Log in

Relevant bibliographies by topics / Homeolog / Journal articles

Journal articles on the topic 'Homeolog'

To see the other types of publications on this topic, follow the link: Homeolog.

Author: Grafiati

Published: 10 December 2022

Last updated: 29 January 2023

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the top 50 journal articles for your research on the topic 'Homeolog.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.

1

Kuo, Tony C. Y., Masaomi Hatakeyama, Toshiaki Tameshige, Kentaro K. Shimizu, and Jun Sese. "Homeolog expression quantification methods for allopolyploids." Briefings in Bioinformatics 21, no. 2 (December 27, 2018): 395–407. http://dx.doi.org/10.1093/bib/bby121.

Full text

Abstract:

Abstract Genome duplication with hybridization, or allopolyploidization, occurs in animals, fungi and plants, and is especially common in crop plants. There is an increasing interest in the study of allopolyploids because of advances in polyploid genome assembly; however, the high level of sequence similarity in duplicated gene copies (homeologs) poses many challenges. Here we compared standard RNA-seq expression quantification approaches used currently for diploid species against subgenome-classification approaches which maps reads to each subgenome separately. We examined mapping error using our previous and new RNA-seq data in which a subgenome is experimentally added (synthetic allotetraploid Arabidopsis kamchatica) or reduced (allohexaploid wheat Triticum aestivum versus extracted allotetraploid) as ground truth. The error rates in the two species were very similar. The standard approaches showed higher error rates (>10% using pseudo-alignment with Kallisto) while subgenome-classification approaches showed much lower error rates (<1% using EAGLE-RC, <2% using HomeoRoq). Although downstream analysis may partly mitigate mapping errors, the difference in methods was substantial in hexaploid wheat, where Kallisto appeared to have systematic differences relative to other methods. Only approximately half of the differentially expressed homeologs detected using Kallisto overlapped with those by any other method in wheat. In general, disagreement in low-expression genes was responsible for most of the discordance between methods, which is consistent with known biases in Kallisto. We also observed that there exist uncertainties in genome sequences and annotation which can affect each method differently. Overall, subgenome-classification approaches tend to perform better than standard approaches with EAGLE-RC having the highest precision.

APA, Harvard, Vancouver, ISO, and other styles

2

Nakade, Shota, Tetsushi Sakuma, Yuto Sakane, Yoshihiro Hara, Atsushi Kurabayashi, Keiko Kashiwagi, Akihiko Kashiwagi, Takashi Yamamoto, and Masanobu Obara. "Homeolog-specific targeted mutagenesis in Xenopus laevis using TALENs." In Vitro Cellular & Developmental Biology - Animal 51, no. 9 (April 29, 2015): 879–84. http://dx.doi.org/10.1007/s11626-015-9912-0.

Full text

APA, Harvard, Vancouver, ISO, and other styles

3

Zhao, Na, Qianli Dong, Brian D. Nadon, Xiaoyang Ding, Xutong Wang, Yuzhu Dong, Bao Liu, Scott A. Jackson, and Chunming Xu. "Evolution of Homeologous Gene Expression in Polyploid Wheat." Genes 11, no. 12 (November 25, 2020): 1401. http://dx.doi.org/10.3390/genes11121401.

Full text

Abstract:

Polyploidization has played a prominent role in the evolutionary history of plants. Two recent and sequential allopolyploidization events have resulted in the formation of wheat species with different ploidies, and which provide a model to study the effects of polyploidization on the evolution of gene expression. In this study, we identified differentially expressed genes (DEGs) between four BBAA tetraploid wheats of three different ploidy backgrounds. DEGs were found to be unevenly distributed among functional categories and duplication modes. We observed more DEGs in the extracted tetraploid wheat (ETW) than in natural tetraploid wheats (TD and TTR13) as compared to a synthetic tetraploid (AT2). Furthermore, DEGs showed higher Ka/Ks ratios than those that did not show expression changes (non-DEGs) between genotypes, indicating DEGs and non-DEGs experienced different selection pressures. For A-B homeolog pairs with DEGs, most of them had only one differentially expressed copy, however, when both copies of a homeolog pair were DEGs, the A and B copies were more likely to be regulated to the same direction. Our results suggest that both cis- and inter-subgenome trans-regulatory changes are important drivers in the evolution of homeologous gene expression in polyploid wheat, with ploidy playing a significant role in the process.

APA, Harvard, Vancouver, ISO, and other styles

4

Ludman, Márta, and Károly Fátyol. "The virological model plant, Nicotiana benthamiana expresses a single functional RDR6 homeolog." Virology 537 (November 2019): 143–48. http://dx.doi.org/10.1016/j.virol.2019.08.017.

Full text

APA, Harvard, Vancouver, ISO, and other styles

5

Boatwright, J. Lucas, Lauren M. McIntyre, Alison M. Morse, Sixue Chen, Mi-Jeong Yoo, Jin Koh, Pamela S. Soltis, Douglas E. Soltis, and W. Brad Barbazuk. "A Robust Methodology for Assessing Differential Homeolog Contributions to the Transcriptomes of Allopolyploids." Genetics 210, no. 3 (September 13, 2018): 883–94. http://dx.doi.org/10.1534/genetics.118.301564.

Full text

APA, Harvard, Vancouver, ISO, and other styles

6

Akama, Satoru, Rie Shimizu-Inatsugi, Kentaro K. Shimizu, and Jun Sese. "Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis." Nucleic Acids Research 42, no. 6 (January 13, 2014): e46-e46. http://dx.doi.org/10.1093/nar/gkt1376.

Full text

APA, Harvard, Vancouver, ISO, and other styles

7

Sigel, Erin M., Joshua P. Der, Michael D. Windham, and Kathleen M. Pryer. "Expression Level Dominance and Homeolog Expression Bias in Recurrent Origins of the Allopolyploid Fern Polypodium hesperium." American Fern Journal 109, no. 3 (September 17, 2019): 224. http://dx.doi.org/10.1640/0002-8444-109.3.224.

Full text

APA, Harvard, Vancouver, ISO, and other styles

8

Hughes, Thomas E., Jane A. Langdale, and Steven Kelly. "The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize." Genome Research 24, no. 8 (April 30, 2014): 1348–55. http://dx.doi.org/10.1101/gr.172684.114.

Full text

APA, Harvard, Vancouver, ISO, and other styles

9

Yoo, Mi-Jeong, Tianyi Ma, Ning Zhu, Lihong Liu, Alice C. Harmon, Qiaomei Wang, and Sixue Chen. "Genome-wide identification and homeolog-specific expression analysis of the SnRK2 genes in Brassica napus guard cells." Plant Molecular Biology 91, no. 1-2 (February 22, 2016): 211–27. http://dx.doi.org/10.1007/s11103-016-0456-9.

Full text

APA, Harvard, Vancouver, ISO, and other styles

10

Sri, Tanu, Pratiksha Mayee, and Anandita Singh. "Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas." Development Genes and Evolution 225, no. 5 (August 15, 2015): 287–303. http://dx.doi.org/10.1007/s00427-015-0513-4.

Full text

APA, Harvard, Vancouver, ISO, and other styles

11

Koh, Jin, Pamela S. Soltis, and Douglas E. Soltis. "Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae)." BMC Genomics 11, no. 1 (2010): 97. http://dx.doi.org/10.1186/1471-2164-11-97.

Full text

APA, Harvard, Vancouver, ISO, and other styles

12

Slotte, Tanja, Hui-Run Huang, Karl Holm, Alf Ceplitis, Kate St Onge, Jun Chen, Ulf Lagercrantz, and Martin Lascoux. "Splicing Variation at a FLOWERING LOCUS C Homeolog Is Associated With Flowering Time Variation in the Tetraploid Capsella bursa-pastoris." Genetics 183, no. 1 (July 6, 2009): 337–45. http://dx.doi.org/10.1534/genetics.109.103705.

Full text

APA, Harvard, Vancouver, ISO, and other styles

13

Thomas, B. C. "Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes." Genome Research 16, no. 7 (July 1, 2006): 934–46. http://dx.doi.org/10.1101/gr.4708406.

Full text

APA, Harvard, Vancouver, ISO, and other styles

14

Nagy, Istvan, Susanne Barth, Jeanne Mehenni-Ciz, Michael T. Abberton, and Dan Milbourne. "A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover." BMC Genomics 14, no. 1 (2013): 100. http://dx.doi.org/10.1186/1471-2164-14-100.

Full text

APA, Harvard, Vancouver, ISO, and other styles

15

Silkova, Olga G., Yulia N. Ivanova, Dina B. Loginova, Lilia A. Solovey, Elena A. Sycheva, and Nadezhda I. Dubovets. "Karyotype Reorganization in Wheat–Rye Hybrids Obtained via Unreduced Gametes: Is There a Limit to the Chromosome Number in Triticale?" Plants 10, no. 10 (September 29, 2021): 2052. http://dx.doi.org/10.3390/plants10102052.

Full text

Abstract:

To date, few data have been accumulated on the contribution of meiotic restitution to the formation of Triticum aestivum hybrid karyotypes. In this study, based on FISH and C-banding, karyotype reorganization was observed in three groups of F5 wheat–rye hybrids 1R(1A) × R. Aberrations, including aneuploidy, telocentrics, and Robertsonian translocations, were detected in all groups. Some of the Group 1 plants and all of the Group 2 plants only had a 4R4R pair (in addition to 1R1R), which was either added or substituted for its homeolog in ABD subgenomes. In about 82% of meiocytes, 4R4R formed bivalents, which indicates its competitiveness. The rest of the Group 1 plants had 2R and 7R chromosomes in addition to 1R1R. Group 3 retained all their rye chromosomes, with a small aneuploidy on the wheat chromosomes. A feature of the meiosis in the Group 3 plants was asynchronous cell division and omission of the second division. Diploid gametes did not form because of the significant disturbances during gametogenesis. As a result, the frequency of occurrence of the formed dyads was negatively correlated (r = −0.73) with the seed sets. Thus, meiotic restitution in the 8n triticale does not contribute to fertility or increased ploidy in subsequent generations.

APA, Harvard, Vancouver, ISO, and other styles

16

Fonsêca, Artur, and Andrea Pedrosa-Harand. "Karyotype stability in the genus Phaseolus evidenced by the comparative mapping of the wild species Phaseolus microcarpus." Genome 56, no. 6 (June 2013): 335–43. http://dx.doi.org/10.1139/gen-2013-0025.

Full text

Abstract:

The genus Phaseolus L. (Fabaceae) is monophyletic and comprises approximately 75 species distributed into two principal clades. The five cultivated species, including the common bean (Phaseolus vulgaris), were placed in clade B. Clade A comprises only wild species, with more limited distribution. In the present work, bacterial artificial chromosomes (BACs) previously mapped in common bean (2n = 22) were used as probes in fluorescent in situ hybridization (FISH) in this comparative study of Phaseolus microcarpus (2n = 22), a species from clade A. We also analyzed the chromomycin A3 (CMA)/4′,6-diamidino-2-phenylindole (DAPI) banding pattern and the localization of rDNA and telomeric DNA sites. The single 45S rDNA site from P. microcarpus was mapped to chromosome 6, showing conservation to the P. vulgaris homeolog. Of the two 5S rDNA sites identified in both species, only the site on chromosome 10 appeared conserved. In spite of the phylogenetic distance between the two species, all of the single-copy BACs demonstrated conservation of synteny. However, four collinearity breaks were observed, probably caused by para- and pericentric inversions. Some variation in the repetitive fraction of the genome was also observed. Thus, a broader analysis of the genus confirms that few, rare inversions seem to represent the main karyotype changes during the evolution of this genus.

APA, Harvard, Vancouver, ISO, and other styles

17

Wang, Ming-Tao, Zhi Li, Miao Ding, Tian-Zi Yao, Sheng Yang, Xiao-Juan Zhang, Chun Miao, et al. "Two duplicated gsdf homeologs cooperatively regulate male differentiation by inhibiting cyp19a1a transcription in a hexaploid fish." PLOS Genetics 18, no. 6 (June 29, 2022): e1010288. http://dx.doi.org/10.1371/journal.pgen.1010288.

Full text

Abstract:

Although evolutionary fates and expression patterns of duplicated genes have been extensively investigated, how duplicated genes co-regulate a biological process in polyploids remains largely unknown. Here, we identified two gsdf (gonadal somatic cell-derived factor) homeologous genes (gsdf-A and gsdf-B) in hexaploid gibel carp (Carassius gibelio), wherein each homeolog contained three highly conserved alleles. Interestingly, gsdf-A and gsdf-B transcription were mainly activated by dmrt1-A (dsx- and mab-3-related transcription factor 1) and dmrt1-B, respectively. Loss of either gsdf-A or gsdf-B alone resulted in partial male-to-female sex reversal and loss of both caused complete sex reversal, which could be rescued by a nonsteroidal aromatase inhibitor. Compensatory expression of gsdf-A and gsdf-B was observed in gsdf-B and gsdf-A mutants, respectively. Subsequently, we determined that in tissue culture cells, Gsdf-A and Gsdf-B both interacted with Ncoa5 (nuclear receptor coactivator 5) and blocked Ncoa5 interaction with Rora (retinoic acid-related orphan receptor-alpha) to repress Rora/Ncoa5-induced activation of cyp19a1a (cytochrome P450, family 19, subfamily A, polypeptide 1a). These findings illustrate that Gsdf-A and Gsdf-B can regulate male differentiation by inhibiting cyp19a1a transcription in hexaploid gibel carp and also reveal that Gsdf-A and Gsdf-B can interact with Ncoa5 to suppress cyp19a1a transcription in vitro. This study provides a typical case of cooperative mechanism of duplicated genes in polyploids and also sheds light on the conserved evolution of sex differentiation.

APA, Harvard, Vancouver, ISO, and other styles

18

Conner, Joann A., Patrick Conner, Mikhail E. Nasrallah, and June B. Nasrallah. "Comparative Mapping of the Brassica S Locus Region and Its Homeolog in Arabidopsis: Implications for the Evolution of Mating Systems in the Brassicaceae." Plant Cell 10, no. 5 (May 1998): 801. http://dx.doi.org/10.2307/3870666.

Full text

APA, Harvard, Vancouver, ISO, and other styles

19

Conner, Joann A., Patrick Conner, Mikhail E. Nasrallah, and June B. Nasrallah. "Comparative Mapping of the Brassica S Locus Region and Its Homeolog in Arabidopsis: Implications for the Evolution of Mating Systems in the Brassicaceae." Plant Cell 10, no. 5 (May 1998): 801–12. http://dx.doi.org/10.1105/tpc.10.5.801.

Full text

APA, Harvard, Vancouver, ISO, and other styles

20

El Hassouni, Khaoula, Muhammad Afzal, Kim A. Steige, Malte Sielaff, Valentina Curella, Manjusha Neerukonda, Stefan Tenzer, Detlef Schuppan, Carl Friedrich Horst Longin, and Patrick Thorwarth. "Multiomics Based Association Mapping in Wheat Reveals Genetic Architecture of Quality and Allergenic Related Proteins." International Journal of Molecular Sciences 24, no. 2 (January 12, 2023): 1485. http://dx.doi.org/10.3390/ijms24021485.

Full text

Abstract:

Wheat is an important staple crop since its proteins contribute to human and animal nutrition and are important for its end-use quality. However, wheat proteins can also cause adverse human reactions for a large number of people. We performed a genome wide association study (GWAS) on 114 proteins quantified by LC-MS-based proteomics and expressed in an environmentally stable manner in 148 wheat cultivars with a heritability > 0.6. For 54 proteins, we detected quantitative trait loci (QTL) that exceeded the Bonferroni-corrected significance threshold and explained 17.3–84.5% of the genotypic variance. Proteins in the same family often clustered at a very close chromosomal position or the potential homeolog. Major QTLs were found for four well-known glutenin and gliadin subunits, and the QTL segregation pattern in the protein encoding the high molecular weight glutenin subunit Dx5 could be confirmed by SDS gel-electrophoresis. For nine potential allergenic proteins, large QTLs could be identified, and their measured allele frequencies open the possibility to select for low protein abundance by markers as long as their relevance for human health has been conclusively demonstrated. A potential allergen was introduced in the beginning of 1980s that may be linked to the cluster of resistance genes introgressed on chromosome 2AS from Triticum ventricosum. The reported sequence information for the 54 major QTLs can be used to design efficient markers for future wheat breeding.

APA, Harvard, Vancouver, ISO, and other styles

21

Magwanga, Richard Odongo, Pu Lu, Joy Nyangasi Kirungu, Qi Dong, Xiaoyan Cai, Zhongli Zhou, Xingxing Wang, et al. "Knockdown of Cytochrome P450 Genes Gh_D07G1197 and Gh_A13G2057 on Chromosomes D07 and A13 Reveals Their Putative Role in Enhancing Drought and Salt Stress Tolerance in Gossypium hirsutum." Genes 10, no. 3 (March 18, 2019): 226. http://dx.doi.org/10.3390/genes10030226.

Full text

Abstract:

We identified 672, 374, and 379 CYPs proteins encoded by the CYPs genes in Gossypium hirsutum, Gossypium raimondii, and Gossypium arboreum, respectively. The genes were found to be distributed in all 26 chromosomes of the tetraploid cotton, with chrA05, chrA12, and their homeolog chromosomes harboring the highest number of genes. The physiochemical properties of the proteins encoded by the CYP450 genes varied in terms of their protein lengths, molecular weight, isoelectric points (pI), and even grand hydropathy values (GRAVY). However, over 99% of the cotton proteins had GRAVY values below 0, which indicated that the majority of the proteins encoded by the CYP450 genes were hydrophilic in nature, a common property of proteins encoded by stress-responsive genes. Moreover, through the RNA interference (RNAi) technique, the expression levels of Gh_D07G1197 and Gh_A13G2057 were suppressed, and the silenced plants showed a higher concentration of hydrogen peroxide (H2O2) with a significant reduction in the concentration levels of glutathione (GSH), ascorbate peroxidase (APX), and proline compared to the wild types under drought and salt stress conditions. Furthermore, the stress-responsive genes 1-Pyrroline–5-Carboxylate Synthetase (GhP5CS), superoxide dismutase (GhSOD), and myeloblastosis (GhMYB) were downregulated in VIGS plants, but showed upregulation in the leaf tissues of the wild types under drought and salt stress conditions. In addition, CYP450-silenced cotton plants exhibited a high level of oxidative injury due to high levels of oxidant enzymes, in addition to negative effects on CMS, ELWL, RLWC, and chlorophyll content The results provide the basic foundation for future exploration of the proteins encoded by the CYP450 genes in order to understand the physiological and biochemical mechanisms in enhancing drought and salt stress tolerance in plants.

APA, Harvard, Vancouver, ISO, and other styles

22

Kuzay, Saarah, Huiqiong Lin, Chengxia Li, Shisheng Chen, Daniel P. Woods, Junli Zhang, Tianyu Lan, Maria von Korff, and Jorge Dubcovsky. "WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat." PLOS Genetics 18, no. 1 (January 13, 2022): e1009747. http://dx.doi.org/10.1371/journal.pgen.1009747.

Full text

Abstract:

Improving our understanding of the genes regulating grain yield can contribute to the development of more productive wheat varieties. Previously, a highly significant QTL affecting spikelet number per spike (SNS), grain number per spike (GNS) and grain yield was detected on chromosome arm 7AL in multiple genome-wide association studies. Using a high-resolution genetic map, we established that the A-genome homeolog of WHEAT ORTHOLOG OF APO1 (WAPO-A1) was a leading candidate gene for this QTL. Using mutants and transgenic plants, we demonstrate in this study that WAPO-A1 is the causal gene underpinning this QTL. Loss-of-function mutants wapo-A1 and wapo-B1 showed reduced SNS in tetraploid wheat, and the effect was exacerbated in wapo1 combining both mutations. By contrast, spikes of transgenic wheat plants carrying extra copies of WAPO-A1 driven by its native promoter had higher SNS, a more compact spike apical region and a smaller terminal spikelet than the wild type. Taken together, these results indicate that WAPO1 affects SNS by regulating the timing of terminal spikelet formation. Both transgenic and wapo1 mutant plants showed a wide range of floral abnormalities, indicating additional roles of WAPO1 on wheat floral development. Previously, we found three widespread haplotypes in the QTL region (H1, H2 and H3), each associated with particular WAPO-A1 alleles. Results from this and our previous study show that the WAPO-A1 allele in the H1 haplotype (115-bp deletion in the promoter) is expressed at significantly lower levels in the developing spikes than the alleles in the H2 and H3 haplotypes, resulting in reduced SNS. Field experiments also showed that the H2 haplotype is associated with the strongest effects in increasing SNS and GNS (H2>H3>H1). The H2 haplotype is already present in most modern common wheat varieties but is rare in durum wheat, where it might be particularly useful to improve grain yield.

APA, Harvard, Vancouver, ISO, and other styles

23

Ulloa, Mauricio, Amanda M. Hulse-Kemp, Luis M. De Santiago, David M. Stelly, and John J. Burke. "Insights Into Upland Cotton (Gossypium hirsutum L.) Genetic Recombination Based on 3 High-Density Single-Nucleotide Polymorphism and a Consensus Map Developed Independently With Common Parents." Genomics Insights 10 (January 1, 2017): 117863101773510. http://dx.doi.org/10.1177/1178631017735104.

Full text

Abstract:

High-density linkage maps are vital to supporting the correct placement of scaffolds and gene sequences on chromosomes and fundamental to contemporary organismal research and scientific approaches to genetic improvement, especially in paleopolyploids with exceptionally complex genomes, eg, upland cotton ( Gossypium hirsutum L., “2n = 52”). Three independently developed intraspecific upland mapping populations were analyzed to generate 3 high-density genetic linkage single-nucleotide polymorphism (SNP) maps and a consensus map using the CottonSNP63K array. The populations consisted of a previously reported F2, a recombinant inbred line (RIL), and reciprocal RIL population, from “Phytogen 72” and “Stoneville 474” cultivars. The cluster file provided 7417 genotyped SNP markers, resulting in 26 linkage groups corresponding to the 26 chromosomes (c) of the allotetraploid upland cotton (AD)1 arisen from the merging of 2 genomes (“A” Old World and “D” New World). Patterns of chromosome-specific recombination were largely consistent across mapping populations. The high-density genetic consensus map included 7244 SNP markers that spanned 3538 cM and comprised 3824 SNP bins, of which 1783 and 2041 were in the At and Dt subgenomes with 1825 and 1713 cM map lengths, respectively. Subgenome average distances were nearly identical, indicating that subgenomic differences in bin number arose due to the high numbers of SNPs on the Dt subgenome. Examination of expected recombination frequency or crossovers (COs) on the chromosomes within each population of the 2 subgenomes revealed that COs were also not affected by the SNPs or SNP bin number in these subgenomes. Comparative alignment analyses identified historical ancestral At-subgenomic translocations of c02 and c03, as well as of c04 and c05. The consensus map SNP sequences aligned with high congruency to the NBI assembly of Gossypium hirsutum. However, the genomic comparisons revealed evidence of additional unconfirmed possible duplications, inversions and translocations, and unbalance SNP sequence homology or SNP sequence/loci genomic dominance, or homeolog loci bias of the upland tetraploid At and Dt subgenomes. The alignments indicated that 364 SNP-associated previously unintegrated scaffolds can be placed in pseudochromosomes of the NBI G hirsutum assembly. This is the first intraspecific SNP genetic linkage consensus map assembled in G hirsutum with a core of reproducible mendelian SNP markers assayed on different populations and it provides further knowledge of chromosome arrangement of genic and nongenic SNPs. Together, the consensus map and RIL populations provide a synergistically useful platform for localizing and identifying agronomically important loci for improvement of the cotton crop.

APA, Harvard, Vancouver, ISO, and other styles

24

Nelson, H. H., D. B. Sweetser, and J. A. Nickoloff. "Effects of terminal nonhomology and homeology on double-strand-break-induced gene conversion tract directionality." Molecular and Cellular Biology 16, no. 6 (June 1996): 2951–57. http://dx.doi.org/10.1128/mcb.16.6.2951.

Full text

Abstract:

Double-strand breaks (DSBs) greatly enhance gene conversion in the yeast Saccharomyces cerevisiae. In prior plasmid x chromosome crosses, conversion tracts were often short ( < 53 bp) and usually extended in only one direction from a DSB in an HO recognition sequence inserted into ura3. To allow fine-structure analysis of short and unidirectional tracts, phenotypically silent markers were introduced at 3- and 6-bp intervals flanking the HO site. These markers, which created a 70-bp homeologous region (71% homology), greatly increased the proportion of bidirectional tracts. Among products with short or unidirectional tracts, 85% were highly directional, converting markers on only one side (the nearest marker being 6 bp from the HO site). A DSB in an HO site insertion creates terminal nonhomologies. The high degree of directionality is a likely consequence of the precise cleavage at homology/nonhomology borders in hybrid DNA by Rad1/10 endonuclease. In contrast, terminal homeology alone yielded mostly unidirectional tracts. Thus, nonhomology flanked by homeology yields primarily bidirectional tracts, but terminal homeology or nonhomology alone yields primarily unidirectional tracts. These results are inconsistent with uni- and bidirectional tracts arising from one- and two-ended invasion mechanisms, respectively, as reduced homology would be expected to favor one-ended events. Tract spectra with terminal homeology alone with similar in RAD1 and rad1 cells, indicating that the high proportion of bidirectional tracts seen with homeology flanking nonhomology is not a consequence of Rad1/10 cleavage at homology/homeology boundaries. Instead, tract directionality appears to reflect the influence of the degree of broken-end homology on mismatch repair.

APA, Harvard, Vancouver, ISO, and other styles

25

Krumlauf, Robb, and Alex Gould. "Homeobox cooperativity." Trends in Genetics 8, no. 9 (September 1992): 297–300. http://dx.doi.org/10.1016/0168-9525(92)90259-7.

Full text

APA, Harvard, Vancouver, ISO, and other styles

26

Reilly, Molly B., Tessa Tekieli, Cyril Cros, G. Robert Aguilar, James Lao, Itai Antoine Toker, Berta Vidal, et al. "Widespread employment of conserved C. elegans homeobox genes in neuronal identity specification." PLOS Genetics 18, no. 9 (September 30, 2022): e1010372. http://dx.doi.org/10.1371/journal.pgen.1010372.

Full text

Abstract:

Homeobox genes are prominent regulators of neuronal identity, but the extent to which their function has been probed in animal nervous systems remains limited. In the nematode Caenorhabditis elegans, each individual neuron class is defined by the expression of unique combinations of homeobox genes, prompting the question of whether each neuron class indeed requires a homeobox gene for its proper identity specification. We present here progress in addressing this question by extending previous mutant analysis of homeobox gene family members and describing multiple examples of homeobox gene function in different parts of the C. elegans nervous system. To probe homeobox function, we make use of a number of reporter gene tools, including a novel multicolor reporter transgene, NeuroPAL, which permits simultaneous monitoring of the execution of multiple differentiation programs throughout the entire nervous system. Using these tools, we add to the previous characterization of homeobox gene function by identifying neuronal differentiation defects for 14 homeobox genes in 24 distinct neuron classes that are mostly unrelated by location, function and lineage history. 12 of these 24 neuron classes had no homeobox gene function ascribed to them before, while in the other 12 neuron classes, we extend the combinatorial code of transcription factors required for specifying terminal differentiation programs. Furthermore, we demonstrate that in a particular lineage, homeotic identity transformations occur upon loss of a homeobox gene and we show that these transformations are the result of changes in homeobox codes. Combining the present with past analyses, 113 of the 118 neuron classes of C. elegans are now known to require a homeobox gene for proper execution of terminal differentiation programs. Such broad deployment indicates that homeobox function in neuronal identity specification may be an ancestral feature of animal nervous systems.

APA, Harvard, Vancouver, ISO, and other styles

27

Nunes, Fabio Daumas, Fernanda Campos Souza de Almeida, Renata Tucci, and Suzana Cantanhede Orsini Machado de Sousa. "Homeobox genes: a molecular link between development and cancer." Pesquisa Odontológica Brasileira 17, no. 1 (March 2003): 94–98. http://dx.doi.org/10.1590/s1517-74912003000100018.

Full text

Abstract:

Homeobox genes are regulatory genes encoding nuclear proteins that act as transcription factors, regulating aspects of morphogenesis and cell differentiation during normal embryonic development of several animals. Vertebrate homeobox genes can be divided in two subfamilies: clustered, or HOX genes, and nonclustered, or divergent, homeobox genes. During the last decades, several homeobox genes, clustered and nonclustered ones, were identified in normal tissue, in malignant cells, and in different diseases and metabolic alterations. Homeobox genes are involved in the normal teeth development and in familial teeth agenesis. Normal development and cancer have a great deal in common, as both processes involve shifts between cell proliferation and differentiation. The literature is accumulating evidences that homeobox genes play an important role in oncogenesis. Many cancers exhibit expression of or alteration in homeobox genes. Those include leukemias, colon, skin, prostate, breast and ovarian cancers, among others. This review is aimed at introducing readers to some of the homeobox family functions in normal tissues and especially in cancer.

APA, Harvard, Vancouver, ISO, and other styles

28

Yamashita, Keishi, Hiroshi Katoh, and Masahiko Watanabe. "The Homeobox Only Protein Homeobox (HOPX) and Colorectal Cancer." International Journal of Molecular Sciences 14, no. 12 (November 25, 2013): 23231–43. http://dx.doi.org/10.3390/ijms141223231.

Full text

APA, Harvard, Vancouver, ISO, and other styles

29

Nagel, Stefan. "The Role of NKL Homeobox Genes in T-Cell Malignancies." Biomedicines 9, no. 11 (November 12, 2021): 1676. http://dx.doi.org/10.3390/biomedicines9111676.

Full text

Abstract:

Homeobox genes encode transcription factors controlling basic developmental processes. The homeodomain is encoded by the homeobox and mediates sequence-specific DNA binding and interaction with cofactors, thus operating as a basic regulatory platform. Similarities in their homeobox sequences serve to arrange these genes in classes and subclasses, including NKL homeobox genes. In accordance with their normal functions, deregulated homeobox genes contribute to carcinogenesis along with hematopoietic malignancies. We have recently described the physiological expression of eleven NKL homeobox genes in the course of hematopoiesis and termed this gene expression pattern NKL-code. Due to the developmental impact of NKL homeobox genes these data suggest a key role for their activity in the normal regulation of hematopoietic cell differentiation including T-cells. On the other hand, aberrant overexpression of NKL-code members or ectopical activation of non-code members has been frequently reported in lymphoid and myeloid leukemia/lymphoma, demonstrating their oncogenic impact in the hematopoietic compartment. Here, we provide an overview of the NKL-code in normal hematopoiesis and discuss the oncogenic role of deregulated NKL homeobox genes in T-cell malignancies.

APA, Harvard, Vancouver, ISO, and other styles

30

Wu, Yingyong, and Jinyun Peng. "miR-27b Targets HOXB8 to Inhibit Malignant Behaviors of Osteosarcoma." Technology in Cancer Research & Treatment 18 (January 1, 2019): 153303381987079. http://dx.doi.org/10.1177/1533033819870791.

Full text

Abstract:

MicroRNAs function as either tumor suppressor or oncogene in human cancers. This study aimed to explore the role of miR-27b in osteosarcoma. Expression of miR-27b or homeobox B8 in osteosarcoma cell lines was analyzed by quantitative real-time polymerase chain reaction and Western blot, respectively. Luciferase activity reporter assay and Western blot were conducted to explore the association between miR-27b and homeobox B8. Cell Counting Kit-8, colony formation assay, and wound-healing assay were performed to investigate the role of miR-27b or homeobox B8 on cell proliferation, colony formation, and cell migration. Expression of miR-27b was significantly reduced, while homeobox B8 was increased in osteosarcoma cell lines. In addition, homeobox B8 was validated as a direct target of homeobox B8. Moreover, miR-27b regulates osteosarcoma cell proliferation, colony formation, and migration through targeting homeobox B8. Taken together, our study provides novel insight into the progression of osteosarcoma, and the miR-27b–homeobox B8 axis identified may be developed as therapeutic targets against hepatocellular carcinoma in the future.

APA, Harvard, Vancouver, ISO, and other styles

31

Falzon, M., and S. Y. Chung. "The expression of rat homeobox-containing genes is developmentally regulated and tissue specific." Development 103, no. 3 (July 1, 1988): 601–10. http://dx.doi.org/10.1242/dev.103.3.601.

Full text

Abstract:

Seven rat homeobox-containing sequences have been isolated by screening a genomic library with a probe derived from a Drosophila antennapedia cDNA clone. The characterization of two of these homeobox-containing clones has been described (Falzon, M., Sanderson, N.D. and Chung, S. Y. (1987) Gene 54, 23–32). Sequence analysis of the remaining five homeobox regions reveals a 180 bp domain sharing 70–95% identity at the amino acid level with the homeodomain from the Drosophila antennapedia gene and with the homeodomains from other metazoan species. Genomic blot analysis shows that each of the homeobox-containing DNA segments is probably present in a single copy per haploid genome. Northern blot analysis of RNA transcripts indicates that the rat homeobox-containing sequences are expressed during embryogenesis and in newborn and adult tissues in a tissue-specific manner; RNA expression is predominantly detected in spinal cord and kidney. Moreover, the pattern of RNA transcripts observed is distinct for each homeobox sequence, indicating differential regulation. Among the seven rat homeobox-containing sequences, the flanking sequences of five of the clones have no obvious sequence similarity with previously published sequences of homeobox-containing genes from other species. Two of the rat clones have been identified as potential homologues to mouse homeobox-containing sequences. For both pairs, a high degree of amino acid conservation (greater than 95%) is observed within the homeodomain and its immediate flanking regions between the putative homologous genes in mouse and rat. This strengthens the assertion that some of the mammalian homeobox-containing genes encode highly conserved proteins and may serve important biological functions.

APA, Harvard, Vancouver, ISO, and other styles

32

BÜRGLIN, T. R., G. RUVKUN, A. COULSON, N. C. HAWKINS, J. D. MCGHEE, D. SCHALLER, C. WITTMANN, F. MÜLLER, and R. H. WATERSTON. "Nematode homeobox cluster." Nature 351, no. 6329 (June 1991): 703. http://dx.doi.org/10.1038/351703a0.

Full text

APA, Harvard, Vancouver, ISO, and other styles

33

Wright, Christopher V. E. "Vertebrate homeobox genes." Current Biology 2, no. 1 (January 1992): 22. http://dx.doi.org/10.1016/0960-9822(92)90417-9.

Full text

APA, Harvard, Vancouver, ISO, and other styles

34

Wright, Christopher V. E. "Vertebrate homeobox genes." Current Opinion in Cell Biology 3, no. 6 (December 1991): 976–82. http://dx.doi.org/10.1016/0955-0674(91)90116-g.

Full text

APA, Harvard, Vancouver, ISO, and other styles

35

Boncinelli, Edoardo, Antonio Mallamaci, and Giovanni Lavorgna. "Vertebrate homeobox genes." Genetica 94, no. 2-3 (June 1994): 127–40. http://dx.doi.org/10.1007/bf01443427.

Full text

APA, Harvard, Vancouver, ISO, and other styles

36

Gehring, Walter J. "Exploring the homeobox." Gene 135, no. 1-2 (December 1993): 215–21. http://dx.doi.org/10.1016/0378-1119(93)90068-e.

Full text

APA, Harvard, Vancouver, ISO, and other styles

37

Laughon, Allen S., and Sean B. Carroll. "INSIDE THE HOMEOBOX." Sciences 28, no. 2 (March 4, 1988): 42–49. http://dx.doi.org/10.1002/j.2326-1951.1988.tb03008.x.

Full text

APA, Harvard, Vancouver, ISO, and other styles

38

Whiteley, Mary, and John B. Armstrong. "Isolation and characterization of a developmentally regulated homeobox sequence in the Mexican axolotl Ambystoma mexicanum." Biochemistry and Cell Biology 68, no. 3 (March 1, 1990): 622–29. http://dx.doi.org/10.1139/o90-088.

Full text

Abstract:

A homeobox-containing genomic DNA fragment was isolated from the Mexican axolotl. This clone was obtained from a partial genomic library enriched for sequences that cross-hybridized with the Drosophila Antp homeobox under low stringency hybridization conditions. DNA sequence analysis revealed that this sequence (Ahox1) was 66% homologous to the Antp homeobox sequence and was most closely related to the mouse Hox-1.6 (84% identity) and Drosophila lab (79% identity) homeobox sequences. Several cross-hybridizing fragments to Ahox1 were detected in both mouse and axolotl genomic DNA. This sequence was also shown to be conserved in other Ambystoma species. Northern blot analysis revealed that genes containing this sequence are developmentally regulated. Transcripts hybridizing to the Ahox1 homeobox probe were detected during the neurula and tail bud stages of development.Key words: axolotl, homeobox, mouse, Drosophila, gene expression.

APA, Harvard, Vancouver, ISO, and other styles

39

Kovalenko, L. P., E. A. Ivanova, A. S. Lapickaya, K. V. Korzhova, and R. V. Zhurikov. "Evaluation of allergenic properties and immunotoxicity of Homeovox." Pharmacokinetics and Pharmacodynamics, no. 4 (April 28, 2020): 45–48. http://dx.doi.org/10.37489/2587-7836-2019-4-45-48.

Full text

Abstract:

Homeovox, a multicomponent homeopathic treatment for laryngitis of various etiologies, was tested for allergenic properties and immunotoxicity.Methods. 80 male albino guinea pigs and 180 male СВА, C57BL/6 and F1 hybrid (CBAхС57BL/6) mice were used in the study. In order to assess immunotoxicity, Homeovox was administrated orally to mice for 14 days at doses of 100 mg/kg and 1 000 mg/kg. To assess the allergenic properties of Homeovox, albino guinea pigs were also given the drug at doses of 100 mg/kg and 1 000 mg/kg according to the standard immunization schedules.Results. Oral administration of Homeovox to mice for 14 days at doses of 100 mg/kg and 1 000 mg/kg did not cause significant changes in the main characteristics of immune response compared to controls. When assessing allergenicity, Homeovox at doses 100 mg/kg and 1 000 mg/kg administered according to the standard immunization schedules did not induce systemic anaphylaxis or active skin anaphylaxis in albino guinea pigs. The immunization of guinea pigs by Homeovox at the same doses in a mixture with Freund's complete adjuvant caused no delayed allergic reactions. Homeovox at a single oral dose of 1 000 mg/kg significantly decreased concanavalin A-induced inflammation in CBA mice by 58.4 %.Conclusion. Within the dosage range investigated, Homeovox does not induce immunotoxicity, immediate- or delayed-type allergic or pseudoallergic reactions.

APA, Harvard, Vancouver, ISO, and other styles

40

Nagel, Stefan. "The NKL- and TALE-Codes Represent Hematopoietic Gene Signatures to Evaluate Deregulated Homeobox Genes in Hodgkin Lymphoma." Hemato 3, no. 1 (February 2, 2022): 122–30. http://dx.doi.org/10.3390/hemato3010011.

Full text

Abstract:

Homeobox genes encode transcription factors which control basic processes in development and differentiation. Concerning the sequence conservation in their homeobox, these genes are arranged into particular groups sharing evolutionary ancestry and resembling in function. We have recently described the physiological expression patterns of two homeobox gene groups, NKL and TALE, in early hematopoiesis and subsequent lymphopoiesis. The hematopoietic activities of eleven NKL and nine TALE homeobox genes have been termed as NKL- and TALE-codes, respectively. Due to the developmental impact of homeobox genes, these expression data indicate a key role for their activity in normal hematopoietic differentiation processes, including B-cell development. On the other hand, aberrant expression of NKL- and TALE-code members or ectopic activation of non-code members have been frequently reported in lymphoid malignancies, demonstrating their oncogenic potential in the hematopoietic compartment. Here, we provide an overview of the established NKL- and TALE-codes in normal lymphopoiesis and of deregulated homeobox genes in Hodgkin lymphoma, demonstrating the capability of gene codes to identify homeo-oncogenes in lymphoid malignancies.

APA, Harvard, Vancouver, ISO, and other styles

41

Mahon, Kathleen A., Heiner Westphal, and Peter Gruss. "Expression of homeobox gene Hox 1.1 during mouse embryogenesis." Development 104, Supplement (October 1, 1988): 187–95. http://dx.doi.org/10.1242/dev.104.supplement.187.

Full text

Abstract:

Many of the genes controlling segmentation and pattern formation in Drosophila contain a conserved 183 bp sequence known as the homeobox. Homeobox sequences have been found in a range of metazoan species, including the vertebrates mouse and man. This striking conservation suggests that homeobox genes may play a fundamental role in developmental processes. If this is the case then it might be expected that vertebrate homeobox genes will be differentially expressed during embryogenesis and that the timing of their expression will coincide with major morphogenetic events. Here the spatial and temporal patterns of expression of murine homeobox genes will be explored, concentrating on the Hox 1.1 gene as an example. Using in situ hybridization to localize RNA transcripts, it has been found that Hox 1.1 is expressed in a region-specific manner during the formation and differentiation of the embryonic anteroposterior axis. Although striking patterns of expression of Hox 1.1 and other homeobox genes are seen in overtly segmented structures of the embryo (i.e. somites, prevertebral elements, neural tube and dorsal spinal ganglia) expression is also seen in tissues with no obvious segmental origin. The results suggest that homeobox genes probably do not play an exclusive role in segmentation in vertebrates, but are consistent with a role in the assignment of positional identity along the axis of the embryo.

APA, Harvard, Vancouver, ISO, and other styles

42

Chang, Wai Hoong, and Alvina G. Lai. "A TALE of shrimps: Genome-wide survey of homeobox genes in 120 species from diverse crustacean taxa." F1000Research 7 (January 17, 2018): 71. http://dx.doi.org/10.12688/f1000research.13636.1.

Full text

Abstract:

The homeodomain-containing proteins are an important group of transcription factors found in most eukaryotes including animals, plants and fungi. Homeobox genes are responsible for a wide range of critical developmental and physiological processes, ranging from embryonic development, innate immune homeostasis to whole-body regeneration. With continued fascination on this key class of proteins by developmental and evolutionary biologists, multiple efforts have thus far focused on the identification and characterization of homeobox orthologs from key model organisms in attempts to infer their evolutionary origin and how this underpins the evolution of complex body plans. Despite their importance, the genetic complement of homeobox genes has yet been described in one of the most valuable groups of animals representing economically important food crops. With crustacean aquaculture being a growing industry worldwide, it is clear that systematic and cross-species identification of crustacean homeobox orthologs is necessary in order to harness this genetic circuitry for the improvement of aquaculture sustainability. Using publicly available transcriptome data sets, we identified a total of 4183 putative homeobox genes from 120 crustacean species that include food crop species, such as lobsters, shrimps, crayfish and crabs. Additionally, we identified 717 homeobox orthologs from 6 other non-crustacean arthropods, which include the scorpion, deer tick, mosquitoes and centipede. This high confidence set of homeobox genes will now serve as a key resource to the broader community for future functional and comparative genomics studies.

APA, Harvard, Vancouver, ISO, and other styles

43

Mackem, S., and K. A. Mahon. "Ghox 4.7: a chick homeobox gene expressed primarily in limb buds with limb-type differences in expression." Development 112, no. 3 (July 1, 1991): 791–806. http://dx.doi.org/10.1242/dev.112.3.791.

Full text

Abstract:

Homeobox genes play a key role in specifying the segmented body plan of Drosophila, and recent work suggests that at least several homeobox genes may play a regulatory role during vertebrate limb morphogenesis. We have used degenerate oligonucleotide primers from highly conserved domains in the homeobox motif to amplify homeobox gene segments from chick embryo limb bud cDNAs using the polymerase chain reaction. Expression of a large number of homeobox genes (at least 17) is detected using this approach. One of these genes contains a novel homeobox loosely related to the Drosophila Abdominal B class, and was further analyzed by determining its complete coding sequence and evaluating its expression during embryogenesis by in situ hybridization. Based on sequence and expression patterns, we have designated this gene as Ghox 4.7 and believe that it is the chick homologue of the murine Hox 4.7 gene (formerly Hox 5.6). Ghox 4.7 is expressed primarily in limb buds during development and shows a striking spatial restriction to the posterior zone of the limb bud, suggesting a role in specifying anterior-posterior pattern formation. In chick, this gene also displays differences in expression between wing and leg buds, raising the possibility that it may participate in specifying limb-type identity.

APA, Harvard, Vancouver, ISO, and other styles

44

G., H. "Hydra and the homeobox." Nature 358, no. 6387 (August 1992): 539. http://dx.doi.org/10.1038/358539a0.

Full text

APA, Harvard, Vancouver, ISO, and other styles

45

Abate-Shen, Cory. "Homeobox genes and cancer." Cancer Cell 4, no. 5 (November 2003): 329–30. http://dx.doi.org/10.1016/s1535-6108(03)00277-0.

Full text

APA, Harvard, Vancouver, ISO, and other styles

46

Boncinelli, Edoardo. "Homeobox genes and disease." Current Opinion in Genetics & Development 7, no. 3 (June 1997): 331–37. http://dx.doi.org/10.1016/s0959-437x(97)80146-3.

Full text

APA, Harvard, Vancouver, ISO, and other styles

47

Kehrl, John H. "Homeobox genes in hematopoiesis." Critical Reviews in Oncology/Hematology 16, no. 2 (April 1994): 145–56. http://dx.doi.org/10.1016/1040-8428(94)90046-9.

Full text

APA, Harvard, Vancouver, ISO, and other styles

48

Scott, Matthew P. "Vertebrate homeobox gene nomenclature." Cell 71, no. 4 (November 1992): 551–53. http://dx.doi.org/10.1016/0092-8674(92)90588-4.

Full text

APA, Harvard, Vancouver, ISO, and other styles

49

Gehring, Walter J. "The homeobox in perspective." Trends in Biochemical Sciences 17, no. 8 (August 1992): 277–80. http://dx.doi.org/10.1016/0968-0004(92)90434-b.

Full text

APA, Harvard, Vancouver, ISO, and other styles

50

Marsh, Eric D., and Jeffrey A. Golden. "Aristaless-related homeobox mutations." Epilepsia 51 (December 2010): 70. http://dx.doi.org/10.1111/j.1528-1167.2010.02856.x.

Full text

APA, Harvard, Vancouver, ISO, and other styles

We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!