scholarly journals Leaf Trichome Distribution Pattern in Arabidopsis Reveals Gene Expression Variation Associated with Environmental Adaptation

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 909
Author(s):  
Shotaro Okamoto ◽  
Kohei Negishi ◽  
Yuko Toyama ◽  
Takeo Ushijima ◽  
Kengo Morohashi
Keyword(s):  
Gene Expression ◽  
Distribution Pattern ◽  
Higher Plants ◽  
Reaction Diffusion ◽  
Distribution Patterns ◽  
Environmental Adaptation ◽  
Stochastic Variation ◽  
Biological Relevance ◽  
Homogeneous Cell ◽  
Multicellular Organisms

Gene expression varies stochastically even in both heterogenous and homogeneous cell populations. This variation is not simply useless noise; rather, it is important for many biological processes. Unicellular organisms or cultured cell lines are useful for analyzing the variation in gene expression between cells; however, owing to technical challenges, the biological relevance of this variation in multicellular organisms such as higher plants remain unclear. Here, we addressed the biological relevance of this variation between cells by examining the genetic basis of trichome distribution patterns in Arabidopsis thaliana. The distribution pattern of a trichome on a leaf is stochastic and can be mathematically represented using Turing’s reaction-diffusion (RD) model. We analyzed simulations based on the RD model and found that the variability in the trichome distribution pattern increased with the increase in stochastic variation in a particular gene expression. Moreover, differences in heat-dependent variability of the trichome distribution pattern between the accessions showed a strong correlation with environmental factors to which each accession was adapted. Taken together, we successfully visualized variations in gene expression by quantifying the variability in the Arabidopsis trichome distribution pattern. Thus, our data provide evidence for the biological importance of variations in gene expression for environmental adaptation.

scholarly journals Leaf trichome distribution pattern in Arabidopsis reveals gene expression variation associated with environmental adaptation

2020 ◽  
Author(s):  
Shotaro Okamoto ◽  
Kohei Negishi ◽  
Yuko Toyama ◽  
Takeo Ushijima ◽  
Kengo Morohashi
Keyword(s):  
Gene Expression ◽  
Distribution Pattern ◽  
Higher Plants ◽  
Reaction Diffusion ◽  
Distribution Patterns ◽  
Environmental Adaptation ◽  
Stochastic Variation ◽  
Biological Relevance ◽  
Homogeneous Cell ◽  
Multicellular Organisms

AbstractGene expression varies stochastically even in both heterogenous and homogeneous cell populations. This variation is not simply useless noise; rather, it is important for many biological processes. Unicellular organisms or cultured cell lines are useful for analyzing the variation in gene expression between cells; however, owing to technical challenges, the biological relevance of this variation in multicellular organisms such as higher plants remains unclear. Here, we addressed the biological relevance of this variation between cells by examining the genetic basis of trichome distribution patterns in Arabidopsis thaliana. The distribution pattern of a trichome on a leaf is stochastic and can be mathematically represented using Turing’s reaction-diffusion (RD) model. We analyzed simulations based on the RD model and found that the variability in the trichome distribution pattern increased with the increase in stochastic variation in a particular gene expression. Moreover, differences in heat-dependent variability of the trichome distribution pattern between the accessions showed a strong correlation with environmental factors to which each accession was adapted. Taken together, we successfully visualized variations in gene expression by quantifying the variability in the Arabidopsis trichome distribution pattern. Thus, our data provide evidence for the biological importance of variations in gene expression for environmental adaptation.

Analisis Rantai Nilai Komoditas Cabai Merah

2019 ◽  
Vol 2 (1) ◽  
pp. 336-346
Author(s):  
Dhamon Oridilla B
Keyword(s):  
Distribution Pattern ◽  
Distribution Patterns ◽  
Added Value ◽  
Commodity Chain ◽  
Market Prices ◽  
Data Analyst ◽  
Bargaining Position ◽  
Agricultural Business ◽  
The Government ◽  
Red Peppers

Candi Village in Bandungan District is one of the Chili Supply Sub-district for Semarang Regency and surrounding area has agro-climate suitable for the development of various agricultural commodities supported by wide market opportunity, so it is suitable for agricultural business development. The purpose of this research is to identify the distribution pattern of red pepper, to know each value of commodity chains and distribution, to design alternative distribution pattern of red pepper.Population in this research is 88 respondents from 735 of member of chilli farmer in Desa Candi with total area of 150,3 hectare consisting of rice field, moor and yard. Methods of data analyst using quantitative approach is done by using Margin Marketing Analysis. The results include: (1) The pattern of distribution of existing farming business grows naturally in accordance with the developments and needs of the perpetrators, the actors in this pattern are farmers, wholesalers, collectors, wholesalers, retailers, consumers. (2) The value of the red chili commodity chain in this naturally grown pattern often makes pricing more dominant by traders, so farmers receive prices slightly lower than market prices. (3) Some obstacles faced in distributing red peppers are the difficulty of changing the mindset of the community about advanced farming, this is best utilized by market participants (chain of distribution) who are more informed and always keep abreast of market dynamics. Conventional marketing pattern by farmer cause price level accepted by farmer in general relatively smaller compared to price received by trader. Suggestions shorten the chain of distribution patterns, increase the added value of products and improve the bargaining position of farmers and for the government always guide / accompany farmers in getting accurate market information, which can be used as farmers in bargaining, Increased market transparency can act as a trigger for the functioning of a market, improved competition and increased adaptation to meet the needs of supply and opportunity to compete with market prices. Desa Candi di Kabupaten Bandungan adalah salah satu Kecamatan Penyedia Cabai untuk Kabupaten Semarang dan sekitarnya memiliki agroklimat yang cocok untuk pengembangan berbagai komoditas pertanian yang didukung oleh peluang pasar yang luas, sehingga sangat cocok untuk pengembangan bisnis pertanian. Tujuan dari penelitian ini adalah untuk mengidentifikasi pola distribusi cabai merah, untuk mengetahui masing-masing nilai rantai komoditas dan distribusi, untuk merancang alternatif pola distribusi cabai merah. Populasi dalam penelitian ini adalah 88 responden dari 735 anggota petani cabai di Desa Candi dengan total luas 150,3 hektar yang terdiri dari sawah, tegalan dan pekarangan. Metode analis data menggunakan pendekatan kuantitatif dilakukan dengan menggunakan Analisis Pemasaran Margin. Hasil meliputi: (1) Pola distribusi usaha pertanian yang ada tumbuh secara alami sesuai dengan perkembangan dan kebutuhan pelaku, pelaku dalam pola ini adalah petani, pedagang besar, pengumpul, pedagang besar, pedagang besar, pengecer, konsumen. (2) Nilai rantai komoditas cabai merah dalam pola yang dikembangkan secara alami ini sering membuat penetapan harga lebih dominan oleh para pedagang, sehingga petani menerima harga yang sedikit lebih rendah daripada harga pasar. (3) Beberapa kendala yang dihadapi dalam mendistribusikan paprika merah adalah sulitnya mengubah pola pikir masyarakat tentang pertanian maju, hal ini paling baik digunakan oleh pelaku pasar (rantai distribusi) yang lebih banyak informasi dan selalu mengikuti perkembangan dinamika pasar. Pola pemasaran konvensional oleh petani menyebabkan tingkat harga yang diterima petani pada umumnya relatif lebih kecil dibandingkan dengan harga yang diterima pedagang. Saran mempersingkat rantai pola distribusi, meningkatkan nilai tambah produk dan meningkatkan posisi tawar petani dan bagi pemerintah selalu membimbing / menemani petani dalam mendapatkan informasi pasar yang akurat, yang dapat digunakan sebagai petani dalam tawar-menawar, Peningkatan transparansi pasar dapat bertindak sebagai pemicu berfungsinya pasar, meningkatnya kompetisi dan peningkatan adaptasi untuk memenuhi kebutuhan pasokan dan peluang untuk bersaing dengan harga pasar.

Freezing

2017 ◽  
Author(s):  
Andrew Clarke
Keyword(s):  
Thermal Hysteresis ◽  
Higher Plants ◽  
Terrestrial Environment ◽  
Cold Temperatures ◽  
Cellular Dehydration ◽  
A Cell ◽  
Unicellular Organisms ◽  
Cell Cytosol ◽  
Freezing Temperatures ◽  
Multicellular Organisms

Freezing is a widespread ecological challenge, affecting organisms in over half the terrestrial environment as well as both polar seas. With very few exceptions, if a cell freezes internally, it dies. Polar teleost fish in shallow waters avoid freezing by synthesising a range of protein or glycoprotein antifreezes. Terrestrial organisms are faced with a far greater thermal challenge, and exhibit a more complex array of responses. Unicellular organisms survive freezing temperatures by preventing ice nucleating within the cytosol, and tolerating the cellular dehydration and membrane disruption that follows from ice forming in the external environment. Multicellular organisms survive freezing temperatures by manipulating the composition of the extracellular body fluids. Terrestrial organisms may freeze at high subzero temperatures, often promoted by ice nucleating proteins, and small molecular mass cryoprotectants (often sugars and polyols) moderate the osmotic stress on cells. A range of chaperone proteins (dehydrins, LEA proteins) help maintain the integrity of membranes and macromolecules. Thermal hysteresis (antifreeze) proteins prevent damaging recrystallisation of ice. In some cases arthropods and higher plants prevent freezing in their extracellular fluids and survive by supercooling. Vitrification of extracellular water, or of the cell cytosol, may be a more widespread response to very cold temperatures than recognised to date.

scholarly journals The secreted endoribonuclease ENDU-2 from the soma protects germline immortality in C. elegans

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Wenjing Qi ◽  
Erika D. V. Gromoff ◽  
Fan Xu ◽  
Qian Zhao ◽  
Wei Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Small Rnas ◽  
C Elegans ◽  
Cleavage Activity ◽  
Response To Temperature ◽  
Multicellular Organisms ◽  
Cell Immortality ◽  
Mature Mrnas ◽  
Endoribonuclease Activity

AbstractMulticellular organisms coordinate tissue specific responses to environmental information via both cell-autonomous and non-autonomous mechanisms. In addition to secreted ligands, recent reports implicated release of small RNAs in regulating gene expression across tissue boundaries. Here, we show that the conserved poly-U specific endoribonuclease ENDU-2 in C. elegans is secreted from the soma and taken-up by the germline to ensure germline immortality at elevated temperature. ENDU-2 binds to mature mRNAs and negatively regulates mRNA abundance both in the soma and the germline. While ENDU-2 promotes RNA decay in the soma directly via its endoribonuclease activity, ENDU-2 prevents misexpression of soma-specific genes in the germline and preserves germline immortality independent of its RNA-cleavage activity. In summary, our results suggest that the secreted RNase ENDU-2 regulates gene expression across tissue boundaries in response to temperature alterations and contributes to maintenance of stem cell immortality, probably via retaining a stem cell specific program of gene expression.

scholarly journals Melatonin as Master Regulator in Plant Growth, Development and Stress Alleviator for Sustainable Agricultural Production: Current Status and Future Perspectives

2020 ◽  
Vol 13 (1) ◽  
pp. 294
Author(s):  
Khadija Nawaz ◽  
Rimsha Chaudhary ◽  
Ayesha Sarwar ◽  
Bushra Ahmad ◽  
Asma Gul ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Growth ◽  
Crop Production ◽  
Higher Plants ◽  
Regulation Of Gene Expression ◽  
Current Status ◽  
Master Regulator ◽  
Abiotic Stressors ◽  
Pathogenesis Related Protein ◽  
Growth Development

Melatonin, a multifunctional signaling molecule, is ubiquitously distributed in different parts of a plant and responsible for stimulating several physiochemical responses against adverse environmental conditions in various plant systems. Melatonin acts as an indoleamine neurotransmitter and is primarily considered as an antioxidant agent that can control reactive oxygen and nitrogen species in plants. Melatonin, being a signaling agent, induces several specific physiological responses in plants that might serve to enhance photosynthesis, growth, carbon fixation, rooting, seed germination and defense against several biotic and abiotic stressors. It also works as an important modulator of gene expression related to plant hormones such as in the metabolism of indole-3-acetic acid, cytokinin, ethylene, gibberellin and auxin carrier proteins. Additionally, the regulation of stress-specific genes and the activation of pathogenesis-related protein and antioxidant enzyme genes under stress conditions make it a more versatile molecule. Because of the diversity of action of melatonin, its role in plant growth, development, behavior and regulation of gene expression it is a plant’s master regulator. This review outlines the main functions of melatonin in the physiology, growth, development and regulation of higher plants. Its role as anti-stressor agent against various abiotic stressors, such as drought, salinity, temperatures, UV radiation and toxic chemicals, is also analyzed critically. Additionally, we have also identified many new aspects where melatonin may have possible roles in plants, for example, its function in improving the storage life and quality of fruits and vegetables, which can be useful in enhancing the environmentally friendly crop production and ensuring food safety.

scholarly journals Computational design and experimental characterization of a photo-controlled mRNA-cap guanine-N7 methyltransferase

2021 ◽  
Author(s):  
Dennis Reichert ◽  
Helena Schepers ◽  
Julian Simke ◽  
Horst Lechner ◽  
Wolfgang Dörner ◽  
...  
Keyword(s):  
Gene Expression ◽  
Computational Design ◽  
Eukaryotic Cells ◽  
Transcriptional Level ◽  
Experimental Characterization ◽  
Temporal Control ◽  
Control Of Gene Expression ◽  
Multicellular Organisms

The spatial and temporal control of gene expression at the post-transcriptional level is essential in eukaryotic cells and developing multicellular organisms. In recent years optochemical and optogenetic tools have enabled...

scholarly journals Environmental RNAi pathways in the two-spotted spider mite

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Mosharrof Mondal ◽  
Jacob Peter ◽  
Obrie Scarbrough ◽  
Alex Flynt
Keyword(s):  
Gene Expression ◽  
Small Rna ◽  
Spider Mite ◽  
Genetic Manipulation ◽  
Model Organisms ◽  
Rnai Pathway ◽  
Plant Host ◽  
Rnai Technology ◽  
Two Spotted Spider Mite ◽  
Multicellular Organisms

Abstract Background RNA interference (RNAi) regulates gene expression in most multicellular organisms through binding of small RNA effectors to target transcripts. Exploiting this process is a popular strategy for genetic manipulation and has applications that includes arthropod pest control. RNAi technologies are dependent on delivery method with the most convenient likely being feeding, which is effective in some animals while others are insensitive. The two-spotted spider mite, Tetranychus urticae, is prime candidate for developing RNAi approaches due to frequent occurrence of conventional pesticide resistance. Using a sequencing-based approach, the fate of ingested RNAs was explored to identify features and conditions that affect small RNA biogenesis from external sources to better inform RNAi design. Results Biochemical and sequencing approaches in conjunction with extensive computational assessment were used to evaluate metabolism of ingested RNAs in T. urticae. This chelicerae arthropod shows only modest response to oral RNAi and has biogenesis pathways distinct from model organisms. Processing of synthetic and plant host RNAs ingested during feeding were evaluated to identify active substrates for spider mite RNAi pathways. Through cataloging characteristics of biochemically purified RNA from these sources, trans-acting small RNAs could be distinguished from degradation fragments and their origins documented. Conclusions Using a strategy that delineates small RNA processing, we found many transcripts have the potential to enter spider mite RNAi pathways, however, trans-acting RNAs appear very unstable and rare. This suggests potential RNAi pathway substrates from ingested materials are mostly degraded and infrequently converted into regulators of gene expression. Spider mites infest a variety of plants, and it would be maladaptive to generate diverse gene regulators from dietary RNAs. This study provides a framework for assessing RNAi technology in organisms where genetic and biochemical tools are absent and benefit rationale design of RNAi triggers for T.urticae.

scholarly journals High resolution spatial transcriptome analysis by photo-isolation chemistry

2020 ◽  
Author(s):  
Mizuki Honda ◽  
Shinya Oki ◽  
Akihito Harada ◽  
Kazumitsu Maehara ◽  
Kaori Tanaka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Transcriptome Profiling ◽  
Tissue Sections ◽  
Complex Functions ◽  
Multicellular Organisms

ABSTRACTIn multicellular organisms, individual cells are characterized by their gene expression profiles and the spatial interactions among cells enable the elaboration of complex functions. Expression profiling in spatially defined regions is crucial to elucidate cell interactions and functions. Here, we established a transcriptome profiling method coupled with photo-isolation chemistry (PIC) that allows the determination of expression profiles specifically from photo-irradiated regions of whole tissues. PIC uses photo-caged oligodeoxynucleotides for in situ reverse transcription. After photo-irradiation of limited areas, gene expression was detected from at least 10 cells in the tissue sections. PIC transcriptome analysis detected genes specifically expressed in small distinct areas of the mouse embryo. Thus, PIC enables transcriptome profiles to be determined from limited regions at a spatial resolution up to the diffraction limit.

Sign in / Sign up

Export Citation Format

Share Document