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https://www.readbyqxmd.com/read/29232619/engineering-of-protein-nanopores-for-sequencing-chemical-or-protein-sensing-and-disease-diagnosis
#1
REVIEW
Shaoying Wang, Zhengyi Zhao, Farzin Haque, Peixuan Guo
Biological systems contain highly-ordered structures performing diverse functions. The elegant structures of biomachines have inspired the development of nanopores as single molecule sensors. Over the years, the utility of nanopores for detecting a wide variety of analytes have rapidly emerged for sensing, sequencing and diagnostic applications. Several protein channels with diverse shapes and sizes, such as motor channels from bacteriophage Phi29, SPP1, T3, and T4, as well as α-hemolysin, MspA, aerolysin, FluA, OmpF/G, CsgG, ClyA, have been continually investigated and developed as nanopores...
December 9, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29232197/dna-based-construction-at-the-nanoscale-emerging-trends-and-applications
#2
Lourdu Xavier Paulraj, Arun Richard Chandrasekaran
The field of structural DNA nanotechnology has reached adolescence - starting with the creation of artificial immobile junctions leading to the recent DNA-protein hybrid nanoscale shapes - in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields...
December 12, 2017: Nanotechnology
https://www.readbyqxmd.com/read/29231155/pedobacter-quisquiliarum-sp-nov-isolated-from-activated-sludge
#3
Bo Zhang, Zhi-Qiang Liu, Yu-Guo Zheng
A Gram-stain-negative, aerobic, rod-shaped, bacterium, C62-2T, was isolated from activated sludge in Fujian Province, China. Phylogenetic analysis of the 16S rRNA gene sequences showed that it was closely related to Pedobacter duraquae WB 2.1-25T (97.92 %), Pedobacter bambusae THG-G118T (97.40 %), Pedobacter cryoconitis A37T (97.37 %) and Pedobacter caeni LMG 22862T (97.3 %). Cells grew aerobically at 20-37 °C (optimum, 30 °C), pH 5.0-8.0 (optimum, pH 7.0) and in the presence of 0-3.0 % (w/v) NaCl...
December 12, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29230285/cellular-senescence-associated-immune-responses-in-liver-cancer
#4
REVIEW
Tim F Greten, Tobias Eggert
Cellular senescence is a stress-induced cell-cycle arrest program that prevents malignant transformation of senescent cells following oncogenic pathway activation and DNA damage. Senescent cells are metabolically active and secrete cytokines and chemokines that shape the function and composition of their microenvironment. These cytokines can recruit immune cells such as lymphocytes and myeloid cells that depending on the context can either promote or inhibit liver tumor development and progression. Accordingly, pharmacologically targeting of secreted cytokines or reprogramming the expression of these cytokines in senescent cells represents a promising approach to skew senescence-associated immune responses toward cancer cell killing...
October 2017: Hepatic Oncology
https://www.readbyqxmd.com/read/29229931/brain-gene-expression-signature-on-primate-genomic-sequence-evolution
#5
Shahar Barbash, Thomas P Sakmar
Considering the overwhelming changes that occurred during primate evolution in brain structure and function, one might expect corresponding changes at the molecular level. Surprisingly, a relatively constrained gene expression pattern is observed in brain compared with other tissues among primates, an observation that calls for reassessment of RNA expression influence on primate genome evolution. We built phylogenetic trees based on genomic sequences of functional genomic regions and tissue-specific RNA expression in eight tissue types for six primate species...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29228286/cut-and-paste-transposons-in-fungi-with-diverse-lifestyles
#6
Anna Muszewska, Kamil Steczkiewicz, Marta Stepniewska-Dziubinska, Krzysztof Ginalski
Transposons (TEs) shape genomes via recombination and transposition, lead to chromosomal rearrangements, create new gene neighbourhoods and alter gene expression. They play key roles in adaptation either to symbiosis in Amanita genus or to pathogenicity in Pyrenophora tritici-repentis. Despite growing evidence of their importance, the abundance and distribution of mobile elements replicating in a "cut and paste" fashion is barely described so far. In order to improve our knowledge on this old and ubiquitous class of transposable elements, 1,730 fungal genomes were scanned using both de novo and homology-based approaches...
December 8, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29225179/synthesis-of-novel-benzodioxane-midst-piperazine-moiety-decorated-chitosan-silver-nanoparticle-against-biohazard-pathogens-and-as-potential-anti-inflammatory-candidate-a-molecular-docking-studies
#7
C S Karthik, H M Manukumar, A P Ananda, S Nagashree, K P Rakesh, L Mallesha, Hua-Li Qin, S Umesha, P Mallu, N B Krishnamurthy
Nanoparticles (NPs) are currently being investigated along with the use of biodegradable polymer containing active agents in many areas of medicine for targeted applications. The present study was aimed to synthesize novel compound Benzodioxane midst piperazine (BP) and characterization of a BP decorated chitosan silver nanoparticles (BP*C@AgNPs) and shown effective against hazardous pathogens, and also having anti-inflammatory property. It was further evaluated for molecular docking proofs, and toxicity. The BP*C@AgNPs had spherical shape with size of 36...
December 7, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29222499/crystal-structure-of-an-rna-cleaving-dnazyme
#8
Hehua Liu, Xiang Yu, Yiqing Chen, Jing Zhang, Baixing Wu, Lina Zheng, Phensinee Haruehanroengra, Rui Wang, Suhua Li, Jinzhong Lin, Jixi Li, Jia Sheng, Zhen Huang, Jinbiao Ma, Jianhua Gan
In addition to storage of genetic information, DNA can also catalyze various reactions. RNA-cleaving DNAzymes are the catalytic DNAs discovered the earliest, and they can cleave RNAs in a sequence-specific manner. Owing to their great potential in medical therapeutics, virus control, and gene silencing for disease treatments, RNA-cleaving DNAzymes have been extensively studied; however, the mechanistic understandings of their substrate recognition and catalysis remain elusive. Here, we report three catalytic form 8-17 DNAzyme crystal structures...
December 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/29220522/meta-analysis-of-genome-wide-association-studies-identifies-8-novel-loci-involved-in-shape-variation-of-human-head-hair
#9
Fan Liu, Yan Chen, Gu Zhu, Pirro G Hysi, Sijie Wu, Kaustubh Adhikari, Krystal Breslin, Ewelina Pospiech, Merel A Hamer, Fuduan Peng, Charanya Muralidharan, Victor Acuna-Alonzo, Samuel Canizales-Quinteros, Gabriel Bedoya, Carla Gallo, Giovanni Poletti, Francisco Rothhammer, Maria Catira Bortolini, Rolando Gonzalez-Jose, Changqing Zeng, Shuhua Xu, Li Jin, André G Uitterlinden, M Arfan Ikram, Cornelia M van Duijn, Tamar Nijsten, Susan Walsh, Wojciech Branicki, Sijia Wang, Andrés Ruiz-Linares, Timothy D Spector, Nicholas G Martin, Sarah E Medland, Manfred Kayser
Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28,964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21...
December 6, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29219968/programmable-self-assembly-of-three-dimensional-nanostructures-from-10-000-unique-components
#10
Luvena L Ong, Nikita Hanikel, Omar K Yaghi, Casey Grun, Maximilian T Strauss, Patrick Bron, Josephine Lai-Kee-Him, Florian Schueder, Bei Wang, Pengfei Wang, Jocelyn Y Kishi, Cameron Myhrvold, Allen Zhu, Ralf Jungmann, Gaetan Bellot, Yonggang Ke, Peng Yin
Nucleic acids (DNA and RNA) are widely used to construct nanometre-scale structures with ever increasing complexity, with possible application in fields such as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early kilodalton-scale examples containing typically tens of unique DNA strands. The introduction of DNA origami, which uses many staple strands to fold one long scaffold strand into a desired structure, has provided access to megadalton-scale nanostructures that contain hundreds of unique DNA strands...
December 6, 2017: Nature
https://www.readbyqxmd.com/read/29219966/gigadalton-scale-shape-programmable-dna-assemblies
#11
Klaus F Wagenbauer, Christian Sigl, Hendrik Dietz
Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging...
December 6, 2017: Nature
https://www.readbyqxmd.com/read/29219808/ferrovibrio-soli-sp-nov-a-novel-cellulolytic-bacterium-isolated-from-stream-bank-soil
#12
Ram Hari Dahal, Jaisoo Kim
Two isolates of bacterial strains A15T and A17 were isolated from stream bank soil in Kyonggi University. Cells were aerobic, Gram-stain-negative, oxidase- and catalase-positive, motile, non-spore-forming, rod-shaped, opaque, and cream coloured. Both strains hydrolysed CM-cellulose. Strains were able to grow at 20-42 °C, pH 5.5-10.0 and at 1.5 % NaCl concentration (w/v). Indole test was positive. Analyses of phylogenetic trees based on its 16S rRNA gene sequences indicated that strain A15T formed a lineage within the family Rhodospirillaceae of the phylum Proteobacteria which was distinct from Ferrovibrio denitrificans S3T (98...
December 8, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29219806/mucilaginibacter-amnicola-sp-nov-isolated-from-a-freshwater-creek
#13
Wen-Ming Chen, Tsai-Ying Hsieh, Shih-Yi Sheu
A pink-coloured bacterial strain, TAPP7T, was isolated from a freshwater creek in Taiwan. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TAPP7T belonged to the genus Mucilaginibacter and showed highest similarity with Mucilaginibacter ginsengisoli B4Y-8T (97.6 %) and Mucilaginibacter carri PR0008KT (96.9 %). Cells of strain TAPP7T were Gram-staining-negative, aerobic, poly-β-hydroxybutyrate-accumulating and short-rod-shaped. Growth occurred at 10-30 °C (optimum, 15-20 °C), at pH 4-8 (optimum, pH 6) and with 0-1 % NaCl (optimum, 0...
December 8, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29219804/pseudooceanicola-lipolyticus-sp-nov-a-marine-alphaproteobacterium-reclassification-of-oceanicola-flagellatus-as-pseudooceanicola-flagellatus-comb-nov-and-emended-description-of-the-genus-pseudooceanicola
#14
Meng-Meng Huang, Li-Li Guo, Yue-Hong Wu, Qi-Liang Lai, Zong-Ze Shao, Chun-Sheng Wang, Min Wu, Xue-Wei Xu
A Gram-stain-negative, rod-shaped bacterium, designated 157T, was isolated from seawater collected from the Philippine Sea. Cells of strain 157T grew in medium containing 0.5-10.0 % NaCl (w/v, optimum 3 %), at pH 6.0-8.5 (optimum 7.0) and at 15-40 °C (optimum 30 °C). Tweens 20, 40 and 80 as well as urea were hydrolysed. The 16S rRNA gene sequence of strain 157T had a high sequence similarity with respect to Pseudooceanicola marinus AZO-CT (97.2 %), and exhibited less than 97.0 % sequence similarity to other type strains of the species with validly published names...
December 8, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29218341/templated-co-assembly-into-nanorods-of-polyanions-and-artificial-virus-capsid-proteins
#15
A Hernandez-Garcia, M A Cohen Stuart, R de Vries
Recombinant triblock polypeptides C-Sn-B, where C is a 400 amino acid long hydrophilic random coil block, Sn is a multimer of the silk-like octapeptide S = (GAGAGAGQ), and B = K12 is an oligolysine, have previously been shown to encapsulate double stranded DNA into rod-shaped, virus-like particles. In order to gain insight of the co-assembly process, and in order to be able to use these proteins for templating other types of nanorods, we here explore their co-assembly with a range of polyanionic templates: poly(acrylic acids) (PAA) of a wide range of lengths, poly(styrene sulphonate) (PSS) and the stiff anionic polysaccharide xanthan...
December 8, 2017: Soft Matter
https://www.readbyqxmd.com/read/29217658/nucleic-acid-based-nanotechnology-the-ability-of-dna-and-rna-to-fold-into-precise-and-complex-shapes-can-be-exploited-for-applications-both-in-biology-and-electronics
#16
https://www.readbyqxmd.com/read/29216758/iron-age-italic-population-genetics-the-piceni-from-novilara-8th-7th-century-bc
#17
P Serventi, C Panicucci, R Bodega, S De Fanti, S Sarno, M Fondevila Alvarez, F Brisighelli, B Trombetta, P Anagnostou, G Ferri, A Vazzana, C Delpino, G Gruppioni, D Luiselli, E Cilli
BACKGROUND: Archaeological data provide evidence that Italy, during the Iron Age, witnessed the appearance of the first communities with well defined cultural identities. To date, only a few studies report genetic data about these populations and, in particular, the Piceni have never been analysed. AIMS: To provide new data about mitochondrial DNA (mtDNA) variability of an Iron Age Italic population, to understand the contribution of the Piceni in shaping the modern Italian gene pool and to ascertain the kinship between some individuals buried in the same grave within the Novilara necropolis...
December 7, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/29214493/virgibacillus-kimchii-sp-nov-a-halophilic-bacterium-isolated-from-kimchi
#18
Young Joon Oh, Ja-Young Jang, Seul Ki Lim, Min-Sung Kwon, Jieun Lee, NamHee Kim, Mi-Young Shin, Hyo Kyeong Park, Myung-Ji Seo, Hak-Jong Choi
A Gram-stain-positive, halophilic, rod-shaped, non-motile, spore forming bacterium, strain NKC1-2T, was isolated from kimchi, a Korean fermented food. Comparative analysis based on 16S rRNA gene sequence demonstrated that the isolated strain was a species of the genus Virgibacillus. Strain NKC1-2T exhibited high level of 16S rRNA gene sequence similarity with the type strains of Virgibacillus xinjiangensis SL6-1T (96.9%), V. sediminis YIM kkny3T (96.8%), and V. salarius SA-Vb1T (96.7%). The isolate grew at pH 6...
December 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/29214490/spirosoma-migulaei-sp-nov-isolated-from-soil
#19
Joseph Okiria, Leonid N Ten, Su-Jin Park, Seung-Yeol Lee, Dong Hoon Lee, In-Kyu Kang, Dae Sung Lee, Hee-Young Jung
A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, aerobic bacterium, designated 15J9-8T, was isolated from soil on Jeju Island, Republic of Korea. The isolate was able to grow between 10 and 30°C, pH 6.5-8.5, and in presence of 0-1% (w/v) NaCl. The results of comparative 16S rRNA gene sequence analysis indicated that strain 15J9-8T represented a member of the family Cytophagaceae, phylum Bacteroidetes, and was most closely related to Spirosoma aerophilum 5516J-17T (96.1% similarity), Spirosoma pulveris JSH5-14T (95...
December 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/29212941/a-novel-sulfolobus-virus-with-an-exceptional-capsid-architecture
#20
Haina Wang, Zhenqian Guo, Hongli Feng, Yufei Chen, Xiuqiang Chen, Zhimeng Li, Walter Hernández-Ascencio, Xin Dai, Zhenfeng Zhang, Xiaowei Zheng, Marielos Mora-López, Yu Fu, Chuanlun Zhang, Ping Zhu, Li Huang
A novel archaeal virus, denoted Sulfolobus ellipsoid virus 1 (SEV1), was isolated from an acidic hot spring in Costa Rica. The morphologically unique virion of SEV1 contains a protein capsid with 16 regularly spaced striations and an 11-nm-thick envelope. The capsid exhibits an unusual architecture in which the viral DNA, probably in the form of a nucleoprotein filament, wraps around the longitudinal axis of the virion in a plane to form a multilayered disk-like structure with a central hole, and 16 of these structures are stacked to generate a spool-like capsid...
December 6, 2017: Journal of Virology
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