scholarly journals Nucleus Specific expression in the multinucleated mushroom-forming fungusAgaricus bisporusreveals different nuclear regulatory programs

2017 ◽  
Author(s):  
Thies Gehrmann ◽  
Jordi F. Pelkmans ◽  
Robin A. Ohm ◽  
Aurin M. Vos ◽  
Anton S. M. Sonnenberg ◽  
...  
Keyword(s):  
Nutrient Recycling ◽  
Specific Expression ◽  
Phenotypic Differences ◽  
Metabolic Genes ◽  
Genes Encoding ◽  
Nuclear Separation ◽  
Cultivated Mushroom ◽  
A Cell ◽  
Novel Method ◽  
Upregulated Genes

AbstractMotivationFungi are essential in nutrient recycling in nature. They also form symbiotic, commensal, parasitic and pathogenic interactions with other organisms including plants, animals and humans. Many fungi are polykaryotic, containing multiple nuclei per cell. In the case of heterokaryons, there are even different nuclear types within a cell. It is unknown what the different nuclear types contribute in terms of mRNA expression levels in fungal heterokaryons. Each cell of the cultivated, mushroom forming basidiomyceteAgaricus bisporuscontains 2 to 25 nuclei of two nuclear types,P1orP2,that originate from two parental strains. Using RNA-Seq data, we wish to assess the differential mRNA contribution of individual nuclear types in heterokaryotic cells and its functional impact.ResultsWe studied differential expression between genes of the two nuclear types throughout mushroom development ofA. bisporusin various tissue types. The two nuclear types, produced specific mRNA profiles which changed through development of the mushroom. The differential regulation occurred at a gene and multi-gene locus level, rather than the chromosomal or nuclear level. Although the P1 nuclear type dominates the mRNA production throughout development, the P2 type showed more differentially upregulated genes in important functional groups including genes involved in metabolism and genes encoding secreted proteins. Out of 5,090 karyolelle pairs, i.e. genes with different alleles in the two nuclear types, 411 were differentially expressed, of which 246 were up-regulated by the P2 type. In the vegetative mycelium, the P2 nucleus up-regulated almost three-fold more metabolic genes and cazymes than P1, suggesting phenotypic differences in growth. A total of 10% of the differential karyollele expression is associated with differential methylation states, indicating that epigenetic mechanisms may be partly responsible for nuclear specific expression.ConclusionWe have identified widespread transcriptomic variation between the two nuclear types ofA. bisporus. Our novel method enables studying karyollelle specific expression which likely influences the phenotype of a fungus in a polykaryotic stage. This is thus relevant for the performance of these fungi as a crop and for improving this species for breeding. Our findings could have a wider impact to better understand fungi as pathogens. This work provides the first insight into the transcriptomic variation introduced by genomic nuclear separation.

scholarly journals Nucleus-specific expression in the multinuclear mushroom-forming fungusAgaricus bisporusreveals different nuclear regulatory programs

2018 ◽  
Vol 115 (17) ◽  
pp. 4429-4434 ◽  
Author(s):  
Thies Gehrmann ◽  
Jordi F. Pelkmans ◽  
Robin A. Ohm ◽  
Aurin M. Vos ◽  
Anton S. M. Sonnenberg ◽  
...  
Keyword(s):  
Agaricus Bisporus ◽  
Sequencing Data ◽  
Carbohydrate Active Enzymes ◽  
Nuclear Level ◽  
Specific Expression ◽  
Phenotypic Differences ◽  
Gene Level ◽  
Nuclear Separation ◽  
Insight Into ◽  
Specific Mrna

Many fungi are polykaryotic, containing multiple nuclei per cell. In the case of heterokaryons, there are different nuclear types within a single cell. It is unknown what the different nuclear types contribute in terms of mRNA expression levels in fungal heterokaryons. Each cell of the mushroomAgaricus bisporuscontains two to 25 nuclei of two nuclear types originating from two parental strains. Using RNA-sequencing data, we assess the differential mRNA contribution of individual nuclear types and its functional impact. We studied differential expression between genes of the two nuclear types, P1 and P2, throughout mushroom development in various tissue types. P1 and P2 produced specific mRNA profiles that changed through mushroom development. Differential regulation occurred at the gene level, rather than at the locus, chromosomal, or nuclear level. P1 dominated mRNA production throughout development, and P2 showed more differentially up-regulated genes in important functional groups. In the vegetative mycelium, P2 up-regulated almost threefold more metabolism genes and carbohydrate active enzymes (cazymes) than P1, suggesting phenotypic differences in growth. We identified widespread transcriptomic variation between the nuclear types ofA. bisporus. Our method enables studying nucleus-specific expression, which likely influences the phenotype of a fungus in a polykaryotic stage. Our findings have a wider impact to better understand gene regulation in fungi in a heterokaryotic state. This work provides insight into the transcriptomic variation introduced by genomic nuclear separation.

scholarly journals Identification of Candidate Genes Involved in Fruit Ripening and Crispness Retention Through Transcriptome Analyses of a ‘Honeycrisp’ Population

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1335
Author(s):  
Hsueh-Yuan Chang ◽  
Cindy B. S. Tong
Keyword(s):  
Cell Wall ◽  
Fruit Ripening ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Phenotypic Differences ◽  
Genes Encoding ◽  
A Cell ◽  
Phenotypic Groups

Crispness retention is a postharvest trait that fruit of the ’Honeycrisp’ apple and some of its progeny possess. To investigate the molecular mechanisms of crispness retention, progeny individuals derived from a ’Honeycrisp’ × MN1764 population with fruit that either retain crispness (named “Retain”), lose crispness (named “Lose”), or that are not crisp at harvest (named “Non-crisp”) were selected for transcriptomic comparisons. Differentially expressed genes (DEGs) were identified using RNA-Seq, and the expression levels of the DEGs were validated using nCounter®. Functional annotation of the DEGs revealed distinct ripening behaviors between fruit of the “Retain” and “Non-crisp” individuals, characterized by opposing expression patterns of auxin- and ethylene-related genes. However, both types of genes were highly expressed in the fruit of “Lose” individuals and ’Honeycrisp’, which led to the potential involvements of genes encoding auxin-conjugating enzyme (GH3), ubiquitin ligase (ETO), and jasmonate O-methyltransferase (JMT) in regulating fruit ripening. Cell wall-related genes also differentiated the phenotypic groups; greater numbers of cell wall synthesis genes were highly expressed in fruit of the “Retain” individuals and ’Honeycrisp’ when compared with “Non-crisp” individuals and MN1764. On the other hand, the phenotypic differences between fruit of the “Retain” and “Lose” individuals could be attributed to the functioning of fewer cell wall-modifying genes. A cell wall-modifying gene, MdXTH, was consistently identified as differentially expressed in those fruit over two years in this study, so is a major candidate for crispness retention.

scholarly journals A cell type‐specific expression map of NCoR1 and SMRT transcriptional co‐repressors in the mouse brain

2020 ◽  
Vol 528 (13) ◽  
pp. 2218-2238 ◽  
Author(s):  
Attilio Iemolo ◽  
Patricia Montilla‐Perez ◽  
I‐Chi Lai ◽  
Yinuo Meng ◽  
Syreeta Nolan ◽  
...  
Keyword(s):  
Mouse Brain ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
A Cell ◽  
Cell Type Specific

scholarly journals A novel method for processing adipose-derived stromal stem cells using a closed cell washing concentration device with a hollow fiber membrane module

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Shinji Hayashi ◽  
Rieko Yagi ◽  
Shuhei Taniguchi ◽  
Masami Uji ◽  
Hidaka Urano ◽  
...  
Keyword(s):  
Stem Cells ◽  
Hollow Fiber ◽  
Hollow Fiber Membrane ◽  
Membrane Module ◽  
Fiber Membrane ◽  
Cell Processing ◽  
Closed Cell ◽  
A Cell ◽  
Novel Method ◽  
Stromal Stem Cells

AbstractCell-assisted lipotransfer (CAL) is an advanced lipoinjection method that uses autologous lipotransfer with addition of a stromal vascular fraction (SVF) containing adipose-derived stromal stem cells (ASCs). The CAL procedure of manual isolation of cells from fat requires cell processing to be performed in clean environment. To isolate cells from fat without the need for a cell processing center, such as in a procedure in an operation theater, we developed a novel method for processing SVF using a closed cell washing concentration device (CCD) with a hollow fiber membrane module. The CCD consists of a sterilized closed circuit, bags and hollow fiber, semi-automatic device and the device allows removal of >99.97% of collagenase from SVF while maintaining sterility. The number of nucleated cells, ASCs and viability in SVF processed by this method were equivalent to those in SVF processed using conventional manual isolation. Our results suggest that the CCD system is as reliable as manual isolation and may also be useful for CAL. This approach will help in the development of regenerative medicine at clinics without a cell processing center.

Dark-Field X-Ray Microscopy of Immunogold-Labeled Cells

1996 ◽  
Vol 2 (2) ◽  
pp. 53-62 ◽  
Author(s):  
Henry N. Chapman ◽  
Jenny Fu ◽  
Chris Jacobsen ◽  
Shawn Williams
Keyword(s):  
Colloidal Gold ◽  
Dark Field Image ◽  
Dark Field ◽  
X Rays ◽  
X Ray ◽  
Scanning Transmission ◽  
A Cell ◽  
Specific Antigens ◽  
Genetic Sequences ◽  
Novel Method

The methods of immunolabeling make visible the presence of specific antigens, proteins, genetic sequences, or functions of a cell. In this paper we present examples of imaging immunolabels in a scanning transmission x-ray microscope using the novel method of dark-field contrast. Colloidal gold, or silver-enhanced colloidal gold, is used as a label, which strongly scatters x-rays. This leads to a high-contrast dark-field image of the label and reduced radiation dose to the specimen. The x-ray images are compared with electron micrographs of the same labeled, unsectioned, whole cell. It is verified that the dark-field x-ray signal is primarily due to the label and the bright-field x-ray signal, showing absorption due to carbon, is largely unaffected by the label. The label can be well visualized even when it is embedded in or laying behind dense material, such as the cell nucleus. The resolution of the images is measured to be 60 nm, without the need for computer processing. This figure includes the x-ray microscope resolution and the accuracy of the label positioning. The technique should be particularly useful for the study of relatively thick (up to 10 μm), wet, or frozen hydrated specimens.

scholarly journals Six mouse alpha-tubulin mRNAs encode five distinct isotypes: testis-specific expression of two sister genes.

1986 ◽  
Vol 6 (7) ◽  
pp. 2409-2419 ◽  
Author(s):  
A Villasante ◽  
D Wang ◽  
P Dobner ◽  
P Dolph ◽  
S A Lewis ◽  
...  
Keyword(s):  
Duplication Event ◽  
Developmental Expression ◽  
Untranslated Regions ◽  
Coding Region ◽  
Specific Expression ◽  
Translational Initiation ◽  
Alpha Tubulin ◽  
Tubulin Isotypes ◽  
Tubulin Isotype ◽  
Genes Encoding

Five mouse alpha-tubulin isotypes are described, each distinguished by the presence of unique amino acid substitutions within the coding region. Most, though not all of these isotype-specific amino acids, are clustered at the carboxy terminus. One of the alpha-tubulin isotypes described is expressed exclusively in testis and is encoded by two closely related genes (M alpha 3 and M alpha 7) which have homologous 3' untranslated regions but which differ at multiple third codon positions and in their 5' untranslated regions. We show that a subfamily of alpha-tubulin genes encoding the same testis-specific isotype also exists in humans. Thus, we conclude that the duplication event leading to a pair of genes encoding a testis-specific alpha-tubulin isotype predated the mammalian radiation, and both members of the duplicated sequence have been maintained since species divergence. A second alpha-tubulin gene, M alpha 6, is expressed ubiquitously at a low level, whereas a third gene, M alpha 4, is unique in that it does not encode a carboxy-terminal tyrosine residue. This gene yields two transcripts: a 1.8-kilobase (kb) mRNA that is abundant in muscle and a 2.4-kb mRNA that is abundant in testis. Whereas the 1.8-kb mRNA encodes a distinct alpha-tubulin isotype, the 2.4-kb mRNA is defective in that the methionine residue required for translational initiation is missing. Patterns of developmental expression of the various alpha-tubulin isotypes are presented. Our data support the view that individual tubulin isotypes are capable of conferring functional specificity on different kinds of microtubules.

scholarly journals Construction of a weight-based seed sorting system for the third-generation hybrid rice

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jianxin Wu ◽  
Shijun Qiu ◽  
Menglong Wang ◽  
Chunjue Xu ◽  
Xing Wang Deng ◽  
...  
Keyword(s):  
Hybrid Rice ◽  
Pollen Grains ◽  
Third Generation ◽  
Male Sterile ◽  
Specific Expression ◽  
The Third ◽  
Genes Encoding ◽  
Wild Type Male ◽  
Sorting System ◽  
Generation Hybrid

Abstract Background The third-generation hybrid rice technology can be constructed by transforming a recessive nuclear male sterile (NMS) mutant with a transgenic cassette containing three functional modules: the wild type male fertility gene to restore the fertility of the mutant, the pollen killer gene that specifically kills the pollen grains carrying the transgene, and the red fluorescence protein (RFP) gene to mark the transgenic seed (maintainer). The transgenic plant produces 1:1 NMS seeds and maintainer seeds that can be distinguished by the RFP signal. However, the RFP signals in the partially filled or pathogen-infected maintainer seeds are often too weak to be detected by RFP-based seed sorting machine, resulting in intermingling of the maintainer seeds with NMS seeds. Results Here we constructed a weight-based seed sorting system for the third-generation hybrid rice technology by silencing the genes encoding ADP-glucose pyrophosphorylase (AGP) essential for endosperm starch biosynthesis via endosperm-specific expression of artificial microRNAs (amiRNAs). In this system, the NMS seeds have normal endosperm and are heavy, but the maintainer seeds have shrunken endosperms and are light-weighted. The maintainer seeds can be easily and accurately sorted out from the NMS seeds by weight-sorting machines, so pure and fully filled NMS seeds are available. Conclusions The weight-based seed sorting system shows obvious advantages over the RFP-based seed sorting system in accuracy, efficiency, and cost for propagation of pure male sterile seeds. These characteristics will significantly increase the value and transgenic safety of the third-generation hybrid rice technology.

scholarly journals Maternal immune activation induces methylation changes in schizophrenia genes

2022 ◽  
Author(s):  
Tom Johnson ◽  
Defne Saatci ◽  
Lahiru Handunnetthi
Keyword(s):  
Environmental Risk ◽  
Immune Activation ◽  
Pyramidal Neurons ◽  
Fold Change ◽  
Adult Brain ◽  
Maternal Immune Activation ◽  
Differentially Methylated Genes ◽  
A Cell ◽  
Layer V ◽  
Upregulated Genes

Susceptibility to schizophrenia is mediated by genetic and environmental risk factors. Infection driven maternal immune activation (MIA) during pregnancy is a key environmental risk factor. However, little is known about how MIA during pregnancy could contribute to adult-onset schizophrenia. In this study, we investigated if maternal immune activation induces changes in methylation of genes linked to schizophrenia. We found that differentially expressed genes in schizophrenia brain were significantly enriched among MIA induced differentially methylated genes in the foetal brain in a cell-type-specific manner. Upregulated genes in layer V pyramidal neurons were enriched among hypomethylated genes at gestational day 9 (fold change = 1.57 , FDR = 0.049) and gestational day 17 (fold change = 1.97 , FDR = 0.0006). We also found that downregulated genes in GABAergic Rosehip interneurons were enriched among hypermethylated genes at gestational day 17 (fold change = 1.62, FDR= 0.03). Collectively, our results highlight a connection between MIA driven methylation changes during gestation and schizophrenia gene expression signatures in the adult brain. These findings carry important implications for early preventative strategies in schizophrenia.

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