scholarly journals Grain Dispersal Mechanism In Cereals Arose From a Genome Duplication Followed By Changes in Spatial Expression of Genes Involved In Pollen Development

2021 ◽  
Author(s):  
Arthur Cross ◽  
John Baijun ◽  
Robbie Waugh ◽  
Agnieszka Golicz ◽  
Mohammad Pourkheirandish
Keyword(s):  
Expression Profile ◽  
Pollen Development ◽  
Developmental Stages ◽  
Biological Function ◽  
Natural Mode ◽  
Cell Wall Modification ◽  
Spatial Expression ◽  
Dispersal Mechanism ◽  
A Genome ◽  
Ancestral Function

Abstract One of the most critical events in the process of cereal domestication was the loss of the natural mode of grain dispersal. Grain dispersal in barley is controlled by two major genes, Btr1 and Btr2, which affect the thickness of cell walls around the disarticulation zone. The barley genome also encodes Btr1-like and Btr2-like genes, which have been shown to be the ancestral copies. While Btr and Btr-like genes are non-redundant, the biological function of Btr-like genes is unknown. We explored the potential biological role of the Btr-like genes by surveying their expression profile across 212 publicly available transcriptome datasets representing diverse organs, developmental stages and stress conditions. We found that Btr1-like and Btr2-like are expressed exclusively in immature anther samples throughout Prophase I of meiosis within the meiocyte. The similar and restricted expression profile of these two genes suggests they are involved in a common biological function. Further analysis revealed 141 genes co-expressed with Btr1-like and 122 genes co-expressed with Btr2-like, with 105 genes in common, supporting Btr-like genes involvement in a shared molecular pathway. We hypothesize that the Btr-like genes play a crucial role in pollen development by facilitating the formation of the callose wall around the meiocyte or in the secretion of callase by the tapetum. Our data suggest that Btr genes retained an ancestral function in cell wall modification and gained a new role in grain dispersal due to changes in their spatial expression becoming spike specific after gene-duplication.

scholarly journals F-Box Genes in the Wheat Genome and Expression Profiling in Wheat at Different Developmental Stages

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1154
Author(s):  
Min Jeong Hong ◽  
Jin-Baek Kim ◽  
Yong Weon Seo ◽  
Dae Yeon Kim
Keyword(s):  
Developmental Stages ◽  
Brachypodium Distachyon ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
Post Translational Modification ◽  
Genome Wide ◽  
A Genome ◽  
High Sequence Homology ◽  
Wide Scale

Genes of the F-box family play specific roles in protein degradation by post-translational modification in several biological processes, including flowering, the regulation of circadian rhythms, photomorphogenesis, seed development, leaf senescence, and hormone signaling. F-box genes have not been previously investigated on a genome-wide scale; however, the establishment of the wheat (Triticum aestivum L.) reference genome sequence enabled a genome-based examination of the F-box genes to be conducted in the present study. In total, 1796 F-box genes were detected in the wheat genome and classified into various subgroups based on their functional C-terminal domain. The F-box genes were distributed among 21 chromosomes and most showed high sequence homology with F-box genes located on the homoeologous chromosomes because of allohexaploidy in the wheat genome. Additionally, a synteny analysis of wheat F-box genes was conducted in rice and Brachypodium distachyon. Transcriptome analysis during various wheat developmental stages and expression analysis by quantitative real-time PCR revealed that some F-box genes were specifically expressed in the vegetative and/or seed developmental stages. A genome-based examination and classification of F-box genes provide an opportunity to elucidate the biological functions of F-box genes in wheat.

scholarly journals Prediction of cell position using single-cell transcriptomic data: an iterative procedure

F1000Research ◽  
2020 ◽  
Vol 8 ◽  
pp. 1775
Author(s):  
Andrés M. Alonso ◽  
Alejandra Carrea ◽  
Luis Diambra
Keyword(s):  
Single Cell ◽  
Expression Profile ◽  
Iterative Procedure ◽  
Cellular Heterogeneity ◽  
Spatial Expression ◽  
Transcriptomic Data ◽  
Cell Localization ◽  
Cell Position ◽  
Small Set ◽  
New Algorithms

Single-cell sequencing reveals cellular heterogeneity but not cell localization. However, by combining single-cell transcriptomic data with a reference atlas of a small set of genes, it would be possible to predict the position of individual cells and reconstruct the spatial expression profile of thousands of genes reported in the single-cell study. With the purpose of developing new algorithms, the Dialogue for Reverse Engineering Assessments and Methods (DREAM) consortium organized a crowd-sourced competition known as DREAM Single Cell Transcriptomics Challenge (SCTC). Within this context, we describe here our proposed procedures for adequate reference genes selection, and an iterative procedure to predict spatial expression profile of other genes.

scholarly journals Expression profile and biological function of miR‑455‑5p in colorectal carcinoma

2018 ◽  
Author(s):  
Jinqiu Wang ◽  
Yang Lu ◽  
Yiyong Zeng ◽  
Leming Zhang ◽  
Kongliang Ke ◽  
...  
Keyword(s):  
Colorectal Carcinoma ◽  
Expression Profile ◽  
Biological Function

scholarly journals Genome-Wide Association Study for Maize Leaf Cuticular Conductance Identifies Candidate Genes Involved in the Regulation of Cuticle Development

2020 ◽  
Vol 10 (5) ◽  
pp. 1671-1683 ◽  
Author(s):  
Meng Lin ◽  
Susanne Matschi ◽  
Miguel Vasquez ◽  
James Chamness ◽  
Nicholas Kaczmar ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Crop Productivity ◽  
Genome Wide Association ◽  
Cell Wall Modification ◽  
Major Barrier ◽  
Maize Leaf ◽  
Genome Wide ◽  
A Genome

The cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed at night and under water-limited conditions. Elucidating the genetic architecture of natural variation for leaf cuticular conductance (gc) is important for identifying genes relevant to improving crop productivity in drought-prone environments. To this end, we conducted a genome-wide association study of gc of adult leaves in a maize inbred association panel that was evaluated in four environments (Maricopa, AZ, and San Diego, CA, in 2016 and 2017). Five genomic regions significantly associated with gc were resolved to seven plausible candidate genes (ISTL1, two SEC14 homologs, cyclase-associated protein, a CER7 homolog, GDSL lipase, and β-D-XYLOSIDASE 4). These candidates are potentially involved in cuticle biosynthesis, trafficking and deposition of cuticle lipids, cutin polymerization, and cell wall modification. Laser microdissection RNA sequencing revealed that all these candidate genes, with the exception of the CER7 homolog, were expressed in the zone of the expanding adult maize leaf where cuticle maturation occurs. With direct application to genetic improvement, moderately high average predictive abilities were observed for whole-genome prediction of gc in locations (0.46 and 0.45) and across all environments (0.52). The findings of this study provide novel insights into the genetic control of gc and have the potential to help breeders more effectively develop drought-tolerant maize for target environments.

scholarly journals Twinfilin is required for actin-dependent developmental processes in Drosophila

2001 ◽  
Vol 155 (5) ◽  
pp. 787-796 ◽  
Author(s):  
Gudrun Wahlström ◽  
Maria Vartiainen ◽  
Lumi Yamamoto ◽  
Pieta K. Mattila ◽  
Pekka Lappalainen ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Biological Function ◽  
Actin Monomer ◽  
Wild Type ◽  
Developmental Processes ◽  
Developmental Defects ◽  
Actin Bundles ◽  
Morphological Processes ◽  
Encoding Gene ◽  
Different Tissues

The actin cytoskeleton is essential for cellular remodeling and many developmental and morphological processes. Twinfilin is a ubiquitous actin monomer–binding protein whose biological function has remained unclear. We discovered and cloned the Drosophila twinfilin homologue, and show that this protein is ubiquitously expressed in different tissues and developmental stages. A mutation in the twf gene leads to a number of developmental defects, including aberrant bristle morphology. This results from uncontrolled polymerization of actin filaments and misorientation of actin bundles in developing bristles. In wild-type bristles, twinfilin localizes diffusively to cytoplasm and to the ends of actin bundles, and may therefore be involved in localization of actin monomers in cells. We also show that twinfilin and the ADF/cofilin encoding gene twinstar interact genetically in bristle morphogenesis. These results demonstrate that the accurate regulation of size and dynamics of the actin monomer pool by twinfilin is essential for a number of actin-dependent developmental processes in multicellular eukaryotes.

scholarly journals How to use new biology to guide therapy in multiple myeloma

Hematology ◽  
2012 ◽  
Vol 2012 (1) ◽  
pp. 342-349 ◽  
Author(s):  
Gareth J. Morgan ◽  
Martin F. Kaiser
Keyword(s):  
Multiple Myeloma ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Survival Rates ◽  
Current Treatment ◽  
Next Generation ◽  
Molecular Subgroups ◽  
Treatment Protocols ◽  
Sequencing Technologies ◽  
A Genome

Abstract Recent advances in multiple myeloma (MM) therapy have led to significantly longer median survival rates and some patients being cured. At the same time, our understanding of MM biology and the molecular mechanisms driving the disease is constantly improving. Next-generation sequencing technologies now allow insights into the genetic aberrations in MM at a genome-wide scale and across different developmental stages in the course of an individual tumor. This improved knowledge about MM biology needs to be rapidly translated and transformed into diagnostic and therapeutic applications to finally achieve cure in a larger proportion of patients. As a part of these translational efforts, novel drugs that inhibit oncogenic proteins overexpressed in defined molecular subgroups of the disease, such as FGFR3 and MMSET in t(4;14) MM, are currently being developed. The potential of targeted next-generation diagnostic tests to rapidly identify clinically relevant molecular subgroups is being evaluated. The technical tools to detect and define tumor subclones may potentially become clinically relevant because intraclonal tumor heterogeneity has become apparent in many cancers. The emergence of different MM subclones under the selective pressure of treatment is important in MM, especially in the context of maintenance therapy and treatment for asymptomatic stages of the disease. Finally, novel diagnostic and therapeutic achievements have to be implemented into innovative clinical trial strategies with smaller trials for molecularly defined high-risk patients and large trials with a long follow-up for the patients most profiting from the current treatment protocols. These combined approaches will hopefully transform the current one-for-all care into a more tailored, individual therapeutic strategy for MM patients.

scholarly journals A quantitative RT-PCR study of the mRNA expression profile of the IGF axis during mammary gland development

2004 ◽  
Vol 33 (1) ◽  
pp. 195-207 ◽  
Author(s):  
M Boutinaud ◽  
JH Shand ◽  
MA Park ◽  
K Phillips ◽  
J Beattie ◽  
...  
Keyword(s):  
Mammary Gland ◽  
Mrna Expression ◽  
Expression Profile ◽  
Mammary Gland Development ◽  
Developmental Stages ◽  
Normal Mammary Gland ◽  
Rt Pcr ◽  
Mrna Expression Profile ◽  
Igf I ◽  
Gland Development

We have used quantitative RT-PCR to analyse the mRNA expression profile of the major components of the IGF axis in different stages of murine mammary gland development, including late pregnancy, lactation and involution. We have shown that all the genes studied, IGF-I, IGF-II, IGF receptor (IGFR) and IGF-binding protein (IGFBP)-1 to -6, were expressed in every stage, albeit at greatly differing levels and displaying unique expression profiles between developmental stages. IGF-I was always expressed at significantly higher levels than either IGF-II or IGFR. This suggests that IGF-I may be the more important IGF during mammary morphogenesis. Overall, IGFBP-3 demonstrated the highest level of expression of any of the IGFBP genes throughout all the developmental stages studied. However, within developmental stages, by far the highest level of expression of any of the IGFBPs was that of IGFBP-5 at day 2 of involution; this was almost an order of magnitude higher than any of the other IGFBP levels recorded. This corroborated our previous findings that the levels of IGFBP-5 protein are highly elevated in the involuting mammary gland, and demonstrated that this up-regulation of IGFBP-5 operates at the level of transcriptional control or message stability. Comparison of the expression profile for these different genes would strongly suggest that they are likely to have differential functions throughout mammary gland development, and also highlights potential interactions and co-regulation between different members of this axis. In addition, our results have identified some similarities and differences in the expression of IGFBPs between the mouse mammary epithelial cell line, HC11, and the normal mammary gland which are worthy of study, most notably the differential regulation of IGFBP-2 and the site of expression of IGFBP-4 and -6. Overall, this study has demonstrated the importance and complexity of the IGF axis during mammary gland development and provides a valuable resource for future research in this area.

Analysis of gene expression profile in pollen development of recessive genic male sterile Brassica napus L. line S45A

2009 ◽  
Vol 28 (9) ◽  
pp. 1363-1372 ◽  
Author(s):  
Yuning Chen ◽  
Shaolin Lei ◽  
Zhengfu Zhou ◽  
Fangqin Zeng ◽  
Bin Yi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Pollen Development ◽  
Male Sterile ◽  
Brassica Napus L

Male cone morphogenesis, pollen development and pollen dispersal mechanism in Ginkgo biloba L.

2011 ◽  
Vol 91 (6) ◽  
pp. 971-981 ◽  
Author(s):  
Y. Lu ◽  
L. Wang ◽  
D. Wang ◽  
Y. Wang ◽  
M Zhang ◽  
...  
Keyword(s):  
Ginkgo Biloba ◽  
Pollen Development ◽  
Pollen Dispersal ◽  
Sporogenous Cell ◽  
Outermost Layer ◽  
Male Cone ◽  
Dispersal Mechanism ◽  
Morphological Adaptations ◽  
Male Cones ◽  
Sporangial Wall

Lu, Y., Wang, L., Wang, D., Wang, Y., Zhang, M., Jin, B. and Chen, P. 2011. Male cone morphogenesis, pollen development and pollen dispersal mechanism in Ginkgo biloba L. Can. J. Plant Sci. 91: 971–981. Ginkgo biloba L. is one of the oldest gymnosperms. Male cone morphogenesis, pollen development and dispersal are important for successful pollination and reproduction. In this study, we investigated the development of male cone, pollen and the sporangial wall in detail. The results indicate that: (1) The primordia of male cones and leaves begin to differentiate in early June and remain open until the following March. The male cones then mature and release pollen in mid-April. The male cones are drooped and approximately perpendicular to the leaves during pollination. (2) The microsporocytes develop from the sporogenous cell and form a tetrahedral tetrad after two simultaneous asymmetrically meioses, then produce a matured four-cell pollen after three polar mitotic divisions. The matured pollen is hemispheric in shape with a large aperture area and three pollen wall layers; once released from the microsporangia, the pollen becomes boat-like in shape. (3) The sporangial walls are eusporangiate and consist of epidermis, endothecium and tapetum. The differentiation of the tapetum occurs separately from that of the epidermis and endothecium, and originates from the outermost layer of sporogenous cells. The sporangial walls exhibit shrinkage of the epidermis, fibrous thickening of the endothecium, and enzymic dissolution of the tapetum during pollen dispersal, which contributes to microsporangia opening. Based on these results, we conclude that there many unique and primitive characteristics of the development of the male cones, pollen and sporangial wall of G. biloba. In addition, we also found that the male cones, pollen and sporangial walls have evolved efficient structural and morphological adaptations to anemophily.

scholarly journals Odorant Binding Protein C17 Contributes to the Response to Artemisia vulgaris Oil in Tribolium castaneum

2021 ◽  
Vol 3 ◽  
Author(s):  
Shan-Shan Gao ◽  
Rui-Min Li ◽  
Shuang Xue ◽  
Yuan-Chen Zhang ◽  
Yong-Lei Zhang ◽  
...  
Keyword(s):  
Tribolium Castaneum ◽  
Expression Profile ◽  
Developmental Stages ◽  
Fat Body ◽  
Profile Analysis ◽  
Control Group ◽  
Contact Toxicity ◽  
Artemisia Vulgaris ◽  
Plant Oil ◽  
Odorant Binding

The red flour beetle, Tribolium castaneum (T. castaneum), generates great financial losses to the grain storage and food processing industries. Previous studies have shown that essential oil (EO) from Artemisia vulgaris (A. vulgaris) has strong contact toxicity to larvae of the beetle, and odorant-binding proteins (OBPs) contribute to the defense of larvae against A. vulgaris. However, the functions of OBPs in insects defending against plant oil is still not clear. Here, expression of one OBP gene, TcOBPC17, was significantly induced 12–72 h after EO exposure. Furthermore, compared to the control group, RNA interference (RNAi) against TcOBPC17 resulted in a higher mortality rate after EO treatment, which suggests that TcOBPC17 involves in the defense against EO and induces a declining sensitivity to EO. In addition, the tissue expression profile analysis revealed that the expression of TcOBPC17 was more abundant in the metabolic detoxification organs of the head, fat body, epidermis, and hemolymph than in other larval tissue. The expression profile of developmental stages showed that TcOBPC17 had a higher level in early and late adult stages than in other developmental stages. Taken together, these results suggest that TcOBPC17 could participate in the sequestration process of exogenous toxicants in T. castaneum larvae.

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