scholarly journals Single-cell transcriptome profiling of buffelgrass (Cenchrus ciliaris) eggs unveils apomictic parthenogenesis signatures

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuji Ke ◽  
Maricel Podio ◽  
Joann Conner ◽  
Peggy Ozias-Akins
Keyword(s):  
De Novo ◽  
Transcriptome Profiling ◽  
Pathway Engineering ◽  
Future Research ◽  
Egg Cell ◽  
Cenchrus Ciliaris ◽  
Functional Roles ◽  
Gene Expression Studies ◽  
Cell Transcriptome ◽  
Parthenogenetic Egg

AbstractApomixis, a type of asexual reproduction in angiosperms, results in progenies that are genetically identical to the mother plant. It is a highly desirable trait in agriculture due to its potential to preserve heterosis of F1 hybrids through subsequent generations. However, no major crops are apomictic. Deciphering mechanisms underlying apomixis becomes one of the alternatives to engineer self-reproducing capability into major crops. Parthenogenesis, a major component of apomixis, commonly described as the ability to initiate embryo formation from the egg cell without fertilization, also can be valuable in plant breeding for doubled haploid production. A deeper understanding of transcriptional differences between parthenogenetic and sexual or non-parthenogenetic eggs can assist with pathway engineering. By conducting laser capture microdissection-based RNA-seq on sexual and parthenogenetic egg cells on the day of anthesis, a de novo transcriptome for the Cenchrus ciliaris egg cells was created, transcriptional profiles that distinguish the parthenogenetic egg from its sexual counterpart were identified, and functional roles for a few transcription factors in promoting natural parthenogenesis were suggested. These transcriptome data expand upon previous gene expression studies and will be a resource for future research on the transcriptome of egg cells in parthenogenetic and sexual genotypes.

scholarly journals Leaves and Roots of Micropropagated Plants Adopt Different Pathways for Withanolide Biosynthesis in Withania Coagulans: A Comparative Transcriptome Study

2021 ◽  
Author(s):  
Swati Gupta ◽  
Manoj Kumar Bohra ◽  
Kalpna sharma ◽  
Sumita Kachhwaha ◽  
Shanker Lal Kothari ◽  
...  
Keyword(s):  
De Novo ◽  
Pathway Engineering ◽  
Future Research ◽  
Withania Coagulans ◽  
Micropropagated Plants ◽  
Leaves And Roots ◽  
Salvage Pathways ◽  
Cellular Components ◽  
Rate Limiting ◽  
Selection Of

Abstract Withania coagulans (Stocks) Dunal commonly known as paneerbandh due to its milk coagulating properties, is a widely used medicinal herb, and micropropagated plants of the plant to produce some novel withanolides. Trasncscriptome sequencing of leaves and roots of micropropagated plants of W. coagulans assembled total 8.08 and 6.35 GB of raw reads into 292,074 and 16,474 high quality reads, out of which 267,119 and 15,758 unigenes were identified in WcL and WcR, respectively. Further, 40.6% WcL and 55.05% WcR unigenes were annotated using more than one database. Metabolic process and cellular components were identified as dominant categories in gene ontology, while total 20,927 WcL and 2,474 WcR unigenes were mapped to different biological pathways. KEGG classification aided in identification of genes involved in biosynthesis of withanolide precursor, 24-methylenecholesterol. All the genes related to withanolide precursor biosynthesis were present only in WcL, indicating de novo biosynthesis of withanolides, while absence of some rate limiting enzymes in WcR indicated towards biosynthesis of withanolides through salvage pathways. GTs, MTs and CYP450s were identified as putative genes involved in conversion of 24-methylenecholesterol to different withanolides. Differential expression of these genes further revealed details of enzymes involved in biosynthesis of tissue-specific withanolides. Further, withanolide profiling through HPLC analysis ascertained the differential biosynthesis and accumulation of withanolides in both the tissues in relatively very less concentration confirmed their biosynthesis through salvage mechanism in roots. Therefore, the present study can be fruitful for future research and product development of W. coagulans through pathway engineering. Moreover, the SSRs identified in this study can be used in marker assisted breeding and selection of biochemically elite varieties of W. coagulans.

scholarly journals Single-cell proteomics reveals downregulation of TMSB4X to drive actin release for stereocilia assembly

2019 ◽  
Author(s):  
Ying Zhu ◽  
Mirko Scheibinger ◽  
Daniel C. Ellwanger ◽  
Jocelyn F. Krey ◽  
Dongseok Choi ◽  
...  
Keyword(s):  
Single Cell ◽  
Progenitor Cells ◽  
Hair Cells ◽  
De Novo ◽  
Single Cells ◽  
Transcriptome Profiling ◽  
Developmental Trajectory ◽  
Sensory Hair ◽  
Hair Cell Differentiation ◽  
Cell Transcriptome

AbstractHearing and balance rely on small sensory hair cells that reside in the inner ear. To explore dynamic changes in the abundant proteins present in differentiating hair cells, we used nanoliter-scale shotgun mass spectrometry of single cells, each ∼1 picoliter, from utricles of embryonic day 15 chickens. We identified unique constellations of proteins or protein groups from presumptive hair cells and from progenitor cells. The single-cell proteomes enabled the de novo reconstruction of a developmental trajectory. Inference of protein expression dynamics revealed that the actin monomer binding protein thymosin β4 (TMSB4X) was present in progenitors but dropped precipitously during hair-cell differentiation. Complementary single-cell transcriptome profiling showed downregulation of TMSB4X mRNA during maturation of hair cells. We propose that most actin is sequestered by TMSB4X in progenitor cells, but upon differentiation to hair cells, actin is released to build the sensory hair bundle.

scholarly journals Single-cell proteomics reveals changes in expression during hair-cell development

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Ying Zhu ◽  
Mirko Scheibinger ◽  
Daniel Christian Ellwanger ◽  
Jocelyn F Krey ◽  
Dongseok Choi ◽  
...  
Keyword(s):  
Single Cell ◽  
Hair Cells ◽  
De Novo ◽  
Single Cells ◽  
Transcriptome Profiling ◽  
Developmental Trajectory ◽  
Proteomics Data ◽  
Sensory Hair Cells ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Hearing and balance rely on small sensory hair cells that reside in the inner ear. To explore dynamic changes in the abundant proteins present in differentiating hair cells, we used nanoliter-scale shotgun mass spectrometry of single cells, each ~1 picoliter, from utricles of embryonic day 15 chickens. We identified unique constellations of proteins or protein groups from presumptive hair cells and from progenitor cells. The single-cell proteomes enabled the de novo reconstruction of a developmental trajectory using protein expression levels, revealing proteins that greatly increased in expression during differentiation of hair cells (e.g., OCM, CRABP1, GPX2, AK1, GSTO1) and those that decreased during differentiation (e.g., TMSB4X, AGR3). Complementary single-cell transcriptome profiling showed corresponding changes in mRNA during maturation of hair cells. Single-cell proteomics data thus can be mined to reveal features of cellular development that may be missed with transcriptomics.

scholarly journals Transcriptome profiling of Lymnaea stagnalis (Gastropoda) for ecoimmunological research

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Otto Seppälä ◽  
Jean-Claude Walser ◽  
Teo Cereghetti ◽  
Katri Seppälä ◽  
Tiina Salo ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Individual Variation ◽  
Lymnaea Stagnalis ◽  
De Novo ◽  
Transcriptome Profiling ◽  
Snail Species ◽  
Immune Defence ◽  
Immune Activity ◽  
Self Recognition ◽  
Immune Assays

Abstract Background Host immune function can contribute to numerous ecological/evolutionary processes. Ecoimmunological studies, however, typically use one/few phenotypic immune assays and thus do not consider the complexity of the immune system. Therefore, “omics” resources that allow quantifying immune activity across multiple pathways are needed for ecoimmunological models. We applied short-read based RNAseq (Illumina NextSeq 500, PE-81) to characterise transcriptome profiles of Lymnaea stagnalis (Gastropoda), a multipurpose model snail species. We used a genetically diverse snail stock and exposed individuals to immune elicitors (injury, bacterial/trematode pathogens) and changes in environmental conditions that can alter immune activity (temperature, food availability). Results Immune defence factors identified in the de novo assembly covered elements broadly described in other gastropods. For instance, pathogen-recognition receptors (PRR) and lectins activate Toll-like receptor (TLR) pathway and cytokines that regulate cellular and humoral defences. Surprisingly, only modest diversity of antimicrobial peptides and fibrinogen related proteins were detected when compared with other taxa. Additionally, multiple defence factors that may contribute to the phenotypic immune assays used to quantify antibacterial activity and phenoloxidase (PO)/melanisation-type reaction in this species were found. Experimental treatments revealed factors from non-self recognition (lectins) and signalling (TLR pathway, cytokines) to effectors (e.g., antibacterial proteins, PO enzymes) whose transcription depended on immune stimuli and environmental conditions, as well as components of snail physiology/metabolism that may drive these effects. Interestingly, the transcription of many factors (e.g., PRR, lectins, cytokines, PO enzymes, antibacterial proteins) showed high among-individual variation. Conclusions Our results indicate several uniform aspects of gastropod immunity, but also apparent differences between L. stagnalis and some previously examined taxa. Interestingly, in addition to immune defence factors that responded to immune elicitors and changes in environmental conditions, many factors showed high among-individual variation across experimental snails. We propose that such factors are highly important to be included in future ecoimmunological studies because they may be the key determinants of differences in parasite resistance among individuals both within and between natural snail populations.

scholarly journals Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tongqing Zhang ◽  
Jiawen Yin ◽  
Shengkai Tang ◽  
Daming Li ◽  
Xiankun Gu ◽  
...  
Keyword(s):  
De Novo ◽  
Corbicula Fluminea ◽  
Gene Families ◽  
Ruditapes Philippinarum ◽  
Genomic Sequences ◽  
Future Research ◽  
Asian Clam ◽  
Sequencing Technologies ◽  
East And Southeast Asia ◽  
Clam Corbicula

AbstractThe Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.

scholarly journals Cohort profile of Acutelines: a large data/biobank of acute and emergency medicine

BMJ Open ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. e047349
Author(s):  
Ewoud ter Avest ◽  
Barbara C van Munster ◽  
Raymond J van Wijk ◽  
Sanne Tent ◽  
Sanne Ter Horst ◽  
...  
Keyword(s):  
Acute Care ◽  
De Novo ◽  
Medical Center ◽  
Large Data ◽  
Future Research ◽  
Imaging Data ◽  
Novel Studies ◽  
Long Term Follow Up ◽  
Registration Number

PurposeResearch in acute care faces many challenges, including enrolment challenges, legal limitations in data sharing, limited funding and lack of singular ownership of the domain of acute care. To overcome these challenges, the Center of Acute Care of the University Medical Center Groningen in the Netherlands, has established a de novo data, image and biobank named ‘Acutelines’.ParticipantsClinical data, imaging data and biomaterials (ie, blood, urine, faeces, hair) are collected from patients presenting to the emergency department (ED) with a broad range of acute disease presentations. A deferred consent procedure (by proxy) is in place to allow collecting data and biomaterials prior to obtaining written consent. The digital infrastructure used ensures automated capturing of all bed-side monitoring data (ie, vital parameters, electrophysiological waveforms) and securely importing data from other sources, such as the electronic health records of the hospital, ambulance and general practitioner, municipal registration and pharmacy. Data are collected from all included participants during the first 72 hours of their hospitalisation, while follow-up data are collected at 3 months, 1 year, 2 years and 5 years after their ED visit.Findings to dateEnrolment of the first participant occurred on 1 September 2020. During the first month, 653 participants were screened for eligibility, of which 180 were approached as potential participants. In total, 151 (84%) provided consent for participation of which 89 participants fulfilled criteria for collection of biomaterials.Future plansThe main aim of Acutelines is to facilitate research in acute medicine by providing the framework for novel studies and issuing data, images and biomaterials for future research. The protocol will be extended by connecting with central registries to obtain long-term follow-up data, for which we already request permission from the participant.Trial registration numberNCT04615065.

scholarly journals Glycosylation of Cancer Extracellular Vesicles: Capture Strategies, Functional Roles and Potential Clinical Applications

Cells ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 109
Author(s):  
Álvaro M. Martins ◽  
Cátia C. Ramos ◽  
Daniela Freitas ◽  
Celso A. Reis
Keyword(s):  
Extracellular Vesicles ◽  
Biomarker Discovery ◽  
De Novo ◽  
Recipient Cell ◽  
Cell Communication ◽  
Cancer Biomarkers ◽  
Functional Roles ◽  
Molecular Information ◽  
Glycosylation Pathway ◽  
Organ Tropism

Glycans are major constituents of extracellular vesicles (EVs). Alterations in the glycosylation pathway are a common feature of cancer cells, which gives rise to de novo or increased synthesis of particular glycans. Therefore, glycans and glycoproteins have been widely used in the clinic as both stratification and prognosis cancer biomarkers. Interestingly, several of the known tumor-associated glycans have already been identified in cancer EVs, highlighting EV glycosylation as a potential source of circulating cancer biomarkers. These particles are crucial vehicles of cell–cell communication, being able to transfer molecular information and to modulate the recipient cell behavior. The presence of particular glycoconjugates has been described to be important for EV protein sorting, uptake and organ-tropism. Furthermore, specific EV glycans or glycoproteins have been described to be able to distinguish tumor EVs from benign EVs. In this review, the application of EV glycosylation in the development of novel EV detection and capture methodologies is discussed. In addition, we highlight the potential of EV glycosylation in the clinical setting for both cancer biomarker discovery and EV therapeutic delivery strategies.

scholarly journals Validation of Reference Genes for Studying Different Abiotic Stresses in oat (Avena sativa L.) by RT-qPCR

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1272
Author(s):  
Judit Tajti ◽  
Magda Pál ◽  
Tibor Janda
Keyword(s):  
Gene Expression ◽  
Avena Sativa ◽  
Abiotic Stresses ◽  
Reference Genes ◽  
Nutritional Value ◽  
Tissue Type ◽  
Future Research ◽  
Experimental Conditions ◽  
Expression Studies ◽  
Gene Expression Studies

Oat (Avena sativa L.) is a widely cultivated cereal with high nutritional value and it is grown mainly in temperate regions. The number of studies dealing with gene expression changes in oat continues to increase, and to obtain reliable RT-qPCR results it is essential to establish and use reference genes with the least possible influence caused by experimental conditions. However, no detailed study has been conducted on reference genes in different tissues of oat under diverse abiotic stress conditions. In our work, nine candidate reference genes (ACT, TUB, CYP, GAPD, UBC, EF1, TBP, ADPR, PGD) were chosen and analysed by four statistical methods (GeNorm, Normfinder, BestKeeper, RefFinder). Samples were taken from two tissues (leaves and roots) of 13-day-old oat plants exposed to five abiotic stresses (drought, salt, heavy metal, low and high temperatures). ADPR was the top-rated reference gene for all samples, while different genes proved to be the most stable depending on tissue type and treatment combinations. TUB and EF1 were most affected by the treatments in general. Validation of reference genes was carried out by PAL expression analysis, which further confirmed their reliability. These results can contribute to reliable gene expression studies for future research in cultivated oat.

scholarly journals Transcriptome Analysis of Ramie (Boehmeria niveaL. Gaud.) in Response to Ramie Moth (Cocytodes coeruleaGuenée) Infestation

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Liangbin Zeng ◽  
Airong Shen ◽  
Jia Chen ◽  
Zhun Yan ◽  
Touming Liu ◽  
...  
Keyword(s):  
Protein Function ◽  
Molecular Mechanisms ◽  
Defense Mechanism ◽  
Natural Fiber ◽  
De Novo ◽  
Average Length ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Cdna Libraries ◽  
Pcr Analysis

The ramie mothCocytodes coeruleaGuenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore,de novoassembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

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