent-conjugation-of-cutinase-from-fusarium-sp-ict-sac1-with-pectin-for-enhanced-stability-process-minutiae-kinetics-thermodynamics-and-structural-study
#13
Abhijeet B Muley, Sandeep A Chaudhari, Rekha S Singhal
Cutinase, a member of α/β-fold hydrolase family possess potentially diverse applications in several industrial processes and products. The present work aims towards thermo-stabilization of cutinase from novel source Fusarium sp. ICT SAC1 via non-covalent interaction with polysaccharides. Although all six polysaccharides chosen for study enhanced the thermal stability, pectin was found to be most promising. The interaction protocol for cutinase with pectin was optimized sequentially with respect to the ratio of enzyme to pectin, solution pH, and buffer strength...
April 22, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28440695/size-variable-zone-in-v3-region-of-16s-rrna
#14
Francisco Vargas-Albores, Luis Enrique Ortiz-Suárez, Enrique Villalpando-Canchola, Marcel Martínez-Porchas
The size distribution of complete 16S-rRNA sequences from the SILVA-database and nucleotide shifts that might interfere with the secondary structure of the molecules were evaluated. Overall, 513,309 sequences recorded in SILVA were used to estimate the size of hypervariable regions of the gene. Redundant sequences were treated as a single sequence to achieve a better representation of the molecular diversity. Nucleotides found in each position in 95% of the sequences were considered the consensus sequences for different size-groups (consensus95)...
April 25, 2017: RNA Biology
https://www.readbyqxmd.com/read/28439280/insights-on-structure-and-function-of-a-late-embryogenesis-abundant-protein-from-amaranthus-cruentus-an-intrinsically-disordered-protein-involved-in-protection-against-desiccation-oxidant-conditions-and-osmotic-stress
#15
Alma L Saucedo, Eric E Hernández-Domínguez, Luis A de Luna-Valdez, Angel A Guevara-García, Abraham Escobedo-Moratilla, Esaú Bojorquéz-Velázquez, Federico Del Río-Portilla, Daniel A Fernández-Velasco, Ana P Barba de la Rosa
Late embryogenesis abundant (LEA) proteins are part of a large protein family that protect other proteins from aggregation due to desiccation or osmotic stresses. Recently, the Amaranthus cruentus seed proteome was characterized by 2D-PAGE and one highly accumulated protein spot was identified as a LEA protein and was named AcLEA. In this work, AcLEA cDNA was cloned into an expression vector and the recombinant protein was purified and characterized. AcLEA encodes a 172 amino acid polypeptide with a predicted molecular mass of 18...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28438793/brassinosteroid-biosynthesis-is-modulated-via-a-transcription-factor-cascade-of-cog1-pif4-and-pif5
#16
Zhuoyun Wei, Tong Yuan, Danuše Tarkowská, Jeongsik Kim, Hong Gil Nam, Ondřej Novák, Kai He, Xiaoping Gou, Jia Li
Brassinosteroids (BRs) are essential phytohormones regulating various developmental and physiological processes during normal growth and development. cog1-3D (cogwheel 1-3D) was identified as an activation-tagged genetic modifier of bri1-5, an intermediate BR receptor mutant. COG1 encodes a Dof-type transcription factor previously found to act as a negative regulator of the phytochrome signaling pathway. cog1-3D single mutants show an elongated hypocotyl phenotype under light conditions. Loss-of-function by ethylmethanoesulfonate (EMS) mutation or inducible expression of a dominant-negative form of COG1 results in an opposite phenotype...
April 24, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28438792/reconstitution-of-abscisic-acid-signaling-from-the-receptor-to-dna-via-bhlh-transcription-factors
#17
Yohei Takahashi, Yuta Ebisu, Ken-Ichiro Shimazaki
The plant hormone abscisic acid (ABA) confers drought tolerance in plants through stomatal closure and regulation of gene expression. The complex consisting of the ABA receptor PYRABACTIN RESISTANCE/REGULATORY COMPONENTS OF ABA RECEPTOR (PYR/RCAR), type 2C protein phosphatase (PP2C), and SNF1-related protein kinase 2 (SnRK2) has a key role in ABA signaling. Basic helix-loop-helix (bHLH) transcriptional activator ABA-RESPONSIVE KINASE SUBSTRATE1 (AKS1, also known as FBH3), is released from DNA by phosphorylation-induced monomerization in response to ABA in guard cells...
April 24, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28438686/expression-purification-and-molecular-characterization-of-a-novel-endoglucanase-protein-from-bacillus-subtilis-sb13
#18
Xuefang Guan, Penglian Chen, Qingxian Xu, Lei Qian, Juqing Huang, Bin Lin
Bacillus subtilis strain SB13 which is isolated in our previous work was confirmed to produce endoglucanase. In this study, a novel endoglucanase gene (accession number: KX576676) was identified and cloned from SB13. Compared with other consensus sequence of reported endoglucanase genes in the GenBank database, this gene displays five differences (including T740C,A874G,A983G, T1210G and T1301C), which leading to five amino acid changes. Homology modeling has indicated that these five changes were located in the α-helix and random coil regions of the glycosyl hydrolase family 5 (GH5) domain, the random coil and β-sandwich of the type 3 carbohydrate-binding module (CBM3) domain, and the random coil domain...
April 21, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28438092/characterization-by-lectin-histochemistry-of-two-subpopulations-of-parietal-cells-in-the-rat-gastric-glands
#19
Laura Gómez-Santos, Edurne Alonso, Lucio Díaz-Flores, Juan F Madrid, Francisco J Sáez
Parietal cells undergo a differentiation process while they move from the isthmus toward the pits and the base region of the gastric gland. The aim of this work was to analyze the rat gastric glands by lectin histochemistry to show the glycans expressed by upper (young) and lower (old) parietal cells. We used lectins recognizing the most frequent sugar moieties in mammals. Each lectin was assayed alone and in combination with several deglycosylation pretreatments: (1) β-elimination, which removes O-linked oligosaccharides; (2) incubation with Peptide-N-glycosidase F, to remove N-linked glycans; (3) acid hydrolysis, which removes terminal sialic acid moieties; (4) methylation-saponification, to remove sulfate groups from sugar residues; and (5) glucose oxidase, a technique carried out with the lectin concanavalin A to convert glucose into gluconic acid...
May 2017: Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society
https://www.readbyqxmd.com/read/28437792/phase-plate-cryo-em-structure-of-a-class-b-gpcr-g-protein-complex
#20
Yi-Lynn Liang, Maryam Khoshouei, Mazdak Radjainia, Yan Zhang, Alisa Glukhova, Jeffrey Tarrasch, David M Thal, Sebastian G B Furness, George Christopoulos, Thomas Coudrat, Radostin Danev, Wolfgang Baumeister, Laurence J Miller, Arthur Christopoulos, Brian K Kobilka, Denise Wootten, Georgios Skiniotis, Patrick M Sexton
Class B G-protein-coupled receptors are major targets for the treatment of chronic diseases, such as osteoporosis, diabetes and obesity. Here we report the structure of a full-length class B receptor, the calcitonin receptor, in complex with peptide ligand and heterotrimeric Gαsβγ protein determined by Volta phase-plate single-particle cryo-electron microscopy. The peptide agonist engages the receptor by binding to an extended hydrophobic pocket facilitated by the large outward movement of the extracellular ends of transmembrane helices 6 and 7...
April 24, 2017: Nature
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