Elimination of micronuclear specific DNA sequences early in anlagen development

After conjugation in Tetrahymena thermophila, the old macronuclei degenerate, and new macronuclei (anlagen) develop. During anlagen development a number of DNA sequences found in the micronuclear genome (micronuclear limited sequences) are eliminated from the anlagen. A cloned copy of a repetitive micronuclear limited sequence has been used to determine the developmental stage at which micronuclear limited sequences are eliminated. DNAs from anlagen of various developmental stages were examined by Southern analysis. It was found that micronuclear limited sequences are present in 4C anlagen and essentially absent in 8C and 16C anlagen. The precipitous loss of these sequences in the 8C anlagen rules out under-replication as the mechanism for the loss and suggests that these sequences are specifically degraded early during anlagen development.

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Elimination of micronuclear specific DNA sequences early in anlagen development.

Molecular and Cellular Biology ◽

10.1128/mcb.5.1.93 ◽

1985 ◽

Vol 5 (1) ◽

pp. 93-98 ◽

Cited By ~ 14

Author(s):

C F Brunk ◽

R K Conover

Keyword(s):

Developmental Stage ◽

Dna Sequences ◽

Developmental Stages ◽

Tetrahymena Thermophila ◽

Southern Analysis ◽

Limited Sequence

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Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza

Scientific Reports ◽

10.1038/s41598-020-79298-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yuping Li ◽

Xiaoju Liang ◽

Xuguo Zhou ◽

Yu An ◽

Ming Li ◽

...

Keyword(s):

Gene Expression ◽

Developmental Stage ◽

Reference Genes ◽

Developmental Stages ◽

Individual Factors ◽

Congeneric Species ◽

Spatio Temporal ◽

The Stability ◽

Different Tissues ◽

Selection Of

AbstractGlycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate measurement of their expression profiles. Reverse transcription quantitative real-time PCR (RT-qPCR) is a primary tool, which requires stably expressed reference genes to serve as the internal references to normalize the target gene expression. In this study, the stability of 14 candidate reference genes from the two congeneric species G. uralensis and G. inflata, including ACT, CAC, CYP, DNAJ, DREB, EF1, RAN, TIF1, TUB, UBC2, ABCC2, COPS3, CS, R3HDM2, were evaluated across different tissues and throughout various developmental stages. More importantly, we investigated the impact of interactions between tissue and developmental stage on the performance of candidate reference genes. Four algorithms, including geNorm, NormFinder, BestKeeper, and Delta Ct, were used to analyze the expression stability and RefFinder, a comprehensive software, provided the final recommendation. Based on previous research and our preliminary data, we hypothesized that internal references for spatio-temporal gene expression are different from the reference genes suited for individual factors. In G. uralensis, the top three most stable reference genes across different tissues were R3HDM2, CAC and TUB, while CAC, CYP and ABCC2 were most suited for different developmental stages. CAC is the only candidate recommended for both biotic factors, which is reflected in the stability ranking for the spatio (tissue)-temporal (developmental stage) interactions (CAC, R3HDM2 and DNAJ). Similarly, in G. inflata, COPS3, R3HDM2 and DREB were selected for tissues, while RAN, COPS3 and CS were recommended for developmental stages. For the tissue-developmental stage interactions, COPS3, DREB and ABCC2 were the most suited reference genes. In both species, only one of the top three candidates was shared between the individual factors and their interactions, specifically, CAC in G. uralensis and COPS3 in G. inflata, which supports our overarching hypothesis. In summary, spatio-temporal selection of reference genes not only lays the foundation for functional genomics research in Glycyrrhiza, but also facilitates these traditional medicinal herbs to reach/maximize their pharmaceutical potential.

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Islands of complex DNA are widespread in Drosophila centric heterochromatin.

Genetics ◽

10.1093/genetics/141.1.283 ◽

1995 ◽

Vol 141 (1) ◽

pp. 283-303

Author(s):

M H Le ◽

D Duricka ◽

G H Karpen

Keyword(s):

Dna Sequences ◽

Structure And Function ◽

Southern Analysis ◽

Cloning And Sequencing ◽

Pulsed Field ◽

Drosophila Heterochromatin ◽

And Function ◽

Heterochromatin Structure ◽

Derivatives Of ◽

Eukaryotic Genomes

Abstract Heterochromatin is a ubiquitous yet poorly understood component of multicellular eukaryotic genomes. Major gaps exist in our knowledge of the nature and overall organization of DNA sequences present in heterochromatin. We have investigated the molecular structure of the 1 Mb of centric heterochromatin in the Drosophila minichromosome Dp1187. A genetic screen of irradiated minichromosomes yielded rearranged derivatives of Dp1187 whose structures were determined by pulsed-field Southern analysis and PCR. Three Dp1187 deletion derivatives and an inversion had one breakpoint in the euchromatin and one in the heterochromatin, providing direct molecular access to previously inaccessible parts of the heterochromatin. End-probed pulsed-field restriction mapping revealed the presence of at least three "islands" of complex DNA, Tahiti, Moorea, and Bora Bora, constituting approximately one half of the Dp1187 heterochromatin. Pulsed-field Southern analysis demonstrated that Drosophila heterochromatin in general is composed of alternating blocks of complex DNA and simple satellite DNA. Cloning and sequencing of a small part of one island, Tahiti, demonstrated the presence of a retroposon. The implications of these findings to heterochromatin structure and function are discussed.

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Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants

Scientific Reports ◽

10.1038/s41598-021-88055-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hangxia Jin ◽

Xiaomin Yu ◽

Qinghua Yang ◽

Xujun Fu ◽

Fengjie Yuan

Keyword(s):

Developmental Stage ◽

Phytic Acid ◽

Differentially Expressed Genes ◽

Transcriptome Analysis ◽

Defense Mechanisms ◽

Developmental Stages ◽

Sucrose Metabolism ◽

Differentially Expressed ◽

Sequencing Analysis ◽

Seed Developmental Stage

AbstractPhytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3–InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.

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Micronuclear DNA sequences from Tetrahymena do not confer mitotic stability on ARS plasmids in Saccharomyces

Genome ◽

10.1139/g88-116 ◽

1988 ◽

Vol 30 (5) ◽

pp. 690-696 ◽

Cited By ~ 3

Author(s):

Wendy H. Horsfall ◽

Ronald E. Pearlman

Keyword(s):

Saccharomyces Cerevisiae ◽

Dna Sequences ◽

Copy Number ◽

Tetrahymena Thermophila ◽

Assay System ◽

Mitotic Stability ◽

Yeast Saccharomyces Cerevisiae ◽

Genomic Libraries ◽

Ade2 Gene

Genomic libraries containing micronuclear DNA sequences from Tetrahymena thermophila have been constructed in a vector containing ARS1, SUP11, and ura3 sequences from the yeast Saccharomyces cerevisiae. When transformed into a strain of S. cerevisiae carrying a suppressible ochre mutation in the ade2 gene, viable transformants are obtained only if the transforming plasmid is maintained at a copy number of one or two per cell. Mitotic segregation of the plasmid is easily assessed in a colour assay of transformants. Using this assay system, we showed that micronuclear DNA from Tetrahymena does not contain sequences that confer mitotic stability on yeast ARS-containing plasmids; i.e., sequences that function analogously to yeast centromere sequences. One transformant was analyzed that carries Tetrahymena sequences that maintain the copy number of the ARS plasmid at one or two per cell. However, these sequences do not confer mitotic stability on the transformants and they confer a phenotype in this assay similar to that of the REP3 gene of the yeast 2 μm plasmid.Key words: mitotic stability, centromere, Tetrahymena, Saccharomyces.

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Safe-Site Effects on Rhizosphere Bacterial Communities in a High-Altitude Alpine Environment

BioMed Research International ◽

10.1155/2014/480170 ◽

2014 ◽

Vol 2014 ◽

pp. 1-9 ◽

Cited By ~ 9

Author(s):

Sonia Ciccazzo ◽

Alfonso Esposito ◽

Eleonora Rolli ◽

Stefan Zerbe ◽

Daniele Daffonchio ◽

...

Keyword(s):

High Altitude ◽

Developmental Stage ◽

Bacterial Communities ◽

Developmental Stages ◽

Gene Diversity ◽

Intergenic Spacer ◽

Intermediate Stage ◽

Plant Colonization ◽

Early Developmental Stage ◽

Rrna Gene

The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites) which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS) site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P<0.05) on 16S rRNA gene diversity revealed significant differences (P<0.05) between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

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Association between floral bud size and developmental stage in soybean microspores

Brazilian Archives of Biology and Technology ◽

10.1590/s1516-89132003000400004 ◽

2003 ◽

Vol 46 (4) ◽

pp. 515-520 ◽

Cited By ~ 21

Author(s):

Mozart da Silva Lauxen ◽

Eliane Kaltchuk- Santos ◽

Ching -yeh Hu ◽

Sidia Maria Callegari- Jacques ◽

Maria Helena Bodanese-Zanettini

Keyword(s):

Developmental Stage ◽

Anther Culture ◽

Developmental Stages ◽

Size Group ◽

Soybean Cultivars ◽

Advanced Stages ◽

Bud Size ◽

Microspore Stage ◽

Floral Bud

This study was carried out to establish the association between floral bud size and the corresponding microspore developmental stages for Brazilian soybean cultivars. Microspore developmental stage distributions were examined in young buds from cv Década, IAS5 and RS7. The data indicated that for a given bud-size group, the microspores of different cultivars were at different developmental stages, with cv RS7 and Década distributed at the youngest and cv IAS5 at the most advanced stages. Microspore stages distribution were also compared among the ten anthers of the same bud of the above cultivars. The ten anthers from a given bud were clearly distributed at different developmental stages. Caution should be exercised when adopting the standard anther culture practice of using the microspore stage of one anther to represent the entire bud.

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A method for mapping germ line sequences in Tetrahymena thermophila using the polymerase chain reaction.

Genetics ◽

10.1093/genetics/137.1.95 ◽

1994 ◽

Vol 137 (1) ◽

pp. 95-106 ◽

Cited By ~ 1

Author(s):

D Cassidy-Hanley ◽

M C Yao ◽

P J Bruns

Keyword(s):

Polymerase Chain Reaction ◽

Dna Sequences ◽

Tetrahymena Thermophila ◽

Germ Line ◽

Repetitive Sequences ◽

Mapping Technique ◽

Ciliated Protozoan ◽

Chain Reaction ◽

Polymerase Chain ◽

Template Dna

Abstract A method for mapping DNA sequences to specific germinal chromosomes in the ciliated protozoan Tetrahymena thermophila has been developed. This mapping technique (PCR mapping) utilizes the polymerase chain reaction and template DNA derived from nullisomic strains to directly assign micronuclear DNA sequences to specific micronuclear chromosomes. Using this technique, a number of unique sequences and short repetitive sequences flanked by unique sequences have been mapped to four of the five germinal chromosomes.

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Plant Developmental Stage Drives the Differentiation in Ecological Role of Plant Bacterial and Fungal Microbiomes

10.21203/rs.3.rs-241147/v1 ◽

2021 ◽

Author(s):

Chao Xiong ◽

Brajesh K. Singh ◽

Ji-Zheng He ◽

Yan-Lai Han ◽

Pei-Pei Li ◽

...

Keyword(s):

Developmental Stage ◽

Plant Development ◽

Late Stage ◽

Developmental Stages ◽

Early Stage ◽

Alpha Diversity ◽

Microbial Interactions ◽

Disease Suppression ◽

Fungal Communities ◽

Ecological Role

Abstract BackgroundPlants live with diverse microbial communities which profoundly affect multiple facets of host performance such as nutrition acquisition, disease suppression and productivity, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils (rhizosphere and bulk soil), plant epiphytic and endophytic niches (phylloplane, rhizoplane, leaf and root endosphere), and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics.ResultsOur results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartment niches than in soils, with the strongest effect in the phylloplane. Air (represented by fake plants) was an important source of phylloplane microbiomes which were co-shaped by both plant development and seasonal environmental factors. Further, we demonstrated that bacterial and fungal communities in plant compartment niches exhibited contrasting response to host developmental stages, with higher alpha diversity and stronger deterministic assembly within bacterial microbiomes at the early stage but a similar pattern within mycobiomes at the late stage. Moreover, we found that bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity and functional genes involved in nutrient provision and disease resistance at the early stage than the late stage. ConclusionsOur results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different plant development stages. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection to meet the physiological requirement of plant developmental stages. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity.

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2 CORRELATION BETWEEN OXYGEN RESPIRATION RATES AND MORPHOLOGY, SEX, DIAMETER AND DEVELOPMENTAL STAGE OF SINGLE BOVINE IVP-EMBRYOS

Reproduction Fertility and Development ◽

10.1071/rdv17n2ab2 ◽

2005 ◽

Vol 17 (2) ◽

pp. 151 ◽

Cited By ~ 1

Author(s):

A.S. Lopes ◽

N. Ramsing ◽

L.H. Larsen ◽

M. Räty ◽

J. Peippo ◽

...

Keyword(s):

Developmental Stage ◽

Respiration Rate ◽

Developmental Stages ◽

Glass Tube ◽

Outer Diameter ◽

Bovine Embryos ◽

Embryo Viability ◽

Concentration Gradients ◽

Cell Stage ◽

Respiration Rates

A simple, non-invasive, rapid and sensitive oxygen microsensor system was developed to investigate correlations between oxygen respiration rates of individual bovine embryos and their morphology, sex, diameter and developmental stage. Bovine IVP-embryos (n = 78; Holm et al. Theriogenology 52, 683–700) were analysed around the 8-cell stage (Day 3; n = 18) and at various blastocyst stages (Day 7; n = 60). Each embryo was morphologically evaluated, its outer diameter measured and was then loaded into a glass tube (i.d. 0.68 mm, length 3 mm). After 1 h, oxygen concentration gradients generated by the embryo’s respiration were measured over app. 8 min with an oxygen microelectrode (www.unisense.com). Five embryos were measured in one round together with an empty tube as control. The procedure was repeated twice for each embryo with app. 1 h interval. Individual respiration rates in nL O2/embryo/h (nL/h) were calculated from these gradients. The measurements were performed at 38.5°C under constant flow of humidified 5% CO2 in air (app. 19% O2). After this, 64 embryos (14 Day 3; 50 Day 7) were lysed for sex diagnosis by PCR. Values are given as mean ± SD. The sensitivity of the oxygen measurement system was high (controls: 0.034 ± 0.035 nL/h, n = 15) and its repeatability from 1st to 2nd measurement was 99.7 ± 9.8% (n = 71). The average embryo respiration rate was 0.39 ± 0.05 nLl/h on Day 3 (n = 18) and 1.31 ± 0.52 nLl/h on Day 7 (n = 60). For Day 7 embryos, the respiration rates varied according to their morphological quality, being 1.87 ± 0.46a (n = 18), 1.17 ± 0.32b (n = 23), 0.95 ± 0.27b,c (n = 14) and 0.72 ± 0.24c (n = 4) nL/h for quality 1, 2, 3, and 4 embryos, respectively (Proc Mixed,a,b,c: P < 0.05; values with different superscripts differ significantly). The sex ratio (male:female) was 9:5 (Day 3) and 32:18 (Day 7), and on Day 7 this ratio varied between qualities: 11:2, 12:8, 8:4, and 1:3 for quality 1, 2, 3, and 4, respectively. The average respiration rate on day 3 was the same for males and females, as it was on day 7 (1.22 ± 0.43 nL/h (females) and 1.31 ± 0.58 nL/h (males), P > 0.05). There was a correlation between embryo diameter and respiration rate (r2 = 0.65, n = 74), which was even stronger for Day 7 male embryos (r2 = 0.72, n = 32). In conclusion, a highly reliable, repeatable and sensitive system was established for measuring respiration rates in single bovine embryos, even at early developmental stages. The respiration rate was lower on day 3 compared to Day 7 embryos, and it was correlated with the morphological embryo quality on Day 7. Oxygen consumption could be a valuable supplementary indicator of embryo viability, especially in difficult evaluations (e.g. quality 2 and 3 after IVP). It remains to be demonstrated if such measurements can also reveal quality differences already at Day 3, which would be of interest in, e.g. the human field. ASL is supported by FCT, Portugal.

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