scholarly journals Transcriptomic Analysis of the Pistacia vera (L.) Fruits Enable the Identification of Genes and Hormone-Related Gene Linked to Inflorescence Bud Abscission

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 60
Author(s):  
Jubina Benny ◽  
Antonio Giovino ◽  
Francesco Paolo Marra ◽  
Bipin Balan ◽  
Federico Martinelli ◽  
...  
Keyword(s):  
Transcription Factors ◽  
De Novo ◽  
Sugar Metabolism ◽  
Transcriptomic Analysis ◽  
Pistacia Vera ◽  
Alternate Bearing ◽  
Hormone Biosynthesis ◽  
The Individual ◽  
Axillary Inflorescence ◽  
Insight Into

Pistacia vera (L.) is an alternate bearing species. The tree produces axillary inflorescence buds every year. Still, they abscise in “ON” overloaded shoots, causing a limited production in the following “OFF” year, causing a significant and unfavorable production fluctuation. In this work, we carried out de novo discovery and transcriptomic analysis in fruits of “ON” and “OFF” shoots of the cultivar Bianca. We also investigated whether the fruit signaling pathway and hormone biosynthesis directly or indirectly linked to the premature fall of the inflorescence buds causing alternate bearing. We identified 1536 differentially expressed genes (DEGs) in fruits of “ON” vs. “OFF” shoots, which are involved primarily in sugar metabolism, plant hormone pathways and transcription factors. The premature bud abscission linked to the phenomenon is attributable to a lack of nutrients (primarily sugar) and the possible competition between the same branches’ sinks (fruits vs. inflorescence buds). Hormone pathways are involved as a response to signals degradation and remobilization of carbon and nutrients due to the strengthening of the developing embryos. Genes of the secondary metabolism and transcription factors are also involved in tailoring the individual branches response to the nutritional stress and sink competition. Crosstalk among sugar and various hormone-related genes, e.g., ethylene, auxin, ABA and cytokinin, were determined. The discovery of putative biomarkers like callose synthase 5, trehalose-6-phosphate synthase, NAD(P)-linked oxidoreductase and MIOX2, Jasmonate, and salicylic acid-related genes can help to design precision farming practices to mitigate the alternate bearing phenomenon to increase farming profitability. The aim of the analysis is to provide insight into the gene expression profiling of the fate of “ON” and “OFF” fruits associated with the alternate bearing in the pistachio.

Complementary transcriptome and proteome analyses provide insight into floral transition in Bamboo (Dendrocalamus latiflorus Munro)

2020 ◽  
Author(s):  
Xiaoyan Wang ◽  
Yujiao Wang ◽  
Guoqian Yang ◽  
Lei Zhao ◽  
Dezhu Li ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Large Scale ◽  
De Novo ◽  
Sugar Metabolism ◽  
Floral Transition ◽  
Growth Phases ◽  
Vegetable Growth ◽  
Plant Maturity ◽  
Woody Bamboos ◽  
Insight Into

Abstract Background Most woody bamboos flower only once after long vegetable growth phases and die immediately afterward. It is difficult to know the timing of the floral transition, as little information is available on the molecular mechanism of plant maturity in bamboos. Results In this study, through RNA sequencing of leaves of D. latiflorus during floral transition and de novo assembly, a final set of 155,494 unigenes were obtained with N50 of 2,069 bp. We identified a lot of flowering time-associated and flowering integration genes and the continued increase and decrease genes were screened as flowering biomarker genes, such as MADS14, bHLH13, ABA-related genes. The different genes were assigned to specific metabolic pathways by Kyoto Encyclopedia of Genes and Genomes (KEGG) and the photoperiod pathways depending on the circadian rhythm may play an essential role in the bamboo floral transition. In addition, a total of 721 different expressed proteins of leaves from the vegetable-to-reproductive stages in the same flowering clumps were identified using iTRAQ technique. The correlations between the expression levels of a transcript and the abundance of its corresponding protein were observed infrequently, but the very strong correlation in the specific metabolic process was observed, such as carbon metabolism, sugar metabolism, and photosynthesis, underlining the importance of these metabolic pathways during floral transition. Conclusions In this report, we combined transcriptome with large-scale quantitative proteomes to investigate the flower transition of D. latiflorus. This work will provide insights into mechanism of floral transition for bamboos, and management of forest breeding.

scholarly journals De novo transcriptomic analysis of light-induced flavonoid pathway, transcription factors in the flower buds of Lonicera japonica

Trees ◽  
2019 ◽  
Vol 34 (1) ◽  
pp. 267-283
Author(s):  
Hailing Fang ◽  
Xiwu Qi ◽  
Yiming Li ◽  
Xu Yu ◽  
Dongbei Xu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
De Novo ◽  
Transcriptomic Analysis ◽  
Lonicera Japonica ◽  
Flavonoid Pathway ◽  
Flower Buds

scholarly journals Transcriptome Analysis of Pistacia vera Inflorescence Buds in Bearing and Non-Bearing Shoots Reveals the Molecular Mechanism Causing Premature Flower Bud Abscission

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 851 ◽  
Author(s):  
Jubina Benny ◽  
Francesco Paolo Marra ◽  
Antonio Giovino ◽  
Bipin Balan ◽  
Tiziano Caruso ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Sugar Metabolism ◽  
Mineral Elements ◽  
Pistacia Vera ◽  
Alternate Bearing ◽  
Tor Signaling ◽  
Flower Bud ◽  
Shed Light

The alteration of heavy (“ON/bearing”) and light (“OFF/non-bearing”) yield in pistachio (Pistacia vera L.) has been reported to result from the abscission of inflorescence buds on high yielding trees during the summer, but the regulatory mechanisms involved in this bud abscission remain unclear. The analysis provides insights into the transcript changes between inflorescence buds on bearing and non-bearing shoots, that we indicated as “ON” and “OFF”, and shed light on the molecular mechanisms causing premature inflorescence bud abscission in the pistachio cultivar “Bianca” which can be related to the alternate bearing behavior. In this study, a transcriptome analysis was performed in inflorescence buds of “ON” and “OFF” shoots. A total of 14,330 differentially expressed genes (DEGs), most of which are involved in sugar metabolism, plant hormone pathways, secondary metabolism and oxidative stress pathway, were identified. Our results shed light on the molecular mechanisms underlying inflorescence bud abscission in pistachio and we proposed a hypothetical model behind the molecular mechanism causing this abscission in “ON” shoots. Results highlighted how changes in genes expressed in nutrient pathways (carbohydrates and mineral elements) in pistachio “ON” vs. “OFF” inflorescence buds triggers a cascade of events involving trehalose-6-phosphate and target of rapamycin (TOR) signaling, SnRK1 complex, hormones, polyamines and ROS which end, through programmed cell death and autophagy phenomena, with the abscission of inflorescence buds. This is the first study reporting gene expression profiling of the fate of “ON” and “OFF” inflorescence buds associated with the alternate bearing in the pistachio.

What Can Economists Contribute to the Common Good Tradition?

2017 ◽  
Author(s):  
Andrew M. Yuengert
Keyword(s):  
Common Good ◽  
Common Pool Resources ◽  
Economic Approach ◽  
Public And Private ◽  
Private Provision ◽  
The Public ◽  
The Common Good ◽  
The Common ◽  
The Individual ◽  
Insight Into

Although most economists are skeptical of or puzzled by the Catholic concept of the common good, a rejection of the economic approach as inimical to the common good would be hasty and counterproductive. Economic analysis can enrich the common good tradition in four ways. First, economics embodies a deep respect for economic agency and for the effects of policy and institutions on individual agents. Second, economics offers a rich literature on the nature of unplanned order and how it might be shaped by policy. Third, economics offers insight into the public and private provision of various kinds of goods (private, public, common pool resources). Fourth, recent work on the development and logic of institutions and norms emphasizes sustainability rooted in the good of the individual.

scholarly journals Intra-Colonial Viral Infections in Western Honey Bees (Apis mellifera)

2021 ◽  
Vol 9 (5) ◽  
pp. 1087
Author(s):  
Loreley Castelli ◽  
María Laura Genchi García ◽  
Anne Dalmon ◽  
Daniela Arredondo ◽  
Karina Antúnez ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Viral Infections ◽  
Sampling Period ◽  
Virus Genome ◽  
The Individual ◽  
Bee Virus ◽  
Insight Into ◽  
Bee Viruses

RNA viruses play a significant role in the current high losses of pollinators. Although many studies have focused on the epidemiology of western honey bee (Apis mellifera) viruses at the colony level, the dynamics of virus infection within colonies remains poorly explored. In this study, the two main variants of the ubiquitous honey bee virus DWV as well as three major honey bee viruses (SBV, ABPV and BQCV) were analyzed from Varroa-destructor-parasitized pupae. More precisely, RT-qPCR was used to quantify and compare virus genome copies across honey bee pupae at the individual and subfamily levels (i.e., patrilines, sharing the same mother queen but with different drones as fathers). Additionally, virus genome copies were compared in cells parasitized by reproducing and non-reproducing mite foundresses to assess the role of this vector. Only DWV was detected in the samples, and the two variants of this virus significantly differed when comparing the sampling period, colonies and patrilines. Moreover, DWV-A and DWV-B exhibited different infection patterns, reflecting contrasting dynamics. Altogether, these results provide new insight into honey bee diseases and stress the need for more studies about the mechanisms of intra-colonial disease variation in social insects.

scholarly journals Genomic Characterization Provides an Insight into the Pathogenicity of the Poplar Canker Bacterium Lonsdalea populi

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 246
Author(s):  
Xiaomeng Chen ◽  
Rui Li ◽  
Yonglin Wang ◽  
Aining Li
Keyword(s):  
Genome Sequence ◽  
Extracellular Enzymes ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Hybrid Poplars ◽  
A Genome ◽  
Conserved Genes ◽  
Genomic Characterization ◽  
Molecular Bases ◽  
Insight Into

An emerging poplar canker caused by the gram-negative bacterium, Lonsdalea populi, has led to high mortality of hybrid poplars Populus × euramericana in China and Europe. The molecular bases of pathogenicity and bark adaptation of L. populi have become a focus of recent research. This study revealed the whole genome sequence and identified putative virulence factors of L. populi. A high-quality L. populi genome sequence was assembled de novo, with a genome size of 3,859,707 bp, containing approximately 3434 genes and 107 RNAs (75 tRNA, 22 rRNA, and 10 ncRNA). The L. populi genome contained 380 virulence-associated genes, mainly encoding for adhesion, extracellular enzymes, secretory systems, and two-component transduction systems. The genome had 110 carbohydrate-active enzyme (CAZy)-coding genes and putative secreted proteins. The antibiotic-resistance database annotation listed that L. populi was resistant to penicillin, fluoroquinolone, and kasugamycin. Analysis of comparative genomics found that L. populi exhibited the highest homology with the L. britannica genome and L. populi encompassed 1905 specific genes, 1769 dispensable genes, and 1381 conserved genes, suggesting high evolutionary diversity and genomic plasticity. Moreover, the pan genome analysis revealed that the N-5-1 genome is an open genome. These findings provide important resources for understanding the molecular basis of the pathogenicity and biology of L. populi and the poplar-bacterium interaction.

Enhanced accumulation of pinosylvin stilbenes and related gene expression in Pinus strobus after infection of pine wood nematode

2021 ◽  
Author(s):  
Hwan-Su Hwang ◽  
Jung Yeon Han ◽  
Yong Eui Choi
Keyword(s):  
Transcription Factors ◽  
Defense Mechanisms ◽  
De Novo ◽  
Pinus Strobus ◽  
Pine Wilt Disease ◽  
Monomethyl Ether ◽  
Bursaphelenchus Xylophilus ◽  
Nematicidal Activity ◽  
Dependent Manner ◽  
Pine Wood

Abstract Pine wood nematodes (PWNs: Bursaphelenchus xylophilus) infect pine trees and cause serious pine wilt disease. Eastern white pine (Pinus strobus) has resistance to PWN. However, the detailed defense mechanisms of P. strobus against PWN are not well known. When P. strobus plants were infected with PWNs, the accumulation of stilbenoids, dihydropinosylvin monomethyl ether (DPME) and pinosylvin monomethyl ether (PME), were increased remarkably. DPME and PME had the high nematicidal activity. Interestingly, the nematicidal activity of the two compounds was resulted in a developmental stage-dependent manner. PME was more toxic to adult PWNs than juveniles, whereas DPME was found more toxic to juvenile PWNs than the adults. The genes involved in PME and DPME biosynthesis such as phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), pinosylvin synthase (STS), and pinosylvin O-methyltransferase (PMT) were isolated using de novo sequencing of the transcriptome in P. strobus. In addition, transcription factors (bHLH, MYB and WRKY) related to stilbene biosynthesis were isolated. qPCR analyses of the selected genes (PAL, 4CL, STS, and PMT) including transcription factors (bHLH, MYB and WRKY) revealed that the expression level of the selected genes highly enhanced after PWN infection. Our results suggest that pinosylvin-type stilbenoid biosynthesis is highly responsive to PWN infection and plays an important role in PWN resistance of P. strobus trees.

scholarly journals Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fengbin Wang ◽  
Ordy Gnewou ◽  
Charles Modlin ◽  
Leticia C. Beltran ◽  
Chunfu Xu ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Synthetic Peptide ◽  
Quaternary Structure ◽  
De Novo ◽  
Rational Approach ◽  
Lateral Interactions ◽  
Protein Assemblies ◽  
Self Assembling ◽  
Arginine Residues ◽  
Insight Into

AbstractThe exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.

scholarly journals A Synergistic Anti-Diabetic Effect by Ginsenosides Rb1 and Rg3 through Adipogenic and Insulin Signaling Pathways in 3T3-L1 Cells

2021 ◽  
Vol 11 (4) ◽  
pp. 1725
Author(s):  
Hee-Do Hong ◽  
Sun-Il Choi ◽  
Ok-Hwan Lee ◽  
Young-Cheul Kim
Keyword(s):  
Transcription Factors ◽  
Insulin Signaling ◽  
Adipocyte Differentiation ◽  
Red Ginseng ◽  
Inhibitory Effects ◽  
Rt Pcr ◽  
High Concentration ◽  
Expression Of Genes ◽  
The Individual ◽  
Maximal Expression

Although ginsenosides Rb1 and Rg3 have been identified as the significant ginsenosides found in red ginseng that confer anti-diabetic actions, it is unclear whether insulin-sensitizing effects are mediated by the individual compounds or by their combination. To determine the effect of ginsenosides Rb1 and Rg3 on adipocyte differentiation, 3T3-L1 preadipocytes were induced to differentiate the standard hormonal inducers in the absence or presence of ginsenosides Rb1 or Rg3. Additionally, we determined the effects of Rb1, Rg3, or their combination on the expression of genes related to adipocyte differentiation, adipogenic transcription factors, and the insulin signaling pathway in 3T3-L1 cells using semi-quantitative RT-PCR. Rb1 significantly increased the expression of CEBPα, PPARγ, and aP2 mRNAs. However, Rg3 exerted its maximal stimulatory effect on these genes at 1 μM concentration, while a high concentration (50 μM) showed inhibitory effects. Similarly, treatment with Rb1 and Rg3 (1 μM) increased the expression of IRS-1, Akt, PI3K, GLUT4, and adiponectin. Importantly, co-treatment of Rb1 and Rg3 (9:1) induced the maximal expression levels of these mRNAs. Our data indicate that the anti-diabetic activity of red ginseng is, in part, mediated by synergistic actions of Rb1 and Rg3, further supporting the significance of minor Rg3.

Sign in / Sign up

Export Citation Format

Share Document