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At least 19 recordsLinked to original sources
PubMed2004

Hereditary variation and genetic recombination in Koji-molds (Aspergillus oryzae and Asp. sojae). I. Natural variation.

Natural variation in monospore lines of Koji-molds (Asp. oryzae and Asp. sojae), isolated from commercial Koji material or soil and from laboratory stock cultures, has been observed. We can divide the 58 strains of Koji-molds investigated into two groups; one group consists of inconstant strains which are very liable to produce natural variants, and the other consists of strains which remain constant through successive single spore culture. The inconstant strains develop colonies bearing various proportions of conidia and aerial mycelium (X-type). They generally form large conidia (Asp. oryzae var. magnasporus) but sometimes medium sized conidia (Asp. oryzae s. str.), which produce large conidia occasionally. The colonies of the constant strains show abundant conidial formation and smooth surfaces (C-type). The conidia are mostly small (Asp. oryzae var. microsporus) but sometimes medium in size (Asp. oryzae s. str.). The colony types of the variants are as follows: C (Conidial type, whole colony covered with conidia), M (mycelial type), R (restricted in growth rate), St (sterile type, little sporulation on all media tested), Nit (requiring reduced nitrate, very faint growth on Czapek's agar), and LS (semi lethal, growth cease immediately after germination). Pedigree cultures of the 8 inconstant strains have been made, but no definite segregation ratios for each variant type have been recognized through successive generations. The LS and N types commonly occur spontaneously from the M-type.

Aspergillus↗
PubMed2006

Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis.

Genomic studies of natural variation in model organisms provide a bridge between molecular analyses of gene function and evolutionary investigations of adaptation and natural selection. In the model plant species Arabidopsis thaliana, recent studies of natural variation have led to the identification of genes underlying ecologically important complex traits, and provided new insights about the processes of genome evolution, geographic population structure, and the selective mechanisms shaping complex trait variation in natural populations. These advances illustrate the potential for a new synthesis to elucidate mechanisms for the adaptive evolution of complex traits from nucleotide sequences to real-world environments.

Adaptation, Biological↗
PubMed2002

The control of natural variation in cytosine methylation in Arabidopsis.

We explore the extent and sources of epigenetic variation in cytosine methylation in natural accessions of the flowering plant, Arabidopsis thaliana, by focusing on the methylation of the major rRNA gene repeats at the two nucleolus organizer regions (NOR). Our findings indicate that natural variation in NOR methylation results from a combination of genetic and epigenetic mechanisms. Genetic variation in rRNA gene copy number and trans-acting modifier loci account for some of the natural variation in NOR methylation. Our results also suggest that divergence and inheritance of epigenetic information, independent of changes in underlying nucleotide sequence, may play an important role in maintaining natural variation in cytosine methylation.

Arabidopsis↗
PubMed2006

Using DNA microarrays to study natural variation.

The emerging field of genomics examines the relationship between genetic and phenotypic variation by describing and analyzing patterns of natural variation on a genome-wide scale. In this endeavor, an important tool is the use of microarrays, which enable simultaneous screening of thousands of assays. Microarrays were originally designed for the detection of differences between samples and are thus ideally suited to high-throughput studies of natural variation. Novel microarray platforms enable the high throughput survey of variation at multiple levels, including DNA sequences, gene expression, protein binding, and methylation. However, most microarray data analysis tools, notably normalization methods, were developed for experiments in which only few features differed between samples. In studies of natural variation, this assumption does not always hold, raising a number of new challenges.

Animals↗
PubMed2003

Natural variation for seed oil composition in Arabidopsis thaliana.

The biochemical pathways involved in the biosynthesis and accumulation of storage lipids in seeds have been extensively studied. However, the regulatory mechanisms of those pathways, their environmental interactions and the ecological implications of variation are poorly understood. We have initiated a new approach: the analysis of natural variation in Arabidopsis thaliana. Three hundred and sixty accessions were surveyed for content of oil, very long chain fatty acids (VLCFAs) and polyunsaturated fatty acids (PUFAs) in their seeds. The results revealed extensive natural variation. A core set of accessions, the seeds of which reproducibly contain extreme amounts of oil, VLCFAs and PUFAs have been identified. Reproducible oil content ranged from 34.6 to 46.0% of seed dry weight. VLCFA content ranged from 13.0 to 21.2% of total fatty acids. PUFA content, ranged from 53.3 to 66.1% of total fatty acids. Interactions were also identified for PUFA and VLCFA content of seeds with vernalisation of plants. Mapping of the regions of the genome involved in controlling the traits was conducted in an F(2) population and indicated that natural variation at the loci FAE1 and FAD3 might be involved in the regulation of VLCFA and PUFA content, respectively. A set of accessions, which capture a broad range of the natural variation for these traits available in A. thaliana, has been selected to form a core set which can be used to further dissect the genetics of the regulation of seed lipid traits and to identify the genes involved.

Analysis of Variance↗
PubMedDate not supplied

Natural variation of cervical range of motion: a one-way repeated-measures design.

OBJECTIVE: To describe the natural variation of the active and passive cervical range of motion (ROM) in asymptomatic subjects over a 3-wk period. STUDY DESIGN: One-way repeated measures of active and passive cervical ROM. SETTING: Institute of Medical Biology (Center of Biomechanics) at Odense University, Denmark. PARTICIPANTS: Forty asymptomatic students from the University of Odense. Male/female ratio, 20:20; mean age, 23.9 yr (range, 20-30 yr). INTERVENTION: Measurements of the active and passive cervical ROM were taken using the electrogoniometer CA-6000 Spine Motion Analyzer. Each subject was measured six times during a 3-wk period. The measurements were performed at the same time of the day. The device gives the maximum end ROM for the motion plane examined. RESULTS: The natural variation in active and passive ROM was found to be in the order of chi +/- 20 degrees for flexion/extension, chi +/- 12 degrees for lateral flexion and chi +/- 14 degrees for rotation. CONCLUSION: In asymptomatic subjects, the individual natural variation is quite large for active and passive cervical flexion/extension, lateral flexion and rotation. When measuring individual patients, one should allow for a natural variation of 12-20 degrees.

Adult↗
PubMedDate not supplied

Mass spectrometry and natural variations of iron isotopes.

Although the processes that govern iron isotope variations in nature are just beginning to be understood, multiple studies attest of the virtue of this system to solve important problems in geosciences and biology. In this article, we review recent advances in the geochemistry, cosmochemistry, and biochemistry of iron isotopes. In Section 2, we briefly address the question of the nucleosynthesis of Fe isotopes. In Section 3, we describe the different methods for purifying Fe and analyzing its isotopic composition. The methods of SIMS, RIMS, and TIMS are presented but more weight is given to measurements by MC-ICPMS. In Section 4, the isotope anomalies measured in extraterrestrial material are briefly discussed. In Section 5, we show how high temperature processes like evaporation, condensation, diffusion, reduction, and phase partitioning can affect Fe isotopic composition. In Section 6, the various low temperature processes causing Fe isotopic fractionation are presented. These involve aqueous and biologic systems.

Journal Article↗
PubMed1990

Serial bone scans in Paget's disease: development of new lesions, natural variation in lesion intensity and nature of changes seen after treatment.

Serial radionuclide bone scans (n = 96) of 40 patients with Paget's disease were studied and tracer uptake graded using a four-point subjective scale. In nine patients studied without treatment the serial scan appearance improved in some, remained unchanged in others and deteriorated in yet others. Similarly individual lesions demonstrated increased, decreased or unchanged tracer uptake. One lesion disappeared without treatment but no new lesions developed. After treatment with aminohydroxypropylidene bisphosphonate (APD) or ethanehydroxy bisphosphonate (EHDP) the overall scan appearance improved in the majority of patients treated (n = 34), but individual lesions demonstrated increased (n = 20), unchanged (n = 79) or decreased uptake (n = 86). The mean reduction in tracer was 32% and 20 lesions reverted to normal intensity. The site of the lesion or the initial intensity of tracer uptake did not influence response to therapy. New lesions developed in five patients after therapy. There was variable correspondence between scintigraphic changes and biochemical parameters of response. From our study we conclude that serial bone scans must be used with caution when interpreting the response of Paget's disease to therapy.

Aged↗
PubMed1997

Ecological and evolutionary physiology of heat shock proteins and the stress response in Drosophila: complementary insights from genetic engineering and natural variation.

Classical adaptational and genetic engineering approaches offer complementary insights to understanding biological variation: the former elucidates the origins, magnitude and ecological context of natural variation, while the latter establishes which genes can underlie natural variation. Studies of the stress or heat shock response in Drosophila illustrate this point. At the cellular level, heat shock proteins (Hsps) function as molecular chaperones, minimizing aggregation of peptides in non-native conformations. To understand the adaptive significance of Hsps, we have characterized thermal stress that Drosophila experience in nature, which can be substantial. We used these findings to design ecologically relevant experiments with engineered Drosophila strains generated by unequal site-specific homologous recombination; these strains differ in hsp70 copy number but share sites of transgene integration. hsp70 copy number markedly affects Hsp70 levels in intact Drosophila, and strains with extra hsp70 copies exhibit corresponding differences in inducible thermotolerance and reactivation of a key enzyme after thermal stress. Elevated Hsp70 levels, however, are not without penalty; these levels retard growth and increase mortality. Transgenic variation in hsp70 copy number has counterparts in nature: isofemale lines from nature vary significantly in Hsp70 expression, and this variation is also correlated with both inducible thermotolerance and mortality in the absence of stress.

Animals↗
PubMed2006

Natural variation in replicative and chronological life spans of Saccharomyces cerevisiae.

Natural variation in the lifespan of natural yeast populations has not been systematically investigated. Here, we have quantified the variation in the replicative and chronological life spans (RLS and CLS) in natural isolates of Saccharomyces cerevisiae and found that genotypic variation accounts for about 22% of the total variation of RLS. Strikingly, the average RLS of 14 natural isolates is about 30% longer than that of 13 laboratory strains (32 versus 21 cell divisions). As is the case for aging in mammals, there is a negative correlation between the logarithmic transformation of the initial mortality rate and the Gompertz coefficient for RLS. Thus this characteristic feature of aging is conserved from yeast to mammals. The average CLS of the natural isolates is about 7 days, significantly shorter than that of the laboratory strains. There is no correlation between RLS and CLS in natural isolates. Possible reasons for the differences between natural and laboratory strains are discussed.

Cellular Senescence↗
PubMed1970

Deuterium: natural variations used as a biological tracer.

The suggestion is made that isotope tracing be carried out by monitoring the natural variations in deuterium concentrations. As an example, the natural variations in deuterium concentrations between food and water collected in Illinois and food and water collected in Colorado were used to determine the residence time of water in the blood and urine of rats. We observed not only a 5(1/2)-day turnover time of water in the blood and urine, but also evidence for the influx of water vapor from the atmosphere through the lungs into the blood.

Animals↗
PubMed2026

Natural variation in Miniature5 determines mitochondrial nad1 splicing and seed development in maize.

Seed size is a key determinant of cereal grain yield, but natural variations in defective-kernel genes have rarely been applied in maize breeding. Here, we report the positional cloning of maize Miniature5 (Mn5), which encodes a mitochondrial-targeted P-class pentatricopeptide repeat (PPR) protein. Further analysis shows that a missense mutation of Mn5, Mn5Val109, presents in maize populations and correlates with reduced seed size. The Mn5Val109 variant exhibits compromised function in the miniature5 (mn5-ref) mutant, failing to trans-splice mitochondrial nad1 intron1, drastically reducing the abundance and activity of respiratory complex I, accompanied by disorganized mitochondrial cristae. Mn5 directly binds to domain IV of the pre-nad1.1 transcript. Notably, this binding site is located downstream of the previously presumed 3'-terminus bound by MITOCHONDRIA STABILITY/PROCESSING PPR FACTOR1 (MSP1), thus redefining the 3'-end of the nad1.1 pre-RNA. Furthermore, Mn5 physically interacts with the maturases ZmnMAT1 and ZmnMAT3, as well as the PPR proteins PPR-SMR1 and SPR2, which are broadly involved in organellar group II intron splicing. Together, our results suggest that Mn5 recruits maturases and PPR proteins to form spliceosomal complexes responsible for the trans-splicing of nad1 intron1. Importantly, natural variations in Mn5 confer differences in seed size control, offering potential for breeding high-yield maize varieties.

Zea mays↗
PubMed1998

Functional and evolutionary implications of natural variation in clock genes.

Nearly all studies of natural variation within clock genes involve the period (per) locus, which was originally isolated in the fruit-fly. Intra- and interspecific work on per has focused mostly on a region of Thr-Gly or Ser-Gly repeats, which show rapid length and sequence evolution. The functional implications of nucleotide variation in this repetitive array have been characterised using behavioural, molecular, ecological, structural and statistical analyses. A population genetics approach to variation in per has also been useful in defining species histories within Drosophilids and, in some cases, in implicating selective processes in the evolution of the per gene. Interspecific analysis of per expression patterns reveals evolutionary alterations in this clock gene's regulation.

Animals↗
PubMed2025

Natural variation in the cytokinin oxidase gene ZmCKX6 influences leaf morphology and yield-related traits in maize.

Leaf width (LW) is a critical determinant of maize architecture and yield. To uncover its genetic basis, we performed a genome-wide association study (GWAS) on 348 maize inbred lines and identified ZmCKX6, encoding cytokinin oxidase/dehydrogenase, as a key gene associated with LW. Natural variation in the ZmCKX6 promoter significantly influenced its expression levels, leading to differences in LW across various haplotypes. Functional validation using CRISPR/Cas9 revealed that ZmCKX6 knockout results in pleiotropic effects, including narrower leaves, reduced plant height, and decreased grain yield components. These phenotypes were accompanied by elevated levels of active cytokinins but reduced levels of auxin, gibberellins, and salicylic acid. Transcriptome analysis revealed a significant downregulation of photosynthesis-related genes, corresponding to reduced photosynthetic rates in knockout lines. Evolutionary analysis demonstrated that the allele associated with narrower leaves were preferentially selected during maize domestication and breeding. This study highlights the role of ZmCKX6 in modulating cytokinin homeostasis and its subsequent impact on multiple agronomic traits in maize, providing insights into the complex genetic control of plant architecture and yield. The identified natural variations could be valuable for marker-assisted selection aimed at optimizing plant architecture and improving yield.

Zea mays↗
PubMed2003

Genomic approaches to analyzing natural variation in Arabidopsis thaliana.

The genomics tools available for studying Arabidopsis thaliana are a great resource for researchers trying to characterize and understand the genetic basis of natural variation. Abundant polymorphic markers aid quantitative trait locus (QTL) mapping, the fully sequenced genome provides rapid identification of candidate loci, and extensive knockout collections allow those candidate loci to be tested. Combining QTL mapping of classic phenotypic traits with biochemical or expression analysis is providing mechanistic insight into the traits of interest. Conversely, natural variation studies are now being done on genomic traits such as methylation or chiasma frequency.

Arabidopsis↗
PubMed2024

Natural variation of immune epitopes reveals intrabacterial antagonism.

Plants and animals detect biomolecules termed Microbe-Associated Molecular Patterns (MAMPs) and induce immunity. Agricultural production is severely impacted by pathogens which can be controlled by transferring immune receptors. However, most studies use a single MAMP epitope and the impact of diverse multi-copy MAMPs on immune induction is unknown. Here we characterized the epitope landscape from five proteinaceous MAMPs across 4,228 plant-associated bacterial genomes. Despite the diversity sampled, natural variation was constrained and experimentally testable. Immune perception in both Arabidopsis and tomato depended on both epitope sequence and copy number variation. For example, Elongation Factor Tu is predominantly single copy and 92% of its epitopes are immunogenic. Conversely, 99.9% of bacterial genomes contain multiple Cold Shock Proteins and 46% carry a non-immunogenic form. We uncovered a new mechanism for immune evasion, intrabacterial antagonism, where a non-immunogenic Cold Shock Protein blocks perception of immunogenic forms encoded in the same genome. These data will lay the foundation for immune receptor deployment and engineering based on natural variation.

comparative genomics↗
PubMed2024

Natural variation of immune epitopes reveals intrabacterial antagonism.

Plants and animals detect biomolecules termed microbe-associated molecular patterns (MAMPs) and induce immunity. Agricultural production is severely impacted by pathogens which can be controlled by transferring immune receptors. However, most studies use a single MAMP epitope and the impact of diverse multicopy MAMPs on immune induction is unknown. Here, we characterized the epitope landscape from five proteinaceous MAMPs across 4,228 plant-associated bacterial genomes. Despite the diversity sampled, natural variation was constrained and experimentally testable. Immune perception in both Arabidopsis and tomato depended on both epitope sequence and copy number variation. For example, Elongation Factor Tu is predominantly single copy, and 92% of its epitopes are immunogenic. Conversely, 99.9% of bacterial genomes contain multiple cold shock proteins, and 46% carry a nonimmunogenic form. We uncovered a mechanism for immune evasion, intrabacterial antagonism, where a nonimmunogenic cold shock protein blocks perception of immunogenic forms encoded in the same genome. These data will lay the foundation for immune receptor deployment and engineering based on natural variation.

Epitopes↗