scholarly journals Molecular Mechanisms Underlying Increase in Lysine Content of Waxy Maize through the Introgression of the opaque2 Allele

2019 ◽  
Vol 20 (3) ◽  
pp. 684 ◽  
Author(s):  
Wei Wang ◽  
Suzhen Niu ◽  
Yi Dai ◽  
Xinmi Zhai ◽  
Mingchun Wang ◽  
...  
Keyword(s):  
Nutritional Value ◽  
Molecular Mechanisms ◽  
Endosperm Development ◽  
Content Increase ◽  
Lysine Content ◽  
Biological Processes ◽  
Rna Seq ◽  
Waxy Maize ◽  
Marker Assisted Backcrossing

The opaque2 (o2) mutation in maize is associated with high lysine content in endosperm and good nutritional value. To improve the nutritional quality of waxy maize, the o2 allele was introgressed into the wxwx line using marker-assisted backcrossing selection technology. The lysine content of o2o2wxwx lines was higher than that of the wxwx line. To reveal the mechanism of increasing lysine content through introgression of the o2 in waxy maize, the transcriptome on kernels (18th day after pollination) of the o2o2wxwx and parent lines was analyzed using RNA-sequencing (RNA-Seq). The RNA-Seq analysis revealed 49 differentially expressed genes (DEGs). Functional analysis showed that these DEGs were mostly related to the catalytic activity and metabolic processes. The O2 gene regulated multiple metabolic pathways related to biological processes (BP) and molecular function (MP) during waxy maize endosperm development. In particular, in the o2o2wxwx lines, the two genes that encode the EF-1α and LHT1 were up-regulated, but the gene that encodes sulfur-rich proteins was down-regulated, raising the grain lysine content. These findings are of great importance for understanding the molecular mechanism underlying the lysine content increase due to o2 allele introgression into waxy maize.

scholarly journals Transcriptome Dynamics of Double Recessive Mutant, o2o2o16o16, Reveals the Transcriptional Mechanisms in the Increase of Its Lysine and Tryptophan Content in Maize

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 316 ◽  
Author(s):  
Wei Wang ◽  
Yi Dai ◽  
Mingchun Wang ◽  
Wenpeng Yang ◽  
Degang Zhao
Keyword(s):  
Molecular Mechanisms ◽  
Degradation Pathway ◽  
Endosperm Development ◽  
Rna Seq ◽  
Wild Type ◽  
Genes Encoding ◽  
Recessive Mutant ◽  
Lysine Degradation ◽  
Tryptophan Content

In maize, pyramiding of o2 and o16 alleles can greatly improve the nutritional quality of grains. To dissect its molecular mechanism, we created a double recessive mutant line, o2o2o16o16, by introgression of the o2 and o16 alleles into the wild-type maize inbred line, by molecular marker-assisted backcross selection. The kernels (18 day after pollination (DAP), 28 DAP, and 38 DAP) of the o2o2o16o16 mutant and its parent lines were subject to RNA sequencing (RNA-Seq). The RNA-Seq analysis revealed that 59 differentially expressed genes (DEGs) were involved in lysine metabolism and 43 DEGs were involved in tryptophan metabolism. Among them, the genes encoding AK, ASADH, and Dap-F in the lysine synthesis pathway were upregulated at different stages of endosperm development, promoting the synthesis of lysine. Meanwhile, the genes encoding LKR/SDH and L-PO in the lysine degradation pathway were downregulated, inhibiting the degradation of lysine. Moreover, the genes encoding TAA and YUC in the tryptophan metabolic pathway were downregulated, restraining the degradation of tryptophan. Thus, pyramiding o2 and o16 alleles could increase the lysine and tryptophan content in maize. These above results would help to uncover the molecular mechanisms involved in the increase in lysine and the tryptophan content, through the introgression of o2 and o16 alleles into the wild-type maize.

scholarly journals Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines

2020 ◽  
Author(s):  
Mikhail G. Dozmorov ◽  
Katarzyna M. Tyc ◽  
Nathan C. Sheffield ◽  
David C. Boyd ◽  
Amy L. Olex ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Genetic Material ◽  
Human Tumor ◽  
Chromatin Conformation ◽  
Library Preparation ◽  
Rna Seq ◽  
Chromatin Conformation Capture ◽  
Alignment Strategy ◽  
Preparation Strategy

AbstractSequencing of patient-derived xenograft (PDX) mouse models allows investigation of the molecular mechanisms of human tumor samples engrafted in a mouse host. Thus, both human and mouse genetic material is sequenced. Several methods have been developed to remove mouse sequencing reads from RNA-seq or exome sequencing PDX data and improve the downstream signal. However, for more recent chromatin conformation capture technologies (Hi-C), the effect of mouse reads remains undefined.We evaluated the effect of mouse read removal on the quality of Hi-C data using in silico created PDX Hi-C data with 10% and 30% mouse reads. Additionally, we generated two experimental PDX Hi-C datasets using different library preparation strategies. We evaluated three alignment strategies (Direct, Xenome, Combined) and three processing pipelines (Juicer, HiC-Pro, HiCExplorer) on the quality of Hi-C data.Removal of mouse reads had little-to-no effect on data quality than the results obtained with Direct alignment strategy. Juicer pipeline extracted the most useful information from PDX Hi-C data. However, library preparation strategy had the largest effect on all quality metrics. Together, our study presents comprehensive guidelines on PDX Hi-C data processing.

scholarly journals ClusterMap: Comparing analyses across multiple Single Cell RNA-Seq profiles

2018 ◽  
Author(s):  
Xin Gao ◽  
Deqing Hu ◽  
Madelaine Gogol ◽  
Hua Li
Keyword(s):  
Single Cell ◽  
Molecular Mechanisms ◽  
Population Level ◽  
Marker Genes ◽  
Rna Seq ◽  
Matching Problem ◽  
Cut Method ◽  
Underlying Mechanisms

AbstractSingle cell RNA-Seq facilitates the characterization of cell type heterogeneity and developmental processes. Further study of single cell profiles across different conditions enables the understanding of biological processes and underlying mechanisms at the sub-population level. However, developing proper methodology to compare multiple scRNA-Seq datasets remains challenging. We have developed ClusterMap, a systematic method and workflow to facilitate the comparison of scRNA profiles across distinct biological contexts. Using hierarchical clustering of the marker genes of each sub-group, ClusterMap matches the sub-types of cells across different samples and provides “similarity” as a metric to quantify the quality of the match. We introduce a purity tree cut method designed specifically for this matching problem. We use Circos plot and regrouping method to visualize the results concisely. Furthermore, we propose a new metric “separability” to summarize sub-population changes among all sample pairs. In three case studies, we demonstrate that ClusterMap has the ability to offer us further insight into the different molecular mechanisms of cellular sub-populations across different conditions. ClusterMap is implemented in R and available at https://github.com/xgaoo/ClusterMap.

scholarly journals Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination

2019 ◽  
Vol 116 (34) ◽  
pp. 17121-17126 ◽  
Author(s):  
Diógenes S. de Lima ◽  
Lucas E. Cardozo ◽  
Vinicius Maracaja-Coutinho ◽  
Andreas Suhrbier ◽  
Karim Mane ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Host Responses ◽  
Biological Processes ◽  
Rna Seq ◽  
Altered Expression ◽  
Live Attenuated Influenza Vaccine ◽  
Induced Immunity ◽  
Blood Transcriptome

Understanding the mechanisms of vaccine-elicited protection contributes to the development of new vaccines. The emerging field of systems vaccinology provides detailed information on host responses to vaccination and has been successfully applied to study the molecular mechanisms of several vaccines. Long noncoding RNAs (lncRNAs) are crucially involved in multiple biological processes, but their role in vaccine-induced immunity has not been explored. We performed an analysis of over 2,000 blood transcriptome samples from 17 vaccine cohorts to identify lncRNAs potentially involved with antibody responses to influenza and yellow fever vaccines. We have created an online database where all results from this analysis can be accessed easily. We found that lncRNAs participate in distinct immunological pathways related to vaccine-elicited responses. Among them, we showed that the expression of lncRNA FAM30A was high in B cells and correlates with the expression of immunoglobulin genes located in its genomic vicinity. We also identified altered expression of these lncRNAs in RNA-sequencing (RNA-seq) data from a cohort of children following immunization with intranasal live attenuated influenza vaccine, suggesting a common role across several diverse vaccines. Taken together, these findings provide evidence that lncRNAs have a significant impact on immune responses induced by vaccination.

scholarly journals Transcriptomic profiling revealed key signaling pathways for cold tolerance and acclimation of two carp species

2019 ◽  
Author(s):  
Guodong Ge ◽  
Yong Long ◽  
Lianyu Shi ◽  
Jing Ren ◽  
Junjun Yan ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Cold Acclimation ◽  
Cold Tolerance ◽  
Drug Transport ◽  
Molecular Mechanisms ◽  
Secondary Alcohol ◽  
Enrichment Analysis ◽  
Biological Processes ◽  
Rna Seq ◽  
Mirror Carp

Abstract Background Closely related species of the carp family ( Cyprinidae ) have evolved distinctive abilities to survive under cold stress, but molecular mechanisms underlying the generation of cold resistance remain largely unknow. In this study, we compared transcriptomic profiles of two carp species to identify key factors and pathways for cold tolerance and acclimation. Results Larvae of Songpu mirror carp and Barbless carp that were pretreated at 18°C for 24 hours significantly improved their survival rates under lethal cold temperature at 8°C or 10°C, indicating that two carp species possess the ability of cold acclimation. However, Songpu mirror carp exhibited stronger abilities of cold tolerance and acclimation than Barbless carp. Transcriptomic profiles of Songpu mirror carp and Barbless carp larvae at 28°C and 18°C were compared during cold acclimation through RNA-seq. Differentially expressed genes that are closely associated with the differences in cold acclimation between two carp species were identified through bioinformatics and Venn's diagram analysis. GO enrichment analysis of these genes indicated that cellular component assembly involved in morphogenesis, secondary alcohol metabolism and drug transport were the most up-regulated biological processes during cold acclimation of Songpu mirror carp. Conversely, positive regulation of macroautophagy, intracellular protein transport, and organonitrogen compound catabolism were the most down-regulated biological processes during cold acclimation of Barbless carp. KEGG enrichment analysis revealed that factors in the FoxO-related signaling pathways are mainly responsible for the development of differences in cold tolerance and acclimation between two carp species since altering the phosphorylation of key proteins in the FoxO-related signaling pathways with inhibitors or an activator significantly decreased the cold tolerance and acclimation of Songpu mirror carp. These data provided key clues for dissection of molecular mechanisms underlying the development of cold tolerance and acclimation in carps. Conclusions These findings indicate that larvae of two carp species possess different abilities of cold tolerance and can build cold acclimation under mild low temperature. Multiple biological processes and FoxO-related signaling pathways are closely associated with the development of differences in cold tolerance and acclimation between two carp species. Keywords: Carp; cold tolerance; cold acclimation; RNA-Seq; biological process; signaling pathways

scholarly journals Advances in Biosynthesis and Biological Functions of Proanthocyanidins in Horticultural Plants

Foods ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1774
Author(s):  
Dan Yu ◽  
Ting Huang ◽  
Bin Tian ◽  
Jicheng Zhan
Keyword(s):  
Nutritional Value ◽  
Biosynthetic Pathway ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Future Research ◽  
Plant Metabolites ◽  
Secondary Plant Metabolites ◽  
New Findings ◽  
Processed Products

Proanthocyanidins are colorless flavonoid polymers condensed from flavan-3-ol units. They are essential secondary plant metabolites that contribute to the nutritional value and sensory quality of many fruits and the related processed products. Mounting evidence has shown that the accumulation of proanthocyanidins is associated with the resistance of plants against a broad spectrum of abiotic and biotic stress conditions. The biosynthesis of proanthocyanidins has been examined extensively, allowing for identifying and characterizing the key regulators controlling the biosynthetic pathway in many plants. New findings revealed that these specific regulators were involved in the proanthocyanidins biosynthetic network in response to various environmental conditions. This paper reviews the current knowledge regarding the control of key regulators in the underlying proanthocyanidins biosynthetic and molecular mechanisms in response to environmental stress. Furthermore, it discusses the directions for future research on the metabolic engineering of proanthocyanidins production to improve food and fruit crop quality.

scholarly journals Whole transcriptome analysis of the fasting and fed Burmese python heart: insights into extreme physiological cardiac adaptation

2011 ◽  
Vol 43 (2) ◽  
pp. 69-76 ◽  
Author(s):  
Christopher E. Wall ◽  
Steven Cozza ◽  
Cecilia A. Riquelme ◽  
W. Richard McCombie ◽  
Joseph K. Heimiller ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Differential Expression ◽  
Molecular Mechanisms ◽  
Biological Processes ◽  
Rna Seq ◽  
Cardiac Adaptation ◽  
Python Molurus ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome ◽  
Novel Model

The infrequently feeding Burmese python ( Python molurus ) experiences significant and rapid postprandial cardiac hypertrophy followed by regression as digestion is completed. To begin to explore the molecular mechanisms of this response, we have sequenced and assembled the fasted and postfed Burmese python heart transcriptomes with Illumina technology using the chicken ( Gallus gallus ) genome as a reference. In addition, we have used RNA-seq analysis to identify differences in the expression of biological processes and signaling pathways between fasted, 1 day postfed (DPF), and 3 DPF hearts. Out of a combined transcriptome of ∼2,800 mRNAs, 464 genes were differentially expressed. Genes showing differential expression at 1 DPF compared with fasted were enriched for biological processes involved in metabolism and energetics, while genes showing differential expression at 3 DPF compared with fasted were enriched for processes involved in biogenesis, structural remodeling, and organization. Moreover, we present evidence for the activation of physiological and not pathological signaling pathways in this rapid, novel model of cardiac growth in pythons. Together, our data provide the first comprehensive gene expression profile for a reptile heart.

scholarly journals The parent-of-origin lncRNA MISSEN regulates rice endosperm development

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yan-Fei Zhou ◽  
Yu-Chan Zhang ◽  
Yu-Meng Sun ◽  
Yang Yu ◽  
Meng-Qi Lei ◽  
...  
Keyword(s):  
Essential Role ◽  
Molecular Mechanisms ◽  
Histone H3 ◽  
Noncoding Rnas ◽  
Endosperm Development ◽  
Biological Processes ◽  
Rice Endosperm ◽  
Family Protein ◽  
Potential Applications ◽  
Parent Of Origin

AbstractThe cereal endosperm is a major factor determining seed size and shape. However, the molecular mechanisms of endosperm development are not fully understood. Long noncoding RNAs (lncRNAs) function in various biological processes. Here we show a lncRNA, MISSEN, that plays an essential role in early endosperm development in rice (Oryza sativa). MISSEN is a parent-of-origin lncRNA expressed in endosperm, and negatively regulates endosperm development, leading to a prominent dent and bulge in the seed. Mechanistically, MISSEN functions through hijacking a helicase family protein (HeFP) to regulate tubulin function during endosperm nucleus division and endosperm cellularization, resulting in abnormal cytoskeletal polymerization. Finally, we revealed that the expression of MISSEN is inhibited by histone H3 lysine 27 trimethylation (H3K27me3) modification after pollination. Therefore, MISSEN is the first lncRNA identified as a regulator in endosperm development, highlighting the potential applications in rice breeding.

Variations in Mineral/heavy metals profiling and preventive role of trichomes in Peach Fruits treated with CaC2

2020 ◽  
Vol 23 ◽  
Author(s):  
Muhammad Irfan ◽  
Safdar Abbas ◽  
Beenish Jehan Azhar ◽  
Shakeel Ahmad ◽  
Hafsa Muhammad ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Nutritional Value ◽  
Fine Powder ◽  
Calcium Carbide ◽  
Control Group ◽  
Tandem Accelerator ◽  
Health Promoting ◽  
Elemental Profiling

Background: Phytonutrients in peach fruits have health promoting antioxidants against various chronic diseases. However, there is no extensive data to show the nutritional values of Local peach cultivars after post-harvest treatments. Objective: Mainly this study was objective to determine the effect of calcium carbide on nutritional value and quality of fruits of Pakistani peach cultivars. Methods: The peach fruits were collected from three different peach orchids of KPK and the fruits were divided into 4 groups while 5th group was collected from local fruit shop. Each experimental group was treated with different concentration of calcium carbide whereas control group was not treated. The peel and pulp samples were oven dried and ground to fine powder separately. The elemental compositions were determined using Particle Induced X-ray emission and Pelletron Tandem Accelerator. Result: Sixteen elements were identified in peach fruits and the elements were Al, P, S, Cl, K, Ca, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, and Se. In peel, concentration of some elements increased or decreased after treatment with CaC2 while in pulp the conc. of nearly all detected elements was increased in treated samples. We found significantly high amount of heavy metals traces including As, Se, Co, Si, and P in peach fruits treated with CaC2. Interestingly, the presence of trichomes in peach skin prevents the transfer of these heavy metals deep into the pulp which was also verified by the elemental profiling of nectarines. Conclusion: Conclusively, the artificial ripening with CaC2 changed the nutritional value of peach fruits that has higher health risks if consume with the peel. According to our best knowledge, this is the first report that highlights the effects of CaC2 which deteriorate the nutritional value of peach fruits in Pakistan.

scholarly journals Molecular regulation of Snai2 in development and disease

2019 ◽  
Vol 132 (23) ◽  
Author(s):  
Wenhui Zhou ◽  
Kayla M. Gross ◽  
Charlotte Kuperwasser
Keyword(s):  
Transcription Factor ◽  
Cell Biology ◽  
Molecular Mechanisms ◽  
Epithelial To Mesenchymal Transition ◽  
Zinc Finger Protein ◽  
Main Role ◽  
Biological Processes ◽  
Developmental Defects ◽  
Mesenchymal Transition ◽  
Damage Repair

ABSTRACT The transcription factor Snai2, encoded by the SNAI2 gene, is an evolutionarily conserved C2H2 zinc finger protein that orchestrates biological processes critical to tissue development and tumorigenesis. Initially characterized as a prototypical epithelial-to-mesenchymal transition (EMT) transcription factor, Snai2 has been shown more recently to participate in a wider variety of biological processes, including tumor metastasis, stem and/or progenitor cell biology, cellular differentiation, vascular remodeling and DNA damage repair. The main role of Snai2 in controlling such processes involves facilitating the epigenetic regulation of transcriptional programs, and, as such, its dysregulation manifests in developmental defects, disruption of tissue homeostasis, and other disease conditions. Here, we discuss our current understanding of the molecular mechanisms regulating Snai2 expression, abundance and activity. In addition, we outline how these mechanisms contribute to disease phenotypes or how they may impact rational therapeutic targeting of Snai2 dysregulation in human disease.

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