scholarly journals Or22 allelic variation alone does not explain differences in discrimination of yeast-produced volatiles byD. melanogaster

2017 ◽  
Author(s):  
Carolyn Elya ◽  
Allison S. Quan ◽  
Kelly M. Schiabor ◽  
Michael B. Eisen
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Sequence Variation ◽  
Allelic Variation ◽  
Odorant Receptor ◽  
Fruit Fly ◽  
Nucleotide Polymorphisms ◽  
Enhanced Sensitivity ◽  
Yeast Ecology ◽  
Primary Driver ◽  
Increased Sensitivity

AbstractDifferent lines of the fruit flyDrosophila melanogastershow variation in the ability to discriminate between volatiles produced by the yeastSaccharomyces cerevisiaeunder natural (nitrogen-limiting, YVN) or laboratory (sugar-limiting, YVL) conditions. Previous work in our laboratory uncovered a strong correlation between heightened sensitivity to YVN wildD. melanogasterlines that harbored a chimeric variant of the highly variable odorant receptor 22 (Or22) locus ofD. melanogaster. We sought to determine if this trend held for an extended set ofD. melanogasterlines, if observed variation within chimeric and non-chimeric lines could be explained by nucleotide polymorphisms and if replacing Or22 with a chimeric allele in a non-chimeric background could confer the enhanced ability to detect YVN. In parallel, we performed crosses of chimeric and non-chimeric fly lines and assayed the behavior of their progeny for enhanced sensitivity to YVN to assess the heritability of the Or22 locus. Ultimately, we found that, while the overall trend of increased sensitivity to YVN in chimeric lines persists, there are exceptions and variation that cannot be explained by sequence variation at the Or22 locus. In addition, we did not observe increased sensitivity for YVN upon replacing the Or22 allele in a non-chimeric line (OreR) with that from our most YVN-sensitive, chimeric line (ME). Though our results do not support our hypothesis that Or22 is the primary driver of sensitivity to YVN, Or22 remains an interesting locus in the context of fly-yeast ecology.

scholarly journals Synonymous single nucleotide polymorphism in arsenic (+3) methyltransferase of the Western mosquitofish (Gambusia affinis) and its gene expression among field populations

Ecotoxicology ◽  
2021 ◽  
Author(s):  
Daesik Park ◽  
Catherine R. Propper ◽  
Guangning Wang ◽  
Matthew C. Salanga
Keyword(s):  
Gene Expression ◽  
Sequence Variation ◽  
Allelic Variation ◽  
Arsenic Concentration ◽  
Gambusia Affinis ◽  
Contamination Level ◽  
Water Medium ◽  
Single Nucleotide ◽  
Wide Range ◽  
High Arsenic

AbstractNaturally occurring arsenic is toxic at extremely low concentrations, yet some species persist even in high arsenic environments. We wanted to test if these species show evidence of evolution associated with arsenic exposure. To do this, we compared allelic variation across 872 coding nucleotides of arsenic (+3) methyltransferase (as3mt) and whole fish as3mt gene expression from three field populations of Gambusia affinis, from water sources containing low (1.9 ppb), medium-low (3.3 ppb), and high (15.7 ppb) levels of arsenic. The high arsenic site exceeds the US EPA’s Maximum Contamination Level for drinking water. Medium-low and high populations exhibited homozygosity, and no sequence variation across all animals sampled. Eleven of 24 fish examined (45.8%) in the low arsenic population harbored synonymous single nucleotide polymorphisms (SNPs) in exons 4 and/or 10. SNP presence in the low arsenic population was not associated with differences in as3mt transcript levels compared to fish from the medium-low site, where SNPs were noted; however, as3mt expression in fish from the high arsenic concentration site was significantly lower than the other two sites. Low sequence variation in fish populations from sites with medium-low and high arsenic concentrations suggests greater selective pressure on this allele, while higher variation in the low population suggests a relaxed selection. Our results suggest gene regulation associated with arsenic detoxification may play a more crucial role in influencing responses to arsenic than polymorphic gene sequence. Understanding microevolutionary processes to various contaminants require the evaluation of multiple populations across a wide range of pollution exposures.

scholarly journals Tempo and Mode of Ty Element Evolution in Saccharomyces cerevisiae

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1341-1351 ◽  
Author(s):  
I King Jordan ◽  
John F McDonald
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Negative Selection ◽  
Sequence Variation ◽  
Size Variation ◽  
Sequence Comparisons ◽  
Ty Elements ◽  
Ty Element ◽  
Amino Acid Sequence Variation ◽  
Element Evolution ◽  
High Level

Abstract The Saccharomyces cerevisiae genome contains five families of long terminal repeat (LTR) retrotransposons, Ty1–Ty5. The sequencing of the S. cerevisiae genome provides an unprecedented opportunity to examine the patterns of molecular variation existing among the entire genomic complement of Ty retrotransposons. We report the results of an analysis of the nucleotide and amino acid sequence variation within and between the five Ty element families of the S. cerevisiae genome. Our results indicate that individual Ty element families tend to be highly homogenous in both sequence and size variation. Comparisons of within-element 5′ and 3′ LTR sequences indicate that the vast majority of Ty elements have recently transposed. Furthermore, intrafamily Ty sequence comparisons reveal the action of negative selection on Ty element coding sequences. These results taken together suggest that there is a high level of genomic turnover of S. cerevisiae Ty elements, which is presumably in response to selective pressure to escape host-mediated repression and elimination mechanisms.

scholarly journals Screening for Modulators of Spermine Tolerance Identifies Sky1, the SR Protein Kinase of Saccharomyces cerevisiae, as a Regulator of Polyamine Transport and Ion Homeostasis

2001 ◽  
Vol 21 (1) ◽  
pp. 175-184 ◽  
Author(s):  
Omri Erez ◽  
Chaim Kahana
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Kinase ◽  
Osmotic Shock ◽  
Ion Homeostasis ◽  
Inorganic Ions ◽  
Yeast Cells ◽  
Wild Type ◽  
Sr Protein ◽  
Polyamine Transport ◽  
Increased Sensitivity

ABSTRACT Although most cells are capable of transporting polyamines, the mechanism that regulates polyamine transport in eukaryotes is still largely unknown. Using a genetic screen for clones capable of restoring spermine sensitivity to spermine-tolerant mutants ofSaccharomyces cerevisiae, we have demonstrated that Sky1p, a recently identified SR protein kinase, is a key regulator of polyamine transport. Yeast cells deleted for SKY1 developed tolerance to toxic levels of spermine, while overexpression of Sky1p in wild-type cells increased their sensitivity to spermine. Expression of the wild-type Sky1p but not of a catalytically inactive mutant restored sensitivity to spermine. SKY1 disruption results in dramatically reduced uptake of spermine, spermidine, and putrescine. In addition to spermine tolerance, sky1Δ cells exhibit increased tolerance to lithium and sodium ions but somewhat increased sensitivity to osmotic shock. The observed halotolerance suggests potential regulatory interaction between the transport of polyamines and inorganic ions, as suggested in the case of the Ptk2p, a recently described regulator of polyamine transport. We demonstrate that these two kinases act in two different signaling pathways. While deletion or overexpression of SKY1 did not significantly affect Pma1p activity, the ability of overexpressed Sky1p, Ptk1p, and Ptk2p to increase sensitivity to LiCl depends on the integrity ofPPZ1 but not of ENA1.

GENETIC VARIATION IN RARE AND WIDESPREAD LOMATIUM SPECIES (APIACEAE): A COMPARISON OF AFLP AND SSCP DATA

2001 ◽  
Vol 58 (2) ◽  
pp. 347-356 ◽  
Author(s):  
M. A. GITZENDANNER ◽  
P. S. SOLTIS
Keyword(s):  
Rare Species ◽  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Allelic Variation ◽  
Plant Conservation ◽  
Single Copy ◽  
Small Populations ◽  
Nucleotide Polymorphisms ◽  
Widespread Species ◽  
Low Levels

Plant conservation genetics has been hampered by a lack of markers for studies of levels and patterns of variation in rare species. We investigated the levels of variation in several rare and widespread species of the western North American genus Lomatium Raf. (Apiaceae) using two relatively new molecular markers: AFLPs and single-strand conformation polymorphisms (SSCPs). For each species, approximately 150 AFLP loci have been scored, yielding estimates of species-level percent polymorphic loci in rare species ranging from near zero to over 80%. Levels of AFLP diversity were similar in two of the rare species, L. bradshawii (Rose ex Mathias) Mathas & Constance and L. ochocense Helliwell & Constance, and the widespread species. The third rare species, L. cookii Kagan, which has small populations, has low levels of diversity based on AFLPs. We also examined nucleotide diversity at the single-copy nuclear-DNA locus glyceraldehyde 3-phosphate dehydrogenase (Gap-C). PCR-amplified segments were analysed for allelic variation using SSCPs, and intrapopulational nucleotide polymorphisms were identified in both L. bradshawii and L. cookii. In the 211bp segment of Gap-C analysed, five nucleotide sites were segregating within populations of L. bradshawii and two in L. cookii.

scholarly journals Single Nucleotide Polymorphism in SMAD7 and CHI3L1 and Colorectal Cancer Risk

2018 ◽  
Vol 2018 ◽  
pp. 1-23 ◽  
Author(s):  
Amal Ahmed Abd El-Fattah ◽  
Nermin Abdel Hamid Sadik ◽  
Olfat Gamil Shaker ◽  
Amal Mohamed Kamal
Keyword(s):  
Colorectal Cancer ◽  
Genetic Variation ◽  
Sequence Variation ◽  
Regulatory Protein ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
The Third ◽  
Common Cancer ◽  
Cancer Initiation

Colorectal cancer (CRC) is one of the leading cancers throughout the world. It represents the third most common cancer and the fourth in mortality. Most of CRC are sporadic, arise with no known high-penetrant genetic variation and with no previous family history. The etiology of sporadic CRC is considered to be multifactorial and arises from the interaction of genetic variants of low-penetrant genes and environmental risk factors. The most common well-studied genetic variation is single nucleotide polymorphisms (SNPs). SNP arises as a point mutation. If the frequency of the sequence variation reaches 1% or more in the population, it is referred to as polymorphism, but if it is lower than 1%, the allele is typically considered as a mutation. Lots of SNPs have been associated with CRC development and progression, for example, genes of TGF-β1 and CHI3L1 pathways. TGF-β1 is a pleiotropic cytokine with a dual role in cancer development and progression. TGF-β1 mediates its actions through canonical and noncanonical pathways. The most important negative regulatory protein for TGF-β1 activity is termed SMAD7. The production of TGF-βcan be controlled by another protein called YKL-40. YKL-40 is a glycoprotein with an important role in cancer initiation and metastasis. YKL-40 is encoded by the CHI3L1 gene. The aim of the present review is to give a brief introduction of CRC, SNP, and examples of some SNPs that have been documented to be associated with CRC. We also discuss two important signaling pathways TGF-β1 and CHI3L1 that influence the incidence and progression of CRC.

A recording porometer with detachable cups operating on four separate leaves

1962 ◽  
Vol 156 (962) ◽  
pp. 1-13 ◽  
Keyword(s):  
Carbon Dioxide ◽  
Carbon Dioxide Concentration ◽  
Ambient Air ◽  
Short Supply ◽  
Enhanced Sensitivity ◽  
Stomatal Behaviour ◽  
New Instrument ◽  
Leaf Surfaces ◽  
Increased Sensitivity ◽  
Experimental Treatments

A new form of recording resistance porometer is described which enables records of stomatal behaviour to be obtained concurrently from four different leaves; the porometer cups are automatically detached between readings, exposing the leaf surfaces to the ambient air in order to avoid artifacts due to changes in carbon dioxide concentration. The readings are recorded for the four leaves seriatim , the cup for each remaining attached for 3 min out of every ½ h. The results of several of the preliminary experiments carried out to test the new instrument are presented: 1. Continuous records for periods up to 6 days appear to have no serious effect on the functioning of the stomata under normal conditions. With Taraxacum officinale slightly greater stomatal opening was recorded on the fifth day than on the first; for wheat a slight falling off occurred on the third and fourth days, possibly due to ageing of the leaves. 2. The stomata of similar leaves on different plants which have been subjected throughout to the same sequence of conditions show remarkable uniformity of behaviour at any one time; a great increase in the precision of comparisons of experimental treatments should thus be achieved by applying them to such leaves and recording the results concurrently. 3. Experiments with plants of T . officinale , wheat and Xanthium pennsylvanicum subjected to increasing water strain have shown a marked closing response to the process of taking a reading (which involves forcing air through the leaf). This closing response is first seen some time before visible wilting occurs and for X. pennsylvanicum has been shown to be mainly if not entirely due to a greatly increased sensitivity to carbon dioxide. The biological implica­tions of this are discussed. The stomata (e. g. of T. officinale ) may not re-open fully for 2 or 3 days after re-watering, when the plant is recovering from water strain, but the enhanced sensitivity to readings is only shown while water is actually in short supply, and not during the period of recovery.

scholarly journals Allelic variation contributes to bacterial host specificity

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Min Yue ◽  
Xiangan Han ◽  
Leon De Masi ◽  
Chunhong Zhu ◽  
Xun Ma ◽  
...  
Keyword(s):  
Allelic Variation ◽  
Multinomial Logistic Regression ◽  
Gene Gain ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Serovar Typhimurium ◽  
Functional Analyses ◽  
High Degree

Abstract Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

scholarly journals Associations between Oxytocin Receptor Gene Polymorphisms, Empathy towards Animals and Implicit Associations towards Animals

Animals ◽  
2018 ◽  
Vol 8 (8) ◽  
pp. 140 ◽  
Author(s):  
Melanie Connor ◽  
Alistair Lawrence ◽  
Sarah Brown
Keyword(s):  
Social Behaviour ◽  
Allelic Variation ◽  
Receptor Gene ◽  
Oxytocin Receptor ◽  
Implicit Associations ◽  
Nucleotide Polymorphisms ◽  
Psychological Variables ◽  
Oxytocin Receptor Gene ◽  
Receptor Gene Polymorphisms ◽  
Human Social Behaviour

Oxytocin has been well researched in association with psychological variables and is widely accepted as a key modulator of human social behaviour. Previous work indicates involvement of oxytocin receptor gene (OXTR) single nucleotide polymorphisms (SNPs) in human-human empathy, however little is known about associations of OXTR SNPs with empathy and affective reactions of humans towards animals. Five OXTR SNPs previously found to associate with human social behaviour were genotyped in 161 students. Empathy towards animals and implicit associations were evaluated. A General Linear Model was used to investigate the OXTR alleles and allelic combinations along with socio-demographic variables and their influence on empathy towards animals. Empathy towards animals showed a significant association with OXTR SNP rs2254298; homozygous G individuals reported higher levels of empathy towards animals than heterozygous (GA). Our preliminary findings show, for the first time, that between allelic variation in OXTR and animal directed empathy in humans maybe associated, suggesting that OXTRs social behaviour role crosses species boundaries, warranting independent replication.

A novel role for DNA photolyase: binding to DNA damaged by drugs is associated with enhanced cytotoxicity in Saccharomyces cerevisiae

1994 ◽  
Vol 14 (12) ◽  
pp. 8071-8077
Author(s):  
M E Fox ◽  
B J Feldman ◽  
G Chu
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Uv Radiation ◽  
Excision Repair ◽  
Yeast Cells ◽  
Repair System ◽  
Dna Photolyase ◽  
Yeast Saccharomyces Cerevisiae ◽  
Pyrimidine Dimers ◽  
Increased Sensitivity ◽  
Nitroquinoline Oxide

DNA photolyase binds to and repairs cyclobutane pyrimidine dimers induced by UV radiation. Here we demonstrate that in the yeast Saccharomyces cerevisiae, photolyase also binds to DNA damaged by the anticancer drugs cis-diamminedichloroplatinum (cis-DDP) and nitrogen mustard (HN2) and by the alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Surprisingly, mutations in photolyase were associated with resistance of yeast cells to cis-DDP, MNNG, 4-nitroquinoline oxide (4NQO), and HN2. Transformation of yeast photolyase mutants with the photolyase gene increased sensitivity to these agents. Thus, while the binding of photolyase to DNA damaged by UV radiation aids survival of the cell, binding to DNA damaged by other agents may interfere with cell survival, perhaps by making the lesions inaccessible to the nucleotide excision repair system.

scholarly journals The P5A ATPase Spf1p is stimulated by phosphatidylinositol 4-phosphate and influences cellular sterol homeostasis

2019 ◽  
Vol 30 (9) ◽  
pp. 1069-1084 ◽  
Author(s):  
Danny Mollerup Sørensen ◽  
Henrik Waldal Holen ◽  
Jesper Torbøl Pedersen ◽  
Helle Juel Martens ◽  
Daniele Silvestro ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Endoplasmic Reticulum ◽  
Marked Change ◽  
Hydrolytic Activity ◽  
Genetic Interactions ◽  
Eukaryotic Cells ◽  
Lipid Bodies ◽  
Increased Sensitivity ◽  
Phosphatidylinositol 4 ◽  
P Type

P5A ATPases are expressed in the endoplasmic reticulum (ER) of all eukaryotic cells, and their disruption results in severe ER stress. However, the function of these ubiquitous membrane proteins, which belong to the P-type ATPase superfamily, is unknown. We purified a functional tagged version of the Saccharomyces cerevisiae P5A ATPase Spf1p and observed that the ATP hydrolytic activity of the protein is stimulated by phosphatidylinositol 4-phosphate (PI4P). Furthermore, SPF1 exhibited negative genetic interactions with SAC1, encoding a PI4P phosphatase, and with OSH1 to OSH6, encoding Osh proteins, which, when energized by a PI4P gradient, drive export of sterols and lipids from the ER. Deletion of SPF1 resulted in increased sensitivity to inhibitors of sterol production, a marked change in the ergosterol/lanosterol ratio, accumulation of sterols in the plasma membrane, and cytosolic accumulation of lipid bodies. We propose that Spf1p maintains cellular sterol homeostasis by influencing the PI4P-induced and Osh-mediated export of sterols from the ER.

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