scholarly journals Coexpression analysis of a large-scale transcriptome identified a calmodulin-like protein regulating the development of adventitious roots in poplar

2020 ◽  
Vol 40 (10) ◽  
pp. 1405-1419
Author(s):  
Zheng’ang Xiao ◽  
Yan Zhang ◽  
Meifeng Liu ◽  
Chang Zhan ◽  
Xiaoqing Yang ◽  
...  
Keyword(s):  
Adventitious Roots ◽  
Large Scale ◽  
Expression Profiles ◽  
Reduction Process ◽  
High Association ◽  
Coexpression Analysis ◽  
Key Factor ◽  
Transgenic Lines ◽  
Poplar Cuttings ◽  
Growing Conditions

Abstract Poplars are important woody plants, and the ability to form adventitious roots (ARs) is the key factor for their cultivation because most poplars are propagated by cloning. In previous studies, Ca2+ was confirmed to regulate AR formation in poplar. In this study, wild-type poplar cuttings grown in 1.0 mM Ca2+ solution showed the best visible performance of AR development. Coexpression analysis of a large-scale RNA-Seq transcriptome was conducted to identify Ca2+-related genes that regulate AR development in poplar. A total of 15 coexpression modules (CMs) were identified, and two CMs showed high association with AR development. Functional analysis identified a number of biological pathways, including ‘oxidation-reduction process’, ‘response to biotic stimulus’ and ‘metabolic process’, in tissues of AR development. The Ca2+-related pathway was specifically selected, and its regulation in poplar AR development was predicted. A Ca2+ sensor, PdeCML23-1, which is a member of the calmodulin-like protein (CML) family, was found to promote AR development by phenotypic assay of overexpressed PdeCML23-1 transgenic lines at various growing conditions. By measuring cytosolic Ca2+ in AR tips, PdeCML23-1 seemed to play a role in decreasing cytosolic Ca2+ concentration. Additionally, the expression profiles of some genes and phytohormone indole acetic acid (IAA) were also changed in the overexpressed PdeCML23-1 transgenic lines. According to this study, we were able to provide a global view of gene regulation for poplar AR development. Moreover, we also observed the regulation of cytosolic Ca2+ concentration by PdeCML23-1, and this regulation was involved in AR development in poplar. We also predicted that PdeCML23-1 possibly regulates AR development by modulating IAA content in poplar.

Going the Distance

2020 ◽  
Author(s):  
Ron Harris
Keyword(s):  
Large Scale ◽  
Western Europe ◽  
Family Firms ◽  
Global Trade ◽  
Long Distance ◽  
Business Corporation ◽  
Modern Economy ◽  
Key Factor ◽  
Silk Route ◽  
Passive Investors

Before the seventeenth century, trade across Eurasia was mostly conducted in short segments along the Silk Route and Indian Ocean. Business was organized in family firms, merchant networks, and state-owned enterprises, and dominated by Chinese, Indian, and Arabic traders. However, around 1600 the first two joint-stock corporations, the English and Dutch East India Companies, were established. This book tells the story of overland and maritime trade without Europeans, of European Cape Route trade without corporations, and of how new, large-scale, and impersonal organizations arose in Europe to control long-distance trade for more than three centuries. It shows that by 1700, the scene and methods for global trade had dramatically changed: Dutch and English merchants shepherded goods directly from China and India to northwestern Europe. To understand this transformation, the book compares the organizational forms used in four major regions: China, India, the Middle East, and Western Europe. The English and Dutch were the last to leap into Eurasian trade, and they innovated in order to compete. They raised capital from passive investors through impersonal stock markets and their joint-stock corporations deployed more capital, ships, and agents to deliver goods from their origins to consumers. The book explores the history behind a cornerstone of the modern economy, and how this organizational revolution contributed to the formation of global trade and the creation of the business corporation as a key factor in Europe's economic rise.

scholarly journals LncGSEA: a versatile tool to infer lncRNA associated pathways from large-scale cancer transcriptome sequencing data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yanan Ren ◽  
Ting-You Wang ◽  
Leah C. Anderton ◽  
Qi Cao ◽  
Rendong Yang
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Clinical Samples ◽  
Sequencing Data ◽  
Multiple Cancer ◽  
Regulatory Pathways ◽  
Cancer Transcriptome ◽  
Versatile Tool

Abstract Background Long non-coding RNAs (lncRNAs) are a growing focus in cancer research. Deciphering pathways influenced by lncRNAs is important to understand their role in cancer. Although knock-down or overexpression of lncRNAs followed by gene expression profiling in cancer cell lines are established approaches to address this problem, these experimental data are not available for a majority of the annotated lncRNAs. Results As a surrogate, we present lncGSEA, a convenient tool to predict the lncRNA associated pathways through Gene Set Enrichment Analysis of gene expression profiles from large-scale cancer patient samples. We demonstrate that lncGSEA is able to recapitulate lncRNA associated pathways supported by literature and experimental validations in multiple cancer types. Conclusions LncGSEA allows researchers to infer lncRNA regulatory pathways directly from clinical samples in oncology. LncGSEA is written in R, and is freely accessible at https://github.com/ylab-hi/lncGSEA.

scholarly journals Trace element catalyses mineral replacement reactions and facilitates ore formation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yanlu Xing ◽  
Joël Brugger ◽  
Barbara Etschmann ◽  
Andrew G. Tomkins ◽  
Andrew J. Frierdich ◽  
...  
Keyword(s):  
Mass Transfer ◽  
Trace Elements ◽  
Fluid Flow ◽  
Large Scale ◽  
Metal Accumulation ◽  
Nucleation And Growth ◽  
Reaction Interface ◽  
Ore Formation ◽  
Key Factor ◽  
Mineral Replacement

AbstractReaction-induced porosity is a key factor enabling protracted fluid-rock interactions in the Earth’s crust, promoting large-scale mineralogical changes during diagenesis, metamorphism, and ore formation. Here, we show experimentally that the presence of trace amounts of dissolved cerium increases the porosity of hematite (Fe2O3) formed via fluid-induced, redox-independent replacement of magnetite (Fe3O4), thereby increasing the efficiency of coupled magnetite replacement, fluid flow, and element mass transfer. Cerium acts as a catalyst affecting the nucleation and growth of hematite by modifying the Fe2+(aq)/Fe3+(aq) ratio at the reaction interface. Our results demonstrate that trace elements can enhance fluid-mediated mineral replacement reactions, ultimately controlling the kinetics, texture, and composition of fluid-mineral systems. Applied to some of the world’s most valuable orebodies, these results provide new insights into how early formation of extensive magnetite alteration may have preconditioned these ore systems for later enhanced metal accumulation, contributing to their sizes and metal endowment.

High nitrate inhibited adventitious roots formation in apple rootstock by altering hormonal contents and miRNAs expression profiles

2021 ◽  
Vol 286 ◽  
pp. 110230
Author(s):  
Muhammad Mobeen Tahir ◽  
Shaohuan Li ◽  
Jiangping Mao ◽  
Yu Liu ◽  
Ke Li ◽  
...  
Keyword(s):  
Adventitious Roots ◽  
Expression Profiles ◽  
Apple Rootstock ◽  
Mirnas Expression

Large-scale prediction of aboveground biomass in heterogeneous mountain forests by means of airborne laser scanning

2016 ◽  
Vol 46 (9) ◽  
pp. 1138-1144 ◽  
Author(s):  
M. Maltamo ◽  
O.M. Bollandsås ◽  
T. Gobakken ◽  
E. Næsset
Keyword(s):  
Aboveground Biomass ◽  
Laser Scanning ◽  
Large Scale ◽  
Airborne Laser Scanning ◽  
Mountain Forests ◽  
Airborne Laser ◽  
Model Predictions ◽  
Growing Conditions ◽  
Southern Norway ◽  
Forest Conditions

This study considered airborne laser scanning (ALS) based aboveground biomass (AGB) prediction in mountain forests. The study area consisted of a long transect from southern Norway to northern parts of the country with wide ranges of elevation along a long latitudinal gradient (58°N–69°N). This transect was covered by ALS data and field data from 238 plots. AGB was modeled using different types of predictor variables, namely ALS metrics, variables related to growing conditions (elevation, latitude, and climatic variables), and tree species information. Modelling of AGB in the long transect covering diverse mountainous forest conditions was challenging: the RMSE values were rather large (37%–70%). The effects of growing conditions on model predictions were minor. However, species information was essential to improve accuracy. The analysis revealed that when doing inventories of spruce-dominated areas, all plots should be pooled together when the models are developed, whereas if pine or deciduous species dominate the area in question, separate dominant species-wise models should be constructed.

scholarly journals Analysis of blood-based gene expression in idiopathic Parkinson disease

Neurology ◽  
2017 ◽  
Vol 89 (16) ◽  
pp. 1676-1683 ◽  
Author(s):  
Ron Shamir ◽  
Christine Klein ◽  
David Amar ◽  
Eva-Juliane Vollstedt ◽  
Michael Bonin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Parkinson Disease ◽  
Gene Networks ◽  
Large Scale ◽  
Expression Profiles ◽  
Area Under The Curve ◽  
Gene Expression Profiles ◽  
Gene Signature ◽  
Gene Profiles ◽  
Independent Test

Objective:To examine whether gene expression analysis of a large-scale Parkinson disease (PD) patient cohort produces a robust blood-based PD gene signature compared to previous studies that have used relatively small cohorts (≤220 samples).Methods:Whole-blood gene expression profiles were collected from a total of 523 individuals. After preprocessing, the data contained 486 gene profiles (n = 205 PD, n = 233 controls, n = 48 other neurodegenerative diseases) that were partitioned into training, validation, and independent test cohorts to identify and validate a gene signature. Batch-effect reduction and cross-validation were performed to ensure signature reliability. Finally, functional and pathway enrichment analyses were applied to the signature to identify PD-associated gene networks.Results:A gene signature of 100 probes that mapped to 87 genes, corresponding to 64 upregulated and 23 downregulated genes differentiating between patients with idiopathic PD and controls, was identified with the training cohort and successfully replicated in both an independent validation cohort (area under the curve [AUC] = 0.79, p = 7.13E–6) and a subsequent independent test cohort (AUC = 0.74, p = 4.2E–4). Network analysis of the signature revealed gene enrichment in pathways, including metabolism, oxidation, and ubiquitination/proteasomal activity, and misregulation of mitochondria-localized genes, including downregulation of COX4I1, ATP5A1, and VDAC3.Conclusions:We present a large-scale study of PD gene expression profiling. This work identifies a reliable blood-based PD signature and highlights the importance of large-scale patient cohorts in developing potential PD biomarkers.

scholarly journals Discovering Distinct Patterns in Gene Expression Profiles

2008 ◽  
Vol 5 (2) ◽  
Author(s):  
Li Teng ◽  
Laiwan Chan
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Clustering Methods ◽  
Gene Expressions ◽  
Real Gene ◽  
Large Scale Dataset ◽  
Coexpressed Genes

SummaryTraditional analysis of gene expression profiles use clustering to find groups of coexpressed genes which have similar expression patterns. However clustering is time consuming and could be diffcult for very large scale dataset. We proposed the idea of Discovering Distinct Patterns (DDP) in gene expression profiles. Since patterns showing by the gene expressions reveal their regulate mechanisms. It is significant to find all different patterns existing in the dataset when there is little prior knowledge. It is also a helpful start before taking on further analysis. We propose an algorithm for DDP by iteratively picking out pairs of gene expression patterns which have the largest dissimilarities. This method can also be used as preprocessing to initialize centers for clustering methods, like K-means. Experiments on both synthetic dataset and real gene expression datasets show our method is very effective in finding distinct patterns which have gene functional significance and is also effcient.

What determines a boundary for navigating a complex street network: evidence from London taxi drivers

2021 ◽  
pp. 1-20
Author(s):  
Eva-Maria Griesbauer ◽  
Ed Manley ◽  
Daniel McNamee ◽  
Jeremy Morley ◽  
Hugo Spiers
Keyword(s):  
Urban Space ◽  
Large Scale ◽  
Route Planning ◽  
Taxi Drivers ◽  
Street Networks ◽  
Planning Models ◽  
Key Factor ◽  
Efficient Planning ◽  
Regent's Park ◽  
Insight Into

Abstract Spatial boundaries play an important role in defining spaces, structuring memory and supporting planning during navigation. Recent models of hierarchical route planning use boundaries to plan efficiently first across regions and then within regions. However, it remains unclear which structures (e.g. parks, rivers, major streets, etc.) will form salient boundaries in real-world cities. This study tested licensed London taxi drivers, who are unique in their ability to navigate London flexibly without physical navigation aids. They were asked to indicate streets they considered as boundaries for London districts or dividing areas. It was found that agreement on boundary streets varied considerably, from some boundaries providing almost no consensus to some boundaries consistently noted as boundaries. Examining the properties of the streets revealed that a key factor in the consistent boundaries was the near rectilinear nature of the designated region (e.g. Mayfair and Soho) and the distinctiveness of parks (e.g. Regent's Park). Surprisingly, the River Thames was not consistently considered as a boundary. These findings provide insight into types of environmental features that lead to the perception of explicit boundaries in large-scale urban space. Because route planning models assume that boundaries are used to segregate the space for efficient planning, these results help make predictions of the likely planning demands of different routes in such complex large-scale street networks. Such predictions could be used to highlight information used for navigation guidance applications to enable more efficient hierarchical planning and learning of large-scale environments.

Neural system-enriched gene expression: relationship to biological pathways and neurological diseases

2004 ◽  
Vol 18 (2) ◽  
pp. 167-183 ◽  
Author(s):  
Jianhua Zhang ◽  
Amy Moseley ◽  
Anil G. Jegga ◽  
Ashima Gupta ◽  
David P. Witte ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
Intracellular Signaling ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene List ◽  
Structure And Function ◽  
System Structure ◽  
Psychiatric Disease ◽  
And Function

To understand the commitment of the genome to nervous system differentiation and function, we sought to compare nervous system gene expression to that of a wide variety of other tissues by gene expression database construction and mining. Gene expression profiles of 10 different adult nervous tissues were compared with that of 72 other tissues. Using ANOVA, we identified 1,361 genes whose expression was higher in the nervous system than other organs and, separately, 600 genes whose expression was at least threefold higher in one or more regions of the nervous system compared with their median expression across all organs. Of the 600 genes, 381 overlapped with the 1,361-gene list. Limited in situ gene expression analysis confirmed that identified genes did represent nervous system-enriched gene expression, and we therefore sought to evaluate the validity and significance of these top-ranked nervous system genes using known gene literature and gene ontology categorization criteria. Diverse functional categories were present in the 381 genes, including genes involved in intracellular signaling, cytoskeleton structure and function, enzymes, RNA metabolism and transcription, membrane proteins, as well as cell differentiation, death, proliferation, and division. We searched existing public sites and identified 110 known genes related to mental retardation, neurological disease, and neurodegeneration. Twenty-one of the 381 genes were within the 110-gene list, compared with a random expectation of 5. This suggests that the 381 genes provide a candidate set for further analyses in neurological and psychiatric disease studies and that as a field, we are as yet, far from a large-scale understanding of the genes that are critical for nervous system structure and function. Together, our data indicate the power of profiling an individual biologic system in a multisystem context to gain insight into the genomic basis of its structure and function.

scholarly journals Synthesis of the Sparse Uniform-Amplitude Concentric Ring Transmitting Array for Optimal Microwave Power Transmission

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
Hua-Wei Zhou ◽  
Xue-Xia Yang ◽  
Sajjad Rahim
Keyword(s):  
Microwave Power ◽  
Large Scale ◽  
Power Transmission ◽  
Synthesis Method ◽  
Pso Algorithm ◽  
Practical Significance ◽  
Concentric Ring ◽  
Swarm Optimization ◽  
Key Factor ◽  
Feed Network

Beam capture efficiency (BCE) is one key factor of the overall efficiency for a microwave power transmission (MPT) system, while sparsification of a large-scale transmitting array has a practical significance. If all elements of the transmitting array are excited uniformly, the fabrication, maintenance, and feed network design would be greatly simplified. This paper describes the synthesis method of the sparse uniform-amplitude transmitting array with concentric ring layout using particle swarm optimization (PSO) algorithm while keeping a higher BCE. Based on this method, uniform exciting strategy, reduced number of elements, and a higher BCE are achieved simultaneously for optimal MPT. The numerical results of the sparse uniform-amplitude concentric ring arrays (SUACRAs) optimized by the proposed method are compared with those of the random-located uniform-amplitude array (RLUAA) and the stepped-amplitude array (SAA), both being reported in the literatures for the maximum BCE. Compared to the RLUAA, the SUACRA saves 32% elements with a 1.1% higher BCE. While compared to the SAA, the SUACRA saves 29.1% elements with a bit higher BCE. The proposed SUACRAs have higher BCEs, simple array arrangement and feed network, and could be used as the transmitting array for a large-scale MPT system.

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