scholarly journals Molecular Mechanism of Vegetative Growth Advantage in Allotriploid Populus

2020 ◽  
Vol 21 (2) ◽  
pp. 441 ◽  
Author(s):  
Kang Du ◽  
Ting Liao ◽  
Yongyu Ren ◽  
Xining Geng ◽  
Xiangyang Kang
Keyword(s):  
Signaling Pathways ◽  
Vegetative Growth ◽  
Growth Regulation ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Starch Synthesis ◽  
Control Process ◽  
Network Models ◽  
Specific Gene ◽  
Functional Control

Allotriploid poplar has a prominent vegetative growth advantage that impacts dramatically on lumber yield. The growth regulation is complex which involves abundant genes, metabolic and signaling pathways, while the information about the functional control process is very little. We used high-throughput sequencing and physiological index measurement to obtain a global overview of differences between allotriploid and diploid Populus. The genes related to plant growth advantage show a higher expression compared to diploid, and most of them are revolved around hormones, photosynthesis and product accumulation. Thus, allotriploid Populus showed more efficient photosynthesis, carbon fixation, sucrose and starch synthesis, and metabolism as well as augmented biosynthesis of auxin, cytokinin, and gibberellin. These data enable the connection of metabolic processes, signaling pathways, and specific gene activity, which will underpin the development of network models to elucidate the process of triploid Populus advantage growth.

scholarly journals MiRNA-Regulated Pathways for Hypertrophic Cardiomyopathy: Network-Based Approach to Insight into Pathogenesis

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 2016
Author(s):  
German Osmak ◽  
Natalia Baulina ◽  
Ivan Kiselev ◽  
Olga Favorova
Keyword(s):  
Hypertrophic Cardiomyopathy ◽  
Signaling Pathways ◽  
Protein Interactions ◽  
Target Gene ◽  
High Throughput Sequencing ◽  
Point Of View ◽  
Specific Gene ◽  
Protein Protein Interactions ◽  
Insight Into ◽  
Sarcomeric Genes

Hypertrophic cardiomyopathy (HCM) is the most common hereditary heart disease. The wide spread of high-throughput sequencing casts doubt on its monogenic nature, suggesting the presence of mechanisms of HCM development independent from mutations in sarcomeric genes. From this point of view, HCM may arise from the interactions of several HCM-associated genes, and from disturbance of regulation of their expression. We developed a bioinformatic workflow to study the involvement of signaling pathways in HCM development through analyzing data on human heart-specific gene expression, miRNA-target gene interactions, and protein–protein interactions, available in open databases. Genes regulated by a pool of miRNAs contributing to human cardiac hypertrophy, namely hsa-miR-1-3p, hsa-miR-19b-3p, hsa-miR-21-5p, hsa-miR-29a-3p, hsa-miR-93-5p, hsa-miR-133a-3p, hsa-miR-155-5p, hsa-miR-199a-3p, hsa-miR-221-3p, hsa-miR-222-3p, hsa-miR-451a, and hsa-miR-497-5p, were considered. As a result, we pinpointed a module of TGFβ-mediated SMAD signaling pathways, enriched by targets of the selected miRNAs, that may contribute to the cardiac remodeling in HCM. We suggest that the developed network-based approach could be useful in providing a more accurate glimpse on pathological processes in the disease pathogenesis.

scholarly journals Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

2021 ◽  
Vol 9 (2) ◽  
pp. 211
Author(s):  
Jie Gao ◽  
Miao Liu ◽  
Sixue Shi ◽  
Ying Liu ◽  
Yu Duan ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Microbial Community Composition ◽  
Ecosystem Functions ◽  
Microbial Composition ◽  
Wetland Ecosystems ◽  
Soil Microbial ◽  
Geochemical Properties ◽  
Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

scholarly journals Transcriptome analysis of lateral buds from Phyllostachys edulis rhizome during germination and early shoot stages

2020 ◽  
Author(s):  
Yuting Shou ◽  
Yihua Zhu ◽  
Yulong Ding
Keyword(s):  
Signaling Pathways ◽  
High Throughput Sequencing ◽  
Stem Elongation ◽  
Rapid Development ◽  
Development Stage ◽  
Fast Growth ◽  
Moso Bamboo ◽  
Phyllostachys Edulis ◽  
Lateral Buds ◽  
Meristem Development

Abstract Background: The vegetative growth is an important stage for plants when they conduct photosynthesis, accumulate and collect all resources needed and prepare for reproduction stage. Bamboo is one of the fastest growing plant species. The rapid growth of Phyllostachys edulis results from the expansion of intercalary meristem at the basal part of nodes, which are differentiated from the apical meristem of rhizome lateral buds. However, little is known about the major signaling pathways and players involved during this rapid development stage of bamboo. To study this question, we adopted the high-throughput sequencing technology and compared the transcriptomes of Moso bamboo rhizome buds in germination stage and late development stage. Results: We found that the development of Moso bamboo rhizome lateral buds was coordinated by multiple pathways, including meristem development, sugar metabolism and phytohormone signaling. Phytohormones have fundamental impacts on the plant development. We found the evidence of several major hormones participating in the development of Moso bamboo rhizome lateral bud. Furthermore, we showed direct evidence that Gibberellic Acids (GA) signaling participated in the Moso bamboo stem elongation. Conclusion: Significant changes occur in various signaling pathways during the development of rhizome lateral buds. It is crucial to understand how these changes are translated to Phyllostachys edulis fast growth. These results expand our knowledge on the Moso bamboo internodes fast growth and provide research basis for further study.

scholarly journals Hipertrofia muscular esquelética humana induzida pelo exercício físico/Exercise-induced human skeletal muscle hypertrophy

2011 ◽  
Vol 1 (2) ◽  
pp. 52-61
Author(s):  
Bernardo Neme Ide ◽  
Fernanda Lorenzi Lazarim ◽  
Denise Vaz de Macedo
Keyword(s):  
Protein Synthesis ◽  
Resistance Training ◽  
Signaling Pathways ◽  
Gene Transcription ◽  
Satellite Cells ◽  
Physical Training ◽  
Molecular Mechanisms ◽  
Enzyme Activation ◽  
Specific Gene ◽  
Adaptation Process

A resposta adaptativa ao treinamento físico é determinada pelo tipo, volume e frequência de aplicação dos estímulos, que ativam vias de sinalização distintas, a transcrição de genes específicos e posterior síntese protéica. O treinamento resistido está relacionado à ativação da enzima mTOR, proporcionada pelo hormônio IGF-1 e estimulada pela insulina, quando um carboidrato é consumido após a atividade física. Estas vias de sinalização levam à inibição da transcrição de genes relacionados à atrofia e aumento da síntese de proteínas contráteis e metabólicas, proporcionando um aumento da massa muscular, conhecido como hipertrofia. Atualmente, evidências sugerem que, além das sinalizações dos hormônios, os estímulos mecânicos (mecanotransdução) também podem influenciar a ativação gênica durante o processo hipertrófico. A ativação de células satélites, proporcionada pelo estresse mecânico, fatores de crescimento, radicais livres e citocinas é de suma importância para o crescimento muscular. Devido à relevância deste assunto, o presente trabalho traz uma revisão da literatura a respeito dos processos envolvidos na resposta hipertrófica, em decorrência do treinamento físico. Embora o processo hipertrófico seja bastante estudado, os mecanismos moleculares, tanto em nível gênico quanto protéico, envolvidos no processo adaptativo ainda não são totalmente compreendidos. Neste sentido, o avanço nas técnicas de biologia molecular como genômica, transcriptoma e proteômica abrem caminhos para futuras investigações nesta área.Palavras-chave: treino resistido, adaptações ao treinamento de força, células satélites, IGF-1, síntese protéica.The adaptation process to physical training is determined by the type, volume and frequency of stimulation, activating distinct signaling pathways, specific gene transcription and then protein synthesis. Resistance-training is related to mTOR enzyme activation induced by IGF-1 and stimulated by insulin when carbohydrates are consumed after physical activity. These pathways, may lead to the inhibition of gene transcription related to atrophy and the increment of contractile and metabolic protein synthesis causing an increase on muscle mass known as hypertrophy. Presently, there is evidence to suggest that besides hormone signaling pathways, mechanical stimulation (mechanotransduction) may also influence the gene activation during the hypertrophic process. The satellite cells activation induced by mechanical stress, growth factors, free radicals, and cytokines is crucial for muscle growth. Due to the importance of this topic, the present study, proposes a literature review about the processes related to the hypertrophic responses to physical training. Despite the frequent studies on the hypertrophic process, the molecular mechanisms (both at gene and protein levels) involved in the adaptation process is yet to be fully understood. Thus, advances in molecular biology techniques such as genomic, transcriptoma and proteomic open ways for future investigations in this area.Key words: Resistance-training, strength training adaptations, satellite cells, IGF-1, protein synthesis.

scholarly journals Composition and predictive functional analysis of bacterial communities in the surface seawater of the Changjiang Estuary

2017 ◽  
Author(s):  
Dong-Mei Wu ◽  
Jian-Xin Wang ◽  
Xiao-Hui Liu ◽  
Ying-Ping Fan ◽  
Ran Jiang ◽  
...  
Keyword(s):  
Dissolved Oxygen ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Oxygen Demand ◽  
Environmental Parameters ◽  
Changjiang Estuary ◽  
Surface Seawater ◽  
The Changjiang Estuary

The objective of this study was to characterize the structure and function of microbial communities in surface seawater from the Changjiang Estuary and adjacent areas, China. Sample water was collected at 12 sites and environmental parameters were measured. Community structure was analyzed using high-throughput sequencing of 16S rDNA genes. Predictive metagenomic approach was used to predict the function of bacterial communities. Result showed that sample site A0102 had the highest bacterial abundance and diversity. The heatmap indicated that different samples could be clustered into six groups. Phylogenetic analysis showed that Proteobacteria was the predominant phylum in all samples, followed by Bacteroidetes and Actinobacteria. Alphaproteobacteria and Gammaproteobacteria were the dominant classes. The analysis of predictive metagenomic showed carbon fixation pathways in prokaryotes, nitrogen metabolism, carbon fixation in photosynthetic organisms, photosynthesis and polycyclic aromatic hydrocarbon degradation were enriched in all samples. Redundancy analysis (RDA) identified that dissolved oxygen (DO) and PO43– concentration had positive correlations with the bacterial communities while chemical oxygen demand (COD), dissolved oxygen (DO) and PO43– concentration were significantly associated with microbial functional diversity. This study adds to our knowledge of functional and taxonomic composition of microbial communities.

scholarly journals Developmental control of transcription of a retina-specific gene, QR1, during differentiation: involvement of factors from the POU family.

1995 ◽  
Vol 15 (2) ◽  
pp. 642-652 ◽  
Author(s):  
A Pierani ◽  
C Pouponnot ◽  
G Calothy
Keyword(s):  
Transcriptional Control ◽  
Growth Regulation ◽  
Late Phase ◽  
Regulatory Region ◽  
Neural Retina ◽  
Specific Gene ◽  
Postnatal Life ◽  
Developmental Control ◽  
Control Of Gene Expression

Developmental control of gene expression often results from the coupling of growth arrest with the establishment of differentiation programs. QR1 is a gene specifically expressed in retinas during the late phase of embryogenesis. At this stage neuroectodermal precursors have reached terminal mitosis and are undergoing differentiation into distinct cell types. Transcription of the QR1 gene is tightly regulated during retinal development: this gene is expressed between embryonic day 9 (ED9) and ED17 and is completely repressed at hatching in quail. Moreover, QR1 transcription is downregulated when postmitotic neural retina cells are induced to proliferate by pp60v-src. We studied the stage-dependent transcriptional control of this gene during quail neural retina (QNR) cell development. Transient transfection experiments with QR1/CAT constructs at various stages of development showed that a region located between -935 and -1265 bp upstream of the transcription start site is necessary to promote transcription in retina cells during the late phase of embryonal development (QNR9, corresponding to ED9). By in vivo footprinting assays we identified at least two elements that are occupied by DNA-protein complexes in QNR cells: the A and B boxes. The A box allows formation of several biochemically distinct complexes: C1, C2, C3, and C4. Formation of the C2 complex mainly during early stages (ED7) and of C2, C3, and C4 complexes during postnatal life correlates with repression of QR1 transcription, whereas the C1 complex is strongly induced at ED11 when the QR1 gene is expressed. We previously showed that C1 was involved in downregulation of QR1 transcription by pp60v-src. Several complexes are also formed on the B box. We show that these complexes are exclusively present in neural tissues and that they involve members of the POU family of transcription factors. Mutations of each one of the two regions which abolish the binding of the C1 factor(s) on the A box and of the POU factor(s) on the B box also prevent stimulation of QR1 transcription in QNR9. Therefore, both elements appear to be required for the stage-specific transcription of the QR1 gene. We also show that the regulatory region from position -1265 to position -935 is able to confer stage-specific transcription upon a heterologous promoter (thymidine kinase). Indeed, this region stimulates transcription in differentiating retinas (QNR9) and represses transcription in terminally differentiated retinas (QNR17, corresponding to postnatal life). Our results suggest that cell growth regulation and developmental control are coordinated through the A and B boxes in regulating QR1 transcription during retinal differentiation.

Regulation of assimilate partitioning in leaves

2000 ◽  
Vol 27 (6) ◽  
pp. 507 ◽  
Author(s):  
Charlotte E. Lewis ◽  
Graham Noctor ◽  
David Causton ◽  
Christine H. Foyer
Keyword(s):  
Carbon Fixation ◽  
Starch Synthesis ◽  
Co2 Concentration ◽  
Building Blocks ◽  
Energy Budgets ◽  
Assimilate Partitioning ◽  
Fixed Carbon ◽  
Carbon And Nitrogen ◽  
Cellular Energy ◽  
Photosynthetic Carbon

Concepts of the regulation of assimilate partitioning in leaves frequently consider only the allocation of carbon between sucrose and starch synthesis, storage and export. While carbohydrate metabolism accounts for a large proportion of assimilated carbon, such analyses provide only a restricted view of carbon metabolism and partitioning in leaf cells since photosynthetic carbon fixation provides precursors for all other biosynthetic pathways in the plant. Most of these precursors are required for biosynthesis of amino acids that form the building blocks for many compounds in plants. We have used leaf carbon : nitrogen ratios to calculate the allocation of photosynthetic electrons to the assimilation of nitrogen necessary for amino acid formation, and conclude that this allocation is variable but may be higher than values often quoted in the literature. Respiration is a significant fate of fixed carbon. In addition to supplying biosynthetic precursors, respiration is required for energy production and may also act, in both light and dark, to balance cellular energy budgets. We have used growth CO2 concentration and irradiance to modify source activity in Lolium temulentum in order to explore the interactions between photosynthetic carbon and nitrogen assimilation, assimilate production, respiration and export. It is demonstrated that there is a robust correlation between source activity and foliar respiration rates. Under some conditions concomitant increases in source activity and respiration may be necessary to support faster growth. In other conditions, increases in respiration appear to result from internal homeostatic mechanisms that may be candidate targets for increasing yield.

scholarly journals Induction of Postmitotic Neuroretina Cell Proliferation by Distinct Ras Downstream Signaling Pathways

2000 ◽  
Vol 20 (19) ◽  
pp. 7068-7079 ◽  
Author(s):  
Carole Peyssonnaux ◽  
Sylvain Provot ◽  
Marie Paule Felder-Schmittbuhl ◽  
Georges Calothy ◽  
Alain Eychène
Keyword(s):  
Cell Proliferation ◽  
Cell Division ◽  
Signaling Pathways ◽  
Cell Transformation ◽  
Primary Cultures ◽  
Dominant Negative ◽  
Specific Gene ◽  
Mitogenic Effect ◽  
Downstream Signaling ◽  
Ras Effectors

ABSTRACT Ras-induced cell transformation is mediated through distinct downstream signaling pathways, including Raf, Ral-GEFs-, and phosphatidylinositol 3-kinase (PI 3-kinase)-dependent pathways. In some cell types, strong activation of the Ras–Raf–MEK–extracellular signal-regulated kinase (ERK) cascade leads to cell cycle arrest rather than cell division. We previously reported that constitutive activation of this pathway induces sustained proliferation of primary cultures of postmitotic chicken neuroretina (NR) cells. We used this model system to investigate the respective contributions of Ras downstream signaling pathways in Ras-induced cell proliferation. Three RasV12 mutants (S35, G37, and C40) which differ by their ability to bind to Ras effectors (Raf, Ral-GEFs, and the p110 subunit of PI 3-kinase, respectively) were able to induce sustained NR cell proliferation, although none of these mutants was reported to transform NIH 3T3 cells. Furthermore, they all repressed the promoter of QR1, a neuroretina growth arrest-specific gene. Overexpression of B-Raf or activated versions of Ras effectors Rlf-CAAX and p110-CAAX also induced NR cell division. The mitogenic effect of the RasC40–PI 3-kinase pathway appears to involve Rac and RhoA GTPases but not the antiapoptotic Akt (protein kinase B) signaling. Division induced by RasG37-Rlf appears to be independent of Ral GTPase activation and presumably requires an unidentified mechanism. Activation of either Ras downstream pathway resulted in ERK activation, and coexpression of a dominant negative MEK mutant or mKsr-1 kinase domain strongly inhibited proliferation induced by the three Ras mutants or by their effectors. Similar effects were observed with dominant negative mutants of Rac and Rho. Thus, both the Raf-MEK-ERK and Rac-Rho pathways are absolutely required for Ras-induced NR cell division. Activation of these two pathways by the three distinct Ras downstream effectors possibly relies on an autocrine or paracrine loop, implicating endogenous Ras, since the mitogenic effect of each Ras effector mutant was inhibited by RasN17.

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