Comparative expression profiling of three early inflorescence stages of oil palm indicates that vegetative to reproductive phase transition of meristem is regulated by sugar balance

2015 ◽  
Vol 42 (6) ◽  
pp. 589 ◽  
Author(s):  
Walter Ajambang ◽  
Sintho W. Ardie ◽  
Hugo Volkaert ◽  
Georges F. Ngando-Ebongue ◽  
Sudarsono Sudarsono
Keyword(s):  
Oil Palm ◽  
Rna Seq ◽  
Illumina Platform ◽  
Reproductive Phase ◽  
Underlying Network ◽  
Highly Expressed Genes ◽  
Three Stages ◽  
Stage 1 ◽  
And Control ◽  
Gene Expression Levels

Breeding and seed production activities in oil palm have been hampered because of the inability of the male parent Pisifera to produce male inflorescence as source of pollen under normal conditions. Researchers are using complete defoliation to induce male inflorescences, but the biological and molecular processes responsible for this morphological change are yet to be revealed. To understand the underlying network of genes that initiate and control this phenotypically documented activity, we initiated a study aimed at identifying differentially expressed genes (DEGs) in three stages of an oil palm inflorescence under complete defoliation stress using RNA-seq. Sequencing on an Illumina platform produced 82 631 476 reads consisting of 8 345 779 076 bases. A total of 60 700 genes were obtained after transcript filtering and normalisation and 54% of them were downregulated. Differences in gene expression levels were significant between tissues under stress. The farther the distance between tissues, the more DEGs recorded. Comparison between stage 2 and stage 1 induced 3893 DEGs whereas 10 136 DEGs were induced between stage 3 and stage 1. Stress response genes and flower development genes were among the highly expressed genes. This study suggests a link between complete defoliation and meristem differentiation from vegetative to reproductive phase in oil palm.

scholarly journals 3 Stages of a Pan-African Identity Framework for Establishing Self-Sovereign Identity With Blockchain

2021 ◽  
Vol 4 ◽  
Author(s):  
S. Solomon Darnell ◽  
Joseph Sevilla
Keyword(s):  
Smart Phone ◽  
General Data Protection Regulation ◽  
African Identity ◽  
Pan African ◽  
Security Hardening ◽  
Sanitation And Hygiene ◽  
Identification Documents ◽  
Three Stages ◽  
Stage 1 ◽  
And Control

The African continent (specifically its overwhelming in(animate) resources) is often referred to as the sleeping giant by magazines, blogs, research presentations and articles, and NGOs [such as World Bank]. Reasons for this moniker/title include the continent’s plentiful natural resources, its large and quickly growing young population, and the young population’s quick adoption and acclimatization to technology. Most countries on the continent are known as developing countries due to lack of access to safe drinking water, reliable electricity and roads, sanitation and hygiene, and a high number of people with tropical/infectious diseases. However, due to the usefulness of cellular phones and technology, several countries and companies within them have focused on cell phone proliferation (91% in Kenya). Smart phone usage allows Kenyans access to the world’s information and potentially endless innovation. Given that a large number of Kenyans with smartphones use social media, coupled with the advent of Europe’s GDPR (general data protection regulation), African identity and its associated data became an area of great interest. As the world is quickly progressing into a digital economy, a solution must be created that allows us to regain and control our identities, doing our best to ensure losing such is infinitely close to computationally and probabilistically impossible/improbable. Developing a blockchain-based identity backbone using biometrics and historical family information while allowing government-based identification documents is the best way forward. Three stages have been identified as necessities to accomplish the development of this system before opening it further beyond the pan-African worldwide community. The three stages are defined by systems that allow for biometric/demographic registration (stage 1), interoperability and security hardening (stage 2), and biometric modality data analysis/organization/association (stage 3).

scholarly journals The effects of the neonicotinoid imidacloprid on gene expression and DNA methylation in the buff-tailed bumblebee Bombus terrestris

2019 ◽  
Vol 286 (1905) ◽  
pp. 20190718 ◽  
Author(s):  
P. S. A. Bebane ◽  
B. J. Hunt ◽  
M. Pegoraro ◽  
A. R. C Jones ◽  
H. Marshall ◽  
...  
Keyword(s):  
Sublethal Effects ◽  
Bombus Terrestris ◽  
Low Doses ◽  
Large Array ◽  
Epigenetic Changes ◽  
Rna Seq ◽  
Nicotinic Acetylcholine ◽  
Horticultural Crops ◽  
Highly Expressed Genes ◽  
And Control

Neonicotinoids are effective insecticides used on many important arable and horticultural crops. They are nicotinic acetylcholine receptor agonists which disrupt the function of insect neurons and cause paralysis and death. In addition to direct mortality, there are numerous sublethal effects of low doses of neonicotinoids on bees. We hypothesize that some of these large array of effects could be a consequence of epigenetic changes in bees induced by neonicotinoids. We compared whole methylome (BS-seq) and RNA-seq libraries of the brains of buff-tailed bumblebee Bombus terrestris workers exposed to field-realistic doses of the neonicotinoid imidacloprid to libraries from control workers. We found numerous genes which show differential expression between neonicotinoid-treated bees and control bees, but no differentially methylated cytosines in any context. We found CpG methylation to be focused mainly in exons and associated with highly expressed genes. We discuss the implications of our results for future legislation.

scholarly journals The SPEECHLESS-induced stomatal increase is required for the salt tolerance of oil palm

2021 ◽  
Author(s):  
Zhuojun Song ◽  
Le Wang ◽  
Chong Cheong Lai ◽  
Zituo Yang ◽  
May Lee ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Oil Palm ◽  
Cellular Response ◽  
Stomatal Density ◽  
Stomatal Development ◽  
Rna Seq ◽  
Underlying Mechanisms ◽  
And Control ◽  
Different Levels

Oil palm is the most productive oil producing plant. Salt stress leads to growth damage and decrease in yield of oil palm. However, the physiological responses of oil palm to salt stress and their underlying mechanisms are not clear. RNA-Seq for leaf samples from young palms challenged under three levels of salts (100, 250 and 500 mM NaCl) and control for 14 days was conducted. Diverse signalling pathways were involved in responses to different levels of salt stress. All the three levels of salt stress activated EgSPCH expression and induced stomatal density of oil palm, which was contrasting to that in Arabidopsis. Under strong salt stress group, oil palm removed excessive salt via stomata. Overexpression of EgSPCH in Arabidopsis increased the stomatal production but lowered the salt tolerance. These data suggest that in oil palm, salt activates EgSPCH to generate more stomata in response to salt stress. Our results shed a light on the cellular response to salt stress of oil palm and provide new insights into the mechanisms of different salt-induced stomatal development between halophytes and glycophytes.

scholarly journals The effects of the neonicotinoid imidacloprid on gene expression and DNA methylation in the buff-tailed bumblebee Bombus terrestris

2019 ◽  
Author(s):  
P.S.A Bebane ◽  
B.J. Hunt ◽  
M. Pegoraro ◽  
A.R.C Jones ◽  
H. Marshall ◽  
...  
Keyword(s):  
Sublethal Effects ◽  
Bombus Terrestris ◽  
Low Doses ◽  
Large Array ◽  
Epigenetic Changes ◽  
Rna Seq ◽  
Nicotinic Acetylcholine ◽  
Horticultural Crops ◽  
Highly Expressed Genes ◽  
And Control

AbstractNeonicotinoids are effective insecticides used on many important arable and horticultural crops. They are nicotinic acetylcholine receptor agonists which disrupt the function of insect neurons and cause paralysis and death. In addition to direct mortality, there are numerous sublethal effects of low doses of neonicotinoids on bees. We hypothesize that some of these large array of effects could be a consequence of epigenetic changes in bees induced by neonicotinoids. We compared whole methylome (BS-seq) and RNA-seq libraries of the brains of buff tailed bumblebee Bombus terrestris workers exposed to field realistic doses of the neonicotinoid imidacloprid to libraries from control workers. We found numerous genes which show differential expression between neonicotinoid treated bees and control bees, but no differentially methylated cytosines in any context. We found CpG methylation to be focused mainly in exons and associated with highly expressed genes. We discuss the implications of our results for future legislation.

scholarly journals Investigating viral attenuation by promoter knockout: a systems approach

2017 ◽  
Author(s):  
Matthew L Paff ◽  
Benjamin R. Jack ◽  
Daniel R Boutz ◽  
Bartram L Smith ◽  
Claus O Wilke ◽  
...  
Keyword(s):  
Genome Editing ◽  
Systems Approach ◽  
A Priori ◽  
Rna Seq ◽  
Genome Composition ◽  
T7 Promoter ◽  
Highly Expressed Genes ◽  
The One ◽  
Viral Attenuation ◽  
Gene Expression Levels

Live attenuated viral vaccines provide the most robust and longest lasting immune response. Yet designing them a priori to have reduced growth capacity and also to be robust to evolutionary reversion can be challenging. On the one hand, genome editing methods now enable us to create almost any conceivable viral genome composition. Yet understanding and predicting how engineered genomes will behave and evolve is a challenge. Here we adopt a systems approach in studying a simple attenuation design in bacteriophage T7: promoter knockout. Either or both promoters for the two most highly expressed genes were abolished. Overall fitnesses, major phenotypes and gene expression levels were measured for all initial genomes and for genomes evolved toward for fitness recovery. Initial genomes behaved broadly as expected, but the genomes showed an unexpected ability to evolve back to high fitness. Genome sequences, RNA Seq and proteomics reveal the molecular foundations of the attenuations and recoveries. Overall, the work suggests that a systems approach is ultimately yielding to understanding, if not predicting the consequences of genome editing and evolutionary recoveries of simple genomes.

scholarly journals Investigating viral attenuation by promoter knockout: a systems approach

2017 ◽  
Author(s):  
Matthew L Paff ◽  
Benjamin R. Jack ◽  
Daniel R Boutz ◽  
Bartram L Smith ◽  
Claus O Wilke ◽  
...  
Keyword(s):  
Genome Editing ◽  
Systems Approach ◽  
A Priori ◽  
Rna Seq ◽  
Genome Composition ◽  
T7 Promoter ◽  
Highly Expressed Genes ◽  
The One ◽  
Viral Attenuation ◽  
Gene Expression Levels

Live attenuated viral vaccines provide the most robust and longest lasting immune response. Yet designing them a priori to have reduced growth capacity and also to be robust to evolutionary reversion can be challenging. On the one hand, genome editing methods now enable us to create almost any conceivable viral genome composition. Yet understanding and predicting how engineered genomes will behave and evolve is a challenge. Here we adopt a systems approach in studying a simple attenuation design in bacteriophage T7: promoter knockout. Either or both promoters for the two most highly expressed genes were abolished. Overall fitnesses, major phenotypes and gene expression levels were measured for all initial genomes and for genomes evolved toward for fitness recovery. Initial genomes behaved broadly as expected, but the genomes showed an unexpected ability to evolve back to high fitness. Genome sequences, RNA Seq and proteomics reveal the molecular foundations of the attenuations and recoveries. Overall, the work suggests that a systems approach is ultimately yielding to understanding, if not predicting the consequences of genome editing and evolutionary recoveries of simple genomes.

Design of objective lens for 200-kV high-resolution electron microscopes

1983 ◽  
Vol 41 ◽  
pp. 314-315
Author(s):  
K. Tsuno ◽  
T. Honda ◽  
Y. Harada ◽  
M. Naruse
Keyword(s):  
Optical Properties ◽  
Computer Technology ◽  
Axial Magnetic Field ◽  
Chromatic Aberration ◽  
Objective Lens ◽  
Resolution Electron ◽  
Correction Of Astigmatism ◽  
Three Stages ◽  
Electron Microscopes ◽  
Stage 1

Developement of computer technology provides much improvements on electron microscopy, such as simulation of images, reconstruction of images and automatic controll of microscopes (auto-focussing and auto-correction of astigmatism) and design of electron microscope lenses by using a finite element method (FEM). In this investigation, procedures for simulating the optical properties of objective lenses of HREM and the characteristics of the new lens for HREM at 200 kV are described.The process for designing the objective lens is divided into three stages. Stage 1 is the process for estimating the optical properties of the lens. Firstly, calculation by FEM is made for simulating the axial magnetic field distributions Bzc of the lens. Secondly, electron ray trajectory is numerically calculated by using Bzc. And lastly, using Bzc and ray trajectory, spherical and chromatic aberration coefficients Cs and Cc are numerically calculated. Above calculations are repeated by changing the shape of lens until! to find an optimum aberration coefficients.

scholarly journals A COVID-19 Lockdown Tabletop Exercise in New Taipei City, Taiwan

2021 ◽  
pp. 1-19
Author(s):  
I-Tien Lo ◽  
Ching-Yuan Lin ◽  
Ming-Tai Cheng
Keyword(s):  
Policy Making ◽  
Large City ◽  
Strategic Plan ◽  
Government Control ◽  
Subject Knowledge ◽  
All Solutions ◽  
Taipei City ◽  
Returning To Work ◽  
Three Stages ◽  
Stage 1

Abstract Objectives: This exercise aimed to validate New Taipei City’s strategic plan for a city lockdown in response to COVID-19. The main goal of all solutions was the principle of “reducing citizen activity and strengthening government control”. Methods: We created a suitable exercise, and creating 15 hypothetical situations for three stages. All participating units designed and proposed policy plans and execution protocols according to each situation. Results: In the course of the exercise, many existing policies and execution protocols were validated to address. Situations occurring in Stage 1, when the epidemic was spreading to the point of lockdown preparations, approaches to curb the continued spread of the epidemic in Stage 2, and returning to work after the epidemic is controlled and lockdown is lifted in Stage 3. Twenty response units participated in the exercise. Although favourable outcomes were obtained, the evaluators provided comments suggesting further improvements. Conclusions: Our exercise demonstrated a successful example to help policy making and revision in a large city over 4 million population during COVID-19 pandemic. It also enhanced participants’ subject knowledge and familiarity with the implementation of a city lockdown. For locations intending to go into lockdown, similar tabletop exercises are an effective verification option.

scholarly journals High heterogeneity undermines generalization of differential expression results in RNA-Seq analysis

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Weitong Cui ◽  
Huaru Xue ◽  
Lei Wei ◽  
Jinghua Jin ◽  
Xuewen Tian ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Small Sample ◽  
Differentially Expressed ◽  
Cancer Type ◽  
Rna Seq ◽  
Sample Sizes ◽  
Large Sample ◽  
Expression Levels ◽  
Gene Expression Levels

Abstract Background RNA sequencing (RNA-Seq) has been widely applied in oncology for monitoring transcriptome changes. However, the emerging problem that high variation of gene expression levels caused by tumor heterogeneity may affect the reproducibility of differential expression (DE) results has rarely been studied. Here, we investigated the reproducibility of DE results for any given number of biological replicates between 3 and 24 and explored why a great many differentially expressed genes (DEGs) were not reproducible. Results Our findings demonstrate that poor reproducibility of DE results exists not only for small sample sizes, but also for relatively large sample sizes. Quite a few of the DEGs detected are specific to the samples in use, rather than genuinely differentially expressed under different conditions. Poor reproducibility of DE results is mainly caused by high variation of gene expression levels for the same gene in different samples. Even though biological variation may account for much of the high variation of gene expression levels, the effect of outlier count data also needs to be treated seriously, as outlier data severely interfere with DE analysis. Conclusions High heterogeneity exists not only in tumor tissue samples of each cancer type studied, but also in normal samples. High heterogeneity leads to poor reproducibility of DEGs, undermining generalization of differential expression results. Therefore, it is necessary to use large sample sizes (at least 10 if possible) in RNA-Seq experimental designs to reduce the impact of biological variability and DE results should be interpreted cautiously unless soundly validated.

scholarly journals Genome-Wide Expression and Alternative Splicing in Domesticated Sunflowers (Helianthus annuus L.) under Flooding Stress

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 92
Author(s):  
Joon Seon Lee ◽  
Lexuan Gao ◽  
Laura Melissa Guzman ◽  
Loren H. Rieseberg
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Mixed Model ◽  
Agricultural Land ◽  
Alcohol Fermentation ◽  
Expression Levels ◽  
Flooding Stress ◽  
Genome Wide ◽  
And Control ◽  
Gene Expression Levels

Approximately 10% of agricultural land is subject to periodic flooding, which reduces the growth, survivorship, and yield of most crops, reinforcing the need to understand and enhance flooding resistance in our crops. Here, we generated RNA-Seq data from leaf and root tissue of domesticated sunflower to explore differences in gene expression and alternative splicing (AS) between a resistant and susceptible cultivar under both flooding and control conditions and at three time points. Using a combination of mixed model and gene co-expression analyses, we were able to separate general responses of sunflower to flooding stress from those that contribute to the greater tolerance of the resistant line. Both cultivars responded to flooding stress by upregulating expression levels of known submergence responsive genes, such as alcohol dehydrogenases, and slowing metabolism-related activities. Differential AS reinforced expression differences, with reduced AS frequencies typically observed for genes with upregulated expression. Significant differences were found between the genotypes, including earlier and stronger upregulation of the alcohol fermentation pathway and a more rapid return to pre-flooding gene expression levels in the resistant genotype. Our results show how changes in the timing of gene expression following both the induction of flooding and release from flooding stress contribute to increased flooding tolerance.

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