keyword
MENU ▼
Read by QxMD icon Read
search

Yeast

keyword
https://www.readbyqxmd.com/read/29149597/structural-basis-for-shelterin-bridge-assembly
#1
Jin-Kwang Kim, Jinqiang Liu, Xichan Hu, Clinton Yu, Kyle Roskamp, Banumathi Sankaran, Lan Huang, Elizabeth A Komives, Feng Qiao
Telomere elongation through telomerase enables chromosome survival during cellular proliferation. The conserved multifunctional shelterin complex associates with telomeres to coordinate multiple telomere activities, including telomere elongation by telomerase. Similar to the human shelterin, fission yeast shelterin is composed of telomeric sequence-specific double- and single-stranded DNA-binding proteins, Taz1 and Pot1, respectively, bridged by Rap1, Poz1, and Tpz1. Here, we report the crystal structure of the fission yeast Tpz1(475-508)-Poz1-Rap1(467-496) complex that provides the structural basis for shelterin bridge assembly...
November 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29149300/the-effect-of-non-reversibility-on-inferring-rooted-phylogenies
#2
Svetlana Cherlin, Sarah E Heaps, Tom M W Nye, Richard J Boys, Tom A Williams, T Martin Embley
Most phylogenetic models assume that the evolutionary process is stationary and reversible. In addition to being biologically improbable, these assumptions also impair inference by generating models under which the likelihood does not depend on the position of the root. Consequently, the root of the tree cannot be inferred as part of the analysis. Yet identifying the root position is a key component of phylogenetic inference because it provides a point of reference for polarising ancestor/descendant relationships and therefore interpreting the tree...
November 15, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29149297/dna-knots-occur-in-intracellular-chromatin
#3
Antonio Valdés, Joana Segura, Sílvia Dyson, Belén Martínez-García, Joaquim Roca
In vivo DNA molecules are narrowly folded within chromatin fibers and self-interacting chromatin domains. Therefore, intra-molecular DNA entanglements (knots) might occur via DNA strand passage activity of topoisomerase II. Here, we assessed the presence of such DNA knots in a variety of yeast circular minichromosomes. We found that small steady state fractions of DNA knots are common in intracellular chromatin. These knots occur irrespective of DNA replication and cell proliferation, though their abundance is reduced during DNA transcription...
November 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29149190/improved-capture-of-drosophila-suzukii-by-a-trap-baited-with-two-attractants-in-the-same-device
#4
Rodrigo Lasa, Eduardo Tadeo, Ricardo A Toledo-Hérnandez, Lino Carmona, Itzel Lima, Trevor Williams
The improvement of trap-lure combinations is an important part of integrated pest management programs that involve monitoring pests for timely insecticide applications, or for their use in control strategies such as mass trapping or bait stations. In this study improvements in the capture of Drosophila suzukii were not observed following the inclusion of different color stimuli with respect to a red-black stripe cup trap. This red-black stripe trap with a hemispherical dome-shaped lid had a significantly improved physical retention of flies compared to traps fitted with a flat lid...
2017: PloS One
https://www.readbyqxmd.com/read/29149170/vibrio-parahaemolyticus-vtra-is-a-membrane-bound-regulator-and-is-activated-via-oligomerization
#5
Ryu Okada, Shigeaki Matsuda, Tetsuya Iida
Vibrio parahaemolyticus is a Gram-negative pathogen that causes food-borne gastroenteritis. A major virulence determinant of the organism is a type III secretion system (T3SS2) encoded on a pathogenicity island, Vp-PAI. Vp-PAI gene expression is regulated by two transcriptional regulators, VtrA and VtrB, whose N-terminal regions share homology with an OmpR-family DNA-binding domain. VtrA activates the gene expression of VtrB, which in turn activates Vp-PAI gene expression; however, the mechanism of this transcriptional activation by VtrA is not well understood...
2017: PloS One
https://www.readbyqxmd.com/read/29149055/exploration-for-the-salinity-tolerance-related-genes-from-xero-halophyte-atriplex-canescens-exploiting-yeast-functional-screening-system
#6
Gang Yu, Jingtao Li, Xinhua Sun, Yanzhi Liu, Xueliang Wang, Hao Zhang, Hongyu Pan
Plant productivity is limited by salinity stress, both in natural and agricultural systems. Identification of salt stress-related genes from halophyte can provide insights into mechanisms of salt stress tolerance in plants. Atriplex canescens is a xero-halophyte that exhibits optimum growth in the presence of 400 mM NaCl. A cDNA library derived from highly salt-treated A. canescens plants was constructed based on a yeast expression system. A total of 53 transgenic yeast clones expressing enhanced salt tolerance were selected from 10⁵ transformants...
November 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29149016/oleanane-type-saponins-from-the-roots-of-ligulariopsis-shichuana-and-their-%C3%AE-glucosidase-inhibitory-activities
#7
Hai-Bo Wu, Ting-Ting Liu, Wen-Shu Wang, Jin-Chao Feng, Hong-Mei Tian
Five new oleanane-type saponins, named ligushicosides A-E, and three known oleanane-type saponins were isolated from the roots of Ligulariopsis shichuana. Their structures were established by a combination of spectroscopic techniques, including 1D and 2D NMR and high resolution electrospray ionization mass spectroscopy (HR-ESI-MS). Furthermore, all isolates were evaluated for their yeast α-glucosidase inhibitory effects and exhibited potent inhibition against α-glucosidase, while compounds 1 and 2 showed excellent inhibitory activities...
November 17, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29148740/effect-of-an-imposed-contact-on-secondary-structure-in-the-denatured-state-of-yeast-iso-1-cytochome-c
#8
Travis A Danielson, Jessica M Stine, Tanveer A Dar, Klara Briknarova, Bruce E Bowler
There is considerable evidence that long-range interactions stabilize residual protein structure under denaturing conditions. However, evaluation of the effect of a specific contact on structure in the denatured state has been difficult. Iso-1-cytochrome c variants with a Lys54-->His mutation form a particularly stable His-heme loop in the denatured state, suggestive of loop-induced residual structure. We have used multidimensional NMR methods to assign (1)H and (15)N backbone amide and (13)C backbone and side chain chemical shifts in the denatured state of iso-1-cytochrome c carrying the Lys54-->His mutation in 3 and 6 M guanidine hydrochloride and at both pH 6...
November 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/29148054/transcriptome-analysis-unravels-an-ethylene-response-factor-involved-in-regulating-fruit-ripening-in-pear
#9
Ping-Ping Hao, Guo-Ming Wang, Hai-Yan Cheng, Ya-Qi Ke, Kai-Jie Qi, Chao Gu, Shao-Ling Zhang
Ethylene response factor (ERF) has been widely studied in regulating fruit ripening in tomato, apple, banana and kiwifruit, but little is known in pear. In this study 1-methylcyclopropene (1-MCP) treatment, an inhibitor of ethylene perception, was conducted at approximately 30 days before harvest to delay fruit ripening in a climacteric white pear cultivar Yali. Transcriptome libraries were constructed and sequenced in pre-ripening, ripening, and 1-MCP treated fruits. Data analysis showed that 73 candidate genes related to fruit ripening were induced by 1-MCP, among which two were positively related, namely 1-aminocyclopropane-1-carboxyla oxidase and an ERF gene (designated as ACO54 and ERF24)...
November 16, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/29147986/leachability-and-potential-ecotoxic-impact-of-trifluralin-impregnated-mulch
#10
Kevin J Bisceglia, Monika Dharia, Manpreet Kaur, Francesca A Pavlovici
The leachability, potential ecotoxicity, and photolysis of trifluralin-impregnated mulch, a popular retail consumer gardening product, were investigated under environmentally realistic conditions. Leachability of trifluralin from impregnated mulch was low (< 1% of total extractable compound) and in the range of reported values for agricultural soils. No trifluralin transformation products were detected in mulch leachate. Yeast-based estrogenicity and androgenicity screens indicated that aqueous trifluralin is not estrogenic but is moderately androgenic at concentrations ~ 1e - 5 M...
November 16, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29147976/evaluation-of-microbial-consortia-and-chemical-changes-in-spontaneous-maize-bran-fermentation
#11
Marilù Decimo, Mattia Quattrini, Giovanni Ricci, Maria Grazia Fortina, Milena Brasca, Tiziana Silvetti, Federica Manini, Daniela Erba, Franca Criscuoli, Maria Cristina Casiraghi
Sustainable exploitation of agro-industrial by-products has attracted great interest in cereal bran valorization. In this research, a polyphasic approach has been carried out to characterize maize bran at microbiological and chemical level during a sourdough like fermentation process, in order to enhance its technological and nutritional properties. Autochthonous microbiota was isolated at different refreshment steps and subjected to identification and molecular characterization. Fermentation was characterized by a rapid increase in lactic acid bacteria and yeasts, with a co-dominance, at the initial stage, of Weissella spp...
November 16, 2017: AMB Express
https://www.readbyqxmd.com/read/29147867/population-structure-of-candida-parapsilosis-no-genetic-difference-between-french-and-urugayan-isolates-using-microsatellite-length-polymorphism
#12
Marie Desnos-Ollivier, Victoria Bórmida, Philippe Poirier, Céline Nourrisson, Dinorah Pan, Stéphane Bretagne, Andrès Puime, Françoise Dromer
Candida parapsilosis is a human commensal yeast, frequently involved in infection worldwide and especially in neonates. It is the second species responsible for bloodstream infections in Uruguay and the third species in France. We were interested in knowing whether the population structure of isolates responsible for candidemia in France and in Uruguay was different. Genotyping methods based on microsatellite length polymorphism (MLP) have been described and are especially used for investigation of local outbreaks...
November 16, 2017: Mycopathologia
https://www.readbyqxmd.com/read/29147558/discovery-and-design-of-self-assembling-peptides
#13
REVIEW
Shuguang Zhang
Peptides are ubiquitous in nature and useful in many fields, from agriculture as pesticides, in medicine as antibacterial and antifungal drugs founded in the innate immune systems, to medicinal chemistry as hormones. However, the concept of peptides as materials was not recognized until 1990 when a self-assembling peptide as a repeating segment in a yeast protein was serendipitously discovered. Peptide materials are so called because they have bona fide materials property and are made from simple amino acids with well-ordered nanostructures under physiological conditions...
December 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/29147007/modulating-cellular-balance-of-rps3-mono-ubiquitination-by-both-hel2-e3-ligase-and-ubp3-deubiquitinase-regulates-protein-quality-control
#14
Youjin Jung, Hag Dong Kim, Hee Woong Yang, Hye Jin Kim, Chang-Young Jang, Joon Kim
When a ribosome complex is stalled during the translation elongation process in eukaryotes, the mono-ubiquitination of Rps3 has recently been shown to be critical to ribosome quality control. We have discovered that the regulatory role of Rps3 mono-ubiquitination is controlled by a deubiquitinase. We also showed that an autophagic signal appears to be coupled to the mono-ubiquitination of Rps3p through the entrance of Ubp3p into the autophagosome in yeasts. The mono-ubiquitination of the Rps3 protein is tightly modulated by reciprocal action between the Hel2p E3 ligase and the Ubp3p deubiquitinase in yeasts and the reciprocal action between the RNF123 E3 ligase and the USP10 deubiquitinase in mammalian cells...
November 17, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/29146944/structure-of-the-transcription-activator-target-tra1-within-the-chromatin-modifying-complex-saga
#15
Grigory Sharov, Karine Voltz, Alexandre Durand, Olga Kolesnikova, Gabor Papai, Alexander G Myasnikov, Annick Dejaegere, Adam Ben Shem, Patrick Schultz
The transcription co-activator complex SAGA is recruited to gene promoters by sequence-specific transcriptional activators and by chromatin modifications to promote pre-initiation complex formation. The yeast Tra1 subunit is the major target of acidic activators such as Gal4, VP16, or Gcn4 but little is known about its structural organization. The 430 kDa Tra1 subunit and its human homolog the transformation/transcription domain-associated protein TRRAP are members of the phosphatidyl 3-kinase-related kinase (PIKK) family...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29146901/genome-driven-evolutionary-game-theory-helps-understand-the-rise-of-metabolic-interdependencies-in-microbial-communities
#16
Ali R Zomorrodi, Daniel Segrè
Metabolite exchanges in microbial communities give rise to ecological interactions that govern ecosystem diversity and stability. It is unclear, however, how the rise of these interactions varies across metabolites and organisms. Here we address this question by integrating genome-scale models of metabolism with evolutionary game theory. Specifically, we use microbial fitness values estimated by metabolic models to infer evolutionarily stable interactions in multi-species microbial "games". We first validate our approach using a well-characterized yeast cheater-cooperator system...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29146871/postcatalytic-spliceosome-structure-reveals-mechanism-of-3-splice-site-selection
#17
Max E Wilkinson, Sebastian M Fica, Wojciech P Galej, Christine M Norman, Andrew J Newman, Kiyoshi Nagai
Introns are removed from eukaryotic mRNA precursors by the spliceosome in two transesterification reactions-branching and exon ligation. The mechanism of 3'-splice site recognition during exon ligation has remained unclear. Here we present the 3.7Å cryo-EM structure of the yeast P complex spliceosome immediately after exon ligation. The 3'-splice site AG dinucleotide is recognized through non-Watson-Crick pairing with the 5'-splice site and the branch point adenosine. After the branching reaction protein factors work together to remodel the spliceosome and stabilize a conformation competent for 3'-splice site docking, thereby promoting exon ligation...
November 16, 2017: Science
https://www.readbyqxmd.com/read/29146870/structure-of-the-yeast-spliceosomal-postcatalytic-p-complex
#18
Shiheng Liu, Xueni Li, Lingdi Zhang, Jiansen Jiang, Ryan C Hill, Yanxiang Cui, Kirk C Hansen, Z Hong Zhou, Rui Zhao
The spliceosome undergoes dramatic changes in a splicing cycle. Structures of B, B(act), C, C*, and ILS complexes revealed mechanisms of 5' splice site (ss) recognition, branching, and intron release, but lacked information on 3' ss recognition, exon ligation and release. Here, we report a cryoEM structure of the postcatalytic P complex at 3.3Å resolution, revealing that 3' ss is mainly recognized through non-Watson-Crick basepairing with the 5' ss and branch point. Furthermore, an unidentified protein becomes stably associated with the P complex, securing the 3' exon and potentially regulating Prp22 activity...
November 16, 2017: Science
https://www.readbyqxmd.com/read/29146766/lipid-droplet-biogenesis-is-spatially-coordinated-at-er-vacuole-contacts-under-nutritional-stress
#19
Hanaa Hariri, Sean Rogers, Rupali Ugrankar, Yang Lydia Liu, J Ryan Feathers, W Mike Henne
Eukaryotic cells store lipids in cytosolic organelles known as lipid droplets (LDs). Lipid droplet bud from the endoplasmic reticulum (ER), and may be harvested by the vacuole for energy during prolonged periods of starvation. How cells spatially coordinate LD production is poorly understood. Here, we demonstrate that yeast ER-vacuole contact sites (NVJs) physically expand in response to metabolic stress, and serve as sites for LD production. NVJ tether Mdm1 demarcates sites of LD budding, and interacts with fatty acyl-CoA synthases at the NVJ periphery...
November 16, 2017: EMBO Reports
https://www.readbyqxmd.com/read/29146582/elucidation-of-the-two-h3k36me3-histone-methyltransferases-set2-and-ash1-in-fusarium-fujikuroi-unravels-their-different-chromosomal-targets-and-a-major-impact-of-ash1-on-genome-stability
#20
Slavica Janevska, Leonie Baumann, Christian M K Sieber, Martin Münsterkötter, Jonas Ulrich, Jörg Kämper, Ulrich Güldener, Bettina Tudzynski
In this work, we present a comprehensive analysis of the H3K36 histone methyltransferases Set2 and Ash1 in the filamentous ascomycete Fusarium fujikuroi In Saccharomyces cerevisiae, one single methyltransferase, Set2, confers all H3K36 methylation, while there are two members of the Set2 family in filamentous fungi, and even more H3K36 methyltransferases in higher eukaryotes. Whereas the yeast Set2 homolog has been analyzed in fungi previously, the second member of the Set2 family, designated Ash1, has not been described for any filamentous fungus...
November 16, 2017: Genetics
keyword
keyword
5203
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"