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https://www.readbyqxmd.com/read/29474735/mads-box-genes-and-crop-domestication-the-jack-of-all-traits
#1
Susanne Schilling, Sirui Pan, Alice Kennedy, Rainer Melzer
MADS-box genes are key regulators of virtually every aspect of plant reproductive development. They play especially prominent roles in flowering time control, inflorescence architecture, floral organ identity determination, and seed development. The developmental and evolutionary importance of MADS-box genes is widely acknowledged. However, their role during flowering plant domestication is less well recognized. Here, we provide an overview illustrating that MADS-box genes have been important targets of selection during crop domestication and improvement...
February 21, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29474620/a-conserved-leucine-zipper-like-motif-accounts-for-strong-tetramerization-capabilities-of-sepallata-like-mads-domain-transcription-factors
#2
Florian Rümpler, Günter Theißen, Rainer Melzer
The development of angiosperm flowers is regulated by homeotic MIKC-type MADS-domain transcription factors that activate or repress target genes via the formation of DNA-bound, organ specific tetrameric complexes. The protein-protein interaction (PPI) capabilities differ considerably between different MIKC-type proteins. The floral homeotic protein SEPALLATA3 (SEP3) acts as a hub that incorporates numerous other MADS-domain proteins into tetrameric complexes that would otherwise not form. However, the molecular mechanisms that underlie these promiscuous interactions remain largely unknown...
February 21, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29473821/luteimonas-rhizosphaerae-sp-nov-isolated-from-the-rhizosphere-of-triticum-aestivum-l
#3
Guo-Yan Zhao, Fei Shao, Mi Zhang, Xue-Jie Zhang, Jing-Yuan Wang, Shou-Jin Fan, Mei-Xue Dai
A Gram-stain-negative, rod-shaped bacterium, strain 4-12T , was isolated from the rhizosphere of Triticum aestivum L. from the Xiaokai River irrigation area, China. The isolate grew optimally at 30 °C, pH 7.5-8.0 and with 1.0 % (w/v) NaCl. Based on the 16S rRNA gene sequence and phylogenetic analysis, strain 4-12T belonged to the genus Luteimonas with the highest degree of 16S rRNA gene sequence similarity to Luteimonas tolerans UM1T (97.68 %), followed by Luteimonas terrae THG-MD21T (97.67 %), Lysobacter panaciterrae Gsoil 068T (97...
February 23, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29472273/a-unified-approach-for-quantifying-and-interpreting-dna-shape-readout-by-transcription-factors
#4
H Tomas Rube, Chaitanya Rastogi, Judith F Kribelbauer, Harmen J Bussemaker
Transcription factors (TFs) interpret DNA sequence by probing the chemical and structural properties of the nucleotide polymer. DNA shape is thought to enable a parsimonious representation of dependencies between nucleotide positions. Here, we propose a unified mathematical representation of the DNA sequence dependence of shape and TF binding, respectively, which simplifies and enhances analysis of shape readout. First, we demonstrate that linear models based on mononucleotide features alone account for 60-70% of the variance in minor groove width, roll, helix twist, and propeller twist...
February 22, 2018: Molecular Systems Biology
https://www.readbyqxmd.com/read/29469688/bizionia-berychis-sp-nov-isolated-from-intestinal-tract-of-a-splendid-alfonsino-beryx-splendens
#5
Young-Ok Kim, In-Suk Park, Sooyeon Park, Bo-Hye Nam, Dong-Gyun Kim, Seok-Gwan Choi, Jin-Woo Bae, Jung-Hoon Yoon
A Gram-stain-negative, non-motile, aerobic and rod-shaped bacterial strain, designated RA3-3-1T , was isolated from splendid alfonsino (Beryxsplendens) collected from the North Pacific Ocean. Strain RA3-3-1T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 1.0-3.0 % (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain RA3-3-1T belonged to the genus Bizionia, clustering with the type strain of Bizionia fulviae. Strain RA3-3-1T exhibited 16S rRNA gene sequence similarities of 98...
February 22, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29468317/paucibacter-aquatile-sp-nov-isolated-from-freshwater-of-the-nakdong-river-republic-of-korea
#6
Young Ho Nam, Ahyoung Choi, Jung Moon Hwang, Kyung June Yim, Jee-Hwan Kim, Gang-Guk Choi, Eu Jin Chung
A Gram-negative, aerobic, motile, and rod-shaped bacterial strain designated CR182T was isolated from freshwater of the Nakdong River, Republic of Korea. Optimal growth conditions for this novel strain were found to be: 25-30 °C, pH 6.5-8.5, and 3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicates that the strain CR182T belongs to type strains of genus Paucibacter. Strain CR182T showed 98.0% 16S rRNA gene sequence similarity with Paucibacter oligotrophus CHU3T and formed a robust phylogenetic clade with this species...
February 21, 2018: Archives of Microbiology
https://www.readbyqxmd.com/read/29467794/detection-of-potential-problematic-cytb-gene-sequences-of-fishes-in-genbank
#7
Xiaobing Li, Xuejuan Shen, Xiao Chen, Dan Xiang, Robert W Murphy, Yongyi Shen
Fishes are, by far, the most diverse group of vertebrates. Their classification relies heavily on morphology. In practice, the correct morphological identification of species often depends on personal experience because many species vary in their body shape, color and other external characters. Thus, the identification of a species may be prone to errors. Due to the rapid development of molecular biology, the number of sequences of fishes deposited in GenBank has grown explosively. These published data likely contain errors owing to invalid or incorrectly identified species...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29467738/worlds-apart-transcriptome-profiles-of-key-oral-microbes-in-the-periodontal-pocket-compared-to-single-laboratory-culture-reflect-synergistic-interactions
#8
Zhi-Luo Deng, Helena Sztajer, Michael Jarek, Sabin Bhuju, Irene Wagner-Döbler
Periodontitis is a worldwide prevalent oral disease which results from dysbiosis of the periodontal microbiome. Some of the most active microbial players, e.g., Porphyromonas gingivalis, Treponema denticola , and Fusobacterium nucleatum , have extensively been studied in the laboratory, but it is unclear to which extend these findings can be transferred to in vivo conditions. Here we show that the transcriptional profiles of P. gingivalis, T. denticola , and F. nucleatum in the periodontal niche are distinct from those in single laboratory culture and exhibit functional similarities...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29467457/adenylosuccinate-lyase-enhances-aggressiveness-of-endometrial-cancer-by-increasing-killer-cell-lectin-like-receptor-c3-expression-by-fumarate
#9
Haengki Park, Kenji Ohshima, Satoshi Nojima, Shinichiro Tahara, Masako Kurashige, Yumiko Hori, Daisuke Okuzaki, Naoki Wada, Jun-Ichiro Ikeda, Eiichi Morii
Adenylosuccinate lyase (ADSL) is an enzyme that plays important roles in de novo purine synthesis. Although ADSL was reported to be upregulated in various malignancies, such as colorectal, breast, and prostate cancer, as well as gliomas, the mechanism by which elevated ADSL expression contributes to cancer has not been elucidated. We previously performed a shotgun proteomics analysis to characterize specific proteins associated with the properties of the aldehyde dehydrogenase (ALDH)-high cell population, which was reported to be involved in tumorigenic potential, and showed that ADSL expression is upregulated in the ALDH-high population of endometrial cancer...
February 21, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/29466359/cdk-activity-provides-temporal-and-quantitative-cues-for-organizing-genome-duplication
#10
Anthony Perrot, Christopher Lee Millington, Blanca Gómez-Escoda, Diane Schausi-Tiffoche, Pei-Yun Jenny Wu
In eukaryotes, the spatial and temporal organization of genome duplication gives rise to distinctive profiles of replication origin usage along the chromosomes. While it has become increasingly clear that these programs are important for cellular physiology, the mechanisms by which they are determined and modulated remain elusive. Replication initiation requires the function of cyclin-dependent kinases (CDKs), which associate with various cyclin partners to drive cell proliferation. Surprisingly, although we possess detailed knowledge of the CDK regulators and targets that are crucial for origin activation, little is known about whether CDKs play a critical role in establishing the genome-wide pattern of origin selection...
February 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29465340/bacillus-alkalitolerans-sp-nov-isolated-from-marine-sediment-near-a-hydrothermal-vent
#11
Yan Liu, Min Yu, Xiao-Hua Zhang
A Gram-stain-positive, endospore-forming, rod-shaped, motile and strictly aerobic strain, designated T3-209T , was isolated from sediment sampled at a water depth of 1206 m of the southern Okinawa Trough at station T1 (25.07° N, 122.58° E) near the Tangyin hydrothermal vent during an expedition on the R/V Kexue in May 2014. The strain was able to grow at a temperature range of 10-42 °C (optimum 28 °C). Growth was observed at NaCl concentrations (w/v) of 0-6 % (optimum 0 %). The pH range for growth was 7...
February 21, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29465339/edaphobacter-lichenicola-sp-nov-a-member-of-the-family-acidobacteriaceae-from-lichen-dominated-forested-tundra
#12
Svetlana E Belova, Natalia E Suzina, W Irene C Rijpstra, Jaap S Sinninghe Damsté, Svetlana N Dedysh
An isolate of aerobic, Gram-stain-negative, rod-shaped, non-motile and light-pink pigmented bacteria, designated SBC68T , was obtained from slightly decomposed thalli of the lichen Cladonia sp. collected from the forested tundra of north-western Siberia. Cells of this isolate occurred singly, in pairs or in rosettes. These bacteria were acidophilic (optimum growth at pH 4.3-5.6) and mesophilic (optimum growth at 20-30 °C) but were also capable of growth at low temperatures, down to 7 °C. The preferred growth substrates were sugars, some organic acids and lichenan...
February 21, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29465222/dna-nanotechnology-enabled-drug-delivery-systems
#13
Qinqin Hu, Hua Li, Lihua Wang, Hongzhou Gu, Chunhai Fan
Over the past decade, we have seen rapid advances in applying nanotechnology in biomedical areas including bioimaging, biodetection, and drug delivery. As an emerging field, DNA nanotechnology offers simple yet powerful design techniques for self-assembly of nanostructures with unique advantages and high potential in enhancing drug targeting and reducing drug toxicity. Various sequence programming and optimization approaches have been developed to design DNA nanostructures with precisely engineered, controllable size, shape, surface chemistry, and function...
February 21, 2018: Chemical Reviews
https://www.readbyqxmd.com/read/29464363/corallibacterium-pacifica-gen-nov-sp-nov-a-novel-bacterium-of-the-family-vibrionaceae-isolated-from-hard-coral
#14
Sachithra Amarin Hettiarachchi, Su-Jin Lee, Youngdeuk Lee, Young-Kyung Kwon, Kae Kyoung Kwon, Sung-Hyun Yang, Eunyoung Jo, Do-Hyung Kang, Chulhong Oh
A gram-negative, rod-shaped, motile, oxidase- and catalase-positive, non-pigmented marine bacterium, designated strain OS-11M-2T , was isolated from a coral sample collected from the Osakura coastal area in Micronesia. Phylogenetic analysis based on 16S ribosomal RNA (rRNA) gene sequences indicated that strain OS-11M-2T is a member of the family Vibrionaceae, its closest neighbors being Photobacterium damselae subsp. piscicida NCIMB 2058T (94.9%), Photobacterium damselae subsp. damselae CIP 102761T (94.75%), Grimontia marina IMCC5001T (94...
February 20, 2018: Current Microbiology
https://www.readbyqxmd.com/read/29464361/flavobacterium-chungangensis-sp-nov-a-bacterium-isolated-from-soil-of-chinese-cabbage-garden
#15
Md Amdadul Huq, Shahina Akter, Sun-Young Lee
A novel bacterial strain MAH-10T was isolated from soil sample of a Chinese cabbage garden, Republic of Korea and was characterized using a polyphasic approach. Cells were Gram-staining negative, rod-shaped, yellowish orange colored, and motile. The strain was aerobic, catalase and oxidase are positive, and optimum growth temperature and pH were 28 °C and 6.5, respectively. Flexirubin-type pigments were found to be present. On the basis of 16S rRNA gene sequence analysis, strain MAH-10T belongs to the genus Flavobacterium and is most closely related to Flavobacterium tyrosinilyticum KCTC 42726T (98...
February 20, 2018: Current Microbiology
https://www.readbyqxmd.com/read/29463659/a-near-complete-haplotype-phased-genome-of-the-dikaryotic-wheat-stripe-rust-fungus-puccinia-striiformis-f-sp-tritici-reveals-high-interhaplotype-diversity
#16
Benjamin Schwessinger, Jana Sperschneider, William S Cuddy, Diana P Garnica, Marisa E Miller, Jennifer M Taylor, Peter N Dodds, Melania Figueroa, Robert F Park, John P Rathjen
A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high-quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here, we present a diploid-aware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long reads using the FALCON-Unzip assembler...
February 20, 2018: MBio
https://www.readbyqxmd.com/read/29463315/x-chromosome-dosage-and-presence-of-sry-shape-sex-specific-differences-in-dna-methylation-at-an-autosomal-region-in-human-cells
#17
Bianca Ho, Keelin Greenlaw, Abeer Al Tuwaijri, Sanny Moussette, Francisco Martínez, Elisa Giorgio, Alfredo Brusco, Giovanni Battista Ferrero, Natália D Linhares, Eugênia R Valadares, Marta Svartman, Vera M Kalscheuer, Germán Rodríguez Criado, Catherine Laprise, Celia M T Greenwood, Anna K Naumova
BACKGROUND: Sexual dimorphism in DNA methylation levels is a recurrent epigenetic feature in different human cell types and has been implicated in predisposition to disease, such as psychiatric and autoimmune disorders. To elucidate the genetic origins of sex-specific DNA methylation, we examined DNA methylation levels in fibroblast cell lines and blood cells from individuals with different combinations of sex chromosome complements and sex phenotypes focusing on a single autosomal region--the differentially methylated region (DMR) in the promoter of the zona pellucida binding protein 2 (ZPBP2) as a reporter...
February 20, 2018: Biology of Sex Differences
https://www.readbyqxmd.com/read/29462174/exposure-to-1-8-ghz-electromagnetic-fields-affects-morphology-dna-related-raman-spectra-and-mitochondrial-functions-in-human-lympho-monocytes
#18
M Lasalvia, R Scrima, G Perna, C Piccoli, N Capitanio, P F Biagi, L Schiavulli, T Ligonzo, M Centra, G Casamassima, A Ermini, V Capozzi
Blood is a fluid connective tissue of human body, where it plays vital functions for the nutrition, defense and well-being of the organism. When circulating in peripheral districts, it is exposed to some physical stresses coming from outside the human body, as electromagnetic fields (EMFs) which can cross the skin. Such fields may interact with biomolecules possibly inducing non thermal-mediated biological effects at the cellular level. In this study, the occurrence of biochemical/biological modifications in human peripheral blood lympho-monocytes exposed in a reverberation chamber for times ranging from 1 to 20 h to EMFs at 1...
2018: PloS One
https://www.readbyqxmd.com/read/29462164/phylogeography-and-dna-based-species-delimitation-provide-insight-into-the-taxonomy-of-the-polymorphic-rose-chafer-protaetia-potosia-cuprea-species-complex-coleoptera-scarabaeidae-cetoniinae-in-the-western-palearctic
#19
Dominik Vondráček, Aneta Fuchsová, Dirk Ahrens, David Král, Petr Šípek
The development of modern methods of species delimitation, unified under the "integrated taxonomy" approach, allows a critical examination and re-evaluation of complex taxonomic groups. The rose chafer Protaetia (Potosia) cuprea is a highly polymorphic species group with a large distribution range. Despite its overall commonness, its taxonomy is unclear and subject to conflicting hypotheses, most of which largely fail to account for its evolutionary history. Based on the sequences of two mitochondrial markers from 65 individuals collected across the species range, and a detailed analysis of morphological characters including a geometric morphometry approach, we infer the evolutionary history and phylogeography of the P...
2018: PloS One
https://www.readbyqxmd.com/read/29461184/cryobacterium-aureum-sp-nov-a-psychrophilic-bacterium-isolated-from-glacier-ice-collected-from-the-ice-tongue-surface
#20
Qing Liu, Yu-Hua Xin, Xiu-Ling Chen, Hong-Can Liu, Yu-Guang Zhou, Wen-Xin Chen
A psychrophilic, Gram-stain-positive, rod-shaped bacterium, designated strain Hh31T , was isolated from Xinjiang No. 1 Glacier in China. Strain Hh31T was catalase-positive, oxidase-negative and able to grow at between 0-18 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Hh31T belonged to the genus Cryobacterium and was most closely related to the type strains of Cryobacterium levicorallinum, Cryobacterium luteum and Cryobacterium flavum. DNA-DNA hybridization, calculation of average nucleotide identity and digital DNA-DNA hybridization revealed that strain Hh31T was distinct from its closest phylogenetic neighbours...
February 20, 2018: International Journal of Systematic and Evolutionary Microbiology
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