Molecular and Behavioral Analysis of Four period Mutants in Drosophila melanogaster Encompassing Extreme Short, Novel Long, and Unorthodox Arrhythmic Types

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 165-178
Author(s):  
Melanie J Hamblen ◽  
Neal E White ◽  
Philip T J Emery ◽  
Kim Kaiser ◽  
Jeffrey C Hall
Keyword(s):  
Drosophila Melanogaster ◽  
Constant Darkness ◽  
Aberrant Splicing ◽  
Single Nucleotide ◽  
Long Period ◽  
Single Nucleotide Change ◽  
Short Novel ◽  
Evening Peak ◽  
Period Mutants ◽  
Clock Protein

Abstract Of the mutationally defined rhythm genes in Drosophila melanogaster, period (per) has been studied the most. We have molecularly characterized three older per mutants—perT, perClk, and per04—along with a novel long-period one (perSLIH). Each mutant is the result of a single nucleotide change. perT, perClk, and perSLIH are accounted for by amino acid substitutions; per04 is altered at a splice site acceptor and causes aberrant splicing. perSLIH exhibits a long period of 27 hr in constant darkness and entrains to light/dark (L/D) cycles with a later-than-normal evening peak of locomotion. perSLIH males are more rhythmic than females. perSLIH's clock runs faster at higher temperatures and slower at lower ones, exhibiting a temperature-compensation defect opposite to that of perLong. The per-encoded protein (PER) in the perT mutant cycles in L/D with an earlier-than-normal peak; this peak in perSLIH is later than normal, and there was a slight difference in the PER timecourse of males vs. females. PER in per04 was undetectable. Two of these mutations, perSLIH and perClk, lie within regions of PER that have not been studied previously and may define important functional domains of this clock protein.

scholarly journals Isolation and Analysis of Six timeless Alleles That Cause Short- or Long-Period Circadian Rhythms in Drosophila

Genetics ◽  
2000 ◽  
Vol 156 (2) ◽  
pp. 665-675
Author(s):  
Adrian Rothenfluh ◽  
Marla Abodeely ◽  
Jeffrey L Price ◽  
Michael W Young
Keyword(s):  
Nuclear Translocation ◽  
Phase Response Curve ◽  
Fixed Number ◽  
Constant Darkness ◽  
Genetic Screens ◽  
Protein Levels ◽  
Long Period ◽  
Short Period ◽  
Molecular Oscillation ◽  
New Alleles

Abstract In genetic screens for Drosophila mutations affecting circadian locomotion rhythms, we have isolated six new alleles of the timeless (tim) gene. Two of these mutations cause short-period rhythms of 21–22 hr in constant darkness, and four result in long-period cycles of 26–28 hr. All alleles are semidominant. Studies of the genetic interactions of some of the tim alleles with period-altering period (per) mutations indicate that these interactions are close to multiplicative; a given allele changes the period length of the genetic background by a fixed percentage, rather than by a fixed number of hours. The timL1 allele was studied in molecular detail. The long behavioral period of timL1 is reflected in a lengthened molecular oscillation of per and tim RNA and protein levels. The lengthened period is partly caused by delayed nuclear translocation of TIML1 protein, shown directly by immunocytochemistry and indirectly by an analysis of the phase response curve of timL1 flies.

scholarly journals Impact of a Single Nucleotide Change or Non-Nucleoside Modifications in G-Rich Region on the Quadruplex–Duplex Hybrid Formation

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1236
Author(s):  
Dorota Gudanis ◽  
Karolina Zielińska ◽  
Daniel Baranowski ◽  
Ryszard Kierzek ◽  
Piotr Kozłowski ◽  
...  
Keyword(s):  
Target Sequence ◽  
Rich Region ◽  
Rna Sequences ◽  
Single Nucleotide ◽  
Alternative Structures ◽  
Single Nucleotide Change ◽  
G Quadruplex ◽  
Quadruplex Formation ◽  
Target Rna ◽  
Insight Into

In this paper, a method to discriminate between two target RNA sequences that differ by one nucleotide only is presented. The method relies on the formation of alternative structures, i.e., quadruplex–duplex hybrid (QDH) and duplex with dangling ends (Dss), after hybridization of DNA or RNA G-rich oligonucleotides with target sequences containing 5′–GGGCUGG–3′ or 5′–GGGCGGG–3′ fragments. Using biophysical methods, we studied the effect of oligonucleotide types (DNA, RNA), non-nucleotide modifications (aliphatic linkers or abasic), and covalently attached G4 ligand on the ability of G-rich oligonucleotides to assemble a G-quadruplex motif. We demonstrated that all examined non-nucleotide modifications could mimic the external loops in the G-quadruplex domain of QDH structures without affecting their stability. Additionally, some modifications, in particular the presence of two abasic residues in the G-rich oligonucleotide, can induce the formation of non-canonical QDH instead of the Dss structure upon hybridization to a target sequence containing the GGGCUGG motif. Our results offer new insight into the sequential requirements for the formation of G-quadruplexes and provide important data on the effects of non-nucleotide modifications on G-quadruplex formation.

scholarly journals Altered Utilization of N-Acetyl-d-Galactosamine by Escherichia coli O157:H7 from the 2006 Spinach Outbreak

2007 ◽  
Vol 190 (5) ◽  
pp. 1710-1717 ◽  
Author(s):  
Amit Mukherjee ◽  
Mark K. Mammel ◽  
J. Eugene LeClerc ◽  
Thomas A. Cebula
Keyword(s):  
Escherichia Coli ◽  
Gene Cluster ◽  
Culture Collection ◽  
Base Substitution ◽  
Phosphotransferase System ◽  
Single Nucleotide ◽  
E Coli ◽  
Single Nucleotide Change ◽  
Phenotype Comparison ◽  
In Silico Analyses

ABSTRACT In silico analyses of previously sequenced strains of Escherichia coli O157:H7, EDL933 and Sakai, localized the gene cluster for the utilization of N-acetyl-d-galactosamine (Aga) and d-galactosamine (Gam). This gene cluster encodes the Aga phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) and other catabolic enzymes responsible for transport and catabolism of Aga. As the complete coding sequences for enzyme IIA (EIIA)Aga/Gam, EIIBAga, EIICAga, and EIIDAga of the Aga PTS are present, E. coli O157:H7 strains normally are able to utilize Aga as a sole carbon source. The Gam PTS complex, in contrast, lacks EIICGam, and consequently, E. coli O157:H7 strains cannot utilize Gam. Phenotypic analyses of 120 independent isolates of E. coli O157:H7 from our culture collection revealed that the overwhelming majority (118/120) displayed the expected Aga+ Gam− phenotype. Yet, when 194 individual isolates, derived from a 2006 spinach-associated E. coli O157:H7 outbreak, were analyzed, all (194/194) displayed an Aga− Gam− phenotype. Comparison of aga/gam sequences from two spinach isolates with those of EDL933 and Sakai revealed a single nucleotide change (G:C→A:T) in the agaF gene in the spinach-associated isolates. The base substitution in agaF, which encodes EIIAAga/Gam of the PTS, changes a conserved glycine residue to serine (Gly91Ser). Pyrosequencing of this region showed that all spinach-associated E. coli O157:H7 isolates harbored this same G:C→A:T substitution. Notably, when agaF + was cloned into an expression vector and transformed into six spinach isolates, all (6/6) were able to grow on Aga, thus demonstrating that the Gly91Ser substitution underlies the Aga− phenotype in these isolates.

scholarly journals Identification of Genes Contributing to a Long Circadian Period in Drosophila Melanogaster

2020 ◽  
pp. 074873042097594
Author(s):  
Shailesh Kumar ◽  
Ilker Tunc ◽  
Terry R. Tansey ◽  
Mehdi Pirooznia ◽  
Susan T. Harbison
Keyword(s):  
Locomotor Activity ◽  
Genome Wide Association Study ◽  
Clock Genes ◽  
Critical Role ◽  
Constant Darkness ◽  
Circadian Period ◽  
Wild Type ◽  
Genetic Rescue ◽  
Long Period ◽  
Activity Behavior

The endogenous circadian period of animals and humans is typically very close to 24 h. Individuals with much longer circadian periods have been observed, however, and in the case of humans, these deviations have health implications. Previously, we observed a line of Drosophila with a very long average period of 31.3 h for locomotor activity behavior. Preliminary mapping indicated that the long period did not map to known canonical clock genes but instead mapped to multiple chromosomes. Using RNA-Seq, we surveyed the whole transcriptome of fly heads from this line across time and compared it with a wild-type control. A three-way generalized linear model revealed that approximately two-thirds of the genes were expressed differentially among the two genotypes, while only one quarter of the genes varied across time. Using these results, we applied algorithms to search for genes that oscillated over 24 h, identifying genes not previously known to cycle. We identified 166 differentially expressed genes that overlapped with a previous Genome-wide Association Study (GWAS) of circadian behavior, strongly implicating them in the long-period phenotype. We tested mutations in 45 of these genes for their effect on the circadian period. Mutations in Alk, alph, CG10089, CG42540, CG6034, Kairos ( CG6123), CG8768, klg, Lar, sick, and tinc had significant effects on the circadian period, with seven of these mutations increasing the circadian period of locomotor activity behavior. Genetic rescue of mutant Kairos restored the circadian period to wild-type levels, suggesting it has a critical role in determining period length in constant darkness.

scholarly journals Molecular basis for the human erythrocyte glycophorin specifying the Miltenberger class I (MiI) phenotype

Blood ◽  
1992 ◽  
Vol 80 (1) ◽  
pp. 257-263 ◽  
Author(s):  
CH Huang ◽  
P Spruell ◽  
JJ Moulds ◽  
OO Blumenfeld
Keyword(s):  
Molecular Basis ◽  
Consensus Sequence ◽  
Direct Repeat ◽  
Single Copy ◽  
Class I ◽  
Blood Group System ◽  
White Family ◽  
Single Nucleotide ◽  
Single Nucleotide Change ◽  
Polymerase Chain

Abstract Human glycophorin Mil (HGpMil) is a structural variant of the MNSs blood group system that specifies the Miltenberger class I phenotype. We report here the molecular basis of the HGpMil gene identified in a white family in which the first homozygote was encountered. Immunoblotting analysis showed the expression of HGpMil and HGpB but the absence of HGpA on the homozygous Mil erythrocytes. Southern blot analysis detected no gross alterations in gene structure or band intensity. Genomic sequences encompassing exons II and III of the HGpMil gene were amplified by single-copy polymerase chain reaction. Restriction digestion and direct DNA sequence analysis showed that HGpMil gene is derived from an alpha N allele of HGpA and differs from the latter in the third exon by a single nucleotide change. In HGpMil, the presence of a deoxythymidine at the second position of codon 28 (ATG) not only resulted in a methionine substitution but also altered the consensus sequence for N-glycosylation from Asn-Asp-Thr to Asn-Asp- Met. These data are consistent with the occurrence of Mil on the red blood cell membrane as a variant deficient in the asparagine-linked carbohydrate unit. Significantly, this particular point mutation lies in between the two half-sites of a direct repeat that has been implicated to facilitate the recombination events leading to several other glycophorin genes of the Miltenberger series. Based on this relatedness, we propose an untemplated nucleotide replacement resulting from a gene conversion event as the molecular basis for the origin of HGpMil gene.

Novel single-nucleotide change inGYP*Ain a person who made an alloantibody to a new high-prevalence MNS antigen called ENEV

Transfusion ◽  
2010 ◽  
Vol 50 (4) ◽  
pp. 856-860 ◽  
Author(s):  
Randall W. Velliquette ◽  
Zong Hu ◽  
Christine Lomas-Francis ◽  
Kim Hue-Roye ◽  
Jean L. Allen ◽  
...  
Keyword(s):  
Nucleotide Change ◽  
Single Nucleotide ◽  
Single Nucleotide Change ◽  
High Prevalence

A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome

Genome ◽  
2004 ◽  
Vol 47 (2) ◽  
pp. 389-398 ◽  
Author(s):  
Joanne Russell ◽  
Allan Booth ◽  
John Fuller ◽  
Brian Harrower ◽  
Peter Hedley ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Wild Barley ◽  
Genomic Ssrs ◽  
Dna Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Change ◽  
Single Nucleotide ◽  
Single Nucleotide Change ◽  
Haplotype Data ◽  
Fertile Crescent

Direct estimates of sequence diversity provides an abundant source of DNA polymorphisms based on single nucleotide polymorphisms (SNPs). The frequency and distribution of nucleotide diversity within 23 genes associated with grain germination in barley were determined in a sample of accessions representing European cultivars, landraces, and wild barley accessions from throughout the fertile crescent. The overall nucleotide diversity ranged from 0.0021 to 0.0189 with a single nucleotide change being detected every 78 bp and insertion–deletion events being observed every 680 bp. Within the cultivated (H. vulgare) genepool, a small number of haplotypes were detected, the total number of haplotypes observed in H. spontaneum was almost double that detected in H. vulgare (46 and 26, respectively). Distinct haplotypes were observed in the H. spontaneum and landrace genepools, which are highly divergent from H. vulgare. A comparison of SNP-based haplotype data with EST-derived SSRs and genomic SSRs revealed a similar trend of decreasing variability in the cultivated genepool. However, the number of unique alleles identified in the cultivated sample was much greater with genomic SSRs (18%) compared with only 2.1% for SNPs and 3.8% for EST-derived SSRs. The potential utility of SNPs and EST-derived SSRs for association mapping in barley is discussed.Key words: SNPs, haplotype, SSRs, barley.

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