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https://www.readbyqxmd.com/read/28335556/trm5-and-trmd-two-enzymes-from-distinct-origins-catalyze-the-identical-trna-modification-m%C3%A2-g37
#1
REVIEW
Sakurako Goto-Ito, Takuhiro Ito, Shigeyuki Yokoyama
The N¹-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m¹G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome. Interestingly, Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. In this review, we describe the different strategies utilized by Trm5 and TrmD to recognize their substrate tRNAs, mainly based on their crystal structures complexed with substrate tRNAs...
March 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28335421/pamam-dendrimers-cross-the-blood-brain-barrier-when-administered-through-the-carotid-artery-in-c57bl-6j-mice
#2
Bhairavi Srinageshwar, Sarah Peruzzaro, Melissa Andrews, Kayla Johnson, Allison Hietpas, Brittany Clark, Crystal McGuire, Eric Petersen, Jordyn Kippe, Andrew Stewart, Olivia Lossia, Abeer Al-Gharaibeh, Aaron Antcliff, Rebecca Culver, Douglas Swanson, Gary Dunbar, Ajit Sharma, Julien Rossignol
Drug delivery into the central nervous system (CNS) is challenging due to the blood-brain barrier (BBB) and drug delivery into the brain overcoming the BBB can be achieved using nanoparticles such as dendrimers. The conventional cationic dendrimers used are highly toxic. Therefore, the present study investigates the role of novel mixed surface dendrimers, which have potentially less toxicity and can cross the BBB when administered through the carotid artery in mice. In vitro experiments investigated the uptake of amine dendrimers (G1-NH₂ and G4-NH₂) and novel dendrimers (G1-90/10 and G4-90/10) by primary cortical cultures...
March 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335409/the-formyl-peptide-receptors-diversity-of-ligands-and-mechanism-for-recognition
#3
REVIEW
Hui-Qiong He, Richard D Ye
The formyl peptide receptors (FPRs) are G protein-coupled receptors that transduce chemotactic signals in phagocytes and mediate host-defense as well as inflammatory responses including cell adhesion, directed migration, granule release and superoxide production. In recent years, the cellular distribution and biological functions of FPRs have expanded to include additional roles in homeostasis of organ functions and modulation of inflammation. In a prototype, FPRs recognize peptides containing N-formylated methionine such as those produced in bacteria and mitochondria, thereby serving as pattern recognition receptors...
March 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28335391/new-metabolites-and-bioactive-chlorinated-benzophenone-derivatives-produced-by-a-marine-derived-fungus-pestalotiopsis-heterocornis
#4
Hui Lei, Xiuping Lin, Li Han, Jian Ma, Qingjuan Ma, Jialiang Zhong, Yonghong Liu, Tiemin Sun, Jinhui Wang, Xueshi Huang
Four new compounds, including two isocoumarins, pestaloisocoumarins A and B (1, 2), one sesquiterpenoid degradation, isopolisin B (4), and one furan derivative, pestalotiol A (5), together with one known isocoumarin, gamahorin (3), and three chlorinated benzophenone derivatives, pestalachloride B (6), pestalachloride E (7) and a mixture of pestalalactone atropisomers (8a/8b), were isolated from a culture of the fungus Pestalotiopsis heterocornis associated with sponge Phakellia fusca. These new chemical structures were established using NMR and MS spectroscopic data, as well as single-crystal X-ray crystallographic analysis and CD Cotton effects...
March 13, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28335369/effect-of-nano-sio%C3%A2-on-the-hydration-and-microstructure-of-portland-cement
#5
Liguo Wang, Dapeng Zheng, Shupeng Zhang, Hongzhi Cui, Dongxu Li
This paper systematically studied the modification of cement-based materials by nano-SiO₂ particles with an average diameter of about 20 nm. In order to obtain the effect of nano-SiO₂ particles on the mechanical properties, hydration, and pore structure of cement-based materials, adding 1%, 3%, and 5% content of nano-SiO₂ in cement paste, respectively. The results showed that the reaction of nano-SiO₂ particles with Ca(OH)₂ (crystal powder) started within 1 h, and formed C-S-H gel. The reaction speed was faster after aging for three days...
December 15, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335359/temperature-and-angle-dependent-magnetic-properties-of-ni-nanotube-arrays-fabricated-by-electrodeposition-in-polycarbonate-templates
#6
Yonghui Chen, Chen Xu, Yibo Zhou, Khan Maaz, Huijun Yao, Dan Mo, Shuangbao Lyu, Jinglai Duan, Jie Liu
Parallel arrays of Ni nanotubes with an external diameter of 150 nm, a wall thickness of 15 nm, and a length of 1.2 ± 0.3 µm were successfully fabricated in ion-track etched polycarbonate (PC) templates by electrochemical deposition. The morphology and crystal structure of the nanotubes were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), and X-ray diffraction (XRD). Structural analyses indicate that Ni nanotubes have a polycrystalline structure with no preferred orientation...
December 1, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335357/the-assembly-of-dna-amphiphiles-at-liquid-crystal-aqueous-interface
#7
Jingsheng Zhou, Yuanchen Dong, Yiyang Zhang, Dongsheng Liu, Zhongqiang Yang
In this article, we synthesized a type of DNA amphiphiles (called DNA-lipids) and systematically studied its assembly behavior at the liquid crystal (LC)-aqueous interface. It turned out that the pure DNA-lipids at various concentrations cannot trigger the optical transition of liquid crystals from planar anchoring to homeotropic anchoring at the liquid crystal-aqueous interface. The co-assembly of DNA-lipid and l-dilauroyl phosphatidylcholine (l-DLPC) indicated that the DLPC assembled all over the LC-aqueous interface, and DNA-lipids prefer to couple with LC in certain areas, particularly in polarized and fluorescent image, forming micron sized net-like structures...
December 1, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335337/effect-of-crystal-orientation-on-self-assembly-nanocones-formed-on-tungsten-surface-induced-by-helium-ion-irradiation-and-annealing
#8
Shilin Huang, Guang Ran, Penghui Lei, Shenghua Wu, Nanjun Chen, Ning Li
The self-assembly nanocone structures on the surface of polycrystalline tungsten were created by He⁺ ion irradiation and then annealing, and the resulting topography and morphology were characterized using atomic force microscopy and scanning electron microscopy. The cross-sectional samples of the self-assembly nanocones were prepared using an in situ-focused ion beam and then observed using transmission electron microscopy. The self-assembly nanocones were induced by the combined effect of He⁺ ion irradiation, the annealing process and the chromium impurity...
November 12, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335322/black-phosphorus-critical-review-and-potential-for-water-splitting-photocatalyst
#9
REVIEW
Tae Hyung Lee, Soo Young Kim, Ho Won Jang
A century after its first synthesis in 1914, black phosphorus has been attracting significant attention as a promising two-dimensional material in recent years due to its unique properties. Nowadays, with the development of its exfoliation method, there are extensive applications of black phosphorus in transistors, batteries and optoelectronics. Though, because of its hardship in mass production and stability problems, the potential of the black phosphorus in various fields is left unexplored. Here, we provide a comprehensive review of crystal structure, electronic, optical properties and synthesis of black phosphorus...
October 29, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335303/detection-of-prohibited-fish-drugs-using-silver-nanowires-as-substrate-for-surface-enhanced-raman-scattering
#10
Jia Song, Yiqun Huang, Yuxia Fan, Zhihui Zhao, Wansong Yu, Barbara A Rasco, Keqiang Lai
Surface-enhanced Raman scattering or surface-enhanced Raman spectroscopy (SERS) is a promising detection technology, and has captured increasing attention. Silver nanowires were synthesized using a rapid polyol method and optimized through adjustment of the molar ratio of poly(vinyl pyrrolidone) and silver nitrate in a glycerol system. Ultraviolet-visible spectrometry, X-ray diffraction, and transmission electron microscopy were used to characterize the silver nanowires. The optimal silver nanowires were used as a SERS substrate to detect prohibited fish drugs, including malachite green, crystal violet, furazolidone, and chloramphenicol...
September 21, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335295/investigation-of-the-band-structure-of-graphene-based-plasmonic-photonic-crystals
#11
Pingping Qiu, Weibin Qiu, Zhili Lin, Houbo Chen, Yixin Tang, Jia-Xian Wang, Qiang Kan, Jiao-Qing Pan
In this paper, one-dimensional (1D) and two-dimensional (2D) graphene-based plasmonic photonic crystals (PhCs) are proposed. The band structures and density of states (DOS) have been numerically investigated. Photonic band gaps (PBGs) are found in both 1D and 2D PhCs. Meanwhile, graphene-based plasmonic PhC nanocavity with resonant frequency around 175 THz, is realized by introducing point defect, where the chemical potential is from 0.085 to 0.25 eV, in a 2D PhC. Also, the bending wvaguide and the beam splitter are realized by introducing the line defect into the 2D PhC...
September 9, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335281/study-on-utilization-of-carboxyl-group-decorated-carbon-nanotubes-and-carbonation-reaction-for-improving-strengths-and-microstructures-of-cement-paste
#12
Xiantong Yan, Hongzhi Cui, Qinghua Qin, Waiching Tang, Xiangming Zhou
Carbon nanotubes (CNTs) have excellent mechanical properties and can be used to reinforce cement-based materials. On the other hand, the reaction product of carbonation with hydroxides in hydrated cement paste can reduce the porosity of cement-based materials. In this study, a novel method to improve the strength of cement paste was developed through a synergy of carbon nanotubes decorated with carboxyl group and carbonation reactions. The experimental results showed that the carboxyl group (-COOH) of decorated carbon nanotubes and the surfactant can control the morphology of the calcium carbonate crystal of carbonation products in hydrated cement paste...
August 19, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335254/quaternized-chitosan-capped-mesoporous-silica-nanoparticles-as-nanocarriers-for-controlled-pesticide-release
#13
Lidong Cao, Huirong Zhang, Chong Cao, Jiakun Zhang, Fengmin Li, Qiliang Huang
Nanotechnology-based pesticide formulations would ensure effective utilization of agricultural inputs. In the present work, mesoporous silica nanoparticles (MSNs) with particle diameters of ~110 nm and pore sizes of ~3.7 nm were synthesized via a liquid crystal templating mechanism. A water-soluble chitosan (CS) derivative (N-(2-hydroxyl)propyl-3-trimethyl ammonium CS chloride, HTCC) was successfully capped on the surface of pyraclostrobin-loaded MSNs. The physicochemical and structural analyses showed that the electrostatic interactions and hydrogen bonding were the major forces responsible for the formation of HTCC-capped MSNs...
June 28, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335231/enhanced-activity-of-supported-ni-catalysts-promoted-by-pt-for-rapid-reduction-of-aromatic-nitro-compounds
#14
Huishan Shang, Kecheng Pan, Lu Zhang, Bing Zhang, Xu Xiang
To improve the activities of non-noble metal catalysts is highly desirable and valuable to the reduced use of noble metal resources. In this work, the supported nickel (Ni) and nickel-platinum (NiPt) nanocatalysts were derived from a layered double hydroxide/carbon composite precursor. The catalysts were characterized and the role of Pt was analysed using X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM), energy dispersive X-ray spectroscopy (EDS) mapping, and X-ray photoelectron spectroscopy (XPS) techniques...
June 4, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28334966/structural-and-mechanistic-insights-into-regulation-of-hbo1-histone-acetyltransferase-activity-by-brpf2
#15
Ye Tao, Chen Zhong, Junjun Zhu, Shutong Xu, Jianping Ding
HBO1, a member of the MYST family of histone acetyltransferases (HATs), is required for global acetylation of histone H3K14 and embryonic development. It functions as a catalytic subunit in multisubunit complexes comprising a BRPF1/2/3 or JADE1/2/3 scaffold protein, and two accessory proteins. BRPF2 has been shown to be important for the HAT activity of HBO1 toward H3K14. Here we demonstrated that BRPF2 can regulate the HAT activity of HBO1 toward free H3 and H4, and nucleosomal H3. Particularly, a short N-terminal region of BRPF2 is sufficient for binding to HBO1 and can potentiate its activity toward H3K14...
February 24, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334932/ribosome-dependent-vibrio-cholerae-mrnase-higb2-is-regulated-by-a-%C3%AE-strand-sliding-mechanism
#16
San Hadži, Abel Garcia-Pino, Sarah Haesaerts, Dukas Jurenas, Kenn Gerdes, Jurij Lah, Remy Loris
Toxin-antitoxin (TA) modules are small operons involved in bacterial stress response and persistence. higBA operons form a family of TA modules with an inverted gene organization and a toxin belonging to the RelE/ParE superfamily. Here, we present the crystal structures of chromosomally encoded Vibrio cholerae antitoxin (VcHigA2), toxin (VcHigB2) and their complex, which show significant differences in structure and mechanisms of function compared to the higBA module from plasmid Rts1, the defining member of the family...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334863/consecutive-non-natural-pz-nucleobase-pairs-in-dna-impact-helical-structure-as-seen-in-50-%C3%AE-s-molecular-dynamics-simulations
#17
Robert W Molt, Millie M Georgiadis, Nigel G J Richards
Little is known about the influence of multiple consecutive 'non-standard' ( , 6-amino-5-nitro-2(1H)-pyridone, and , 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one) nucleobase pairs on the structural parameters of duplex DNA. nucleobase pairs follow standard rules for Watson-Crick base pairing but have rearranged hydrogen bonding donor and acceptor groups. Using the X-ray crystal structure as a starting point, we have modeled the motions of a DNA duplex built from a self-complementary oligonucleotide (5΄-CTTATPPPZZZATAAG-3΄) in water over a period of 50 μs and calculated DNA local parameters, step parameters, helix parameters, and major/minor groove widths to examine how the presence of multiple, consecutive nucleobase pairs might impact helical structure...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334829/structure-of-the-sac3-rna-binding-m-region-in-the-saccharomyces-cerevisiae-trex-2-complex
#18
James M B Gordon, Shintaro Aibara, Murray Stewart
Transcription-export complex 2 (TREX-2, or THSC) facilitates localization of actively transcribing genes such as GAL1 to the nuclear periphery, contributes to the generation of export-competent mRNPs and influences gene expression through interactions with Mediator. TREX-2 is based on a Sac3 scaffold to which Thp1, Sem1, Cdc31 and Sus1 bind and consists of three modules: the N-region (Sac3∼1-100), which binds mRNA export factor Mex67:Mtr2; the M-region, in which Thp1 and Sem1 bind to Sac3∼100-550; and the CID region in which Cdc31 and two Sus1 chains bind to Sac3∼720-805...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334766/crystal-structure-of-the-n-terminal-domain-of-human-timeless-and-its-interaction-with-tipin
#19
Sandro Holzer, Gianluca Degliesposti, Mairi L Kilkenny, Sarah L Maslen, Dijana Matak-Vinkovíc, Mark Skehel, Luca Pellegrini
Human Timeless is involved in replication fork stabilization, S-phase checkpoint activation and establishment of sister chromatid cohesion. In the cell, Timeless forms a constitutive heterodimeric complex with Tipin. Here we present the 1.85 Å crystal structure of a large N-terminal segment of human Timeless, spanning amino acids 1-463, and we show that this region of human Timeless harbours a partial binding site for Tipin. Furthermore, we identify minimal regions of the two proteins that are required for the formation of a stable Timeless-Tipin complex and provide evidence that the Timeless-Tipin interaction is based on a composite binding interface comprising different domains of Timeless...
February 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334691/dna-functionalized-photonic-crystal-microspheres-for-multiplex-detection-of-toxic-metal-ions
#20
Zhengyu Yan, Chunqing Tian, Xincheng Qu, Weiyang Shen, Baofen Ye
A novel type of suspension array for multiplex detection of heavy metal ions with photonic crystal hydrogel microspheres was reported. The photonic crystal hydrogel microspheres have close-packed photonic crystal particles as their encoding units and ssDNA-functionalized hydrogel as the sensing units. The developed microspheres were successfully applied in multiplex detection of heavy metal ions.
March 8, 2017: Colloids and Surfaces. B, Biointerfaces
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