keyword
MENU ▼
Read by QxMD icon Read
search

Yeast

keyword
https://www.readbyqxmd.com/read/28655158/coretracker-accurate-codon-reassignment-prediction-applied-to-mitochondrial-genomes
#1
Noutahi Emmanuel, Calderon Virginie, Blanchette Mathieu, Lang B Franz, El-Mabrouk Nadia
Motivation: Codon reassignments have been reported across all domains of life. With the increasing number of sequenced genomes, the development of systematic approaches for genetic code detection is essential for accurate downstream analyses. Three automated prediction tools exist so far: FACIL, GenDecoder and Bagheera; the last two respectively restricted to metazoan mitochondrial genomes and CUG reassignments in yeast nuclear genomes. These tools can only analyze a single genome at a time and are often not followed by a validation procedure, resulting in a high rate of false positives...
June 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28654906/p53-p63-and-p73-in-the-wonderland-of-s-cerevisiae
#2
REVIEW
Olivier Billant, Marc Blondel, Cécile Voisset
Since its discovery in 1979, p53 has been on the forefront of cancer research. It is considered a master gene of cancer suppression and is found mutated in around 50% of all human tumors. In addition, the progressive identification of p53-related transcription factors p63 and p73 as well as their multiple isoforms have added further layers of complexity to an already dense network. Among the numerous models used to unravel the p53 family mysteries, S. cerevisiae has been particularly useful. This seemingly naive model allows the expression of a functional human p53 and thus the assessment of p53 intrinsic transcriptional activity...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28654751/substrate-recognition-mechanism-of-the-putative-yeast-carnosine-n-methyltransferase
#3
Xiwen Liu, Jialiang Wu, Yujie Sun, Wei Xie
Anserine (β-alanyl-N(Pi) -methyl-L-histidine) is a natural metabolite present in skeletal muscle and the central nervous system of vertebrates, and plays important physiological roles in living organisms. The production of anserine is catalyzed by carnosine N-methyltransferases, which transfer a methyl group to carnosine (β-alanyl-L-histidine). However, the structural basis of the substrate recognition for the enzymes is unknown. We present the crystal structure of the putative carnosine N-methyltransferase from yeast named YNL092W in complex with SAH, solved by the single-wavelength anomalous dispersion (SAD) method...
June 27, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28654660/isolation-and-characterization-of-gmmybj3-an-r2r3-myb-transcription-factor-that-affects-isoflavonoids-biosynthesis-in-soybean
#4
Mingzhu Zhao, Tianliang Wang, Ping Wu, Wenyun Guo, Liantai Su, Ying Wang, Yajing Liu, Fan Yan, Qingyu Wang
Isoflavonoids are secondary metabolites that play a variety of roles in plant-microbe interactions and plant defenses against abiotic stresses. Here we report a new MYB transcription factor (TF) gene, GmMYBJ3, that is involved in the isoflavonoids biosynthesis. The GmMYBJ3 gene is 1,002 bp long and encodes a protein of 333 amino acids. Amino acid sequence analysis showed that GmMYBJ3 is a typical R2R3 MYB TF. Yeast expression experiment demonstrated that GmMYBJ3 has its transcription activity in the nucleus and is transiently expressed in onion epidermal cells...
2017: PloS One
https://www.readbyqxmd.com/read/28654659/environmental-change-drives-accelerated-adaptation-through-stimulated-copy-number-variation
#5
Ryan M Hull, Cristina Cruz, Carmen V Jack, Jonathan Houseley
Copy number variation (CNV) is rife in eukaryotic genomes and has been implicated in many human disorders, particularly cancer, in which CNV promotes both tumorigenesis and chemotherapy resistance. CNVs are considered random mutations but often arise through replication defects; transcription can interfere with replication fork progression and stability, leading to increased mutation rates at highly transcribed loci. Here we investigate whether inducible promoters can stimulate CNV to yield reproducible, environment-specific genetic changes...
June 2017: PLoS Biology
https://www.readbyqxmd.com/read/28654248/multiplexed-sequence-specific-capture-of-chromatin-and-mass-spectrometric-discovery-of-associated-proteins
#6
Yunxiang Dai, Julia Kennedy-Darling, Michael R Shortreed, Mark Scalf, Audrey P Gasch, Lloyd M Smith
Comprehensive understanding of a gene's expression and regulation at the molecular level requires identification of all proteins interacting with the gene. HyCCAPP (Hybridization Capture of Chromatin Associated Proteins for Proteomics) is an approach that uses single-stranded DNA oligonucleotides to capture specific genomic sequences in cross-linked chromatin fragments, and identify associated proteins by mass spectrometry. Previous studies have shown HyCCAPP to provide useful information on protein-DNA interactions, revealing the proteins associated with the Gal1-10 region in yeast...
June 27, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28653998/cell-free-production-of-pentacyclic-triterpenoid-compound-betulinic-acid-from-betulin-by-the-engineered-saccharomyces-cerevisiae
#7
Jianan Wu, Yongwu Niu, Abdelmoneim Bakur, Hao Li, Qihe Chen
Betulinic acid is a product of plant secondary metabolism which has shown various bioactivities. Several CYP716A subfamily genes were recently characterized encoding multifunctional oxidases capable of C-28 oxidation. CYP716A12 was identified as betulin C-28 oxidase, capable of modifying betulin. This study aimed to induce the transformation of betulin to betulinic acid by co-expressing enzymes CYP716A12 from Medicago truncatula and ATR1 from Arabidopsis thaliana in Saccharomyces cerevisiae. The microsome protein extracted from the transgenic yeast successfully catalyzed the transformation of betulin to betulinic acid...
June 27, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28653743/genetic-diversity-and-pectinolytic-activity-of-epiphytic-yeasts-from-grape-carposphere
#8
M Cilião Filho, M B D Bertéli, J S Valle, L D Paccola-Meirelles, G A Linde, F G Barcellos, N B Colauto
The genetic diversity of epiphytic yeasts from grape carposphere is susceptible to environmental variations that determine the predominant carposphere microbiota. Understanding the diversity of yeasts that inhabit grape carposphere in different environments and their pectinolytic activity is a way to understand the biotechnological potential that surrounds us and help improve winemaking. Therefore, this study aimed to evaluate the pectinolytic activity and characterize the genetic diversity of isolated epiphytic yeasts from grape carposphere...
June 20, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28653724/probing-functional-roles-of-wilson-disease-protein-atp7b-copper-binding-domains-in-yeast
#9
Kumaravel Ponnandai Shanmugavel, Dina Petranovic, Pernilla Wittung-Stafshede
After Ctr1-mediated uptake into human cells, copper (Cu) ions are transported by the cytoplasmic Cu chaperone Atox1 to the Wilson disease protein (ATP7B) in the Golgi network. Cu transfer occurs via direct protein-protein interactions and leads to incorporation of Cu into Cu-dependent enzymes. ATP7B is a large multi-domain membrane-spanning protein which, in contrast to homologs, has six cytoplasmic metal-binding domains (MBDs). The reason for multiple MBDs is proposed to be indirect modulation of activity but mechanistic studies of full-length ATP7B are limited...
June 27, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28653109/the-life-of-psi
#10
REVIEW
Brian Cox, Mick Tuite
The AAA+ disaggregase Hsp104 is essential for the maintenance and inheritance of nearly all known prions of the yeast Saccharomyces cerevisiae. Uniquely for [PSI (+)], the prion form of the Sup35 protein, there seem to be two activities, involving differing co-chaperones, by which Hsp104 affects the inheritance of [PSI (+)], the prion form of the Sup35 protein. Each pathway is also involved in protection against ageing, one through disaggregation of damaged proteins and the other through their retention in the mother cell during budding...
June 26, 2017: Current Genetics
https://www.readbyqxmd.com/read/28652865/crispr-cas9-enabled-genetic-disruptions-for-understanding-ethanol-and-ethyl-acetate-biosynthesis-in-kluyveromyces-marxianus
#11
Ann-Kathrin Löbs, Ronja Engel, Cory Schwartz, Andrew Flores, Ian Wheeldon
BACKGROUND: The thermotolerant yeast Kluyveromyces marxianus shows promise as an industrial host for the biochemical production of fuels and chemicals. Wild-type strains are known to ferment high titers of ethanol and can effectively convert a wide range of C5, C6, and C12 sugars into the volatile short-chain ester ethyl acetate. Strain engineering, however, has been limited due to a lack of advanced genome-editing tools and an incomplete understanding of ester and ethanol biosynthesis...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28652824/fungal-endophthalmitis-in-an-elderly-woman-differing-responses-in-each-eye
#12
Rei Sakata, Jiro Numaga
Candida endophthalmitis is caused by hematogenous metastasis of the yeast. To ensure early diagnosis, serodiagnosis, or surveillance culturing is usually performed. If fungemia is apparent upon successive serological testing (in at least two tests: blood culture and/or measurement of β-d-glucan level), ophthalmic consultation is necessary, even if no ophthalmic complaint is evident. This is because early detection with prompt prescription of systemic antifungal agents inhibits progression of the distinctive cholioretinitis...
2017: International Medical Case Reports Journal
https://www.readbyqxmd.com/read/28652406/deciphering-the-role-of-the-signal-and-sty1-kinase-dependent-phosphorylation-of-the-stress-responsive-transcription-factor-atf1-on-gene-activation
#13
Clàudia Salat-Canela, Esther Paulo, Laura Sánchez-Mir, Mercè Carmona, José Ayté, Baldo Oliva, Elena Hidalgo
Adaptation to stress triggers the most dramatic shift in gene expression in fission yeast (Schizosaccharomyces pombe), and this response is driven by signaling via the MAPK Sty1. Upon activation, Sty1 accumulates in the nucleus, and stimulates expression of hundreds of genes via the nuclear transcription factor Atf1, including expression of atf1 itself. However, the role of stress-induced, Sty1-mediated Atf1 phosphorylation in transcriptional activation is unclear. To this end, we expressed Atf1 phosphorylation mutants from a constitutive promoter, to uncouple Atf1 activity from endogenous, stress-activated Atf1 expression...
June 26, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28652389/structural-differences-between-yeast-and-mammalian-microtubules-revealed-by-cryo-em
#14
Stuart C Howes, Elisabeth A Geyer, Benjamin LaFrance, Rui Zhang, Elizabeth H Kellogg, Stefan Westermann, Luke M Rice, Eva Nogales
Microtubules are polymers of αβ-tubulin heterodimers essential for all eukaryotes. Despite sequence conservation, there are significant structural differences between microtubules assembled in vitro from mammalian or budding yeast tubulin. Yeast MTs were not observed to undergo compaction at the interdimer interface as seen for mammalian microtubules upon GTP hydrolysis. Lack of compaction might reflect slower GTP hydrolysis or a different degree of allosteric coupling in the lattice. The microtubule plus end-tracking protein Bim1 binds yeast microtubules both between αβ-tubulin heterodimers, as seen for other organisms, and within tubulin dimers, but binds mammalian tubulin only at interdimer contacts...
June 26, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28652377/causal-genetic-variation-underlying-metabolome-differences
#15
Devjanee Swain-Lenz, Igor Nikolisky, Jiye Cheng, Priya Sudarsanam, Darcy Nayler, Max V Staller, Barak A Cohen
An ongoing challenge in biology is to predict the phenotypes of individuals from their genotypes. Genetic variants that cause disease often change an individual's total metabolite profile, or metabolome. In light of our extensive knowledge of metabolic pathways, genetic variants that alter the metabolome may help predict novel phenotypes. To link genetic variants to changes in the metabolome, we studied natural variation in the yeast Saccharomyces cerevisiae We used an untargeted mass spectrometry method to identify dozens of metabolite Quantitative Trait Loci (mQTL), genomic regions containing genetic variation that control differences in metabolite levels between individuals...
June 26, 2017: Genetics
https://www.readbyqxmd.com/read/28652264/analysis-of-the-zar1-immune-complex-reveals-determinants-for-immunity-and-molecular-interactions
#16
Maël Baudin, Jana A Hassan, Karl Schreiber, Jennifer D Lewis
Plants depend on innate immunity to prevent disease. Plant pathogenic bacteria, like Pseudomonas syringae and Xanthomonas campestris, use the type III secretion system as a molecular syringe to inject type III secreted effector (T3SE) proteins in plants. The primary function of most T3SEs is to suppress immunity, however the plant can evolve NBD-LRR domain-containing (NLR) proteins to recognize specific T3SEs. The AtZAR1 NLR induces strong defense responses against P. syringae and X. campestris. The P. syringae T3SE HopZ1a is an acetyltransferase that acetylates the pseudokinase AtZED1, and triggers recognition by AtZAR1...
June 26, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28652237/the-candidate-antimalarial-drug-mmv665909-causes-oxygen-dependent-mrna-mistranslation-and-synergises-with-quinoline-derived-antimalarials
#17
Cindy Vallières, Simon V Avery
To cope with growing resistance to current antimalarials, new drugs with novel modes of action are urgently needed. Molecules targeting protein synthesis appear to be promising candidates. We identified a compound (MMV665909) from the MMV Malaria Box of candidate antimalarials that could produce synergistic growth inhibition with the aminoglycoside antibiotic paromomycin, suggesting a possible action of the compound in mRNA mistranslation. This mechanism of action was substantiated with the yeast cell model using available reporters of mistranslation and other genetic tools...
June 26, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28652216/fungemia-and-necrotic-lymph-node-infection-with-sporopachydermia-cereana-in-a-patient-with-acute-myeloid-leukemia
#18
Craig Kingston, Michael Medinger, Florian Banderet-Uglioni, Stefano Bassetti, Mario Bargetzi, Sebastian Haubitz, Christoph A Fux, Veronika Bättig, Daniel Goldenberger, Jakob Passweg, Marc Heizmann
Sporopachydermia cereana is a rare yeast found in necrotic cactus-tissue, predominantly in the Americas. Infection in humans with clinical data has only been reported in four patients so far, all of whom died, either directly from the pathogen or from other complications of immunosuppression. Treatment of the yeast is complicated by difficulties in identification of the pathogen with conventional diagnostic techniques and by intrinsic resistance to echinocandins. We present herewith the first patient who survived a disseminated infection with S...
June 23, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/28652019/sphingolipids-from-the-human-fungal-pathogen-aspergillus-fumigatus
#19
REVIEW
Thierry Fontaine
Sphingolipids (SPLs) are key components of the plasma membrane in yeast and filamentous fungi. These molecules are involved in a number of cellular processes, and particularly, SGLs are essential components of the highly polarized fungal growth where they are required for the formation of the polarisome organization at the hyphal apex. Aspergillus fumigatus, a human fungal pathogen, produce SGLs that are discriminated into neutral cerebrosides, glycosylinositolphosphoceramides (GIPCs) and glycosylphosphatidylinositol (GPI) anchors...
June 23, 2017: Biochimie
https://www.readbyqxmd.com/read/28651982/design-and-optimization-of-highly-selective-broad-spectrum-fungal-cyp51-inhibitors
#20
Christopher M Yates, Edward P Garvey, Sammy R Shaver, Robert J Schotzinger, William J Hoekstra
While the orally-active azoles such as fluconazole and posaconazole are effective antifungal agents, they potently inhibit a broad range of off-target human cytochrome P450 enzymes (CYPs) leading to various safety issues (e.g., drug-drug interactions, liver, and reproductive toxicities). Recently we described the rationally-designed, antifungal agent VT-1161 that is more selective for fungal CYP51 than related human CYP enzymes such as CYP3A4. Herein, we describe the use of a homology model of Aspergillus fumigatus to design and optimize a novel series of highly selective, broad spectrum fungal CYP51 inhibitors...
June 15, 2017: Bioorganic & Medicinal Chemistry Letters
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"