Liquid profiling in plants: identification and analysis of extracellular metabolites and miRNAs in pollination drops of Ginkgo biloba

2020 ◽  
Vol 40 (10) ◽  
pp. 1420-1436 ◽  
Author(s):  
Zhaogeng Lu ◽  
Bei Jiang ◽  
Beibei Zhao ◽  
Xinyu Mao ◽  
Jinkai Lu ◽  
...  
Keyword(s):  
Organic Acids ◽  
Carbohydrate Metabolism ◽  
Ginkgo Biloba ◽  
Target Prediction ◽  
Gas Chromatography Mass Spectrometry ◽  
Critical Feature ◽  
Functional Roles ◽  
Extracellular Mirna ◽  
And Function ◽  
Pollination Systems

Abstract The pollination drop (PD), also known as an ovular secretion, is a critical feature of most wind-pollinated gymnosperms and function as an essential component of pollination systems. However, the metabolome and small RNAs of gymnosperm PDs are largely unknown. We employed gas chromatography–mass spectrometry to identify a total of 101 metabolites in Ginkgo biloba L. PDs. The most abundant metabolites were sugars (45.70%), followed by organic acids (15.94%) and alcohols (15.39%) involved in carbohydrate metabolism, glycine, serine and threonine metabolism. Through pollen culture of the PDs, we further demonstrated that the metabolic components of PDs are indispensable for pollen germination and growth; in particular, organic acids and fatty acids play defensive roles against microbial activity. In addition, we successfully constructed a small RNA library and detected 45 known and 550 novel miRNAs in G. biloba PDs. Interestingly, in a comparative analysis of miRNA expression between PDs and ovules, we found that most of the known miRNAs identified in PDs were also expressed in the ovules, implying that miRNAs in PDs may originate from ovules. Further, combining with potential target prediction, degradome validation and transcriptome sequencing, we identified that the interactions of several known miRNAs and their targets in PDs are involved in carbohydrate metabolism, hormone signaling and defense response pathways, consistent with the metabolomics results. Our results broaden the knowledge of metabolite profiling and potential functional roles in gymnosperm PDs and provide the first evidence of extracellular miRNA functions in ovular secretions from gymnosperms.

Computational Approaches to Predict the Non-canonical DNAs

2019 ◽  
Vol 14 (6) ◽  
pp. 470-479 ◽  
Author(s):  
Nazia Parveen ◽  
Amen Shamim ◽  
Seunghee Cho ◽  
Kyeong Kyu Kim
Keyword(s):  
Computational Methods ◽  
Genetic Instability ◽  
Computational Prediction ◽  
Structure And Function ◽  
Sequence Motifs ◽  
Computational Approaches ◽  
Functional Roles ◽  
And Function ◽  
Genetic Events ◽  
Insight Into

Background: Although most nucleotides in the genome form canonical double-stranded B-DNA, many repeated sequences transiently present as non-canonical conformations (non-B DNA) such as triplexes, quadruplexes, Z-DNA, cruciforms, and slipped/hairpins. Those noncanonical DNAs (ncDNAs) are not only associated with many genetic events such as replication, transcription, and recombination, but are also related to the genetic instability that results in the predisposition to disease. Due to the crucial roles of ncDNAs in cellular and genetic functions, various computational methods have been implemented to predict sequence motifs that generate ncDNA. Objective: Here, we review strategies for the identification of ncDNA motifs across the whole genome, which is necessary for further understanding and investigation of the structure and function of ncDNAs. Conclusion: There is a great demand for computational prediction of non-canonical DNAs that play key functional roles in gene expression and genome biology. In this study, we review the currently available computational methods for predicting the non-canonical DNAs in the genome. Current studies not only provide an insight into the computational methods for predicting the secondary structures of DNA but also increase our understanding of the roles of non-canonical DNA in the genome.

scholarly journals The Evolving Roles of Cardiac Macrophages in Homeostasis, Regeneration, and Repair

2021 ◽  
Vol 22 (15) ◽  
pp. 7923
Author(s):  
Santiago Alvarez-Argote ◽  
Caitlin C. O’Meara
Keyword(s):  
Cardiac Injury ◽  
Cardiac Regeneration ◽  
Normal Function ◽  
Cardiac Conduction ◽  
Cell Detection ◽  
Fate Mapping ◽  
The Novel ◽  
Functional Roles ◽  
Macrophage Populations ◽  
And Function

Macrophages were first described as phagocytic immune cells responsible for maintaining tissue homeostasis by the removal of pathogens that disturb normal function. Historically, macrophages have been viewed as terminally differentiated monocyte-derived cells that originated through hematopoiesis and infiltrated multiple tissues in the presence of inflammation or during turnover in normal homeostasis. However, improved cell detection and fate-mapping strategies have elucidated the various lineages of tissue-resident macrophages, which can derive from embryonic origins independent of hematopoiesis and monocyte infiltration. The role of resident macrophages in organs such as the skin, liver, and the lungs have been well characterized, revealing functions well beyond a pure phagocytic and immunological role. In the heart, recent research has begun to decipher the functional roles of various tissue-resident macrophage populations through fate mapping and genetic depletion studies. Several of these studies have elucidated the novel and unexpected roles of cardiac-resident macrophages in homeostasis, including maintaining mitochondrial function, facilitating cardiac conduction, coronary development, and lymphangiogenesis, among others. Additionally, following cardiac injury, cardiac-resident macrophages adopt diverse functions such as the clearance of necrotic and apoptotic cells and debris, a reduction in the inflammatory monocyte infiltration, promotion of angiogenesis, amelioration of inflammation, and hypertrophy in the remaining myocardium, overall limiting damage extension. The present review discusses the origin, development, characterization, and function of cardiac macrophages in homeostasis, cardiac regeneration, and after cardiac injury or stress.

Functional Roles of Chelated Magnesium Ions in RNA Folding and Function

Biochemistry ◽  
2021 ◽  
Author(s):  
Ryota Yamagami ◽  
Jacob P. Sieg ◽  
Philip C. Bevilacqua
Keyword(s):  
Rna Folding ◽  
Magnesium Ions ◽  
Functional Roles ◽  
And Function

scholarly journals Biodistribution and function of extracellular miRNA-155 in mice

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Shashi Bala ◽  
Timea Csak ◽  
Fatemeh Momen-Heravi ◽  
Dora Lippai ◽  
Karen Kodys ◽  
...  
Keyword(s):  
Extracellular Mirna ◽  
And Function

On the 3D Correlation between Myofibroblast Shape and Contraction

2021 ◽  
Author(s):  
Alex Khang ◽  
Emma Lejeune ◽  
Ali Abbaspour ◽  
Daniel Howsmon ◽  
Michael Sacks
Keyword(s):  
Cell Shape ◽  
Interstitial Cell ◽  
Stable State ◽  
Stress Fiber ◽  
Poly Ethylene Glycol ◽  
Critical Feature ◽  
Peg Hydrogels ◽  
Poly Ethylene ◽  
And Function ◽  
The Relationship

Abstract Cell shape is known to correlate closely with stress-fiber geometry and function, and is thus a critical feature of cell biophysical state. However, the relationship between myofibroblast shape and contraction is complex, even as well in regards to steady-state contractile level (basal tonus). At present, the relationship between myofibroblast shape and basal tonus in 3D is poorly understood. Herein, we utilize the aortic valve interstitial cell (AVICs) as a representative myofibroblast to investigate the relationship between basal tonus and overall cell shape. AVICs were embedded within 3D poly (ethylene glycol) (PEG) hydrogels containing degradable peptide crosslinkers, adhesive peptide sequences, and sub-micron fluorescent micro-spheres to track the local displacement field. We then developed a methodology to evaluate the correlation between overall AVIC shape and basal tonus induced contraction. We computed a volume averaged stretch tensor <U> for the volume occupied by the AVIC, which had three distinct eigenvalues (1.08, 0.99, and 0.89), suggesting that AVIC shape is a result of anisotropic contraction. Furthermore, the direction of maximum contraction correlated closely with the longest axis of a bounding ellipsoid enclosing the AVIC. As gel--imbedded AVIC are known to be in a stable state by three days of incubation used herein, this finding suggests that the overall quiescent AVIC shape is driven by the underlying stress-fiber directional structure and possibly contraction level.

scholarly journals miRador: a fast and precise tool for the prediction of plant miRNAs

2021 ◽  
Author(s):  
Reza K Hammond ◽  
Parth Patel ◽  
Pallavi Gupta ◽  
Blake C. Meyers
Keyword(s):  
Stress Responses ◽  
Target Prediction ◽  
Accurate Identification ◽  
Rna Molecules ◽  
Prediction Tools ◽  
Novel Mirna ◽  
Precise Tool ◽  
Computationally Intensive ◽  
And Function ◽  
Post Transcriptional Regulation

Plant microRNAs (miRNAs) are short, non-coding RNA molecules that restrict gene expression via post-transcriptional regulation and function in several essential pathways including development, growth, and stress responses. Accurately identifying miRNAs in populations of small RNA (sRNA) sequencing libraries is a computationally intensive process which has resulted in the misidentification of inaccurately annotated miRNA sequences. In recent years, criteria for miRNA annotation have been refined to reduce these misannotations. Here, we describe miRador, a novel miRNA identification tool that utilizes the most up-to-date, community-established criteria for accurate identification of miRNAs in plants. We combine target prediction and Parallel Analysis of RNA Ends (PARE) data to assess the precision of the miRNAs identified by miRador. We compare miRador to other commonly used miRNA prediction tools and we find that miRador is at least as precise as other prediction tools while being significantly faster than other tools.

scholarly journals Multilevel regulation of the glass locus during Drosophila eye development

2019 ◽  
Author(s):  
Cornelia Fritsch ◽  
F. Javier Bernardo-Garcia ◽  
Tim-Henning Humberg ◽  
Sara Miellet ◽  
Silvia Almeida ◽  
...  
Keyword(s):  
Cell Fate ◽  
Molecular Mechanisms ◽  
Eye Development ◽  
Fruit Fly ◽  
Protein Isoforms ◽  
Critical Feature ◽  
Reading Frame ◽  
Cis Acting ◽  
Temporal Gene Expression ◽  
And Function

ABSTRACTDevelopment of eye tissue is initiated by a conserved set of transcripton factors termed retinal determination network (RDN). In the fruit fly Drosophila melanogaster, the zinc-finger transcription factor Glass acts directly downstream of the RDN to control idendity of photoreceptor as well as non-photoreceptors cells. Tight control of spatial and temporal gene expression is a critical feature during development, cell-fate determination as well as maintainance of differentiated tissues. The molecular mechanisms that control expression of glass, however remain largely unknown. We here identify complex regulatory mechanisms controlling expression of the glass locus. All information to recapitulate glass expression are contained in a compact 5.2 kb cis-acting genomic element by combining different cell-type specific and general enhancers with repressor elements. Moreover, the immature RNA of the locus contains an alterantive small open reading frame (smORF) upstream of the actual glass translation start, resulting in a small peptide instead of the three possible glass protein isoforms. CRISPR/Cas9-based mutagenesis shows that the smORF is not required for the formation of functioning photoreceptors, but to attenuate effects of glass misexpression. Furthermore, editing the genome to generate glass loci eliminating either one or two isoforms shows that only one of the three proteins is critical for formation of functioning photoreceptors, while removing the two other isoforms did not cause defects in developmental or photoreceptor function. Our results show that eye development and function is surprisingly robust and appears buffered to targeted manipulations of critical features of the glass transcript, suggesting a strong selection pressure to allow the formation of a functioning eye.

scholarly journals Cuticular hydrocarbon profile for queen recognition in the termite Reticulitermes speratus

2021 ◽  
Author(s):  
Yuki Mitaka ◽  
Tadahide Fujita
Keyword(s):  
Cuticular Hydrocarbon ◽  
Gas Chromatography Mass Spectrometry ◽  
Reticulitermes Speratus ◽  
Recognition Mechanism ◽  
The Social ◽  
Queen Succession ◽  
Queen Recognition ◽  
And Function ◽  
Reproductive Division Of Labor ◽  
Reproductive Division

Abstract Chemical communication underlies the sophisticated colony organization of social insects. In these insects, cuticular hydrocarbons (CHCs) play central roles in nestmate, task, and caste recognition, which contribute to maintenance of the social and reproductive division of labor. Queen-specific CHCs reflect queen fertility status and function as a queen recognition pheromone, triggering aggregation responses around the queens. However, there are only a few studies about the royal recognition mechanism in termites, and particularly, no study has reported about queen-specific CHCs in the species using asexual queen succession (AQS) system, in which the primary queen is replaced by neotenic queens produced parthenogenetically. In this study, we identified the CHC pheromone for neotenic queen recognition in the AQS termite species Reticulitermes speratus. Gas chromatography-mass spectrometry analyses revealed that the relative amount of n-pentacosane was disproportionately greater in the CHC profiles of queens than in the CHC profiles of kings, soldiers, and workers. Furthermore, we investigated the cuticular chemicals of the queen aggregate workers; bioassays demonstrated that n-pentacosane shows a worker arrestant activity in the presence of workers’ cuticular extract. These results suggest that R. speratus workers identify whether each individual is a neotenic queen by recognizing the relatively higher ratio of n-pentacosane in the conspecific CHC background. Moreover, they suggest that termites have evolved queen recognition behavior, independently of social hymenopterans.

scholarly journals The STAGA Subunit ADA2b Is an Important Regulator of Human GCN5 Catalysis

2008 ◽  
Vol 29 (1) ◽  
pp. 266-280 ◽  
Author(s):  
Armin M. Gamper ◽  
Jaehoon Kim ◽  
Robert G. Roeder
Keyword(s):  
Saga Complex ◽  
Histone Tails ◽  
Functional Roles ◽  
Enzymatic Function ◽  
Core Histones ◽  
Human Proteins ◽  
Important Regulator ◽  
And Function

ABSTRACT Human STAGA is a multisubunit transcriptional coactivator containing the histone acetyltransferase GCN5L. Previous studies of the related yeast SAGA complex have shown that the yeast Gcn5, Ada2, and Ada3 components form a heterotrimer that is important for the enzymatic function of SAGA. Here, we report that ADA2a and ADA2b, two human homologues of yeast Ada2, each have the ability to form a heterotrimer with ADA3 and GCN5L but that only the ADA2b homologue is found in STAGA. By comparing the patterns of acetylation of several substrates, we found context-dependent requirements for ADA2b and ADA3 for the efficient acetylation of histone tails by GCN5. With human proteins, unlike yeast proteins, the acetylation of free core histones by GCN5 is unaffected by ADA2b or ADA3. In contrast, the acetylation of mononucleosomal substrates by GCN5 is enhanced by ADA2b, with no significant additional effect of ADA3, and the efficient acetylation of nucleosomal arrays (chromatin) by GCN5 requires both ADA2b and ADA3. Thus, ADA2b and ADA3 appear to act at two different levels of histone organization within chromatin to facilitate GCN5 function. Interestingly, although ADA2a forms a complex(es) with GCN5 and ADA3 both in vitro and in vivo, ADA2a-containing complexes are unable to acetylate nucleosomal H3. We have also shown the preferential recruitment of ADA2b, relative to ADA2a, to p53-dependent genes. This finding indicates that the previously demonstrated presence and function of GCN5 on these promoters reflect the action of STAGA and that the ADA2a and ADA2b paralogues have nonredundant functional roles.

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